https://github.com/geodynamics/citcoms
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Tip revision: fdc93a2ec0da55afe41fd1c325f60df300f79b47 authored by Eric Heien on 19 July 2011, 18:34 UTC
Reverted development code to fix bugs
Tip revision: fdc93a2
ChangeLog
2009-06-10 20:42  tan2

	* configure.ac: Added COND_GGRD flags; removed redundant LIBS

2009-06-10 20:41  tan2

	* configure.ac: Checking malloc.h earlier to initialize even when
	  not using pyre

2009-06-10 17:49  tan2

	* configure.ac: checking netcdf header and library

2009-06-10 04:11  tan2

	* configure.ac: Append GMTHOME/lib to LD path

2009-06-09 23:47  tan2

	* configure.ac: Adding ggrd compilation support

2009-06-08 21:03  tan2

	* NEWS: One more feature and mention where to find the features in
	  the cookbooks.

2009-06-08 18:11  tan2

	* CitcomS/Coupler/EmbeddedCoupler.py: Added a safe guard

2009-06-04 21:04  tan2

	* examples/Cookbook9/cookbook9.cfg: Reordering parameter

2009-06-03 21:08  tan2

	* module/Exchanger/BoundarySVTInlet.cc,
	  module/Exchanger/SVTInlet.cc, module/Exchanger/SVTInlet.h: Update
	  SVTInlet to inherit from BaseSVTInlet

2009-06-03 21:07  tan2

	* module/Exchanger/Makefile.am: adding files to makefile

2009-06-02 22:58  tan2

	* tests/coupled.cfg, tests/exchange.py: update to current coupler

2009-06-02 22:58  tan2

	* examples/Cookbook9/cookbook9.cfg: reducing the accuracy of
	  solvers, otherwise, they will converge to the wrong result

2009-06-02 22:56  tan2

	* CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py,
	  CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/Coupler/Inlet.py,
	  CitcomS/Coupler/Outlet.py, CitcomS/Solver/CoupledSolver.py,
	  module/Exchanger/AreaWeightedNormal.cc,
	  module/Exchanger/AreaWeightedNormal.h,
	  module/Exchanger/BaseSVTInlet.cc,
	  module/Exchanger/BaseSVTInlet.h,
	  module/Exchanger/BoundarySVTInlet.cc,
	  module/Exchanger/BoundarySVTInlet.h,
	  module/Exchanger/BoundaryVTInlet.cc,
	  module/Exchanger/CitcomInterpolator.cc,
	  module/Exchanger/Makefile.am, module/Exchanger/PInlet.cc,
	  module/Exchanger/PInlet.h, module/Exchanger/PInterior.cc,
	  module/Exchanger/PInterior.h, module/Exchanger/POutlet.cc,
	  module/Exchanger/POutlet.h, module/Exchanger/bindings.cc,
	  module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h,
	  module/Exchanger/inlets_outlets.cc,
	  module/Exchanger/inlets_outlets.h: Added parameters
	  'amending_outflow' and 'exchange_pressure' to help the
	  convergence of esolver
	  
	  When 'amending_outflow' is set to true, the imposed velocity BC
	  will be amended slightly to be divergence-free. (The divergence,
	  e.g. outflow, is caused by the combination of solver inaccuracy
	  and interpolation inaccuracy.)
	  
	  When 'exchange_pressure' is set to true, the initial pressure (at
	  element level) of the embedded solver is taken from the pressure
	  solution of the containing solver.

2009-06-02 22:09  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h:
	  Boundary for global mesh, not sure whether it works with
	  interpolator or not

2009-06-02 21:58  tan2

	* lib/Instructions.c: init'd E->output.seismic and
	  E->output.coord_bin

2009-06-02 21:58  tan2

	* examples/Cookbook10/cookbook10.cfg: refining cookbook10

2009-05-28 01:50  leif

	* configure.ac, lib/General_matrix_functions.c, lib/Makefile.am,
	  lib/cgrad_kernel.cu: CUDA-ized e_assemble_del2_u(), and ran it
	  successfully -- and slowly! -- under the device emulator. Added a
	  new 'configure' option: "--with-cuda".

2009-05-27 02:32  leif

	* lib/cgrad_kernel.cu: Parallelized strip_bcs_from_residual().

2009-05-27 01:28  leif

	* lib/cgrad_kernel.cu: Sketched data-parallel version of
	  e_assemble_del2_u().

2009-05-26 15:21  becker

	* lib/Initial_temperature.c, lib/convection_variables.h: Added
	  blob_bc_persist parameter (default = off) to allow assigning
	  blob-like temperature anomalies to BCs.

2009-05-26 15:03  becker

	* lib/Initial_temperature.c, lib/Pan_problem_misc_functions.c:
	  Fixed typo in blob temperature assignment.
	  
	  Changed conversion of coordinates, now assignment works.

2009-05-21 23:16  tan2

	* NEWS: add changes in r14999

2009-05-15 22:32  tan2

	* visual/project_geoid.c: ignoring the degree-0 and degree-1
	  components of geoid

2009-05-10 23:18  tan2

	* NEWS: add more chaanges in v3.1.0

2009-05-10 16:37  tan2

	* configure.ac, setup.py: Change version number for v3.1.0 alpha
	  release

2009-05-10 16:35  tan2

	* NEWS: Summary of changes in this release

2009-05-01 22:19  tan2

	* examples/Cookbook10, examples/Cookbook10/cookbook10.cfg: Adding
	  cookbook for synthetic seismogram, mostly copied from cookbook7

2009-05-01 22:18  tan2

	* lib/Mineral_physics_models.c: Depth is measured from r=1.0, not
	  outer radius, because in coupled model, the outer radius can be <
	  1.0.

2009-05-01 22:17  tan2

	* lib/Instructions.c: Printing a big warning when plate velocity is
	  imposed but remove_angular_momentum or remove_rigid_rotation is
	  on.

2009-05-01 22:15  tan2

	* lib/Drive_solvers.c: Removing angular momentum in pseudo free
	  surface case

2009-05-01 22:14  tan2

	* visual/parser.py: ignore anything after ';'

2009-05-01 22:13  tan2

	* INSTALL: explicitly add Python.h to requirement

2009-04-28 22:53  leif

	* lib/cgrad_kernel.cu: For my own sanity, simplified code assuming
	  the following:
	  
	  E->sphere.caps_per_proc == 1 E->parallel.nproc == 1
	  E->mesh.levmax == 0 E->mesh.nsd == 3

2009-04-27 20:15  leif

	* lib/cgrad_kernel.cu: Moved malloc/free calls outside of kernel.
	  (The amount of memory allocated appears to be invariant.)

2009-04-27 18:39  leif

	* lib/cgrad_kernel.cu: Consolidated calls to malloc/free.

2009-04-24 18:37  becker

	* lib/Instructions.c, lib/Viscosity_structures.c,
	  lib/global_defs.h: Added flag to allow using the more precise
	  method of computing strain-rates throughout the globe, and not
	  just close to the poles.
	  
	  precise_strain_rate=on
	  
	  will select this, default is "odd", i.e. poles only as before.

2009-04-23 02:32  leif

	* lib/cgrad_kernel.cu: Don't call through function pointers --
	  otherwise, 'nvcc' crashes!

2009-04-23 02:22  leif

	* lib/cgrad_kernel.cu: Proposed CUDA kernel for conjugate gradient
	  solver.

2009-04-22 00:59  leif

	* lib/Instructions.c: Avoid core dump in record() when E->fp hasn't
	  been set yet.

2009-04-21 22:29  leif

	* configure.ac: The new Python.h header check reorders this script
	  somewhat. CIT_CHECK_PYTHON_HEADER must follow AC_PROG_CC, and
	  precede CIT_PYTHON_EGG_SETUP.

2009-04-21 19:33  leif

	* configure.ac: Issue45: Check for Python.h.

2009-04-17 03:37  becker

	* lib/Viscosity_structures.c: Added viscosity options 9 and 10 for
	  TDPEPV which are identical to 3 and 8 but temperature is not
	  limited to [0;1]. This is cumbersome, but perhaps needed for
	  backward compatibility.

2009-04-16 18:24  tan2

	* CitcomS/Components/IC.py, CitcomS/Components/Param.py,
	  examples/Cookbook6/cookbook6.cfg, lib/Initial_temperature.c,
	  lib/Lith_age.c, lib/Output_h5.c, lib/global_defs.h,
	  module/Exchanger/initTemperature.cc, module/setProperties.c: Move
	  parameter "mantle_temp" from CitcomS.solver.param to
	  CitcomS.solver.ic. Renamed E->control.lith_age_mantle_temp to
	  E->control.mantle_temp.

2009-04-16 18:23  tan2

	* examples/Cookbook8/cookbook8.cfg: update cookbook8 with the
	  manual

2009-04-16 18:22  tan2

	* module/Exchanger/Makefile.am: Add -DUSE_HDF5 to CPPFLAGS in
	  module/Exchanger

2009-04-16 18:21  tan2

	* examples/Cookbook7/cookbook7.cfg: change the viscosity section to
	  be the same as that in cookbook3.

2009-04-16 18:20  tan2

	* examples/Cookbook4/cookbook4.cfg,
	  examples/Cookbook5/cookbook5.cfg: Removed domain extents, since
	  they are determined by coor_file.

2009-04-16 18:07  tan2

	* INSTALL: Removed instructions to 'make install', 'make clean' and
	  'make distclean'. Added dependencies.

2009-04-09 20:53  tan2

	* lib/Instructions.c, module/setProperties.c: Fixed a bug in cgrad
	  solver introduced in r13270.

2009-04-09 20:39  becker

	* lib/Output.c: Left debugging output in, now cleaned up

2009-04-09 20:37  becker

	* bin/Citcom.c, lib/Instructions.c, lib/Output.c: Fixed file output
	  issue which caused vtk log file I/O to bomb during Citcom
	  finalize.

2009-04-08 23:39  tan2

	* CitcomS/BaseApplication.py, CitcomS/Controller.py,
	  CitcomS/Solver/CoupledFullSolver.py,
	  CitcomS/Solver/CoupledRegionalSolver.py,
	  CitcomS/Solver/FullSolver.py, CitcomS/Solver/RegionalSolver.py,
	  CitcomS/Solver/Solver.py, bin/Citcom.c, lib/Instructions.c,
	  lib/Viscosity_structures.c, lib/citcom_init.h,
	  module/initial_conditions.c: Sync'ing C and Pyre and adding
	  comments

2009-04-08 23:38  tan2

	* CitcomS/Controller.py, CitcomS/Solver/CoupledSolver.py,
	  CitcomS/Solver/Solver.py, bin/Citcom.c, lib/Citcom_init.c,
	  lib/Parallel_util.c, lib/citcom_init.h, lib/parallel_related.h,
	  module/bindings.c, module/initial_conditions.c, module/misc.c,
	  module/misc.h, module/outputs.c, module/outputs.h: Added a
	  function citcom_finalize() to close files and MPI before exit.
	  Return 0 when the code is finished normally. Rearrang
	  post_processing and stokes_flow_only.

2009-04-08 23:34  tan2

	* examples/Full/input.sample, examples/Regional/input.sample,
	  lib/Convection.c, lib/Instructions.c, lib/Viscosity_structures.c,
	  lib/global_defs.h, module/advdiffu.c, module/bindings.c,
	  module/misc.c, module/misc.h: Clean up.

2009-04-08 23:31  tan2

	* CitcomS/Components/Stokes_solver/Incompressible.py,
	  lib/Construct_arrays.c, lib/Full_parallel_related.c,
	  lib/Full_version_dependent.c, lib/General_matrix_functions.c,
	  lib/Instructions.c, lib/Regional_parallel_related.c,
	  lib/Regional_sphere_related.c, lib/Regional_version_dependent.c,
	  lib/Size_does_matter.c, lib/Solver_conj_grad.c,
	  lib/Solver_multigrid.c, lib/global_defs.h, module/bindings.c,
	  module/stokes_solver.c, module/stokes_solver.h: Removed
	  multigrid-el option of stokes solver, which is broken for a long
	  time and not used by anyone.

2009-04-08 23:27  tan2

	* lib/Instructions.c: Moved where to call read_rayleigh_from_file()
	  earlier. I hope this doesn't break the ray_control stuff.

2009-04-08 20:24  becker

	* lib/Ggrd_handling.c: Fixed bug in vtop assignment.

2009-04-07 22:50  tan2

	* examples/Makefile.am: Revert the unintended modification of
	  examples/Makefile.am

2009-04-07 22:45  tan2

	* examples/Cookbook3/cookbook3.cfg,
	  examples/Cookbook4/cookbook4.cfg, examples/Makefile.am: Change
	  the viscosity option in cookbook3 and cookbook4

2009-04-07 22:44  tan2

	* examples/Cookbook2/cookbook2.cfg: Change the mesh size in
	  cookbook2

2009-04-04 00:59  tan2

	* lib/Makefile.am, lib/Mineral_physics_models.c,
	  lib/Seismic_model.c: Renamed Seismic_model.c to
	  Mineral_physics_models.c

2009-04-04 00:57  tan2

	* lib/Output.c, lib/Seismic_model.c: Fixed a few bugs in seismic
	  output
	  
	  * fixed errors in the coefficient table * fixed typos *
	  normalized drho by reference density profile * more digits in the
	  prem radius table * added two specfem flags in PREM calculation.
	  * "dv" output for debugging purpose, disabled.

2009-04-04 00:52  tan2

	* examples/example0.cfg: Inconsisent parameters with the manual

2009-03-28 02:29  becker

	* lib/Full_tracer_advection.c, lib/Ggrd_handling.c,
	  lib/Tracer_setup.c: Modified the way the compositional init with
	  ggrd tracer can now select either a range of layers (>0) or a
	  specific layer (<0).

2009-03-20 23:36  tan2

	* CitcomS/Components/Stokes_solver/Incompressible.py,
	  lib/General_matrix_functions.c, lib/Instructions.c,
	  lib/global_defs.h, module/setProperties.c: limiting the number of
	  multigrid cycles in solve_del2_u().
	  
	  A new input parameter solver.vsolver.max_mg_cycles (default to
	  50) controls the max. number of multigrid cycles when solving the
	  velocity. Without this parameter, when the stiffness matrix is
	  near singular, the the multigrid solver may become an infinite
	  loop.

2009-03-18 19:39  tan2

	* CitcomS/Components/Sphere/Sphere.py, module/setProperties.c:
	  Remove mgunitx etc from pyre input. This restores the behavior in
	  v3.0 and earlier version.
	  
	  In pyre version, the mesh size is always specified by nodex etc.
	  In C version, the mesh size is specified by nodex if
	  Solver=cgrad, and by mgunitx and levels if Solver=multigrid.

2009-03-17 23:42  tan2

	* lib/Output.c: Rollback the unintended change in velo output.

2009-03-17 00:18  tan2

	* lib/Full_read_input_from_files.c, lib/Full_version_dependent.c,
	  lib/Initial_temperature.c, lib/Lith_age.c,
	  lib/Material_properties.c, lib/Output_gzdir.c,
	  lib/Problem_related.c, lib/Regional_read_input_from_files.c,
	  lib/Regional_sphere_related.c, lib/Regional_version_dependent.c:
	  Check return values of sscanf/fscanf. This fixs issue265.

2009-03-17 00:17  tan2

	* lib/Obsolete.c, lib/Pan_problem_misc_functions.c: Removed
	  obsolete function read_previous_field()

2009-03-17 00:16  tan2

	* CitcomS/Components/Stokes_solver/Incompressible.py,
	  examples/Cookbook8/cookbook8.cfg, lib/Drive_solvers.c,
	  lib/Global_operations.c, lib/Instructions.c, lib/Output_gzdir.c,
	  lib/Tracer_setup.c, lib/global_defs.h, module/setProperties.c:
	  remove angular momentum from stokes solution by setting
	  solver.vsolver.remove_angular_mementum=1

2009-03-16 23:17  tan2

	* CitcomS/Components/Param.py, lib/Instructions.c, lib/Makefile.am,
	  lib/Output.c, lib/Output_gzdir.c, lib/Output_h5.c,
	  lib/Seismic_model.c, lib/global_defs.h, lib/output.h,
	  module/setProperties.c: Converting temperature/composition fields
	  to seismic velocities, in a format that specfem3d portal and v4.1
	  can understand.
	  
	  * solver.param.mineral_physics_mode: default to 3, the model of
	  Tramper, Vacher and Vlaar's PEPI 2001. * output_optional=seismic
	  will write coordinates and seismic velocities in binary files for
	  specfem comsumption. * domain bounds file "datafile.domain":
	  binary file with nproc * 10 doubles. The 10 doubles are (rmin,
	  rmax) and four (theta, phi) pairs for the four bottom corner
	  nodes. This file is written by rank-0 processor only.

2009-03-16 22:52  tan2

	* lib/Initial_temperature.c, tests/stokes,
	  tests/stokes/bousinessq.cfg, tests/stokes/tala.cfg: add test
	  cases for the stokes solver under bousinessq approximation and
	  truncated anelastic liquid approximation

2009-03-16 22:50  tan2

	* CitcomS/Components/Sphere/Sphere.py, CitcomS/Solver/Solver.py,
	  lib/Full_geometry_cartesian.c, lib/Full_sphere_related.c,
	  lib/Instructions.c, lib/Regional_geometry_cartesian.c,
	  lib/Regional_sphere_related.c, module/bindings.c,
	  module/mesher.c, module/mesher.h, module/setProperties.c:
	  seperate initialization and parameter input

2009-03-16 22:44  tan2

	* CitcomS/Components/Sphere/Sphere.py: change the default of mgunit

2009-03-16 22:43  tan2

	* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
	  CitcomS/Components/Sphere/Sphere.py,
	  CitcomS/Components/Stokes_solver/Incompressible.py,
	  CitcomS/Solver/Solver.py: Make the initialization step in pyre
	  conforms to C version. This fixs a bug in r13270.

2009-03-10 00:58  tan2

	* lib/Determine_net_rotation.c: Disable HC related stuff if
	  USE_GGRD is not set

2009-03-04 23:45  becker

	* bin/Citcom.c, lib/Checkpoints.c, lib/Full_tracer_advection.c,
	  lib/Regional_tracer_advection.c, lib/Tracer_setup.c: Changed ic
	  flavors from 100 to 99 as per Eh's request

2009-03-04 23:00  becker

	* bin/Citcom.c, lib/Checkpoints.c, lib/Full_tracer_advection.c,
	  lib/Regional_tracer_advection.c, lib/Tracer_setup.c: Changed ggrd
	  flavor init for tracers with checkpoint override from 2 to 100 as
	  per Eh's request.

2009-02-28 21:23  becker

	* bin/Citcom.c, lib/Checkpoints.c, lib/Composition_related.c,
	  lib/Determine_net_rotation.c, lib/Full_tracer_advection.c,
	  lib/Instructions.c, lib/Tracer_setup.c: Added
	  ic_method_for_flavors=2, which works like the ggrd based tracer
	  flavor init method ic_method_for_flavors=1 but overrides restart
	  settings for tracers. This allows a compositional restart of a
	  purely thermal run.

2009-02-20 00:09  tan2

	* CitcomS/Components/Tracer.py, lib/Full_tracer_advection.c,
	  lib/Process_buoyancy.c, lib/Tracer_setup.c, lib/tracer_defs.h,
	  module/setProperties.c: Partially back out r19268,r9272,r11215,
	  since the AVM stuff is redesigned.

2009-02-19 23:46  tan2

	* lib/Full_tracer_advection.c, lib/Process_buoyancy.c,
	  lib/Tracer_setup.c: Partially back out r11218, since the AVM
	  stuff is redesigned.

2009-02-19 23:41  tan2

	* CitcomS/BaseApplication.py, CitcomS/Controller.py,
	  lib/Process_buoyancy.c, module/initial_conditions.c: Partially
	  back out r11221, since the AVM stuff is redesigned.

2009-02-19 23:35  tan2

	* lib/Process_buoyancy.c: Back out r11279, since the AVM stuff is
	  redesigned.

2009-02-13 03:46  leif

	* lib/Checkpoints.c: Fixed minor bug exposed by C-to-C++
	  translation (r14045).

2009-02-06 19:51  tan2

	* lib/Instructions.c, lib/Stokes_flow_Incomp.c: Emit the warning
	  message from a different place to get rid of static variables.
	  Also, the macros TRUE and FALSE are undefined unless configured
	  with GMT.

2008-12-22 18:48  tan2

	* lib/Viscosity_structures.c: Fixed a bug in viscosity rheol=7. Bug
	  reported by Laura Alisic.

2008-11-19 06:49  tan2

	* lib/General_matrix_functions.c: Fixed two bugs in lg_pow(a, n),
	  which computes a^n.
	  
	  One bug is when n=0, it returned a, instead of 1 Another bug is
	  a^(n-1) was returned

2008-11-18 23:56  tan2

	* lib/Topo_gravity.c: One more fix to zero geoid arrays

2008-11-18 22:58  tan2

	* lib/Topo_gravity.c: Zero'ed geoid arrays.

2008-11-18 06:55  becker

	* lib/Ggrd_handling.c, lib/Instructions.c,
	  lib/Stokes_flow_Incomp.c, lib/global_defs.h: Patched up
	  Ggrd_handling for velocity grids close to pole.
	  
	  Addded flag to suppress check of incompressibility and pressure
	  convergence. Partially, this is because for kinematic BCs
	  pressure will only be constrained up to a constant, partially
	  because mixed density/plate flow models show very poor
	  convergence, still to be checked.

2008-11-11 02:55  becker

	* lib/Initial_temperature.c: blob parameters were required even if
	  tic_method != 2, changed such that the parameters were only read
	  in if tic_method == 2

2008-11-11 02:48  becker

	* lib/Initial_temperature.c: Minor fix to allow compilation with
	  USE_GGRD

2008-11-07 23:35  tan2

	* module/setProperties.c: forget to check in module/setProperties.c

2008-11-07 23:32  tan2

	* CitcomS/Components/IC.py, examples/Cookbook6/cookbook6.cfg,
	  lib/Full_solver.c, lib/Full_version_dependent.c,
	  lib/Initial_temperature.c, lib/Regional_solver.c,
	  lib/Regional_version_dependent.c, lib/solver.h: * Reserved
	  'tic_method=100' for user-defined initial temperature. * Read all
	  parameters related to initial temperature regardless which
	  tic_method is used. This will make the life easier when adding
	  new tic_method. * Fixed a bug in 'tic_method=0' for regional
	  model. The bug causes that the sinosoidal temperature
	  perturbation is applied at 0th processor only. * Fixed a bug in
	  'tic_method=1' for regional model. 'tic_method=1' should generate
	  a top TBL according to the input parameter 'half_space_age'.
	  However, the code effectively multiply 25x to the age. Cookbook6
	  is using this tic_method, so its half_space_age needs to become
	  2500 to get the original temperature. * In 'tic_method=2',
	  compute distance in Cartesian coordinate, instead of spherical
	  coordinate. * Refactoring codes for temperature initial
	  conditions. * Merged regional_construct_tic_from_input() and
	  full_construct_tic_from_input() to construct_tic_from_input().

2008-11-07 23:32  tan2

	* lib/Viscosity_structures.c: Reserved 'rheol=100' for user-defined
	  viscosity law.

2008-11-07 23:31  tan2

	* CitcomS/Components/Output.py, module/setProperties.c: Added
	  parameter 'use_cbf_topo' to pyre binding, default to off.

2008-11-07 23:14  tan2

	* CitcomS/Components/Sphere/Sphere.py, CitcomS/Solver/Solver.py,
	  examples/Full/input.sample, examples/Regional/input.sample,
	  lib/Full_solver.c, lib/Full_version_dependent.c,
	  lib/Instructions.c, lib/Regional_solver.c,
	  lib/Regional_version_dependent.c, lib/solver.h,
	  module/setProperties.c: * Added back parameters
	  mgunitx/mgunity/mgunitz. This partly reverts r13256. * Under
	  pyre, uses mgunitx/mgunity/mgunitz and levels to compute
	  nodex/nodey/nodez in multigrid solver. * Merged
	  regional_global_derived_values() and full_global_derived_values()
	  to global_derived_values().

2008-11-05 00:19  tan2

	* lib/Full_version_dependent.c: Minor fix on node counting

2008-11-04 22:50  tan2

	* visual/pasteCitcomData.py: Added a missing import

2008-11-04 21:02  tan2

	* visual/zslice.py: zslice.py will slice opt files if present

2008-11-04 21:01  tan2

	* CitcomS/Solver/Solver.py, examples/Full/input.sample,
	  examples/Regional/input.sample, lib/Instructions.c,
	  module/bindings.c, module/misc.c, module/misc.h: Removed input
	  parameters "mgunitx", "mgunity" and "mgunitz". Their values are
	  inferred from other parameters. Also, the code checks that
	  "levels" > 1 when multigrid solver is used.

2008-11-04 21:00  tan2

	* lib/Output.c: Fixed a bug in outputting comp_el

2008-11-01 18:37  becker

	* lib/Full_sphere_related.c, lib/Full_version_dependent.c,
	  lib/Instructions.c, lib/Stokes_flow_Incomp.c: Fixed two typos,
	  velocity norm function was called where pressure norm should have
	  been called. This leads to core dumps, all seems to be working
	  now.

2008-10-31 20:18  tan2

	* lib/Full_version_dependent.c, lib/Regional_version_dependent.c:
	  Reporting correct nno and nel (number of nodes and elements)

2008-10-29 23:22  tan2

	* lib/global_defs.h: (for r13196) Fixing convergence criterion for
	  Stokes solver.
	  
	  * New functions global_v_norm2(), global_p_norm2(),
	  global_div_norm2() compute the L2 norm of velocity, pressure, and
	  divergence. * The L2 norm of the vector f is defined as:
	  \sum_{all elements} ( \int_{element} (f*f dA) ) / A where A is
	  the volume of the domain. * The convergence criterion is
	  controlled by parameter "accuracy" under
	  "[CitcomS.solver.vsolver]". The iteration stops if
	  (norm(div(rho*V))/norm(V) < accuracy) or ( (norm(dV)/norm(V) <
	  accuracy) and (norm(dP)/norm(P) < accuracy) for the last two
	  iterations ) * The default value of "accuracy" becomes 1e-4. *
	  The input parameters "tole_compressibility" and
	  "relative_err_accuracy" under "[CitcomS.solver.vsolver]" are
	  gone. * The mass matrix E->MASS becomes double precision (was
	  single precision).

2008-10-29 23:17  tan2

	* CitcomS/Components/Stokes_solver/Incompressible.py,
	  examples/Cookbook6/cookbook6.cfg,
	  examples/Cookbook7/cookbook7.cfg,
	  examples/Cookbook8/cookbook8.cfg,
	  examples/Cookbook9/cookbook9.cfg, examples/Full/input.sample,
	  examples/Regional/input.sample, lib/Checkpoints.c,
	  lib/Element_calculations.c, lib/General_matrix_functions.c,
	  lib/Global_operations.c, lib/Instructions.c, lib/Output_h5.c,
	  lib/Output_vtk.c, lib/Size_does_matter.c,
	  lib/Stokes_flow_Incomp.c, lib/global_defs.h,
	  module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/misc.cc,
	  module/setProperties.c, tests/coupled.cfg,
	  tests/multicoupled.cfg, tests/test2.sh, tests/test5.sh: Fixed two
	  bugs in vtk velocity output

2008-10-23 23:35  becker

	* lib/Ggrd_handling.c, lib/Initial_temperature.c,
	  lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c,
	  lib/Topo_gravity.c, lib/Viscosity_structures.c,
	  lib/global_defs.h: Initial test implementation of netcdf grd
	  based assignment of designated Euler vectors based on a code grd.

2008-09-04 22:46  tan2

	* lib/Viscosity_structures.c: multi-component chemical viscosity

2008-09-04 20:18  tan2

	* lib/Regional_sphere_related.c: Fixed issue 158: incorrect
	  E->control.fi_max with coor=1

2008-09-04 00:20  tan2

	* lib/Instructions.c, lib/Makefile.am, lib/Output_vtk.c: Some basic
	  VTK parallel XML output
	  
	  * output in vts/pvts Structured VTK XML format * only these
	  fields are available: coordinate, temperature, velocity and
	  viscosity * coordinate and velocity are in Cartesian coordinates
	  
	  Some notes for future tasks: * adding other node- or
	  element-based fields (pressure, stress, comp_nd, comp_el) is easy
	  * tracer output should be in vtp format * surf, botm, and
	  horiz_avg will be in vts format * geoid will still be as an ascii
	  table

2008-09-04 00:12  tan2

	* lib/global_defs.h: forgot to checkin this change in r12799

2008-09-04 00:11  tan2

	* CitcomS/Components/Output.py, module/setProperties.c: pyre input
	  for "self_gravitation"

2008-09-04 00:10  tan2

	* lib/Sphere_harmonics.c, lib/Topo_gravity.c: self-gravitation
	  geoid stuff
	  
	  * compute geoid due to internal buoyancy at the bottom * get rid
	  of stress arrays * seperating topo effect on surface geoid into
	  two part: surface topo and CMB topo.

2008-07-24 18:42  tan2

	* module/setProperties.c: E->viscosity.zbase_layer is not init'd in
	  pyre version. This fixes issue 155.

2008-07-24 18:21  becker

	* lib/Instructions.c: Both Eh and I were right and now the z_layer
	  check should be finally fixed.

2008-07-24 18:13  becker

	* lib/Instructions.c, lib/Viscosity_structures.c: Fixed typo that
	  provided assignment of zbase_layer thanks to Eh.

2008-07-24 01:00  becker

	* bin/Citcom.c, lib/Ggrd_handling.c, lib/Instructions.c,
	  lib/Pan_problem_misc_functions.c, lib/Viscosity_structures.c,
	  lib/viscosity_descriptions.h: Added rheology option eight. The
	  other merges are surprising.

2008-06-30 15:49  becker

	* lib/Output.c, lib/Output_gzdir.c, lib/Output_h5.c: Moved the
	  stress computation into stress output subroutine, for consistency
	  with the style of the Output...c files.

2008-06-30 02:12  becker

	* lib/Construct_arrays.c, lib/Ggrd_handling.c,
	  lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c,
	  lib/Output_gzdir.c, lib/Output_h5.c, lib/Topo_gravity.c,
	  lib/Viscosity_structures.c, lib/global_defs.h,
	  lib/viscosity_descriptions.h: Made CBF topography method and call
	  to E->solver.parallel_communication_routs_s contingent on a
	  "use_cbf_topo" parameter which is for now, by default, off, until
	  the potential remaining memory bug (?) is tracked down.
	  
	  Made sure the stress tensor is computed before stress output, as
	  CBF topo does not require the computation of the stress tensor.
	  
	  Added a z_layer input flag for zbase_layer other than the four
	  layers used for the control of phase boundary depth. (Default is
	  backward compatible.)

2008-06-27 00:53  becker

	* lib/Global_operations.c: Check in of proper version for
	  elliptical net rotation correction.

2008-06-26 23:56  becker

	* lib/Global_operations.c, lib/Instructions.c,
	  lib/Pan_problem_misc_functions.c, lib/global_defs.h: Reordered
	  loop in get_buoyancy to speed up array access.
	  
	  Fixed omission of one elliptical correction, added a flag.

2008-06-26 23:04  becker

	* lib/Determine_net_rotation.c, lib/Drive_solvers.c,
	  lib/Full_sphere_related.c, lib/Full_version_dependent.c,
	  lib/Global_operations.c, lib/Instructions.c, lib/Nodal_mesh.c,
	  lib/Output_gzdir.c, lib/Pan_problem_misc_functions.c,
	  lib/Regional_version_dependent.c, lib/Size_does_matter.c,
	  lib/global_defs.h: Replaced several trig function evaluations in
	  Size_does_matter.c witht he precomputed SinCos arrays for
	  speedup.
	  
	  Experimental ellipticity implementation has been improved
	  somewhat, and made accessible only when -DALLOW_ELLIPTICAL is
	  set. This was necessary to not slow the spherical version of the
	  code down with if statements.

2008-06-25 01:13  becker

	* lib/Determine_net_rotation.c, lib/Element_calculations.c,
	  lib/Ggrd_handling.c, lib/Global_operations.c, lib/Instructions.c,
	  lib/Output.c, lib/Output_gzdir.c,
	  lib/Pan_problem_misc_functions.c, lib/Size_does_matter.c,
	  lib/Topo_gravity.c, lib/Tracer_setup.c: Modified net rotation
	  computation for ellipticity.
	  
	  Minor additions (prototypes) to make the code compile smoothly
	  under PGI.

2008-06-24 21:18  tan2

	* lib/Construct_arrays.c, lib/Full_parallel_related.c: Modified
	  routs_s for lines. Added some debugging output and updated
	  comments.

2008-06-24 21:11  tan2

	* lib/Topo_gravity.c: Only top/bottom processors need to
	  communicate

2008-06-21 22:28  becker

	* lib/Full_boundary_conditions.c, lib/Full_parallel_related.c,
	  lib/Full_read_input_from_files.c, lib/Full_version_dependent.c,
	  lib/Ggrd_handling.c, lib/Initial_temperature.c,
	  lib/Instructions.c, lib/Regional_boundary_conditions.c,
	  lib/Regional_read_input_from_files.c, lib/global_defs.h:
	  Assignment of velocity boundary condition only called once at the
	  top multigrid level during boundary condition assignment.
	  
	  Experimental implementation of mixed velocity/free slip boundary
	  condition based on netcdf grids, in Ggrd_handling.

2008-06-20 23:01  tan2

	* lib/Output.c, lib/Output_gzdir.c, lib/Output_h5.c: Enable CBF
	  topography

2008-06-20 22:51  tan2

	* lib/Topo_gravity.c: Added back get_CBF_topo(), from Shijie Zhong,
	  with some minor modifications.
	  
	  Minor modifications: * some double arrays -> float arrays *
	  calling exchange_snode_d() -> calling *_exchange_snode_f()

2008-06-20 22:50  tan2

	* lib/Full_parallel_related.c, lib/Regional_parallel_related.c:
	  Resurrected full_parallel_communication_routs_s(), which is
	  needed by CBF topo.
	  
	  Renamed exchange_snode_f() to full_exchange_snode_f() and
	  regional_exchange_snode_f().

2008-06-20 22:42  tan2

	* lib/Size_does_matter.c: Added get_global_1d_shape_fn_L() from
	  Shijie Zhong

2008-06-20 22:41  tan2

	* lib/Shape_functions.c: Compute E->L and E->Lx 1d shape functions
	  (1d is a misnomer, they are 2d actually).

2008-06-20 19:08  tan2

	* lib/Full_version_dependent.c: The function declaration was put at
	  a wrong place.

2008-06-19 22:20  tan2

	* visual/project_geoid.c: Change back the order of input arguments
	  to match the manual.

2008-06-19 21:43  tan2

	* lib/Viscosity_structures.c: The comment in rheol=4 doesn't match
	  the code and is removed.
	  
	  Added option rheol=7, with a complete temperature- and
	  pressure-dependent Arrhenius law.
	  
	  This fixed issue152.

2008-06-19 21:42  tan2

	* lib/Full_version_dependent.c, lib/Sphere_harmonics.c: Added
	  debugging (but disabled) function for spherical harmonics
	  expansion.

2008-06-19 01:05  tan2

	* lib/Global_operations.c, lib/Topo_gravity.c: Send geoid arrays to
	  vertical columns of processors. After this fix, the geoid output
	  is the same for nprocz=1 and nprocz>1.

2008-06-19 01:04  tan2

	* lib/Size_does_matter.c, lib/Sphere_harmonics.c: Compute
	  E->surf_det (top surface area, ie. surface jacobian, of an
	  element) on a unit sphere.
	  
	  Use E->surf_det, instead of the surface jacobian returned by
	  get_global_1d_shape_fn(), to expand spherical harmonics.
	  
	  The surface jacobian returned by get_global_1d_shape_fn() is
	  defined at the top radius of the current mesh. When nprocz>1, the
	  top radius is not the same as the outer radius of the sphere for
	  processors. As a result, the spherical harmonics expansion gave
	  incorrect result when nprocz>1 in the previous revisions.

2008-06-18 22:35  becker

	* lib/Global_operations.c: Speed up of computation by precomputing
	  constants.

2008-06-17 21:23  tan2

	* lib/General_matrix_functions.c, lib/Output.c, lib/Output_gzdir.c,
	  lib/Output_h5.c, lib/Sphere_harmonics.c, lib/Topo_gravity.c,
	  lib/global_defs.h: Compute geoid with self gravitation. Code
	  contributed by Shijie Zhong.

2008-06-17 20:31  becker

	* lib/Drive_solvers.c, lib/General_matrix_functions.c,
	  lib/Instructions.c, lib/Output.c, lib/Size_does_matter.c,
	  lib/Solver_conj_grad.c, lib/Solver_multigrid.c,
	  lib/Sphere_harmonics.c, lib/Topo_gravity.c, lib/global_defs.h:
	  Added a few more comments and made a few loops more efficient.

2008-06-14 00:00  becker

	* bin/Citcom.c, lib/Full_read_input_from_files.c,
	  lib/Ggrd_handling.c, lib/Instructions.c,
	  lib/Pan_problem_misc_functions.c, lib/Problem_related.c,
	  lib/global_defs.h: Added a few comments on Rayleigh number netcdf
	  control.

2008-06-13 23:36  tan2

	* NEWS: update NEWS item

2008-06-13 23:35  tan2

	* lib/Ggrd_handling.c, lib/Global_operations.c, lib/Output_gzdir.c:
	  Replaced MPI_COMM_WORLD by E->parallel.world.
	  
	  MPI_COMM_WORLD is the global communicator. E->parallel.world is
	  the communicator for the current solver. These two are different
	  in a coupled run. Before this fix, full-regional coupling will
	  dead lock.

2008-06-13 23:34  tan2

	* bin/Citcom.c: Added some comments

2008-06-13 23:33  tan2

	* CitcomS/Controller.py: To be consistent with C version, disable
	  checkpoint point output at 0th step if restarting.

2008-06-13 23:32  tan2

	* lib/Construct_arrays.c, lib/Drive_solvers.c,
	  lib/Full_parallel_related.c, lib/Full_version_dependent.c,
	  lib/General_matrix_functions.c, lib/Regional_parallel_related.c,
	  lib/Regional_version_dependent.c, lib/Stokes_flow_Incomp.c:
	  Correctly counting the global number of equations. This will
	  slightly affect the results of the stokes solver.
	  
	  This avoid double counting the overlapping nodes between
	  processors and the global norm of velocity vector.

2008-06-13 23:25  tan2

	* module/Exchanger/Boundary.cc: Using firewall channel, since error
	  channel doesn't stop the code.

2008-06-13 23:24  tan2

	* lib/Stokes_flow_Incomp.c: Decalred variables as double to avoid
	  float-double conversion later in the loop.

2008-06-13 19:14  tan2

	* visual/project_geoid.c: update the help message

2008-06-12 21:22  becker

	* bin/Citcom.c, lib/Checkpoints.c, lib/Construct_arrays.c,
	  lib/Determine_net_rotation.c, lib/Drive_solvers.c,
	  lib/Full_boundary_conditions.c, lib/Full_read_input_from_files.c,
	  lib/Full_sphere_related.c, lib/Full_version_dependent.c,
	  lib/Ggrd_handling.c, lib/Instructions.c, lib/Output.c,
	  lib/Output_gzdir.c, lib/Pan_problem_misc_functions.c,
	  lib/Process_buoyancy.c, lib/Regional_boundary_conditions.c,
	  lib/Size_does_matter.c, lib/Topo_gravity.c, lib/Tracer_setup.c,
	  lib/global_defs.h, visual/project_geoid.c: Added tentative
	  implementation of a rotating, elliptical Earth.
	  
	  Made restart for constant viscosity cases possible.
	  
	  Added alternative geoid computation place holder for
	  self-gravitating mantle, to be filled out by Shijie's old code.

2008-05-30 18:42  becker

	* visual/project_geoid.c: Fixed typo in memory allocation procedure
	  that led to core dump.

2008-05-12 21:22  gurnis

	* NEWS: fixed typo

2008-05-12 21:16  gurnis

	* NEWS: Just a place holder for the next release

2008-05-05 19:17  gurnis

	* lib/Regional_read_input_from_files.c: Bug Fix

2008-05-01 22:59  tan2

	* CitcomS/Components/BC.py, CitcomS/Solver/Solver.py,
	  module/bindings.c, module/misc.c, module/misc.h: Add python
	  binding to update top surface temperatures

2008-05-01 22:56  gurnis

	* bin/Citcom.c, lib/Full_boundary_conditions.c,
	  lib/Full_read_input_from_files.c, lib/Problem_related.c,
	  lib/Regional_boundary_conditions.c,
	  lib/Regional_read_input_from_files.c, lib/Viscosity_structures.c:
	  More additions to allow top surface temperatures to be read in a
	  each time step. Should read in every time step for C only
	  version. Additional changes for Pyre version to follow; will test
	  more once these changes are made.
	  
	  Small changes to viscosity structures when reading in materials
	  for each element. More documentation to follow.

2008-05-01 00:51  tan2

	* CitcomS/Components/Param.py, lib/Instructions.c, lib/Output_h5.c,
	  module/setProperties.c: Inputing tbcs_file &
	  temperature_boundary_file

2008-04-30 23:11  gurnis

	* lib/global_defs.h: Start to add new features for reading surface
	  temperature for all top surface node points
	  
	  Added new variables to the CONTROL structure vbcs_file &
	  temperature_boundary_fi le

2008-04-06 21:58  becker

	* bin/Citcom.c, lib/Advection_diffusion.c,
	  lib/Full_read_input_from_files.c, lib/Ggrd_handling.c,
	  lib/Instructions.c, lib/Pan_problem_misc_functions.c,
	  lib/Problem_related.c, lib/Regional_read_input_from_files.c,
	  lib/ggrd_handling.h, lib/global_defs.h,
	  lib/viscosity_descriptions.h: GMT/Netcdf grd input can now deal
	  with velocity boundary conditions, material dependence, and local
	  Rayleigh number in surface layers.

2008-03-05 21:15  tan2

	* lib/Instructions.c: Close trace_log files when finalizing

2008-03-05 21:07  tan2

	* lib/Full_sphere_related.c, lib/Full_version_dependent.c,
	  lib/General_matrix_functions.c, lib/Instructions.c,
	  lib/Obsolete.c, lib/Regional_version_dependent.c,
	  lib/global_defs.h: Clean up unused arrays and functions

2008-03-05 21:06  tan2

	* lib/Tracer_setup.c: Write exclusive tracer time every 20 steps

2008-03-05 21:04  tan2

	* examples/Makefile.am, lib/Full_sphere_related.c,
	  lib/Full_version_dependent.c, lib/General_matrix_functions.c,
	  lib/Instructions.c, lib/Obsolete.c,
	  lib/Regional_version_dependent.c, lib/Tracer_setup.c,
	  lib/global_defs.h, visual/Makefile.am: Revert r11328

2008-03-05 20:50  tan2

	* examples/Makefile.am, lib/Full_sphere_related.c,
	  lib/Full_version_dependent.c, lib/General_matrix_functions.c,
	  lib/Instructions.c, lib/Obsolete.c,
	  lib/Regional_version_dependent.c, lib/Tracer_setup.c,
	  lib/global_defs.h, visual/Makefile.am: Write exclusive tracer
	  time every 20 steps

2008-02-28 01:03  tan2

	* lib/Composition_related.c: Removed artificial tolerance of empty
	  elements. This greatly decreases the minimal number of tracers
	  per element required for a given mesh.
	  
	  This fixed issue140.

2008-02-28 01:00  tan2

	* lib/Process_buoyancy.c: Minor tweak

2008-02-27 07:42  becker

	* lib/Full_read_input_from_files.c, lib/Ggrd_handling.c,
	  lib/Initial_temperature.c, lib/Instructions.c, lib/Lith_age.c,
	  lib/Output_gzdir.c, lib/Pan_problem_misc_functions.c,
	  lib/Regional_read_input_from_files.c, lib/Tracer_setup.c,
	  lib/ggrd_handling.h: Built surface velocity BC support via Netcdf
	  grd files back in. This needs more testing, but it would be good
	  to have the framework in place before new additions are made.
	  Also, age control is not yet implemented, but will be soon.

2008-02-21 01:25  tan2

	* bin/Citcom.c: Removed unnecessary call to construct_mat_group()

2008-02-21 01:03  tan2

	* CitcomS/BaseApplication.py, CitcomS/Controller.py,
	  lib/Full_tracer_advection.c, lib/Process_buoyancy.c,
	  module/initial_conditions.c: Finished interpolating fields onto
	  tracers

2008-02-21 01:02  tan2

	* lib/Full_tracer_advection.c: Renamed fix_phi() to fix_angle()

2008-02-21 01:01  tan2

	* lib/Full_tracer_advection.c: Fixed issue139. Bug for tracers near
	  South pole.

2008-02-21 01:00  tan2

	* lib/Full_tracer_advection.c, lib/Process_buoyancy.c,
	  lib/Tracer_setup.c: Get new tracers in post processing stage

2008-02-21 00:56  tan2

	* lib/Pan_problem_misc_functions.c, lib/Tracer_setup.c: Read
	  multiple extraq

2008-02-21 00:55  tan2

	* lib/Composition_related.c, lib/Instructions.c, lib/Output.c,
	  lib/Output_gzdir.c: Write averaged composition in horiz_avg
	  output. The HDF5 part of output is not implemented...

2008-02-21 00:54  tan2

	* lib/Process_buoyancy.c: Removed horizontal average from
	  output_interpolated_fields()

2008-02-21 00:53  tan2

	* lib/Instructions.c, lib/Process_buoyancy.c, lib/global_defs.h:
	  Compute horizontal average for composition fields

2008-02-17 00:14  becker

	* bin/Citcom.c, lib/Full_read_input_from_files.c,
	  lib/Ggrd_handling.c, lib/Initial_temperature.c,
	  lib/Instructions.c, lib/Regional_read_input_from_files.c,
	  lib/Viscosity_structures.c, lib/convection_variables.h,
	  lib/global_defs.h: Modified Citcom.c such that E->mat gets
	  assigned based on element depth (as was default before), even if
	  mat_control is not selected.
	  
	  Added (back in?) ggrd netcdf type VIP prefactor material control
	  via ggrd_mat_control flags (as documented in Instructions.c)
	  
	  Renamed some of the ggrd stuff to make it more modular.

2008-02-09 00:14  tan2

	* lib/Process_buoyancy.c: Interpolate fields in post_processing()
	  
	  * The parameter "itracer_interpolate_fields" is the same as
	  "model_type" in the AVM code. * If itracer_interpolate_fields is
	  1, 2, or 3, it interpolates temperature and compositions. The
	  horizonal average is not removed yet.

2008-02-08 23:58  tan2

	* lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c:
	  Refactored the functions.
	  
	  * get shape functions on tracer location * interpolate data using
	  acquired shape functions

2008-02-08 23:56  tan2

	* CitcomS/Solver/Solver.py, bin/Citcom.c, module/bindings.c,
	  module/initial_conditions.c, module/initial_conditions.h: Added
	  binding for post_processing(). Exit program after post processing
	  and saving results.

2008-02-08 23:54  tan2

	* lib/Full_tracer_advection.c, lib/global_defs.h: * Using a
	  different reference point for uv space. This fixed a nasty bug
	  when some cap extends over ~pi/2.
	  
	  * A bunch of debugging output (disabled)
	  
	  * Disable more debugging output

2008-02-08 23:50  tan2

	* CitcomS/Components/Tracer.py, lib/Full_tracer_advection.c,
	  lib/Tracer_setup.c, lib/tracer_defs.h, module/setProperties.c:
	  Added new parameter: itracer_interpolate_fields
	  
	  When it is 0 (default), nothing is done. Otherwise, the
	  convection fields are interpolated onto the location of tracers.

2008-02-04 23:23  tan2

	* examples/Makefile.am, visual/Makefile.am: Reverted part of
	  unwannted change

2008-02-04 23:21  tan2

	* examples/Makefile.am, module/misc.c, visual/Makefile.am: Fixed
	  potential memory leak

2008-02-04 23:13  tan2

	* module/Exchanger/exchangers.cc: Fixed bugs in managing reference
	  counts and potential double-free

2008-02-04 20:40  tan2

	* lib/Initial_temperature.c: Fixed a regression reported by Lydia
	  Dicaprio.
	  
	  The initial temperature should be constructured in this order: 1.
	  if tic_method=-1, read from velo files. 2. if lith_age=1,
	  read/constructed from lith_age files. 3. otherwise, call
	  {full,regional}_construct_tic_from_input()

2008-01-22 19:52  tan2

	* lib/Advection_diffusion.c, lib/Element_calculations.c,
	  lib/Size_does_matter.c, lib/Topo_gravity.c,
	  lib/Viscosity_structures.c: Renamed functions

2008-01-22 19:38  tan2

	* lib/Advection_diffusion.c, lib/Element_calculations.c,
	  lib/Global_operations.c, lib/Instructions.c, lib/Obsolete.c,
	  lib/Process_buoyancy.c, lib/Size_does_matter.c,
	  lib/Topo_gravity.c, lib/Viscosity_structures.c,
	  lib/global_defs.h: Computes the derivatives of shape functions
	  and jacobians only once and stores them for later use. This
	  reduces the total cpu time of cookbook8 by 13%.
	  
	  - get_global_shape_fn_sph() computes and stores the derivatives
	  of shape functions and jacobians.
	  
	  - Moved get_global_shape_fn() to Obsolete.c
	  
	  - Calling construct_shape_function_derivatives() in
	  initial_mesh_solver_setup(). This function call
	  get_global_shape_fn_sph() for each element.
	  
	  - get_rtf_at_vpts() and get_rtf_at_ppts() are for coord.
	  transformation matrix at vpts and ppts respectively
	  
	  - Passed arguments by references in PG solvers instead of by
	  values to avoid copying.

2008-01-17 02:06  becker

	* lib/Full_tracer_advection.c, lib/global_defs.h: Changed GNOMONIC
	  to CITCOM_GNOMONIC to avoid namespace conflict with GMT gmt.h

2008-01-16 20:53  tan2

	* lib/Tracer_setup.c: Forgot to checkin this file

2008-01-16 20:34  tan2

	* lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c,
	  lib/tracer_defs.h: Added timing information for tracer module.
	  The timing is reported in *.tracer_log.* files.

2008-01-16 20:30  tan2

	* lib/Full_tracer_advection.c, lib/global_defs.h,
	  lib/tracer_defs.h: A more memory efficient way to find shape
	  function for tracers.
	  
	  - Migrated E->tracer.UV to E->gnomonic. The reference point is
	  the 1st node of the local mesh. The 0th element of E->gnomonic
	  stores the sine of cosine of reference theta. - Convertd
	  shape_coefs array from size of nel to size of snel to save
	  memory.

2008-01-15 23:36  tan2

	* AUTHORS: Added Luis Armendariz to the author list

2008-01-15 23:11  tan2

	* lib/Full_sphere_related.c: Simplified loop over levels

2008-01-15 23:05  tan2

	* examples/Makefile.am, lib/Full_sphere_related.c,
	  lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c,
	  lib/Tracer_setup.c, lib/global_defs.h, lib/tracer_defs.h,
	  visual/Makefile.am: Reverted previous checkin

2008-01-15 23:01  tan2

	* examples/Makefile.am, lib/Full_sphere_related.c,
	  lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c,
	  lib/Tracer_setup.c, lib/global_defs.h, lib/tracer_defs.h,
	  visual/Makefile.am: Simplified loop over levels

2008-01-15 00:29  tan2

	* lib/Full_sphere_related.c: Forgot to rename variables

2008-01-14 23:03  tan2

	* lib/Full_sphere_related.c: Fixed 2 bugs in full_coord_of_cap().
	  
	  1. x and y arrays were overridden in the loop of level. 2. Choice
	  of reference point was not optimal and may cause round off
	  problem.

2008-01-03 19:51  tan2

	* lib/Construct_arrays.c, lib/Full_geometry_cartesian.c,
	  lib/Full_sphere_related.c, lib/Full_tracer_advection.c,
	  lib/Full_version_dependent.c, lib/Output_h5.c,
	  lib/Regional_version_dependent.c, lib/Sphere_harmonics.c,
	  lib/Sphere_util.c, lib/global_defs.h: Re-applied patches that got
	  reverted in r8973

2007-12-29 07:02  becker

	* lib/Construct_arrays.c, lib/Full_geometry_cartesian.c,
	  lib/Full_sphere_related.c, lib/Full_tracer_advection.c,
	  lib/Full_version_dependent.c, lib/Instructions.c,
	  lib/Output_h5.c, lib/Regional_version_dependent.c,
	  lib/Sphere_harmonics.c, lib/Sphere_util.c, lib/global_defs.h:
	  Trying to sync back up, those should be old changes, I hope.

2007-12-20 20:30  tan2

	* lib/Full_sphere_related.c, lib/Full_tracer_advection.c,
	  lib/Full_version_dependent.c, lib/Sphere_harmonics.c,
	  lib/Sphere_util.c, lib/global_defs.h, tests/gnomonic.c: Generated
	  global mesh by great circles. Tracer module can split the cap in
	  the map view now.

2007-12-20 20:27  tan2

	* lib/Full_geometry_cartesian.c: Fine tune the mesh so that each
	  cap has the same surface area

2007-12-20 20:26  tan2

	* lib/Regional_version_dependent.c: Removed obsolete code

2007-12-20 20:25  tan2

	* lib/Construct_arrays.c: Fixed a redundant cast

2007-12-17 22:06  tan2

	* lib/Output_h5.c: Fixed phase change width

2007-11-12 22:42  tan2

	* NEWS, configure.ac: Updated the version number and file NEWS

2007-11-12 22:38  tan2

	* module/Exchanger/Makefile.am: Added mishing header file to the
	  makefile, also avoided compiling unused code.

2007-11-11 20:37  becker

	* lib/Construct_arrays.c, lib/Full_obsolete.c, lib/Ggrd_handling.c,
	  lib/Material_properties.c, lib/global_defs.h: Synching with the
	  new release, none of those changes should be relevant.

2007-11-08 22:41  tan2

	* ChangeLog: Updated file ChangeLog to r8244

2007-11-08 22:31  tan2

	* lib/Instructions.c, lib/Pan_problem_misc_functions.c: Replaced a
	  system call by std C library remove() and disabled another system
	  call (backup input file). Partially fixed issue130. All remaining
	  system calls are in lib/Output_gzdir.c.

2007-11-08 21:38  tan2

	* ChangeLog: Updated file ChangeLog to r8242

2007-11-08 21:36  tan2

	* examples/Makefile.am: Removed binary checkpoint files from
	  makefile, as the file size is too big for distribution.

2007-11-08 21:17  tan2

	* ChangeLog: Updated file ChangeLog to r8240

2007-11-08 19:19  tan2

	* configure.ac: Update the version number

2007-11-08 19:18  tan2

	* NEWS: Update NEWS

2007-11-08 19:18  tan2

	* examples/Cookbook5/cookbook5.cfg: Dereased the timestep size to
	  reduce artifacts in advection

2007-11-07 19:52  tan2

	* examples/Cookbook4/cookbook4.cfg: Decreased the # of processors.
	  This is the only way I can reproduce single-cell convection as in
	  the manual.

2007-11-07 19:52  tan2

	* CitcomS/Components/Output.py, lib/Output.c: Removed comp_el from
	  default output, since it is not required for restart anymore.

2007-11-07 19:51  tan2

	* lib/Stokes_flow_Incomp.c: Print a warning when matrix eqn solver
	  not converging

2007-11-06 23:18  tan2

	* examples/Cookbook7/cookbook7.cfg: Added cgrad solver convergence
	  parameters, increased buoyancy_ratio and lower the # of steps

2007-11-06 23:18  tan2

	* examples/Cookbook6/cookbook6.cfg: Removed unused multigrid
	  parameters

2007-11-06 23:18  tan2

	* examples/Full/input.sample, examples/Regional/input.sample:
	  Increase vlowstep to match the default value in pyre

2007-11-06 23:17  tan2

	* visual/project_geoid.c: Fixed a few memory errors

2007-11-06 01:04  tan2

	* lib/Output.c: Init'd some variables about vtk_io, which might be
	  accessed with uninit'd values in output_finalize()

2007-11-06 01:04  tan2

	* lib/Full_obsolete.c, lib/Global_operations.c, lib/Obsolete.c,
	  lib/Sphere_harmonics.c, lib/Topo_gravity.c: Shrank the size of
	  sph. harm arrays

2007-11-06 01:03  tan2

	* lib/Regional_obsolete.c: Removed functions related sph. harm in
	  lib/Regional_obsolete.c

2007-11-06 01:03  tan2

	* lib/Topo_gravity.c: Scaled topo with variable gravity. Fixed an
	  error in comment. Rearranged computation.

2007-11-01 23:33  tan2

	* lib/Full_version_dependent.c: Fixed an error in comment

2007-11-01 23:33  tan2

	* lib/Stokes_flow_Incomp.c: Print dv/v=dp/p=1.0 for the 1st Uzawa
	  iteraion

2007-10-30 22:29  tan2

	* visual/Makefile.am: Minor modification

2007-10-30 21:54  tan2

	* visual/Makefile.am: Added the C program project_geoid to the
	  makefile

2007-10-30 21:53  tan2

	* visual/project_geoid.c: A post-processing program to project
	  geoid coefficents onto a regular (longitude, latitude) mesh

2007-10-30 21:50  tan2

	* lib/Topo_gravity.c: Fixed a bug in dimensionalizing density.
	  Provided the formula of geoid calculation in the comments.
	  Rearranged the order of functions.

2007-10-30 21:49  tan2

	* lib/Element_calculations.c, lib/Instructions.c: Compute
	  d(rho)/dr/rho from rho(r)

2007-10-22 20:57  tan2

	* ChangeLog: Updated file ChangeLog to r8170

2007-10-22 20:26  tan2

	* NEWS: Updated NEWS

2007-10-22 19:46  tan2

	* AUTHORS, configure.ac: Minor update

2007-10-22 19:44  tan2

	* INSTALL, README: Simpilify INSTALL

2007-10-22 19:03  tan2

	* lib/Advection_diffusion.c: Eliminated unnecessary computation

2007-10-22 19:03  tan2

	* lib/Advection_diffusion.c: Variable material properties in latent
	  heat correction on adiabatic cooling

2007-10-22 19:02  tan2

	* lib/Advection_diffusion.c, lib/Phase_change.c: Added some
	  comments

2007-10-19 19:24  tan2

	* lib/Advection_diffusion.c, lib/Phase_change.c, lib/global_defs.h,
	  module/setProperties.c: Renamed control.width* ->
	  control.inv_width* for clarity

2007-10-18 18:53  tan2

	* CitcomS/Coupler/Coupler.py, module/Exchanger/Convertor.cc,
	  module/Exchanger/Convertor.h, module/Exchanger/exchangers.cc:
	  Renamed coupler inventory: dimensional -> si_unit and
	  transformational -> cartesian

2007-10-17 22:44  tan2

	* examples/Cookbook5/cookbook5.cfg,
	  examples/Cookbook9/cookbook9.cfg: Minor change in the examples

2007-10-17 20:56  tan2

	* bin/Citcom.c: Added comments on where C code is replaced by
	  python code in Citcom.c

2007-10-17 20:55  tan2

	* lib/Determine_net_rotation.c, lib/Drive_solvers.c,
	  lib/Output_gzdir.c, lib/Stokes_flow_Incomp.c,
	  lib/Viscosity_structures.c, lib/viscosity_descriptions.h: Put the
	  rest of r8111 back

2007-10-17 20:33  tan2

	* examples/Full/input.sample, examples/Regional/input.sample: Fixed
	  input diffusivity parameter in the examples, from r8111.

2007-10-17 20:32  tan2

	* lib/Drive_solvers.c, lib/Global_operations.c,
	  lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c:
	  Added back minor modification from r8111

2007-10-17 18:40  tan2

	* examples/Cookbook9/cookbook9.cfg: Fixed a typo in the example

2007-10-17 18:36  tan2

	* lib/Global_operations.c: Fixed a bug in remove_rigid_rot()

2007-10-17 18:35  tan2

	* bin/Citcom.c, examples/Full/input.sample,
	  lib/Determine_net_rotation.c, lib/Drive_solvers.c,
	  lib/Full_version_dependent.c, lib/Global_operations.c,
	  lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c,
	  lib/Output_gzdir.c, lib/Stokes_flow_Incomp.c,
	  lib/Viscosity_structures.c, lib/viscosity_descriptions.h: Roll
	  back r8111, reading velo files for init. temperature stays as
	  tic_method=-1. Other changes in r8111 will be put back later.

2007-10-13 19:07  becker

	* bin/Citcom.c, examples/Full/input.sample,
	  lib/Determine_net_rotation.c, lib/Drive_solvers.c,
	  lib/Full_version_dependent.c, lib/Global_operations.c,
	  lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c,
	  lib/Output_gzdir.c, lib/Stokes_flow_Incomp.c,
	  lib/Viscosity_structures.c, lib/viscosity_descriptions.h: Fixed
	  rigid rotation code bug. Added restart=2 option which will not
	  use checkpoints, but tic_method=-1 style temperature input
	  (formally realized via tic_method=-1, but this should be cleaner)
	  fixed input diffusivity parameter in full example file.

2007-10-12 20:24  tan2

	* tests/coupled.cfg: Turn off monitor_max_T in the test

2007-10-12 20:23  tan2

	* module/Exchanger/Boundary.cc: Boundary class is for regional
	  model only, add a checking for it.

2007-10-11 01:23  tan2

	* examples/Cookbook9, examples/Cookbook9/cookbook9.cfg,
	  examples/Cookbook9/ic, examples/Cookbook9/ic/cntn.velo.0.0,
	  examples/Cookbook9/ic/cntn.velo.1.0,
	  examples/Cookbook9/ic/embd.velo.0.0,
	  examples/Cookbook9/ic/embd.velo.1.0, examples/Cookbook9/velocity,
	  examples/Cookbook9/velocity/bvel.dat0,
	  examples/Cookbook9/velocity/bvel.dat1, examples/Makefile.am:
	  Cookbook 9: nested solver coupling + coor_refine + tsolver tuning

2007-10-11 00:03  becker

	* lib/Process_buoyancy.c: Wiser now, commented in the E->fp output

2007-10-10 23:40  becker

	* bin/Citcom.c, lib/Construct_arrays.c,
	  lib/Full_version_dependent.c, lib/Ggrd_handling.c,
	  lib/Initial_temperature.c, lib/Instructions.c,
	  lib/Pan_problem_misc_functions.c, lib/Process_buoyancy.c,
	  lib/Regional_sphere_related.c, lib/Regional_version_dependent.c,
	  lib/Viscosity_structures.c, lib/convection_variables.h,
	  lib/global_defs.h: Added coor=3 option for radial node spacing a
	  la CitcomCU. Streamlined ggrd temperature init. Added file flush
	  to heat flow output.

2007-10-10 21:00  tan2

	* CitcomS/Coupler/Coupler.py: Add an assertion

2007-10-10 20:11  tan2

	* CitcomS/Components/Stokes_solver/Incompressible.py,
	  examples/Cookbook8/cookbook8.cfg, examples/Full/input.sample,
	  examples/Regional/input.sample, lib/Drive_solvers.c,
	  lib/Global_operations.c, lib/Instructions.c, lib/global_defs.h,
	  module/setProperties.c: Remove rigid body rotation from the
	  velocity solution from global model.
	  
	  A input parameter 'solver.vsolver.remove_rigid_rotation', default
	  to on, indicate whether to remove the rigid body rotation. For
	  free-slip model, this parameter should be on. For model with
	  imposed plate velocity, it is advised to turn off this parameter.

2007-10-05 20:02  tan2

	* CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py,
	  CitcomS/Coupler/EmbeddedCoupler.py,
	  CitcomS/Solver/CoupledSolver.py: Renamed excludeTop ->
	  exclude_top, and excludeBottom -> exclude_bottom. (No other
	  CitcomS parameter uses CamelCase.)
	  
	  Reworked the interaction of initial temperature and coupling.
	  Created a new parameter exchange_initial_temperature.

2007-10-05 20:00  tan2

	* CitcomS/Components/Stokes_solver/Incompressible.py: Strengthen
	  the default convergence criterion for the 3rd iteration in
	  compressible cg solver

2007-10-05 19:58  tan2

	* lib/Regional_read_input_from_files.c: Disable a debugging output

2007-10-05 19:58  tan2

	* CitcomS/Coupler/MultiC_Coupler.py,
	  CitcomS/Coupler/MultiE_Coupler.py: Add licence text to the
	  multi-couplers

2007-10-05 19:57  tan2

	* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
	  lib/Advection_diffusion.c: Turn off filter_temp by default since
	  it's not in the energy equation

2007-10-04 19:35  becker

	* lib/Viscosity_structures.c: Fxied material assignment bug in
	  PDEPV (0 vs. 1 array issue...)

2007-10-01 20:38  tan2

	* examples/Cookbook1/cookbook1.cfg,
	  examples/Cookbook2/cookbook2.cfg,
	  examples/Cookbook4/cookbook4.cfg,
	  examples/Cookbook5/cookbook5.cfg, examples/Cookbook5/ic,
	  examples/Cookbook5/restart_files,
	  examples/Cookbook6/cookbook6.cfg,
	  examples/Cookbook7/cookbook7.cfg, examples/Makefile.am,
	  examples/example1.cfg: Updated the cookbook scripts

2007-10-01 19:26  tan2

	* examples/Cookbook8, examples/Cookbook8/cookbook8.cfg,
	  examples/Cookbook8/coord.dat, examples/Cookbook8/restart,
	  examples/Cookbook8/restart/cookbook8.chkpt.0.9000,
	  examples/Cookbook8/restart/cookbook8.chkpt.1.9000,
	  examples/Cookbook8/restart/cookbook8.chkpt.10.9000,
	  examples/Cookbook8/restart/cookbook8.chkpt.11.9000,
	  examples/Cookbook8/restart/cookbook8.chkpt.2.9000,
	  examples/Cookbook8/restart/cookbook8.chkpt.3.9000,
	  examples/Cookbook8/restart/cookbook8.chkpt.4.9000,
	  examples/Cookbook8/restart/cookbook8.chkpt.5.9000,
	  examples/Cookbook8/restart/cookbook8.chkpt.6.9000,
	  examples/Cookbook8/restart/cookbook8.chkpt.7.9000,
	  examples/Cookbook8/restart/cookbook8.chkpt.8.9000,
	  examples/Cookbook8/restart/cookbook8.chkpt.9.9000,
	  examples/Makefile.am: Added Cookbook8 for compressible model +
	  geoid + checkpoint + vsolver tuning

2007-09-28 23:36  becker

	* lib/Full_version_dependent.c, lib/Initial_temperature.c,
	  lib/Output_gzdir.c: Fixed restart I/O bug in Output_gzdir.

2007-09-27 19:33  tan2

	* bin/Citcom.c, lib/Output_gzdir.c: Added function prototype and
	  fixed a few errors

2007-09-27 19:07  tan2

	* lib/Checkpoints.c, lib/Composition_related.c, lib/Tracer_setup.c,
	  lib/composition_related.h: Shrink the size of checkpoint files

2007-09-27 19:07  tan2

	* CitcomS/Components/Sphere/Sphere.py,
	  lib/Regional_sphere_related.c, module/setProperties.c: Enable
	  coor_refine for regional model, only radial coordinate is refined

2007-09-25 19:40  tan2

	* lib/Instructions.c: Fixed a bug in vtkio

2007-09-25 01:31  tan2

	* CitcomS/Components/Param.py, lib/Instructions.c,
	  lib/Material_properties.c, lib/global_defs.h,
	  module/setProperties.c: Introducing choice of reference state:
	  
	  When solver.param.reference_state=0, the reference state is read
	  from a file (solver.param.refstate_file)
	  
	  When solver.param.reference_state=1 (default), the reference
	  state is calculated using Adams-Williamson equation of state.

2007-09-24 21:29  tan2

	* configure.ac, lib/Output_gzdir.c: Detect the presence of libz and
	  enable ascii-gz at configure time

2007-09-24 21:28  tan2

	* lib/Instructions.c, lib/Material_properties.c, lib/global_defs.h:
	  Comment out varialbe thermal conductivity. Removed unused struct
	  members.

2007-09-24 21:28  tan2

	* lib/Advection_diffusion.c: Multiply rho*cp to DT/dt

2007-09-19 20:34  tan2

	* lib/Material_properties.c: Don't write to log file, since only
	  rank-0 proc can access it

2007-09-19 20:34  tan2

	* lib/Composition_related.c, lib/Instructions.c: Set default value
	  for tracer/composition flags earlier

2007-09-19 20:33  tan2

	* lib/Checkpoints.c: Shrink the size of arrays

2007-09-19 20:31  tan2

	* lib/Instructions.c: Shrink the size of arrays

2007-09-19 20:30  tan2

	* lib/Output.c, lib/Output_gzdir.c, lib/Output_h5.c,
	  lib/Topo_gravity.c: Fixed uninit'd heat flux and geoid arrays
	  bugs, as reported by valgrind

2007-09-19 00:28  becker

	* lib/Advection_diffusion.c, lib/Output_gzdir.c: Minor bug fix in
	  Output_gzidir, output_heating function didn't work.

2007-09-18 23:08  tan2

	* lib/Checkpoints.c: Fixed a memory bug in checkpoint

2007-09-18 23:07  tan2

	* lib/Regional_tracer_advection.c: Setup composition for regional
	  model

2007-09-18 01:52  leif

	* configure.ac, setup.py: Fix for Issue129: "CitcomS configured
	  without exchanger still links with -lExchanger". Also, use
	  CIT_HEADER_MPI so that configuring --with-exchanger using MPICH2
	  works (see Issue14 and Issue57).

2007-09-17 20:30  tan2

	* lib/Composition_related.c: Generalized init. composition from
	  neighbors for multi-component composition

2007-09-17 19:07  tan2

	* lib/Composition_related.c: Using neighboring elements to
	  determine the initial composition, if only a few elements are
	  empty.

2007-09-15 00:17  tan2

	* lib/Tracer_setup.c: Revert accidental commit in part of r7957

2007-09-14 23:39  tan2

	* lib/Advection_diffusion.c, lib/Phase_change.c: Rearranged
	  computation of latent heat and the test condition of phase change

2007-09-14 23:11  tan2

	* lib/Advection_diffusion.c: Added the contribution of latent heat
	  to the diffusion term

2007-09-14 23:11  tan2

	* lib/Obsolete.c, lib/Phase_change.c: Replace abs() by fabs()

2007-09-14 23:10  tan2

	* lib/Advection_diffusion.c: Consevert energy (sum of rho*cp*T)
	  instead of temperature (sum of T) in the Lenardic filter, also
	  fixed a long-standing bug (abs -> fabs)

2007-09-14 23:09  tan2

	* lib/Advection_diffusion.c: Changed the magic numbers (0.0 and
	  1.0) to const variables, reindent the code.

2007-09-13 22:36  tan2

	* CitcomS/Solver/Solver.py, lib/Instructions.c,
	  lib/Material_properties.c, lib/global_defs.h,
	  module/setProperties.c: Comment out adiabatic temperature profile
	  for now, since it is not used in the code.

2007-09-12 19:24  tan2

	* visual/parser.py: Fixed a problem when the input string is empty

2007-09-12 19:24  tan2

	* lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c,
	  lib/Tracer_setup.c, lib/global_defs.h: Added heating file to
	  optional output

2007-09-12 19:24  tan2

	* lib/Stokes_flow_Incomp.c: Keep the load vector intact in the bicg
	  solver

2007-09-12 19:23  tan2

	* lib/Composition_related.c, lib/Full_tracer_advection.c,
	  lib/Tracer_setup.c: Using drand48() instead of rand() to improve
	  the quality of random tracers. Added some debugging output if the
	  tracer count is low.

2007-09-12 19:22  tan2

	* CitcomS/Components/Tracer.py, lib/Composition_related.c,
	  lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c,
	  lib/Tracer_setup.c, module/setProperties.c: Add new input boolean
	  parameter 'itracer_warnings'. Default to on. When it is off, the
	  exit condition of tracer is relaxed.

2007-09-12 19:19  tan2

	* lib/Stokes_flow_Incomp.c: Removed the test for F=0 load vector
	  bug. The bug was fixed in r7940.

2007-09-07 22:53  tan2

	* lib/Advection_diffusion.c, lib/Size_does_matter.c: Fixed tsolver.
	  
	  Fixed a bug in TMass and another in convert element # to nz.

2007-09-05 22:35  tan2

	* lib/Checkpoints.c, lib/Construct_arrays.c, lib/Drive_solvers.c,
	  lib/Element_calculations.c, lib/Full_obsolete.c,
	  lib/Full_parallel_related.c, lib/General_matrix_functions.c,
	  lib/Instructions.c, lib/Obsolete.c, lib/Regional_obsolete.c,
	  lib/Regional_parallel_related.c, lib/Solver_multigrid.c,
	  lib/Stokes_flow_Incomp.c: Fixed a few memory problems.
	  
	  Shrink the size of several arrays related to Stokes eqn.
	  
	  Moved jacobi() to Obsolete.c

2007-09-05 22:21  tan2

	* module/Exchanger/SIUnit.cc: Forgot to update surfacee_tem

2007-09-05 22:20  tan2

	* lib/Viscosity_structures.c: Set the min of 2nd strain rate
	  invariant to 1e-16 to prevent infinite viscosity when SDEPV=on

2007-09-05 22:20  tan2

	* lib/Convection.c: Init'd timestep variables

2007-09-04 23:09  becker

	* lib/Full_tracer_advection.c, lib/Instructions.c,
	  lib/Stokes_flow_Incomp.c: Added test for F=0 load vector bug,
	  moved open_qfiles to after set_elapsed time.

2007-08-29 23:50  tan2

	* examples/Makefile.am: Forgot to update the makefile

2007-08-29 23:39  tan2

	* examples/Cookbook5/velocity/bvel.dat57,
	  examples/Cookbook5/velocity/bvel.dat58,
	  examples/Cookbook5/velocity/bvel.dat59,
	  examples/Cookbook5/velocity/bvel.dat60,
	  examples/Cookbook5/velocity/bvel.dat61,
	  examples/Cookbook5/velocity/bvel.dat62,
	  examples/Cookbook5/velocity/bvel.dat63,
	  examples/Cookbook5/velocity/bvel.dat64,
	  examples/Cookbook5/velocity/bvel.dat65,
	  examples/Cookbook5/velocity/bvel.dat66,
	  examples/Cookbook5/velocity/bvel.dat67,
	  examples/Cookbook5/velocity/bvel.dat68,
	  examples/Cookbook5/velocity/bvel.dat69,
	  examples/Cookbook5/velocity/bvel.dat70,
	  examples/Cookbook5/velocity/bvel.dat71: Removed unused velocity
	  bc files

2007-08-29 23:18  tan2

	* doc/CitcomS, doc: Restructing the repository layout for CitcomS
	  documentation

2007-08-29 20:55  tan2

	* lib/Instructions.c: Forgot to update r7902

2007-08-29 20:48  tan2

	* lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c,
	  lib/Regional_obsolete.c, lib/Viscosity_structures.c,
	  lib/output.h: Replaced output_open() with output_open_mode()
	  
	  Append the log and time files if restarting

2007-08-29 20:47  tan2

	* lib/Advection_diffusion.c: Minor fix

2007-08-29 01:46  becker

	* lib/Instructions.c: Missed to merge one modification after the
	  conflict.

2007-08-29 00:51  becker

	* bin/Citcom.c, lib/Full_version_dependent.c, lib/Ggrd_handling.c,
	  lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c,
	  lib/Output_gzdir.c, lib/Output_h5.c, lib/Process_buoyancy.c,
	  lib/Regional_version_dependent.c, lib/Viscosity_structures.c,
	  lib/convection_variables.h, lib/global_defs.h: When checking in
	  my changes, I had to resolve a conflict for lib/Instructions.c by
	  hand, which I hope I did properly. Here are my changes:
	  
	  - renamed CONTOL structure members ORTHO and ORTHOZ to
	  CITCOM_ORTHO and CITCOM_ORTHOZ Those were never used and
	  conflicted with definitions in GMT gmt.h
	  
	  - Added a higher frequency heat flow output option like so:
	  
	  write_q_files=1 # option to write heat flux to files qt.dat and
	  qb.dat # at intervals smaller than storage_spacing (0)
	  
	  - Added the capability to read in initial temperatures from
	  netcdf grd files, if -USE_GGRD is used. Lot of options, like so:
	  
	  # # read initial temperature conditions from grd files (default
	  values in parentheses) # tic_method=4 # read initial temperature
	  from netcdf GRD files (off)
	  
	  ggrd_tinit_scale_with_prem=off # scale the temperature with PREM
	  densities (off)
	  
	  ggrd_tinit_scale=1.0 # scaling factor to apply to read in scalars
	  f (1.0)
	  
	  ggrd_tinit_offset=-0.5 # offset, T = f * scale + offset + tm
	  (0.0) # where tm is the mean between top and bottom TBC values #
	  if the bottom is flux, will use 1 for bottom TBC value
	  
	  ggrd_tinit_gfile="../../data/tomography/s20a_smean_new_age/t" #
	  prefix of grd files, will # try to read t.1.grd, t.2.grd ...
	  t.n.grd # where n is the number of layers in the depth file
	  ggrd_tinit_dfile="../../data/tomography/s20a_smean_new_age/tdepth.dat"
	  # file with layer depths in km from bottom up
	  
	  ggrd_tinit_prem_file="../../progs/src/hc-svn/prem/prem.dat" #
	  PREM data file ggrd_tinit_override_tbc=on # override temperature
	  boundary conditions (off)

2007-08-28 01:10  tan2

	* CitcomS/Solver/Solver.py, lib/Instructions.c: Defaulting
	  datadir_old to the current directory

2007-08-28 01:09  tan2

	* CitcomS/Components/Const.py, CitcomS/Solver/Solver.py,
	  lib/Advection_diffusion.c, lib/Instructions.c,
	  lib/Material_properties.c, lib/Output_h5.c, lib/global_defs.h,
	  module/setProperties.c: Added various heating term to the energy
	  equation.
	  
	  A new input parameter: solver.surfaceT for non-dimensional
	  surface temperature.
	  
	  Removed old (and unused) input parameter: solver.const.surf_temp.

2007-08-27 19:34  tan2

	* lib/Stokes_flow_Incomp.c: Fixed a index bug in stokes solver

2007-08-27 19:34  tan2

	* CitcomS/Components/Output.py, CitcomS/Components/Tracer.py,
	  CitcomS/Components/Visc.py, lib/Advection_diffusion.c,
	  module/setProperties.c: Add pyre input for new parameters
	  introduced by TWB

2007-08-27 19:34  tan2

	* lib/Advection_diffusion.c, lib/Checkpoints.c,
	  lib/Construct_arrays.c, lib/Determine_net_rotation.c,
	  lib/Drive_solvers.c, lib/Full_geometry_cartesian.c,
	  lib/Full_lith_age_read_files.c, lib/Full_tracer_advection.c,
	  lib/General_matrix_functions.c, lib/Instructions.c,
	  lib/Lith_age.c, lib/Pan_problem_misc_functions.c, lib/Parsing.c,
	  lib/Regional_lith_age_read_files.c,
	  lib/Regional_sphere_related.c, lib/Regional_tracer_advection.c,
	  lib/Regional_version_dependent.c, lib/Tracer_setup.c,
	  lib/Viscosity_structures.c, lib/output.h, module/setProperties.c:
	  Clean up the code and declared function prototypes to avoid
	  compiler warnings

2007-08-23 20:20  tan2

	* lib/Advection_diffusion.c: Compute total visc and adi heating

2007-08-23 20:19  tan2

	* lib/Advection_diffusion.c, lib/Parsing.c: Minor refactoring

2007-08-23 20:18  tan2

	* lib/Pan_problem_misc_functions.c, lib/Phase_change.c: Compute
	  phase change wrt reference density and gravity profiles.

2007-08-23 20:18  tan2

	* lib/Composition_related.c, lib/Tracer_setup.c,
	  module/setProperties.c: Avoid reading unused input parameters

2007-08-23 20:17  tan2

	* CitcomS/Controller.py, CitcomS/Coupler/Coupler.py,
	  CitcomS/Coupler/EmbeddedCoupler.py,
	  CitcomS/Coupler/MultiC_Coupler.py,
	  CitcomS/Solver/CoupledSolver.py: assert
	  solver.tsolver.monitor_max_T is off in coupled run and remove
	  debugging output

2007-08-23 20:16  tan2

	* lib/Advection_diffusion.c, lib/Instructions.c, lib/Output_h5.c,
	  lib/advection.h, lib/global_defs.h, module/setProperties.c:
	  Renamed E->control.filter_temperature to
	  E->advection.filter_temperature

2007-08-23 20:16  tan2

	* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
	  lib/Advection_diffusion.c, lib/advection.h,
	  module/setProperties.c: Added new input parameter
	  solver.tsolver.monitor_max_T
	  
	  When it is on (default), if the max temperature changes too much
	  between timestep, the temperature field is restored at the
	  tsolver is called using half of the timestep size.

2007-08-23 20:15  tan2

	* lib/Advection_diffusion.c, lib/advection.h: Removed unused var.
	  in struct advection

2007-08-23 20:14  tan2

	* lib/Size_does_matter.c: A new way to compute TMass

2007-08-23 20:14  tan2

	* lib/Advection_diffusion.c, lib/Material_properties.c,
	  lib/Pan_problem_misc_functions.c, lib/Process_buoyancy.c,
	  lib/Size_does_matter.c, lib/global_defs.h, module/mesher.c: Minor
	  refactoring: add comments, rename variables

2007-08-22 01:00  becker

	* lib/Advection_diffusion.c, lib/Determine_net_rotation.c,
	  lib/Instructions.c, lib/Makefile.am, lib/Output.c,
	  lib/Output_gzdir.c, lib/Pan_problem_misc_functions.c,
	  lib/Tracer_setup.c, lib/global_defs.h: Added an option to remove
	  net rotations of the whole model before ascii-gz output. This
	  might be something of interest for other output options as well,
	  but is still experimental. Obvisouly, NR motions could be removed
	  in a post-processing step, but it is useful to monitor how those
	  develop during a model run. (Particularly pronounced for strong
	  lateral viscosity variations based on composition.)

2007-08-21 22:42  tan2

	* lib/Stokes_flow_Incomp.c: Removed the 2nd exit condition for bicg
	  solver because the convergence criterion is hard to determine.

2007-08-21 22:41  tan2

	* lib/Topo_gravity.c: Fixed the scaling constants in geoid
	  calculation with reference state

2007-08-21 22:41  tan2

	* lib/Pan_problem_misc_functions.c, lib/Phase_change.c: Disable
	  phase change in compressible flow

2007-08-21 20:28  tan2

	* AUTHORS: Added Wei Leng to author list

2007-08-21 20:27  tan2

	* CitcomS/Components/Stokes_solver/Incompressible.py,
	  lib/Instructions.c, lib/Stokes_flow_Incomp.c, lib/global_defs.h,
	  module/setProperties.c: A new input parameter to specify which
	  compressible solver
	  
	  If solver.vsolver.uzawa == "cg", Wei Leng's implementation is
	  used. If solver.vsolver.uzawa == "bicg", Eh Tan's implementation
	  is used.

2007-08-21 20:26  tan2

	* lib/Stokes_flow_Incomp.c: Refactored non-newtonian stokes solver
	  and iter-CG compressible stokes solver

2007-08-20 19:44  becker

	* lib/Viscosity_structures.c: Forgot this file.

2007-08-20 18:11  tan2

	* lib/Instructions.c: Added #ifdef block around vtk_io in
	  output_finalize()

2007-08-20 00:11  becker

	* lib/Advection_diffusion.c, lib/Tracer_setup.c: Made CDEPV and
	  Q0.enriched work only with ncomp=1 for now.

2007-08-19 23:54  becker

	* lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c,
	  lib/Output_h5.c, lib/Parsing.c: - merged changes with Eh's
	  additions
	  
	  - added coor=2 option (for full citcom) to assign finer radial
	  node spacing to top and lower layers of shell. The
	  coor_refine=0.1,0.15,0.1,0.2 parameter specifies the radius
	  fraction of the bottom layer [0], the fraction of the nodes in
	  this layer [1], the top layer fraction [2], and the top layer
	  node fraction [3]. I.e. the defaults will put 15% of all nz nodes
	  into the 10% lower layer, 20% in the top 10% upper layer, and the
	  rest in between.
	  
	  - renamed gzipped output option ascii-gz
	  
	  - built in restart facilities for temperature and tracers when
	  using gzdir I/O
	  
	  - added a composition viscosity function, CDEPV, based on two
	  tracer flavors
	  
	  - for this to work, I had to move viscosity_input() *behind*
	  tic_input() and tracer_input() in instructions
	  
	  - added tracer_enriched option. If tracer = on and
	  tracer_enriched = on, will reader Q0_enriched and vary the
	  element heat production between Q0 for C = 0 and Q0_enriched for
	  C = 1. I.e. this only works if C varies between 0 and 1.
	  
	  - added an experimental option to write to a single VTK file
	  (note caveats!) if ascii-gz is activated
	  
	  gzdir_vtkio = 2, will try to write VTK straight (experimental)
	  
	  the VTK output is of the "legacy", serial type, and requires that
	  all processors see the same filesystem. This will likely lead to
	  a bottleneck for larg CPU computations as each processor has to
	  wait til the previous is done.

2007-08-17 21:41  tan2

	* tests/checkpoint/run.sh: Added excutable permission to testing
	  shell script

2007-08-17 21:39  tan2

	* tests/checkpoint/restart.cfg: Added comments to restart example

2007-08-17 18:35  tan2

	* lib/Advection_diffusion.c, lib/Output.c, lib/Output_gzdir.c,
	  lib/Viscosity_structures.c: Converting TWB's ascii-gz and vtkio
	  output and CDEPV and tracer_enriched for multi-component chemical
	  convection.

2007-08-17 18:33  tan2

	* CitcomS/Components/Tracer.py, lib/Checkpoints.c,
	  lib/Composition_related.c, lib/Full_tracer_advection.c,
	  lib/Output.c, lib/Pan_problem_misc_functions.c,
	  lib/Regional_tracer_advection.c, lib/Tracer_setup.c,
	  lib/global_defs.h, lib/tracer_defs.h, module/setProperties.c,
	  tests/checkpoint/tracer.cfg, visual/autocombine.py,
	  visual/batchcombine.py, visual/dxgeneral.py: Multi-component
	  chemical convection.
	  
	  By setting tracer_flavors > 2, one can enable multi-component
	  chemical convection. See tests/checkpoint/tracer.cfg for example
	  input.

2007-08-16 21:36  tan2

	* CitcomS/Components/IC.py, CitcomS/Components/Tracer.py,
	  CitcomS/Controller.py, CitcomS/Solver/CoupledSolver.py,
	  CitcomS/Solver/Solver.py, bin/Citcom.c,
	  examples/Cookbook5/cookbook5.cfg, lib/Checkpoints.c,
	  lib/Composition_related.c, lib/Full_tracer_advection.c,
	  lib/Initial_temperature.c, lib/Instructions.c, lib/Lith_age.c,
	  lib/Makefile.am, lib/Output.c, lib/Problem_related.c,
	  lib/Regional_tracer_advection.c, lib/Tracer_setup.c,
	  lib/Viscosity_structures.c, lib/checkpoints.h, lib/global_defs.h,
	  lib/initial_temperature.h, lib/lith_age.h, module/bindings.c,
	  module/initial_conditions.c, module/initial_conditions.h,
	  module/outputs.c, module/outputs.h, module/setProperties.c,
	  tests/checkpoint, tests/checkpoint/restart.cfg,
	  tests/checkpoint/run.sh, tests/checkpoint/tracer.cfg: Merging the
	  checkpoint branch to trunk.
	  
	  The checkpoint file is called [datafile].chkpt.[rank].[step] and
	  is outputed with an interval of controller.checkpointFrequency.
	  
	  To read back the checkpoint file, set solver.ic.restart=on. The
	  old checkpoint file,
	  [datafile_old].chkpt.[rank].[solution_cycles_init] will be read
	  in.
	  
	  The old way of restarting (read in temperature from the velo
	  files) will still be available through solver.ic.tic_method=-1.
	  
	  Setting solver.tracer.ic_method=2 will read the old *.tracer.*
	  files as before, but the composition field will be calculated
	  according to the tracers, not read from the *.comp_el.* files.
	  The parameter solver.tracer.reset_initial_composition becomes
	  obsolete.

2007-08-16 20:10  tan2

	* lib/Element_calculations.c, lib/Viscosity_structures.c: When the
	  element is close to the poles, use a more precise method to
	  compute the strain rate.

2007-08-16 19:38  tan2

	* lib/Material_properties.c, lib/material_properties.h: Forgot to
	  add two files to the repository

2007-08-16 19:28  tan2

	* CitcomS/Components/Stokes_solver/Incompressible.py,
	  lib/Construct_arrays.c, lib/Element_calculations.c,
	  lib/Instructions.c, lib/Output_h5.c,
	  lib/Pan_problem_misc_functions.c, lib/Stokes_flow_Incomp.c,
	  lib/Topo_gravity.c, lib/Viscosity_structures.c,
	  lib/global_defs.h, module/setProperties.c,
	  visual/pasteCitcomData.py: Merging compressible branch to trunk.
	  
	  The TALA solver is working. Two new input parameters:
	  dissipation_number and gruneisen.

2007-08-16 01:42  tan2

	* examples/Cookbook5/cookbook5.cfg,
	  examples/Cookbook5/restart_files/cookbook5.velo.0.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.1.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.10.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.11.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.12.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.13.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.14.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.15.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.16.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.17.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.18.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.19.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.2.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.20.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.21.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.22.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.23.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.24.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.25.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.26.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.27.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.28.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.29.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.3.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.30.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.31.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.32.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.33.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.34.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.35.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.36.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.37.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.38.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.39.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.4.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.40.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.41.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.42.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.43.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.44.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.45.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.46.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.47.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.48.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.49.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.5.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.50.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.51.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.52.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.53.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.54.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.55.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.56.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.57.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.58.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.59.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.6.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.60.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.61.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.62.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.63.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.7.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.8.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.9.0,
	  examples/Makefile.am: Updated Cookbook5 so that it uses only 2
	  processors.

2007-08-16 00:27  tan2

	* CitcomS/Solver/Solver.py, lib/Advection_diffusion.c,
	  lib/Construct_arrays.c, lib/Convection.c, lib/Drive_solvers.c,
	  lib/Element_calculations.c, lib/Full_version_dependent.c,
	  lib/Instructions.c, lib/Makefile.am, lib/Obsolete.c,
	  lib/Output.c, lib/Output_h5.c, lib/Pan_problem_misc_functions.c,
	  lib/Process_buoyancy.c, lib/Regional_obsolete.c,
	  lib/Regional_version_dependent.c, lib/Size_does_matter.c,
	  lib/Stokes_flow_Incomp.c, lib/Topo_gravity.c,
	  lib/Viscosity_structures.c, lib/global_defs.h, module/mesher.c,
	  module/setProperties.c: Merging compressible branch (up to r6584)
	  to trunk.

2007-08-14 03:33  becker

	* lib/Advection_diffusion.c, lib/Full_version_dependent.c,
	  lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c,
	  lib/Pan_problem_misc_functions.c, lib/Problem_related.c,
	  lib/Process_buoyancy.c, lib/Regional_sphere_related.c,
	  lib/Regional_version_dependent.c, lib/Tracer_setup.c,
	  lib/global_defs.h: - added coor=2 option (for full citcom) to
	  assign finer radial node spacing to top and lower layers of
	  shell. The coor_refine=0.1,0.15,0.1,0.2 parameters specify the
	  radius fraction of the bottom layer [0], the fraction of the
	  nodes in this layer [1], the top layer fraction [2], and the top
	  layer node fraction [3]. I.e. the defaults will put 15% of all nz
	  nodes into the 10% lower layer, 20% in the top 10% upper layer,
	  and the rest in between.
	  
	  - renamed gzipped output version with sub-directory storage
	  ascii-gz
	  
	  - built in restart facilities for temperature and tracers when
	  using ascii-gz I/O with vtkio != 2
	  
	  - added a composition viscosity function, CDEPV, based on two
	  tracer flavors
	  
	  - for this to work, I had to move viscosity_input() *behind*
	  tic_input() and tracer_input() in instructions
	  
	  - added tracer_enriched option for internal heating. If tracer =
	  on and tracer_enriched = on, will reader Q0_enriched and vary the
	  element heat production between Q0 for C = 0 and Q0_enriched for
	  C = 1. I.e. this only works if C varies between 0 and 1.
	  
	  - added an option to write from all processros to a single VTK
	  file, if ascii-gz is activated, and vtkio = 2. The VTK output is
	  of the "legacy", serial, single-file type, and requires that all
	  processors see the same filesystem.
	  
	  This will lead to a bottleneck for large # of CPU computations as
	  each processor has to wait til the previous is done.
	  
	  More efficient I/O should be possible by using the distributed
	  storage version of VTK, but I have no clue how this works.
	  Anyone?

2007-08-13 22:55  tan2

	* lib/Global_operations.c, lib/Nodal_mesh.c, lib/Obsolete.c,
	  lib/Pan_problem_misc_functions.c, lib/Stokes_flow_Incomp.c: Minor
	  refactoring, clean-up and moving functions between files

2007-08-13 21:43  tan2

	* lib/Obsolete.c, lib/Phase_change.c: Moved obsolete functions
	  phae_change_* from Phase_change.c to Obsolete.c and declared
	  private functions to be static

2007-08-10 23:56  tan2

	* AUTHORS: Update the author list

2007-08-10 23:56  sue

	* doc/manual/citcoms.lyx: additions per becker, tan2

2007-08-10 23:44  tan2

	* lib/Drive_solvers.c, lib/Global_operations.c: Fixed two
	  type-mismatch errors. Issue127 is fixed by this change and r7802.

2007-08-10 23:43  tan2

	* lib/Stokes_flow_Incomp.c: Prevent the original force vector being
	  modified by Uzawa solver. This is needed for the non-Newtonian
	  iterations.

2007-08-10 20:51  becker

	* lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c,
	  lib/Problem_related.c, lib/Tracer_setup.c: - renamed gzipped
	  output option ascii-gz
	  
	  - built in restart facilities for temperature and tracers when
	  using gzdir I/O
	  
	  - added a composition viscosity function, CDEPV, based on two
	  tracer flavors
	  
	  - for this to work, I had to move viscosity_input() *behind*
	  tic_input() and tracer_input() in instructions

2007-08-09 01:27  becker

	* lib/Initial_temperature.c, lib/Instructions.c,
	  lib/Output_gzdir.c, lib/Problem_related.c, lib/Tracer_setup.c,
	  lib/Viscosity_structures.c, lib/viscosity_descriptions.h: - added
	  a compositional viscosity function, CDEPV, based on two tracer
	  flavors
	  
	  - for this to work, I had to move viscosity_input() *behind*
	  tic_input() and tracer_input() in Instructions.c
	  
	  - built in restart facilities for temperature and tracers when
	  using gzdir I/O

2007-08-08 22:55  becker

	* doc/manual/citcoms.lyx, lib/Composition_related.c,
	  lib/Construct_arrays.c, lib/Full_tracer_advection.c,
	  lib/General_matrix_functions.c, lib/Ggrd_handling.c,
	  lib/Instructions.c, lib/Makefile.am, lib/Output.c,
	  lib/Output_gzdir.c, lib/Pan_problem_misc_functions.c,
	  lib/Tracer_setup.c, lib/Viscosity_structures.c,
	  lib/global_defs.h, lib/tracer_defs.h: - added new routine
	  Ggrd_handling which will take care of netcdf grd input. For now,
	  only the tracer innitial conditions can be set by using, for
	  example,
	  
	  ictracer_grd_layers=2 ictracer_grd_file="tmask.grd"
	  
	  for this to work, the ggrd libraries from HC, as well as the
	  -lgmt and -lnetcdf need to be linked, and -DUSE_GGRD needs to be
	  defined on compile time.
	  
	  - rewrote TDEPV viscosity options 3 and 4 slightly to make them
	  more efficient
	  
	  - added TDEPV viscosity option 6
	  
	  eta = N_0 exp(E(T_0-T) + (1-z) Z_0 )
	  
	  - took layers subroutine in Construct_arrays.c apart to allow
	  calling the same function in a more flexible from other
	  subroutines
	  
	  - addded error handling routine "myerror" to
	  Pan_problem_misc_functions
	  
	  - made the output behavior of the multigrid solver convergence
	  parameters consisent with verbosity setting (ie. use report
	  instead of always stderr output)
	  
	  - changed tracer input parameter "tracer" and "chemical_buoyancy"
	  to boolean routine for added flexibility (I hope)
	  
	  - made check_initial_composition consistent with tracer
	  advection, exits after warning only for
	  E->trace.itracer_warnings==1
	  
	  - debugging output in Full_tracer_advection.c and Tracer_setup
	  only gets printed to file for E->control.verbose == 1
	  
	  - fixed some typos in Output_gzdir (that might have been
	  introduced by asynchronous svn updating or something like that)

2007-08-08 16:41  becker

	* lib/Output_gzdir.c: Forgot to actually add the new file that is
	  needed for gzipped and "vtk" I/O.

2007-08-08 05:58  becker

	* lib/Advection_diffusion.c, lib/Drive_solvers.c,
	  lib/Instructions.c, lib/Makefile.am, lib/Output.c,
	  lib/Pan_problem_misc_functions.c, lib/Stokes_flow_Incomp.c,
	  lib/Viscosity_structures.c, lib/global_defs.h, lib/output.h,
	  lib/viscosity_descriptions.h: - added functions rtp2xyz,
	  calc_cbase_at_tp, and convert_pvec_to_cvec for spherical to
	  Cartesian vector conversion to Pan_problem_functions.c
	  
	  Added "safe_malloc" to the same file because I didn't like the
	  way Malloc1 uses int as arguments (64 bit issues).
	  
	  - added support for gzipped ascii output into subdirectories of
	  data_dir, option gzdir. To use, need to compile with USE_GZDIR
	  and link with the -lz zlib libraries. Within gzdir output mode,
	  selected by
	  
	  output_format=gzdir user can define vtk I/O (gzdir_vtkio=1) to
	  write Cartesian coordinates and velocities that are easy to
	  combine to a single vtk file in a post-processing step.
	  
	  If gzlib_vtkio=0 the gzdir output option is meant to be identical
	  to the original ascii output, but files are all gzipped on the
	  fly, and the output that changes with each cycle is placed into
	  subdirectories of data_dir/ called data_dir/cycles/ For gzdir
	  I/O, data_name is not used at all, all single output files are
	  placed in the data_dir/ directory without prefix.
	  
	  - added a new rheology option, PDEPV, for pseudo-plasticity and
	  added a corresponding description to the manual.
	  
	  - Modified Drive_solver stderr output to show v.v, and not only
	  dv.dv/v.v

2007-08-02 22:44  luis

	* .gitignore: Ignore most files generated by build system

2007-07-27 23:33  hlin

	* module/Exchanger/Boundary.cc: M Boundary.cc fixed a bug on topbc

2007-07-26 00:20  tan2

	* examples/Cookbook5/cookbook5.cfg: Fixed a typo, which was
	  introduced in svn r5399

2007-07-26 00:13  tan2

	* visual/batchcombine.py, visual/combine.py: Fixed a bug that
	  *opt*.general files are mistakenly named. This bug is introduced
	  by svn r7236

2007-07-25 23:19  tan2

	* visual/dxgeneral.py: Fixed a bug in ordering of mesh nodes. The
	  bug was introduced in svn r6510.

2007-07-23 19:50  hlin

	* tests/coupled.cfg, tests/multicoupled.cfg: M
	  tests/multicoupled.cfg M tests/coupled.cfg
	  
	  The code has passed a test on a regional containing solver.
	  Timestep will sync and initial condition will match.
	  
	  Going to use a full containing solver with embedded solvers at
	  Hawaii and Reunion in next revision.

2007-07-20 21:52  hlin

	* tests/coupled.cfg: M coupled.cfg alligned nodes in the solvers
	  for comparing velocity directly.

2007-07-19 18:51  tan2

	* module/advdiffu.c: Fixed a bug in setting stable timestep

2007-07-19 18:51  tan2

	* CitcomS/CoupledApp.py, CitcomS/MultiCoupledApp.py,
	  tests/coupled.cfg, tests/multicoupled.cfg: Changed the name
	  attribute of all application classes to 'CitcomS'. This allows
	  the users to specify the same launcher parameters for all
	  application in their ~/.pyre/CitcomS/CitcomS.cfg.

2007-07-19 18:37  hlin

	* CitcomS/Controller.py, CitcomS/Coupler/EmbeddedCoupler.py,
	  CitcomS/Coupler/MultiC_Coupler.py,
	  CitcomS/Coupler/MultiE_Coupler.py, CitcomS/Coupler/__init__.py,
	  CitcomS/MultiCoupledApp.py, CitcomS/Solver/CoupledSolver.py: M
	  trunk/CitcomS/Coupler/MultiE_Coupler.py M
	  trunk/CitcomS/Coupler/__init__.py M
	  trunk/CitcomS/Coupler/EmbeddedCoupler.py M
	  trunk/CitcomS/Coupler/MultiC_Coupler.py M
	  trunk/CitcomS/Solver/CoupledSolver.py M
	  trunk/CitcomS/Controller.py M trunk/CitcomS/MultiCoupledApp.py
	  
	  solved the synchronization issue. There are some bugs in the log
	  of time.

2007-07-18 23:06  hlin

	* CitcomS/Coupler/MultiC_Coupler.py,
	  CitcomS/Coupler/MultiE_Coupler.py: A Coupler/MultiE_Coupler.py M
	  Coupler/MultiC_Coupler.py
	  
	  Fixed the synchronization part. Need to test on it. Now Embedded
	  Couplers will wait until containing coupler make a decision.

2007-07-18 21:01  tan2

	* bin/Makefile.am, bin/citcoms.in, bin/coupledcitcoms.in: Unify
	  bin/citcoms with bin/coupledcitcoms scripts. Users can run
	  'bin/citcoms --coupled' to launch a coupled run and 'bin/citcoms
	  --multicoupled' to launch a multicoupled run.

2007-07-17 22:49  tan2

	* tests/multicoupled.cfg: An input file for multicoupled run

2007-07-17 22:48  tan2

	* CitcomS/Coupler/MultiC_Coupler.py, CitcomS/Coupler/__init__.py,
	  CitcomS/MultiCoupledApp.py: Fixed a few typos and attached
	  MultiC_Coupler as the default factory for the ccoupler facility

2007-07-17 22:48  tan2

	* CitcomS/Solver/MultiC_FullSolver.py,
	  CitcomS/Solver/MultiC_RegionalSolver.py,
	  CitcomS/Solver/MultiC_Solver.py, CitcomS/Solver/__init__.py:
	  Simplified the MultiC_*Solver classes

2007-07-16 23:45  hlin

	* CitcomS/Solver/MultiC_FullSolver.py,
	  CitcomS/Solver/MultiC_RegionalSolver.py,
	  CitcomS/Solver/MultiC_Solver.py: A
	  Solver/MultiC_RegionalSolver.py A Solver/MultiC_FullSolver.py A
	  Solver/MultiC_Solver.py
	  
	  ideally these files works as the solvers I needed for the
	  project.

2007-07-16 21:21  hlin

	* CitcomS/Coupler/MultiC_Coupler.py, CitcomS/MultiLayout.py: M
	  CitcomS/MultiLayout.py trivial comment change
	  
	  M CitcomS/Coupler/MultiC_Coupler.py a nearly complete version.
	  Although I am not sure how most of the things works , I managed
	  to create a copy of everything.initTemperature,
	  restartTemperature , and modifyT not defined.

2007-07-13 23:24  hlin

	* CitcomS/Coupler/ContainingCoupler.py: M
	  Coupler/ContainingCoupler.py trivial modification on comments

2007-07-13 23:23  hlin

	* CitcomS/Coupler/MultiC_Coupler.py: M Coupler/MultiC_Coupler.py
	  add __init__, initialize, createMesh some of createMesh are
	  commented out because I do not understand it.

2007-07-13 21:09  hlin

	* CitcomS/Coupler/MultiC_Coupler.py: A Coupler/MultiC_Coupler.py
	  It's a child of Containing Coupler It has nothing now.

2007-07-11 20:17  tan2

	* module/Exchanger/Boundary.cc,
	  module/Exchanger/CitcomInterpolator.cc,
	  module/Exchanger/CitcomSource.cc, module/Exchanger/SVTInlet.cc,
	  module/Exchanger/SVTOutlet.cc: Added some comments

2007-07-10 20:08  tan2

	* CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py,
	  CitcomS/Coupler/EmbeddedCoupler.py: Renamed variables for
	  clarification

2007-07-09 22:03  tan2

	* CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py,
	  CitcomS/Coupler/EmbeddedCoupler.py: Small changes in *Coupler
	  class. * consolidated __init__() and initialize() * renamed
	  numSrc -> remoteSize, boundary -> remoteBdryList, interior ->
	  remoteIntrList * defaulted the dimensional and transformational
	  properties to False

2007-07-06 20:48  tan2

	* CitcomS/MultiCoupledApp.py, CitcomS/MultiLayout.py: Added
	  svn:keywords Id

2007-07-06 20:46  tan2

	* CitcomS/MultiCoupledApp.py, CitcomS/MultiLayout.py: Debugged
	  MultiLayout.initialize() and MultiCoupledApp.findLayout(). Fixed
	  some typos.

2007-07-06 18:00  tan2

	* CitcomS/CoupledApp.py: Using log() instead of line() to flush the
	  journal buffer, otherwise no output at all.

2007-07-06 17:50  hlin

	* CitcomS/MultiCoupledApp.py, CitcomS/MultiLayout.py: fix myPlus
	  and remotePlus and report in MultiCoupledApp edit some comments
	  in MultiLayout

2007-07-05 23:45  hlin

	* CitcomS/MultiCoupledApp.py, CitcomS/MultiLayout.py: add
	  MultiLayout not sure about number of processor, currently assign
	  1-10 for ccom 11 for ecom1, and 12 for ecom2

2007-07-05 22:36  hlin

	* CitcomS/MultiCoupledApp.py:

2007-07-05 20:49  hlin

	* CitcomS/MultiCoupledApp.py:

2007-07-04 00:02  hlin

	* CitcomS/MultiCoupledApp.py: a draft for multicoupled application

2007-07-02 22:21  tan2

	* doc/manual/citcoms.lyx: Removing outdated and redundant
	  documentation

2007-07-02 22:21  tan2

	* CitcomS/SimpleApp.py: Using log() instead of line() to flush the
	  journal buffer, otherwise no output at all.

2007-06-28 19:35  tan2

	* CitcomS/Layout.py, tests/coupled.cfg: Renamed ccomm ->
	  containing_group and ecomm -> embedded_group. Added more checks
	  to the groups

2007-06-27 01:04  tan2

	* CitcomS/BaseApplication.py, CitcomS/Controller.py,
	  CitcomS/CoupledApp.py, CitcomS/Coupler/ContainingCoupler.py,
	  CitcomS/Coupler/Coupler.py, CitcomS/Coupler/EmbeddedCoupler.py,
	  CitcomS/Layout.py, CitcomS/SimpleApp.py,
	  CitcomS/Solver/CoupledSolver.py: Added/updated a bunch of
	  comments, renamed variables

2007-06-26 00:37  tan2

	* doc/manual/graphics/citcoms_cover-layers.pdf,
	  doc/manual/graphics/citcoms_cover.pdf: Added mime-type property
	  to the PDF files

2007-06-23 00:33  tan2

	* CitcomS/CoupledApp.py, CitcomS/Coupler/ContainingCoupler.py,
	  CitcomS/Coupler/Coupler.py, CitcomS/Coupler/EmbeddedCoupler.py,
	  CitcomS/SimpleApp.py, CitcomS/Solver/CoupledSolver.py,
	  module/Exchanger/BoundaryVTInlet.cc,
	  module/Exchanger/CitcomSource.cc, module/Exchanger/SVTOutlet.cc,
	  module/Exchanger/exchangers.cc, module/Exchanger/misc.cc,
	  tests/array2d.cc, tests/coupled.cfg: Giving
	  Exchanger/Coupler/CoupledApp as new life. The testing script
	  tests/coupled.cfg finished successfully.

2007-06-23 00:30  tan2

	* lib/Citcom_init.c: Useful debuggin output, but disabled

2007-06-23 00:29  tan2

	* configure.ac: Print CXX and CXXFLAGS after finishing configure

2007-06-23 00:28  tan2

	* lib/Viscosity_structures.c: Removed the back-and-forth
	  interpolation of viscosity, which smoothes the viscosity field
	  unnecessarily

2007-06-22 23:43  tan2

	* module/setProperties.c: Forgot to commit module/setProperties.c
	  in r7289. This should fix issue115 in the pyre version also.

2007-06-22 04:36  leif

	* .: Added BuildBot config.

2007-06-21 22:35  hlin

	* tests/test1.sh: Resolved the conflict

2007-06-21 22:25  tan2

	* tests/test1.sh: Preparing a conflict test, again

2007-06-21 22:22  tan2

	* tests/test1.sh: Preparing a conflict test, again

2007-06-21 22:19  tan2

	* tests/test1.sh: Preparing a conflict test

2007-06-18 23:21  tan2

	* CitcomS/CoupledApp.py, CitcomS/Coupler/Coupler.py,
	  CitcomS/Layout.py, etc/full.odb, etc/regional.odb: Renamed 'XXX1'
	  -> 'cXXX' and 'XXX2' -> 'eXXX'

2007-06-18 23:06  tan2

	* lib/Instructions.c, lib/Tracer_setup.c: Fixing issue115:
	  interference between restart=1 & tracer_ic_method
	  
	  Previously, when "restart" is set, tracer_ic_method will be set
	  to 2 (restart tracers) by the code. Now, these two options are
	  independent.

2007-06-15 18:01  leif

	* bin/dummy.cc: Fix for problem with GCC 3.4.5 (observed on
	  CITerra):
	  
	  mv: cannot stat `.deps/dummy.Tpo': No such file or directory

2007-06-14 21:38  tan2

	* lib/Topo_gravity.c: Zeroing geoid arrays before every geoid
	  calculation. This fixes issue114

2007-06-14 17:55  tan2

	* visual/autocombine.py, visual/batchcombine.py,
	  visual/pasteCitcomData.py: A better fix for issue110

2007-06-14 01:36  tan2

	* visual/pasteCitcomData.py: Fixing issue111: Expanding %RANK in
	  autocombine.py

2007-06-13 17:55  hlin

	* tests/test1.sh: A trivial change

2007-06-12 00:05  tan2

	* module/setProperties.c: Fixing issue112

2007-05-11 20:19  leif

	* bin/Makefile.am: Fixed LINK problem w/Automake.

2007-05-11 02:02  leif

	* CitcomS/CoupledApp.py, bin/Makefile.am, bin/coupledcitcoms.in,
	  bin/dummy.cc, bin/pycitcoms.c, configure.ac,
	  module/Exchanger/AreaWeightedNormal.cc,
	  module/Exchanger/Boundary.cc,
	  module/Exchanger/BoundaryVTInlet.cc,
	  module/Exchanger/CitcomInterpolator.cc,
	  module/Exchanger/CitcomSource.cc, module/Exchanger/Convertor.cc,
	  module/Exchanger/Exchangermodule.cc,
	  module/Exchanger/Exchangermodule.h, module/Exchanger/Interior.cc,
	  module/Exchanger/Makefile.am, module/Exchanger/SIUnit.cc,
	  module/Exchanger/SInlet.cc, module/Exchanger/SVTInlet.cc,
	  module/Exchanger/SVTOutlet.cc, module/Exchanger/TInlet.cc,
	  module/Exchanger/TOutlet.cc, module/Exchanger/VOutlet.cc,
	  module/Exchanger/VTInlet.cc, module/Exchanger/VTOutlet.cc,
	  module/Exchanger/bindings.cc, module/Exchanger/exceptions.cc,
	  module/Exchanger/exchangers.cc, module/Exchanger/global_bbox.cc,
	  module/Exchanger/initTemperature.cc,
	  module/Exchanger/inlets_outlets.cc, module/Exchanger/misc.cc,
	  module/Makefile.am, setup.py: Build with Exchanger, if available.
	  The Exchanger package will be automatically detected if it is
	  installed on your PYTHONPATH. The preprocessor & link flags for
	  compiling/linking with Exchanger are handled automatically.
	  
	  To my chagrin, this change increases the CitcomS language count
	  back up to 3 again (C, C++, Python). Even with the aid of the
	  'cproto' tool, it would take many hours of work to make the C
	  code in 'lib' compile using a C++ compiler.

2007-04-11 00:40  tan2

	* tests/Makefile.am: Forgot to update the makefile in r6541

2007-04-10 21:59  tan2

	* lib/Tracer_setup.c: Finding the min/max of the Cartesian
	  coordinates. The min/max values provide the bounding box for
	  random tracer generation. This will speed up the tracer
	  generation, and should avoid a potential problem of "too many
	  tries?" error when the domain size of a processor is much smaller
	  (<1%) than the size of the whole sphere.

2007-04-10 21:58  tan2

	* tests/asap.py, tests/hrothgar.py: Removed obsolete pyre
	  components in tests/

2007-04-05 22:21  tan2

	* visual/Makefile.am, visual/autocombine.py,
	  visual/batchcombine.py, visual/batchpaste.sh, visual/combine.py,
	  visual/dxgeneral.py, visual/dxgeneral.sh, visual/execpaste.py,
	  visual/pasteCitcomData.py, visual/pasteCitcomData.sh: Adding the
	  ability to combine optional fields to the post-processing
	  scripts.
	  
	  autocombine.py will read the parameter 'output_optional' from the
	  cfg file and combine the optional fields (can be pressure,
	  stress, comp_nd, or a combination of the three) into a file. The
	  file is named similar to the cap file, with 'cap' replaced by
	  'opt'. A .general file is also created, which describes the
	  content, shape, and structure of the opt file.

2007-03-27 20:54  sue

	* doc/manual/graphics/citcoms_cover-layers.pdf: standardized
	  typefaces on cover

2007-03-27 06:51  sue

	* doc/manual/citcoms.pdf,
	  doc/manual/graphics/citcoms_cover-layers.pdf,
	  doc/manual/graphics/citcoms_cover.pdf: changed version to 2.2.1
	  per tan2

2007-03-27 04:39  tan2

	* ChangeLog: Regenerated ChangeLog upto r6417

2007-03-27 04:37  tan2

	* NEWS, configure.ac, doc/manual/citcoms.lyx: Updated NEWS for the
	  upcoming 2.2.1

2007-03-27 04:20  tan2

	* examples/Makefile.am: Forgot to add cookbook7.cfg to the file
	  list

2007-03-26 18:48  tan2

	* ChangeLog: Regenerated ChangeLog upto r6409

2007-03-26 18:45  tan2

	* lib/Makefile.am: Forgot to add a header file to the file list

2007-03-26 18:25  tan2

	* ChangeLog: Regenerated ChangeLog upto r6403

2007-03-26 18:20  tan2

	* visual/plot_annulus.py: Set the length unit to cm to fit within
	  the page

2007-03-26 18:11  tan2

	* visual/plot_layer.py: Changed the size of gmt plots to fit within
	  the page

2007-03-26 18:05  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: restored edits to
	  stable copy; regen pdf, images showing

2007-03-26 06:01  tan2

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: Enlarged the
	  figure of cookbook7. Rephrased the description of the
	  low-viscosity-zone parameters, per Sue's suggestion.

2007-03-26 00:23  sue

	* doc/manual/citcoms.pdf: chasing down image problem

2007-03-25 23:07  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: changed verbage
	  in History 1.2, paragraphs on version 2.1, to past tense, since
	  notes on 2.2 should be only ones in present tense \c

2007-03-25 22:55  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: edits of new
	  copy; attempt to fix an image that is not displaying, still
	  unresolved

2007-03-24 23:05  tan2

	* doc/manual/citcoms.lyx: Finished Cookbook7

2007-03-24 23:03  tan2

	* README, configure.ac, setup.py: Changed the version number to 2.2

2007-03-24 00:02  tan2

	* examples/Cookbook7, examples/Cookbook7/cookbook7.cfg: Added new
	  cookbook7

2007-03-23 22:21  tan2

	* NEWS, doc/manual/citcoms.lyx: Updated the NEWS for v2.2.0

2007-03-23 22:21  tan2

	* doc/manual/citcoms.lyx, examples/Full/input.sample,
	  examples/Regional/input.sample: Added new parameter 'adv_gamme'
	  to the manual and input samples. Documented a new tic_method=3

2007-03-23 21:06  tan2

	* doc/manual/citcoms.lyx: Added description to the tracer and
	  composition input/output files

2007-03-23 20:40  tan2

	* doc/manual/citcoms.lyx, examples/Full/input.sample,
	  examples/Regional/input.sample: Added the tracer parameters to
	  the manual and sample input files

2007-03-23 20:39  tan2

	* CitcomS/Components/Tracer.py, lib/Full_tracer_advection.c,
	  module/setProperties.c: Disable the parameter
	  "analytical_tracer_test", and make "chemical_buoyancy" a boolean

2007-03-23 19:37  tan2

	* doc/manual/citcoms.lyx, examples/Full/input.sample,
	  examples/Regional/input.sample: Added the low-visc-zone
	  parameters to the manual and the sample input files

2007-03-23 05:31  tan2

	* doc/manual/graphics/cookbook7.jpg: Added the image for cookbook7
	  (thermo-chemical convection

2007-03-23 05:30  tan2

	* doc/manual/citcoms.lyx, doc/manual/graphics/cookbook6.eps,
	  doc/manual/graphics/cookbook7.eps: When I renamed the old
	  Cookbook7/ directory to Cookbook6/, I forgot to rename
	  cookbook7.eps to cookbook6.eps. Now it is done.

2007-03-23 05:25  tan2

	* doc/manual/graphics/cookbook6.2.eps,
	  doc/manual/graphics/cookbook6.eps: These two EPS files are the
	  leftover of an old cookbook

2007-03-23 05:22  tan2

	* lib/Tracer_setup.c: Gather theta and phi only in
	  get_neighboring_caps()

2007-03-23 05:21  tan2

	* lib/Composition_related.c, lib/Output.c: Changed the header
	  format of comp_* output to be consistent with other data files

2007-03-22 22:11  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf,
	  doc/manual/graphics/citcoms_cover-layers.pdf,
	  doc/manual/graphics/citcoms_cover.pdf: added bib entry per eh,
	  changed cover to citcoms (rem .py), changed to 2.2.0, todo
	  notation removed; regen pdf

2007-03-22 19:58  tan2

	* lib/Stokes_flow_Incomp.c: Make the output of 1st iteration
	  consistent with later iterations

2007-03-22 19:57  tan2

	* lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c,
	  lib/Tracer_setup.c: Calling find_tracers() and
	  count_tracers_of_flavors() in initialize_tracers(), so that the
	  former two functions can become static/private

2007-03-22 19:55  tan2

	* lib/Tracer_setup.c: Renamed initialize_tracer_arrays() to
	  allocate_tracer_arrays()

2007-03-21 22:46  tan2

	* doc/manual/citcoms.lyx: Updated the version number to 2.2.0

2007-03-21 22:46  tan2

	* doc/manual/citcoms.lyx: Updated the dependency information

2007-03-21 22:46  tan2

	* doc/manual/citcoms.lyx: Added chemical Rayleigh number to the
	  equations

2007-03-21 22:45  tan2

	* doc/manual/citcoms.lyx: Added history of v2.2 release

2007-03-21 22:45  tan2

	* doc/manual/citcoms.lyx: Added citation to McNamara & Zhong 2004

2007-03-21 19:30  tan2

	* lib/Full_tracer_advection.c: Added a safeguard against nprocx or
	  nprocy greater than 1

2007-03-20 06:34  tan2

	* lib/Full_tracer_advection.c: full_lost_souls() now works for
	  nprocz>1 as well

2007-03-20 06:27  tan2

	* CitcomS/Components/Tracer.py, lib/Full_tracer_advection.c,
	  lib/Regional_tracer_advection.c, lib/Tracer_setup.c,
	  lib/tracer_defs.h, module/setProperties.c: Removed the
	  'tracer_interpolation_scheme' and 'tracer_advection_scheme'
	  parameters

2007-03-20 06:26  tan2

	* lib/Viscosity_structures.c: Reporting error if low viscosity
	  channel/wedge is turned on, but tracer is turned off

2007-03-19 23:49  tan2

	* lib/Full_tracer_advection.c, lib/Global_operations.c,
	  lib/Regional_parallel_related.c, lib/Regional_tracer_advection.c,
	  lib/Tracer_setup.c, lib/tracer_defs.h: lost_souls() cannot be
	  shared by both versions. The parallel communications of both
	  versions are too different. So, the original lost_souls() is
	  renamed to full_lost_souls(). A new regional_lost_souls() is
	  implemented. This code has been tested in 3x3x3 processors,
	  running over 100 timesteps. The number of total tracers is
	  conserved.

2007-03-19 23:44  tan2

	* module/setProperties.c: Init'd
	  E->composition.icompositional_rheology to 0

2007-03-19 23:42  tan2

	* lib/Composition_related.c, lib/composition_related.h: * Init'd
	  E->composition.icompositional_rheology to 0 * Write composition
	  instruction only if it is turned on * Clean up the code a bit

2007-03-19 23:29  tan2

	* lib/Composition_related.c: Removing read_comp(), which is not
	  used anymore

2007-03-19 23:25  tan2

	* CitcomS/Solver/Solver.py: Advect the tracers right after
	  temperature advection, before solving velocity

2007-03-19 23:08  tan2

	* lib/Regional_parallel_related.c: Replaced for-loop by an if,
	  which matchs the intention better

2007-03-19 22:53  tan2

	* lib/Advection_diffusion.c, lib/Convection.c: Init'd
	  advection.timestep and advection.timesteps earlier. The time
	  output uses these parameters.

2007-03-19 22:51  tan2

	* lib/Viscosity_structures.c: Reimplemented my version of
	  low_viscosity_channel_factor() and low_viscosity_wedge_factor()

2007-03-19 22:50  tan2

	* lib/Full_tracer_advection.c, lib/Tracer_setup.c: Clean up the
	  function prototype declaration

2007-03-19 22:48  tan2

	* lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c,
	  lib/Tracer_setup.c: Moving tracer initialization code to a
	  function

2007-03-19 22:45  tan2

	* lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c,
	  lib/Size_does_matter.c, lib/Tracer_setup.c, lib/global_defs.h:
	  Compute the volume of the mesh, use it to estimate the # of
	  tracers in the proc. make_tracer_array() now works for both
	  versions

2007-03-17 00:38  tan2

	* lib/Pan_problem_misc_functions.c: Apply chemical buoyancy only
	  when using tracer

2007-03-17 00:21  tan2

	* bin/Citcom.c, lib/Full_obsolete.c, lib/Full_tracer_advection.c,
	  lib/Output.c, lib/Output_h5.c, lib/Regional_tracer_advection.c,
	  lib/Tracer_setup.c, lib/Viscosity_structures.c,
	  lib/global_defs.h, lib/tracer_defs.h, module/misc.c,
	  module/setProperties.c: Merged the regional and global tracer
	  codes.
	  
	  Basically, Vlad's code is mostly gone and is replaced by Allen's
	  and mine code. A few functions, eg. analytical_test(),
	  low_viscosity_*_factor(), are disabled, need to work on them
	  later.

2007-03-15 02:51  leif

	* CitcomS/BaseApplication.py: Removed broken usage() method.
	  (Pythia v0.8.1.3 will have a reasonable default for this method.)

2007-03-13 00:56  gurnis

	* lib/Full_read_input_from_files.c,
	  lib/Regional_lith_age_read_files.c,
	  lib/Regional_read_input_from_files.c: Refactored the regional
	  parts of the code so that the age grids are read in from the same
	  code as are the velocity and material files. Moved the guts of
	  Regional_lith_age_read_files.c to
	  Regional_read_input_from_files.c. This nearly makes the structure
	  of Full and Regional the same -- refactoring that Leif initiated
	  last year

2007-03-12 23:27  tan2

	* CitcomS/Components/Tracer.py, lib/Composition_related.c,
	  module/setProperties.c: Commented out code about
	  compositional_rheology, which is not implemented

2007-03-12 23:11  tan2

	* lib/Composition_related.c, lib/Full_tracer_advection.c: Removed
	  static variables, added some code documentation

2007-03-12 22:14  tan2

	* CitcomS/Components/Tracer.py, lib/Composition_related.c,
	  lib/Full_tracer_advection.c, lib/composition_related.h,
	  lib/global_defs.h, lib/tracer_defs.h, module/setProperties.c: A
	  new input parameter "ic_method_for_flavors", to specify which way
	  to initialize the flavors when the tracers are init'd randomly
	  
	  Currrently, only ic_method_for_flavors=0 is allowed, which
	  produces a layered structure, any tracer above z_interface is of
	  flavor 0, below z_interface is of flavor 1.

2007-03-12 22:07  tan2

	* lib/Composition_related.c, lib/Full_tracer_advection.c,
	  lib/composition_related.h: Initial bulk composition

2007-03-12 22:06  tan2

	* lib/Full_tracer_advection.c, lib/Output.c, lib/tracer_defs.h:
	  Output the total composition information to the log file, get rid
	  of extra file handles in trace struct

2007-03-12 22:05  tan2

	* lib/Full_tracer_advection.c, lib/Stokes_flow_Incomp.c,
	  lib/tracer_defs.h: Compute the Cartesian velocity on the fly, not
	  storing it in a seperated array

2007-03-12 20:08  gurnis

	* lib/Advection_diffusion.c, lib/Lith_age.c,
	  lib/Regional_lith_age_read_files.c,
	  lib/Regional_read_input_from_files.c: Modified
	  Regional_read_input_from_files.c so that it now opens and reads
	  in material files. Material files are organized by elements.
	  Previsouly only worked for Full

2007-03-11 05:27  tan2

	* CitcomS/Components/Tracer.py, lib/Composition_related.c,
	  lib/Full_tracer_advection.c, lib/Output.c, lib/global_defs.h,
	  lib/tracer_defs.h, module/setProperties.c: A new way to compute
	  composition.
	  
	  Each tracer has a "flavor" (can only be either 0 or 1 currently).
	  In the ratio method, the composition of an element is determined
	  by: (# of tracers of flavor i)/(# of total tracers)

2007-03-11 05:20  tan2

	* CitcomS/Components/Tracer.py, lib/Composition_related.c,
	  lib/Full_obsolete.c, lib/Full_tracer_advection.c, lib/Output.c,
	  lib/Pan_problem_misc_functions.c, lib/global_defs.h,
	  lib/tracer_defs.h, module/setProperties.c: * Unifying output for
	  extra tracer quantities * Renamed rtrac to basicq, etrac to
	  extraq, to match the basic/extra quantities for advection *
	  Renamed itrac to ielement, itracsize to ielementsize,
	  ielementsize to max_ntracers * A new member for the # of tracers
	  * Removed some unused members in trace struct * Untabify and
	  indent the code

2007-03-09 00:26  tan2

	* AUTHORS: Add Vlad to the author list

2007-03-09 00:25  tan2

	* AUTHORS, CitcomS/Components/Output.py,
	  CitcomS/Components/Tracer.py, lib/Composition_related.c,
	  lib/Element_calculations.c, lib/Full_obsolete.c,
	  lib/Full_tracer_advection.c, lib/Global_operations.c,
	  lib/Instructions.c, lib/Makefile.am, lib/Output.c,
	  lib/Pan_problem_misc_functions.c, lib/Stokes_flow_Incomp.c,
	  lib/Viscosity_structures.c, lib/composition_related.h,
	  lib/global_defs.h, lib/tracer_defs.h, module/setProperties.c: A
	  big patch for tracers and composition:
	  
	  * Seperating composition codes from tracer codes, several struct
	  members in E->trace are moved to E->composition * Add chemical
	  buoyancy term * Renamed thermal_buoyancy() to get_buoyancy() to
	  reflect the fact that this function computes buoyancy according
	  to temperature/composition/phase * Fix and optimize the fix_*()
	  functions * Remove some static variables, or converte them to
	  const * Change the type of E->SinCos from float to double, and
	  replace E->trace.DSinCos * Provide default values for "required"
	  input parameters * Renamed tracer_restart to tracer_ic_method,
	  also remapped the options * Removed option for Cartesian tracer
	  input and trace.iwrite_tracers_every * Replaced
	  trace.itracer_type by composition.ichemical_buoyancy * Optionally
	  output tracers and composition fields

2007-03-08 00:35  leif

	* bin/Makefile.am: Minor Makefile fix I made while working on
	  Nemesis (i.e. with embedding disabled).

2007-03-02 00:09  tan2

	* lib/Full_tracer_advection.c, lib/tracer_defs.h: * Simplified
	  checking in the radial direction * Removed obsolete variables in
	  trace struct

2007-03-01 21:23  tan2

	* lib/Full_tracer_advection.c: Finally, exchanging tracers between
	  processors works, at least in 12-proc cases

2007-03-01 21:21  tan2

	* lib/Full_tracer_advection.c, lib/Output.c, lib/tracer_defs.h: *
	  Communicate cap boundary information with neighboring processors.
	  This information will be used in icheck_cap() later * Update
	  icheck_cap() for our paralleism * Disable composition-related
	  output

2007-03-01 21:17  tan2

	* lib/Full_tracer_advection.c: Fixed two errors reported by icc

2007-03-01 21:16  tan2

	* CitcomS/Components/Tracer.py, lib/Full_tracer_advection.c,
	  module/setProperties.c: * Create pyre inventory for tracer input
	  * Changed the default values of some tracer parameters to be
	  consistent with pyre inventory

2007-03-01 21:15  tan2

	* bin/Citcom.c, lib/Full_tracer_advection.c,
	  lib/Full_version_dependent.c, lib/Global_operations.c,
	  lib/Instructions.c, lib/Tracer_setup.c,
	  lib/Viscosity_structures.c, lib/global_defs.h, lib/tracer_defs.h,
	  module/initial_conditions.c: Migrating the tracer code (not
	  finished)

2007-03-01 21:02  tan2

	* lib/Full_tracer_advection.c, lib/Global_operations.c,
	  lib/Makefile.am, lib/global_defs.h, lib/tracer_defs.h: Copied
	  from Allen McNamara's tracer code. The code will fail to compile

2007-02-16 17:44  leif

	* module/Exchanger: Resurrected Exchanger source.

2007-02-08 00:15  tan2

	* lib/Advection_diffusion.c: Spherical version of the temperature
	  solver

2007-02-08 00:14  tan2

	* visual/execpaste.py: Removed the use of a new feature in python
	  2.4 ("substring" in "string")

2007-02-06 02:23  tan2

	* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
	  lib/Advection_diffusion.c, lib/Convection.c,
	  module/setProperties.c: Added input parameters that controlling
	  the predictor-corrector scheme

2007-02-06 02:22  tan2

	* lib/Full_version_dependent.c: Fixed a bug when reading coor_file
	  in full CitcomS

2007-02-06 02:22  tan2

	* lib/Solver_multigrid.c: Changed smoothing method for viscosity to
	  be consistent with CitcomCU

2007-02-02 23:30  tan2

	* CitcomS/Components/IC.py, lib/Full_version_dependent.c,
	  lib/Initial_temperature.c, lib/Regional_version_dependent.c,
	  module/setProperties.c: A new option for initial temperature,
	  which is used in Shijie's benchmark
	  
	  When tic_method==3, the initial temperature is a linear profile
	  plus mag * modified_plgndr_a(ll, mm, theta) * (cos(mm*phi) +
	  sin(mm*phi)) * sin(M_PI * (r - E->sphere.ri) / (E->sphere.ro -
	  E->sphere.ri))

2007-02-02 20:10  tan2

	* CitcomS/Solver/Solver.py: Disable pid output for processors of
	  rank>0

2007-01-31 20:46  tan2

	* CitcomS/Solver/Solver.py: Removed spaces around the equal sign
	  when writing pid file, which confused parser.py

2007-01-30 21:16  leif

	* configure.ac: Moved Python egg stuff into our Autoconf macro
	  library.

2007-01-30 19:29  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: added spaces
	  after = in sec b.2; redid table in c.4.9 prev updated by eh;
	  regen pdf

2007-01-30 19:04  tan2

	* lib/Viscosity_structures.c: Compute the 2nd invariant of strain
	  rate tensor in spherical coordinate

2007-01-29 20:51  gurnis

	* lib/Full_read_input_from_files.c: The functionality of this
	  routine is now expanded so that for evey time step the element
	  materials are read in. The code for determining the material file
	  names and opening the file name and then reading in the element
	  files is placed in the same code that the age grids and velocity
	  files are processed. Obviously, reading in materials currently
	  only works for Full; fill be working on Regional next.

2007-01-29 20:46  gurnis

	* lib/Advection_diffusion.c, lib/BC_util.c, lib/Instructions.c,
	  lib/Problem_related.c: Changed the seequence placement in the
	  time step when the age grids are assimilated into the temperature
	  field. Previously, going back to the original code contributed by
	  CC, the assimilation occurred avery time the temperature BCs were
	  set (meaning multiple times in a PC loop). Now assimilation
	  happens only once at the end of the time step. This is placed at
	  the end of the routine PG_time_step_solve. Once we have worked
	  with this some more, we will want to expose this code at a higher
	  level so that assimulation will work properly from either plain C
	  code or the Pyre version. Currently only tested with Full.

2007-01-29 20:37  gurnis

	* lib/Lith_age.c: A minor change so that restart now works properly
	  when lith_age=1. Now restart from old temperature fields appear
	  to work without any obvious corruption of the Temp field. Only
	  tested with Full.

2007-01-29 20:32  gurnis

	* lib/Viscosity_structures.c: Small change for rheol=5 to use
	  harmonic mean when element materials are read in. Also, this
	  involved a minor conflict resolution with Eh s recent change to
	  this file

2007-01-26 21:32  tan2

	* CitcomS/Solver/Solver.py: Write controller inventory to pid file.
	  This is a heck!

2007-01-25 23:30  tan2

	* lib/Stokes_flow_Incomp.c: Compute the velocity in Cartesian coord
	  on the fly.
	  
	  The previous code computed and stored the Cartesian velocity in
	  E->temp in v_from_vector() and accessed E->temp in
	  velo_from_element. This is bug prone. E->temp is a temporary
	  array and should be used for storage.
	  
	  Also, in previous code, if E->sphere.cap[m].V is modified, one
	  has to recompute E->temp. Otherwise, the Cartesian velocity will
	  be incorrect.

2007-01-25 01:38  tan2

	* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
	  bin/Citcom.c, lib/Advection_diffusion.c, lib/Convection.c,
	  lib/Solver_multigrid.c, lib/global_defs.h: Get rid of static
	  variables

2007-01-25 00:57  tan2

	* CitcomS/Solver/Solver.py, bin/Citcom.c,
	  lib/Advection_diffusion.c, lib/Convection.c,
	  lib/Full_geometry_cartesian.c, lib/Instructions.c,
	  lib/Regional_geometry_cartesian.c, module/advdiffu.c,
	  module/mesher.c, module/setProperties.c: Refactoring various
	  functions to simplify their pyre counterpart

2007-01-17 20:02  tan2

	* lib/Viscosity_structures.c: Fixed a bug in locating elements
	  right above tracers

2007-01-17 01:54  tan2

	* lib/Instructions.c, lib/Pan_problem_misc_functions.c: Replaced
	  'exit(0)' with correct MPI exit, related to issue69

2007-01-16 20:37  tan2

	* lib/Full_read_input_from_files.c,
	  lib/Regional_read_input_from_files.c: Fixed issue77 - velocity
	  b.c not scaled correctly when age becomes negative

2007-01-16 19:49  tan2

	* CitcomS/Components/IC.py, module/setProperties.c: Read input
	  parameter 'half_space_age' when tic_method=1

2007-01-16 18:50  tan2

	* lib/Regional_tracer_advection.c: Fixed incorrect prototype

2007-01-16 18:43  tan2

	* lib/Regional_version_dependent.c: When "tic_method=1", the
	  temperature is isothermal (== bottom b.c.) with a uniformly cold
	  plate (thickness specified by 'half_space_age')

2007-01-16 17:41  tan2

	* CitcomS/Components/Visc.py, lib/Regional_tracer_advection.c,
	  lib/Viscosity_structures.c, lib/viscosity_descriptions.h,
	  module/setProperties.c: Tracer-defined rheology -- low viscosity
	  channel/wedge

2007-01-15 21:42  tan2

	* lib/Makefile.am, lib/Regional_tracer_advection.c,
	  lib/Tracer_advection.c, lib/Tracer_setup.c, lib/tracer_defs.h,
	  module/misc.c: Added regional (passive) tracers

2007-01-09 21:11  tan2

	* lib/Problem_related.c: Fix for time-invariant velocity boundary
	  conditions, issue75

2007-01-08 23:09  tan2

	* doc/manual/citcoms.lyx: Another document fix for issue75, related
	  to "how to specify time-invariant velocity boundary conditions?"

2007-01-08 22:19  tan2

	* doc/manual/citcoms.lyx: 1. Fixed a reference error, "Section 1.6"
	  should be "Equation 1.6" 2. Velocity BC input and geoid output
	  are dimensional. The units were undocumented in previous release.
	  This fix the issue75. 3. More information about geoid output: the
	  meaning of each column and how to compute the geoid field.

2007-01-08 22:19  tan2

	* visual/plot_annulus.py, visual/plot_layer.py: Truncate the
	  temperature grd file at specified min/max
	  
	  Sometimes the temperature field has overshoot/undershoot, which
	  would be leave a blank area in the contour plot. This is a simple
	  workaround.

2007-01-05 22:33  tan2

	* visual/batchpaste.sh: Fix for issue73 "problems with
	  autocombine.py in single workstation mode"
	  
	  $HOSTNAME is not defined in the non-interactive shell in Ubuntu
	  6.10. Need to put a quote around it.

2007-01-05 00:06  leif

	* Makefile.am: Fix for issue72: "'make install' broken for
	  non-pyred CitcomS".

2006-12-20 22:13  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: added note about
	  updating to 2.10.3

2006-12-09 00:26  tan2

	* ChangeLog: Regenerated ChangeLog upto r5565

2006-12-09 00:22  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: gurnis final
	  changes; image resize; ready for release

2006-12-08 23:50  sue

	* doc/manual/citcoms.lyx: small text changes; image resize

2006-12-08 23:45  tan2

	* doc/manual/citcoms.lyx: Added "created by OpenDX" on several
	  figure captions

2006-12-08 23:36  tan2

	* doc/manual/citcoms.lyx, doc/manual/graphics/mayavi2.png: Updated
	  MayaVi2 section

2006-12-08 23:30  tan2

	* visual/Makefile.am,
	  visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py,
	  visual/mayavi2_citcoms_display.py: Renamed the MayaVi launching
	  script and move it to visual/

2006-12-08 23:26  tan2

	* visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py: Added
	  executable bit to file permission

2006-12-08 22:44  luis

	* visual/Makefile.am: Add plugins for MayaVi2 to installation

2006-12-08 22:27  luis

	* visual/Mayavi2/README, visual/Mayavi2/citcoms_display/README,
	  visual/Mayavi2/citcoms_plugins/README: Added README files

2006-12-08 22:00  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: fixed image size,
	  text size and other small text changes

2006-12-08 21:16  luis

	* visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py: Removing
	  reduce filter from comments, as it is currently obsolete.

2006-12-08 21:15  luis

	* doc/manual/citcoms.lyx: Added MayaVi screenshot to manual, along
	  with a couple of other fixes.

2006-12-08 20:03  luis

	* visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py,
	  visual/Mayavi2/citcoms_plugins/plugins/OpenCitcomSFILES.py: Last
	  set of patches to citcoms_plugins * Display filename in mayavi
	  pipeline * Changed glob pattern so that only HDF5 timestep files
	  can be selected

2006-12-08 19:47  luis

	* visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py,
	  visual/Mayavi2/citcoms_plugins/custom_ui.py,
	  visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py,
	  visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSFilterActions.py,
	  visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSreduce.py,
	  visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSshowCaps.py,
	  visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomsCapFilter.py,
	  visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomsReduceFilter.py:
	  Forgot to rename data filters.

2006-12-08 17:53  luis

	* doc/manual/graphics/mayavi2.png: Added MayaVi2 screenshot for the
	  manual.

2006-12-08 17:44  luis

	* visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py,
	  visual/Mayavi2/citcoms_plugins/custom_ui.py,
	  visual/Mayavi2/citcoms_plugins/plugins/CitcomSHDFUgrid.py,
	  visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py,
	  visual/Mayavi2/citcoms_plugins/plugins/OpenCitcomSFILES.py,
	  visual/Mayavi2/citcoms_plugins/utils.py: Various patches.

2006-12-08 17:40  luis

	* visual/Mayavi2/citcoms_plugins,
	  visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py,
	  visual/Mayavi2/citcoms_plugins/__init__.py,
	  visual/Mayavi2/citcoms_plugins/plugins,
	  visual/Mayavi2/citcoms_plugins/plugins/CitcomSHDFUgrid.py,
	  visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py,
	  visual/Mayavi2/citcoms_plugins/plugins/OpenCitcomSFILES.py,
	  visual/Mayavi2/citcoms_plugins/plugins/__init__.py,
	  visual/Mayavi2/citcoms_plugins/plugins/filter,
	  visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSFilterActions.py,
	  visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSSphere.py,
	  visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSreduce.py,
	  visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSshowCaps.py,
	  visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSshowSurface.py,
	  visual/Mayavi2/citcoms_plugins/plugins/filter/__init__.py:
	  Forking original plugins

2006-12-08 17:32  luis

	* visual/Mayavi2/Martin, visual/Mayavi2/original_plugins,
	  visual/Mayavi2/original_plugins/README: Archiving original
	  plugins.

2006-12-08 17:31  luis

	* visual/Mayavi2/mayavi_custom_ui.py: Modify plugins directory

2006-12-08 17:29  luis

	* visual/Mayavi2/Martin/README: Explain contents of each directory.

2006-12-08 02:29  leif

	* configure.ac: Made 'install_deps' actually do what 'configure'
	  says it's doing (*missing* deps, not *all*).

2006-12-07 23:26  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf,
	  doc/manual/graphics/regtest.100.z005.jpg: reinstated a few lost
	  changes; changed caption position on fig 5.3 on request; enlarged
	  fig 5.4; regen pdf

2006-12-07 22:34  tan2

	* doc/manual/citcoms.lyx: chapter 5 * Added MayaVi2 in the
	  introduction * Added links to MayaVi2 installation

2006-12-07 22:19  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: fixed image size;
	  regen pdf

2006-12-07 22:09  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: text fixes to
	  recent additions

2006-12-07 21:30  tan2

	* doc/manual/citcoms.lyx, doc/manual/graphics/hdfview.png: * Put
	  back the HDFView sections * Added a screenshot of HDFView * Added
	  a warning on "-O3" compiler flag

2006-12-07 05:03  sue

	* doc/manual/citcoms.lyx: text edits to appendices and bib

2006-12-07 00:12  sue

	* doc/manual/citcoms.lyx: small changes to chapt 6; standardized
	  cross refference style; sstandardized code spacing

2006-12-06 23:31  sue

	* doc/manual/citcoms.lyx: enumerating several sections of the
	  instructions in chap 5 for clarity, and a few minor text fixes

2006-12-06 20:59  sue

	* doc/manual/citcoms.lyx: a few text fixes in chapter 3

2006-12-06 20:33  sue

	* doc/manual/citcoms.lyx: a few text fixes, preface to end of chapt
	  2

2006-12-06 18:59  sue

	* doc/manual/citcoms.lyx: gurnis corrections and some other fixes

2006-12-06 08:52  luis

	* visual/Makefile.am: Temporarily removing Mayavi2 files from
	  Makefile.am

2006-12-06 08:23  luis

	* visual/Mayavi2/Citcoms_Hdf2Vtk.c,
	  visual/Mayavi2/Citcoms_Hdf2Vtk.py,
	  visual/Mayavi2/Citcoms_HdfDisplay.py,
	  visual/Mayavi2/Citcoms_VtkDisplay.py, visual/Mayavi2/Martin,
	  visual/Mayavi2/Martin/Citcoms_Hdf2Vtk.c,
	  visual/Mayavi2/Martin/Citcoms_Hdf2Vtk.py,
	  visual/Mayavi2/Martin/Citcoms_HdfDisplay.py,
	  visual/Mayavi2/Martin/Citcoms_VtkDisplay.py,
	  visual/Mayavi2/Martin/README, visual/Mayavi2/Martin/__init__.py,
	  visual/Mayavi2/Martin/plugins, visual/Mayavi2/README,
	  visual/Mayavi2/__init__.py, visual/Mayavi2/plugins: Archive files
	  created during Martin Weier's internship

2006-12-06 08:16  luis

	* visual/Mayavi2/citcoms_display/plugins,
	  visual/Mayavi2/citcoms_display/plugins/HDF5FileReader.py,
	  visual/Mayavi2/citcoms_display/plugins/HDF5UGrid.py,
	  visual/Mayavi2/citcoms_display/plugins/ReduceFilter.py,
	  visual/Mayavi2/citcoms_display/plugins/ShowCapsFilter.py,
	  visual/Mayavi2/citcoms_display/plugins/ShowSurfaceFilter.py,
	  visual/Mayavi2/citcoms_display/plugins/Sphere.py,
	  visual/Mayavi2/citcoms_display/plugins/UGridThread.py,
	  visual/Mayavi2/citcoms_display/plugins/VTKFileReader.py,
	  visual/Mayavi2/citcoms_display/plugins/__init__.py: Reorganized
	  structure of the Mayavi2 plugin modules

2006-12-06 08:13  luis

	* visual/Mayavi2/citcoms_display/custom_ui.py,
	  visual/Mayavi2/citcoms_display/mayavi_custom_ui.py,
	  visual/Mayavi2/mayavi_custom_ui.py: Simplified the file that will
	  be be copied to user's ~/.mayavi2 directory.

2006-12-06 06:55  luis

	* visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Group all
	  CitcomS options under a single menu group.

2006-12-06 05:58  luis

	* doc/manual/citcoms.lyx: Quick fixes to manual.

2006-12-06 01:08  leif

	* CitcomS/Makefile.am, module/Regionalmodule.c, visual/Makefile.am:
	  Adding missing files to tarball ("make dist"), including the
	  'Mayavi2' directory, which is now installed under share/CitcomS.
	  Also deleted 'Regionalmodule.c', which is no longer used.

2006-12-06 00:49  sue

	* doc/manual/citcoms.lyx: small changes in one image caption and in
	  citation

2006-12-06 00:42  leif

	* Makefile.am, bin/Makefile.am, configure.ac: Fix for eggs not
	  being installed by "make install" when builddir == srcdir. This
	  change also re-fixes the setup.py infinite regress in a cleaner
	  way.

2006-12-06 00:18  luis

	* visual/Mayavi2/citcoms_display/actions.py,
	  visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Added actions
	  for ReduceFilter and ShowCapsFilter

2006-12-05 23:13  leif

	* Makefile.am, setup.py: Require final release version of Pythia.
	  Include egg-related files in release tarball ("make dist").

2006-12-05 20:46  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: edited text and
	  images placement in 5.8

2006-12-05 20:34  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: slghtly widened
	  l. col in appendix a tables as using typewriter widened lines;
	  fixed other formatting issues in appendices

2006-12-05 20:11  sue

	* doc/manual/citcoms.lyx: changing font style to typewriter small
	  in appendix a tablesi and a few typos

2006-12-05 19:19  sue

	* doc/manual/citcoms.lyx: small fixes to chap 4, text and table
	  placement

2006-12-05 18:04  sue

	* doc/manual/citcoms.lyx: making use of typewriter font and quotes
	  consistent in appendix a

2006-12-05 07:09  tan2

	* doc/manual/citcoms.lyx: Updated Chapter 4

2006-12-05 06:17  tan2

	* visual/samples/cookbook1.100.h5, visual/samples/cookbook1.h5:
	  Example h5 files including all optional output

2006-12-05 06:14  tan2

	* visual/Makefile.am: Forgot to update the makefile

2006-12-05 05:04  tan2

	* doc/manual/citcoms.lyx: Removed sections about HDFView.
	  
	  HDFView by default displays the dataset in a 2D table, which can
	  be very confusing when working on multidimensional dataset.
	  
	  "h5ls -r" is a better tool for discovering the group structure
	  and dataset dimension.

2006-12-05 04:19  tan2

	* visual/estimate.py, visual/estimate_size.py: * Renamed
	  estimate.py to estimate_size.py * Added license text * Update for
	  new HDF5 layout

2006-12-05 00:46  luis

	* doc/manual/citcoms.lyx: Changed code in A.1.1 and A.1.2 to use
	  small font with typewriter style.

2006-12-05 00:40  tan2

	* NEWS: Mentioned change of naming scheme for capfiles in NEWS

2006-12-05 00:31  sue

	* doc/manual/citcoms.lyx: fixed quotes; added degree symbols as
	  requested

2006-12-05 00:14  tan2

	* doc/manual/citcoms.lyx,
	  doc/manual/graphics/fulltest.xsect.100.jpg,
	  doc/manual/graphics/regtest.100.z005.jpg: Finished the GMT script
	  section

2006-12-04 23:47  tan2

	* visual/plot_annulus.py: Renamed "center" to "starting point"

2006-12-04 22:42  sue

	* doc/manual/citcoms.lyx: minor sentence/word form changes in 5.1
	  and 5.2

2006-12-04 22:33  sue

	* doc/manual/citcoms.lyx: reformatted column names in c.4.9

2006-12-04 22:19  tan2

	* doc/manual/citcoms.lyx: Revised Chapter 5 and Appendix A * Minor
	  revision of post-processing * Update OpenDX section for new HDF5
	  layout * Briefly mentioned GMT scripts (unfinished) * Described
	  new viscosity laws * Using Greek letter eta in the viscosity
	  equations

2006-12-04 20:33  sue

	* doc/manual/citcoms.lyx: fixed more quotes, fixed table breaks,
	  lines in table missing, other minor format problems

2006-12-04 19:48  luis

	* visual/Mayavi2/citcoms_display/__init__.py,
	  visual/Mayavi2/citcoms_display/actions.py,
	  visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Added
	  OpenHDF5 and OpenVTK actions for mayavi2

2006-12-04 17:24  luis

	* doc/manual/citcoms.lyx: Fixes to manual

2006-12-04 17:24  luis

	* NEWS: Fixed typos

2006-12-04 16:54  luis

	* visual/h5tocap.c: Added vim modeline

2006-12-04 14:21  luis

	* visual/Mayavi2/citcoms_display/__init__.py,
	  visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Mayavi2 UI
	  customizations

2006-12-04 14:11  luis

	* visual/Mayavi2/citcoms_display: Added python module namespace for
	  the citcoms mayavi2 plugins

2006-12-04 13:43  luis

	* visual/Mayavi2/__init__.py,
	  visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
	  visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py,
	  visual/Mayavi2/plugins/__init__.py,
	  visual/Mayavi2/plugins/filter/__init__.py: Removed executable
	  permissions

2006-12-02 07:41  tan2

	* doc/manual/graphics/CitcomSImportHDF5.net.gif,
	  visual/OpenDXMacro/CitcomSImportHDF5.net.in: Update for new HDF5
	  layout

2006-12-02 07:14  tan2

	* examples/Full/input.sample, examples/Regional/input.sample: *
	  Removed obsolete parameters * Added new parameters * Only one
	  "parameter=value" per line

2006-12-02 06:04  tan2

	* visual/h5tocap.c: Updated for new HDF5 layout

2006-12-02 06:04  tan2

	* visual/h5util.c, visual/h5util.h: Minor tweaks

2006-12-02 04:43  tan2

	* visual/Makefile.am, visual/h5tovelo.c, visual/h5util.c,
	  visual/h5util.h: Moved utility functions to h5util.c

2006-12-02 04:15  tan2

	* visual/h5tovelo.c: Fixed a bug of counting argc

2006-12-02 00:57  tan2

	* lib/Viscosity_structures.c: Added more rheology options, which is
	  required for benchmarks
	  
	  rheol=1: visc = visc0 * exp(viscE * (viscT - T)) rheol=2: visc =
	  visc0 * exp(-T / viscT)

2006-12-02 00:38  tan2

	* visual/h5tocap.py: Updated h5tocap.py for new layout of HDF5
	  files

2006-12-02 00:03  tan2

	* visual/Makefile.am, visual/h5tovelo.c: Added a program to convert
	  h5 file to velo files for restart

2006-12-01 23:34  sue

	* doc/manual/citcoms.lyx: removed todo at 4.5.1, no issue there

2006-12-01 22:00  leif

	* configure.ac: Fix for infinite regress when builddir == srcdir.
	  !@#$%*
	  
	  The .pth/sitedir/sys.path/PYTHONPATH aspect of eggs is really
	  irritating. I hope setuptools becomes a part of the standard
	  Python distro, as the Python core developers are likely to accept
	  it uncritically and unmodified (as they are wont to do,
	  apparently -- judging by all the other crap that is in the
	  standard library). God willing, this will further accelerate the
	  death of the language.

2006-12-01 21:56  tan2

	* visual/Makefile.am, visual/samples/cookbook1.100.h5,
	  visual/samples/cookbook1.h5: Added samples of HDF5 output

2006-12-01 21:33  leif

	* bin/Makefile.am, configure.ac: builddir != srcdir works again.
	  
	  The use of setup.py/distutils/setuptools forces the creation of
	  files in srcdir. This bugs me.

2006-12-01 04:40  leif

	* Makefile.am, configure.ac: The "make install" command now works
	  again.

2006-11-30 23:38  sue

	* doc/manual/citcoms.lyx: fixed sentence in A.1.2 last row

2006-11-30 23:08  tan2

	* doc/manual/citcoms.lyx: Updated Chapter 6 * sync'd the manual
	  with the cookbook scripts * improving the resolution of
	  cookbook5.2.eps is left until the next release
	  
	  Also, fixed table borders in Appendix A.

2006-11-30 22:55  tan2

	* examples/Cookbook5/cookbook5.cfg: Moved path name of restart file
	  to "datadir_old"

2006-11-30 22:53  tan2

	* examples/Cookbook1/cookbook1.cfg,
	  examples/Cookbook2/cookbook2.cfg,
	  examples/Cookbook3/cookbook3.cfg,
	  examples/Cookbook4/cookbook4.cfg,
	  examples/Cookbook5/cookbook5.cfg: Fixed issue63, Change
	  "monitoringfrequency" comment in citcoms cookbooks

2006-11-30 22:21  luis

	* doc/manual/citcoms.lyx: Done with Chapter 4 references.

2006-11-30 21:16  tan2

	* doc/manual/citcoms.lyx: The concept of caps is explained in
	  section 1.7

2006-11-30 21:10  luis

	* visual/Makefile.am, visual/h5steps.c: Removing obsolete program
	  h5steps.c

2006-11-30 20:57  tan2

	* doc/manual/citcoms.lyx: Updated Appendices

2006-11-30 20:26  tan2

	* doc/manual/citcoms.lyx: Updated section 3.6.1

2006-11-28 23:28  leif

	* CitcomS/Components/IC.py,
	  CitcomS/Components/Sphere/FullSphere.py,
	  CitcomS/Components/Sphere/RegionalSphere.py,
	  CitcomS/Solver/Solver.py, module/bindings.c,
	  module/getProperty.h, module/misc.c, module/misc.h,
	  module/setProperties.c: Fixed some bugs, some of which were
	  introduced during the C -> C++ transition.
	  
	  Using a pidXXXX.cfg file as input should "work" now, although it
	  still doesn't reproduce the original simulation, since at least
	  one parameter is missing ('steps'). I maintain that dumping the
	  configuration is really the job of the framework (Pyre).
	  Unfortunately, Pyre's current capabilities in this area are buggy
	  in the case of '.pml' files, and non-existent in the case of
	  '.cfg' files.
	  
	  Note: 'nproc_surf' is now a real inventory item, instead of a
	  fake one. It looks like it doesn't belong in the inventory at
	  all, though. (I left it there to avoid breakage.)

2006-11-28 21:08  leif

	* doc/manual/citcoms.lyx: Checked-in a virus, a worm, a Trojan
	  horse, and some other malware. LyX doesn't support copy & paste
	  between applications, so this check-in may have introduced some
	  bugs as well.

2006-11-28 19:26  sue

	* doc/manual/citcoms.lyx: various edits to 3.6.1 and 3.7

2006-11-28 07:33  leif

	* lib/Instructions.c: Rewrote expand_str() in order to: 1) avoid
	  potential buffer overflow; 2) avoid the use of non-standard
	  strndup(); 3) avoid the use of the heap altogether. (Prompted by
	  unresolved strndup on Mac OS X.)

2006-11-28 05:00  tan2

	* examples/Cookbook2/cookbook2.cfg: Clarified the comment

2006-11-28 04:42  tan2

	* NEWS: Updated for new features

2006-11-28 04:41  tan2

	* README: Added a reference to NEWS

2006-11-28 03:34  tan2

	* doc/manual/citcoms.lyx: Chapter 3 updated

2006-11-28 03:01  leif

	* CitcomS/CoupledApp.py, CitcomS/SimpleApp.py, bin/citcoms.in,
	  setup.py: Changes related to Pythia v0.8.1.0b7, which CitcomS now
	  requires: 'journal' is no longer a part of an application's
	  inventory, and pyre.applications.start() is now responsible for
	  calling run().

2006-11-28 02:57  tan2

	* examples/Cookbook6/cookbook6.cfg, examples/Full/input.sample,
	  examples/Regional/input.sample: Updated the dimensional const

2006-11-28 02:55  tan2

	* examples/example1.cfg: Updated to be consistent with the manual

2006-11-27 23:09  tan2

	* CitcomS/Solver/Solver.py, lib/Instructions.c: Changed the default
	  value of "datadir" to "."

2006-11-27 22:37  tan2

	* visual/Makefile.am, visual/autocombine.py,
	  visual/batchcombine.py, visual/batchpaste.sh,
	  visual/batchpaste2.sh, visual/execpaste.py: Changed
	  postprocessing scripts for the new "datadir" parameter

2006-11-27 21:27  tan2

	* visual/pasteCitcomData.sh: Fix for POSIX-compliant arithmetic
	  expression
	  
	  The "sh" shell on my Ubuntu 6.10 doesn't have the "let" command.
	  That's how I found that "let" is not in the POSIX standard. Use
	  "$((expression))" instead.

2006-11-27 20:05  tan2

	* visual/citcoms_datadir: Added extern program to determine
	  "datadir"

2006-11-27 20:05  tan2

	* CitcomS/Components/Output.py, CitcomS/Solver/Solver.py,
	  lib/Instructions.c, lib/Output.c, lib/global_defs.h,
	  module/setProperties.c: Changes how to specify output directory
	  
	  * "output_format" must be either "ascii" (the default) or "hdf5",
	  the "ascii-local" option is gone * "datafile" becomes the prefix
	  of the filename and cannot contain "/" * "datadir" becomes
	  mandatory input parameters * If "datadir" is "%DATADIR", the
	  output directory is determined by an external program
	  "citcoms_datadir" * Special substrings "%RANK", "%HOSTNAME" in
	  datadir will be substituted by mpi rank, machine's hostname,
	  $DATADIR environment variable, respectively. * These special
	  strings start with "%", rather than "$", becuase it's very
	  difficult to input "$" from the command line.

2006-11-22 21:26  tan2

	* lib/Stokes_flow_Incomp.c: Changed the convergence criterion of
	  Stokes solver: * stop iterations if delta(v) or delta(p) becomes
	  too small (i.e., v or p has converged) * this is suggested by
	  Shijie Zhong

2006-11-22 21:25  tan2

	* lib/Full_parallel_related.c: Ignoring overlapping nodes when
	  counting # of global nodes

2006-11-22 20:25  sue

	* doc/manual/citcoms.lyx: typo; made references into an itemized
	  list

2006-11-22 20:05  tan2

	* lib/Full_parallel_related.c, lib/Full_version_dependent.c,
	  lib/Makefile.am, lib/Regional_parallel_related.c,
	  lib/Regional_version_dependent.c, lib/global_defs.h,
	  lib/temperature_descriptions.h: Removed unused codes and files

2006-11-22 19:41  tan2

	* lib/Output.c, lib/Output_h5.c, lib/Sphere_harmonics.c,
	  lib/Topo_gravity.c, lib/global_defs.h: Refactored geoid
	  calculation

2006-11-21 23:03  luis

	* doc/manual/citcoms.lyx: Expanded section on optimizing parallel
	  I/O.

2006-11-21 20:18  tan2

	* visual/plot_annulus.py, visual/plot_layer.py, visual/zslice.py:
	  Added scripts for 2D temperature plots, using GMT commands

2006-11-20 19:24  tan2

	* lib/Sphere_harmonics.c: Forgot to declare function prototype

2006-11-18 05:17  tan2

	* lib/Sphere_harmonics.c: Disabled a debugging output, which is not
	  protected by a "if(E->control.verbose)" and caused Segmentation
	  Fault.

2006-11-18 01:29  leif

	* bin/pycitcoms.c: The function loadObject() has been moved from
	  Pythia to Merlin.

2006-11-18 00:48  tan2

	* examples/Full/input.sample, examples/Full/velbc/README,
	  examples/Full/velbc/velbc_full.tar.gz, examples/Makefile.am:
	  Updated the vbc files and input file

2006-11-18 00:41  tan2

	* examples/Regional/input.sample, examples/Regional/velbc/README,
	  examples/Regional/velbc/velbc_regional.tar.gz,
	  examples/Regional/velbc/velbc_regional40,
	  examples/Regional/velbc/velbc_regional41: Updated the vbc files
	  and input file.

2006-11-18 00:20  tan2

	* lib/Instructions.c, lib/Output_h5.c, lib/hdf5_related.h,
	  lib/output_h5.h: HDF5 output for geoid is working

2006-11-17 22:37  luis

	* ., CitcomS, bin, etc, examples, lib, module, tests, visual,
	  visual/OpenDXMacro: Cleaned up 'svn status' by updating
	  svn:ignore property

2006-11-17 20:25  tan2

	* lib/Output_h5.c: HDF5 output of surf, botm, horiz_avg are working
	  now.
	  
	  * Time and timestep infomation is written as scalar attributes
	  "time" and "timestep" in / group. * Set MPI_Info according to
	  input parameters "cb_block_size" and "cb_buffer_size" * I decided
	  not to write surf, botm, and horiz_avg coordinates. This
	  coordinate can be retrieved from the 3D coordinate very easily by
	  this pseudo-code: surf_coord = coord[cap=all, x=all, y=all, z=1]
	  z_coord = coord[cap=1, x=1, y=1, z=all]
	  
	  Remainging works: geoid for hdf5, update the manual

2006-11-17 06:26  tan2

	* lib/Instructions.c, lib/Output_h5.c, lib/hdf5_related.h,
	  lib/output_h5.h: HDF5 output reloaded. See issue4 for reasoning.
	  
	  Most data outputs are working. Remaining works: * How to deal
	  with time output? (Maybe not output at all? Time info is always
	  written in the .time file anyway.) * Where to put 2d and 1d
	  coordinate output? (Maybe output with the data? These datasets
	  are small and won't take too much space anyway.) * Geoid output

2006-11-17 05:34  leif

	* CitcomS/Components/Output.py: Fixed a minor bug in Output.py.

2006-11-17 02:24  leif

	* doc/manual/citcoms.lyx: Revised everything having to do with
	  runtime configuration: launcher.xxx, scheduler.xxx, and job.xxx.
	  
	  Lowered the prominence/importance given to .pml files... and
	  resisted my temptation to delete all reference to them :-)
	  
	  (I think I'm pretty much done with the v2.1 manual at this point.
	  Reading the manual makes me tired, because it reminds me of how
	  much work remains to be done on the code itself. Ease-of-use
	  could be substantially improved...)

2006-11-16 21:58  leif

	* bin/Makefile.am: Reverted another recent decision of mine: Always
	  build the legacy drivers, 'CitcomSFull' and 'CitcomSRegional'. I
	  took these out of the Pyre build to avoid confusion; but now --
	  thinking of shared installations of CitcomS on clusters -- I
	  think they should always be built (as they were before) so that
	  users have the option.

2006-11-16 21:36  leif

	* examples/Makefile.am: Install examples under
	  PREFIX/share/CitcomS/examples, as now documented in the manual.
	  This is for the benefit of users of shared installations of
	  CitcomS. I also sync'd the file list in examples/Makefile.am.
	  
	  Note: the file velbc_regional.tar.gz seems to be corrupt!!!

2006-11-16 21:25  leif

	* doc/manual/citcoms.lyx: Corrections with respect to r5302: the
	  binaries/scripts are now once again built under the 'bin'
	  subdirectory.
	  
	  Also reviewed all references to PREFIX.

2006-11-16 14:40  leif

	* Citcom.c, CitcomSFull.c, CitcomSRegional.c, Makefile.am, bin,
	  bin/Citcom.c, bin/CitcomSFull.c, bin/CitcomSRegional.c,
	  bin/Makefile.am, bin/citcoms.in, bin/pycitcoms.c, citcoms.in,
	  configure.ac, pycitcoms.c: Re-created 'bin' subdirectory to avoid
	  filename conflict on case-sensitive filesystems (Mac, Windows):
	  "CitcomS" == "citcoms".
	  
	  Fixed egg-related bugs which prevented 'configure' from
	  succeeding when buildir != srcdir (another BuildBot test vector).
	  
	  Call addsitedir() in the 'citcoms' script. I guess this is now
	  necessary since "site.py" is no longer in the same directory as
	  "citcoms". (*)
	  
	  Note that there is currently a bug in Merlin which prevents
	  'citcoms' from running ("No module named pkg_resources"). The
	  work-around is to manually add the merlin egg to the
	  merlin-install.pth file.
	  
	  There are more bugs which prevent running on Mac OS X at all
	  (still investigating).
	  
	  (*) I'm becoming annoyed with setuptools' use of .pth files as a
	  sys.path/PYTHONPATH persistence mechanism, mainly because of the
	  accompanying hacks which are used to turn ordinary directories
	  into "site" directories (i.e., directories where .pth files work)
	  -- these ugly, confusing hacks include the fake site.py, "virtual
	  python", etc. I think Merlin will only use .pth files in real
	  site directories. It will use clear, straitforward, direct
	  sys.path manipulation everywhere else.

2006-11-16 03:04  tan2

	* module/setProperties.c: Forgot to commit module/ directory

2006-11-16 03:01  tan2

	* lib/Topo_gravity.c: Declared function prototype at the top

2006-11-16 02:07  tan2

	* CitcomS/Components/Const.py, CitcomS/Components/Output.py,
	  CitcomS/Components/Sphere/Sphere.py: Forgot to commit python
	  files

2006-11-16 02:07  tan2

	* lib/Sphere_harmonics.c: Declared function prototype at the top

2006-11-16 01:52  tan2

	* lib/Element_calculations.c, lib/Full_obsolete.c,
	  lib/Full_parallel_related.c, lib/Full_version_dependent.c,
	  lib/General_matrix_functions.c, lib/Global_operations.c,
	  lib/Instructions.c, lib/Obsolete.c, lib/Output.c,
	  lib/Output_h5.c, lib/Regional_obsolete.c,
	  lib/Regional_parallel_related.c,
	  lib/Regional_version_dependent.c, lib/Sphere_harmonics.c,
	  lib/Topo_gravity.c, lib/global_defs.h: Implemented geoid
	  calculation, see issue64. User visible changes include: *
	  "output_optional" can include string "geoid", which will enable
	  geoid output * new input parameters: radius, density_above,
	  density_below * removed input parameters: layerd, wdensity,
	  llmax, nlong, nlati * moved input parameter "output_ll_max" from
	  Sphere.py to Output.py * sync'd the defalut values of input
	  parameters in Const.py and Instructions.c
	  
	  TODO: h5output_geoid() not finished

2006-11-15 22:01  leif

	* doc/manual/citcoms.lyx: Elaborated a bit on .egg download, and
	  clarified that CitcomS needs Pythia v0.8.1.x (instead of 0.8).

2006-11-15 21:18  leif

	* doc/manual/citcoms.lyx: Re-read the stuff I worked on yesterday,
	  making minor corrections: "is in your PATH" -> "is on your PATH",
	  inserted the word "Section" before section references, other
	  minor changes.

2006-11-15 20:40  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: a few typos
	  fixed, http removed from htmlurl tags (not needed and lengthen
	  name in line); pdf regen

2006-11-15 02:06  leif

	* doc/manual/citcoms.lyx: Corrections to the section, "Changing
	  Parameters".

2006-11-15 01:14  leif

	* doc/manual/citcoms.lyx: Updated the installation chapter.

2006-11-14 03:25  leif

	* Makefile.am, citcoms.in, pycitcoms.c, setup.py: Pythia
	  v0.8.1.0b4: Fixed bugs relating to MPI launching: Fix
	  sys.path/PYTHONPATH automatically; don't touch 'argv' until after
	  MPI_Init().
	  
	  Next, I may try to slurp 'pycitcoms.c' into the framework... it
	  contains a lot of implementation details which have everything to
	  do with Pyre and nothing to do with CitcomS.

2006-11-11 03:34  leif

	* ., configure.ac, ez_setup.py, setup.py: Use the new merlin (the
	  setuptools clone). Download Python dependencies automatically
	  during 'configure' (This doesn't work for "make install" yet.)
	  
	  The Dynamo BuildBot might even succeed after this check-in...
	  fingers crossed...

2006-11-10 19:20  sue

	* doc/manual/citcoms.lyx: created formulas for sec a.1.11

2006-11-10 18:54  sue

	* doc/manual/citcoms.lyx, doc/manual/graphics/cookbook7.eps:
	  cookbook 6 graphic edited, various small tweaks

2006-11-10 01:59  sue

	* doc/manual/citcoms.lyx: finished various typos and fixes after
	  checking with Luis on questions

2006-11-09 19:37  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms_cover-layers.pdf,
	  doc/manual/citcoms_cover.pdf, doc/manual/graphics/c_fig1.eps:
	  various typos and fixes

2006-11-07 19:33  tan2

	* doc/manual/citcoms.lyx: * Fixed a few typos * Added "TODO" in
	  front of all unfinished text.

2006-11-07 02:30  leif

	* Makefile.am, configure.ac, lib/Makefile.am, visual/Makefile.am:
	  Moved CitcomS HDF5 macros to cs/autoconf.

2006-11-07 01:33  leif

	* ., CitcomS/Makefile.am, Makefile.am, bin, citcoms.in,
	  configure.ac, etc/Makefile.am, lib/Makefile.am, module/Exchanger,
	  module/Makefile.am, project.cfg, pycitcoms.c, setup.py,
	  visual/Makefile.am: Took a step backwards so that I can take a
	  more conservative approach to build/install. Also, temporarily
	  deleted 'Exchanger' and all references to it, to avoid confusion.
	  We can always go back in time and retrieve it later.

2006-11-07 00:49  sue

	* doc/manual/citcoms.pdf: pdf generated

2006-11-07 00:49  sue

	* doc/manual/citcoms.lyx, doc/manual/graphics/c_fig1.eps,
	  doc/manual/graphics/cookbook1.eps,
	  doc/manual/graphics/cookbook2.eps: gurnis edits, new pdf

2006-11-06 18:53  sue

	* doc/manual/citcoms.lyx,
	  doc/manual/graphics/citcoms_cover-layers.pdf,
	  doc/manual/graphics/citcoms_cover.pdf: added authors to cover

2006-11-06 18:33  sue

	* doc/manual/citcoms.lyx, doc/manual/graphics/proc_mesh.eps: added
	  new section 1.7 per gurnis and supporting graphic

2006-11-01 20:47  luis

	* doc/manual/citcoms.lyx: Re-typed most of the changes from my copy
	  of the citcoms.lyx file

2006-10-27 21:26  tan2

	* tests/.cvsignore: Removed legacy file .cvsignore

2006-10-27 21:25  tan2

	* doc/.cvsignore: Removed legary file .cvsignore

2006-10-20 19:36  tan2

	* examples/.reset-temporary: This file (examples/.reset-temporary)
	  was checked into svn at the initial import by me. I don't
	  remember what this file was used for.

2006-10-20 19:00  tan2

	* CitcomS/Solver/Solver.py: * Removed extra output_time(), which
	  was used for profiling * Converted tab to 4 spaces

2006-10-20 08:19  leif

	* configure.ac: Fail if MPI lib/header is not found.

2006-10-17 11:00  leif

	* CitcomS/Makefile.am, Makefile.am, bin/Makefile.am,
	  etc/Makefile.am, lib/Makefile.am, module/Makefile.am: Fixed
	  legacy build.

2006-10-17 09:18  leif

	* ., Citcom.c, CitcomSFull.c, CitcomSRegional.c, Makefile.am,
	  bin/Citcom.c, configure.ac, doc/CitComS.doxyconf,
	  lib/Pan_problem_misc_functions.c, lib/Tracer_advection.c,
	  module/CitcomSmodule.c, module/Makefile.am,
	  module/Regionalmodule.c, module/advdiffu.c, module/bindings.c,
	  module/exceptions.c, module/initial_conditions.c,
	  module/mesher.c, module/misc.c, module/outputs.c,
	  module/setProperties.c, module/stokes_solver.c, project.cfg,
	  setup.py, tests/Makefile.am, visual/Makefile.am: Transitioning to
	  Merlin. (Warning: still under construction.)

2006-10-14 00:29  tan2

	* CitcomS/Solver/CoupledSolver.py: Undid the accidental checkin at
	  r4998

2006-10-14 00:27  tan2

	* CitcomS/Solver/Solver.py, doc/manual/citcoms.lyx,
	  lib/Instructions.c, lib/Output.c, lib/Output_h5.c,
	  lib/global_defs.h, visual/estimate.py: Renamed reference of
	  "average" to "horiz_avg"

2006-10-14 00:06  tan2

	* NEWS: Added description on new features and bug fixes for v2.1.0

2006-10-13 23:59  luis

	* lib/Output_h5.c: Settled on /horiz_avg/ instead of /have/

2006-10-13 23:46  sue

	* doc/manual/citcoms.lyx: updated url handling

2006-10-13 23:18  tan2

	* visual/h5tocap.c: * Updated for the new layout of HDF5 group *
	  Changed the order of nodes, so that the output is the same as the
	  cap file from autocombine.py

2006-10-13 07:39  tan2

	* doc/manual/citcoms.lyx: * Fixed a typo "PHDF HOME" -> "PHDF_HOME"
	  * Added a section on using none-pyre version * Undid a xref in
	  section 3.1, which should link to (not-checked-in-yet) "Working
	  with HDF5" chapter * Updated Appendix A and changed the title *
	  Added description on new output files (stress, pressure, average)

2006-10-13 06:43  tan2

	* lib/Full_geometry_cartesian.c, lib/Regional_geometry_cartesian.c,
	  lib/Viscosity_structures.c: Gave default values to several
	  parameters

2006-10-13 04:15  tan2

	* examples/Full/input.sample, examples/Regional/input.sample:
	  Removed obsolete input parameter "maxadvtime" from the input
	  samples

2006-10-13 04:10  tan2

	* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
	  CitcomS/Components/Stokes_solver/Incompressible.py,
	  lib/Output_h5.c, module/setProperties.c: Moved input parameters
	  "aug_lagr" and "aug_number" from tsolver to vsolver, where they
	  really should belong to. These parameters are for augmented
	  lagragian stiffness matrix (I have no idea on what it is...), as
	  indicated in Element_calculations.c.

2006-10-12 21:43  tan2

	* CitcomS/Components/IC.py, module/setProperties.c:
	  'half_space_age' was not used when 'tic_method'=1. So, fixed the
	  comment and removed the conditional input

2006-10-12 14:48  leif

	* CitcomS/BaseApplication.py,
	  CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
	  CitcomS/Components/BC.py, CitcomS/Components/CitcomComponent.py,
	  CitcomS/Components/CodecConfig.py, CitcomS/Components/Const.py,
	  CitcomS/Components/HackedConfigParser.py,
	  CitcomS/Components/IC.py, CitcomS/Components/Launchers.py,
	  CitcomS/Components/Output.py, CitcomS/Components/Param.py,
	  CitcomS/Components/Phase.py, CitcomS/Components/Sphere/Sphere.py,
	  CitcomS/Components/Stokes_solver/Incompressible.py,
	  CitcomS/Components/Tracer.py, CitcomS/Components/Visc.py,
	  CitcomS/CoupledApp.py, CitcomS/SimpleApp.py,
	  CitcomS/Solver/Solver.py, bin/Citcom.c, bin/Makefile.am,
	  bin/citcoms.in, bin/coupledcitcoms.in, bin/pycitcoms.c,
	  bin/pycitcoms.cc, bin/pycppcitcoms.cc, configure.ac,
	  doc/manual/citcoms.lyx, etc/CitcomS.pml.in, etc/Makefile.am,
	  etc/globus.odb, etc/lam-mpi.odb, etc/lsf.odb, etc/mpich.odb,
	  etc/pbs.odb, lib/Advection_diffusion.c, lib/Citcom_init.c,
	  lib/Drive_solvers.c, lib/Full_parallel_related.c,
	  lib/Full_version_dependent.c, lib/Global_operations.c,
	  lib/Instructions.c, lib/Lith_age.c, lib/Output.c,
	  lib/Output_h5.c, lib/Parsing.c, lib/Process_buoyancy.c,
	  lib/Regional_parallel_related.c,
	  lib/Regional_version_dependent.c, lib/Topo_gravity.c,
	  lib/Tracer_advection.c, lib/global_defs.h,
	  lib/sphere_communication.h, module/CitcomSmodule.c,
	  module/CitcomSmodule.cc, module/CitcomSmodule.h,
	  module/Makefile.am, module/PyxMPI, module/Regionalmodule.c,
	  module/Regionalmodule.cc, module/advdiffu.c, module/advdiffu.cc,
	  module/advdiffu.h, module/bindings.c, module/bindings.cc,
	  module/bindings.h, module/exceptions.c, module/exceptions.cc,
	  module/exceptions.h, module/getProperty.h,
	  module/initial_conditions.c, module/initial_conditions.cc,
	  module/initial_conditions.h, module/mesher.c, module/mesher.cc,
	  module/mesher.h, module/misc.c, module/misc.cc, module/misc.h,
	  module/outputs.c, module/outputs.cc, module/outputs.h,
	  module/setProperties.c, module/setProperties.cc,
	  module/setProperties.h, module/stokes_solver.c,
	  module/stokes_solver.cc, module/stokes_solver.h, setup.py: Moved
	  'launcher' and '.cfg' support out of CitcomS and into the
	  framework.
	  
	  As I was revising the "Installation" chapter of the manual (still
	  in progress), I got frustrated with how complicated everything
	  was -- and how difficult it was to document that complexity -- so
	  I did something slightly violent:
	  
	  Converted the CitcomS extension module, 'CitcomSLib', from C++ to
	  C. This is made possible by Pythia 0.8.1.0b2, which replaces
	  _mpimodule with _mpi.pyx, which has a C interface.
	  
	  It is now possible to build CitcomS -- and all its prerequisites
	  (e.g. Python) -- entirely from source, starting with nothing but
	  a C compiler. Exchanger still requires C++, of course. I have yet
	  to test these changes with Exchanger enabled, but I don't
	  anticipate any serious problems.
	  
	  This may have been overkill, but I also cleaned the source of
	  C++-style comments (even though most modern C compilers probably
	  accept them... it became standard in C99 or something).
	  
	  I'll bet you can install CitcomS with GCC 2.x now :-)

2006-10-11 20:01  sue

	* doc/manual/citcoms.lyx: took care of some todo items

2006-10-10 23:48  tan2

	* doc/manual/citcoms.lyx: * Added subsection on installing
	  OpenDXutils package * Aligned figures to the center * Changed the
	  layout of the Appendices

2006-10-10 20:37  sue

	* doc/manual/citcoms.lyx: added hdf5 install and addt tools
	  chapters

2006-10-10 18:42  luis

	* doc/manual/citcoms.lyx: Inserted a few TODO items

2006-10-10 13:00  luis

	* lib/Makefile.am, lib/Output_h5.c, lib/PyTables.c, lib/pytables.h:
	  1. Reorganized routines in a more logical order. 2. Consolidated
	  routines from PyTables.[ch] into Output_h5.c

2006-10-10 11:54  luis

	* lib/Instructions.c, lib/Output_h5.c, lib/output_h5.h: Renamed
	  local function to conform with h5 prefix.

2006-10-10 07:29  luis

	* lib/Output_h5.c, lib/PyTables.c, lib/pytables.h: 1. Added PID to
	  metadata to make it easier to identify the corresponding .cfg
	  file 2. Wrapped most calls to set_attribute() to avoid using
	  addresses as arguments 3. Added
	  set_attribute_{int,float,double}_vector() functions

2006-10-10 00:52  luis

	* lib/Output_h5.c: Forgot to delete reference to obsolete
	  data_group.

2006-10-10 00:52  tan2

	* doc/manual/citcoms_cover-layers.pdf,
	  doc/manual/citcoms_cover.pdf: Set MIME type to pdf

2006-10-10 00:51  tan2

	* doc/manual/graphics/CitcomSImportHDF5.net.gif: Set MIME type to
	  image

2006-10-10 00:48  tan2

	* doc/manual/graphics/c_fig1.eps, doc/manual/graphics/c_fig10.eps,
	  doc/manual/graphics/c_fig2.eps, doc/manual/graphics/c_fig3.jpg,
	  doc/manual/graphics/c_fig4.eps, doc/manual/graphics/c_fig5.eps,
	  doc/manual/graphics/c_fig6.jpg, doc/manual/graphics/c_fig7.eps,
	  doc/manual/graphics/c_fig8.eps, doc/manual/graphics/c_fig9.eps,
	  doc/manual/graphics/cookbook1.2.jpg,
	  doc/manual/graphics/cookbook1.eps,
	  doc/manual/graphics/cookbook1.png,
	  doc/manual/graphics/cookbook2.2.eps,
	  doc/manual/graphics/cookbook2.2eps,
	  doc/manual/graphics/cookbook2.eps,
	  doc/manual/graphics/cookbook3.eps,
	  doc/manual/graphics/cookbook4.eps,
	  doc/manual/graphics/cookbook5.2.eps,
	  doc/manual/graphics/cookbook5.eps,
	  doc/manual/graphics/cookbook6.2.eps,
	  doc/manual/graphics/cookbook6.eps,
	  doc/manual/graphics/cookbook7.eps: Set MIME type to image

2006-10-10 00:45  luis

	* lib/Output_h5.c: Shortened /average/ group into /have/

2006-10-10 00:42  tan2

	* doc/manual/graphics/CitcomSImportHDF5.net.gif: Figure for HDF5
	  visualization

2006-10-10 00:41  tan2

	* doc/manual/citcoms.lyx: Added section on visualizing HDF5 output

2006-10-10 00:38  luis

	* lib/Output_h5.c: Fix mispelling in input parameters (allignment
	  options).

2006-10-09 23:25  tan2

	* doc/manual/citcoms.lyx: * Added documentaion of .pml file, which
	  comes from DANSE FAQ * Added section on visualization of full
	  version * Moved the discussion on .log and .time files from
	  Section 4.2 to Section 3.5.3 * Updated links to equations

2006-10-09 23:14  sue

	* doc/manual/citcoms.lyx: change equation numbering

2006-10-09 20:41  tan2

	* visual/OpenDXMacro/CitcomSImportHDF5.net.in: Changed the order of
	  input parameters

2006-10-09 19:58  tan2

	* visual/OpenDXMacro/CitcomSImportHDF5.net.in: Updated for the new
	  layout of hdf5 output

2006-10-09 00:14  gurnis

	* lib/Full_read_input_from_files.c, lib/Problem_related.c,
	  lib/Viscosity_structures.c: For Viscosity_structures.c, added a
	  new rheology, rheol=5, that is a variant of rheol=3. The
	  difference lay in the way that plate boundaries are weakened.
	  Must set mat_control=1 and enter materials into the VIP array.
	  Removed debug statements from Problem_related.c in preparation of
	  new release.

2006-10-08 12:04  leif

	* configure.ac, setup.py: Pointed CitcomS egg-downloading at the
	  new "Eggs" section on the web site, to insulate CitcomS from the
	  imminent chaos in pythia-dev.

2006-10-07 01:15  tan2

	* visual/h5tocap.py: Updated for the new layout in the h5 file

2006-10-07 00:01  luis

	* lib/Output_h5.c: Eliminated data group in HDF5 file. Main
	  datasets are now on the root-level.

2006-10-06 21:10  tan2

	* lib/Obsolete.c: The type of elt_g should be "higher_precision"
	  instead of "double".

2006-10-06 20:18  tan2

	* lib/Interuption.c: Changed the signature of the signal handler
	  from (void)(interuption(void)) to (void)(interuption(int)) to
	  conform with the C standard

2006-10-06 20:02  tan2

	* lib/element_definitions.h: Missing braces around initializers for
	  array structs node_point[] and offset[]

2006-10-06 17:17  tan2

	* doc/manual/citcoms.lyx: Some minor edits

2006-10-05 20:07  tan2

	* visual/combine.py: Using 2-digit number for the cap filename, eg.
	  prefix.cap00.step

2006-10-05 00:38  tan2

	* visual/visFull.cfg, visual/visFull.net.in,
	  visual/visRegional.cfg, visual/visRegional.net.in: Updated macros
	  to use new samples files and fixed a few stylus issues

2006-10-05 00:15  tan2

	* visual/Makefile.am: Rearranged file list

2006-10-05 00:15  tan2

	* visual/Makefile.am: Updated file list

2006-10-05 00:04  tan2

	* visual/samples/fulltest.cap0.0,
	  visual/samples/fulltest.cap0.0.general,
	  visual/samples/fulltest.cap00.100,
	  visual/samples/fulltest.cap00.100.general,
	  visual/samples/fulltest.cap01.100,
	  visual/samples/fulltest.cap01.100.general,
	  visual/samples/fulltest.cap02.100,
	  visual/samples/fulltest.cap02.100.general,
	  visual/samples/fulltest.cap03.100,
	  visual/samples/fulltest.cap03.100.general,
	  visual/samples/fulltest.cap04.100,
	  visual/samples/fulltest.cap04.100.general,
	  visual/samples/fulltest.cap05.100,
	  visual/samples/fulltest.cap05.100.general,
	  visual/samples/fulltest.cap06.100,
	  visual/samples/fulltest.cap06.100.general,
	  visual/samples/fulltest.cap07.100,
	  visual/samples/fulltest.cap07.100.general,
	  visual/samples/fulltest.cap08.100,
	  visual/samples/fulltest.cap08.100.general,
	  visual/samples/fulltest.cap09.100,
	  visual/samples/fulltest.cap09.100.general,
	  visual/samples/fulltest.cap1.0,
	  visual/samples/fulltest.cap1.0.general,
	  visual/samples/fulltest.cap10.0,
	  visual/samples/fulltest.cap10.0.general,
	  visual/samples/fulltest.cap10.100,
	  visual/samples/fulltest.cap10.100.general,
	  visual/samples/fulltest.cap11.0,
	  visual/samples/fulltest.cap11.0.general,
	  visual/samples/fulltest.cap11.100,
	  visual/samples/fulltest.cap11.100.general,
	  visual/samples/fulltest.cap2.0,
	  visual/samples/fulltest.cap2.0.general,
	  visual/samples/fulltest.cap3.0,
	  visual/samples/fulltest.cap3.0.general,
	  visual/samples/fulltest.cap4.0,
	  visual/samples/fulltest.cap4.0.general,
	  visual/samples/fulltest.cap5.0,
	  visual/samples/fulltest.cap5.0.general,
	  visual/samples/fulltest.cap6.0,
	  visual/samples/fulltest.cap6.0.general,
	  visual/samples/fulltest.cap7.0,
	  visual/samples/fulltest.cap7.0.general,
	  visual/samples/fulltest.cap8.0,
	  visual/samples/fulltest.cap8.0.general,
	  visual/samples/fulltest.cap9.0,
	  visual/samples/fulltest.cap9.0.general,
	  visual/samples/regtest.cap0.0,
	  visual/samples/regtest.cap0.0.general,
	  visual/samples/regtest.cap00.100,
	  visual/samples/regtest.cap00.100.general: Replaced sample files
	  at 0th time step with sample files at 100th time step, which have
	  more interesting features in the visualization,

2006-10-04 18:34  tan2

	* examples/Cookbook1/cookbook1.cfg,
	  examples/Cookbook2/cookbook2.cfg,
	  examples/Cookbook3/cookbook3.cfg,
	  examples/Cookbook4/cookbook4.cfg,
	  examples/Cookbook5/cookbook5.cfg,
	  examples/Cookbook6/cookbook6.cfg: * Removed some unnecessary
	  parameters * Changed the layout slightly * Updated the cookbook
	  scripts to be consistent with the manual

2006-10-04 18:32  tan2

	* doc/manual/citcoms.lyx: Updated the Cookbook chapter

2006-10-04 18:24  tan2

	* doc/manual/graphics/cookbook1.jpg, doc/manual/graphics/eq1.eps,
	  doc/manual/graphics/eq10.eps, doc/manual/graphics/eq11.eps,
	  doc/manual/graphics/eq12.eps, doc/manual/graphics/eq13.eps,
	  doc/manual/graphics/eq14.eps, doc/manual/graphics/eq15.eps,
	  doc/manual/graphics/eq16.eps, doc/manual/graphics/eq17.eps,
	  doc/manual/graphics/eq18.eps, doc/manual/graphics/eq19.eps,
	  doc/manual/graphics/eq2.eps, doc/manual/graphics/eq20.2.eps,
	  doc/manual/graphics/eq20.eps, doc/manual/graphics/eq21.eps,
	  doc/manual/graphics/eq3.eps, doc/manual/graphics/eq4.eps,
	  doc/manual/graphics/eq5.eps, doc/manual/graphics/eq6.eps,
	  doc/manual/graphics/eq7.eps, doc/manual/graphics/eq8.eps,
	  doc/manual/graphics/eq9.eps, doc/manual/graphics/exp1.eps,
	  doc/manual/graphics/exp10.eps, doc/manual/graphics/exp11.eps,
	  doc/manual/graphics/exp12.eps, doc/manual/graphics/exp2.eps,
	  doc/manual/graphics/exp3.eps, doc/manual/graphics/exp4.eps,
	  doc/manual/graphics/exp5.eps, doc/manual/graphics/exp6.eps,
	  doc/manual/graphics/exp7.eps, doc/manual/graphics/exp8.eps,
	  doc/manual/graphics/exp9.eps: Removed unused figures

2006-10-04 01:56  tan2

	* examples/Cookbook6/cookbook6.cfg,
	  examples/Cookbook6/cookbook7.cfg: Renamed file to be consistent
	  with the manual

2006-10-04 01:54  tan2

	* examples/Cookbook6, examples/Cookbook7: Renamed directory to be
	  consistent with the manual

2006-10-02 22:46  tan2

	* examples/Cookbook1/cookbook1.cfg: Using default Rayleigh number,
	  which is stated in the manual. Also updated the comment to be
	  consistent with the manual.

2006-10-02 22:43  tan2

	* doc/manual/citcoms.lyx: Slightly updated postprocessing chapter.
	  Revised Cookbook 1.

2006-09-30 00:56  tan2

	* doc/manual/citcoms.lyx: Updated Chapter 3 "Running CitComS.py"
	  for the .cfg input format, also explained how to launch a
	  parallel job. Some TODO items left.

2006-09-29 23:14  gurnis

	* lib/Full_read_input_from_files.c, lib/Problem_related.c,
	  lib/Regional_lith_age_read_files.c: Fixed age bug in Regional. In
	  Regional_lith_age_read_files.c, find_age_in_MY() was not being
	  converted to a float

2006-09-29 21:50  sue

	* doc/manual/citcoms_cover-layers.pdf,
	  doc/manual/citcoms_cover.pdf: updated version on pdf cover and
	  added pdf layered file

2006-09-28 14:56  luis

	* lib/Output_h5.c, lib/hdf5_related.h: 1. Added a cap dimension for
	  efficient parallel I/O 2. Bulk of data write operations now done
	  in collective mode. 4. Passing various parallel I/O tuning
	  parameters to HDF5 and MPI-IO. 5. Consolidated all data buffers
	  into one (only largest size allocated).

2006-09-28 14:30  luis

	* CitcomS/Components/Output.py, module/setProperties.cc: Fixed typo
	  in names

2006-09-27 23:33  tan2

	* CitcomS/Components/Output.py: * Removed debugging output * Added
	  svn:keywords and svn:mime-type attributes

2006-09-27 20:37  leif

	* setup.py: Relaxed setuptools version requirement to 0.6b1.

2006-09-27 00:24  tan2

	* CitcomS/Components/Output.py, CitcomS/Makefile.am,
	  CitcomS/Solver/Solver.py, lib/Instructions.c, lib/Output.c,
	  lib/Output_h5.c, lib/global_defs.h, lib/output.h,
	  lib/output_h5.h, module/bindings.cc, module/setProperties.cc,
	  module/setProperties.h: * Created new component 'Output.py' for
	  storing output-related properties * Added several input
	  parameters for HDF5 output performance tuning * Moved
	  'output_format' and 'output_optional' form Solver.py to Output.py

2006-09-26 12:20  luis

	* bin/Makefile.am, examples/Makefile.am, lib/Makefile.am,
	  module/Makefile.am, visual/OpenDXMacro/Makefile.am: Fixed broken
	  'make dist'

2006-09-26 01:09  leif

	* bin/Makefile.am, bin/pycitcoms.cc, configure.ac, ez_setup.py,
	  module/Exchanger/Makefile.am, module/Makefile.am, setup.py: Made
	  'Exchanger' optional. Give "--with-exchanger=[yes|no]" as an
	  argument to 'configure' to manually specify whether you want
	  Exchanger; the default is "auto", which means to use Exchanger if
	  it's installed (and on your PYTHONPATH).
	  
	  Egg-ified 'configure' checks for Python packages. This means that
	  CitcomS now requires the egg-ified CIG version of Pythia -- and
	  (optionally) the egg-ified Exchanger. Old Pythia/Exchanger
	  installations will not work, as they lack the egg-metadata
	  ('configure' will act as if they are not installed).
	  
	  Added 'setup.py', which will automatically download and install
	  the egg version of Pythia -- as well as the egg system itself
	  ('setuptools'). If you want Exchanger, you still must install it
	  manually (the way C++ is used prevents complete egg-ification of
	  Exchanger). Note that 'setup.py' actually checks-out the latest
	  Pythia from the SVN repository. The release version of CitcomS
	  will download a packaged Pythia from the website instead.

2006-09-25 19:13  tan2

	* lib/Output.c, lib/Output_h5.c: Disabled material output, since
	  material control is not working (yet)

2006-09-24 07:28  tan2

	* CitcomS/Solver/Solver.py, lib/Instructions.c, lib/Output_h5.c,
	  lib/global_defs.h, module/setProperties.cc: Added new input
	  parameter 'datadir_old' in CitcomS.solver. If output_format=ascii
	  and restart=1, the restart files will be read from
	  ${datadir_old}/${rank}/${datafile_old}.velo.${rank}.${step}. In
	  this case, 'datafile_old' cannot contain '/'. See issue56.

2006-09-22 23:26  tan2

	* CitcomS/Solver/Solver.py, lib/Instructions.c: Write surf and botm
	  output by default (but can be disabled by setting
	  output_optional=''), which is compatible with v2.0.x.

2006-09-22 22:58  tan2

	* lib/Instructions.c: Removed debugging output

2006-09-22 22:29  tan2

	* visual/batchsurf.py: * Fixed issue55 "surf files got deleted by
	  batchsurf.py" * Refactored the codes on machinefile -> nodelist

2006-09-22 22:14  tan2

	* visual/getcoord.sh, visual/getsurf.sh: These scripts accept
	  'localhost' as a valid machine name now

2006-09-22 22:01  luis

	* lib/Output_h5.c: Bug fix: maxdims[0] is set to H5S_UNLIMITED in
	  extendible datasets, so it should never be incremented.

2006-09-22 20:37  tan2

	* visual/autocombine.py, visual/estimate.py, visual/h5tocap.py,
	  visual/miff2avi, visual/miff2mpg, visual/parser.py,
	  visual/zslice.py: Added 'Id' keyword to the files

2006-09-22 19:19  tan2

	* visual/batchpaste.sh, visual/batchpaste2.sh: Fixed two bugs in
	  post-processing scripts

2006-09-21 23:03  tan2

	* visual/autocombine.py, visual/batchcombine.py,
	  visual/batchpaste.sh, visual/batchpaste2.sh: Updated
	  post-processing script for new output_format options. See
	  issue53.

2006-09-21 21:25  luis

	* lib/Output_h5.c: Allow for optional fields when extending
	  datasets.

2006-09-21 21:17  tan2

	* lib/Output.c, lib/Output_h5.c, lib/Process_buoyancy.c: Refactored
	  out the code computing horizontal average of temperature and rms
	  velocity into a function. This fixes the bug in issue46.

2006-09-21 20:08  tan2

	* lib/Instructions.c: Forgot to change the default value in C

2006-09-21 19:57  tan2

	* CitcomS/Solver/Solver.py, lib/Instructions.c, lib/Output.c,
	  lib/Output_h5.c, lib/global_defs.h: Added new option for
	  "output_format". The current behavior is: * If
	  output_format=="ascii-local" (the default), CitcomS will write
	  ascii files to the directory and prefix specified by "datafile",
	  ie., the same behavior as in v2.0 * If output_format=="ascii",
	  CitcomS will write ascii files to the directory specified by
	  "datadir" with the prefix specified by "datafile". In the case,
	  "datafile" cannot contains the '/' (path seperator) character. *
	  If output_format=="hdf5", CitcomS will write singe HDf5 file to
	  the directory and prefix specified by "datafile".

2006-09-21 17:51  tan2

	* visual/parser.py: Parser will skip lines starting with '[', so
	  that it can parse .cfg file correctly

2006-09-21 17:49  tan2

	* module/setProperties.cc: Removed quotes from output string

2006-09-21 00:18  tan2

	* CitcomS/CoupledApp.py, CitcomS/SimpleApp.py,
	  examples/Cookbook1/cookbook1.cfg,
	  examples/Cookbook2/cookbook2.cfg,
	  examples/Cookbook3/cookbook3.cfg,
	  examples/Cookbook4/cookbook4.cfg,
	  examples/Cookbook5/cookbook5.cfg,
	  examples/Cookbook7/cookbook7.cfg, examples/example0.cfg,
	  examples/example1.cfg: Calculate the needed # of cpu according to
	  mesher properties. There is no longer a need to set
	  launcher.nodes.

2006-09-20 22:51  tan2

	* CitcomS/BaseApplication.py, CitcomS/Solver/CoupledFullSolver.py,
	  CitcomS/Solver/CoupledRegionalSolver.py,
	  CitcomS/Solver/CoupledSolver.py: Added svn:keywprds = Id

2006-09-20 20:47  tan2

	* lib/Output_h5.c: Sync'd h5output_meta() with setProperties

2006-09-20 20:45  tan2

	* CitcomS/Components/IC.py: Fixed the comment

2006-09-20 20:34  tan2

	* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
	  lib/Advection_diffusion.c, lib/Output_h5.c,
	  module/setProperties.cc: Removed unused parameter 'maxadvtime'

2006-09-20 20:30  tan2

	* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
	  CitcomS/Components/Const.py, CitcomS/Components/IC.py,
	  CitcomS/Components/Visc.py, module/setProperties.cc: Print out
	  all pyre properties to the pid file

2006-09-20 19:54  tan2

	* lib/Citcom_init.c, lib/Instructions.c, module/mesher.cc,
	  module/setProperties.cc: Saving the input parameters to a unique
	  file 'pidXXXXX.cfg' for archives.

2006-09-19 19:50  luis

	* lib/Output_h5.c: Allocate tensor field buffer only when
	  necessary.

2006-09-19 18:44  tan2

	* citcoms_profile: Since the opendx scripts have the macro path
	  built in the file, there is no need to define $DXMACROS env. var.

2006-09-17 17:32  tan2

	* CitcomS/Solver/Solver.py, examples/Cookbook5/cookbook5.cfg,
	  examples/Full/input.sample, examples/Regional/input.sample,
	  lib/Instructions.c, lib/Output.c, lib/Output_h5.c,
	  lib/global_defs.h, module/setProperties.cc,
	  visual/autocombine.py, visual/batchcombine.py,
	  visual/batchpaste.sh, visual/combine.py,
	  visual/pasteCitcomData.sh: * Added new input parameter 'datadir'
	  in Solver * All outputs are done in 'datadir' directory *
	  Processors write its own ascii output in 'datadir/rank' directory
	  * Post-processing codes and cookbook examples were updated
	  accordingly

2006-09-14 18:14  maweier

	* visual/Mayavi2/Citcoms_Hdf2Vtk.c: added help on usage.

2006-09-13 19:04  maweier

	* visual/Mayavi2/plugins/filter/CitcomSreduce.py: Changed range
	  trait.

2006-09-12 20:50  tan2

	* lib/global_defs.h: Fixed the bug of negative CPU time, which is
	  caused by storing the walltime in insufficient precision

2006-09-11 17:25  maweier

	* visual/Mayavi2/Citcoms_Hdf2Vtk.c: added latest version of file
	  converter in c.

2006-09-11 17:24  maweier

	* visual/Mayavi2/Citcoms_HdfDisplay.py,
	  visual/Mayavi2/Citcoms_VtkDisplay.py,
	  visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
	  visual/Mayavi2/plugins/filter/CitcomSFilterActions.py,
	  visual/Mayavi2/plugins/filter/CitcomSSphere.py,
	  visual/Mayavi2/plugins/filter/CitcomSreduce.py,
	  visual/Mayavi2/plugins/filter/CitcomSshowCaps.py,
	  visual/Mayavi2/plugins/filter/CitcomSshowSurface.py,
	  visual/Mayavi2/plugins/plugin_defs/mayavi_ui_plugin_definition.py:
	  Updated licenses.

2006-09-11 17:23  maweier

	* visual/Mayavi2/Citcoms_Hdf2Vtk.c: Update

2006-09-11 00:17  luis

	* visual/Makefile.am, visual/h5steps.c, visual/h5tocap.c: 1. Added
	  utility to extract steps from CitcomS HDF5 file. 2. Changed
	  h5tocombined.c to h5tocap.c in copyright header.

2006-09-11 00:09  luis

	* visual/h5tocap.c: When no frames are specified, print number of
	  available frames.

2006-09-10 09:50  luis

	* visual/Makefile.am, visual/h5tocap.c: 1. Added h5tocap to build
	  procedure 2. Changed h5tocap to read frames from command-line
	  (instead of steps)

2006-09-10 07:36  luis

	* lib/Output_h5.c, visual/estimate.py: Moved connectivity dataset
	  to root group.

2006-09-09 01:45  tan2

	* configure.ac: * set --with-hdf5=auto as default, which will try
	  to detect HDF5 library, if not found, HDF5 support will be
	  disabled * Reported summary at the end of configure

2006-09-09 00:24  tan2

	* configure.ac: Added $PHDF5_HOME env. variables for the home
	  directory of parallel HDF5 lib

2006-09-08 20:59  tan2

	* visual/Makefile.am: Forgot to rename file

2006-09-08 20:27  luis

	* visual/h5tocap.c, visual/h5tocombined.c: Changed name to
	  h5tocap.c

2006-09-08 19:20  tan2

	* visual/h5tocap.py: Added a comment

2006-09-08 19:18  tan2

	* visual/visRegional.cfg: Reverted the accidental check-in at r4498

2006-09-08 19:14  tan2

	* visual/h52combined.py, visual/h5tocap.py, visual/visRegional.cfg:
	  Renamed the conversion script

2006-09-08 19:14  tan2

	* visual/h52combined.py: * Using 'caps' attribute in the input
	  group * frame -> timestep conversion * Cleaned up the code

2006-09-08 15:53  luis

	* lib/Output_h5.c, lib/pytables.h: Removing unnecessary HDF5
	  attribute.

2006-09-08 15:46  luis

	* lib/Output_h5.c: Fix allocation of buffer for connectivity (done
	  per cap, not globally).

2006-09-07 21:07  maweier

	* visual/Mayavi2/Citcoms_Hdf2Vtk.py,
	  visual/Mayavi2/Citcoms_HdfDisplay.py,
	  visual/Mayavi2/plugins/CitcomSHDFUgrid.py: Fixed connectivity
	  issues. Fixed HdfDisplays wrong status output.

2006-09-06 22:33  maweier

	* visual/Mayavi2/Citcoms_Hdf2Vtk.py,
	  visual/Mayavi2/plugins/CitcomSHDFUgrid.py: Got rid of the
	  iterator to change the order.

2006-09-06 21:01  luis

	* visual/Mayavi2/Citcoms_Hdf2Vtk.c: Added function to retrieve
	  float attributes from HDF5 file.

2006-09-06 20:18  tan2

	* visual/OpenDXMacro/CitcomSImportHDF5.net.in,
	  visual/OpenDXMacro/Makefile.am: * Made CitcomSImportHDF5 accept
	  NULL (default) input for the caplist * Added CitcomSImportHDF5 to
	  the install list

2006-09-06 19:06  tan2

	* CitcomS/Makefile.am: Forgot backslash (line continuation) after
	  Solver/__init__.py. See issue48.

2006-09-06 18:39  tan2

	* visual/OpenDXMacro/CitcomSImportHDF5.net.in: Added an dx macro to
	  import HDF5 output, this module depends on the Cactus OpenDXutils
	  project (http://www.cactuscode.org/Visualization/openDX)

2006-09-06 16:41  maweier

	* visual/Mayavi2/Citcoms_Hdf2Vtk.c: New C version of the Hdf to Vtk
	  converter.

2006-09-05 22:41  maweier

	* visual/Mayavi2/Citcoms_Hdf2Vtk.py, visual/Mayavi2/README:
	  Bugfixes and a new README on how to use the code.

2006-09-05 21:10  maweier

	* visual/Mayavi2/Citcoms_Hdf2Vtk.py,
	  visual/Mayavi2/Citcoms_hdf2vtk.py: Consistency

2006-09-05 20:53  maweier

	* visual/Mayavi2/Citcoms_HdfDisplay.py,
	  visual/Mayavi2/Citcoms_hdf2vtk.py, visual/Mayavi2/__init__.py,
	  visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py,
	  visual/Mayavi2/plugins/filter/CitcomSFilterActions.py,
	  visual/Mayavi2/plugins/filter/CitcomSshowCaps.py,
	  visual/Mayavi2/plugins/filter/CitcomSshowSurface.py,
	  visual/Mayavi2/plugins/filter/__init__.py: Some minor bugfixes

2006-09-05 20:49  maweier

	* visual/Mayavi2/Citcoms_hdf2vtk.py,
	  visual/Mayavi2/citcoms_hdf2vtk.py: Rename for consistence.

2006-09-02 10:11  luis

	* lib/Instructions.c, lib/Output_h5.c, lib/global_defs.h,
	  visual/estimate.py: Added connectivity datasets (per cap) to HDF5
	  optional output.

2006-09-02 09:31  luis

	* visual/h5tocombined.c: Opened all available cap groups outside
	  the main loop.

2006-08-31 23:06  maweier

	* visual/Mayavi2, visual/Mayavi2/Citcoms_HdfDisplay.py,
	  visual/Mayavi2/Citcoms_VtkDisplay.py, visual/Mayavi2/__init__.py,
	  visual/Mayavi2/citcoms_hdf2vtk.py, visual/Mayavi2/plugins,
	  visual/Mayavi2/plugins/CitcomHDFThread.py,
	  visual/Mayavi2/plugins/CitcomSHDFUgrid.py,
	  visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
	  visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py,
	  visual/Mayavi2/plugins/OpenCitcomSFILES.py,
	  visual/Mayavi2/plugins/__init__.py,
	  visual/Mayavi2/plugins/filter,
	  visual/Mayavi2/plugins/filter/CitcomSFilterActions.py,
	  visual/Mayavi2/plugins/filter/CitcomSSphere.py,
	  visual/Mayavi2/plugins/filter/CitcomSreduce.py,
	  visual/Mayavi2/plugins/filter/CitcomSshowCaps.py,
	  visual/Mayavi2/plugins/filter/CitcomSshowSurface.py,
	  visual/Mayavi2/plugins/filter/__init__.py,
	  visual/Mayavi2/plugins/plugin_defs,
	  visual/Mayavi2/plugins/plugin_defs/mayavi_ui_plugin_definition.py:
	  New folder structure.

2006-08-31 23:05  maweier

	* visual/Mayavi2: Complete update to new Folder structure.

2006-08-31 14:56  luis

	* visual/h5tocombined.c: Added ability to output multiple timesteps
	  (specified on command-line).

2006-08-31 13:28  luis

	* visual/h5tocombined.c: 1. Cleaned up code in general. 2. Fixed
	  bug in reading coord dataset (need to do it for each cap!).

2006-08-29 23:44  maweier

	* visual/Mayavi2/citcoms_hdf2vtk.py,
	  visual/Mayavi2/plugins/CitcomSHDFUgrid.py,
	  visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
	  visual/Mayavi2/plugins/filter/CitcomSshowCaps.py: More stable
	  versions. Some performance enhancements.

2006-08-28 23:19  maweier

	* visual/Mayavi2/core/CitcomSHDFUgrid.pyc,
	  visual/Mayavi2/core/__init__.pyc,
	  visual/Mayavi2/filter/CitcomSFilterActions.pyc,
	  visual/Mayavi2/filter/CitcomSSphere.pyc,
	  visual/Mayavi2/filter/CitcomSreduce.pyc,
	  visual/Mayavi2/filter/CitcomSshowCaps.pyc,
	  visual/Mayavi2/filter/__init__.pyc,
	  visual/Mayavi2/plugins/CitcomSHDFUgrid.pyc,
	  visual/Mayavi2/plugins/CitcomS_hdf_file_reader.pyc,
	  visual/Mayavi2/plugins/CitcomS_vtk_file_reader.pyc,
	  visual/Mayavi2/plugins/OpenCitcomSFILES.pyc,
	  visual/Mayavi2/plugins/__init__.pyc,
	  visual/Mayavi2/plugins/filter/CitcomSFilterActions.pyc,
	  visual/Mayavi2/plugins/filter/CitcomSSphere.pyc,
	  visual/Mayavi2/plugins/filter/CitcomSreduce.pyc,
	  visual/Mayavi2/plugins/filter/CitcomSshowCaps.pyc,
	  visual/Mayavi2/plugins/filter/__init__.pyc,
	  visual/Mayavi2/plugins/filter/showcaps.pyc: Deleting Bytecode
	  Files

2006-08-28 23:17  maweier

	* visual/Mayavi2, visual/Mayavi2/HdfDisplay.py,
	  visual/Mayavi2/VtkDisplay.py, visual/Mayavi2/__init__.py,
	  visual/Mayavi2/citcoms_hdf2vtk.py, visual/Mayavi2/core,
	  visual/Mayavi2/core/CitcomSHDFUgrid.py,
	  visual/Mayavi2/core/CitcomSHDFUgrid.pyc,
	  visual/Mayavi2/core/__init__.py,
	  visual/Mayavi2/core/__init__.pyc, visual/Mayavi2/filter,
	  visual/Mayavi2/filter/CitcomSFilterActions.py,
	  visual/Mayavi2/filter/CitcomSFilterActions.pyc,
	  visual/Mayavi2/filter/CitcomSSphere.py,
	  visual/Mayavi2/filter/CitcomSSphere.pyc,
	  visual/Mayavi2/filter/CitcomSreduce.py,
	  visual/Mayavi2/filter/CitcomSreduce.pyc,
	  visual/Mayavi2/filter/CitcomSshowCaps.py,
	  visual/Mayavi2/filter/CitcomSshowCaps.pyc,
	  visual/Mayavi2/filter/CitcomSshowSurface.py,
	  visual/Mayavi2/filter/__init__.py,
	  visual/Mayavi2/filter/__init__.pyc, visual/Mayavi2/plugins,
	  visual/Mayavi2/plugins/CitcomSHDFUgrid.py,
	  visual/Mayavi2/plugins/CitcomSHDFUgrid.pyc,
	  visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
	  visual/Mayavi2/plugins/CitcomS_hdf_file_reader.pyc,
	  visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py,
	  visual/Mayavi2/plugins/CitcomS_vtk_file_reader.pyc,
	  visual/Mayavi2/plugins/OpenCitcomSFILES.py,
	  visual/Mayavi2/plugins/OpenCitcomSFILES.pyc,
	  visual/Mayavi2/plugins/__init__.py,
	  visual/Mayavi2/plugins/__init__.pyc,
	  visual/Mayavi2/plugins/filter,
	  visual/Mayavi2/plugins/filter/CitcomSFilterActions.py,
	  visual/Mayavi2/plugins/filter/CitcomSFilterActions.pyc,
	  visual/Mayavi2/plugins/filter/CitcomSSphere.py,
	  visual/Mayavi2/plugins/filter/CitcomSSphere.pyc,
	  visual/Mayavi2/plugins/filter/CitcomSreduce.py,
	  visual/Mayavi2/plugins/filter/CitcomSreduce.pyc,
	  visual/Mayavi2/plugins/filter/CitcomSshowCaps.py,
	  visual/Mayavi2/plugins/filter/CitcomSshowCaps.pyc,
	  visual/Mayavi2/plugins/filter/CitcomSshowSurface.py,
	  visual/Mayavi2/plugins/filter/__init__.py,
	  visual/Mayavi2/plugins/filter/__init__.pyc,
	  visual/Mayavi2/plugins/filter/showcaps.pyc,
	  visual/Mayavi2/plugins/plugin_defs,
	  visual/Mayavi2/plugins/plugin_defs/mayavi_ui_plugin_definition.py:
	  Files for Mayavi2 plugins

2006-08-28 21:20  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms_cover.pdf: fixed man
	  cover, removed pg no., fixed date, added table of figures,
	  enabled URL hotlinks

2006-08-26 00:49  tan2

	* lib/Full_boundary_conditions.c, lib/Full_parallel_related.c,
	  lib/Full_version_dependent.c, lib/Phase_change.c,
	  lib/Process_buoyancy.c, lib/Regional_boundary_conditions.c,
	  lib/Regional_parallel_related.c,
	  lib/Regional_version_dependent.c, lib/Size_does_matter.c,
	  lib/Viscosity_structures.c: Flushed debugging output

2006-08-25 23:15  tan2

	* doc/manual/citcoms.lyx: Improved the section of full CitcomS
	  visualization. Fixed issue44

2006-08-24 23:46  luis

	* visual/estimate.py: Added script to estimate the size of the
	  output from CitcomS.

2006-08-24 20:08  tan2

	* CitcomS/CoupledApp.py, CitcomS/Layout.py: Renamed some attributes

2006-08-24 20:08  tan2

	* CitcomS/Makefile.am: Updated file list

2006-08-24 19:40  tan2

	* CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py,
	  CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/Coupler/__init__.py:
	  Changed the class names

2006-08-24 19:34  tan2

	* CitcomS/Coupler/CoarseGridExchanger.py,
	  CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py,
	  CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/Coupler/Exchanger.py,
	  CitcomS/Coupler/FineGridExchanger.py: Renamed *Exchanger.py to
	  *Coupler.py

2006-08-24 19:31  tan2

	* CitcomS/Components/Exchanger, CitcomS/Coupler,
	  CitcomS/Coupler.py: Started refactoring Coupler and Exchanger ...

2006-08-24 19:27  tan2

	* CitcomS/BaseApplication.py, CitcomS/CoupledApp.py,
	  CitcomS/SimpleApp.py, CitcomS/Solver/CoupledFullSolver.py,
	  CitcomS/Solver/CoupledRegionalSolver.py,
	  CitcomS/Solver/CoupledSolver.py, CitcomS/Solver/Solver.py,
	  CitcomS/Solver/__init__.py, bin/Makefile.am, bin/citcoms.in,
	  bin/coupledcitcoms.in: * Refactored coupler-related codes from
	  Solver.py to CoupledSolver.py * Created CoupledFullSolver.py and
	  CoupledRegionalSolver.py * Refactored common codes between
	  CoupledApp.py and SimpleApp.py to BaseApplication.py * Changed
	  the facility names in CoupledApp.py * Created a coupledcitcoms
	  script

2006-08-24 02:47  luis

	* lib/Output_h5.c, lib/hdf5_related.h: Added /cap/average/coord
	  dataset

2006-08-23 23:24  luis

	* lib/Output_h5.c: Fixed silly typos.

2006-08-23 23:16  luis

	* lib/Output_h5.c, lib/hdf5_related.h: 1. Grouped horizontal
	  average data into its own HDF5 group. 2. All datasets are
	  referenced using relative paths (to its own cap group).

2006-08-22 18:24  luis

	* lib/Output_h5.c, lib/hdf5_related.h: Data buffer in field_t
	  struct should be a float.

2006-08-22 13:08  luis

	* lib/Output_h5.c: 1. Fixed PyTables attributes for time dataset
	  (bugfix) 2. Added surf and botm data (optional output) 3. Added
	  horizontal averages (optional output)

2006-08-21 22:42  tan2

	* lib/Output_h5.c: Added two attributes to /input group * 'scalev'
	  : velocity scale, in cm/yr * 'scalet' : time scale, in Myrs

2006-08-21 21:38  luis

	* visual/h5tocombined.c: Added program to convert the HDF5 output
	  file to the ASCII combined file, using the HDF5 C-API.

2006-08-18 18:43  tan2

	* bin/Citcom.c, lib/Output.c, lib/Output_h5.c, lib/output.h,
	  lib/output_h5.h, module/outputs.cc: Refactored and Merged
	  output_pseudo_surf with output

2006-08-18 04:59  tan2

	* CitcomS/Solver/Solver.py, bin/Citcom.c, lib/Instructions.c,
	  lib/Output.c, lib/Output_h5.c, lib/global_defs.h,
	  module/outputs.cc, module/setProperties.cc: * Closed E->fp_out
	  properly * Fixed a bug when output_format is illegal * Added new
	  input parameter "output_optional", which is a comma seperated
	  list of fields to output. Currently, supported outputs are
	  "pressure", "stress", "surf", "botm", and "average". * Changed
	  the format of stress output to be consistent with other output

2006-08-15 21:50  sue

	* doc/manual/citcoms2.0.2.lyx, doc/manual/citcoms2.0.2.pdf,
	  doc/manual/citcoms_cover2-0-2.pdf: deleted versioned files

2006-08-15 20:48  tan2

	* lib/Citcom_init.c, lib/Instructions.c: Added 'output_format'
	  input for stand-alone version

2006-08-15 20:46  tan2

	* lib/global_defs.h: Commented out an unused include file

2006-08-15 20:14  sue

	* doc/manual/citcoms.lyx: one more cross-reference fix

2006-08-15 19:46  sue

	* doc/manual/citcoms.lyx: fixed tan's requests and recoded tables
	  to use space better

2006-08-15 18:43  tan2

	* doc/manual/citcoms.lyx: Fixed various typos/inconsistency/errors
	  Added some comments (started with 'tan2:')

2006-08-15 14:02  luis

	* lib/Output_h5.c, lib/PyTables.c, lib/pytables.h: Fixed issues
	  with time dataset.

2006-08-15 12:09  luis

	* lib/Output_h5.c, lib/hdf5_related.h: 1. Introduced field_t
	  object, and updated the appropriate functions to use it. 2.
	  Changed to independent parallel I/O for dataset writes. 3. Using
	  collective calls to extend time-varying datasets (bugfix).

2006-08-15 06:26  tan2

	* doc/manual/citcoms.lyx: Updated the status of multi-grid solver

2006-08-14 22:24  sue

	* doc/manual/citcoms.lyx: restored 2-sided page setting

2006-08-14 19:52  sue

	* doc/manual/citcoms.lyx: got appendices into toc

2006-08-14 19:29  sue

	* doc/manual/citcoms.lyx: changed margins and doc settings as
	  requested

2006-08-14 11:52  luis

	* lib/Output_h5.c: 1. Switching default data transfer property to
	  use independent parallel I/O. 2. Time-varying fields are now
	  created without an extent along time-dimension. 3. Consolidated
	  some debug statements into a single printf.

2006-08-14 11:22  luis

	* lib/Output_h5.c, lib/hdf5_related.h: Added step column to the
	  /time table dataset.

2006-08-14 11:01  luis

	* lib/Output_h5.c: Determine hyperslab block size based on mpi
	  process coordinates, not mpi process rank (bugfix).

2006-08-14 08:38  luis

	* lib/Output_h5.c, lib/PyTables.c, lib/pytables.h: Added some
	  useful set_attribute*() functions.

2006-08-12 22:47  gurnis

	* lib/Full_boundary_conditions.c, lib/Lith_age.c: Fix bug
	  associated with assimilating age grids in global models. Only
	  relevant change was made in the subroutine
	  full_temperature_boundary_condition() in which I now make a call
	  to lith_age_temperature_bound_adj() if lith_age_time is on.

2006-08-12 02:37  luis

	* visual/h52combined.py: Rearranged (i,j,k) indices for
	  consistency, i.e. to correspond to (x,y,z) coords instead of
	  (y,x,z). Also, moved constant format string outside of the loop
	  body.

2006-08-11 21:36  tan2

	* doc/manual/citcoms.lyx: Fixed the status of CitcomS.py on
	  TeraGrid

2006-08-11 20:28  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms_cover.pdf: added
	  leif's gnu build sys additions

2006-08-11 20:05  sue

	* doc/manual/citcoms.lyx: incorporated tan2 changes/comments

2006-08-11 06:11  leif

	* visual/Makefile.am: Whoops -- macro references from visual/*.net
	  must refer to subdirectory 'OpenDXMacro'.

2006-08-11 01:55  leif

	* bin/Makefile.am, bin/citcoms.in, configure.ac,
	  visual/Makefile.am, visual/OpenDXMacro,
	  visual/OpenDXMacro/Makefile.am: Build OpenDX macros in-place
	  during 'make'. Remove 'citcoms' script during 'uninstall'. Also,
	  partial fixes for MPICH2... one still needs to add
	  -DMPICH_SKIP_MPICXX to CPPFLAGS, however; see issue14.

2006-08-10 20:48  sue

	* doc/manual/citcoms2.0.2.lyx, doc/manual/citcoms2.0.2.pdf,
	  doc/manual/citcoms_cover2-0-2.pdf: added 2.0.2 manual draft and
	  cover

2006-08-08 21:24  tan2

	* lib/Output_h5.c, lib/PyTables.c: Made the code compile when
	  configured --with-hdf5=no

2006-08-08 20:47  luis

	* configure.ac: Fix checks for hdf5.h and for parallel HDF5. Should
	  now be performed only if --with-hdf5 is specified.

2006-08-08 04:55  ces74

	* examples/Cookbook7/cookbook7.cfg: * fixed a bug in the module
	  specification: - vsolver --> solver.vsolver - tsolver -->
	  solver.tsolver.

2006-08-07 21:24  luis

	* lib/Output_h5.c, lib/hdf5_related.h: Added time dataset

2006-08-07 06:47  luis

	* configure.ac: Added configure check for Parallel-HDF5

2006-08-07 06:38  luis

	* lib/Makefile.am: Removed reference to nonexistent directory

2006-08-07 06:10  luis

	* bin/Makefile.am, configure.ac, lib/Citcom_init.c,
	  lib/Makefile.am, lib/hdf5_related.h, module/Makefile.am: Changed
	  configure script to compile everything with -DUSE_HDF5 when HDF5
	  support is enabled (--with-hdf5)

2006-08-07 04:56  luis

	* lib/Makefile.am, lib/global_defs.h, lib/hdf5_info.h,
	  lib/hdf5_related.h: Need to maintain multiple structs in header
	  file, so renaming hdf5_info.h to hdf5_related.h

2006-08-07 00:46  luis

	* lib/Output_h5.c: Commented out debug statements

2006-08-05 12:48  luis

	* lib/Output_h5.c: Added h5output_meta(), and saved to the HDF5
	  input group the same input parameters that are used in
	  pyCitcom_*_set_properties().

2006-08-05 12:43  luis

	* lib/PyTables.c, lib/pytables.h: Added set_attribute_numerical*()
	  functions for creating numerical attributes (int, float, double,
	  ...) on a specified HDF5 object.

2006-08-05 00:26  tan2

	* visual/Makefile.am: Added h52combined.py to the install list

2006-08-05 00:14  tan2

	* visual/h52combined.py: Added a script to convert the HDF5 output
	  file to the ASCII combined file, using PyTables extension
	  package.

2006-08-04 23:37  tan2

	* lib/Advection_diffusion.c: Added some comments for filter()

2006-08-04 23:20  luis

	* lib/Output_h5.c: Output viscosity.

2006-08-04 23:13  luis

	* lib/Output_h5.c, lib/hdf5_info.h: Renamed E->hdf5.step to
	  something less confusing: E->hdf5.count

2006-08-04 21:46  tan2

	* CitcomS/Solver/Solver.py, bin/Citcom.c, lib/Output.c,
	  lib/output.h, module/bindings.cc, module/outputs.cc,
	  module/outputs.h: * Fixed skipped time output when
	  monitoringFrequency > 1, which was introduced in r4118 * Forgot
	  to change to the E->output function pointer in r4126

2006-08-03 14:14  luis

	* lib/Output_h5.c: Changed h5output() so that it prints an error if
	  the C macro USE_HDF5 is not defined (and similarly for
	  h5output_pseudo_surf())

2006-08-03 14:03  luis

	* lib/Output_h5.c, lib/hdf5_info.h: Fix bug in behavior for values
	  of monitoringFrequency > 1 by keeping an internal count of steps
	  (Python does not pass monitoringFrequency to C code).

2006-08-03 11:17  luis

	* module/PyxMPI/PyxMPI.c: Regenerated PyxMPI.c with Pyrex 0.9.4 to
	  fix GCC4 lvalue-casting error.

2006-08-03 11:14  luis

	* configure.ac: Fixed typo in configure.ac and added conditional
	  check for hdf5.h header.

2006-08-03 04:22  luis

	* lib/Output_h5.c: 1. Disabled creation of surf & botm (temporary)
	  2. Only outputs (per cap) are currently coord, velocity &
	  temperature fields 3. For clarity, added indentation to the
	  debugging output

2006-08-03 03:05  luis

	* lib/Output_h5.c: Rewrote h5write_field().

2006-08-03 02:31  luis

	* lib/Output_h5.c: Renamed h5write_array_hyperslab() to
	  h5write_dataset() and fixed the comment describing the usage of
	  h5create_field().

2006-08-03 02:15  luis

	* lib/Output_h5.c: Rewrote h5create_field() to use indices instead
	  of if-else branches when building the arguments (dims, maxdims,
	  chunkdims) for dataset creation.

2006-08-03 01:43  luis

	* lib/Output_h5.c: In h5create_dataset(), renamed local variable
	  filespace into dataspace.

2006-08-03 01:42  luis

	* lib/Output_h5.c: Renamed h5create_array() to h5create_dataset()
	  and made sure that the datasets created by that function are
	  compatibles with PyTables.

2006-08-03 01:30  luis

	* lib/Output_h5.c: Updated debug statements.

2006-08-03 01:05  luis

	* lib/Output_h5.c: Added h5create_file() and modified
	  h5create_group() so that the files and groups created with these
	  functions are compatible with PyTables.

2006-08-03 01:04  luis

	* lib/Makefile.am, lib/PyTables.c: Fixed typo in PyTables.c and
	  added it to the sources in Makefile.am

2006-08-02 23:38  sue

	* doc/manual/citcoms.lyx: added cover image

2006-08-02 19:42  sue

	* doc/manual/citcoms.lyx, doc/manual/citcoms_book.xml,
	  doc/manual/graphics.tar.gz: replace manual with lyx manual

2006-08-02 00:17  tan2

	* lib/Instructions.c, lib/Output_h5.c: Open and close HDF5 output
	  properly

2006-08-01 23:25  luis

	* lib/Output_h5.c: Added debug statements.

2006-08-01 23:17  luis

	* lib/pytables.h: Updated prototypes for the pytables-derived
	  functions.

2006-08-01 23:09  luis

	* lib/global_defs.h: Added flags to control which data
	  (viscosity,stress,pressure) gets written to output.

2006-08-01 22:50  luis

	* lib/hdf5_info.h: Consolidated buffers by size instead of by type.

2006-08-01 22:47  luis

	* lib/PyTables.c: Use strings as default HDF5 attribute type.

2006-08-01 19:21  tan2

	* CitcomS/Solver/Solver.py, module/bindings.cc, module/outputs.cc,
	  module/outputs.h: Closing output files in Solver.py

2006-08-01 19:06  tan2

	* CitcomS/Components/Param.py, CitcomS/Solver/Solver.py,
	  module/setProperties.cc: Moved the 'output_format' property from
	  Param.py to Solver.py

2006-08-01 05:57  tan2

	* CitcomS/Components/Param.py, module/outputs.cc,
	  module/setProperties.cc: * Created pyre property for
	  'output_format' * Changed the output function pointer in the
	  python binding

2006-08-01 00:54  luis

	* bin/Makefile.am, configure.ac, lib/Makefile.am: Added --with-hdf5
	  options to configure.ac. Also, modified Makefile.am so that
	  Output_h5.o is compiled.

2006-08-01 00:23  tan2

	* CitcomS/Controller.py, CitcomS/Solver/Solver.py,
	  module/bindings.cc, module/misc.cc, module/misc.h: Completely
	  fixed issue35 (inconsistent times) and related problems * t, dt,
	  step are modified only in the C code. Their python counterparts
	  are read-only * Changed the ancestor of the Controller from
	  Pyre's SimulationController to Pyre's Component, as the
	  SimulationController hinders the use of read-only properties *
	  Changed the ancestor of the Solver from Pyre's Solver to Pyre's
	  Component, as Pyre's Solver hinders the use of read-only
	  properties

2006-07-31 23:07  tan2

	* lib/Instructions.c: Changed the default value of 'layerd' from
	  2800 km (the depth of the mantle) to 6371 km (the radius of the
	  Earth), which is necessary to dimensionalize the time

2006-07-31 23:04  tan2

	* bin/Citcom.c, lib/Instructions.c, lib/global_defs.h,
	  module/mesher.cc: Added logic to switch the E->output function
	  pointer

2006-07-29 00:08  luis

	* lib/Output_h5.c: Added two methods for writing to HDF5 arrays
	  (refactored from CitcomCU).

2006-07-28 22:12  luis

	* lib/Output_h5.c: Fixed typos in h5output_coord()

2006-07-28 22:06  tan2

	* CitcomS/Solver/Solver.py: Removed unused variables due to
	  refactoring of time output

2006-07-28 18:37  tan2

	* lib/Output.c: Flushed the E->fptime stream after each output

2006-07-28 18:36  tan2

	* lib/Instructions.c: Added missing function declaration

2006-07-27 22:02  tan2

	* CitcomS/Controller.py, CitcomS/Solver/Solver.py, bin/Citcom.c,
	  lib/Instructions.c, lib/Output.c, lib/global_defs.h,
	  module/mesher.cc: Moved the responsibility of time output from
	  Citcom.c and Solver.py to Output.c, which includes the following
	  changes * open .time file at either mesher.cc (for pyre run) or
	  Instructions.c (for C run) * .time file is opened and closed only
	  by the rank-0 processor. This will avoid multiple processors
	  opening/writing/closing on the same file. Similar modification is
	  necessary for the .log file. * created two variables
	  E->monitor.cpu_time_at_start and
	  E->monitor.cpu_time_at_last_cycles for storing the wall clock
	  time at startup and last timestep, respectively * output .time
	  file in output_time() in Output.c

2006-07-27 21:06  luis

	* lib/Output_h5.c: Refactored code for array creation.

2006-07-27 21:04  luis

	* lib/hdf5_info.h: Eliminated unecessary buffer arrays.

2006-07-27 19:57  tan2

	* examples/example0.cfg: forgot to change the 'datafile' parameter

2006-07-24 11:22  luis

	* lib/Output_h5.c: Prepare output functions for optional HDF5
	  configuration with autoconf.

2006-07-24 11:18  luis

	* lib/global_defs.h: Added output function pointer to All_variables
	  struct.

2006-07-19 20:19  tan2

	* examples/example0.cfg: example script of single-processor run

2006-07-19 18:42  luis

	* lib/global_defs.h, lib/hdf5_info.h: Created new hdf5 struct
	  member within the All_variables struct.

2006-07-18 23:42  sue

	* doc/manual/graphics, doc/manual/graphics/c_fig1.eps,
	  doc/manual/graphics/c_fig10.eps, doc/manual/graphics/c_fig2.eps,
	  doc/manual/graphics/c_fig3.jpg, doc/manual/graphics/c_fig4.eps,
	  doc/manual/graphics/c_fig5.eps, doc/manual/graphics/c_fig6.jpg,
	  doc/manual/graphics/c_fig7.eps, doc/manual/graphics/c_fig8.eps,
	  doc/manual/graphics/c_fig9.eps,
	  doc/manual/graphics/cookbook1.2.jpg,
	  doc/manual/graphics/cookbook1.eps,
	  doc/manual/graphics/cookbook1.jpg,
	  doc/manual/graphics/cookbook1.png,
	  doc/manual/graphics/cookbook2.2.eps,
	  doc/manual/graphics/cookbook2.2eps,
	  doc/manual/graphics/cookbook2.eps,
	  doc/manual/graphics/cookbook3.eps,
	  doc/manual/graphics/cookbook4.eps,
	  doc/manual/graphics/cookbook5.2.eps,
	  doc/manual/graphics/cookbook5.eps,
	  doc/manual/graphics/cookbook6.2.eps,
	  doc/manual/graphics/cookbook6.eps,
	  doc/manual/graphics/cookbook7.eps, doc/manual/graphics/eq1.eps,
	  doc/manual/graphics/eq10.eps, doc/manual/graphics/eq11.eps,
	  doc/manual/graphics/eq12.eps, doc/manual/graphics/eq13.eps,
	  doc/manual/graphics/eq14.eps, doc/manual/graphics/eq15.eps,
	  doc/manual/graphics/eq16.eps, doc/manual/graphics/eq17.eps,
	  doc/manual/graphics/eq18.eps, doc/manual/graphics/eq19.eps,
	  doc/manual/graphics/eq2.eps, doc/manual/graphics/eq20.2.eps,
	  doc/manual/graphics/eq20.eps, doc/manual/graphics/eq21.eps,
	  doc/manual/graphics/eq3.eps, doc/manual/graphics/eq4.eps,
	  doc/manual/graphics/eq5.eps, doc/manual/graphics/eq6.eps,
	  doc/manual/graphics/eq7.eps, doc/manual/graphics/eq8.eps,
	  doc/manual/graphics/eq9.eps, doc/manual/graphics/exp1.eps,
	  doc/manual/graphics/exp10.eps, doc/manual/graphics/exp11.eps,
	  doc/manual/graphics/exp12.eps, doc/manual/graphics/exp2.eps,
	  doc/manual/graphics/exp3.eps, doc/manual/graphics/exp4.eps,
	  doc/manual/graphics/exp5.eps, doc/manual/graphics/exp6.eps,
	  doc/manual/graphics/exp7.eps, doc/manual/graphics/exp8.eps,
	  doc/manual/graphics/exp9.eps: adding graphics directory

2006-07-18 23:05  sue

	* doc/manual/citcoms_book.xml: updated dtd address

2006-07-18 01:00  luis

	* lib/PyTables.c, lib/pytables.h: Provide an API for creating
	  PyTables-compatible HDF5 files.

2006-07-17 23:31  luis

	* lib/Output_h5.c, lib/output_h5.h: For the new HDF5 output format,
	  use a similar API as in Output.c Copying the bodies from the old
	  functions for now, but prefixing the function name with 'h5'.

2006-07-15 02:14  leif

	* CitcomS/SimpleApp.py: Bug fix in
	  _getPrivateDepositoryLocations(); updated usage().

2006-07-13 23:41  leif

	* examples/Cookbook1/cookbook1.cfg,
	  examples/Cookbook1/cookbook1.sh,
	  examples/Cookbook2/cookbook2.cfg,
	  examples/Cookbook2/cookbook2.sh,
	  examples/Cookbook3/cookbook3.cfg,
	  examples/Cookbook3/cookbook3.sh,
	  examples/Cookbook4/cookbook4.cfg,
	  examples/Cookbook4/cookbook4.sh,
	  examples/Cookbook5/cookbook5.cfg,
	  examples/Cookbook5/cookbook5.sh,
	  examples/Cookbook7/cookbook7.cfg,
	  examples/Cookbook7/cookbook7.sh, examples/example1.sh,
	  tests/Makefile.am, tests/citcomsfull.sh.in,
	  tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Nuked
	  citcoms{full,regional}.sh, coupledcitcoms.sh. Converted cookbook
	  *.sh files to *.cfg files, and sprinkled-in some comments derived
	  from the manual.

2006-07-13 20:06  leif

	* configure.ac: Fix for broken "make install" on Pangu (discovered
	  by Lydia): add both 'pythondir' and 'pyexecdir' to
	  PYTHONPATH/sys.path.

2006-07-07 23:54  leif

	* bin/pycitcoms.cc: Temporary work-around for broken _mpimodule on
	  Pangu.

2006-07-07 23:07  tan2

	* CitcomS/Controller.py: Renamed extension module (see r3983)

2006-07-07 22:35  leif

	* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
	  CitcomS/Components/BC.py, CitcomS/Components/Const.py,
	  CitcomS/Components/Exchanger/Exchanger.py,
	  CitcomS/Components/Exchanger/Inlet.py,
	  CitcomS/Components/Exchanger/Outlet.py, CitcomS/Components/IC.py,
	  CitcomS/Components/Param.py, CitcomS/Components/Phase.py,
	  CitcomS/Components/Sphere/FullSphere.py,
	  CitcomS/Components/Sphere/RegionalSphere.py,
	  CitcomS/Components/Sphere/Sphere.py,
	  CitcomS/Components/Stokes_solver/Incompressible.py,
	  CitcomS/Components/Tracer.py, CitcomS/Components/Visc.py,
	  CitcomS/Makefile.am, CitcomS/SimpleApp.py,
	  CitcomS/Solver/FullSolver.py, CitcomS/Solver/RegionalSolver.py,
	  CitcomS/Solver/Solver.py, bin/Makefile.am, bin/citcoms.in,
	  bin/pycitcoms.cc, module/CitcomSmodule.cc,
	  module/CitcomSmodule.h, module/Exchanger/Exchangermodule.cc,
	  module/Exchanger/Exchangermodule.h, module/Exchanger/Makefile.am,
	  module/Full, module/Makefile.am, module/Regional,
	  module/Regionalmodule.cc, module/advdiffu.cc, module/advdiffu.h,
	  module/bindings.cc, module/bindings.h, module/exceptions.cc,
	  module/exceptions.h, module/initial_conditions.cc,
	  module/initial_conditions.h, module/mesher.cc, module/mesher.h,
	  module/misc.cc, module/misc.h, module/outputs.cc,
	  module/outputs.h, module/setProperties.cc,
	  module/setProperties.h, module/stokes_solver.cc,
	  module/stokes_solver.h, tests/exchange.py: Moved & renamed
	  extension modules:
	  
	  CitcomS.CitcomS -> CitcomsLib CitcomS.Exchanger -> ExchangerLib
	  
	  Top-level modules allow easy toggling between embedding &
	  extending without any special hacks in the embedding case. Also,
	  it allows the Python scripts to be installed under 'libdir'
	  instead of 'libexecdir', although this is a minor issue.
	  
	  Also: moved module/Regional/* source to module/* to really
	  complete the Full/Regional merge (there is only one CitcomS
	  extension module now). Plus, a bug fix in collectUserInput.

2006-07-07 21:36  tan2

	* CitcomS/Controller.py, CitcomS/Solver/Solver.py,
	  module/Regional/bindings.cc, module/Regional/misc.cc,
	  module/Regional/misc.h: A quick fix to issue35 "inconsistent
	  times in C and Pyre"

2006-07-07 00:54  leif

	* bin/Makefile.am, configure.ac, lib/Advection_diffusion.c,
	  lib/BC_util.c, lib/Citcom_init.c, lib/Common,
	  lib/Construct_arrays.c, lib/Convection.c, lib/Drive_solvers.c,
	  lib/Element_calculations.c, lib/Full,
	  lib/Full_boundary_conditions.c, lib/Full_geometry_cartesian.c,
	  lib/Full_lith_age_read_files.c, lib/Full_obsolete.c,
	  lib/Full_parallel_related.c, lib/Full_read_input_from_files.c,
	  lib/Full_solver.c, lib/Full_sphere_related.c,
	  lib/Full_version_dependent.c, lib/General_matrix_functions.c,
	  lib/Global_operations.c, lib/Initial_temperature.c,
	  lib/Instructions.c, lib/Interuption.c, lib/Lith_age.c,
	  lib/Makefile.am, lib/Nodal_mesh.c, lib/Obsolete.c, lib/Output.c,
	  lib/Pan_problem_misc_functions.c, lib/Parallel_util.c,
	  lib/Parsing.c, lib/Phase_change.c, lib/Problem_related.c,
	  lib/Process_buoyancy.c, lib/Regional,
	  lib/Regional_boundary_conditions.c,
	  lib/Regional_geometry_cartesian.c,
	  lib/Regional_lith_age_read_files.c, lib/Regional_obsolete.c,
	  lib/Regional_parallel_related.c,
	  lib/Regional_read_input_from_files.c, lib/Regional_solver.c,
	  lib/Regional_sphere_related.c, lib/Regional_version_dependent.c,
	  lib/Shape_functions.c, lib/Size_does_matter.c,
	  lib/Solver_conj_grad.c, lib/Solver_multigrid.c,
	  lib/Sphere_harmonics.c, lib/Sphere_util.c,
	  lib/Stokes_flow_Incomp.c, lib/Topo_gravity.c,
	  lib/Tracer_advection.c, lib/Viscosity_structures.c,
	  lib/advection.h, lib/advection_diffusion.h, lib/citcom_init.h,
	  lib/convection_variables.h, lib/drive_solvers.h,
	  lib/element_definitions.h, lib/global_defs.h,
	  lib/initial_temperature.h, lib/interuption.h, lib/lith_age.h,
	  lib/output.h, lib/parallel_related.h, lib/parsing.h,
	  lib/phase_change.h, lib/solver.h, lib/sphere_communication.h,
	  lib/temperature_descriptions.h, lib/tracer_defs.h,
	  lib/viscosity_descriptions.h, module/Exchanger/Makefile.am,
	  module/Makefile.am: Avoid shared libraries altogether when
	  embedding. Shared libs are very likely to fail with static
	  MPICH... this was confirmed when the link failed on Eh's iBook.
	  
	  Also completed the Full/Regional merge by flatting the directory
	  structure under 'lib'.

2006-07-06 23:20  leif

	* CitcomS, CitcomS/Components,
	  CitcomS/Components/Advection_diffusion,
	  CitcomS/Components/Exchanger, CitcomS/Components/Sphere,
	  CitcomS/Components/Stokes_solver, CitcomS/Makefile.am,
	  CitcomS/SimpleApp.py, CitcomS/Solver, CitcomS/__init__.py,
	  CitcomS/__init__.py.in, Makefile.am, bin/Makefile.am,
	  configure.ac: Issue32: "make install" is now optional. Users can
	  now simply "configure", "make", and then add the "bin"
	  subdirectory of the source/build directory to their PATH.
	  
	  In this mode, changes to C/C++ simply require a "make" from the
	  top-level directory ("make" from a subdirectory will not work in
	  the near future). Changes to the Python code do not require you
	  to run "make" at all -- simply re-run 'citcoms'.

2006-07-06 22:22  leif

	* CitcomS, bin, drivers, pyre: Renamed directories in preparation
	  for next check-in:
	  
	  pyre -> CitcomS drivers -> bin
	  
	  This is to work-around this error message from 'svn':
	  
	  "new node revision ID without delete".
	  
	  I am not loving Subversion right now. Wasn't the whole point that
	  it handles renames gracefully?

2006-07-06 18:16  leif

	* Make.mm, drivers/Full, drivers/Make.mm, drivers/Regional,
	  drivers/local.def, etc/Make.mm, lib/Common/Make.mm,
	  lib/Common/local.def, lib/Full/Make.mm, lib/Full/local.def,
	  lib/Make.mm, lib/Regional/Make.mm, lib/Regional/local.def,
	  lib/local.def, local.def, module/Exchanger/Make.mm,
	  module/Full/Make.mm, module/Full/local.def, module/Make.mm,
	  module/Regional/Make.mm, module/Regional/local.def,
	  pyre/Components/Advection_diffusion/Make.mm,
	  pyre/Components/Exchanger/Make.mm, pyre/Components/Make.mm,
	  pyre/Components/Sphere/Make.mm,
	  pyre/Components/Stokes_solver/Make.mm, pyre/Make.mm,
	  pyre/Solver/Make.mm, pyre/local.def, tests/Make.mm,
	  tests/local.def, visual/Make.mm: Nuked "Make.mm" files, which are
	  no longer used.

2006-07-06 02:53  leif

	* examples/example1.cfg, pyre/Components/CodecConfig.py,
	  pyre/Components/HackedConfigParser.py, pyre/Makefile.am,
	  pyre/SimpleApp.py: Added the ability to use ".cfg" files instead
	  of clumsy shell scripts for specifying parameters.
	  
	  Example usage:
	  
	  citcoms example1.cfg
	  
	  (The file 'example1.cfg' is checked-in under 'examples'.)
	  
	  The code which made this possible was copied & pasted from
	  Specfem project; it will be factored-out into a shared package at
	  some point...

2006-07-06 02:16  leif

	* Makefile.am, configure.ac, drivers/Citcom.c, drivers/Makefile.am,
	  drivers/citcoms.in, drivers/pycitcoms.cc, etc/CitcomS.pml.in,
	  etc/Makefile.am, lib/Common/Advection_diffusion.c,
	  lib/Common/BC_util.c, lib/Common/Construct_arrays.c,
	  lib/Common/Convection.c, lib/Common/Element_calculations.c,
	  lib/Common/General_matrix_functions.c,
	  lib/Common/Initial_temperature.c, lib/Common/Instructions.c,
	  lib/Common/Lith_age.c, lib/Common/Makefile.am,
	  lib/Common/Nodal_mesh.c, lib/Common/Parallel_util.c,
	  lib/Common/Problem_related.c, lib/Common/Process_buoyancy.c,
	  lib/Common/Size_does_matter.c, lib/Common/Solver_multigrid.c,
	  lib/Common/Sphere_util.c, lib/Common/global_defs.h,
	  lib/Common/lith_age.h, lib/Common/parallel_related.h,
	  lib/Common/solver.h, lib/Full/Boundary_conditions.c,
	  lib/Full/Geometry_cartesian.c, lib/Full/Lith_age.c,
	  lib/Full/Lith_age_read_files.c, lib/Full/Makefile.am,
	  lib/Full/Parallel_related.c, lib/Full/Read_input_from_files.c,
	  lib/Full/Solver.c, lib/Full/Sphere_related.c,
	  lib/Full/Version_dependent.c, lib/Makefile.am,
	  lib/Regional/Boundary_conditions.c,
	  lib/Regional/Geometry_cartesian.c, lib/Regional/Lith_age.c,
	  lib/Regional/Lith_age_read_files.c, lib/Regional/Makefile.am,
	  lib/Regional/Parallel_related.c,
	  lib/Regional/Read_input_from_files.c, lib/Regional/Solver.c,
	  lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c,
	  module/CitcomSmodule.cc, module/CitcomSmodule.h,
	  module/Exchanger/Exchangermodule.cc,
	  module/Exchanger/Exchangermodule.h, module/Exchanger/Makefile.am,
	  module/Full/Makefile.am, module/Makefile.am, module/PyxMPI,
	  module/PyxMPI/PyxMPI.c, module/PyxMPI/PyxMPI.pyx,
	  module/PyxMPI/cmpi.pxd, module/Regional/Makefile.am,
	  module/Regional/bindings.cc, module/Regional/mesher.cc,
	  module/Regional/misc.cc, module/Regional/misc.h,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/BC.py, pyre/Components/CitcomComponent.py,
	  pyre/Components/Const.py, pyre/Components/IC.py,
	  pyre/Components/Launchers.py, pyre/Components/Param.py,
	  pyre/Components/Phase.py, pyre/Components/Sphere/FullSphere.py,
	  pyre/Components/Sphere/RegionalSphere.py,
	  pyre/Components/Sphere/Sphere.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Tracer.py, pyre/Components/Visc.py,
	  pyre/SimpleApp.py, pyre/Solver/FullSolver.py,
	  pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py,
	  tests/Makefile.am, tests/citcomsfull.sh.in,
	  tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Added
	  the capability to embed Python instead of extending it. This
	  creates one, big monolithic executable, 'pycitcoms', which
	  contains all CitcomS code and an embedded Python interpreter.
	  Embedding works-around MPI portability issues. (See issue15 for
	  details.) Embed by default.
	  
	  Configure with '--disable-embedding' to build the old way with
	  ".so" extension modules. This is *NOT* guaranteed to work unless
	  you have a shared MPI library. The ugly hacks which made it work
	  in the past (even with a static "libmpich.a", for example) are no
	  longer supported.
	  
	  Merged "Full" and "Regional" into a single library to cut down on
	  redundancy, both in the source code and in the amount of object
	  code which is produced. (I performed this merge so that I would
	  only need a single 'pycitcoms' intepreter, instead of two.)

2006-06-12 17:43  gurnis

	* lib/Common/Advection_diffusion.c,
	  lib/Common/Initial_temperature.c, lib/Common/Problem_related.c,
	  lib/Full/Read_input_from_files.c, pyre/Solver/Solver.py: Fixed
	  restart_tic() in Initial_temperature.c so that time is correctly
	  read in while using the lith_ages

2006-06-02 23:38  gurnis

	* lib/Full/Boundary_conditions.c, lib/Full/Lith_age.c,
	  lib/Regional/Boundary_conditions.c, lib/Regional/Lith_age.c:
	  Fixed bugs associated assimilating lith_age files into Full.
	  Slightly improved method of assimilating lith_age

2006-05-18 18:05  cassie

	* doc/manual/citcoms_book.xml: typo in manual corrected

2006-05-16 19:50  cassie

	* doc/manual/citcoms_book.xml: additional minor updates to manual

2006-05-16 18:36  cassie

	* doc/manual/citcoms_book.xml: minor updates to manual

2006-04-18 23:34  luis

	* lib/Full/Obsolete.c: Fixed typos.

2006-03-28 19:22  walter

	* .: Changed externals from svn:// to http://

2006-02-14 23:24  leif

	* ChangeLog, NEWS: Updated NEWS and ChangeLog.

2006-02-14 22:24  leif

	* pyre/SimpleApp.py, tests/Makefile.am, tests/citcomsfull.sh.in,
	  tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Merged
	  r2600 (fix for issue13, "make PYTHONPATH automatic") from v2
	  branch to trunk.

2006-02-04 02:11  luis

	* doc/manual/citcoms_book.xml: Fixed about 20 assorted typos.

2006-02-04 00:18  luis

	* lib/Regional/Version_dependent.c: Eliminated the unused local
	  variables lx,ly,lz in global_derived_values().

2006-02-04 00:15  luis

	* lib/Full/Version_dependent.c: The value of max_size needs to be
	  larger by 1, or else we access out-of-bound array elements in the
	  arrays E->boundary.element and E->boundary.normal.
	  
	  Refer to issue10 in roundup for more details.

2006-02-04 00:11  luis

	* lib/Common/global_defs.h: Adjusted size of arrays in struct
	  Shape_function_dA. This fixes a bug involving out-of-bounds array
	  access caused by use of fortran-style indexing.
	  
	  Refer to issue10 in roundup for more information.

2006-02-04 00:04  luis

	* lib/Common/Citcom_init.c: Need to initialize to zero the
	  following variables * E->control.total_iteration_cycles *
	  E->control.total_v_solver_calls

2006-01-31 23:16  leif

	* pyre/Components/Launchers.py: Merged r2575 (fix for issue9, "need
	  a property for extra LSF options") from v2 branch to trunk.

2006-01-31 20:23  leif

	* pyre/Components/Launchers.py: Merged r2573 (fix for issue8,
	  "eliminate CitcomS default time limit for batch jobs") from v2
	  branch to trunk.

2006-01-31 02:54  leif

	* configure.ac, etc/Makefile.am, pyre/Makefile.am,
	  tests/Makefile.am, tests/citcomsfull.sh.in,
	  tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Merged
	  r2565 (fix for issue11, "broken install when 'pkgpyexecdir' is
	  distinct from 'pkgpythondir'") from v2 branch to trunk.

2006-01-31 00:07  leif

	* configure.ac: Merged r2563 (fix for issue7, "CitcomS check_CXX
	  check is broken") from v2 branch to trunk.

2005-11-17 19:14  luis

	* examples/Cookbook2/cookbook2.sh: Corrected typo. Should be:
	  --solver.bc.topvbyval=0

2005-11-17 00:35  luis

	* doc/manual/citcoms_book.xml: boundition --> boundary condition

2005-11-16 02:23  leif

	* pyre/Components/IC.py: Fixed a bug which Luis found
	  ("--solver.ic.help-properties"): bad default values for
	  blob_radius and blob_dT.

2005-11-09 18:53  leif

	* doc/manual/citcoms_book.xml: Regenerated PDF.

2005-11-09 12:15  luis

	* doc/manual/citcoms_book.xml: Fixed example 5.6 in Cookbook 5

2005-11-09 11:45  luis

	* doc/manual/citcoms_book.xml: Fixed a few more typos.

2005-11-09 11:31  luis

	* doc/manual/citcoms_book.xml: Missed a stray =

2005-11-09 11:20  luis

	* doc/manual/citcoms_book.xml: Corrected several typos and
	  mispelling errors.

2005-11-04 19:39  leif

	* doc/manual/citcoms_book.xml: Regenerated PDF: updated date; minor
	  corrections, format tweaks.

2005-11-03 00:26  tan2

	* doc/manual/citcoms_book.xml: fixed a bug in closing <filename>
	  tag

2005-11-01 01:10  tan2

	* doc/manual/citcoms_book.xml: changes in Chapter 4
	  (post-processing) and Appendix C (output format)

2005-10-29 02:16  leif

	* mc/3D/CitcomS/branches/v2/examples/Cookbook1/cookbook1.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook2/cookbook2.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook3/cookbook3.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook4/cookbook4.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook5/cookbook5.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook7/cookbook7.sh,
	  mc/3D/CitcomS/branches/v2/examples/example1.sh,
	  mc/3D/CitcomS/tags/v2.0.1/examples/Cookbook1/cookbook1.sh,
	  mc/3D/CitcomS/tags/v2.0.1/examples/Cookbook2/cookbook2.sh,
	  mc/3D/CitcomS/tags/v2.0.1/examples/Cookbook3/cookbook3.sh,
	  mc/3D/CitcomS/tags/v2.0.1/examples/Cookbook4/cookbook4.sh,
	  mc/3D/CitcomS/tags/v2.0.1/examples/Cookbook5/cookbook5.sh,
	  mc/3D/CitcomS/tags/v2.0.1/examples/Cookbook7/cookbook7.sh,
	  mc/3D/CitcomS/tags/v2.0.1/examples/example1.sh,
	  examples/Cookbook1/cookbook1.sh, examples/Cookbook2/cookbook2.sh:
	  Set svn:executable on all examples and cookbooks.

2005-10-29 02:07  leif

	* doc/manual/citcoms_book.xml: Numerous minor corrections and
	  format tweaks.

2005-10-28 22:58  leif

	* doc/manual/citcoms_book.xml: Minor corrections to Chapter 3,
	  "Running CitComS.py", and a major update to Chapter 4,
	  "Postprocessing and Graphics" (which still contained references
	  to the "regcitcom input file").

2005-10-28 20:06  leif

	* doc/manual/citcoms_book.xml: Minor updates to Chapter 2 -- in
	  particular, removed reference to the separate, sync'd Pythia
	  repository. Also, removed reference to the Python installer.

2005-10-28 19:45  leif

	* doc/manual, doc/manual/citcoms_book.xml,
	  doc/manual/citcoms_cover.pdf, doc/manual/graphics.tar.gz: Added
	  DocBook manual files from Cassie.

2005-10-21 19:35  leif

	* mc/3D/CitcomS/branches/v2/examples/Cookbook1/cookbook1.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook2/cookbook2.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook3/cookbook3.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook4/cookbook4.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook5/cookbook5.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook7/cookbook7.sh,
	  mc/3D/CitcomS/branches/v2/examples/example1.sh,
	  mc/3D/CitcomS/branches/v2/visual/Makefile.am,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSFullImport.net,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSFullImport.net.in,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSImport.net,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSImport.net.in,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceHeatflux.net,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceHeatflux.net.in,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceImport.net,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceImport.net.in,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceTopo.net,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceTopo.net.in,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceVelocity.net,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceVelocity.net.in,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSTemperature.net,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSTemperature.net.in,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSVelocity.net,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSVelocity.net.in,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSViscosity.net,
	  mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSViscosity.net.in,
	  mc/3D/CitcomS/branches/v2/visual/visFull.net,
	  mc/3D/CitcomS/branches/v2/visual/visFull.net.in,
	  mc/3D/CitcomS/branches/v2/visual/visRegional.net,
	  mc/3D/CitcomS/branches/v2/visual/visRegional.net.in,
	  mc/3D/CitcomS/branches/v2/visual/visRegionalSurface.net,
	  mc/3D/CitcomS/branches/v2/visual/visRegionalSurface.net.in,
	  examples/Cookbook1/cookbook1.sh, examples/Cookbook2/cookbook2.sh,
	  examples/Cookbook3/cookbook3.sh, examples/Cookbook4/cookbook4.sh,
	  examples/Cookbook5/cookbook5.sh, examples/Cookbook7/cookbook7.sh,
	  examples/example1.sh, visual/Makefile.am,
	  visual/OpenDXMacro/CitcomSFullImport.net,
	  visual/OpenDXMacro/CitcomSFullImport.net.in,
	  visual/OpenDXMacro/CitcomSImport.net,
	  visual/OpenDXMacro/CitcomSImport.net.in,
	  visual/OpenDXMacro/CitcomSSurfaceHeatflux.net,
	  visual/OpenDXMacro/CitcomSSurfaceHeatflux.net.in,
	  visual/OpenDXMacro/CitcomSSurfaceImport.net,
	  visual/OpenDXMacro/CitcomSSurfaceImport.net.in,
	  visual/OpenDXMacro/CitcomSSurfaceTopo.net,
	  visual/OpenDXMacro/CitcomSSurfaceTopo.net.in,
	  visual/OpenDXMacro/CitcomSSurfaceVelocity.net,
	  visual/OpenDXMacro/CitcomSSurfaceVelocity.net.in,
	  visual/OpenDXMacro/CitcomSTemperature.net,
	  visual/OpenDXMacro/CitcomSTemperature.net.in,
	  visual/OpenDXMacro/CitcomSVelocity.net,
	  visual/OpenDXMacro/CitcomSVelocity.net.in,
	  visual/OpenDXMacro/CitcomSViscosity.net,
	  visual/OpenDXMacro/CitcomSViscosity.net.in, visual/visFull.net,
	  visual/visFull.net.in, visual/visRegional.net,
	  visual/visRegional.net.in, visual/visRegionalSurface.net,
	  visual/visRegionalSurface.net.in: Merged revision 2466 from
	  CitcomS v2.0.1 to v2 branch and trunk.

2005-10-07 12:37  leif

	* mc/3D/CitcomS/branches/v2/pyre/Solver/FullSolver.py,
	  mc/3D/CitcomS/branches/v2/pyre/Solver/RegionalSolver.py,
	  pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py: Don't
	  suppress errors loading Full/Regional module.

2005-10-04 23:58  tan2

	* visual/dxgeneralsurf.sh, visual/pasteCitcomData.sh: changed the
	  argument style of 'head'/'tail' command to conform with the
	  standard

2005-10-04 23:56  tan2

	* visual/dxgeneral.sh: changed 'head -1' to 'head -n 1' to conform
	  with the standard

2005-10-04 22:37  leif

	* mc/3D/CitcomS/branches/v2/Make.mm,
	  mc/3D/CitcomS/branches/v2/Makefile.am,
	  mc/3D/CitcomS/branches/v2/configure.ac,
	  mc/3D/CitcomS/branches/v2/drivers/Citcom.c,
	  mc/3D/CitcomS/branches/v2/drivers/Full/Make.mm,
	  mc/3D/CitcomS/branches/v2/drivers/Full/local.def,
	  mc/3D/CitcomS/branches/v2/drivers/Make.mm,
	  mc/3D/CitcomS/branches/v2/drivers/Makefile.am,
	  mc/3D/CitcomS/branches/v2/drivers/Regional/Make.mm,
	  mc/3D/CitcomS/branches/v2/drivers/Regional/local.def,
	  mc/3D/CitcomS/branches/v2/drivers/local.def,
	  mc/3D/CitcomS/branches/v2/etc/Make.mm,
	  mc/3D/CitcomS/branches/v2/etc/Makefile.am,
	  mc/3D/CitcomS/branches/v2/etc/__vault__.odb,
	  mc/3D/CitcomS/branches/v2/etc/full-sphere.odb,
	  mc/3D/CitcomS/branches/v2/etc/full.odb,
	  mc/3D/CitcomS/branches/v2/etc/globus.odb,
	  mc/3D/CitcomS/branches/v2/etc/incomp-newtonian.odb,
	  mc/3D/CitcomS/branches/v2/etc/incomp-non-newtonian.odb,
	  mc/3D/CitcomS/branches/v2/etc/lam-mpi.odb,
	  mc/3D/CitcomS/branches/v2/etc/lsf.odb,
	  mc/3D/CitcomS/branches/v2/etc/mpich.odb,
	  mc/3D/CitcomS/branches/v2/etc/pbs.odb,
	  mc/3D/CitcomS/branches/v2/etc/regional-sphere.odb,
	  mc/3D/CitcomS/branches/v2/etc/regional.odb,
	  mc/3D/CitcomS/branches/v2/etc/temp.odb,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook1/cookbook1.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook2/cookbook2.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook3/cookbook3.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook4/cookbook4.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook5/cookbook5.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook7/cookbook7.sh,
	  mc/3D/CitcomS/branches/v2/examples/Makefile.am,
	  mc/3D/CitcomS/branches/v2/examples/example1.sh,
	  mc/3D/CitcomS/branches/v2/lib/Common/Advection_diffusion.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Citcom_init.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Construct_arrays.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Convection.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Drive_solvers.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Element_calculations.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/General_matrix_functions.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Global_operations.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Initial_temperature.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Instructions.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Interuption.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Make.mm,
	  mc/3D/CitcomS/branches/v2/lib/Common/Makefile.am,
	  mc/3D/CitcomS/branches/v2/lib/Common/Nodal_mesh.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Obsolete.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Output.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Pan_problem_misc_functions.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Parsing.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Phase_change.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Problem_related.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Process_buoyancy.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Shape_functions.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Size_does_matter.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Solver_conj_grad.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Solver_multigrid.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Sphere_harmonics.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Stokes_flow_Incomp.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Topo_gravity.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Tracer_advection.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Viscosity_structures.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/advection.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/advection_diffusion.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/citcom_init.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/convection_variables.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/drive_solvers.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/element_definitions.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/global_defs.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/initial_temperature.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/interuption.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/lith_age.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/local.def,
	  mc/3D/CitcomS/branches/v2/lib/Common/output.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/parallel_related.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/parsing.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/phase_change.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/sphere_communication.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/temperature_descriptions.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/tracer_defs.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/viscosity_descriptions.h,
	  mc/3D/CitcomS/branches/v2/lib/Full/Boundary_conditions.c,
	  mc/3D/CitcomS/branches/v2/lib/Full/Geometry_cartesian.c,
	  mc/3D/CitcomS/branches/v2/lib/Full/Lith_age.c,
	  mc/3D/CitcomS/branches/v2/lib/Full/Make.mm,
	  mc/3D/CitcomS/branches/v2/lib/Full/Makefile.am,
	  mc/3D/CitcomS/branches/v2/lib/Full/Obsolete.c,
	  mc/3D/CitcomS/branches/v2/lib/Full/Parallel_related.c,
	  mc/3D/CitcomS/branches/v2/lib/Full/Read_input_from_files.c,
	  mc/3D/CitcomS/branches/v2/lib/Full/Sphere_related.c,
	  mc/3D/CitcomS/branches/v2/lib/Full/Version_dependent.c,
	  mc/3D/CitcomS/branches/v2/lib/Full/local.def,
	  mc/3D/CitcomS/branches/v2/lib/Make.mm,
	  mc/3D/CitcomS/branches/v2/lib/Makefile.am,
	  mc/3D/CitcomS/branches/v2/lib/Regional/Boundary_conditions.c,
	  mc/3D/CitcomS/branches/v2/lib/Regional/Geometry_cartesian.c,
	  mc/3D/CitcomS/branches/v2/lib/Regional/Lith_age.c,
	  mc/3D/CitcomS/branches/v2/lib/Regional/Make.mm,
	  mc/3D/CitcomS/branches/v2/lib/Regional/Makefile.am,
	  mc/3D/CitcomS/branches/v2/lib/Regional/Obsolete.c,
	  mc/3D/CitcomS/branches/v2/lib/Regional/Parallel_related.c,
	  mc/3D/CitcomS/branches/v2/lib/Regional/Read_input_from_files.c,
	  mc/3D/CitcomS/branches/v2/lib/Regional/Sphere_related.c,
	  mc/3D/CitcomS/branches/v2/lib/Regional/Version_dependent.c,
	  mc/3D/CitcomS/branches/v2/lib/Regional/local.def,
	  mc/3D/CitcomS/branches/v2/lib/local.def,
	  mc/3D/CitcomS/branches/v2/local.def,
	  mc/3D/CitcomS/branches/v2/module/Full/Fullmodule.cc,
	  mc/3D/CitcomS/branches/v2/module/Full/Make.mm,
	  mc/3D/CitcomS/branches/v2/module/Full/Makefile.am,
	  mc/3D/CitcomS/branches/v2/module/Full/local.def,
	  mc/3D/CitcomS/branches/v2/module/Make.mm,
	  mc/3D/CitcomS/branches/v2/module/Makefile.am,
	  mc/3D/CitcomS/branches/v2/module/Regional/Make.mm,
	  mc/3D/CitcomS/branches/v2/module/Regional/Makefile.am,
	  mc/3D/CitcomS/branches/v2/module/Regional/Regionalmodule.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/advdiffu.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/advdiffu.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/bindings.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/bindings.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/exceptions.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/exceptions.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/initial_conditions.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/initial_conditions.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/local.def,
	  mc/3D/CitcomS/branches/v2/module/Regional/mesher.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/mesher.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/misc.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/misc.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/outputs.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/outputs.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/setProperties.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/setProperties.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/stokes_solver.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/stokes_solver.h,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Advection_diffusion/Make.mm,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Advection_diffusion/__init__.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/BC.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/CitcomComponent.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Const.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/CoarseGridExchanger.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Exchanger.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/FineGridExchanger.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Inlet.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Make.mm,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Outlet.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/__init__.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/IC.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Launchers.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Make.mm,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Param.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Phase.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/FullSphere.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/Make.mm,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/RegionalSphere.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/Sphere.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/__init__.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Stokes_solver/Incompressible.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Stokes_solver/Make.mm,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Stokes_solver/__init__.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Tracer.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Visc.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/__init__.py,
	  mc/3D/CitcomS/branches/v2/pyre/Controller.py,
	  mc/3D/CitcomS/branches/v2/pyre/CoupledApp.py,
	  mc/3D/CitcomS/branches/v2/pyre/Coupler.py,
	  mc/3D/CitcomS/branches/v2/pyre/Layout.py,
	  mc/3D/CitcomS/branches/v2/pyre/Make.mm,
	  mc/3D/CitcomS/branches/v2/pyre/Makefile.am,
	  mc/3D/CitcomS/branches/v2/pyre/SimpleApp.py,
	  mc/3D/CitcomS/branches/v2/pyre/Solver/FullSolver.py,
	  mc/3D/CitcomS/branches/v2/pyre/Solver/Make.mm,
	  mc/3D/CitcomS/branches/v2/pyre/Solver/RegionalSolver.py,
	  mc/3D/CitcomS/branches/v2/pyre/Solver/Solver.py,
	  mc/3D/CitcomS/branches/v2/pyre/Solver/__init__.py,
	  mc/3D/CitcomS/branches/v2/pyre/__init__.py.in,
	  mc/3D/CitcomS/branches/v2/pyre/local.def,
	  mc/3D/CitcomS/branches/v2/tests/Make.mm,
	  mc/3D/CitcomS/branches/v2/tests/Makefile.am,
	  mc/3D/CitcomS/branches/v2/tests/asap.py,
	  mc/3D/CitcomS/branches/v2/tests/citcomsfull.sh.in,
	  mc/3D/CitcomS/branches/v2/tests/citcomsregional.sh.in,
	  mc/3D/CitcomS/branches/v2/tests/hrothgar.py,
	  mc/3D/CitcomS/branches/v2/tests/local.def,
	  mc/3D/CitcomS/branches/v2/tests/signon.py,
	  mc/3D/CitcomS/branches/v2/visual/Make.mm,
	  mc/3D/CitcomS/branches/v2/visual/Makefile.am,
	  mc/3D/CitcomS/branches/v2/visual/autocombine.py,
	  mc/3D/CitcomS/branches/v2/visual/batchcombine.py,
	  mc/3D/CitcomS/branches/v2/visual/batchpaste.sh,
	  mc/3D/CitcomS/branches/v2/visual/batchsurf.py,
	  mc/3D/CitcomS/branches/v2/visual/combine.py,
	  mc/3D/CitcomS/branches/v2/visual/combinesurf.py,
	  mc/3D/CitcomS/branches/v2/visual/dxgeneral.sh,
	  mc/3D/CitcomS/branches/v2/visual/dxgeneralsurf.sh,
	  mc/3D/CitcomS/branches/v2/visual/getcoord.sh,
	  mc/3D/CitcomS/branches/v2/visual/getlog.sh,
	  mc/3D/CitcomS/branches/v2/visual/getsurf.sh,
	  mc/3D/CitcomS/branches/v2/visual/parser.py,
	  mc/3D/CitcomS/branches/v2/visual/pasteCitcomData.sh,
	  mc/3D/CitcomS/branches/v2/visual/zslice.py, Make.mm, Makefile.am,
	  configure.ac, drivers/Citcom.c, drivers/Full/Make.mm,
	  drivers/Full/local.def, drivers/Make.mm, drivers/Makefile.am,
	  drivers/Regional/Make.mm, drivers/Regional/local.def,
	  drivers/local.def, etc/Make.mm, etc/Makefile.am,
	  etc/__vault__.odb, etc/full-sphere.odb, etc/full.odb,
	  etc/globus.odb, etc/incomp-newtonian.odb,
	  etc/incomp-non-newtonian.odb, etc/lam-mpi.odb, etc/lsf.odb,
	  etc/mpich.odb, etc/pbs.odb, etc/regional-sphere.odb,
	  etc/regional.odb, etc/temp.odb, examples/Cookbook1/cookbook1.sh,
	  examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
	  examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh,
	  examples/Cookbook7/cookbook7.sh, examples/Makefile.am,
	  examples/example1.sh, lib/Common/Advection_diffusion.c,
	  lib/Common/Citcom_init.c, lib/Common/Construct_arrays.c,
	  lib/Common/Convection.c, lib/Common/Drive_solvers.c,
	  lib/Common/Element_calculations.c,
	  lib/Common/General_matrix_functions.c,
	  lib/Common/Global_operations.c, lib/Common/Initial_temperature.c,
	  lib/Common/Instructions.c, lib/Common/Interuption.c,
	  lib/Common/Make.mm, lib/Common/Makefile.am,
	  lib/Common/Nodal_mesh.c, lib/Common/Obsolete.c,
	  lib/Common/Output.c, lib/Common/Pan_problem_misc_functions.c,
	  lib/Common/Parsing.c, lib/Common/Phase_change.c,
	  lib/Common/Problem_related.c, lib/Common/Process_buoyancy.c,
	  lib/Common/Shape_functions.c, lib/Common/Size_does_matter.c,
	  lib/Common/Solver_conj_grad.c, lib/Common/Solver_multigrid.c,
	  lib/Common/Sphere_harmonics.c, lib/Common/Stokes_flow_Incomp.c,
	  lib/Common/Topo_gravity.c, lib/Common/Tracer_advection.c,
	  lib/Common/Viscosity_structures.c, lib/Common/advection.h,
	  lib/Common/advection_diffusion.h, lib/Common/citcom_init.h,
	  lib/Common/convection_variables.h, lib/Common/drive_solvers.h,
	  lib/Common/element_definitions.h, lib/Common/global_defs.h,
	  lib/Common/initial_temperature.h, lib/Common/interuption.h,
	  lib/Common/lith_age.h, lib/Common/local.def, lib/Common/output.h,
	  lib/Common/parallel_related.h, lib/Common/parsing.h,
	  lib/Common/phase_change.h, lib/Common/sphere_communication.h,
	  lib/Common/temperature_descriptions.h, lib/Common/tracer_defs.h,
	  lib/Common/viscosity_descriptions.h,
	  lib/Full/Boundary_conditions.c, lib/Full/Geometry_cartesian.c,
	  lib/Full/Lith_age.c, lib/Full/Make.mm, lib/Full/Makefile.am,
	  lib/Full/Obsolete.c, lib/Full/Parallel_related.c,
	  lib/Full/Read_input_from_files.c, lib/Full/Sphere_related.c,
	  lib/Full/Version_dependent.c, lib/Full/local.def, lib/Make.mm,
	  lib/Makefile.am, lib/Regional/Boundary_conditions.c,
	  lib/Regional/Geometry_cartesian.c, lib/Regional/Lith_age.c,
	  lib/Regional/Make.mm, lib/Regional/Makefile.am,
	  lib/Regional/Obsolete.c, lib/Regional/Parallel_related.c,
	  lib/Regional/Read_input_from_files.c,
	  lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c,
	  lib/Regional/local.def, lib/local.def, local.def,
	  module/Exchanger/AreaWeightedNormal.cc,
	  module/Exchanger/AreaWeightedNormal.h,
	  module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/BoundaryVTInlet.cc,
	  module/Exchanger/BoundaryVTInlet.h,
	  module/Exchanger/CitcomInterpolator.cc,
	  module/Exchanger/CitcomInterpolator.h,
	  module/Exchanger/CitcomSource.cc,
	  module/Exchanger/CitcomSource.h, module/Exchanger/Convertor.cc,
	  module/Exchanger/Convertor.h,
	  module/Exchanger/Exchangermodule.cc,
	  module/Exchanger/Interior.cc, module/Exchanger/Interior.h,
	  module/Exchanger/Make.mm, module/Exchanger/Makefile.am,
	  module/Exchanger/SIUnit.cc, module/Exchanger/SIUnit.h,
	  module/Exchanger/SInlet.cc, module/Exchanger/SInlet.h,
	  module/Exchanger/SVTInlet.cc, module/Exchanger/SVTInlet.h,
	  module/Exchanger/SVTOutlet.cc, module/Exchanger/SVTOutlet.h,
	  module/Exchanger/TInlet.cc, module/Exchanger/TInlet.h,
	  module/Exchanger/TOutlet.cc, module/Exchanger/TOutlet.h,
	  module/Exchanger/VOutlet.cc, module/Exchanger/VOutlet.h,
	  module/Exchanger/VTInlet.cc, module/Exchanger/VTInlet.h,
	  module/Exchanger/VTOutlet.cc, module/Exchanger/VTOutlet.h,
	  module/Exchanger/bindings.cc, module/Exchanger/bindings.h,
	  module/Exchanger/exceptions.cc, module/Exchanger/exceptions.h,
	  module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h,
	  module/Exchanger/global_bbox.cc, module/Exchanger/global_bbox.h,
	  module/Exchanger/initTemperature.cc,
	  module/Exchanger/initTemperature.h,
	  module/Exchanger/inlets_outlets.cc,
	  module/Exchanger/inlets_outlets.h, module/Exchanger/misc.cc,
	  module/Exchanger/misc.h, module/Full/Fullmodule.cc,
	  module/Full/Make.mm, module/Full/Makefile.am,
	  module/Full/local.def, module/Make.mm, module/Makefile.am,
	  module/Regional/Make.mm, module/Regional/Makefile.am,
	  module/Regional/Regionalmodule.cc, module/Regional/advdiffu.cc,
	  module/Regional/advdiffu.h, module/Regional/bindings.cc,
	  module/Regional/bindings.h, module/Regional/exceptions.cc,
	  module/Regional/exceptions.h,
	  module/Regional/initial_conditions.cc,
	  module/Regional/initial_conditions.h, module/Regional/local.def,
	  module/Regional/mesher.cc, module/Regional/mesher.h,
	  module/Regional/misc.cc, module/Regional/misc.h,
	  module/Regional/outputs.cc, module/Regional/outputs.h,
	  module/Regional/setProperties.cc,
	  module/Regional/setProperties.h,
	  module/Regional/stokes_solver.cc,
	  module/Regional/stokes_solver.h,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/Advection_diffusion/Make.mm,
	  pyre/Components/Advection_diffusion/__init__.py,
	  pyre/Components/BC.py, pyre/Components/CitcomComponent.py,
	  pyre/Components/Const.py,
	  pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  pyre/Components/Exchanger/Inlet.py,
	  pyre/Components/Exchanger/Make.mm,
	  pyre/Components/Exchanger/Outlet.py,
	  pyre/Components/Exchanger/__init__.py, pyre/Components/IC.py,
	  pyre/Components/Launchers.py, pyre/Components/Make.mm,
	  pyre/Components/Param.py, pyre/Components/Phase.py,
	  pyre/Components/Sphere/FullSphere.py,
	  pyre/Components/Sphere/Make.mm,
	  pyre/Components/Sphere/RegionalSphere.py,
	  pyre/Components/Sphere/Sphere.py,
	  pyre/Components/Sphere/__init__.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Stokes_solver/Make.mm,
	  pyre/Components/Stokes_solver/__init__.py,
	  pyre/Components/Tracer.py, pyre/Components/Visc.py,
	  pyre/Components/__init__.py, pyre/Controller.py,
	  pyre/CoupledApp.py, pyre/Coupler.py, pyre/Layout.py,
	  pyre/Make.mm, pyre/Makefile.am, pyre/SimpleApp.py,
	  pyre/Solver/FullSolver.py, pyre/Solver/Make.mm,
	  pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py,
	  pyre/Solver/__init__.py, pyre/__init__.py.in, pyre/local.def,
	  tests/Make.mm, tests/Makefile.am, tests/array2d.cc,
	  tests/asap.py, tests/citcomsfull.sh.in,
	  tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in,
	  tests/exchange.py, tests/hrothgar.py, tests/local.def,
	  tests/signon.py, tests/test1.sh, tests/test2.sh, tests/test5.sh,
	  visual/Make.mm, visual/Makefile.am, visual/autocombine.py,
	  visual/batchcombine.py, visual/batchpaste.sh,
	  visual/batchsurf.py, visual/combine.py, visual/combinesurf.py,
	  visual/dxgeneral.sh, visual/dxgeneralsurf.sh, visual/getcoord.sh,
	  visual/getlog.sh, visual/getsurf.sh, visual/parser.py,
	  visual/pasteCitcomData.sh, visual/zslice.py: Changed CitcomS
	  license header text to GNU GPL.

2005-10-04 02:53  leif

	* mc/3D/CitcomS/branches/v2/AUTHORS,
	  mc/3D/CitcomS/branches/v2/COPYING,
	  mc/3D/CitcomS/branches/v2/ChangeLog,
	  mc/3D/CitcomS/branches/v2/CitcomS.py-LICENSE.txt,
	  mc/3D/CitcomS/branches/v2/INSTALL,
	  mc/3D/CitcomS/branches/v2/Make.mm,
	  mc/3D/CitcomS/branches/v2/Makefile.am,
	  mc/3D/CitcomS/branches/v2/NEWS, mc/3D/CitcomS/branches/v2/README,
	  mc/3D/CitcomS/branches/v2/citcoms_profile,
	  mc/3D/CitcomS/branches/v2/configure.ac,
	  mc/3D/CitcomS/branches/v2/drivers/Full/Make.mm,
	  mc/3D/CitcomS/branches/v2/drivers/Full/local.def,
	  mc/3D/CitcomS/branches/v2/drivers/Make.mm,
	  mc/3D/CitcomS/branches/v2/drivers/Makefile.am,
	  mc/3D/CitcomS/branches/v2/drivers/Regional/Make.mm,
	  mc/3D/CitcomS/branches/v2/drivers/Regional/local.def,
	  mc/3D/CitcomS/branches/v2/drivers/local.def,
	  mc/3D/CitcomS/branches/v2/etc/CitcomS.pml.in,
	  mc/3D/CitcomS/branches/v2/etc/Make.mm,
	  mc/3D/CitcomS/branches/v2/etc/Makefile.am,
	  mc/3D/CitcomS/branches/v2/etc/__vault__.odb,
	  mc/3D/CitcomS/branches/v2/etc/full-sphere.odb,
	  mc/3D/CitcomS/branches/v2/etc/full.odb,
	  mc/3D/CitcomS/branches/v2/etc/globus.odb,
	  mc/3D/CitcomS/branches/v2/etc/incomp-newtonian.odb,
	  mc/3D/CitcomS/branches/v2/etc/incomp-non-newtonian.odb,
	  mc/3D/CitcomS/branches/v2/etc/lam-mpi.odb,
	  mc/3D/CitcomS/branches/v2/etc/lsf.odb,
	  mc/3D/CitcomS/branches/v2/etc/mpich.odb,
	  mc/3D/CitcomS/branches/v2/etc/pbs.odb,
	  mc/3D/CitcomS/branches/v2/etc/regional-sphere.odb,
	  mc/3D/CitcomS/branches/v2/etc/regional.odb,
	  mc/3D/CitcomS/branches/v2/etc/temp.odb,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook2/cookbook2.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook3/cookbook3.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook4/cookbook4.sh,
	  mc/3D/CitcomS/branches/v2/examples/Cookbook5/cookbook5.sh,
	  mc/3D/CitcomS/branches/v2/examples/Makefile.am,
	  mc/3D/CitcomS/branches/v2/examples/example1.sh,
	  mc/3D/CitcomS/branches/v2/lib/Common/Element_calculations.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Make.mm,
	  mc/3D/CitcomS/branches/v2/lib/Common/Makefile.am,
	  mc/3D/CitcomS/branches/v2/lib/Common/Obsolete.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Pan_problem_misc_functions.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Size_does_matter.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Topo_gravity.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/Tracer_advection.c,
	  mc/3D/CitcomS/branches/v2/lib/Common/advection_diffusion.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/citcom_init.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/drive_solvers.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/global_defs.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/local.def,
	  mc/3D/CitcomS/branches/v2/lib/Common/output.h,
	  mc/3D/CitcomS/branches/v2/lib/Common/parallel_related.h,
	  mc/3D/CitcomS/branches/v2/lib/Full/Boundary_conditions.c,
	  mc/3D/CitcomS/branches/v2/lib/Full/Make.mm,
	  mc/3D/CitcomS/branches/v2/lib/Full/Makefile.am,
	  mc/3D/CitcomS/branches/v2/lib/Full/local.def,
	  mc/3D/CitcomS/branches/v2/lib/Make.mm,
	  mc/3D/CitcomS/branches/v2/lib/Makefile.am,
	  mc/3D/CitcomS/branches/v2/lib/Regional/Boundary_conditions.c,
	  mc/3D/CitcomS/branches/v2/lib/Regional/Make.mm,
	  mc/3D/CitcomS/branches/v2/lib/Regional/Makefile.am,
	  mc/3D/CitcomS/branches/v2/lib/Regional/local.def,
	  mc/3D/CitcomS/branches/v2/lib/local.def,
	  mc/3D/CitcomS/branches/v2/local.def,
	  mc/3D/CitcomS/branches/v2/module/Full/Fullmodule.cc,
	  mc/3D/CitcomS/branches/v2/module/Full/Make.mm,
	  mc/3D/CitcomS/branches/v2/module/Full/Makefile.am,
	  mc/3D/CitcomS/branches/v2/module/Full/local.def,
	  mc/3D/CitcomS/branches/v2/module/Make.mm,
	  mc/3D/CitcomS/branches/v2/module/Makefile.am,
	  mc/3D/CitcomS/branches/v2/module/Regional/Make.mm,
	  mc/3D/CitcomS/branches/v2/module/Regional/Makefile.am,
	  mc/3D/CitcomS/branches/v2/module/Regional/Regionalmodule.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/advdiffu.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/advdiffu.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/bindings.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/bindings.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/exceptions.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/exceptions.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/initial_conditions.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/initial_conditions.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/local.def,
	  mc/3D/CitcomS/branches/v2/module/Regional/mesher.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/mesher.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/misc.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/misc.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/outputs.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/outputs.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/setProperties.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/setProperties.h,
	  mc/3D/CitcomS/branches/v2/module/Regional/stokes_solver.cc,
	  mc/3D/CitcomS/branches/v2/module/Regional/stokes_solver.h,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Advection_diffusion/Make.mm,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Advection_diffusion/__init__.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/BC.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/CitcomComponent.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Const.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/CoarseGridExchanger.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Exchanger.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/FineGridExchanger.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Inlet.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Make.mm,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Outlet.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/__init__.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/IC.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Launchers.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Make.mm,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Param.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Phase.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/FullSphere.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/Make.mm,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/RegionalSphere.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/Sphere.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/__init__.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Stokes_solver/Incompressible.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Stokes_solver/Make.mm,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Stokes_solver/__init__.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Tracer.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/Visc.py,
	  mc/3D/CitcomS/branches/v2/pyre/Components/__init__.py,
	  mc/3D/CitcomS/branches/v2/pyre/CoupledApp.py,
	  mc/3D/CitcomS/branches/v2/pyre/Coupler.py,
	  mc/3D/CitcomS/branches/v2/pyre/Layout.py,
	  mc/3D/CitcomS/branches/v2/pyre/Make.mm,
	  mc/3D/CitcomS/branches/v2/pyre/Makefile.am,
	  mc/3D/CitcomS/branches/v2/pyre/SimpleApp.py,
	  mc/3D/CitcomS/branches/v2/pyre/Solver/FullSolver.py,
	  mc/3D/CitcomS/branches/v2/pyre/Solver/Make.mm,
	  mc/3D/CitcomS/branches/v2/pyre/Solver/RegionalSolver.py,
	  mc/3D/CitcomS/branches/v2/pyre/Solver/Solver.py,
	  mc/3D/CitcomS/branches/v2/pyre/Solver/__init__.py,
	  mc/3D/CitcomS/branches/v2/pyre/__init__.py,
	  mc/3D/CitcomS/branches/v2/pyre/__init__.py.in,
	  mc/3D/CitcomS/branches/v2/pyre/local.def,
	  mc/3D/CitcomS/branches/v2/tests/Make.mm,
	  mc/3D/CitcomS/branches/v2/tests/Makefile.am,
	  mc/3D/CitcomS/branches/v2/tests/asap.py,
	  mc/3D/CitcomS/branches/v2/tests/citcomsfull.sh,
	  mc/3D/CitcomS/branches/v2/tests/citcomsfull.sh.in,
	  mc/3D/CitcomS/branches/v2/tests/citcomsregional.sh,
	  mc/3D/CitcomS/branches/v2/tests/citcomsregional.sh.in,
	  mc/3D/CitcomS/branches/v2/tests/hrothgar.py,
	  mc/3D/CitcomS/branches/v2/tests/local.def,
	  mc/3D/CitcomS/branches/v2/tests/signon.py,
	  mc/3D/CitcomS/branches/v2/visual/Make.mm,
	  mc/3D/CitcomS/branches/v2/visual/Makefile.am,
	  mc/3D/CitcomS/branches/v2/visual/batchcombine.py,
	  mc/3D/CitcomS/branches/v2/visual/batchpaste.sh,
	  mc/3D/CitcomS/branches/v2/visual/batchsurf.py,
	  mc/3D/CitcomS/branches/v2/visual/combine.py,
	  mc/3D/CitcomS/branches/v2/visual/combinesurf.py,
	  mc/3D/CitcomS/branches/v2/visual/dxgeneral.sh,
	  mc/3D/CitcomS/branches/v2/visual/dxgeneralsurf.sh,
	  mc/3D/CitcomS/branches/v2/visual/getcoord.sh,
	  mc/3D/CitcomS/branches/v2/visual/getlog.sh,
	  mc/3D/CitcomS/branches/v2/visual/getsurf.sh,
	  mc/3D/CitcomS/branches/v2/visual/pasteCitcomData.sh, Makefile.am,
	  tests/Make.mm: Ported GNU Build System from CitcomS trunk to v2
	  branch.

2005-10-04 00:34  leif

	* pyre/Controller, pyre/Coupler, pyre/Facilities, pyre/Layout:
	  Nuked empty directories.

2005-10-01 01:17  leif

	* ChangeLog: Strip "mc/3D/CitcomS/trunk" directory prefix. By the
	  way, this file is generated with svn2cl
	  (http://ch.tudelft.nl/~arthur/svn2cl/) using the command "svn log
	  --xml --verbose | xsltproc --stringparam strip-prefix
	  mc/3D/CitcomS/trunk svn2cl.xsl - > ChangeLog".

2005-10-01 01:01  leif

	* AUTHORS, COPYING, ChangeLog, CitcomS.py-LICENSE.txt, INSTALL,
	  NEWS, README: Added various GNU standard files, including the
	  GPL.

2005-09-30 23:48  leif

	* module/Full: Doh! Restored svn:ignore'ing of those ridiculous
	  symlinks used by Make.mm.

2005-09-30 22:39  leif

	* ., drivers, etc, examples, lib, lib/Common, lib/Full,
	  lib/Regional, module, module/Exchanger, module/Full,
	  module/Regional, pyre, tests, visual: Ignore files generated by
	  Autoconf/Automake/Libtool.

2005-09-30 17:59  leif

	* configure.ac: Push/pop C++ around MPI tests, which are now
	  sensitive to the current language. Made sure that
	  '--without-pyre' works in the absence of a C++ compiler (tested
	  on Hrothgar). When building with Pyre modules, fail if a C++
	  compiler is not found.

2005-09-28 23:26  leif

	* configure.ac, etc/CitcomS.pml.in, etc/Make.mm, etc/Makefile.am,
	  pyre/Components/Launchers.py, pyre/CoupledApp.py, pyre/Make.mm,
	  pyre/Makefile.am, pyre/SimpleApp.py, pyre/__init__.py,
	  pyre/__init__.py.in, tests/Make.mm, tests/Makefile.am,
	  tests/citcomsfull.sh.in, tests/citcomsregional.sh.in,
	  tests/coupledcitcoms.sh.in: Add ${pythondir} to PYTHONPATH before
	  checking for Python modules, so that installing multiple packages
	  to a single PREFIX "just works". This also attempts to simulate
	  the final installation environment, which might make a difference
	  in unusual cases. Also, 'sed' the install-time PYTHONPATH into
	  CitComS scripts (instead of an explicit list of @pythondir@'s).
	  
	  Added _getPrivateDepositoryLocations() and CitcomS.pml. Changed
	  "etc/citcoms" to "etc/CitcomS" for consistency with the Python
	  package name. Add PACKAGE_VERSION to __init__.py, and added
	  pyconfig-generated config.py. Freeze the full path to 'mpirun'
	  and 'mpipython.exe' at 'configure' time. First crack at batch
	  system configuration.

2005-09-21 00:03  leif

	* Makefile.am, configure.ac,
	  lib/Common/Pan_problem_misc_functions.c,
	  lib/Common/Tracer_advection.c, module/Exchanger/Makefile.am,
	  module/Full/Makefile.am, module/Regional/Makefile.am,
	  tests/Make.mm, tests/Makefile.am, tests/citcomsfull.sh.in,
	  tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Utilize
	  my new 'pyconfig' facility to automatically slurp config info
	  from Pythia, Exchanger. Changed contact e-mail to cig-mc; other
	  misc. changes.

2005-09-09 19:49  leif

	* Makefile.am, configure.ac, drivers/Makefile.am, etc/Makefile.am,
	  examples/Makefile.am, lib/Common/Makefile.am,
	  lib/Full/Makefile.am, lib/Makefile.am, lib/Regional/Makefile.am,
	  module/Exchanger/Makefile.am, module/Full/Makefile.am,
	  module/Makefile.am, module/Regional/Makefile.am,
	  pyre/Makefile.am, tests/Makefile.am, visual/Makefile.am: Added Id
	  keyword property to configure.ac, Makefile.am.

2005-09-09 19:41  leif

	* ., Makefile.am, configure.ac, drivers/Makefile.am,
	  etc/Makefile.am, examples/Makefile.am, lib/Common/Makefile.am,
	  lib/Full/Makefile.am, lib/Makefile.am, lib/Regional/Makefile.am,
	  module/Exchanger/Makefile.am, module/Full, module/Full/Make.mm,
	  module/Full/Makefile.am, module/Make.mm, module/Makefile.am,
	  module/Regional/Makefile.am, pyre/Components/Launchers.py,
	  pyre/Makefile.am, pyre/Solver/FullSolver.py,
	  pyre/Solver/RegionalSolver.py, tests/Make.mm, tests/Makefile.am,
	  tests/citcomsfull.sh, tests/citcomsfull.sh.in,
	  tests/citcomsregional.sh, tests/citcomsregional.sh.in,
	  tests/coupledcitcoms.sh, tests/coupledcitcoms.sh.in,
	  visual/Makefile.am: Added files for the GNU Build System.

2005-08-29 19:28  leif

	* Make.mm, citcoms_profile, drivers/Full/Make.mm,
	  drivers/Full/local.def, drivers/Make.mm,
	  drivers/Regional/Make.mm, drivers/Regional/local.def,
	  drivers/local.def, etc/Make.mm, etc/__vault__.odb,
	  etc/full-sphere.odb, etc/full.odb, etc/globus.odb,
	  etc/incomp-newtonian.odb, etc/incomp-non-newtonian.odb,
	  etc/lam-mpi.odb, etc/lsf.odb, etc/mpich.odb, etc/pbs.odb,
	  etc/regional-sphere.odb, etc/regional.odb, etc/temp.odb,
	  examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
	  examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh,
	  examples/Cookbook7/cookbook7.sh, examples/example1.sh,
	  lib/Common/Element_calculations.c, lib/Common/Make.mm,
	  lib/Common/Obsolete.c, lib/Common/Size_does_matter.c,
	  lib/Common/Topo_gravity.c, lib/Common/local.def,
	  lib/Full/Boundary_conditions.c, lib/Full/Make.mm,
	  lib/Full/local.def, lib/Make.mm,
	  lib/Regional/Boundary_conditions.c, lib/Regional/Make.mm,
	  lib/Regional/local.def, lib/local.def, local.def,
	  module/Exchanger/AreaWeightedNormal.cc,
	  module/Exchanger/AreaWeightedNormal.h,
	  module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/BoundaryVTInlet.cc,
	  module/Exchanger/BoundaryVTInlet.h,
	  module/Exchanger/CitcomInterpolator.cc,
	  module/Exchanger/CitcomInterpolator.h,
	  module/Exchanger/CitcomSource.cc,
	  module/Exchanger/CitcomSource.h, module/Exchanger/Convertor.cc,
	  module/Exchanger/Convertor.h,
	  module/Exchanger/Exchangermodule.cc,
	  module/Exchanger/Interior.cc, module/Exchanger/Interior.h,
	  module/Exchanger/Make.mm, module/Exchanger/SIUnit.cc,
	  module/Exchanger/SIUnit.h, module/Exchanger/SInlet.cc,
	  module/Exchanger/SInlet.h, module/Exchanger/SVTInlet.cc,
	  module/Exchanger/SVTInlet.h, module/Exchanger/SVTOutlet.cc,
	  module/Exchanger/SVTOutlet.h, module/Exchanger/TInlet.cc,
	  module/Exchanger/TInlet.h, module/Exchanger/TOutlet.cc,
	  module/Exchanger/TOutlet.h, module/Exchanger/VOutlet.cc,
	  module/Exchanger/VOutlet.h, module/Exchanger/VTInlet.cc,
	  module/Exchanger/VTInlet.h, module/Exchanger/VTOutlet.cc,
	  module/Exchanger/VTOutlet.h, module/Exchanger/bindings.cc,
	  module/Exchanger/bindings.h, module/Exchanger/exceptions.cc,
	  module/Exchanger/exceptions.h, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h, module/Exchanger/global_bbox.cc,
	  module/Exchanger/global_bbox.h,
	  module/Exchanger/initTemperature.cc,
	  module/Exchanger/initTemperature.h,
	  module/Exchanger/inlets_outlets.cc,
	  module/Exchanger/inlets_outlets.h, module/Exchanger/misc.cc,
	  module/Exchanger/misc.h, module/Full/Fullmodule.cc,
	  module/Full/Make.mm, module/Full/local.def, module/Make.mm,
	  module/Regional/Make.mm, module/Regional/Regionalmodule.cc,
	  module/Regional/advdiffu.cc, module/Regional/advdiffu.h,
	  module/Regional/bindings.cc, module/Regional/bindings.h,
	  module/Regional/exceptions.cc, module/Regional/exceptions.h,
	  module/Regional/initial_conditions.cc,
	  module/Regional/initial_conditions.h, module/Regional/local.def,
	  module/Regional/mesher.cc, module/Regional/mesher.h,
	  module/Regional/misc.cc, module/Regional/misc.h,
	  module/Regional/outputs.cc, module/Regional/outputs.h,
	  module/Regional/setProperties.cc,
	  module/Regional/setProperties.h,
	  module/Regional/stokes_solver.cc,
	  module/Regional/stokes_solver.h,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/Advection_diffusion/Make.mm,
	  pyre/Components/Advection_diffusion/__init__.py,
	  pyre/Components/BC.py, pyre/Components/CitcomComponent.py,
	  pyre/Components/Const.py,
	  pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  pyre/Components/Exchanger/Inlet.py,
	  pyre/Components/Exchanger/Make.mm,
	  pyre/Components/Exchanger/Outlet.py,
	  pyre/Components/Exchanger/__init__.py, pyre/Components/IC.py,
	  pyre/Components/Launchers.py, pyre/Components/Make.mm,
	  pyre/Components/Param.py, pyre/Components/Phase.py,
	  pyre/Components/Sphere/FullSphere.py,
	  pyre/Components/Sphere/Make.mm,
	  pyre/Components/Sphere/RegionalSphere.py,
	  pyre/Components/Sphere/Sphere.py,
	  pyre/Components/Sphere/__init__.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Stokes_solver/Make.mm,
	  pyre/Components/Stokes_solver/__init__.py,
	  pyre/Components/Tracer.py, pyre/Components/Visc.py,
	  pyre/Components/__init__.py, pyre/CoupledApp.py, pyre/Coupler.py,
	  pyre/Layout.py, pyre/Make.mm, pyre/SimpleApp.py,
	  pyre/Solver/FullSolver.py, pyre/Solver/Make.mm,
	  pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py,
	  pyre/Solver/__init__.py, pyre/__init__.py, pyre/local.def,
	  tests/Make.mm, tests/array2d.cc, tests/asap.py,
	  tests/citcomsfull.sh, tests/citcomsregional.sh,
	  tests/coupledcitcoms.sh, tests/exchange.py, tests/hrothgar.py,
	  tests/local.def, tests/signon.py, tests/test1.sh, tests/test2.sh,
	  tests/test5.sh, visual/Make.mm, visual/autocombine.py,
	  visual/batchcombine.py, visual/batchpaste.sh,
	  visual/batchsurf.py, visual/combine.py, visual/combinesurf.py,
	  visual/dxgeneral.sh, visual/dxgeneralsurf.sh, visual/getcoord.sh,
	  visual/getlog.sh, visual/getsurf.sh, visual/miff2avi,
	  visual/miff2mpg, visual/parser.py, visual/pasteCitcomData.sh,
	  visual/zslice.py: Added executable property and 'Id' keyword
	  expansion.

2005-08-27 03:04  leif

	* lib/Common/advection_diffusion.h, lib/Common/citcom_init.h,
	  lib/Common/drive_solvers.h, lib/Common/global_defs.h,
	  lib/Common/output.h, lib/Common/parallel_related.h,
	  module/Regional/advdiffu.cc,
	  module/Regional/initial_conditions.cc, module/Regional/mesher.cc,
	  module/Regional/misc.cc, module/Regional/outputs.cc,
	  module/Regional/stokes_solver.cc: Avoid 'extern "C" { #include
	  ... }'; it causes problems with mpi++.h/mpicxx.h.

2005-07-27 08:58  leif

	* etc/mpich.odb, pyre/Components/Launchers.py, pyre/SimpleApp.py:
	  Fixed it so that the uniprocessor examples work again. This
	  invovled creating CitcomS's own version of LauncherMPICH, and
	  tweaking the MPI launchers so that CitcomS re-execs itself under
	  'mpipython.exe' when it is run under plain old 'python'. Also:
	  made "--launcher.dry" work; ignore 'nodegen' in LauncherBatch (so
	  that the examples "just work" on the TeraGrid); added some 'tips'
	  ("--launcher.help-properties"); added SimpleApp.usage().

2005-07-23 08:35  leif

	* Make.mm, examples/Cookbook1/cookbook1.sh,
	  examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
	  examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh,
	  examples/example1.sh, tests/Make.mm, tests/array2d.cc,
	  visual/Make.mm: General build clean-up: 'export' all the various
	  scripts to $EXPORT_ROOT/bin, so that goofy relative paths are not
	  needed (e.g., "../tests/citcomsregional.sh"); and so that the
	  'visual' directory doesn't have to be added to the PATH. I also
	  dusted-off 'array2d' -- it compiles and links now.

2005-07-23 08:00  leif

	* module/Regional/misc.cc: Raise an exception -- instead of
	  crashing -- when pyCitcom_citcom_init() is passed a null
	  "mpi::Communicator *" argument.

2005-07-22 10:03  leif

	* pyre/Components/Launchers.py: Switched from Python's '%' operator
	  to pyre.util.expandMacros(), so that I don't have to escape '%'
	  (e.g., --launcher.nodegen="n%03d"). Also, export key environment
	  variables to LAM/MPI jobs.

2005-07-22 05:55  leif

	* lib/Common/Make.mm, lib/Common/local.def, lib/Full/Make.mm,
	  lib/Full/local.def, lib/Regional/Make.mm, lib/Regional/local.def:
	  Build with soflags to produce position-independent code. 'Export'
	  the resulting shared libraries.

2005-07-20 04:23  leif

	* tests/citcomsfull.sh, tests/citcomsregional.sh,
	  tests/coupledcitcoms.sh: Use 'python' instead of 'mpipython.exe'
	  -- on some TeraGrid clusters, MPI programs cannot be run
	  directly.

2005-07-20 04:12  leif

	* examples/ncsa.sh, examples/tacc.sh: Removed sample batch scripts,
	  which are obsoleted by my new launchers. Use "--launcher=pbs" or
	  "--launcher=lsf" on NCSA and TACC, respectively.

2005-07-20 04:07  leif

	* etc/Make.mm, etc/globus.odb, etc/lam-mpi.odb, etc/lsf.odb,
	  etc/mpich.odb, etc/pbs.odb, pyre/Components/Launchers.py,
	  pyre/Components/Make.mm: Added Pyre launchers for LAM/MPI,
	  Globus, LSF, and PBS. This is their temporary home; they should
	  be incorporated into Pyre eventually.

2005-07-20 03:55  leif

	* visual/batchpaste.sh: Merged revision 1.5.2.1 from CitcomS-2_x
	  branch to trunk: tan2: "a fix for single-processor (eg. laptop)".

2005-06-30 08:31  leif

	* lib/Common/global_defs.h, module/Exchanger/Make.mm,
	  module/Full/Make.mm, module/Regional/Make.mm: Changes for Mac OS
	  X build.

2005-08-23 03:42  unknown_user

	* pyre/Facilities/Make.mm, pyre/Facilities/Mesher.py,
	  pyre/Facilities/Solver.py, pyre/Facilities/TSolver.py,
	  pyre/Facilities/VSolver.py, pyre/Facilities/__init__.py: [vcp]
	  delete of edited revision with dead state

2005-06-18 04:24  leif

	* pyre/Facilities/Make.mm, pyre/Facilities/Mesher.py,
	  pyre/Facilities/Solver.py, pyre/Facilities/TSolver.py,
	  pyre/Facilities/VSolver.py, pyre/Facilities/__init__.py,
	  pyre/Make.mm: Removed 'Facilities' directory -- no longer needed
	  under Pythia v0.8.

2005-06-18 04:20  leif

	* examples/ncsa.sh, examples/tacc.sh: Added example batch scripts
	  for NCSA and TACC TeraGrid clusters.

2005-06-18 02:07  ces74

	* visual/visFull.cfg, visual/visFull.net, visual/visRegional.cfg,
	  visual/visRegional.net, visual/visRegionalSurface.cfg,
	  visual/visRegionalSurface.net: * removed default paths to
	  input/output files. * removed absolute paths to macros.

2005-06-16 02:33  tan2

	* visual/autocombine.py: script to automatically read input
	  parameters from input file and call batchcombine.py

2005-06-16 02:33  tan2

	* visual/batchcombine.py: 1. moved parts of the script into
	  functions so that other scripts can import them. 2. raise
	  ValueError when the length of machinefile is not right

2005-06-16 02:30  tan2

	* visual/parser.py: using new-style class

2005-06-16 01:27  tan2

	* pyre/Components/Sphere/Sphere.py, pyre/Solver/Solver.py: print
	  messages to stderr instead of stdout

2005-06-14 23:47  leif

	* module/Full/Make.mm, module/Regional/Make.mm: Corrected use of
	  -Xlinker.

2005-06-10 09:23  leif

	* CitcomS.py-LICENSE.txt, drivers/Citcom.c, drivers/Full/Make.mm,
	  drivers/Full/local.def, drivers/Make.mm,
	  drivers/Regional/Make.mm, drivers/Regional/local.def,
	  drivers/local.def, etc/Make.mm, etc/__vault__.odb,
	  etc/full-sphere.odb, etc/full.odb, etc/incomp-newtonian.odb,
	  etc/incomp-non-newtonian.odb, etc/regional-sphere.odb,
	  etc/regional.odb, etc/temp.odb, examples/Cookbook1/cookbook1.sh,
	  examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
	  examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh,
	  examples/Cookbook7/cookbook7.sh, examples/example1.sh,
	  lib/Common/Advection_diffusion.c, lib/Common/Citcom_init.c,
	  lib/Common/Construct_arrays.c, lib/Common/Convection.c,
	  lib/Common/Drive_solvers.c, lib/Common/Element_calculations.c,
	  lib/Common/General_matrix_functions.c,
	  lib/Common/Global_operations.c, lib/Common/Initial_temperature.c,
	  lib/Common/Instructions.c, lib/Common/Interuption.c,
	  lib/Common/Make.mm, lib/Common/Nodal_mesh.c,
	  lib/Common/Obsolete.c, lib/Common/Output.c,
	  lib/Common/Pan_problem_misc_functions.c, lib/Common/Parsing.c,
	  lib/Common/Phase_change.c, lib/Common/Problem_related.c,
	  lib/Common/Process_buoyancy.c, lib/Common/Shape_functions.c,
	  lib/Common/Size_does_matter.c, lib/Common/Solver_conj_grad.c,
	  lib/Common/Solver_multigrid.c, lib/Common/Sphere_harmonics.c,
	  lib/Common/Stokes_flow_Incomp.c, lib/Common/Topo_gravity.c,
	  lib/Common/Tracer_advection.c, lib/Common/Viscosity_structures.c,
	  lib/Common/advection.h, lib/Common/advection_diffusion.h,
	  lib/Common/citcom_init.h, lib/Common/convection_variables.h,
	  lib/Common/drive_solvers.h, lib/Common/element_definitions.h,
	  lib/Common/global_defs.h, lib/Common/initial_temperature.h,
	  lib/Common/interuption.h, lib/Common/lith_age.h,
	  lib/Common/local.def, lib/Common/output.h,
	  lib/Common/parallel_related.h, lib/Common/parsing.h,
	  lib/Common/phase_change.h, lib/Common/sphere_communication.h,
	  lib/Common/temperature_descriptions.h, lib/Common/tracer_defs.h,
	  lib/Common/viscosity_descriptions.h,
	  lib/Full/Boundary_conditions.c, lib/Full/Geometry_cartesian.c,
	  lib/Full/Lith_age.c, lib/Full/Make.mm, lib/Full/Obsolete.c,
	  lib/Full/Parallel_related.c, lib/Full/Read_input_from_files.c,
	  lib/Full/Sphere_related.c, lib/Full/Version_dependent.c,
	  lib/Full/local.def, lib/Make.mm,
	  lib/Regional/Boundary_conditions.c,
	  lib/Regional/Geometry_cartesian.c, lib/Regional/Lith_age.c,
	  lib/Regional/Make.mm, lib/Regional/Obsolete.c,
	  lib/Regional/Parallel_related.c,
	  lib/Regional/Read_input_from_files.c,
	  lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c,
	  lib/Regional/local.def, lib/local.def, module/Full/Fullmodule.cc,
	  module/Full/Make.mm, module/Full/local.def, module/Make.mm,
	  module/Regional/Make.mm, module/Regional/Regionalmodule.cc,
	  module/Regional/advdiffu.cc, module/Regional/advdiffu.h,
	  module/Regional/bindings.cc, module/Regional/bindings.h,
	  module/Regional/exceptions.cc, module/Regional/exceptions.h,
	  module/Regional/initial_conditions.cc,
	  module/Regional/initial_conditions.h, module/Regional/local.def,
	  module/Regional/mesher.cc, module/Regional/mesher.h,
	  module/Regional/misc.cc, module/Regional/misc.h,
	  module/Regional/outputs.cc, module/Regional/outputs.h,
	  module/Regional/setProperties.cc,
	  module/Regional/setProperties.h,
	  module/Regional/stokes_solver.cc,
	  module/Regional/stokes_solver.h,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/Advection_diffusion/Make.mm,
	  pyre/Components/Advection_diffusion/__init__.py,
	  pyre/Components/BC.py, pyre/Components/CitcomComponent.py,
	  pyre/Components/Const.py,
	  pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  pyre/Components/Exchanger/Inlet.py,
	  pyre/Components/Exchanger/Make.mm,
	  pyre/Components/Exchanger/Outlet.py,
	  pyre/Components/Exchanger/__init__.py, pyre/Components/IC.py,
	  pyre/Components/Make.mm, pyre/Components/Param.py,
	  pyre/Components/Phase.py, pyre/Components/Sphere/FullSphere.py,
	  pyre/Components/Sphere/Make.mm,
	  pyre/Components/Sphere/RegionalSphere.py,
	  pyre/Components/Sphere/Sphere.py,
	  pyre/Components/Sphere/__init__.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Stokes_solver/Make.mm,
	  pyre/Components/Stokes_solver/__init__.py,
	  pyre/Components/Tracer.py, pyre/Components/Visc.py,
	  pyre/Components/__init__.py, pyre/Controller.py,
	  pyre/CoupledApp.py, pyre/Coupler.py, pyre/Facilities/Make.mm,
	  pyre/Facilities/Mesher.py, pyre/Facilities/Solver.py,
	  pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py,
	  pyre/Facilities/__init__.py, pyre/Layout.py, pyre/Make.mm,
	  pyre/SimpleApp.py, pyre/Solver/FullSolver.py,
	  pyre/Solver/Make.mm, pyre/Solver/RegionalSolver.py,
	  pyre/Solver/Solver.py, pyre/Solver/__init__.py, pyre/__init__.py,
	  pyre/local.def, tests/Make.mm, tests/array2d.cc, tests/asap.py,
	  tests/citcomsfull.sh, tests/citcomsregional.sh,
	  tests/coupledcitcoms.sh, tests/exchange.py, tests/hrothgar.py,
	  tests/local.def, tests/signon.py, tests/test1.sh, tests/test2.sh,
	  tests/test5.sh, visual/batchcombine.py, visual/batchpaste.sh,
	  visual/batchsurf.py, visual/combine.py, visual/combinesurf.py,
	  visual/dxgeneral.sh, visual/dxgeneralsurf.sh, visual/getcoord.sh,
	  visual/getlog.sh, visual/getsurf.sh, visual/parser.py,
	  visual/pasteCitcomData.sh, visual/zslice.py: Added license text.

2005-06-08 11:02  tan2

	* examples/Cookbook5/cookbook5.sh: 1. subsitute 'staging' with
	  'launcher' as required by pythia-0.8 2. removed unneccesary input
	  parameters

2005-06-08 08:55  leif

	* pyre/CoupledApp.py, pyre/SimpleApp.py, pyre/Solver/FullSolver.py,
	  pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: Port from
	  pythia-0.4 to pythia-0.8, continued: use "factory=" instead of
	  "default=" in facilities where appropriate. The scripts
	  example1.sh and test5.sh seem to work now.

2005-06-06 06:41  tan2

	* visual/parser.py: Parser class to parse CitcomS input file

2005-06-06 06:13  tan2

	* visual/batchpaste.sh: execute 'cmd_copy' only if 'cmd_paste' was
	  finished without error

2005-06-04 04:51  leif

	* Make.mm, etc, etc/Make.mm, etc/__vault__.odb,
	  etc/full-sphere.odb, etc/full.odb, etc/incomp-newtonian.odb,
	  etc/incomp-non-newtonian.odb, etc/regional-sphere.odb,
	  etc/regional.odb, etc/temp.odb, examples/Cookbook1/cookbook1.sh,
	  examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
	  examples/Cookbook4/cookbook4.sh, examples/Cookbook7/cookbook7.sh,
	  examples/example1.sh, module/Exchanger/AreaWeightedNormal.cc,
	  module/Exchanger/Boundary.cc,
	  module/Exchanger/CitcomInterpolator.cc,
	  module/Exchanger/CitcomSource.cc, module/Exchanger/Convertor.cc,
	  module/Exchanger/Interior.cc, module/Exchanger/Make.mm,
	  module/Exchanger/SInlet.cc, module/Exchanger/SVTInlet.cc,
	  module/Exchanger/SVTOutlet.cc, module/Exchanger/TInlet.cc,
	  module/Exchanger/TOutlet.cc, module/Exchanger/VOutlet.cc,
	  module/Exchanger/VTInlet.cc, module/Exchanger/VTOutlet.cc,
	  module/Exchanger/initTemperature.cc, module/Full/Make.mm,
	  module/Regional/Make.mm,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/BC.py, pyre/Components/Const.py,
	  pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  pyre/Components/IC.py, pyre/Components/Param.py,
	  pyre/Components/Phase.py,
	  pyre/Components/Sphere/RegionalSphere.py,
	  pyre/Components/Sphere/Sphere.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Tracer.py, pyre/Components/Visc.py,
	  pyre/Controller.py, pyre/CoupledApp.py,
	  pyre/Facilities/Mesher.py, pyre/Facilities/Solver.py,
	  pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py,
	  pyre/Layout.py, pyre/SimpleApp.py, pyre/Solver/FullSolver.py,
	  pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py,
	  tests/exchange.py, tests/test1.sh, tests/test2.sh,
	  tests/test5.sh: Initial port from pythia-0.4 to pythia-0.8.

2005-05-28 12:27  ces74

	* lib/Regional/Version_dependent.c,
	  module/Regional/setProperties.cc, pyre/Components/IC.py: * If a
	  user doesn't specify "blob_center", assign [-999.,-999.,-999] as
	  a default values in IC.py. * The real default values are assigned
	  in setProperties.cc * The distance calculation in
	  "construct_tic_from_input" modified. * A bug in
	  non-dimensionalizing half_space_age fixed.

2005-05-28 04:41  vlad

	* examples/example1.sh: *** empty log message ***

2005-05-28 04:11  gurnis

	* examples/Cookbook1/cookbook1.sh: *** empty log message ***

2005-05-28 01:39  vlad

	* examples/Cookbook5/velocity,
	  examples/Cookbook5/velocity/bvel.dat0,
	  examples/Cookbook5/velocity/bvel.dat1,
	  examples/Cookbook5/velocity/bvel.dat10,
	  examples/Cookbook5/velocity/bvel.dat11,
	  examples/Cookbook5/velocity/bvel.dat12,
	  examples/Cookbook5/velocity/bvel.dat13,
	  examples/Cookbook5/velocity/bvel.dat14,
	  examples/Cookbook5/velocity/bvel.dat15,
	  examples/Cookbook5/velocity/bvel.dat16,
	  examples/Cookbook5/velocity/bvel.dat17,
	  examples/Cookbook5/velocity/bvel.dat18,
	  examples/Cookbook5/velocity/bvel.dat19,
	  examples/Cookbook5/velocity/bvel.dat2,
	  examples/Cookbook5/velocity/bvel.dat20,
	  examples/Cookbook5/velocity/bvel.dat21,
	  examples/Cookbook5/velocity/bvel.dat22,
	  examples/Cookbook5/velocity/bvel.dat23,
	  examples/Cookbook5/velocity/bvel.dat24,
	  examples/Cookbook5/velocity/bvel.dat25,
	  examples/Cookbook5/velocity/bvel.dat26,
	  examples/Cookbook5/velocity/bvel.dat27,
	  examples/Cookbook5/velocity/bvel.dat28,
	  examples/Cookbook5/velocity/bvel.dat29,
	  examples/Cookbook5/velocity/bvel.dat3,
	  examples/Cookbook5/velocity/bvel.dat30,
	  examples/Cookbook5/velocity/bvel.dat31,
	  examples/Cookbook5/velocity/bvel.dat32,
	  examples/Cookbook5/velocity/bvel.dat33,
	  examples/Cookbook5/velocity/bvel.dat34,
	  examples/Cookbook5/velocity/bvel.dat35,
	  examples/Cookbook5/velocity/bvel.dat36,
	  examples/Cookbook5/velocity/bvel.dat37,
	  examples/Cookbook5/velocity/bvel.dat38,
	  examples/Cookbook5/velocity/bvel.dat39,
	  examples/Cookbook5/velocity/bvel.dat4,
	  examples/Cookbook5/velocity/bvel.dat40,
	  examples/Cookbook5/velocity/bvel.dat41,
	  examples/Cookbook5/velocity/bvel.dat42,
	  examples/Cookbook5/velocity/bvel.dat43,
	  examples/Cookbook5/velocity/bvel.dat44,
	  examples/Cookbook5/velocity/bvel.dat45,
	  examples/Cookbook5/velocity/bvel.dat46,
	  examples/Cookbook5/velocity/bvel.dat47,
	  examples/Cookbook5/velocity/bvel.dat48,
	  examples/Cookbook5/velocity/bvel.dat49,
	  examples/Cookbook5/velocity/bvel.dat5,
	  examples/Cookbook5/velocity/bvel.dat50,
	  examples/Cookbook5/velocity/bvel.dat51,
	  examples/Cookbook5/velocity/bvel.dat52,
	  examples/Cookbook5/velocity/bvel.dat53,
	  examples/Cookbook5/velocity/bvel.dat54,
	  examples/Cookbook5/velocity/bvel.dat55,
	  examples/Cookbook5/velocity/bvel.dat56,
	  examples/Cookbook5/velocity/bvel.dat57,
	  examples/Cookbook5/velocity/bvel.dat58,
	  examples/Cookbook5/velocity/bvel.dat59,
	  examples/Cookbook5/velocity/bvel.dat6,
	  examples/Cookbook5/velocity/bvel.dat60,
	  examples/Cookbook5/velocity/bvel.dat61,
	  examples/Cookbook5/velocity/bvel.dat62,
	  examples/Cookbook5/velocity/bvel.dat63,
	  examples/Cookbook5/velocity/bvel.dat64,
	  examples/Cookbook5/velocity/bvel.dat65,
	  examples/Cookbook5/velocity/bvel.dat66,
	  examples/Cookbook5/velocity/bvel.dat67,
	  examples/Cookbook5/velocity/bvel.dat68,
	  examples/Cookbook5/velocity/bvel.dat69,
	  examples/Cookbook5/velocity/bvel.dat7,
	  examples/Cookbook5/velocity/bvel.dat70,
	  examples/Cookbook5/velocity/bvel.dat71,
	  examples/Cookbook5/velocity/bvel.dat8,
	  examples/Cookbook5/velocity/bvel.dat9: Velocity files

2005-05-28 01:38  vlad

	* examples/Cookbook5/restart_files,
	  examples/Cookbook5/restart_files/cookbook5.velo.0.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.1.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.10.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.11.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.12.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.13.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.14.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.15.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.16.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.17.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.18.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.19.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.2.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.20.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.21.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.22.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.23.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.24.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.25.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.26.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.27.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.28.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.29.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.3.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.30.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.31.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.32.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.33.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.34.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.35.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.36.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.37.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.38.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.39.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.4.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.40.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.41.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.42.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.43.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.44.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.45.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.46.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.47.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.48.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.49.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.5.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.50.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.51.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.52.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.53.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.54.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.55.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.56.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.57.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.58.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.59.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.6.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.60.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.61.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.62.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.63.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.7.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.8.0,
	  examples/Cookbook5/restart_files/cookbook5.velo.9.0: Restart
	  files

2005-05-28 01:35  vlad

	* examples/Cookbook5, examples/Cookbook5/cookbook5.sh,
	  examples/Cookbook5/coor.dat: Cookbook5 and coordinate files

2005-05-25 08:22  tan2

	* visual/zslice.py: changed the hard-wire path (/usr/bin/python) to
	  run-time dep. path

2005-05-25 04:28  tan2

	* visual/zslice.py: a utility script to slize horizontal layers
	  from CitcomS output. See docstring for usage.

2005-05-25 01:12  leif

	* module/Make.mm: Prefer "$(MM)" to "mm".

2005-05-24 05:15  ces74

	* examples/Cookbook7, examples/Cookbook7/README,
	  examples/Cookbook7/cookbook7.sh, examples/Cookbook7/coord.dat: *
	  adding a script to run the Cookbook7 example and coord.dat file.
	  * README for some additional information.

2005-05-24 05:00  ces74

	* lib/Common/Initial_temperature.c,
	  lib/Common/convection_variables.h, lib/Regional/Sphere_related.c,
	  lib/Regional/Version_dependent.c,
	  module/Regional/setProperties.cc, pyre/Components/IC.py: * added
	  new parameters to control a hot blob as temperature IC. - One can
	  specify three parameters: 1. Coordinates(theta,fi,r) of the
	  center. 2. Radius. 3. The amount of temperature increase/decrease
	  within the blob. - Currently works only for the Regional version.
	  
	  - CitcomS variable name: convection.blob_center,
	  convection.blob_radius, convection.blob_dT - Pyre parameter name:
	  solver.ic.blob_center, solver.ic.blob_radius, solver.ic.blob_dT
	  
	  - it is required to set "solver.ic.tic_method=2"
	  
	  * the format of coordinates file has been modified. - "nsd=1" is
	  not recognized as "%s%d" on some machine. - now it should be
	  "nsd= 1" to be read as "%s %d".

2005-05-20 05:39  leif

	* module/Exchanger/CitcomInterpolator.cc,
	  module/Exchanger/global_bbox.cc,
	  module/Regional/setProperties.cc: Include <cmath> in various
	  files. Fixes compilation errors with GCC v3.4.3.

2005-05-20 05:01  ces74

	* module/Exchanger/initTemperature.cc: * added a new function for
	  the initial temperature field. - called "hot_blob_lith" - Thermal
	  boudnary layer on top + one hot bloc at the center.

2005-05-19 01:27  leif

	* lib/Regional/Boundary_conditions.c: Added a prototype for
	  temperatures_conform_bcs() -- fixes compilation failure with GCC
	  v3.4.3.

2005-05-18 08:57  tan2

	* tests/test5.sh: test for coupled run

2005-05-18 03:54  tan2

	* module/Exchanger/Make.mm: using rpath to specify runtime library
	  path

2005-05-18 02:45  tan2

	* module/Full/Make.mm, module/Regional/Make.mm: using rpath to
	  specify runtime library path

2005-05-17 07:35  tan2

	* module/Full/Make.mm, module/Regional/Make.mm: the full path of
	  shared library is given, otherwise g++ can compile but the
	  program couldn't find the shared library at the run time

2005-05-17 06:53  vlad

	* lib/Common/Output.c, lib/Common/Tracer_advection.c,
	  lib/Common/tracer_defs.h: 3D MPI tracer-advection code

2005-04-11 19:09  steve

	* lib/Common/Make.mm, lib/Full/Make.mm, lib/Regional/Make.mm:
	  facelifted to work with new "config" repository (cvs -d
	  :pserver:config@cvs.cacr.caltech.edu:/config co config).
	  
	  I think this will still work with the old config... Eh you may
	  want to check.

2005-03-30 10:34  vlad

	* lib/Common/Output.c, lib/Common/Tracer_advection.c,
	  lib/Common/tracer_defs.h: *** empty log message ***

2005-03-30 10:27  vlad

	* lib/Common/Output.c, lib/Common/Tracer_advection.c,
	  lib/Common/tracer_defs.h: *** empty log message ***

2005-03-11 12:23  steve

	* module/Exchanger/Make.mm: Added EXCHANGER_INCDIR and
	  EXCHANGER_LIBDIR, as in my case, I do not build exchanger into
	  either pythia's or citcom's build root (but into its own)

2005-03-11 08:24  vlad

	* lib/Common/Output.c, lib/Common/Phase_change.c: *** empty log
	  message ***

2005-03-09 06:24  vlad

	* lib/Common/Tracer_advection.c: The tracer code only works in root
	  processor

2005-02-18 08:13  tan2

	* pyre/Components/IC.py: fixed a bug in the validator of
	  'tic_method'

2005-02-18 07:15  tan2

	* module/Regional/setProperties.cc: added new parameter
	  'tic_method' and 'half_space_age'

2005-02-18 06:57  tan2

	* pyre/Components/IC.py: 1. added validator to some of the input.
	  2. added new parameter 'tic_method' and 'half_space_age'.

2005-02-18 06:14  tan2

	* lib/Full/Version_dependent.c, lib/Regional/Version_dependent.c:
	  implementation of cooling plate temperature is pending.

2005-02-18 06:12  tan2

	* lib/Common/Initial_temperature.c,
	  lib/Common/convection_variables.h: Added new input parameter:
	  tic_method. When it is 0 (default), the temperature is a linear
	  profile + perturbation at some layers. When it is 1, the
	  temperature is isothermal (== bottom b.c.) + uniformly cold plate
	  (thickness specified by 'half_space_age').

2005-02-05 02:51  ces74

	* module/Exchanger/SInlet.cc, module/Exchanger/SInlet.h,
	  module/Exchanger/bindings.cc, module/Exchanger/inlets_outlets.cc,
	  module/Exchanger/inlets_outlets.h: * bindings for the SInlet
	  class added. * setSBCFlag() method added to SInlet.

2005-02-03 05:49  tan2

	* module/Exchanger/Boundary.cc: fixed a bug in finding boundary
	  nodes and rearraged code

2005-01-29 08:23  ces74

	* pyre/Components/Exchanger/Inlet.py: * SInlet class added

2005-01-29 08:15  ces74

	* module/Exchanger/Make.mm, module/Exchanger/SIUnit.cc,
	  module/Exchanger/SInlet.cc, module/Exchanger/SInlet.h: * added a
	  new class SInlet to receive stress from the coupled solver. *
	  "stress_factor" defined in SIUnit.cc

2005-01-29 03:20  tan2

	* module/Exchanger/Make.mm: removed redudant include and library
	  path. PYTHIA_INCDIR and PYTHIA_LIBDIR must be defined.

2005-01-27 06:10  tan2

	* lib/Common/Tracer_advection.c: removed tracer_output(), which is
	  replaced by output_tracer() in Output.c

2005-01-27 06:05  tan2

	* drivers/Citcom.c: removed calls to tracer_output(), which is
	  replaced by output_tracer() in Output.c

2005-01-26 07:01  ces74

	* lib/Common/Instructions.c: * removed a useless block of code

2005-01-26 04:05  tan2

	* lib/Common/Tracer_advection.c: 1. Commented out part of the code
	  that use itcolor, which is the starting age of the tracer. 2.
	  Added a few comments about the code. This should help people to
	  read the code.

2005-01-24 05:20  tan2

	* pyre/Components/Exchanger/Exchanger.py: commented out debugging
	  output

2005-01-21 06:29  tan2

	* module/Regional/setProperties.cc, pyre/Components/Param.py:
	  removed 'tracer' and 'tracer_file' properties from Param class
	  (these properties are moved to Tracer class)

2005-01-21 06:25  tan2

	* pyre/Components/Visc.py: fixed a bug in reading viscZ property

2005-01-20 03:02  ces74

	* pyre/Components/BC.py: * A BC property, "pseudo_free_surf",
	  added. Its default value is False.

2005-01-20 02:55  tan2

	* module/Regional/setProperties.cc, pyre/Components/Visc.py: added
	  new properties visc.viscZ and visc.rheol

2005-01-20 02:35  vlad

	* lib/Common/Viscosity_structures.c: a new viscosity law was added
	  (case 4)

2005-01-19 10:19  tan2

	* lib/Common/Output.c: added function output_tracer()

2005-01-19 10:02  tan2

	* pyre/Components/Tracer.py, pyre/Solver/Solver.py: added Tracer
	  module into Solver

2005-01-19 10:01  tan2

	* module/Regional/bindings.cc, module/Regional/misc.cc,
	  module/Regional/misc.h: added binding to tracer_advection()

2005-01-19 09:05  tan2

	* module/Regional/bindings.cc, module/Regional/setProperties.cc,
	  module/Regional/setProperties.h: added bindings to tracer input

2005-01-19 08:57  tan2

	* pyre/Components/Make.mm: added Tracer.py to file list

2005-01-19 08:44  tan2

	* pyre/Components/Tracer.py: added Tracer module

2005-01-19 08:43  tan2

	* lib/Common/Tracer_advection.c: changed the default value of
	  E->control.tracer_file

2005-01-19 08:38  tan2

	* module/Regional/mesher.cc: modified according to changes in
	  lib/Common/Instructions.c (add tracer module)

2005-01-19 08:36  tan2

	* lib/Common/Instructions.c: fixed a syntax error

2005-01-19 08:35  tan2

	* lib/Common/Instructions.c, lib/Common/Tracer_advection.c: 1.
	  moved input of tracer-related parameters to tracer_input() 2.
	  changed where tracer_initial_settings() is called

2005-01-19 07:19  tan2

	* lib/Common/global_defs.h: fixed a problem in function pointer
	  declaration

2005-01-19 07:19  tan2

	* drivers/Citcom.c: uncommented tracer module

2005-01-19 06:30  vlad

	* examples/Cookbook4, examples/Cookbook4/cookbook4.sh,
	  examples/Cookbook4/coor.dat: new cookbook with a refined mesh

2005-01-19 06:24  tan2

	* tests/signon.py: *** empty log message ***

2005-01-08 11:24  ces74

	* lib/Common/Element_calculations.c: * removed unnecessary
	  debugging output from get_elt_tr()

2005-01-08 11:20  ces74

	* module/Regional/bindings.cc, module/Regional/outputs.cc,
	  module/Regional/outputs.h, module/Regional/stokes_solver.cc,
	  module/Regional/stokes_solver.h: * call Citcom's functions in
	  output, general_stokes_solver, respectively, instead of creating
	  pseudo_surf bindings for each

2005-01-08 11:02  ces74

	* module/Regional/bindings.cc, module/Regional/outputs.cc,
	  module/Regional/outputs.h, module/Regional/setProperties.cc,
	  module/Regional/stokes_solver.cc,
	  module/Regional/stokes_solver.h: * added bindings for new
	  functions for the "pseudo free surface" formulation

2005-01-08 10:57  ces74

	* lib/Common/Instructions.c: * always assign memory for free_surf
	  and Vprev for now. - in the future, need to save memory when
	  pseudo_free_surf is off.

2005-01-08 10:16  ces74

	* drivers/Citcom.c: * modified to enable the "pseudo free surface"
	  mode.

2005-01-08 10:15  ces74

	* lib/Common/Drive_solvers.c, lib/Common/Element_calculations.c,
	  lib/Common/Instructions.c, lib/Common/Output.c,
	  lib/Common/Stokes_flow_Incomp.c, lib/Common/Topo_gravity.c,
	  lib/Common/global_defs.h, lib/Common/output.h: * functions added
	  to track pseudo free surface and compute normal traction from it.

2005-01-05 06:58  tan2

	* module/Exchanger/SVTInlet.cc: removed the declaration of my_tbc()

2005-01-05 06:57  tan2

	* module/Exchanger/SVTInlet.cc: 1. uncommented the journal output
	  2. removed codes about 'upwind bc', as it is proved not accurate.
	  3. removed a call to my_tbc(), which is specific to my Hawaii
	  plume model and sliped through the repository

2005-01-01 03:00  tan2

	* lib/Common/Advection_diffusion.c, lib/Common/Convection.c: move
	  parameter input from Convection.c to Advection_diffusion.c

2004-12-31 09:03  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: fixed
	  a bug when nprocz>1 and excludeTop or/add excludeBottom is turned
	  on

2004-12-28 09:38  tan2

	* module/Exchanger/Boundary.cc: fixed a bug, which causes some
	  nodes being excluded from Boundary when excludeTop or
	  excludeBottom are turned off

2004-12-28 03:49  tan2

	* visual/combine.py: renamed some variables and changed the
	  doc_string

2004-12-03 04:23  tan2

	* pyre/CoupledApp.py, pyre/SimpleApp.py: 1. In findLayput(), assing
	  self.controller 2. In CoupledApp, two controllers are created.
	  So, two controllers can have different output interval
	  (monitoringFrequency).

2004-11-25 05:47  ces74

	* lib/Common/Advection_diffusion.c, lib/Common/Instructions.c,
	  lib/Common/global_defs.h, module/Regional/setProperties.cc,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py: * a
	  new parameter, "filter_temperature" created as a memeber of the
	  "Control" structure. - if it's 1, the function filter() is called
	  to reduce artifical diffusioin. - it's 1 by default.
	  
	  * The command line option for this parameter is "filter_temp" -
	  it belongs to the "Advection_diffusion" class, which is
	  instantiated as "tsolver" in Solver.py. - Usage:
	  --solver.tsolver.filter_temp=True/False

2004-11-16 19:43  steve

	* module/Exchanger/Make.mm, module/Full/Make.mm,
	  module/Regional/Make.mm: made where to find pyre, etc a little
	  more generic

2004-11-09 07:21  ces74

	* visual/miff2avi, visual/miff2mpg: * added appropriate credits for
	  these scripts.

2004-11-07 08:41  ces74

	* visual/miff2avi, visual/miff2mpg: * scripts to make a movie out
	  of images generated by OpenDX -- mjpeg tools are necessary to
	  run.

2004-10-08 07:28  tan2

	* pyre/Solver/Solver.py: don't use exchanger.initTemperature() when
	  restart (use disk file for IC)

2004-10-08 07:25  tan2

	* lib/Common/Process_buoyancy.c: disable writing out surface hear
	  flux information, for processor on the surface usually don't have
	  E->fp ready to use.

2004-10-08 07:21  tan2

	* lib/Common/Construct_arrays.c: get_bcs_id_for_residual() is
	  version independent. Move from Boundary_conditions.c to
	  Common/Construct_arrays.c

2004-10-08 07:20  tan2

	* lib/Common/global_defs.h: temperatures_conform_bcs() is version
	  (Full/Regional) dependent. Make a function pointer for it.

2004-10-08 07:18  tan2

	* lib/Full/Boundary_conditions.c,
	  lib/Regional/Boundary_conditions.c: 1. temperatures_conform_bcs()
	  is version (Full/Regional) dependent. Make a function pointer for
	  it. 2. get_bcs_id_for_residual() is version independent. Move to
	  Common/Construct_arrays.c

2004-10-08 07:11  tan2

	* module/Exchanger/SVTInlet.cc, module/Exchanger/TInlet.cc,
	  module/Exchanger/VTInlet.cc, module/Exchanger/initTemperature.cc:
	  1. temperatures_conform_bcs() is version (Full/Regional)
	  dependent. Make a function pointer for it. 2. in
	  initTemperature.cc, add several new functions of different IC.

2004-10-08 07:08  tan2

	* module/Exchanger/Boundary.cc: 1. fixed a bug: normalFlag was not
	  init'd correctly 2. when excludeBottom is true, bottome edge
	  nodes are still included

2004-09-23 04:31  ces74

	* visual/OpenDXMacro/CitcomSSurfaceHeatflux.net,
	  visual/OpenDXMacro/CitcomSSurfaceImport.net,
	  visual/OpenDXMacro/CitcomSSurfaceTopo.net,
	  visual/OpenDXMacro/CitcomSSurfaceVelocity.net,
	  visual/OpenDXMacro/RTFtoXYZ2D.net,
	  visual/OpenDXMacro/VelocityRTFtoXYZ2D.net,
	  visual/visRegionalSurface.cfg, visual/visRegionalSurface.net: *
	  OpenDX macros and a new visual program for surface data.

2004-09-22 07:16  ces74

	* visual/combinesurf.py: * fixed a bug related to the loop over the
	  surface procs for each cap.

2004-09-22 06:44  ces74

	* visual/batchsurf.py, visual/getcoord.sh: * fixed bugs related to
	  generating a list of surface processors.

2004-08-10 07:22  tan2

	* lib/Common/Initial_temperature.c: Print restart filename to
	  logfile

2004-08-08 05:08  tan2

	* pyre/Components/Exchanger/Exchanger.py, pyre/Controller.py,
	  pyre/Coupler.py, pyre/Solver/Solver.py: Synchronized when to save
	  the result. During a coupled run, when one solver saves the
	  result, the other solver will save too.

2004-08-07 06:25  tan2

	* visual/batchsurf.py: the 1st argument can be either the name of
	  machine file or a quoted machine list(eg. 'n101 n102').

2004-08-07 06:24  tan2

	* visual/combinesurf.py: fixed quite a few bugs. this script is
	  working correctly.

2004-08-07 05:47  tan2

	* pyre/Components/Exchanger/FineGridExchanger.py: VTOutlet was used
	  in creatII, TOutlet is used now.

2004-08-07 03:22  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py: nailed down a
	  big bug. VTInlet was used in creatII, which set temperature bc
	  flag for all interior nodes. TInlet is used now.

2004-08-05 01:29  tan2

	* visual/OpenDXMacro/CitcomSFullImport.net: fixed a bug which
	  incorrectly set cap_start=0

2004-08-04 03:11  tan2

	* module/Regional/setProperties.cc, pyre/Components/Const.py:
	  changed the units of depth parameters to be nondimensional, so
	  that they are consistent with original CitcomS input format

2004-08-02 23:34  ces74

	* pyre/Components/Stokes_solver/Incompressible.py: * some
	  parameters that were hardwired can have user-defined values now.

2004-07-29 00:39  tan2

	* visual/visFull.cfg, visual/visFull.net, visual/visRegional.cfg,
	  visual/visRegional.net: * use the same colormap for temperature
	  cross-section and isosurfaces.

2004-07-28 01:19  tan2

	* module/Exchanger/AreaWeightedNormal.cc,
	  module/Exchanger/AreaWeightedNormal.h: * Change of
	  implementation. Now the weighted normal vectors are taken from
	  CitcomS' internal data (from boundary determinant
	  E->boundary.det, this array has been throughly tested), no needto
	  compute them again. Havn't tested.

2004-07-28 01:14  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: *
	  Fixed a problem in initBBox(). It used to returned a tight
	  boundingbox. So, when excludeTop or excludeBottom is set, the
	  outer and inner radii are not the correct outer and inner radii
	  of the mesh. This can cause confusion and problem in other part
	  of program. * Added a new attribute, bnode. It is the index
	  mapping from CitcomS' node # to Boundary's node #.

2004-07-27 06:56  tan2

	* visual/batchcombine.py: * the 1st argument can be either the name
	  of machine file or a quoted machine list(eg. 'n101 n102'). *
	  modified the doc string

2004-07-09 01:15  tan2

	* lib/Common/Problem_related.c, lib/Full/Lith_age.c,
	  lib/Full/Read_input_from_files.c, lib/Regional/Lith_age.c,
	  lib/Regional/Read_input_from_files.c: Previousely, CitcomS would
	  abort running when age < -1 Ma. This behavior is not desirable.
	  The following fixes change the behavior so that CitcomS will
	  assume age=0 when time has passed present day.
	  
	  1. find_age_in_MY() returns negative age when time has passed
	  present day 2. changed how age is manipulated before reading
	  age-dependet files

2004-07-06 13:32  patrick

	* doc/CitComS.doxyconf, doc/Exchanger.doxyconf: * Renamed
	  Exchanger.doxyconf to CitComS.doxyconf * Set the tags to work
	  properly

2004-07-03 03:47  tan2

	* module/Exchanger/global_bbox.cc: Fixed a bug in
	  fullGlobalBoundedBox(). The first and second dimension of bbox
	  are swapped. This bug makes the interpolator skip some nodes.

2004-06-30 03:25  tan2

	* examples/Cookbook3, examples/Cookbook3/cookbook3.sh: example of
	  temperature-dependent viscosity

2004-06-30 00:25  tan2

	* examples/Cookbook1, examples/Cookbook1/cookbook1.sh,
	  examples/Cookbook2, examples/Cookbook2/cookbook2.sh,
	  examples/example1.sh: more example scripts

2004-06-29 06:04  tan2

	* tests/.cvsignore: tell cvs to ignore output files of test scripts

2004-06-29 05:58  tan2

	* lib/Full/Lith_age.c, lib/Regional/Lith_age.c: calling
	  temperatures_conform_bcs() after init'ed restarted temperature
	  field

2004-06-29 05:29  tan2

	* lib/Full/Lith_age.c: similar changes as in Regional/Lith_age.c

2004-06-29 04:20  tan2

	* lib/Regional/Lith_age.c: 1. fix a bug when init'ing temperature
	  2. read lith_age_file in lith_age_init()

2004-06-29 02:56  tan2

	* drivers/Full/Make.mm, drivers/Regional/Make.mm: changed export
	  rule so that mm will create symbolic links of binary executables
	  in $EXPORT_ROOT/bin

2004-06-29 02:54  tan2

	* module/Regional/mesher.cc: calling lith_age_init() in
	  mehser_init()

2004-06-29 02:53  tan2

	* lib/Common/Instructions.c, lib/Common/lith_age.h,
	  lib/Regional/Lith_age.c: 1. moved initialization of lith_age to
	  lith_age_init() 2. calling lith_age_init() in read_instructions()

2004-06-29 02:49  tan2

	* lib/Regional/Boundary_conditions.c: called
	  temperatures_conform_bcs() after setting tbc

2004-06-29 01:36  tan2

	* lib/Common/Pan_problem_misc_functions.c: bug fix

2004-06-29 01:10  tan2

	* examples/example1.sh: typos fixed

2004-06-27 08:04  tan2

	* module/Regional/initial_conditions.cc: enable lith_age support

2004-06-27 08:03  tan2

	* lib/Regional/Lith_age.c: fixed a 'access unallocated memory' bug

2004-06-27 07:59  tan2

	* lib/Common/Initial_temperature.c,
	  lib/Common/initial_temperature.h: added declaration of
	  restart_tic() and restart_tic() in header

2004-06-26 03:06  tan2

	* visual/visFull.cfg, visual/visFull.net: 1. show (reduced) surface
	  grid 2. make rotating the Plane easier

2004-06-26 01:50  tan2

	* visual/visFull.cfg, visual/visFull.net: new OpenDX network for
	  CitcomS Full

2004-06-26 01:49  tan2

	* visual/visRegional.cfg, visual/visRegional.net: 1. import
	  viscosity 2. changed names of transmitters/receivers

2004-06-26 01:48  tan2

	* visual/OpenDXMacro/CitcomSFullImport.net,
	  visual/OpenDXMacro/CitcomSImport.net,
	  visual/OpenDXMacro/CitcomSViscosity.net: added viscosity import

2004-06-26 01:28  tan2

	* visual/samples/fulltest.cap0.0,
	  visual/samples/fulltest.cap0.0.general,
	  visual/samples/fulltest.cap1.0,
	  visual/samples/fulltest.cap1.0.general,
	  visual/samples/fulltest.cap10.0,
	  visual/samples/fulltest.cap10.0.general,
	  visual/samples/fulltest.cap11.0,
	  visual/samples/fulltest.cap11.0.general,
	  visual/samples/fulltest.cap2.0,
	  visual/samples/fulltest.cap2.0.general,
	  visual/samples/fulltest.cap3.0,
	  visual/samples/fulltest.cap3.0.general,
	  visual/samples/fulltest.cap4.0,
	  visual/samples/fulltest.cap4.0.general,
	  visual/samples/fulltest.cap5.0,
	  visual/samples/fulltest.cap5.0.general,
	  visual/samples/fulltest.cap6.0,
	  visual/samples/fulltest.cap6.0.general,
	  visual/samples/fulltest.cap7.0,
	  visual/samples/fulltest.cap7.0.general,
	  visual/samples/fulltest.cap8.0,
	  visual/samples/fulltest.cap8.0.general,
	  visual/samples/fulltest.cap9.0,
	  visual/samples/fulltest.cap9.0.general: added sample data file of
	  CitcomS Full

2004-06-25 02:38  tan2

	* examples/example1.sh: first example for Cookbook

2005-08-23 03:32  unknown_user

	* examples/Full/Make.mm, examples/Full/local.def, examples/Make.mm,
	  examples/Regional/Make.mm, examples/Regional/local.def,
	  examples/local.def: [vcp] delete of edited revision with dead
	  state

2004-06-25 02:31  tan2

	* Make.mm, examples/Full/Make.mm, examples/Full/local.def,
	  examples/Make.mm, examples/Regional/Make.mm,
	  examples/Regional/local.def, examples/local.def: removed
	  makefiles in examples/

2004-06-25 02:26  tan2

	* pyre/Solver/Solver.py: new default value for Rayleight number

2004-06-25 02:25  tan2

	* pyre/Components/Sphere/RegionalSphere.py: new default values for
	  domain size

2004-06-25 02:24  tan2

	* pyre/Components/IC.py: new default values, number of initial
	  temperature perturbation is default to 1, perturbl and perturbm
	  to 1, perturblayer to 5.

2004-06-12 03:14  tan2

	* module/Exchanger/Make.mm, module/Full/Make.mm,
	  module/Regional/Make.mm: modified library and include pathes

2004-06-11 06:07  tan2

	* visual/visRegional.cfg, visual/visRegional.net: 1. added integer
	  interactor to control the cutting dimension of Slab 2. made the
	  names of interactor more descriptive 3. set the min of slab
	  cutting position to 0 4. set the min and max of slab Autocolor to
	  0 and 1, respectively

2004-06-09 00:40  tan2

	* module/Full/.cvsignore: tell cvs to ignore linked source codes in
	  this directory

2004-06-09 00:32  tan2

	* lib/Common/Output.c: disable pressure and stress output

2004-06-08 08:35  tan2

	* visual/batchsurf.py, visual/combinesurf.py,
	  visual/dxgeneralsurf.sh, visual/getsurf.sh: scripts to get back
	  and combine the surf file (containing x, y, topography, heatflux,
	  vx, vy)

2004-06-08 08:32  tan2

	* visual/getcoord.sh: script to get the coord file

2004-06-08 05:29  tan2

	* visual/batchcombine.py: changed the way to generate machine list

2004-06-08 04:51  tan2

	* visual/batchpaste.sh: Removed hard-wired path. Users have to set
	  CitcomS/visual in their path.

2004-06-08 02:54  tan2

	* visual/batchcombine.py: removed debugging output

2004-06-08 02:45  tan2

	* visual/batchcombine.py: When the length of machinefile mismatch
	  the number of processors, the script will give a warging and try
	  to match number of processors by applying machinefile multiple
	  times.

2004-06-03 04:49  tan2

	* citcoms_profile: environment variables for Pyre-ized CitcomS
	  package. Users need to modify $GEOFRAMEWORK to the installation
	  path

2004-06-03 03:30  tan2

	* module/Exchanger/misc.cc: remove unused header file

2004-06-03 03:28  tan2

	* module/Exchanger/exchangers.cc: fixed a bug in passing int when
	  *int is expected

2004-06-03 03:27  tan2

	* module/Exchanger/Boundary.cc: enable journal output

2004-06-03 03:23  tan2

	* module/Exchanger/CitcomInterpolator.cc: throw an exception if
	  selfTest() is failed

2004-06-02 06:59  tan2

	* Make.mm, local.def: remove incorrect copyright listing

2004-05-29 08:19  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: 1. added new
	  boolean property 'two_way_communication' in Exchanger.py. If it
	  is false, communication is only one way (coarse to fine). 2.
	  added new boolean properties 'excludeTop' and 'excludeBottom' in
	  FineGridExchanger.py. These two are new construtor arguments of
	  Boundary class.

2004-05-29 04:26  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/exchangers.cc: 1. Boundary can be constucted
	  without top or bottom surfaces. This is done through two c'tor
	  argument 'bool excludeTop, excludeBottom'. 2. disable journal

2004-05-27 06:56  tan2

	* module/Regional/bindings.cc, module/Regional/misc.cc,
	  module/Regional/misc.h: split 'BC_update_bc()' into
	  'Visc_update_material()' and 'BC_update_plate_velocity()'

2004-05-27 06:55  tan2

	* pyre/Components/BC.py, pyre/Components/Visc.py,
	  pyre/Solver/Solver.py: split 'BC.updateBC()' into
	  'Visc.updateMaterial()' and 'BC.updatePlateVelocity()'

2004-05-27 06:53  tan2

	* pyre/Components/Advection_diffusion/Advection_diffusion.py: made
	  "fixed_timestep" and "finetunedt" an inventory property (they
	  were ordinary class member).

2004-05-26 05:41  tan2

	* visual/visRegional.net: using relative path to the data files

2004-05-26 05:34  tan2

	* visual/visRegional.cfg, visual/visRegional.net: basic OpenDX
	  network script to visualize result from regional version of
	  CitcomS

2004-05-26 05:24  tan2

	* visual/samples, visual/samples/regtest.cap0.0,
	  visual/samples/regtest.cap0.0.general: added new sample files for
	  visualization

2004-05-25 07:29  tan2

	* module/Exchanger/CitcomSource.cc, module/Exchanger/SVTInlet.cc,
	  module/Exchanger/SVTOutlet.cc: journal is known to leak memory.
	  Commented out journal output before the leak is fixed.

2004-05-25 03:32  tan2

	* module/Regional/bindings.cc, module/Regional/misc.cc,
	  module/Regional/misc.h, pyre/Components/BC.py,
	  pyre/Solver/Solver.py: added support to read vel_bc files at
	  every timestep

2004-05-25 03:30  tan2

	* module/Regional/stokes_solver.cc: added function name in the
	  argument to PyArg_ParseTuple()

2004-05-25 03:27  tan2

	* tests/.cvsignore: tell cvs to ignore files generated by citcoms
	  output

2004-05-25 02:59  tan2

	* module/Exchanger/SVTInlet.cc: Two types of temperature b.c:
	  upwind/normal. In upwind bc, bc can be either fixed
	  temperature/heatflux depending on the direction of flow. In
	  normal bc, bc is always fixed temperature. After more testing, I
	  found normal bc works better than upwind bc.

2004-05-24 02:13  tan2

	* lib/Common/Pan_problem_misc_functions.c: 'side_sbc' is applicable
	  in regional version only. add a sanity check here. also remove
	  some (incorrect) conditional #include

2004-05-24 02:10  tan2

	* lib/Common/Topo_gravity.c, lib/Full/Boundary_conditions.c,
	  lib/Regional/Boundary_conditions.c: fully implemented
	  stress_conform_bcs() and moved it from Boundary_conditions.c to
	  Topo_gravity.c

2004-05-24 01:45  tan2

	* examples/Regional/input.sample: add missing parameter
	  'perturblayer'

2004-05-19 04:21  ces74

	* module/Exchanger/Make.mm, module/Exchanger/bindings.cc,
	  module/Exchanger/inlets_outlets.cc: * bindings for VOutlet, which
	  sends only the velocity to a sink.

2004-05-19 04:18  ces74

	* module/Exchanger/VOutlet.cc, module/Exchanger/VOutlet.h,
	  module/Exchanger/inlets_outlets.h: * Binding for VOutlet created:
	  this send only the velocity to a sink.

2004-05-19 04:15  ces74

	* pyre/Components/Exchanger/Outlet.py: * a class added for
	  exchanging only the velocity.

2004-05-19 03:40  tan2

	* visual/OpenDXMacro/ScaledGlyphs.net: macro that takes two data
	  and plot them as two glyphs that has the same size (eg. length of
	  arrow) scale. The shape (eg. the thickness of arrow) cannot be
	  scaled automaticly though.

2004-05-19 03:38  tan2

	* visual/OpenDXMacro/ShowSphere.net: input1: origin of sphere;
	  default=[0 0 0] input2: radius of sphere; default=0.5 output:
	  sphere object

2004-05-13 02:10  patrick

	* doc/Exchanger.doxyconf: * Updated the package name in the Doxygen
	  docs

2004-05-13 02:05  tan2

	* visual/OpenDXMacro/CitcomSFullImport.net: Added two more inputs.
	  One is an integer indicating the starting cap number. The other
	  is an integer indicating the ending cap number. The default is
	  0-11, ie. all caps. If you wanna plot some specific caps only,
	  change these two values.

2004-05-13 02:01  tan2

	* visual/dxgeneral.sh: Changed the order of 'grid'. Now it is YXZ.
	  Don't know why, but the old XYZ ordering doesn't work.

2004-05-12 02:32  tan2

	* visual/OpenDXMacro, visual/OpenDXMacro/CitcomSFullImport.net,
	  visual/OpenDXMacro/CitcomSImport.net,
	  visual/OpenDXMacro/CitcomSTemperature.net,
	  visual/OpenDXMacro/CitcomSVelocity.net,
	  visual/OpenDXMacro/RTFtoXYZ.net,
	  visual/OpenDXMacro/VelocityRTFtoXYZ.net: * OpenDX macros for
	  importing CitcomS data file * how to use: 1. create the 'cap'
	  files and '.general' files using scripts in CitcomS/visual/
	  directory. 2. use CitcomSImport to import single cap-file. use
	  CitcomSFullImport to import 12 cap-files.

2005-08-23 03:30  unknown_user

	* module/Exchanger/TractionInlet.cc,
	  module/Exchanger/TractionInlet.h,
	  module/Exchanger/TractionOutlet.cc,
	  module/Exchanger/TractionOutlet.h: [vcp] delete of edited
	  revision with dead state

2004-05-12 01:36  tan2

	* module/Exchanger/TractionInlet.cc,
	  module/Exchanger/TractionInlet.h,
	  module/Exchanger/TractionOutlet.cc,
	  module/Exchanger/TractionOutlet.h: obsolete classes

2004-05-12 01:35  tan2

	* module/Exchanger/AreaWeightedNormal.cc,
	  module/Exchanger/AreaWeightedNormal.h,
	  module/Exchanger/BoundaryVTInlet.cc,
	  module/Exchanger/BoundaryVTInlet.h: modified these classes using
	  new base exchanger. these classes are not used currently and I
	  didn't write any binding for them.

2004-05-11 14:59  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  pyre/Components/Exchanger/Inlet.py,
	  pyre/Components/Exchanger/Outlet.py: * using new c++ class
	  hierarchy

2005-08-23 03:30  unknown_user

	* module/Exchanger/AbstractSource.cc,
	  module/Exchanger/AbstractSource.h, module/Exchanger/Array2D.cc,
	  module/Exchanger/Array2D.h, module/Exchanger/BoundedBox.cc,
	  module/Exchanger/BoundedBox.h, module/Exchanger/BoundedMesh.cc,
	  module/Exchanger/BoundedMesh.h,
	  module/Exchanger/CartesianCoord.cc,
	  module/Exchanger/CartesianCoord.h, module/Exchanger/DIM.h,
	  module/Exchanger/FEMInterpolator.cc,
	  module/Exchanger/FEMInterpolator.h, module/Exchanger/Inlet.cc,
	  module/Exchanger/Inlet.h, module/Exchanger/Outlet.cc,
	  module/Exchanger/Outlet.h, module/Exchanger/Sink.cc,
	  module/Exchanger/Sink.h,
	  module/Exchanger/TractionInterpolator.cc,
	  module/Exchanger/TractionInterpolator.h,
	  module/Exchanger/TractionSource.cc,
	  module/Exchanger/TractionSource.h,
	  module/Exchanger/VTInterpolator.cc,
	  module/Exchanger/VTInterpolator.h, module/Exchanger/VTSource.cc,
	  module/Exchanger/VTSource.h, module/Exchanger/utilTemplate.cc,
	  module/Exchanger/utilTemplate.h, module/Exchanger/utility.cc,
	  module/Exchanger/utility.h: [vcp] delete of edited revision with
	  dead state

2004-05-11 14:55  tan2

	* module/Exchanger/AbstractSource.cc,
	  module/Exchanger/AbstractSource.h, module/Exchanger/Array2D.cc,
	  module/Exchanger/Array2D.h, module/Exchanger/Boundary.cc,
	  module/Exchanger/Boundary.h, module/Exchanger/BoundedBox.cc,
	  module/Exchanger/BoundedBox.h, module/Exchanger/BoundedMesh.cc,
	  module/Exchanger/BoundedMesh.h,
	  module/Exchanger/CartesianCoord.cc,
	  module/Exchanger/CartesianCoord.h,
	  module/Exchanger/CitcomInterpolator.cc,
	  module/Exchanger/CitcomInterpolator.h,
	  module/Exchanger/CitcomSource.cc,
	  module/Exchanger/CitcomSource.h, module/Exchanger/Convertor.cc,
	  module/Exchanger/Convertor.h, module/Exchanger/DIM.h,
	  module/Exchanger/FEMInterpolator.cc,
	  module/Exchanger/FEMInterpolator.h, module/Exchanger/Inlet.cc,
	  module/Exchanger/Inlet.h, module/Exchanger/Interior.cc,
	  module/Exchanger/Interior.h, module/Exchanger/Make.mm,
	  module/Exchanger/Outlet.cc, module/Exchanger/Outlet.h,
	  module/Exchanger/SIUnit.cc, module/Exchanger/SIUnit.h,
	  module/Exchanger/SVTInlet.cc, module/Exchanger/SVTInlet.h,
	  module/Exchanger/SVTOutlet.cc, module/Exchanger/SVTOutlet.h,
	  module/Exchanger/Sink.cc, module/Exchanger/Sink.h,
	  module/Exchanger/TInlet.cc, module/Exchanger/TInlet.h,
	  module/Exchanger/TOutlet.cc, module/Exchanger/TOutlet.h,
	  module/Exchanger/TractionInterpolator.cc,
	  module/Exchanger/TractionInterpolator.h,
	  module/Exchanger/TractionSource.cc,
	  module/Exchanger/TractionSource.h, module/Exchanger/VTInlet.cc,
	  module/Exchanger/VTInlet.h, module/Exchanger/VTInterpolator.cc,
	  module/Exchanger/VTInterpolator.h, module/Exchanger/VTOutlet.cc,
	  module/Exchanger/VTOutlet.h, module/Exchanger/VTSource.cc,
	  module/Exchanger/VTSource.h, module/Exchanger/bindings.cc,
	  module/Exchanger/bindings.h, module/Exchanger/exceptions.h,
	  module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h,
	  module/Exchanger/global_bbox.cc, module/Exchanger/global_bbox.h,
	  module/Exchanger/initTemperature.cc,
	  module/Exchanger/initTemperature.h,
	  module/Exchanger/inlets_outlets.cc,
	  module/Exchanger/inlets_outlets.h, module/Exchanger/misc.cc,
	  module/Exchanger/misc.h, module/Exchanger/utilTemplate.cc,
	  module/Exchanger/utilTemplate.h, module/Exchanger/utility.cc,
	  module/Exchanger/utility.h: * New class hierarchy. All base
	  classes are moved to packages/Exchanger, so does
	  non-CitcomS-specific utility classes. * Removed 'mode' argument
	  in VTInlet and VTOutlet c'tors. Every Inlet and Outlet class is
	  reponsible for only one job. * Merged all Interpolator into
	  CitcomInterpolator * Merged all Source into CitcomSource

2004-05-08 01:44  tan2

	* module/Exchanger/SVTInlet.cc: impose temperature b.c. when flow
	  is toward into my domain. Otherwise, impose no-heatflux b.c.

2004-05-08 01:41  tan2

	* module/Exchanger/misc.cc: changed default initial temperature
	  field -- a hot spherical blob below the fine mesh

2004-05-01 01:41  tan2

	* module/Exchanger/Sink.cc: added another self test. This test will
	  make sure that every mesh node is interpolated.

2004-04-30 05:19  tan2

	* lib/Common/Instructions.c: remove debug print out

2004-04-30 04:41  tan2

	* module/Exchanger/SVTInlet.cc: implemented imposeSV(), passed
	  benchmark.

2004-04-30 04:36  tan2

	* module/Exchanger/VTInterpolator.cc: fixed a bug in accessing
	  E->gstress array

2004-04-30 04:35  tan2

	* lib/Common/Topo_gravity.c, lib/Full/Boundary_conditions.c,
	  lib/Regional/Boundary_conditions.c: After stress is calculated,
	  replace stress of boundary nodes with boundary conditions (if
	  stress BC is specified). This is partially done in Regional
	  version (if E->control.side_sbcs is on, should use different bc
	  arrays). Not implemented in Full version.

2004-04-30 03:40  patrick

	* doc, doc/.cvsignore, doc/Exchanger.doxyconf: Commiting Doxygen
	  config file to build the documents for the exchanger

2004-04-29 07:23  tan2

	* pyre/Components/BC.py: side_sbcs default to False

2004-04-29 07:23  tan2

	* lib/Common/Instructions.c: E->control.side_sbcs default to 0

2004-04-29 07:21  tan2

	* lib/Common/Output.c: added new function output_stress()

2004-04-29 07:13  tan2

	* lib/Regional/Version_dependent.c: added some comment for initial
	  temperature in spherical harmonic for future reference

2005-08-23 03:29  unknown_user

	* tests/citcomsfull.py, tests/citcomsregional.py,
	  tests/coupledcitcoms.py: [vcp] delete of edited revision with
	  dead state

2004-04-24 05:15  tan2

	* tests/citcomsfull.py, tests/citcomsfull.sh,
	  tests/citcomsregional.py, tests/citcomsregional.sh,
	  tests/coupledcitcoms.py, tests/coupledcitcoms.sh: update the
	  scripts that executes pyreized versions

2004-04-24 04:15  tan2

	* drivers/Regional/Make.mm: export binary executable

2004-04-23 03:52  tan2

	* drivers/Full/Make.mm: export binary

2004-04-17 02:12  tan2

	* lib/Common/Pan_problem_misc_functions.c: bug fix

2004-04-16 08:17  tan2

	* module/Regional/setProperties.cc, pyre/Components/BC.py: add
	  'side_sbcs' to property list

2004-04-16 07:08  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: use SVTInlet and
	  SVTOutlet as BC

2004-04-16 07:05  tan2

	* pyre/Components/Exchanger/Inlet.py,
	  pyre/Components/Exchanger/Outlet.py: add SVTOutlet and SVTInlet
	  classes and their bindings. These classes are for CitcomS-CitcomS
	  coupling, b.c. with temperature, normal velocity and shear
	  traction

2004-04-16 07:03  tan2

	* module/Exchanger/Make.mm, module/Exchanger/SVTInlet.cc,
	  module/Exchanger/SVTInlet.h, module/Exchanger/SVTOutlet.cc,
	  module/Exchanger/SVTOutlet.h, module/Exchanger/bindings.cc,
	  module/Exchanger/inlets_outlets.cc,
	  module/Exchanger/inlets_outlets.h: add SVTOutlet and SVTInlet
	  classes and their bindings. These classes are for CitcomS-CitcomS
	  coupling, b.c. with temperature, normal velocity and shear
	  traction

2004-04-16 07:01  tan2

	* module/Exchanger/VTSource.cc: add some journal debug output

2004-04-16 01:39  tan2

	* lib/Common/Topo_gravity.c,
	  module/Exchanger/TractionInterpolator.cc: rearranged the order of
	  stress vector so that it conforms with Hugh's convention
	  
	  | 1 4 5 | stress =| 4 2 6 | | 5 6 3 |

2004-04-16 01:35  tan2

	* lib/Common/Make.mm, lib/Common/Process_velocity.c: remove the
	  empty file, Process_velocity.c, from the repository

2004-04-16 01:33  tan2

	* lib/Common/Obsolete.c, lib/Common/Process_velocity.c,
	  lib/Common/Topo_gravity.c: 1. move get_surf_stress() from
	  Process_velocity.c to Topo_gravity.c 2. move get_ele_visc() from
	  Process_velocity.c to Obsolete.c

2004-04-15 03:12  tan2

	* module/Exchanger/VTSource.cc, module/Exchanger/VTSource.h:
	  implement interpolateStress()

2004-04-15 03:06  tan2

	* module/Exchanger/VTInterpolator.cc,
	  module/Exchanger/VTInterpolator.h: implement interpolateStress()

2004-04-15 02:41  tan2

	* module/Exchanger/AbstractSource.h, module/Exchanger/DIM.h,
	  module/Exchanger/FEMInterpolator.h,
	  module/Exchanger/TractionInterpolator.h,
	  module/Exchanger/TractionSource.h,
	  module/Exchanger/VTInterpolator.h, module/Exchanger/VTSource.h:
	  1. add a new constant, 'STRESS_DIM', for the dimension of stress
	  (=6 in 3D) 2. in Interpolator and Source, stress has correct
	  dimension now 3. add virtual function 'interpolateDisplacement'
	  in Source

2004-04-15 01:29  tan2

	* lib/Common/Element_calculations.c, lib/Common/Instructions.c,
	  lib/Common/Pan_problem_misc_functions.c,
	  lib/Common/global_defs.h, lib/Full/Boundary_conditions.c,
	  lib/Regional/Boundary_conditions.c: convert b.c. data structure
	  to support traction b.c. on all sides of a element

2004-04-13 06:30  tan2

	* lib/Common/Element_calculations.c: bug fix

2004-04-13 06:23  tan2

	* lib/Common/Element_calculations.c: modify get_elt_tr() so that it
	  computes traction per side, not per element. Also, some minor
	  speed improvement.

2004-04-10 08:05  tan2

	* module/Exchanger/TractionInterpolator.cc: changes in interfaces
	  of construct_side_c3x3matrix_el() and
	  get_global_side_1d_shape_fn()

2004-04-10 08:03  tan2

	* lib/Common/Size_does_matter.c: change the interface of
	  get_global_side_1d_shape_fn(): NS and far is replaced by side

2004-04-10 07:49  tan2

	* lib/Common/Element_calculations.c, lib/Common/Size_does_matter.c:
	  1. change interface of construct_side_c3x3matrix_el(): NS, far is
	  replaced by side 2. in get_elt_tr(), traction is only imposed on
	  top/bottom sides (will relax this constraint later)

2004-04-10 07:00  tan2

	* lib/Common/Element_calculations.c: bug fix

2004-04-10 06:56  tan2

	* lib/Common/Element_calculations.c, lib/Common/Obsolete.c: move
	  get_elt_h() from Element_calculations.c to Obsolete.c

2004-04-10 06:31  tan2

	* lib/Common/Element_calculations.c: 1. finished get_elt_tr(),
	  which computes RHS vector contributed to traction b.c. 2. remove
	  declaration of unused variables

2004-04-10 06:20  tan2

	* lib/Common/Size_does_matter.c: 1. finished construct_bdry_det()
	  2. modify other functions related to sides 3. remove declaration
	  unused variables

2004-04-10 06:19  tan2

	* lib/Common/element_definitions.h: add/change side definition

2004-04-10 02:05  tan2

	* lib/Common/Element_calculations.c: fixed a bug in calculating RHS
	  force vector due to boundary velocity

2004-04-10 01:39  tan2

	* lib/Common/Element_calculations.c: undo previous (uninit'd
	  memory) bug fix -- it is not a bug

2004-04-09 07:13  tan2

	* lib/Common/Element_calculations.c: fixed a bug in initializing
	  array

2004-04-06 02:36  tan2

	* module/Exchanger/FEMInterpolator.cc: minor modification to
	  previous check-in

2004-04-05 06:03  tan2

	* module/Exchanger/FEMInterpolator.cc: sometimes after coordinate
	  conversion, surface nodes of different solvers won't line up,
	  need this special treatment -- if x is a little bit above my top
	  surface, move it back to the surface

2004-03-29 07:31  tan2

	* module/Regional/mesher.cc: in sphere_launch(), call
	  construct_bdry_det() to compute (6-side) surface determinants of
	  boundary elements

2004-03-29 07:22  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: usage of VTOutlet
	  and VTInlet is replaced by TractionInlet and TractionOutlet.
	  Goal: impose normal velocity and shear traction as bounary
	  conditions

2004-03-29 07:20  tan2

	* pyre/Components/Exchanger/Inlet.py: bug fix

2004-03-29 07:19  tan2

	* module/Exchanger/TractionInterpolator.cc,
	  module/Exchanger/TractionInterpolator.h,
	  module/Exchanger/TractionOutlet.cc,
	  module/Exchanger/TractionOutlet.h,
	  module/Exchanger/TractionSource.cc,
	  module/Exchanger/TractionSource.h,
	  module/Exchanger/exchangers.cc: 1. TractionOutlet c'tor has a new
	  argument to specify 'mode'. Avaiable modes are: 'F': send
	  traction only 'V": send velocity only (this is somewhat
	  duplicated with VTOutlet) 'FV": send both traction and velocity
	  2. TractionSource and TractionInterpolateor have to know how to
	  interpolate velocity (because of 1) 3. remove domian_cutout() 4.
	  restructure TractionInterpolateor class to reuse CitcomS library

2004-03-29 07:05  tan2

	* module/Exchanger/bindings.cc: add bindings to TractionOutlet and
	  TractionInlet

2004-03-29 07:05  tan2

	* module/Exchanger/Make.mm, module/Exchanger/TractionInlet.cc,
	  module/Exchanger/TractionInlet.h,
	  module/Exchanger/inlets_outlets.cc,
	  module/Exchanger/inlets_outlets.h: add new class TractionInlet
	  and its bindings

2004-03-29 07:01  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h:
	  send/recv/broadcast normal array as well

2004-03-27 08:10  steve

	* module/Exchanger/Make.mm: changed from $TOOLS_DIR/lib to
	  $TOOL_LIBDIR

2004-03-27 08:04  tan2

	* lib/Common/Element_calculations.c: 1. extract repeated codes to a
	  new function add_force() 2. remove unused variables 3. add new
	  function to compute RHS of momemtum eqn due to traction b.c. (not
	  finished yet)

2004-03-27 07:42  tan2

	* lib/Common/Size_does_matter.c: 1. move get_global_1d_shape_fn_1()
	  form Size_does_matter.c to Obsolete.c 2. add new function
	  construct_bdry_det() to compute (6-side) surface determinant of
	  boundary element 3. isolate some repeated codes to new function
	  get_x_cart()

2004-03-27 07:41  tan2

	* lib/Common/Obsolete.c: move get_global_1d_shape_fn_1() form
	  Size_does_matter.c to Obsolete.c

2004-03-27 07:39  tan2

	* lib/Common/element_definitions.h: add a section defines the
	  ordering of the 6 surfaces of a element and the ordering of 4
	  nodes within each surface

2004-03-27 07:39  tan2

	* lib/Common/global_defs.h: add definition of new structure Bdry
	  and declaration of E->boundary. This structure is used to mark
	  boundary element and store its (6-side) surface determinants

2004-03-27 07:36  tan2

	* lib/Full/Version_dependent.c, lib/Regional/Version_dependent.c:
	  1. add new function construct_boundary() to find boundary
	  elements 2. fix bug in using fscanf() 3. remove unused variables

2004-03-27 01:53  tan2

	* lib/Common/Instructions.c: 'read uninitialized value' bug fixed

2004-03-26 06:45  tan2

	* lib/Common/Tracer_advection.c: minor bug fixed

2004-03-26 06:42  tan2

	* lib/Regional/Sphere_related.c: minor bug fixed

2004-03-25 04:14  tan2

	* lib/Common/Instructions.c: *** empty log message ***

2004-03-25 04:13  tan2

	* lib/Common/Convection.c, lib/Common/Instructions.c: input of
	  Rayleigh number is moved

2004-03-17 07:17  tan2

	* lib/Common/Topo_gravity.c, lib/Common/global_defs.h,
	  lib/Full/Parallel_related.c, lib/Regional/Parallel_related.c: 1.
	  add function pointers void (* exchange_node_d) and void (*
	  exchange_node_f) in struct All_variables 2. replace calls to
	  exchange_node_d() by void (* exchange_node_d) in Topo_gravity.c.
	  Because exchange_node_d() is version dependent and can't be
	  called from Exchanger.

2004-03-17 05:07  tan2

	* module/Regional/mesher.cc: construct surface arrays and compute
	  surface determinant

2004-03-17 05:03  tan2

	* lib/Common/Construct_arrays.c, lib/Common/Instructions.c,
	  lib/Common/Size_does_matter.c: 1. construct surface node and
	  element array for bookkeeping 2. compute surface determinant

2004-03-14 07:11  tan2

	* lib/Common/Size_does_matter.c: remove debugging print out

2004-03-13 07:13  tan2

	* lib/Common/Topo_gravity.c: another bug fix

2004-03-13 07:05  tan2

	* lib/Common/Topo_gravity.c: restructure function get_STD_topo()

2004-03-13 07:05  tan2

	* lib/Common/Output.c: bug fix

2004-03-13 07:01  tan2

	* lib/Common/Output.c: isolate calculation and output of horizontal
	  average into one function

2004-03-12 07:25  tan2

	* pyre/Components/Exchanger/Inlet.py,
	  pyre/Components/Exchanger/Outlet.py: 1. add TractionInlet class
	  2. simplified bindings for inlets and outlets

2004-03-12 07:23  tan2

	* module/Exchanger/bindings.cc, module/Exchanger/inlets_outlets.cc,
	  module/Exchanger/inlets_outlets.h: simplified bindings to inlets
	  and outlets

2004-03-12 06:50  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: add
	  attribute 'normal_' to indicate the direction of outward normal
	  on each node.

2004-03-12 06:46  tan2

	* module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h: remove obsolete bindings

2004-03-12 06:42  tan2

	* module/Exchanger/Sink.cc, module/Exchanger/VTInlet.cc: bug fixed

2004-03-12 06:36  tan2

	* module/Exchanger/Sink.h, module/Exchanger/VTInlet.cc: change
	  method name: 'recvArray2D' --> 'recv'

2005-08-23 03:27  unknown_user

	* module/Exchanger/BoundaryCondition.cc,
	  module/Exchanger/BoundaryCondition.h,
	  module/Exchanger/InteriorImposing.cc,
	  module/Exchanger/InteriorImposing.h, module/Exchanger/Source.cc,
	  module/Exchanger/Source.h, module/Exchanger/TractionBC.cc,
	  module/Exchanger/TractionBC.h: [vcp] delete of edited revision
	  with dead state

2004-03-12 06:22  tan2

	* module/Exchanger/BoundaryCondition.cc,
	  module/Exchanger/BoundaryCondition.h,
	  module/Exchanger/InteriorImposing.cc,
	  module/Exchanger/InteriorImposing.h, module/Exchanger/Make.mm,
	  module/Exchanger/Source.cc, module/Exchanger/Source.h,
	  module/Exchanger/TractionBC.cc, module/Exchanger/TractionBC.h:
	  remove obsolete files

2004-03-11 09:07  tan2

	* pyre/Components/Exchanger/Inlet.py: method 'storeTimestep' is
	  moved up to the parent class

2004-03-11 09:06  tan2

	* module/Exchanger/Inlet.cc, module/Exchanger/Inlet.h,
	  module/Exchanger/VTInlet.cc, module/Exchanger/VTInlet.h,
	  module/Exchanger/bindings.cc, module/Exchanger/inlets_outlets.cc,
	  module/Exchanger/inlets_outlets.h: 1. move attributes 'fge_t' and
	  'cge_t', methods 'storeTimestep' and 'getFactor' from VTInlet to
	  Inlet. 2. change the binding accordingly

2004-02-27 07:04  tan2

	* module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/initTemperature.cc,
	  module/Exchanger/initTemperature.h: delete
	  initTemperatureSource(), initTemperatureSink() and their
	  bindings.

2004-02-27 06:29  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: use Inlet and
	  Outlet

2004-02-27 06:29  tan2

	* pyre/Components/Exchanger/Inlet.py,
	  pyre/Components/Exchanger/Make.mm,
	  pyre/Components/Exchanger/Outlet.py: add various classes for
	  exchanger

2004-02-27 03:27  tan2

	* module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h:
	  1. remove "before_send_bbox" and "converted_bbox" journal log 2.
	  add 'send' and 'recv' methods

2005-08-23 03:27  unknown_user

	* module/Exchanger/InformationSourceSink.h: [vcp] delete of edited
	  revision with dead state

2004-02-26 07:29  tan2

	* module/Exchanger/InformationSourceSink.h: obsolete (actually
	  never used), replaced by Inlet and Outlet classes.

2004-02-26 07:25  tan2

	* pyre/Components/Exchanger/FineGridExchanger.py: activate
	  journal.info("incompressibility")

2004-02-26 07:24  tan2

	* module/Exchanger/AreaWeightedNormal.cc: outputing outflow
	  information is moved to journal.info category

2004-02-26 07:07  tan2

	* module/Exchanger/Make.mm: add AbstractSource.cc

2004-02-26 07:07  tan2

	* module/Exchanger/AbstractSource.cc,
	  module/Exchanger/AbstractSource.h,
	  module/Exchanger/TractionSource.cc,
	  module/Exchanger/TractionSource.h, module/Exchanger/VTSource.cc,
	  module/Exchanger/VTSource.h: 1. add AbstractSource.cc 2. move
	  initialization of TractionSource and VTSource to AbstractSource

2004-02-25 08:54  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: new Exchanger,
	  using inlets and outlets.

2004-02-25 04:40  tan2

	* module/Exchanger/Make.mm: add new source files

2004-02-25 04:39  tan2

	* module/Exchanger/bindings.cc: add bindings to various inlet and
	  outlet classes in method table

2004-02-25 04:37  tan2

	* module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h:
	  move 'createVTSource' function to inlets_outlets.cc

2004-02-25 04:35  tan2

	* module/Exchanger/inlets_outlets.cc,
	  module/Exchanger/inlets_outlets.h: bindings for various inlets
	  and outlets classes

2004-02-25 04:34  tan2

	* module/Exchanger/BoundaryVTInlet.cc,
	  module/Exchanger/BoundaryVTInlet.h: class which consumes nodal
	  velocities and temperature and enforce imcompressibility
	  constraint, replacing BoundaryConditionSink class.

2004-02-25 04:26  tan2

	* module/Exchanger/VTInlet.cc, module/Exchanger/VTInlet.h: class
	  which consuming nodal velocities and temperature, replacing (part
	  of) BoundaryConditionSink class.

2004-02-25 04:24  tan2

	* module/Exchanger/VTOutlet.cc, module/Exchanger/VTOutlet.h: class
	  which provides nodal velocities and temperature, replacing (part
	  of) BoundaryConditionSource class.

2004-02-25 04:20  tan2

	* module/Exchanger/VTSource.cc, module/Exchanger/VTSource.h: class
	  which sends velocity and temperature across the network,
	  replacing Source class.

2004-02-25 04:14  tan2

	* module/Exchanger/TractionOutlet.cc,
	  module/Exchanger/TractionOutlet.h: class which provides nodal
	  traction, replacing TractionBC class.

2004-02-25 04:09  tan2

	* module/Exchanger/FEMInterpolator.cc: small modification on
	  convergence criterion

2004-02-25 04:03  tan2

	* module/Exchanger/Inlet.cc, module/Exchanger/Inlet.h,
	  module/Exchanger/Outlet.cc, module/Exchanger/Outlet.h: base
	  classes for send/receive/impose exchanged information

2004-02-12 07:34  ces74

	* lib/Common/Output.c: Pressure output added

2004-02-07 07:28  tan2

	* lib/Common/Output.c: increase number of digits for coordinate and
	  viscosity output

2004-02-06 04:17  tan2

	* lib/Common/Initial_temperature.c,
	  lib/Common/convection_variables.h,
	  module/Regional/setProperties.cc: increase max. allowed # of
	  perturbations to 255

2004-02-06 03:56  tan2

	* module/Regional/setProperties.cc: change echo format of
	  get*Property

2004-02-06 03:46  tan2

	* module/Exchanger/misc.cc: allocate and init temperature boundary
	  condition flags

2004-02-06 03:45  tan2

	* module/Exchanger/FEMInterpolator.cc, module/Exchanger/Sink.cc:
	  changes in journal log

2004-02-06 03:06  tan2

	* pyre/Components/IC.py, pyre/Components/Visc.py: use
	  pyre.properties.list instead of pyre.properties.sequence for
	  several component properties because: 1. sequence only accepts
	  integer from command line input 2. list doesn't require '[]'
	  around command line input

2004-02-05 08:46  tan2

	* visual/pasteCitcomData.sh: use space char. as field delimiter
	  instead of tab char.

2004-01-23 04:06  puru

	* module/Exchanger/InteriorImposing.cc,
	  module/Exchanger/InteriorImposing.h: Temporarily setVBCFlag is
	  called inside recvV, which is computationally inefficient for
	  testing purpose.

2004-01-22 11:38  puru

	* module/Exchanger/BoundedBox.cc: Corrected to include the case
	  when one bounded box completely subsumes the other boundedbox

2004-01-22 04:46  tan2

	* module/Exchanger/AreaWeightedNormal.h: #include mpi.h in the
	  header

2004-01-22 02:09  tan2

	* module/Exchanger/Source.h: #include BoundedBox.h in the header

2004-01-22 01:40  tan2

	* module/Exchanger/AreaWeightedNormal.cc,
	  module/Exchanger/AreaWeightedNormal.h: remove Sink from the
	  arguement list of computeWeightedNormal()

2004-01-21 08:13  puru

	* module/Exchanger/InteriorImposing.cc: A typo has been corrected

2004-01-21 08:13  puru

	* module/Exchanger/exchangers.cc: Corrected a typo

2004-01-21 06:57  tan2

	* module/Exchanger/misc.cc: 1. seperate codes that is in original
	  initTemperatureTest() to new functions: hot_blob(),
	  add_hot_blob() and debug_output() 2. add new function
	  five_hot_blob(), which put a hot blob in the center of bbox, and
	  4 hot blobs outside and around bbox.

2004-01-19 05:07  tan2

	* module/Exchanger/FEMInterpolator.cc: add comments

2004-01-18 06:22  ces74

	* module/Exchanger/TractionInterpolator.cc: a bug fixed in traction
	  calculation.

2004-01-17 10:10  puru

	* module/Exchanger/InteriorImposing.cc,
	  module/Exchanger/InteriorImposing.h,
	  module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h: Facility to impose velocity from
	  Snac to Citcom has been added.

2004-01-16 10:05  tan2

	* module/Exchanger/FEMInterpolator.cc: revert to previous version

2004-01-16 09:50  tan2

	* module/Exchanger/FEMInterpolator.cc: changes to make floating
	  point comparison friendly

2004-01-15 11:00  ces74

	* module/Exchanger/TractionInterpolator.h: header file for
	  TractionInterpolator.cc

2004-01-15 10:59  ces74

	* module/Exchanger/TractionBC.cc: converted fbc can be printed out
	  for debugging.

2004-01-15 09:04  ces74

	* module/Exchanger/TractionInterpolator.cc: 1. in
	  initComputeTraction, bbox is now boundedMesh.tightBBox().
	  
	  2. domain_cutout() causes a problem in Citcom. Until fixed, it's
	  not called.

2004-01-15 08:48  tan2

	* visual/batchcombine.py: script to retrieve/combine Citcom data in
	  OpenDX-friendly format

2004-01-15 08:47  tan2

	* visual/batchpaste.sh: run 'rsh ...' in the foreground

2004-01-15 08:17  tan2

	* visual/dxgeneral.sh: can have multiple input files now

2004-01-15 07:22  tan2

	* visual, visual/batchpaste.sh, visual/combine.py,
	  visual/dxgeneral.sh, visual/getlog.sh, visual/pasteCitcomData.sh:
	  add scripts to combine/retrieve Citcom data

2004-01-15 03:07  tan2

	* module/Exchanger/BoundedMesh.cc: small improvement

2004-01-15 02:52  tan2

	* module/Exchanger/Boundary.cc: call tightBBox() to init bbox_

2004-01-15 02:49  tan2

	* module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h:
	  add new method tightBBox() which returns a tight bounding box for
	  current X_

2005-08-23 03:26  unknown_user

	* module/Exchanger/TractionBC.cc~, module/Exchanger/TractionBC.h~:
	  [vcp] delete of edited revision with dead state

2004-01-15 00:52  puru

	* module/Exchanger/TractionBC.cc~, module/Exchanger/TractionBC.h~:
	  TractionBC.cc~ and Traction.h~ have been removed from repository

2004-01-14 10:40  ces74

	* module/Exchanger/TractionBC.cc,
	  module/Exchanger/TractionInterpolator.cc,
	  module/Exchanger/bindings.cc, module/Exchanger/exchangers.h: bug
	  fixed. The changes in the name of classes are corrected.

2004-01-14 10:11  ces74

	* module/Exchanger/Make.mm, module/Exchanger/TractionBC.cc,
	  module/Exchanger/TractionBC.cc~, module/Exchanger/TractionBC.h,
	  module/Exchanger/TractionBC.h~,
	  module/Exchanger/TractionSource.cc,
	  module/Exchanger/TractionSource.h, module/Exchanger/bindings.cc,
	  module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1)
	  New files TractionBC.cc TractionBC.h have been added. 2)
	  sendTraction is now a method of TractionSource.

2004-01-14 08:34  tan2

	* module/Exchanger/initTemperature.cc: add function
	  basal_tbl_central_hot_blob()

2004-01-14 08:34  tan2

	* module/Exchanger/Source.cc, module/Exchanger/Source.h: definition
	  of destructor is moved from Source.h to Source.cc

2004-01-14 02:53  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  pyre/Solver/Solver.py: change Solver attributes so that
	  Exchangers don't access Solver.inventory.IC.inventory directly

2004-01-13 11:55  tan2

	* module/Exchanger/FEMInterpolator.cc,
	  module/Exchanger/FEMInterpolator.h, module/Exchanger/misc.cc: new
	  FEMInterpolator using every element nodes to do interpolation
	  (was using 4 element nodes)

2004-01-13 11:01  ces74

	* pyre/Solver/Solver.py: initialization was improper.

2004-01-13 09:32  tan2

	* drivers/Full/Make.mm, drivers/Regional/Make.mm: when linking
	  binary file, will check dependency on object file

2004-01-13 09:21  ces74

	* module/Exchanger/BoundaryCondition.cc,
	  module/Exchanger/BoundedMesh.cc, module/Exchanger/Interior.cc,
	  module/Exchanger/InteriorImposing.cc, module/Exchanger/Make.mm,
	  module/Exchanger/SIUnit.cc, module/Exchanger/Sink.cc,
	  module/Exchanger/Source.cc, module/Exchanger/exchangers.cc: bugs
	  fixed. For synchronization between users.

2004-01-10 06:42  ces74

	* module/Exchanger/FEMInterpolator.cc: Added a comment line

2004-01-09 14:10  ces74

	* module/Exchanger/CartesianCoord.cc: fixed bugs in degenerate
	  cases.

2004-01-09 09:25  tan2

	* module/Exchanger/Convertor.cc: when unconverting, un-transformate
	  first, then non-dimensionalize next.

2004-01-09 08:38  ces74

	* module/Exchanger/CartesianCoord.cc: fixed bug in degenerate case

2004-01-09 07:43  tan2

	* pyre/Solver/Solver.py: coupler get init'ed after setProperties()
	  is called

2005-08-23 03:25  unknown_user

	* module/Exchanger/Dimensional.cc, module/Exchanger/Dimensional.h:
	  [vcp] delete of edited revision with dead state

2004-01-09 07:31  tan2

	* module/Exchanger/Dimensional.cc, module/Exchanger/Dimensional.h:
	  renamed to SIUnit

2004-01-09 05:19  tan2

	* module/Exchanger/CartesianCoord.cc: 'Array2D: second index out of
	  range' bug fixed

2005-08-23 03:25  unknown_user

	* module/Exchanger/Interpolator.cc,
	  module/Exchanger/Interpolator.h: [vcp] delete of edited revision
	  with dead state

2004-01-09 04:42  tan2

	* module/Exchanger/FEMInterpolator.cc,
	  module/Exchanger/FEMInterpolator.h,
	  module/Exchanger/Interpolator.cc,
	  module/Exchanger/Interpolator.h, module/Exchanger/Make.mm,
	  module/Exchanger/Source.cc, module/Exchanger/Source.h,
	  module/Exchanger/TractionInterpolator.cc,
	  module/Exchanger/TractionInterpolator.h,
	  module/Exchanger/TractionSource.cc,
	  module/Exchanger/VTInterpolator.cc,
	  module/Exchanger/VTInterpolator.h: 1. Interpolator is renamed to
	  VTInterpolator 2. Calculation of shape function is moved to
	  FEMInterpolator 3. VTInterpolator and TractionInterpolatore
	  inherit from FEMInterpolator 4. change Source and TractionSource
	  accordingly

2004-01-09 02:40  tan2

	* module/Exchanger/dimensionalization.h: obsolete

2004-01-09 02:38  tan2

	* module/Exchanger/SIUnit.cc, module/Exchanger/SIUnit.h:
	  dimensionalize temperature is done

2004-01-09 02:37  tan2

	* module/Regional/setProperties.cc: bug fix

2004-01-09 02:26  tan2

	* lib/Common/Instructions.c, module/Regional/setProperties.cc,
	  pyre/Components/Const.py: 1. Const class has new property
	  'surftemp' 2. Instruction.c and setProperties.cc readin
	  E->data.surf_temp and calculate temperature scale from Rayleigh
	  number and other dimensional constants

2004-01-09 02:04  tan2

	* module/Exchanger/Convertor.cc, module/Exchanger/Convertor.h: use
	  plain pointer instead of auto_ptr

2004-01-09 00:28  puru

	* module/Exchanger/CartesianCoord.cc: Bounded box has been
	  transformed while accounting for degenerate cases

2004-01-08 10:29  tan2

	* module/Exchanger/AbstractSource.h,
	  module/Exchanger/BoundaryCondition.cc,
	  module/Exchanger/Convertor.cc, module/Exchanger/Interpolator.cc,
	  module/Exchanger/Sink.cc, module/Exchanger/Sink.h,
	  module/Exchanger/Source.cc, module/Exchanger/Source.h,
	  module/Exchanger/TractionInterpolator.cc,
	  module/Exchanger/TractionSource.cc,
	  module/Exchanger/TractionSource.h: convert (dimensionalization +
	  coordinate transformation) of exchanged velocity/temperature is
	  done

2004-01-08 09:50  tan2

	* module/Exchanger/exchangers.cc: bug fixed

2004-01-08 09:50  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: typo fixed

2004-01-08 07:54  tan2

	* module/Exchanger/InteriorImposing.cc,
	  module/Exchanger/InteriorImposing.h,
	  module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h: 1. remove unnecessary functions in
	  InteriorImposingSink and their bindings 2. convert/unconvert
	  temperature to standard/internal representation

2004-01-08 06:01  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: changes in
	  dimensionalization and coordinate transformation scheme

2004-01-08 05:54  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h,
	  module/Exchanger/CartesianCoord.cc,
	  module/Exchanger/CartesianCoord.h, module/Exchanger/Convertor.cc,
	  module/Exchanger/Convertor.h, module/Exchanger/Interior.cc,
	  module/Exchanger/Interior.h, module/Exchanger/Interpolator.cc,
	  module/Exchanger/Make.mm, module/Exchanger/SIUnit.cc,
	  module/Exchanger/SIUnit.h, module/Exchanger/bindings.cc,
	  module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1.
	  Convertor class will convert
	  coordinate/velocity/traction/time/... from CitcomS' internal
	  representation to some standard representation (currently in SI
	  unit and Cartesian coordinate) 2. change other parts of code
	  accordingly

2004-01-07 16:12  tan2

	* module/Exchanger/exchangers.cc: remove calls to Transformation
	  class

2005-08-23 03:24  unknown_user

	* module/Exchanger/Transformational.h: [vcp] delete of edited
	  revision with dead state

2004-01-07 15:41  tan2

	* module/Exchanger/Transformational.cc,
	  module/Exchanger/Transformational.h: renamed to CartesianCoord

2004-01-07 09:07  tan2

	* module/Exchanger/Interpolator.cc,
	  module/Exchanger/Interpolator.h: remove obsolete function
	  findMaxGridSpacing()

2004-01-07 06:40  puru

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h,
	  module/Exchanger/Interior.cc, module/Exchanger/Interior.h,
	  module/Exchanger/exchangers.cc: Transformation from Spherical
	  coordinate system to Euclidean coordinate is done at citcom end

2004-01-07 06:38  puru

	* module/Exchanger/CartesianCoord.cc,
	  module/Exchanger/CartesianCoord.h,
	  module/Exchanger/Transformational.cc,
	  module/Exchanger/Transformational.h: Added a new cleass
	  Transformational for transforming from one coordinate system to
	  another coordinate system

2003-12-31 05:46  tan2

	* module/Exchanger/BoundaryCondition.cc: temporary fix

2003-12-31 05:46  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/BoundedBox.cc, module/Exchanger/BoundedMesh.cc,
	  module/Exchanger/BoundedMesh.h, module/Exchanger/Interior.cc,
	  module/Exchanger/Interior.h, module/Exchanger/bindings.cc,
	  module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h:
	  optional dimensionalization

2003-12-31 05:44  tan2

	* module/Exchanger/Dimensional.cc, module/Exchanger/Dimensional.h,
	  module/Exchanger/Make.mm, module/Exchanger/SIUnit.cc,
	  module/Exchanger/SIUnit.h: add Dimensional class

2003-12-31 05:42  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: 1. add new
	  property 'dimensional': if it is true, quantities exchanged are
	  dimensional 2. (optional) dimensional BoundedBox, Boundary,
	  Interior and timestep

2003-12-30 08:31  ces74

	* module/Exchanger/BoundedBox.cc: dimensional_len was being used
	  without a value assigned. --> temporarily, not used in
	  regionalGlobalBoundedBox().

2003-12-25 06:46  ces74

	* pyre/Solver/Solver.py: a bug fixed: initTemperature is an
	  attribute of exchanger, not coupler.

2003-12-23 15:02  puru

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: Initial condition
	  initialization has been done at a higher level

2003-12-23 08:42  puru

	* module/Exchanger/Boundary.cc,
	  module/Exchanger/InteriorImposing.cc,
	  module/Exchanger/dimensionalization.h: fixed dimensionalization

2003-12-23 01:47  puru

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: all_variables has
	  been moved from Exchanger to Finegrid and Coarsegrid Exchangers
	  (for CitcomS-Snac Coupling)

2003-12-20 02:21  tan2

	* module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h: add bindings to functions
	  initTemperatureSink(), initTemperatureSource() and modifyT() for
	  exchange initial temperature field between CitcomS-CitcomS

2003-12-19 16:05  tan2

	* module/Exchanger/initTemperature.h: add functions
	  initTemperatureSink(), initTemperatureSource() and modifyT() for
	  exchange initial temperature field between CitcomS-CitcomS

2003-12-19 06:30  puru

	* pyre/Components/Exchanger/__init__.py: Changed __init__.py to
	  export Exchange class

2003-12-17 12:27  puru

	* module/Exchanger/Boundary.cc,
	  module/Exchanger/BoundaryCondition.cc,
	  module/Exchanger/BoundedBox.cc, module/Exchanger/Interior.cc,
	  module/Exchanger/InteriorImposing.cc,
	  module/Exchanger/Interpolator.cc,
	  module/Exchanger/TractionInterpolator.cc,
	  module/Exchanger/dimensionalization.h: 1) Added dimensionalize.h
	  which contains variables for dimensionalizing CitcomS variables
	  2) All variables sent out by Citcom exchanger are dimensionalized
	  3) All variables received in by Citcom exchanger are
	  non-dimensionalized

2003-12-17 09:35  puru

	* module/Exchanger/Interpolator.cc: fixed bug

2003-12-17 03:09  tan2

	* module/Exchanger/Make.mm: add compilation for
	  TractionInterpolator.cc and TractionSource.cc

2003-12-17 03:08  tan2

	* module/Exchanger/Source.cc, module/Exchanger/Source.h: remove
	  functions about traction interpolation (moved to TractionSource)

2003-12-17 02:50  tan2

	* module/Exchanger/TractionSource.cc,
	  module/Exchanger/TractionSource.h: source for CitcomS-Snac
	  coupling

2003-12-16 11:01  puru

	* module/Exchanger/Boundary.cc, module/Exchanger/BoundedBox.cc,
	  module/Exchanger/Interior.cc, module/Exchanger/Interpolator.cc:
	  Dimensionalized exchanger part for the ease of interaction with
	  Snac

2003-12-16 10:14  tan2

	* module/Exchanger/FEMInterpolator.h,
	  module/Exchanger/TractionInterpolator.cc,
	  module/Exchanger/TractionInterpolator.h: 1. remove const-ness in
	  Interpolate*() functions 2. remove passing E in
	  TractionInterpolator 3. remove static qualifier of some local
	  var. in TractionInterpolator

2003-12-04 08:28  puru

	* module/Exchanger/InteriorImposing.cc,
	  module/Exchanger/TractionInterpolator.cc: Conevrsion from
	  dimensional to non-dimensional and vice-versa 1) Forces have been
	  dimensionalized in TractioInterpolator before sent to Snac 2)
	  Velocities have been non-dimensionalized in InteriorImposing
	  after receiving from Snac

2003-11-30 09:22  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: add
	  restartTemperature() for read/send/receive/modify restarted
	  temperature

2003-11-30 09:21  tan2

	* module/Exchanger/initTemperature.cc: add comments and call
	  temperatures_conform_bcs()

2003-11-30 08:12  tan2

	* lib/Common/Process_buoyancy.c: fix a bug of flushing (maybe)
	  non-existing file handle

2003-11-29 06:34  ces74

	* module/Exchanger/TractionInterpolator.cc,
	  module/Exchanger/TractionInterpolator.h: a new class added, but
	  not being used yet.

2003-11-29 06:32  ces74

	* module/Exchanger/Interpolator.cc: interpolateF removed.

2003-11-29 06:32  ces74

	* module/Exchanger/Interpolator.h: interpolateF removed

2003-11-29 06:25  ces74

	* module/Exchanger/exchangers.h: new definitions added for
	  domain_cutout and sendTraction

2003-11-29 06:23  ces74

	* module/Exchanger/exchangers.cc: new bindings added:
	  
	  PyObject * pyExchanger_sendTraction(PyObject *, PyObject *args)
	  PyObject * pyExchanger_domain_cutout(PyObject *, PyObject *args)

2003-11-29 06:21  ces74

	* module/Exchanger/bindings.cc: two entries added: sendTraction and
	  domain_cutout

2003-11-29 06:20  ces74

	* module/Exchanger/BoundaryCondition.h: new functions added: void
	  sendTraction() void domain_cutout()

2003-11-29 06:20  tan2

	* module/Regional/bindings.cc,
	  module/Regional/initial_conditions.cc,
	  module/Regional/initial_conditions.h: add bindings to
	  'restartTemperature()' and 'constructTemperature()', which are
	  used for temperature initial condition

2003-11-29 06:19  ces74

	* module/Exchanger/Source.h: new functions defined:
	  
	  void interpolateF(Array2D<double,DIM>& F, All_variables* E)
	  const; void domain_cutout(const All_variables* E) const;

2003-11-29 06:18  ces74

	* module/Exchanger/Source.cc: new functions added:
	  
	  void Source::interpolateF() void Source::domain_cutout()

2003-11-29 06:18  tan2

	* module/Regional/setProperties.cc: *** empty log message ***

2003-11-29 06:17  tan2

	* pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/IC.py, pyre/Solver/Solver.py: move properties
	  'inputdiffusivity' from Solver to Advecton_diffusion; 'restart',
	  'post_p', 'solution_cycles_init', and 'zero_elapsed_time' from
	  Solver to IC

2003-11-29 06:16  ces74

	* module/Exchanger/BoundaryCondition.cc: The body of the following
	  functions are commented out:
	  
	  void BoundaryConditionSource::sendTraction() void
	  BoundaryConditionSource::domain_cutout()

2003-11-29 06:14  tan2

	* pyre/CoupledApp.py, pyre/SimpleApp.py: add factory functions

2003-11-29 05:42  ces74

	* lib/Common/Size_does_matter.c: two new functions added: 1. void
	  construct_side_c3x3matrix_el() 2. void
	  get_global_side_1d_shape_fn()

2003-11-27 07:27  tan2

	* drivers/Full/Make.mm, drivers/Regional/Make.mm: modify Make.mm so
	  that it always make a new binary file

2003-11-27 07:25  tan2

	* lib/Regional/Parallel_related.c: fix a bug of memory leak

2003-11-27 06:31  tan2

	* lib/Regional/Geometry_cartesian.c: fix a bug when reading input
	  parameters

2003-11-27 05:26  tan2

	* lib/Common/Initial_temperature.c, lib/Full/Version_dependent.c,
	  lib/Regional/Version_dependent.c: 1. combine and move
	  'restart_tic_from_file()' from Version_dependent.c to
	  Initial_temperature.c 2. fix bug in calculating dimensional
	  information: E->data.layer_km is in kilometers, not in meters.

2003-11-27 05:24  tan2

	* lib/Full/Make.mm, lib/Regional/Make.mm: remove options related to
	  library linking

2003-11-26 02:41  puru

	* module/Exchanger/InteriorImposing.cc: fixed a bug

2003-11-26 01:58  puru

	* module/Exchanger/InteriorImposing.cc,
	  module/Exchanger/InteriorImposing.h,
	  module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h: Added facility (recvV) for CitcomS
	  to receive velocity boundary condition in Snac-Citcom coupling

2003-11-25 10:59  tan2

	* module/Exchanger/AbstractSource.h,
	  module/Exchanger/FEMInterpolator.h,
	  module/Exchanger/InformationSourceSink.h: base classes for
	  exchanger

2003-11-25 05:38  ces74

	* lib/Common/Instructions.c: The line for assigning memory to
	  E->traction[] has been removed.

2003-11-25 05:37  ces74

	* lib/Common/global_defs.h: traction[] array removed.

2003-11-25 05:37  ces74

	* lib/Common/Topo_gravity.c: populate E->gstress in get_STD_topo.

2003-11-25 05:26  ces74

	* lib/Common/Instructions.c: memory allocation to "E->gstress" and
	  "E->traction[j]".

2003-11-25 05:25  ces74

	* lib/Common/global_defs.h: new data members, "gstress" and
	  "traction", added to the "All_variables" structure.

2003-11-25 05:22  ces74

	* module/Exchanger/Interpolator.cc: a typo fixed

2003-11-25 05:03  ces74

	* module/Exchanger/Interpolator.h: The prototype of "interpolateF"
	  added to the class "Interpolator" as a public member function.

2003-11-25 05:03  ces74

	* module/Exchanger/Source.h: The prototype of "interpolateF" added
	  to the class "Source" as a public member function.

2003-11-24 03:08  ces74

	* module/Exchanger/exchangers.h: the definition of
	  "pyExchanger_sendTraction" added.

2003-11-24 03:06  ces74

	* module/Exchanger/exchangers.cc: Python binding for sendTraction
	  implemented.

2003-11-24 03:04  ces74

	* module/Exchanger/bindings.cc: "sendTraction" added to Exchanger's
	  method table

2003-11-24 02:25  ces74

	* module/Exchanger/BoundaryCondition.cc: a typo fixed

2003-11-24 02:25  ces74

	* module/Exchanger/BoundaryCondition.cc:
	  BoundaryConditionSource::sendTraction() has been implemented.
	  
	  This is for sending CitcomS' traction to other app as force BC.

2003-11-24 02:21  ces74

	* module/Exchanger/BoundaryCondition.h: 1. A datamember, "fbc",
	  added to the class, "BoundaryConditionSource". 2. A public
	  memberfunction, "sendTraction()" added to
	  "BoundaryConditionSource".
	  
	  These are for sending CitcomS' traction to other app. as force
	  BC.

2003-11-24 02:11  ces74

	* module/Exchanger/Source.cc: a typo fixed

2003-11-24 02:10  ces74

	* module/Exchanger/Source.cc: Source::interpolateF added. This is
	  for sending CitcomS' traction to other app's as force BC.

2003-11-24 02:05  ces74

	* module/Exchanger/Interpolator.cc: a typo fixed

2003-11-24 02:02  ces74

	* module/Exchanger/Interpolator.cc: interpolateF added. This is for
	  sending CitcomS' traction to other app's force BC.

2003-11-23 16:33  steve

	* module/Regional/Make.mm: changed from $(TOOLS_DIR)/lib to
	  $(TOOLS_LIBDIR) as the former is not always true (if you let pyre
	  choose the export dir it will be in .../lib/Linux...)

2003-11-23 16:31  steve

	* module/Full/Make.mm: changed from $(TOOLS_DIR)/lib to
	  $(TOOLS_LIBDIR) as the former is not always true (if you let pyre
	  choose the export dir it will be in .../lib/Linux...)

2003-11-22 07:15  tan2

	* module/Exchanger/AreaWeightedNormal.cc,
	  module/Exchanger/Boundary.cc,
	  module/Exchanger/BoundaryCondition.cc,
	  module/Exchanger/BoundedMesh.h, module/Exchanger/Interior.cc,
	  module/Exchanger/InteriorImposing.cc: 1. attribute name changed:
	  BoundedMesh.meshID ==> BounedMesh.nodeID 2. in
	  BoundaryConditionSink::imposeTBC, call 'temperatures_conform_bcs'

2003-11-20 03:06  tan2

	* lib/Full/Read_input_from_files.c: restart file has cap number
	  0~11 (was 1~12)

2003-11-12 03:45  ces74

	* module/Exchanger/BoundaryCondition.cc: setTBCFlag and imposeTBC
	  completed.

2003-11-12 03:29  tan2

	* module/Exchanger/AreaWeightedNormal.cc,
	  module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h,
	  module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/Interior.cc, module/Exchanger/Interior.h,
	  module/Exchanger/InteriorImposing.cc,
	  module/Exchanger/InteriorImposing.h,
	  module/Exchanger/Interpolator.cc, module/Exchanger/Sink.cc,
	  module/Exchanger/Sink.h, module/Exchanger/Source.h,
	  module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h, module/Exchanger/misc.cc,
	  pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: 2-way
	  communication

2003-11-11 05:59  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: change in
	  BoundaryConditionSink c'tor

2003-11-11 05:55  tan2

	* module/Exchanger/AreaWeightedNormal.cc,
	  module/Exchanger/AreaWeightedNormal.h,
	  module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h,
	  module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/BoundaryCondition.cc,
	  module/Exchanger/BoundaryCondition.h,
	  module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h,
	  module/Exchanger/Interior.h, module/Exchanger/Make.mm,
	  module/Exchanger/Sink.h, module/Exchanger/Source.h,
	  module/Exchanger/exchangers.cc, module/Exchanger/utilTemplate.cc,
	  module/Exchanger/utilTemplate.h, module/Exchanger/utility.cc,
	  module/Exchanger/utility.h: 1. multi-processor AreaWeightedNormal
	  2. small improvements

2003-11-08 05:43  puru

	* module/Exchanger/InteriorImposing.cc,
	  module/Exchanger/InteriorImposing.h,
	  module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h: added bindings for two way
	  communication

2003-11-08 04:41  puru

	* module/Exchanger/Interior.cc: Made it easier to read and
	  initialized bbox_

2003-11-08 04:39  puru

	* module/Exchanger/InteriorImposing.cc,
	  module/Exchanger/InteriorImposing.h: Added InteriorImposing for
	  two-way communication

2003-11-07 13:47  puru

	* module/Exchanger/Interior.cc: fixed the bug

2003-11-07 13:14  puru

	* module/Exchanger/Interior.cc: Set interior nodes for two way
	  communication

2003-11-07 09:20  tan2

	* module/Exchanger/BoundaryCondition.cc,
	  module/Exchanger/BoundaryCondition.h: remove unnecessary base
	  class BoundaryCondition

2005-08-23 03:21  unknown_user

	* module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h,
	  module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h,
	  module/Exchanger/auto_array_ptr.h: [vcp] delete of edited
	  revision with dead state

2003-11-07 09:08  tan2

	* module/Exchanger/AreaWeightedNormal.cc,
	  module/Exchanger/AreaWeightedNormal.h,
	  module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h,
	  module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/BoundaryCondition.cc,
	  module/Exchanger/BoundaryCondition.h,
	  module/Exchanger/BoundedBox.cc, module/Exchanger/BoundedBox.h,
	  module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h, module/Exchanger/DIM.h,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/Exchangermodule.cc,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h,
	  module/Exchanger/Interior.cc, module/Exchanger/Interior.h,
	  module/Exchanger/Interpolator.cc,
	  module/Exchanger/Interpolator.h, module/Exchanger/Make.mm,
	  module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h,
	  module/Exchanger/Sink.cc, module/Exchanger/Sink.h,
	  module/Exchanger/Source.cc, module/Exchanger/Source.h,
	  module/Exchanger/auto_array_ptr.h, module/Exchanger/bindings.cc,
	  module/Exchanger/bindings.h, module/Exchanger/exceptions.cc,
	  module/Exchanger/exceptions.h, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h,
	  module/Exchanger/initTemperature.cc,
	  module/Exchanger/initTemperature.h, module/Exchanger/misc.cc,
	  module/Exchanger/misc.h, module/Exchanger/utilTemplate.cc,
	  module/Exchanger/utilTemplate.h,
	  pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  pyre/CoupledApp.py, pyre/Coupler.py, pyre/Layout.py,
	  pyre/Solver/Solver.py: point-to-point communication

2003-10-31 07:36  tan2

	* module/Exchanger/ExchangerClass.cc, module/Exchanger/Mapping.cc:
	  replace c functions/macros (fabs, min, max) with c++ functions

2003-10-31 07:28  tan2

	* lib/Common/global_defs.h: add "#if defined(__cplusplus)" clause
	  to skip macro (max, min, SWAP) definition when included in C++

2003-10-31 06:45  tan2

	* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: fixed a
	  bug that send/receive used different tag.

2003-10-31 06:25  tan2

	* tests/Make.mm, tests/array2d.cc: add tests for Array2D class

2003-10-31 06:21  tan2

	* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: 1. add
	  non-blocking version of send/receive 2. move inlined function
	  definition from .h to .cc file

2003-10-30 02:40  tan2

	* module/Full/Make.mm, module/Regional/Make.mm,
	  module/Regional/bindings.cc,
	  module/Regional/initial_conditions.cc,
	  module/Regional/initial_conditions.h, module/Regional/mesher.cc,
	  module/Regional/stokes_solver.cc,
	  module/Regional/stokes_solver.h, pyre/Components/IC.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Solver/Solver.py: 1. let IC initialize temperature,
	  pressure, velocity, and viscosity fields 2. let Incompressible
	  call general_stokes_solver_setup() 3. coupler.initTemperature
	  replaces ic.initTemperature

2003-10-30 01:18  tan2

	* module/Exchanger/Array2D.h: index range check when debugging

2003-10-29 09:13  tan2

	* pyre/CoupledApp.py, pyre/Coupler.py, pyre/Solver/Solver.py: bug
	  fix and small improvement

2003-10-29 07:52  tan2

	* module/Regional/bindings.cc, module/Regional/setProperties.cc,
	  module/Regional/setProperties.h: add Solver_set_properties() and
	  its binding

2005-08-23 03:20  unknown_user

	* pyre/Components/Stokes_solver/Stokes_solver.py: [vcp] delete of
	  edited revision with dead state

2003-10-29 07:51  tan2

	* pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/Advection_diffusion/__init__.py,
	  pyre/Components/BC.py, pyre/Components/Const.py,
	  pyre/Components/Exchanger/__init__.py, pyre/Components/IC.py,
	  pyre/Components/Param.py, pyre/Components/Phase.py,
	  pyre/Components/Sphere/RegionalSphere.py,
	  pyre/Components/Sphere/Sphere.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Stokes_solver/Stokes_solver.py,
	  pyre/Components/Stokes_solver/__init__.py,
	  pyre/Components/Visc.py, pyre/CoupledApp.py, pyre/SimpleApp.py,
	  pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py,
	  pyre/Solver/Solver.py: 1. move properties around 2. provide
	  default argurments to all constructors or factories

2003-10-29 03:57  tan2

	* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: 1. add
	  sendSize(), receiveSize(), broadcastSize() and empty() methods 2.
	  send(), receive(), and broadcast() will send/recieve size
	  information and adjust its memory accordingly

2003-10-29 01:24  tan2

	* pyre/Controller.py: *** empty log message ***

2003-10-28 10:34  puru

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h,
	  module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: Two way
	  communication between Coarse and Fine Grid has been incorporated

2003-10-28 09:56  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Solver/Solver.py: fixed bugs in time marching and output

2003-10-28 09:55  tan2

	* pyre/Components/Sphere/__init__.py: add default component name

2003-10-28 09:52  tan2

	* module/Make.mm: change the order of complilation: Exchanger/ is
	  done last

2003-10-28 09:51  tan2

	* module/Exchanger/ExchangerClass.cc: change to Array2D.swap()

2003-10-28 09:51  tan2

	* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: 1.
	  implementation changed: using vector as internal representation
	  2. swap() becomes a member function

2003-10-25 07:45  ces74

	* lib/Full/Version_dependent.c: a bug fixed in
	  global_derived_values(): nox = E->mesh.mgunitx * (int)
	  pow(2.0,(double)i), etc. ===> nox = E->mesh.mgunitx * (int)
	  pow(2.0,(double)i)*E->parallel.nprocx, etc.

2003-10-24 12:23  tan2

	* tests/coupledcitcoms.py, tests/exchange.py, tests/test1.sh,
	  tests/test2.sh: update tests according to changes in module/ and
	  pyre/

2003-10-24 12:04  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  pyre/Components/Exchanger/__init__.py: 1. remove unsed attributes
	  'localLeader' 2. in __init__.py, factory methods now doesn't need
	  any argument

2005-08-23 03:19  unknown_user

	* pyre/Controller/Make.mm, pyre/Controller/__init__.py,
	  pyre/Coupler/Coupler.py, pyre/Coupler/Make.mm,
	  pyre/Coupler/__init__.py, pyre/Layout/Layout.py,
	  pyre/Layout/Make.mm, pyre/Layout/__init__.py: [vcp] delete of
	  edited revision with dead state

2003-10-24 11:55  tan2

	* pyre/Controller.py, pyre/Controller/Controller.py,
	  pyre/Controller/Make.mm, pyre/Controller/__init__.py,
	  pyre/CoupledApp.py, pyre/Coupler.py, pyre/Coupler/Coupler.py,
	  pyre/Coupler/Make.mm, pyre/Coupler/__init__.py, pyre/Layout.py,
	  pyre/Layout/Layout.py, pyre/Layout/Make.mm,
	  pyre/Layout/__init__.py, pyre/Make.mm, pyre/Solver/Solver.py: 1.
	  move Controller.py, Coupler.py, and Layout.py to pyre/ directory
	  2. change Make.mm accordingly 3. remove unused attributes
	  'self.localLeader' in Layout, CoupledApp, and Solver

2003-10-24 11:51  tan2

	* module/Exchanger/AreaWeightedNormal.cc,
	  module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h,
	  module/Exchanger/Boundary.cc,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h,
	  module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h,
	  module/Exchanger/exchangers.cc: 1. add shrink() in Array2D 2. add
	  shrinksize() in Boundary and Mapping 3. write (most) output via
	  journal 4. remove unused attribute 'localLeader' in Exchanger

2003-10-24 02:06  puru

	* module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: fixed
	  bugs

2003-10-24 01:26  puru

	* module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: added
	  FindInteriorNodes

2003-10-23 03:33  ces74

	* module/Exchanger/AreaWeightedNormal.cc: a bug fixed: in
	  AreaWeightedNormal::imposeConstraint()
	  
	  if(outflow > toleranceOutflow_) ==> if (fabs(outflow) >
	  toleranceOutflow_)

2003-10-22 08:15  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: add
	  resize() method

2003-10-22 08:13  tan2

	* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: 1.
	  resize() will copy the old data to new memory location 2. make
	  reset() private (because its syntax in error-prone)

2003-10-22 00:32  tan2

	* tests/test2.sh: with correction on outflow

2003-10-22 00:31  tan2

	* tests/test2.sh: coupled citcoms test (4-proc coarse-grid solver,
	  1-proc fine-grid solver, no correction on outflow)

2003-10-22 00:26  tan2

	* tests/test1.sh: functional test of exchanger

2003-10-21 00:13  tan2

	* module/Exchanger/AreaWeightedNormal.cc,
	  module/Exchanger/AreaWeightedNormal.h,
	  module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm:
	  more small improvements

2003-10-21 00:12  tan2

	* module/Exchanger/Array2D.cc: bug in memory allocation fixed

2003-10-20 02:54  tan2

	* module/Exchanger/Array2D.h, module/Exchanger/Mapping.h: fixed a
	  bug in declaration

2003-10-19 08:01  tan2

	* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h,
	  module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h,
	  module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h,
	  module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h: many many small improvements

2003-10-18 03:18  ces74

	* lib/Common/General_matrix_functions.c: A bug fixed in
	  solve_del2_u(): now multigrid method can be used.

2003-10-17 03:06  tan2

	* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: 1.
	  generalize template Array2D<class T, int N>, T can be double,
	  float, int, or char. 2. using Array2D in class Mapping 3. throw
	  exception when selftest failed

2003-10-16 01:51  tan2

	* module/Exchanger/FineGridExchanger.cc: bug in reduceOutflow()
	  fixed

2003-10-11 07:40  tan2

	* pyre/Components/Exchanger/FineGridExchanger.py: add call to
	  module.imposeConstraint()

2003-10-11 07:38  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm,
	  module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h,
	  module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h: 1. add class 'Mapping' and its
	  derived classes 'CoarseGridMapping' and 'FineGridMapping' 2. move
	  'bid2gid', 'bid2proc', 'bid2elem', and 'shape' from Boundary to
	  Mapping 3. change Exchanger classes accordingly

2003-10-11 07:35  tan2

	* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: add
	  prefix to the output

2003-10-11 01:14  tan2

	* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h: 1. replace 'strcut Data' by
	  'Array2D<int N>', replace 'incoming' and 'outgoing' by
	  'incomingV', 'outgoingV', 'incomingT' and 'outgoingT' 2.
	  decompose 'imposeConstraint()' into 'computeWeightedNormal()',
	  'computeOutflow()', and 'reduceOutflow()'

2003-10-06 11:31  tan2

	* lib/Common/global_defs.h: header guard #define directive is added

2003-10-06 11:30  tan2

	* lib/Common/Viscosity_structures.c: bug preventing viscosity
	  initialization is fixed

2003-10-06 08:09  puru

	* module/Exchanger/Boundary.cc: Bug associated with round off error
	  of degenerate case in fine grid node to Coarse grid element map
	  has been fixed.

2003-10-06 07:53  puru

	* module/Exchanger/ExchangerClass.cc: bug associated switching of
	  indices of theta and of theta fi has been fixed

2003-10-06 01:55  tan2

	* module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h: 1. smoother temperature field
	  in initTemperature() 2. remove obsolete functions

2003-10-05 06:37  puru

	* module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h: added method imposeConstraint
	  to correct velocities which are consistent with incompressibility
	  of the fluid.

2003-10-04 21:24  puru

	* module/Exchanger/ExchangerClass.cc: Boundary conditions for fine
	  mesh have been modified to satisfy incompressiblility constraint
	  in receiveVelocities

2003-10-04 04:50  puru

	* module/Exchanger/ExchangerClass.cc: net outflow corresponding to
	  velocity boundary conditions has been added.

2003-10-04 02:20  tan2

	* module/Exchanger/Boundary.cc: bug fix

2003-10-04 01:36  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: 1.
	  decompose init() to two functions initBound() and
	  findBoundaryNodes() 2. remove init(), all of its functionality is
	  done in mapFindGrid() 3. in mapCoarseGrid(), extend the domain
	  when searching for node mapping 4. use auto_array_ptr for all
	  member arrays to improve exception safety

2003-10-04 01:25  tan2

	* module/Exchanger/auto_array_ptr.h: first import, modified from
	  Jack W. Reeves' code on March 1996 issue of the C++ Report.

2003-10-04 01:18  tan2

	* pyre/Solver/Solver.py: call coupler.launch() right after
	  mesher.run() to set BC flag and reconstruct ID array

2003-10-04 01:17  tan2

	* pyre/Components/Exchanger/FineGridExchanger.py: 1. add call to
	  self.module.setBCFlag() 2. call mapBoundary() before
	  sendBoundary() to reflect change in module/Exchanger/Boundary.cc

2003-10-04 01:12  tan2

	* module/Exchanger/FineGridExchanger.cc: 1. calculate boundary.size
	  in a simplified way 2. remove call to boundary.init() (the job of
	  init() is done in mapFindGrid() now)

2003-10-04 01:10  tan2

	* module/Exchanger/misc.cc: init E->mesh.nno in commonE()

2003-10-02 08:14  tan2

	* module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h, module/Exchanger/Make.mm,
	  module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h: 1. add Exchanger::setBCFlag() to
	  set BC Flag and reconstruct E->ID 2. add binding to
	  Exchanger::setBCFlag()

2003-10-02 05:21  tan2

	* module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
	  module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h:
	  add Exchanger::initTemperature() and its binding

2003-10-02 05:16  tan2

	* pyre/Solver/Solver.py: 1. pass Solver.inventory.datafile to
	  Param.inventory.datafile to get around a bug in pyre 2. add
	  solveVelocities() and solverTemperature() 3. comment out
	  applyBoundaryConditions(). BC is applied by FGE.preVSolverRun()
	  or CGE.postVSolverRun() 4. fix a logical bug, exchanging
	  velocities is done at the correct timestep

2003-10-02 05:07  tan2

	* pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py: add
	  property 'datafile' to get around a bug in pyre

2003-10-02 05:06  tan2

	* pyre/Coupler.py, pyre/Coupler/Coupler.py: 1. remove
	  solveVelocities() 2. add preVSolverRun() and postVSolverRun()

2003-10-02 05:04  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: 1. remove
	  solverVelocities() 2. add preVSolverRun() and postVSolverRun() 3.
	  add attribute 'toApplyBC' in FGE, which flags applying BC or not
	  4. print time marching information

2003-09-30 09:02  puru

	* module/Exchanger/ExchangerClass.cc: fixed degeneracy associated
	  with cge=0

2003-09-30 08:50  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: add
	  solveVelocities() and storeTimestep()

2003-09-30 08:49  tan2

	* pyre/Controller.py, pyre/Controller/Controller.py: disable call
	  to applyBoundaryConditions()

2003-09-30 08:48  tan2

	* pyre/Coupler.py, pyre/Coupler/Coupler.py: add solveVelocities()

2003-09-30 08:47  tan2

	* pyre/Solver/Solver.py: when coupled, call solveVelocities()
	  instead of vsolver.run()

2003-09-30 08:45  puru

	* module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h: Interpolated Boundary
	  conditions for fine mesh from coarse mesh has been added

2003-09-30 08:33  tan2

	* module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
	  module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1.
	  add attributes 'fge_t' and 'cge_t' in Exchanger class 2. init
	  'fge_t' and 'cge_t' in constructor 3. add functions
	  storeTimestep() in Exchanger class 4. add binding to
	  storeTimestep()

2003-09-30 07:48  puru

	* module/Exchanger/Boundary.cc: Modified to account for multiple
	  processes

2003-09-30 07:39  tan2

	* module/Full/Make.mm, module/Regional/Make.mm: bug fixed

2003-09-30 05:31  puru

	* module/Exchanger/Boundary.cc, module/Exchanger/misc.cc: Modified
	  to account for 2*PI crossover in spherical coordinates system

2003-09-30 03:25  tan2

	* module/Full/Make.mm, module/Regional/Make.mm: update library and
	  include path

2003-09-30 03:23  tan2

	* pyre/Layout.py, pyre/Layout/Layout.py: cosmetics

2003-09-30 03:22  tan2

	* pyre/Coupler.py, pyre/Coupler/Coupler.py: bug fix

2003-09-30 03:22  tan2

	* module/Regional/setProperties.cc: bug in output fixed

2003-09-30 03:21  tan2

	* drivers/Citcom.c, lib/Common/Instructions.c,
	  module/Regional/mesher.cc, pyre/Controller.py,
	  pyre/Controller/Controller.py, pyre/Solver/Solver.py: 1. open
	  'fptime' is moved to drivers/Citcom.c 2. rename
	  open_log_and_time() to open_log() 3. add time ouput in pyre
	  version

2003-09-30 01:34  puru

	* module/Exchanger/Boundary.cc: Implemented more efficient search
	  of coarse element for fine mesh nodes

2003-09-30 01:06  tan2

	* module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h: 1. add helper functions
	  printDataT() and printDataV() 2. replace old debugging output by
	  printDataV()

2003-09-30 01:03  tan2

	* module/Exchanger/misc.cc: 1. allocate and initialize
	  E->sphere.cap[].V 2. change debugging output accordingly

2003-09-29 09:52  puru

	* module/Exchanger/CoarseGridExchanger.cc: *** empty log message
	  ***

2003-09-29 09:20  puru

	* module/Exchanger/misc.cc: fixed a bug

2003-09-29 09:09  puru

	* module/Exchanger/misc.cc: converted from cartesian to spherical
	  coordinates

2003-09-29 09:04  puru

	* module/Exchanger/Boundary.cc: Converted from cartesian
	  coordinates to spherical coordinates

2003-09-29 04:44  tan2

	* pyre/CoupledApp.py: change default coarse solver to full version

2003-09-29 04:44  tan2

	* pyre/Controller.py, pyre/Controller/Controller.py: pass
	  'totalTime' and 'steps' to endTimestep()

2003-09-29 04:43  tan2

	* pyre/Coupler.py, pyre/Coupler/Coupler.py: 1. remove call to
	  exchanger.mapBoundary() 2. comment out call to
	  exchanger.initTemperature()

2003-09-29 03:45  tan2

	* module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
	  module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1.
	  wait() and nowait() is replaced by exchangeSignal() 2. add helper
	  functions exchangeInt(), exchangeDouble() and exchangeFloat()

2003-09-29 03:41  tan2

	* module/Exchanger/misc.cc: cosmetics

2003-09-29 03:40  tan2

	* pyre/Controller.py, pyre/Controller/Controller.py,
	  pyre/Coupler.py, pyre/Coupler/Coupler.py, pyre/Solver/Solver.py:
	  1. add attribute 'self.done' in Controller indicating end of
	  simulation 2. change argument list and return list of
	  endTimestep() 3. Coupler can terminate the time marching by
	  returning False at endTimestep() 4. synchronization between
	  solvers is done in endTimestep

2003-09-29 03:36  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  tests/exchange.py: 1. synchronization between solvers is done in
	  endTimestep() (was in NewStep()) 2. pass the test on
	  synchronization 3. delete functions createDataArrays() and
	  deleteDataArrays()

2003-09-28 22:47  tan2

	* module/Exchanger/ExchangerClass.cc: check proc. rank in
	  imposeBC()

2003-09-28 22:36  tan2

	* module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.cc: call createDataArrays()
	  inside mapBoundary()

2003-09-28 13:03  tan2

	* module/Exchanger/misc.cc: allocate and init E->node and E->cap.VB

2003-09-28 13:01  tan2

	* pyre/Components/Exchanger/FineGridExchanger.py: finish test

2003-09-28 07:35  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  tests/exchange.py: 1. rename 'leaderRank' to 'leader' 2. remove
	  unused functions

2003-09-28 07:34  tan2

	* module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h: remove unused bindings

2003-09-28 07:30  tan2

	* pyre/Layout.py, pyre/Layout/Layout.py, pyre/Solver/Solver.py:
	  rename attribute 'leaderRank' to 'leader'

2003-09-28 07:11  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h,
	  module/Exchanger/exchangers.cc: 1. remove attribute 'lrank' in
	  Exchanger class 2. 'rank' is processor rank in local communicator
	  3. modify Exchanger::createDataArray() and
	  Exchanger::deleteDataArray() 4. gather() and distribute() become
	  pure virtual functions 5. finish CGE::gather() 6. rename
	  interpolate() to interpretate() 7. modify CGE::interpretate()

2003-09-28 04:04  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: 1.
	  bid2proc contains current proc. rank (was current capid) 2. add
	  sendBid2proc(), which send bid2proc array of each processor to
	  localLeader 3. add printBid2proc() and printBid2elem() for
	  debugging

2003-09-28 03:52  tan2

	* module/Exchanger/exchangers.cc: change argument list of
	  create*Exchanger()

2003-09-28 03:30  tan2

	* module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h: 1. add attribute
	  'leaderRank' 2. change argument list of constructors 3. rewrite
	  sendVelocities() and receiveVelocities()

2003-09-28 03:24  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  pyre/CoupledApp.py, pyre/Solver/Solver.py: 1. add attribute
	  'leaderRank' 2. pass 'leaderRank' to createExchanger()

2003-09-28 03:17  tan2

	* pyre/Layout.py, pyre/Layout/Layout.py: add attribute 'leaderRank'

2003-09-28 03:16  tan2

	* module/Exchanger/misc.cc: init E->parallel.nproc

2003-09-28 00:12  tan2

	* module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h,
	  module/Exchanger/exchangers.cc: 1. add new attributes 'lrank' 2.
	  change arugment list of consturctors of all exchangers 3.
	  cosmetics

2003-09-27 07:30  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py: remove
	  getBid2crseelem()

2003-09-27 07:29  tan2

	* module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h: add dummy definition of
	  gather() and distribute()

2003-09-27 07:28  tan2

	* module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h: 1. remove binding to
	  CoarseGridExchanger::getBid2crseelem()

2003-09-27 07:27  tan2

	* module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h: 1. sendBoundary() and
	  receiveBoundary() delegate most of their jobs to
	  Boundary::send(), Boundary::receive() and Boundary::broadcast()
	  2. change return type of sendBoundary() from int to void 3.
	  change argument list of mapFineGrid() and mapCoarseGrid() 4.
	  remove CoarseGridExchanger::getBid2crseelem()

2003-09-27 07:09  tan2

	* module/Exchanger/misc.cc: 1. init E->X according domain bound
	  information in commonE() 2. add initialization of
	  E->sphere.capid[] 3. change domain bound in FinereturnE()

2003-09-27 07:05  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: 1.
	  delete attribute 'connectivity' 2. change argument list of
	  mapFineGrid() and mapCoarseGrid() 3. add send(), receive() and
	  broadcast() 4. add printBound() 5. move Tetrahedronvolume() and
	  det3_sub() to private section 6. fix 'delete []' bug in
	  mapFineGrid() 7. remove redundant initialization of X in
	  mapFineGrid() 8. cosmetics

2003-09-27 05:04  puru

	* module/Exchanger/Boundary.cc: bug fixed

2003-09-27 04:54  ces74

	* pyre/Solver/Solver.py: a typo fixed.

2003-09-27 04:11  tan2

	* module/Exchanger/misc.cc: reduce repeated codes and do some
	  cosmetics

2003-09-27 02:04  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  tests/exchange.py: replace self.fine_E and self.coarse_E by
	  self.all_variables

2003-09-27 02:03  tan2

	* pyre/Layout.py, pyre/Layout/Layout.py: change back: 'coarse' is
	  full CitcomS

2003-09-27 01:24  puru

	* module/Exchanger/Boundary.h,
	  module/Exchanger/CoarseGridExchanger.cc: bid2crseelem has been
	  replaced with more obvious bid2elem and bid2proc

2003-09-27 01:23  puru

	* module/Exchanger/Boundary.cc: bid2crseelem with more obvious
	  bid2elem and bid2proc have been introduced

2003-09-27 00:33  tan2

	* module/Exchanger/Boundary.cc: uncomment self test

2003-09-27 00:01  ces74

	* module/Exchanger/ExchangerClass.cc: Exchanger::imposeBC fixed.

2003-09-26 08:05  ces74

	* module/Exchanger/ExchangerClass.cc: ImposeBC now changes flags of
	  boundary nodes.

2003-09-26 05:47  ces74

	* module/Exchanger/CoarseGridExchanger.cc: test output modified in
	  CoarseGridExchanger::interpolate

2003-09-26 05:45  ces74

	* module/Exchanger/Boundary.cc: an error fixed in
	  Boundary::getBid2crseelem

2003-09-26 05:37  ces74

	* module/Exchanger/Boundary.cc: Test part of
	  Boundary::getBid2crseelem() is temporarily commented out.

2003-09-26 05:25  ces74

	* module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/FineGridExchanger.h: gather and distribute are
	  members of Exchanger Class.

2003-09-26 05:14  ces74

	* module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h:
	  CoarseGridExchanger.interpolateTemperature added

2003-09-26 05:14  ces74

	* module/Exchanger/bindings.cc:
	  CoarseGridExchanger.interpolateTemperature addedcc

2003-09-26 02:17  ces74

	* module/Exchanger/CoarseGridExchanger.cc: errors fixed in
	  CoarseGridExchanger::interpolate.

2003-09-26 02:16  ces74

	* module/Exchanger/FineGridExchanger.cc: boundary->bid2gid is
	  transferred from Fine to Coarse Grid.

2003-09-25 10:37  ces74

	* module/Exchanger/Boundary.cc: theta_max, theta_min, fi_max,
	  fi_min, ro ,ri were being redeclared as local variables --> fixed
	  so that they are used only as members of boundary class.

2003-09-25 09:51  ces74

	* module/Exchanger/CoarseGridExchanger.cc: typo fixed.

2003-09-25 03:14  puru

	* module/Exchanger/Boundary.cc,
	  module/Exchanger/CoarseGridExchanger.cc: Interpolation with
	  arbitrary element shapes has been added

2003-09-25 02:42  puru

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/CoarseGridExchanger.cc: interpolation test added

2003-09-24 11:53  puru

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h:
	  interpolation from corase to fine has been added

2003-09-23 01:14  ces74

	* lib/Common/global_defs.h, lib/Regional/Boundary_conditions.c,
	  module/Exchanger/Boundary.cc,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h,
	  module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h, module/Exchanger/misc.cc,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  tests/exchange.py: 1. in Boundary.cc, bid2gid is now generated in
	  a consistent way with assigning boundary.X arrays.
	  
	  2. in ExchangerClass.cc, imposeBC method is added and tested.

2003-09-22 05:24  ces74

	* lib/Common/element_definitions.h, module/Exchanger/Boundary.cc,
	  module/Exchanger/Boundary.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.cc, module/Exchanger/bindings.cc,
	  module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h,
	  module/Exchanger/misc.cc,
	  pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  tests/exchange.py: All the functions needed by Exchanger are
	  created and tested.

2003-09-20 08:32  ces74

	* lib/Common/element_definitions.h, module/Exchanger/Boundary.cc,
	  module/Exchanger/Boundary.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
	  module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h,
	  module/Exchanger/misc.cc,
	  pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  tests/exchange.py: intermediate updates

2003-09-19 13:32  ces74

	* module/Exchanger/Boundary.cc,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
	  module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h,
	  module/Exchanger/misc.cc,
	  pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  tests/exchange.py: send/receive temperature between leader
	  processors tested.

2003-09-19 05:37  ces74

	* module/Exchanger/ExchangerClass.h: *** empty log message ***

2003-09-19 05:03  ces74

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/bindings.cc, module/Exchanger/misc.cc,
	  module/Exchanger/misc.h,
	  pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  tests/exchange.py: intermediate updates

2003-09-19 00:16  puru

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/ExchangerClass.h: Exchanger for Coarse grid has
	  been introduced

2003-09-18 23:12  puru

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.cc: New variables added to
	  Boundary Class

2003-09-18 06:15  ces74

	* module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  tests/exchange.py: two methods for exchanger added: 'gather' and
	  'distribute'

2003-09-12 23:25  tan2

	* tests/citcomsfull.py, tests/citcomsregional.py,
	  tests/coupledcitcoms.py: test

2003-09-12 05:10  tan2

	* module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h: 1. change argument lists of
	  createBoundary(), sendBoundary(), receiveBoundary() and
	  mapBoundary() 2. createBoundary(), sendBoundary(),
	  receiveBoundary() and mapBoundary() have passed test

2003-09-12 04:56  tan2

	* module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h: 1. comment out send() and
	  receive() declaration 2. change argument list of mapBoundary() 3.
	  fix some bugs in sendVelocities() and receiveVelocities() 4.
	  comment out reset_target() 5. add some output in constructor
	  (commented out)

2003-09-12 04:50  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: add
	  printX() and printBid2gid() methods

2003-09-12 04:43  tan2

	* module/Exchanger/exchangers.cc: change the argument lists of
	  createBoundary(), sendBoundary(), receiveBoundary(), and
	  mapBoundary()

2003-09-12 04:41  tan2

	* module/Exchanger/misc.cc: add All_variables data, which is
	  required by Boundary object

2003-09-12 04:33  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: findBoundary will
	  not return boundary object

2003-09-12 04:32  tan2

	* tests/exchange.py: change output slightly

2003-09-11 11:07  puru

	* module/Exchanger/Boundary.cc: duplication of nodes on edges and
	  vertices are removed

2003-09-11 06:40  puru

	* module/Exchanger/Boundary.cc: Duplication of nodes on edges and
	  vertices has been fixed

2003-09-11 04:11  puru

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h: Boundary mapping completed

2003-09-11 01:51  ces74

	* module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/ExchangerClass.cc: Added: functions to
	  send/receive velocities between leader and workers

2003-09-10 11:03  tan2

	* module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
	  module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1.
	  finish exchangeTimestep(), wait() and nowait() to Exchanger, test
	  passed 2. add skeleton of sendTemperature() and
	  receiveTemperature() to Exchanger 3. add bindings to the
	  functions above

2003-09-10 11:01  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: finish
	  stableTimestep() and NewStep()

2003-09-10 11:00  tan2

	* tests/exchange.py: 1. add test for stableTimestep() and NewStep()

2003-09-10 04:08  tan2

	* tests/exchange.py: reflecting changes in Exchanger.py

2003-09-10 04:04  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py, pyre/Coupler.py,
	  pyre/Coupler/Coupler.py, pyre/Solver/Solver.py: 1. remove
	  exchanger.initialize() 2. change argument lists of
	  initTemperature() and applyBoundaryConditions() 3. add more calls
	  to Coupler in Solver

2003-09-10 03:57  tan2

	* module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h,
	  module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h, module/Exchanger/misc.cc,
	  module/Exchanger/misc.h: 1. add boundary as a data member of
	  Exchanger 2. assign boundary at sendBoundary and receiveBoundary
	  3. change argument list of gather, distribute, send and receive
	  functions

2003-09-10 03:41  puru

	* module/Exchanger/FineGridExchanger.cc: global_defs.h has been
	  included

2003-09-10 03:07  puru

	* module/Exchanger/FineGridExchanger.cc: fixed bug

2003-09-10 03:03  puru

	* module/Exchanger/FineGridExchanger.cc: size in
	  FineGridExchanger::createBoundary has been set

2003-09-10 01:25  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h,
	  module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h: 1. declare map() in Boundary class
	  2. changer argument list of several Exchanger functions

2003-09-09 09:35  tan2

	* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
	  module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm,
	  module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h: 1. move declartion and definition
	  of Boundary class to seperated files (was in ExchangerClass.h) 2.
	  add boundary creation and exchanging functions 3. add bindings to
	  boundary creation and exchanging functions

2003-09-09 09:28  tan2

	* tests/exchange.py: add test to Exchanger.findBoundary()

2003-09-09 09:27  tan2

	* pyre/Layout.py, pyre/Layout/Layout.py: createIntercomm() returns
	  mpi.world()

2005-08-23 03:11  unknown_user

	* module/Exchanger/Exchanger.cc, module/Exchanger/Exchanger.h:
	  [vcp] delete of edited revision with dead state

2003-09-09 04:47  tan2

	* module/Exchanger/CoarseGridExchanger.cc,
	  module/Exchanger/CoarseGridExchanger.h,
	  module/Exchanger/Exchanger.cc, module/Exchanger/Exchanger.h,
	  module/Exchanger/ExchangerClass.cc,
	  module/Exchanger/ExchangerClass.h,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm,
	  module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
	  module/Exchanger/exchangers.h, module/Exchanger/misc.cc: 1.
	  change filename Exchanger.* -> ExchangerClass.* to avoid import
	  problem in python 2. add constructors to Exchanger and its child
	  class 3. add bindings to constructors

2003-09-09 04:38  tan2

	* module/Make.mm: add Exchanger module`

2003-09-09 04:37  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py: createExchanger()
	  is done

2003-09-09 04:35  tan2

	* tests/exchange.py: test for Exchanger component

2003-09-07 06:44  tan2

	* module/Exchanger, module/Exchanger/Exchanger.cc,
	  module/Exchanger/Exchanger.h,
	  module/Exchanger/Exchangermodule.cc,
	  module/Exchanger/FineGridExchanger.cc,
	  module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm,
	  module/Exchanger/bindings.cc, module/Exchanger/bindings.h,
	  module/Exchanger/exceptions.cc, module/Exchanger/exceptions.h,
	  module/Exchanger/misc.cc, module/Exchanger/misc.h: original
	  source

2003-09-06 02:49  tan2

	* pyre/Components/Exchanger/CoarseGridExchanger.py,
	  pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/FineGridExchanger.py,
	  pyre/Components/Exchanger/Make.mm,
	  pyre/Components/Exchanger/__init__.py, pyre/CoupledApp.py,
	  pyre/Coupler.py, pyre/Coupler/Coupler.py,
	  pyre/Coupler/__init__.py, pyre/Layout.py, pyre/Layout/Layout.py,
	  pyre/Layout/__init__.py, pyre/Solver/FullSolver.py,
	  pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: add
	  skeletons of coupler and exchanger, change application, layout,
	  and solver accordingly.

2005-08-23 03:10  unknown_user

	* pyre/FullApp.py, pyre/RegionalApp.py: [vcp] delete of edited
	  revision with dead state

2003-09-06 02:26  tan2

	* pyre/FullApp.py, pyre/RegionalApp.py: obsolete

2005-08-23 03:10  unknown_user

	* pyre/CoupledRegionalApp.py: [vcp] delete of edited revision with
	  dead state

2003-09-06 02:25  tan2

	* pyre/CoupledRegionalApp.py: obsolete

2003-09-04 04:18  tan2

	* pyre/CoupledApp.py, pyre/SimpleApp.py: 1. change layout() to
	  findLayout() 2. change calling sequence in initialize()

2003-09-04 04:16  tan2

	* pyre/Layout.py, pyre/Layout/Layout.py: 1. change layout() to
	  initialize() 2. create intercommunicator (not finished)

2003-09-04 04:13  tan2

	* pyre/Controller.py, pyre/Controller/Controller.py: add
	  Controller.initialize()

2003-09-04 04:08  tan2

	* pyre/Solver/Solver.py: Solver is now "coupler-awared". It will
	  initialize/launch coupler and call coupler.stableTimestep() and
	  coupler.applyBoundaryConditions() if necessary.

2003-09-03 11:02  ces74

	* examples/Full/velbc/README: Typos fixed.

2003-09-03 11:01  ces74

	* examples/Regional/velbc/README,
	  examples/Regional/velbc/velbc_regional.tar.gz: 1. Velbc example
	  files are now tarred and compressed.
	  
	  2. README file explains how to untar the provided velbc archive
	  and the naming scheme of the velbc files.

2003-09-03 10:57  ces74

	* examples/Full/input.sample, examples/Full/velbc,
	  examples/Full/velbc/README,
	  examples/Full/velbc/velbc_full.tar.gz: 1. input.sample has been
	  modified to show how to read in velocity b.c. from files.
	  
	  2. The gzipped tar file, velbc_full.tar.gz, contains velbc files
	  for each M.Y. and for each sphereical cap.
	  
	  3. README explains how to untar the velbc files and their naming
	  scheme.

2003-09-03 07:23  ces74

	* examples/Regional/input.sample, examples/Regional/velbc,
	  examples/Regional/velbc/velbc_regional40,
	  examples/Regional/velbc/velbc_regional41: 1. The example input
	  file is modified to show how to use velbc files.
	  
	  2. velbc directory is added together with velbc examples.

2003-09-02 01:30  ces74

	* lib/Common/Problem_related.c, lib/Full/Make.mm,
	  lib/Full/Read_input_from_files.c, lib/Regional/Make.mm,
	  lib/Regional/Read_input_from_files.c: 1. The function to read in
	  velocity boundary conditions for every My is removed from
	  Common/Problem_related.c.
	  
	  2. A new file, Read_input_from_files.c is added to lib/Full/ and
	  lib/Regional/. This file contains a sinlge function
	  'read_input_files_for_timesteps'.
	  
	  3. Full/Make.mm and Regional/Make.mm have been changed
	  accordingly.

2003-09-01 09:02  ces74

	* drivers/Full/Make.mm, drivers/Regional/Make.mm: A bug fixed in
	  the Makefiles:
	  
	  The rule for linking binaries, CitcomSFull and CitcomSRegional,
	  had libCitcomSCommon.a and libCitcomSFull(or Regional).a as
	  dependencies.
	  
	  --> now these are treated as libraries to which Citcom.o is
	  linked.

2005-08-23 03:10  unknown_user

	* pyre/Components/Coupler.py, pyre/Components/Exchanger.py: [vcp]
	  delete of edited revision with dead state

2003-08-30 07:45  tan2

	* pyre/Components/Coupler.py, pyre/Components/Exchanger.py,
	  pyre/Components/Make.mm, pyre/Make.mm: change directory structure

2003-08-30 07:44  tan2

	* pyre/Components/Exchanger/Exchanger.py,
	  pyre/Components/Exchanger/Make.mm,
	  pyre/Components/Exchanger/__init__.py: original source

2003-08-30 07:39  tan2

	* pyre/Components/Exchanger,
	  pyre/Components/Exchanger/Exchanger.py, pyre/CoupledApp.py:
	  original source

2003-08-30 07:37  tan2

	* pyre/Coupler, pyre/Coupler/Make.mm, pyre/Coupler/__init__.py:
	  original source

2003-08-30 07:35  tan2

	* pyre/Layout, pyre/Layout.py, pyre/Layout/Layout.py,
	  pyre/Layout/Make.mm, pyre/Layout/__init__.py: original source

2003-08-30 07:29  ces74

	* pyre/Components/Advection_diffusion/Advection_diffusion.py:
	  'maxadvtime' is removed from Advection_diffusion.inventory.

2003-08-30 07:27  ces74

	* pyre/Components/Param.py: The following five parameters are
	  removed from the Param.inventory.
	  
	  minstep, maxstep, maxtotstep, storage_spacing,
	  cpu_limits_in_seconds

2003-08-30 07:24  ces74

	* drivers/Citcom.c: 1. A step is added to decide whether to proceed
	  time-marching.
	  
	  2. max_dimensionless_time is not a criterion for time-marching
	  any more.

2003-08-30 07:19  ces74

	* lib/Common/Advection_diffusion.c: The following parameters are no
	  more used in PG_timestep_solve:
	  
	  minstep, maxstep, and maxtotstep

2003-08-30 03:41  tan2

	* pyre/SimpleApp.py, pyre/Solver/FullSolver.py,
	  pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: use new
	  interface of Facilities

2003-08-30 03:40  tan2

	* pyre/Facilities/Mesher.py, pyre/Facilities/Solver.py,
	  pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py: change
	  argument list of __init__() to be compatible with pyre facility

2003-08-30 02:46  tan2

	* pyre/Facilities/Make.mm, pyre/Facilities/Solver.py,
	  pyre/SimpleApp.py: add Solver facility and use it in SimpleApp.py

2003-08-30 01:33  tan2

	* pyre/Controller.py, pyre/Controller/Controller.py: 1. change
	  march() so that final step is saved 2. remove
	  run_init_simulation() 3. change the argument list of save()

2003-08-30 01:31  tan2

	* pyre/Solver/Solver.py: merge run_init_simulation() with launch()

2003-08-30 01:06  tan2

	* pyre/SimpleApp.py, pyre/Solver/Solver.py: communicator is
	  assigned in Application

2003-08-29 07:43  tan2

	* pyre/Make.mm: add SimpleApp.py

2003-08-29 07:08  tan2

	* pyre/SimpleApp.py, tests/citcomsregional.py: 1. add SimpleApp,
	  which using Controller and Solver componets 2. change
	  citcomsregional.py accordingly

2003-08-29 06:58  tan2

	* pyre/Controller.py, pyre/Controller/Controller.py,
	  pyre/Solver/Solver.py: fix typos

2003-08-29 06:18  ces74

	* pyre/Solver/Solver.py: bug fixed in the 'advance' method: tsolver
	  and vsolver are now defined before being used.

2003-08-29 06:12  ces74

	* pyre/Controller/__init__.py: bug fixed: Controller is now
	  imported before being used.

2003-08-29 06:10  ces74

	* pyre/Make.mm: Controller is added to 'BLD_DIRS'

2003-08-29 06:04  ces74

	* pyre/Controller.py, pyre/Controller/Controller.py,
	  pyre/Controller/Make.mm, pyre/Controller/__init__.py,
	  pyre/Solver/Solver.py: 1. Controller.py modified:
	  self.solver.start_simulation --> self.solver.launch 2. Solver. py
	  modified: self.start_simulation --> self.launch 3. Make.mm and
	  __init__.py added to CitcomS/pyre/Controller/

2003-08-29 05:53  ces74

	* pyre/Controller, pyre/Controller.py,
	  pyre/Controller/Controller.py: Controller.py newly added. It's a
	  derivation from pyre/components/SimulationController.py.

2003-08-29 05:49  ces74

	* pyre/Solver/Solver.py: method endSimulation modified:
	  endSimulation(self) --> endSimulation(self,step)

2003-08-29 05:37  ces74

	* pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Solver/Solver.py: 1. Solver.py modified to be consistent
	  with 'Controller'.
	  
	  2. Advection_diffusion.py A new method, 'launch', runs
	  PG_timestep_init(). The '_solve' method now executes only
	  PG_timestep_solve()

2005-08-23 03:09  unknown_user

	* pyre/Citcom.py, pyre/CitcomSFull.py, pyre/CitcomSRegional.py:
	  [vcp] delete of edited revision with dead state

2003-08-28 05:24  tan2

	* pyre/Citcom.py, pyre/CitcomSFull.py, pyre/CitcomSRegional.py,
	  pyre/FullApp.py, pyre/Make.mm, pyre/RegionalApp.py,
	  pyre/Solver/FullSolver.py, pyre/Solver/Make.mm,
	  pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py,
	  pyre/Solver/__init__.py: 1. move and rename files: Citcom.py ->
	  Solver/Solver.py CitcomSFull.py -> Solver/FullSolver.py
	  CitcomSRegional.py -> Solver/RegionalSolver.py 2. add Solver
	  module 3. change Make.mm, FullApp.py and RegionalApp.py
	  accordingly

2005-08-23 03:08  unknown_user

	* pyre/Components/Parallel.py: [vcp] delete of edited revision with
	  dead state

2003-08-28 03:52  tan2

	* pyre/Citcom.py, pyre/CitcomSFull.py, pyre/CitcomSRegional.py,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/Advection_diffusion/__init__.py,
	  pyre/Components/BC.py, pyre/Components/CitcomComponent.py,
	  pyre/Components/Const.py, pyre/Components/IC.py,
	  pyre/Components/Parallel.py, pyre/Components/Param.py,
	  pyre/Components/Phase.py, pyre/Components/Sphere/FullSphere.py,
	  pyre/Components/Sphere/RegionalSphere.py,
	  pyre/Components/Sphere/Sphere.py,
	  pyre/Components/Sphere/__init__.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Stokes_solver/__init__.py,
	  pyre/Components/Visc.py, pyre/CoupledRegionalApp.py,
	  pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py,
	  pyre/Solver/Solver.py: simplified components layout

2003-08-27 03:58  tan2

	* pyre/Components/Advection_diffusion/Advection_diffusion.py: add
	  stable_timestep() method

2003-08-27 03:56  tan2

	* lib/Common/Advection_diffusion.c,
	  lib/Common/advection_diffusion.h, module/Regional/advdiffu.cc,
	  module/Regional/advdiffu.h, module/Regional/bindings.cc: add
	  stable_timestep() to lib/ and its binding to module/

2003-08-26 02:34  tan2

	* pyre/CitcomSFull.py, pyre/FullApp.py, pyre/Solver/FullSolver.py:
	  add components CitcomSRegional and CitcomSFull

2005-08-23 03:08  unknown_user

	* pyre/CitcomApp.py: [vcp] delete of edited revision with dead
	  state

2003-08-26 02:16  tan2

	* pyre/Citcom.py, pyre/CitcomApp.py, pyre/CitcomSRegional.py,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/Sphere/Sphere.py,
	  pyre/Components/Stokes_solver/Incompressible.py, pyre/Make.mm,
	  pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py,
	  pyre/Solver/Solver.py: add components CitcomSRegional and
	  CitcomSFull

2003-08-23 05:35  tan2

	* pyre/Citcom.py, pyre/CitcomApp.py, pyre/CitcomSFull.py,
	  pyre/CitcomSRegional.py, pyre/FullApp.py, pyre/RegionalApp.py,
	  pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py,
	  pyre/Solver/Solver.py: fix bug introduced by previous check-in

2003-08-23 05:35  tan2

	* module/Regional/bindings.cc, module/Regional/setProperties.cc,
	  module/Regional/setProperties.h: fix typo

2005-08-23 03:07  unknown_user

	* pyre/Components/Stokes_solver/Imcompressible.py: [vcp] delete of
	  edited revision with dead state

2003-08-23 05:24  tan2

	* pyre/Components/Stokes_solver/Imcompressible.py: rename file

2003-08-23 05:21  tan2

	* drivers/Citcom.c: output is performed every 'storage_spacing'
	  time step

2003-08-23 05:19  tan2

	* tests/citcomsfull.py, tests/citcomsregional.py,
	  tests/coupledcitcoms.py: *** empty log message ***

2005-08-23 03:07  unknown_user

	* pyre/RadiusDepth.py: [vcp] delete of edited revision with dead
	  state

2003-08-23 05:18  tan2

	* pyre/Citcom.py, pyre/CitcomApp.py, pyre/CitcomSFull.py,
	  pyre/CitcomSRegional.py, pyre/Components/Coupler.py,
	  pyre/Components/Exchanger.py, pyre/Components/Make.mm,
	  pyre/CoupledRegionalApp.py, pyre/FullApp.py, pyre/Make.mm,
	  pyre/RadiusDepth.py, pyre/RegionalApp.py,
	  pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py,
	  pyre/Solver/Solver.py: a small step toward coupled application

2003-08-23 05:16  tan2

	* pyre/Facilities/VSolver.py: *** empty log message ***

2003-08-23 05:14  tan2

	* pyre/Components/Stokes_solver/Imcompressible.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Stokes_solver/Make.mm,
	  pyre/Components/Stokes_solver/__init__.py: fix typo

2003-08-21 02:18  tan2

	* lib/Common/Instructions.c, lib/Common/convection_variables.h,
	  lib/Common/global_defs.h: remove several obsolelte variables

2003-08-21 01:54  tan2

	* lib/Regional/Boundary_conditions.c: add open_top velocity
	  boundary condition

2003-08-20 09:45  tan2

	* tests/citcomsfull.py, tests/citcomsregional.py: determine
	  staging.nodes from input parameters automatically

2003-08-20 04:24  tan2

	* pyre/Citcom.py, pyre/CitcomApp.py,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/CitcomComponent.py,
	  pyre/Components/Sphere/FullSphere.py,
	  pyre/Components/Sphere/RegionalSphere.py,
	  pyre/Components/Stokes_solver/Imcompressible.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Solver/Solver.py: create a python variable
	  CitcomApp.all_variables, which holds the C pointer "struct
	  All_varialbes *E". CitcomApp.all_variables is passed as an
	  argument to most CitcomModule functions.

2003-08-20 04:21  tan2

	* module/Regional/advdiffu.cc, module/Regional/mesher.cc,
	  module/Regional/misc.cc, module/Regional/outputs.cc,
	  module/Regional/setProperties.cc,
	  module/Regional/stokes_solver.cc: remove global declaration of
	  "struct All_variables *E", E is passed as an argument to all
	  functions.

2003-08-20 04:20  tan2

	* drivers/Citcom.c, lib/Common/Citcom_init.c,
	  lib/Common/Instructions.c, lib/Common/citcom_init.h: 1. remove
	  declaration of "extern struct All_variables *E" in citcom_init.h
	  2. E is allocated in Citcom_init() and returned to main() 3.
	  change other files accordingly.

2003-08-16 01:59  tan2

	* lib/Common/Drive_solvers.c, lib/Common/drive_solvers.h: *** empty
	  log message ***

2003-08-16 01:56  tan2

	* module/Regional/bindings.cc, module/Regional/stokes_solver.cc,
	  module/Regional/stokes_solver.h: remove obsolete bindings to
	  general_stokes_solver_*()

2003-08-16 01:56  tan2

	* module/Regional/setProperties.cc,
	  module/Regional/setProperties.h: change function name:
	  pyCitcom_Stokes_solver_set_properties() ->
	  pyCitcom_Imcompressible_set_properties()

2003-08-16 01:47  tan2

	* pyre/Components/Stokes_solver/Imcompressible.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Stokes_solver/__init__.py: merge
	  ImcompressibleNewtonian() and ImcompressibleNonNewtonian() to
	  Imcompressible(), Stokes_solver() becomes obsolete.

2003-08-15 07:28  tan2

	* lib/Common/Convection.c, lib/Common/Element_calculations.c,
	  lib/Common/General_matrix_functions.c, lib/Common/global_defs.h,
	  lib/Full/Lith_age.c, lib/Regional/Boundary_conditions.c,
	  lib/Regional/Lith_age.c: eliminate static variables

2003-08-15 05:50  tan2

	* module/Regional/bindings.cc, module/Regional/mesher.cc,
	  module/Regional/stokes_solver.cc,
	  module/Regional/stokes_solver.h,
	  pyre/Components/Stokes_solver/Stokes_solver.py: reflect the
	  change in general_stokes_solver()

2003-08-15 05:43  tan2

	* lib/Common/Construct_arrays.c, lib/Common/Drive_solvers.c,
	  lib/Common/Instructions.c: 1. change the flowline of
	  general_stokes_solver() 2. eliminate static variables in
	  construct_stiffness_B_matrix() 3. add call to
	  general_stokes_solver_setup() in read_instructions()

2003-08-15 01:36  tan2

	* lib/Full/Parallel_related.c: elimanate static variables.

2003-08-15 01:35  tan2

	* module/Full/Make.mm, module/Regional/Make.mm: add
	  $(TOOLS_DIR)/lib to library path

2003-08-13 08:22  tan2

	* module/Full/Make.mm, module/Regional/Make.mm: change the library
	  link paths

2003-08-13 03:43  ces74

	* drivers/Full/Make.mm, drivers/Regional/Make.mm: Modified in order
	  to use separate static libraries:
	  
	  libCitcomSCommon.a, libCitcomSFull.a, and libCitcomSRegional.a

2003-08-13 03:40  ces74

	* lib/Common/Initial_temperature.c: Typo fixed:
	  
	  "Missing input parameter: 'perturbml' -> "Missing input
	  parameter: 'perturbl'

2003-08-12 23:54  ces74

	* lib/Full/Make.mm, lib/Regional/Make.mm: a bug fixed: lib/Common
	  is now included in paths for header files.

2003-08-12 23:34  ces74

	* lib/Common/Make.mm, lib/Full/Make.mm, lib/Make.mm,
	  lib/Regional/Make.mm, module/Full/Make.mm,
	  module/Regional/Make.mm: Makefiles in module/ and lib/ modified
	  to create three separate static libraries: libCitcomSCommon.a,
	  libCitcomSFull.a, and libCitcomSRegional.a
	  
	  These libraries are used when linking *.so objects.

2003-08-10 03:25  tan2

	* lib/Common/Instructions.c, lib/Full/Version_dependent.c,
	  lib/Regional/Version_dependent.c: unifying
	  read_initial_settings()

2003-08-09 05:51  tan2

	* lib/Common/Make.mm, lib/Full/Make.mm, lib/Full/Output.c,
	  lib/Regional/Make.mm, lib/Regional/Obsolete.c,
	  lib/Regional/Output.c: unifying

2003-08-09 05:34  tan2

	* lib/Common/Make.mm, lib/Full/Make.mm,
	  lib/Full/Process_buoyancy.c, lib/Regional/Make.mm,
	  lib/Regional/Process_buoyancy.c: unifying

2005-08-23 03:05  unknown_user

	* pyre/Components/Advection_diffusion/Temperature_diffadv.py: [vcp]
	  delete of edited revision with dead state

2003-08-09 05:13  tan2

	* examples/Full/input.sample, examples/Full/machine.sample,
	  pyre/Components/Advection_diffusion/Temperature_diffadv.py:
	  obsolete

2003-08-09 05:03  tan2

	* lib/Common/Output.c, lib/Common/Problem_related.c,
	  lib/Common/Tracer_advection.c, lib/Common/global_defs.h,
	  lib/Full/Output.c, lib/Full/Parallel_related.c,
	  lib/Regional/Boundary_conditions.c, lib/Regional/Obsolete.c,
	  lib/Regional/Output.c, lib/Regional/Parallel_related.c,
	  lib/Regional/Process_buoyancy.c, lib/Regional/Sphere_related.c,
	  lib/Regional/Version_dependent.c, module/Regional/bindings.cc,
	  module/Regional/setProperties.cc,
	  module/Regional/setProperties.h: 1. eliminate several global
	  variables- parallel: mst, nproc[xyz]l, me_locl sphere:
	  local_capid, pid_surf, cap.connection 2. change the way
	  Regional/Parallel_related.c used to assign me_loc and
	  PROCESSOR.pass

2003-08-08 05:05  tan2

	* module/Make.mm: default action will link files from Regional/ to
	  Full/

2003-08-08 04:34  tan2

	* module/Regional/setProperties.cc: only processor 0 can write to
	  stderr now Note: device /dev/null and /dev/stderr are used, may
	  not portable to non-unix platform

2003-08-08 02:49  tan2

	* drivers/Citcom.c, lib/Common/Instructions.c,
	  lib/Common/Sphere_harmonics.c, lib/Common/parallel_related.h,
	  lib/Full/Obsolete.c, lib/Full/Parallel_related.c,
	  lib/Regional/Obsolete.c, lib/Regional/Parallel_related.c,
	  module/Regional/mesher.cc: *** empty log message ***

2003-08-08 01:41  tan2

	* drivers/Full/Make.mm, drivers/Full/local.def, drivers/Make.mm,
	  drivers/Regional/Make.mm, drivers/Regional/local.def,
	  drivers/local.def, lib/Common/Output.c, lib/Common/global_defs.h,
	  lib/Full/Output.c, lib/Full/global_defs.h, lib/Full/lith_age.h,
	  lib/Full/output.h, lib/Full/parallel_related.h, lib/Make.mm,
	  lib/Regional/global_defs.h, lib/Regional/lith_age.h,
	  lib/Regional/output.h, lib/Regional/parallel_related.h,
	  lib/local.def: move header files global_defs.h, lith_age.h,
	  output.h, and parallel_related.h to Common/

2003-08-07 04:09  tan2

	* lib/Common/Make.mm, lib/Full/Make.mm, lib/Full/Problem_related.c,
	  lib/Regional/Make.mm, lib/Regional/Problem_related.c: unify
	  Problem_related.c

2003-08-07 04:00  tan2

	* lib/Common/Initial_temperature.c, lib/Common/Make.mm,
	  lib/Common/convection_variables.h,
	  lib/Full/Initial_temperature.c, lib/Full/Make.mm,
	  lib/Full/Version_dependent.c, lib/Full/initial_temperature.h,
	  lib/Regional/Initial_temperature.c, lib/Regional/Make.mm,
	  lib/Regional/Version_dependent.c,
	  lib/Regional/initial_temperature.h,
	  module/Regional/setProperties.cc: unify Initial_temperature.c and
	  initial_temperature.h

2003-08-07 01:56  tan2

	* lib/Common/Output.c, lib/Full/Obsolete.c, lib/Full/Output.c: move
	  obsolete functions from Output.c to Obsolete.c

2003-08-07 01:47  tan2

	* lib/Common/Global_operations.c, lib/Common/Make.mm,
	  lib/Full/Global_operations.c, lib/Full/Make.mm,
	  lib/Full/Obsolete.c, lib/Regional/Global_operations.c,
	  lib/Regional/Make.mm, lib/Regional/Obsolete.c: unify two versions
	  of Global_operations.c, and put it to Common/

2003-08-03 07:43  tan2

	* module/Regional/setProperties.cc: bug fixed, tests/citcomsfull.py
	  now gives correct result

2003-08-02 05:57  tan2

	* tests/citcomsfull.py, tests/hrothgar.py: to run a Full version of
	  CitcomS, use the following command: ./citcomsfull.py
	  --staging=hrothgar --param.datafile=/SOME_PATH/test

2005-08-23 03:02  unknown_user

	* module/local.def: [vcp] delete of edited revision with dead state

2003-08-02 05:53  tan2

	* module/Make.mm, module/Regional/Regionalmodule.cc,
	  module/Regional/advdiffu.cc, module/Regional/advdiffu.h,
	  module/Regional/bindings.cc, module/Regional/bindings.h,
	  module/Regional/exceptions.cc, module/Regional/exceptions.h,
	  module/Regional/local.def, module/Regional/mesher.cc,
	  module/Regional/mesher.h, module/Regional/misc.cc,
	  module/Regional/misc.h, module/Regional/outputs.cc,
	  module/Regional/outputs.h, module/Regional/setProperties.cc,
	  module/Regional/setProperties.h,
	  module/Regional/stokes_solver.cc,
	  module/Regional/stokes_solver.h, module/local.def: make some
	  changes in function names so that both Full and Regioanl versions
	  can use the same source code.

2005-08-23 03:02  unknown_user

	* module/Full/bindings.cc, module/Full/bindings.h,
	  module/Full/exceptions.cc, module/Full/exceptions.h,
	  module/Full/misc.cc, module/Full/misc.h: [vcp] delete of edited
	  revision with dead state

2003-08-02 05:52  tan2

	* module/Full/Fullmodule.cc, module/Full/Make.mm,
	  module/Full/bindings.cc, module/Full/bindings.h,
	  module/Full/exceptions.cc, module/Full/exceptions.h,
	  module/Full/local.def, module/Full/misc.cc, module/Full/misc.h:
	  module/Full and module/Regional now use the same files, except
	  $(TYPE)module.cc and Make.mm.
	  
	  ***** Important ***** When you check out this directory
	  (module/Full) in the first time, do 'mm link' in this directory.
	  This will hard-link every source files in module/Regional to this
	  directory.

2003-08-02 05:25  tan2

	* lib/Full/global_defs.h: add some variable declaration which are
	  only used by regional version

2003-08-02 05:24  tan2

	* pyre/Citcom.py, pyre/CitcomApp.py, pyre/CitcomSFull.py,
	  pyre/CitcomSRegional.py, pyre/FullApp.py, pyre/Make.mm,
	  pyre/RegionalApp.py, pyre/Solver/FullSolver.py,
	  pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: 1. add base
	  class CitcomApp 2. derive FullApp and RegionalApp form CitcomApp

2003-08-02 02:05  tan2

	* pyre/Components/Sphere/FullSphere.py,
	  pyre/Components/Sphere/Make.mm,
	  pyre/Components/Sphere/RegionalSphere.py,
	  pyre/Components/Sphere/Sphere.py,
	  pyre/Components/Sphere/__init__.py, pyre/Facilities/Mesher.py: 1.
	  add a base class Sphere for component Sphere 2. add a new
	  component FullSphere for Full version 3. change Make.mm,
	  __init__.py, and the binder of facility Mesher accordingly

2003-08-01 02:41  tan2

	* lib/Common/General_matrix_functions.c,
	  lib/Common/Initial_temperature.c, lib/Common/Instructions.c,
	  lib/Full/Initial_temperature.c, lib/Full/Parallel_related.c,
	  lib/Regional/Initial_temperature.c: bug fix

2003-08-01 02:40  tan2

	* lib/Common/Process_buoyancy.c, lib/Full/Obsolete.c,
	  lib/Full/Process_buoyancy.c: remove obsolete function

2003-07-30 03:54  tan2

	* drivers/Make.mm, lib/Make.mm: *** empty log message ***

2003-07-30 03:54  tan2

	* lib/Common/Output.c, lib/Common/Process_buoyancy.c,
	  lib/Full/Boundary_conditions.c, lib/Full/Global_operations.c,
	  lib/Full/Initial_temperature.c, lib/Full/Lith_age.c,
	  lib/Full/Make.mm, lib/Full/Output.c, lib/Full/Parallel_related.c,
	  lib/Full/Problem_related.c, lib/Full/Process_buoyancy.c,
	  lib/Full/Version_dependent.c, lib/Full/global_defs.h,
	  lib/Full/initial_temperature.h, lib/Full/lith_age.h,
	  lib/Full/output.h, lib/Full/parallel_related.h: copy changes in
	  Regional version to Full version

2003-07-29 06:03  tan2

	* pyre/CitcomSRegional.py,
	  pyre/Components/Advection_diffusion/Make.mm,
	  pyre/Components/Make.mm, pyre/Components/Sphere/Make.mm,
	  pyre/Components/Stokes_solver/Make.mm, pyre/Facilities/Mesher.py,
	  pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py,
	  pyre/Make.mm, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py:
	  change directory structures

2003-07-29 04:57  tan2

	* lib/Common/Convection.c, lib/Common/Solver_multigrid.c,
	  module/Regional/bindings.cc, module/Regional/outputs.cc,
	  module/Regional/outputs.h, module/Regional/setProperties.cc,
	  pyre/CitcomSRegional.py,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/Sphere/RegionalSphere.py,
	  pyre/Components/Stokes_solver/Stokes_solver.py,
	  pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: 1.
	  RegionalApp._setProperties() is called before Component.init() 2.
	  some cosmetics

2003-07-27 04:47  tan2

	* drivers/Citcom.c, lib/Common/Instructions.c,
	  lib/Common/Problem_related.c, lib/Common/Process_velocity.c,
	  lib/Common/output.h, lib/Regional/Obsolete.c,
	  lib/Regional/Output.c, lib/Regional/Problem_related.c,
	  lib/Regional/Process_buoyancy.c,
	  lib/Regional/Version_dependent.c, lib/Regional/output.h,
	  module/Regional/bindings.cc, module/Regional/mesher.cc,
	  module/Regional/misc.cc, module/Regional/misc.h,
	  module/Regional/outputs.cc, module/Regional/outputs.h,
	  pyre/CitcomSRegional.py, pyre/RegionalApp.py,
	  pyre/Solver/RegionalSolver.py: complete output part

2003-07-26 03:43  tan2

	* drivers/Citcom.c, lib/Common/Advection_diffusion.c,
	  lib/Common/Initial_temperature.c,
	  lib/Regional/Initial_temperature.c, module/Regional/advdiffu.cc,
	  module/Regional/bindings.cc, module/Regional/mesher.cc,
	  module/Regional/misc.cc, module/Regional/misc.h,
	  module/Regional/setProperties.cc, pyre/CitcomSRegional.py,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/Advection_diffusion/__init__.py,
	  pyre/Components/BC.py, pyre/Components/Const.py,
	  pyre/Components/Param.py, pyre/Components/Phase.py,
	  pyre/Components/Sphere/RegionalSphere.py,
	  pyre/Components/Stokes_solver/Stokes_solver.py,
	  pyre/Components/Visc.py, pyre/RegionalApp.py,
	  pyre/Solver/RegionalSolver.py: complete VSolver and TSolver

2003-07-26 02:17  tan2

	* lib/Common/Parsing.c: bug fix

2003-07-26 02:13  tan2

	* lib/Common/Parsing.c: cosmetic output

2003-07-25 03:10  tan2

	* lib/Common/Global_operations.c, lib/Regional/Global_operations.c,
	  lib/Regional/Parallel_related.c, module/Regional/bindings.cc,
	  module/Regional/mesher.cc, module/Regional/mesher.h,
	  module/Regional/setProperties.cc, pyre/CitcomSRegional.py,
	  pyre/Components/Sphere/RegionalSphere.py, pyre/RegionalApp.py,
	  pyre/Solver/RegionalSolver.py: finish RegionalSphere.run(), it
	  gives identical results as stand-alone CitcomSRegional

2003-07-25 00:46  tan2

	* pyre/CitcomSRegional.py,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/Advection_diffusion/__init__.py,
	  pyre/Components/BC.py, pyre/Components/CitcomComponent.py,
	  pyre/Components/Const.py, pyre/Components/IC.py,
	  pyre/Components/Make.mm, pyre/Components/Parallel.py,
	  pyre/Components/Param.py, pyre/Components/Phase.py,
	  pyre/Components/Sphere/RegionalSphere.py,
	  pyre/Components/Sphere/__init__.py,
	  pyre/Components/Stokes_solver/Imcompressible.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Stokes_solver/Stokes_solver.py,
	  pyre/Components/Stokes_solver/__init__.py,
	  pyre/Components/Visc.py, pyre/RegionalApp.py,
	  pyre/Solver/RegionalSolver.py, tests/citcomsregional.py,
	  tests/signon.py: 1. remove passing filename to
	  RegionalApp.__init__() 2. add new base component
	  CitcomComponent(), derive every component from CitcomComponent,
	  the interface to __init__ and setProperties are changed

2003-07-24 07:04  tan2

	* module/Regional/advdiffu.cc, module/Regional/advdiffu.h,
	  module/Regional/bindings.cc, module/Regional/misc.cc,
	  module/Regional/misc.h,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py: add
	  binding of set_convection_defaults()

2003-07-24 06:00  tan2

	* lib/Common/Initial_temperature.c,
	  lib/Common/initial_temperature.h,
	  lib/Regional/Initial_temperature.c,
	  lib/Regional/Version_dependent.c,
	  lib/Regional/initial_temperature.h: seperate input and init
	  phases of temperature IC

2003-07-24 05:59  tan2

	* lib/Common/global_defs.h, lib/Regional/global_defs.h,
	  module/Regional/setProperties.cc: remove global variables
	  VERBOSE, DESCRIBE, and BEGINNER

2003-07-24 05:00  tan2

	* module/Regional/bindings.cc, module/Regional/setProperties.cc,
	  module/Regional/setProperties.h, pyre/CitcomSRegional.py,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/Const.py, pyre/Components/Parallel.py,
	  pyre/Components/Param.py,
	  pyre/Components/Sphere/RegionalSphere.py,
	  pyre/Components/Stokes_solver/Stokes_solver.py,
	  pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: finished
	  setting properties

2003-07-24 02:00  tan2

	* pyre/Components/IC.py: typo fixed

2003-07-23 12:29  ces74

	* pyre/Components/BC.py, pyre/Components/Const.py,
	  pyre/Components/IC.py, pyre/Components/Parallel.py,
	  pyre/Components/Param.py, pyre/Components/Phase.py,
	  pyre/Components/Visc.py: '*_set_prop' methods of the 'Regioanl'
	  module are now called
	  
	  '*_set_properties'.

2003-07-23 12:27  ces74

	* lib/Common/global_defs.h, lib/Regional/global_defs.h: New members
	  of the "CONTROL" and the "All_variables" structure added.

2003-07-23 12:26  ces74

	* lib/Common/Initial_temperature.c,
	  lib/Regional/Initial_temperature.c: Originally local variables,
	  
	  number_of_perturbations, perturb_ll, perturb_mm, load_depth, and
	  perturb_mag,
	  
	  are now members of the global "All_variables" structure.

2003-07-23 12:22  ces74

	* lib/Common/Parsing.c: Originally local variables, VERBOSE,
	  DESCRIBE, and BEGINNER,
	  
	  are now global: members of the 'All_variables' structure.

2003-07-23 12:19  ces74

	* module/Regional/bindings.cc, module/Regional/outputs.cc,
	  module/Regional/stokes_solver.cc: function name changed from
	  *_set_prop to *_set_properties.

2003-07-23 12:18  ces74

	* module/Regional/setProperties.cc,
	  module/Regional/setProperties.h: Properties for the following
	  components added: IC, Const, Param, Phase, and Parallel.

2003-07-23 04:58  tan2

	* module/Regional/bindings.cc, module/Regional/mesher.cc,
	  module/Regional/misc.cc, module/Regional/misc.h,
	  pyre/CitcomSRegional.py, pyre/RegionalApp.py,
	  pyre/Solver/RegionalSolver.py: 1. change Citcom_Init() to
	  citcom_init() (finished) 2. add binding to open info_file

2003-07-23 02:52  tan2

	* lib/Common/Advection_diffusion.c, lib/Common/advection.h: ***
	  empty log message ***

2003-07-22 04:58  ces74

	* lib/Common/Drive_solvers.c: Functions uncommented: void
	  general_stokes_solver_init(struct All_variables *E) void
	  general_stokes_solver_fini(struct All_variables *E) void
	  general_stokes_solver_update_velo(struct All_variables *E) void
	  general_stokes_solver_Unorm(struct All_variables *E, double
	  *Udot_mag, double *dUdot_mag) void
	  general_stokes_solver_log(struct All_variables *E, float
	  Udot_mag, float dUdot_mag, int count)

2003-07-22 04:44  tan2

	* lib/Common/output.h, lib/Regional/Boundary_conditions.c,
	  lib/Regional/Obsolete.c, lib/Regional/Output.c,
	  lib/Regional/Parallel_related.c, lib/Regional/output.h: partially
	  eliminate use of static variables

2003-07-19 07:34  tan2

	* lib/Common/Global_operations.c, lib/Common/global_defs.h,
	  lib/Regional/Global_operations.c,
	  lib/Regional/Parallel_related.c, lib/Regional/global_defs.h: add
	  communicators E->parallel.horizontal_comm and
	  E->parallel.vertical_comm and initialize them at
	  set_horizontal_communicator() and set_vertical_communicator()

2003-07-19 05:15  tan2

	* drivers/Citcom.c: change Citcom_Init() to citcom_init()

2003-07-18 07:10  tan2

	* lib/Common/Citcom_init.c, lib/Common/Drive_solvers.c,
	  lib/Common/Element_calculations.c,
	  lib/Common/General_matrix_functions.c, lib/Common/Instructions.c,
	  lib/Common/Interuption.c, lib/Common/Process_velocity.c,
	  lib/Common/Solver_multigrid.c, lib/Common/Stokes_flow_Incomp.c,
	  lib/Common/Tracer_advection.c, lib/Common/Viscosity_structures.c,
	  lib/Common/citcom_init.h, lib/Common/interuption.h: 1. change
	  Citcom_Init() to citcom_init() 2. add interuption.h, header file
	  of Interuption.c 3. partially eliminate use of static variables

2003-07-18 06:31  tan2

	* lib/Common/Global_operations.c, lib/Regional/Global_operations.c:
	  vnorm_nonnewt() returned NaN if there was only one material type.
	  bug? fixed.

2003-07-18 04:19  tan2

	* lib/Regional/Sphere_related.c: memory-leak fixed

2003-07-17 04:52  tan2

	* lib/Common/global_defs.h, lib/Regional/global_defs.h: add
	  argument declaration for function pointers (necessarily when
	  linking with C++)

2003-07-17 04:49  tan2

	* module/Regional/Make.mm, module/Regional/bindings.cc,
	  module/Regional/mesher.cc, module/Regional/mesher.h: add bindings
	  of component RegionalSphere()

2005-08-23 02:55  unknown_user

	* pyre/Components/Mesh.py: [vcp] delete of edited revision with
	  dead state

2003-07-16 04:53  tan2

	* pyre/Components/Make.mm, pyre/Components/Mesh.py: component
	  Mesh() is replaced by component RegionalSphere()

2003-07-16 04:50  tan2

	* pyre/CitcomSRegional.py, pyre/Components/Sphere,
	  pyre/Components/Sphere/Make.mm,
	  pyre/Components/Sphere/RegionalSphere.py,
	  pyre/Components/Sphere/__init__.py, pyre/Facilities/Make.mm,
	  pyre/Facilities/Mesher.py, pyre/RegionalApp.py,
	  pyre/Solver/RegionalSolver.py: add new facility Mesher() and its
	  default component RegionalSphere()

2003-07-16 04:47  tan2

	* pyre/Components/Stokes_solver/Stokes_solver.py: typo fixed

2003-07-16 01:17  ces74

	* module/Regional/bindings.cc: A missing part of the method talbe
	  added: set_cg_defaults, set_mg_defaults, set_mg_el_defaults.

2005-08-23 02:55  unknown_user

	* pyre/Components/Adv_solver.py: [vcp] delete of edited revision
	  with dead state

2003-07-16 01:06  ces74

	* pyre/Components/Adv_solver.py: Binding for advection-diffusion
	  solver is now in pyre/Regional/Facilities/TSolver.py

2003-07-16 01:04  ces74

	* pyre/Facilities/TSolver.py: Binding of TSolver with a component
	  (Temperature_diffadv.py) is implemented.

2003-07-16 01:03  ces74

	* pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/Advection_diffusion/Temperature_diffadv.py,
	  pyre/Components/Advection_diffusion/__init__.py:
	  Temperature_diffadv now can call CitcomS subroutines to
	  initialize and solve for the advection/diffusion of temperature
	  field.

2003-07-16 01:01  ces74

	* pyre/CitcomSRegional.py, pyre/RegionalApp.py,
	  pyre/Solver/RegionalSolver.py: modified to initialize the
	  Advection_diffusion facility

2003-07-15 07:40  tan2

	* module/Regional/Make.mm, module/Regional/bindings.cc,
	  module/Regional/misc.cc, module/Regional/misc.h,
	  module/Regional/stokes_solver.cc,
	  module/Regional/stokes_solver.h, pyre/CitcomSRegional.py,
	  pyre/Components/Stokes_solver/Stokes_solver.py,
	  pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: 1. move
	  bindings related to Stokes_solver() to stokes_solver.cc 2. call
	  set_cg_defaults()/set_mg_defaults() in Stokes_solver.init()

2003-07-15 04:08  tan2

	* lib/Common/Instructions.c, lib/Common/Interuption.c,
	  lib/Common/Make.mm: move everything related to System Signal to
	  interuption.c

2003-07-15 02:44  tan2

	* module/Regional/setProperties.cc: change helper functions to
	  templates

2003-07-14 05:58  tan2

	* module/Regional/bindings.cc, module/Regional/setProperties.cc,
	  module/Regional/setProperties.h, pyre/CitcomSRegional.py,
	  pyre/Components/Visc.py, pyre/RegionalApp.py,
	  pyre/Solver/RegionalSolver.py, tests/signon.py: 1. more helper
	  functions in setProperties.cc 2. Regional.BC_set_prop() and its
	  binding 3. RegionalApp._setProperties() 4. some test in singon.py

2005-08-23 02:54  unknown_user

	* pyre/Components/Stokes_solver.py: [vcp] delete of edited revision
	  with dead state

2003-07-10 02:42  tan2

	* pyre/CitcomSRegional.py, pyre/Components/Adv_solver.py,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/BC.py, pyre/Components/Const.py,
	  pyre/Components/IC.py, pyre/Components/Mesh.py,
	  pyre/Components/Parallel.py, pyre/Components/Param.py,
	  pyre/Components/Phase.py, pyre/Components/Stokes_solver.py,
	  pyre/Components/Stokes_solver/Imcompressible.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Stokes_solver/Stokes_solver.py,
	  pyre/Components/Visc.py, pyre/Facilities/VSolver.py,
	  pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: migrate
	  toward pythia-0.4

2003-07-04 06:56  ces74

	* pyre/CitcomSRegional.py, pyre/RegionalApp.py,
	  pyre/Solver/RegionalSolver.py: Typos corrected

2003-07-04 06:52  ces74

	* pyre/CitcomSRegional.py, pyre/RegionalApp.py,
	  pyre/Solver/RegionalSolver.py: Modified to use the TSolver
	  facility.

2003-07-04 06:43  ces74

	* pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/Advection_diffusion/Make.mm,
	  pyre/Components/Advection_diffusion/Temperature_diffadv.py,
	  pyre/Components/Advection_diffusion/__init__.py: A component of
	  "TSoler" facility added.
	  
	  Advection_diffusion.py is a general class of advection_diffusion
	  solvers.
	  
	  Temperature_diffadv.py is a solver for temperature field.
	  
	  __init__.py exports temperature_diffadv under Advection_diffusion
	  module.

2003-07-04 06:40  ces74

	* pyre/Facilities/Make.mm, pyre/Facilities/TSolver.py: TSolver
	  facility added. Make.mm modified accordingly.

2003-06-27 07:15  tan2

	* module/Regional/Make.mm, module/Regional/bindings.cc,
	  module/Regional/setProperties.cc,
	  module/Regional/setProperties.h, pyre/CitcomSRegional.py,
	  pyre/Components/BC.py, pyre/Components/Make.mm,
	  pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: passing
	  properties of BC() to C variables

2003-06-27 06:14  tan2

	* pyre/Components/Stokes_solver/Imcompressible.py,
	  pyre/Components/Stokes_solver/Incompressible.py:
	  ImcompressibleNonNewtonian() is inherited from
	  ImcompressibleNewtonian() now

2003-06-27 06:14  tan2

	* pyre/Components/Stokes_solver/Stokes_solver.py: remove properties
	  related to viscosity

2003-06-24 04:01  tan2

	* pyre/Facilities/VSolver.py: bug fix

2003-06-24 03:54  tan2

	* pyre/Components/Stokes_solver/Imcompressible.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Stokes_solver/Make.mm,
	  pyre/Components/Stokes_solver/Stokes_solver.py,
	  pyre/Components/Stokes_solver/__init__.py: 1. Stokes_solver() is
	  a Component of new facility VSolver() 2. add properties to
	  Stokes_solver(), including properties belong to (future)
	  Viscosity component 3. change ImcompressibleNewtonian() and
	  ImcompressibleNonNewtonian() accordingly

2003-06-24 03:43  tan2

	* pyre/Facilities, pyre/Facilities/Make.mm,
	  pyre/Facilities/VSolver.py, pyre/Facilities/__init__.py: add new
	  facilities

2003-06-14 00:12  tan2

	* pyre/CitcomSRegional.py, pyre/RegionalApp.py,
	  pyre/Solver/RegionalSolver.py: add facilities

2003-06-14 00:11  tan2

	* tests/citcomsregional.py: tests for facilities

2003-06-13 01:25  tan2

	* pyre/Components/__init__.py, pyre/__init__.py: 1. remove
	  'license_text' 2. add Common/Component/__init__.py

2003-06-12 06:02  tan2

	* pyre/Components/Adv_solver.py, pyre/Components/BC.py,
	  pyre/Components/Const.py, pyre/Components/IC.py,
	  pyre/Components/Make.mm, pyre/Components/Mesh.py,
	  pyre/Components/Parallel.py, pyre/Components/Param.py,
	  pyre/Components/Phase.py, pyre/Components/Stokes_solver.py,
	  pyre/Components/Visc.py: 1. move all components to new directory
	  Component/ 2. all components have a new and shorter name 3.
	  'SimulationSolver' is splited into two components: 'Adv_solver'
	  and 'Stokes_solver' 4. change Make.mm accordingly

2003-06-08 15:11  tan2

	* module/Regional/Make.mm: fixed bug in linking with
	  'libmpimodule.a' (I don't like this solution though)

2003-06-07 02:04  tan2

	* module/Regional/Make.mm, module/Regional/misc.cc: passing mpi
	  communicator to Citcom_Init()

2003-05-24 00:58  tan2

	* tests/asap.py, tests/hrothgar.py: add two staging classes (copied
	  from specfem_globe/tests/)

2003-05-24 00:49  tan2

	* module/Regional/misc.cc, module/Regional/outputs.cc: append
	  function name to the argument of PyArg_ParseTuple()

2003-05-24 00:07  tan2

	* module/Make.mm: fix a typo

2003-05-23 12:12  ces74

	* module/Regional/advdiffu.cc, module/Regional/advdiffu.h,
	  module/Regional/bindings.cc, module/Regional/misc.cc,
	  module/Regional/misc.h: test methods are removed. class
	  PG_timestep now has only two methods: init and solve

2003-05-23 12:11  ces74

	* lib/Common/Drive_solvers.c,
	  lib/Common/General_matrix_functions.c,
	  lib/Common/Stokes_flow_Incomp.c, lib/Common/drive_solvers.h: test
	  functions removed.

2003-05-23 11:47  ces74

	* lib/Common/Advection_diffusion.c, lib/Common/Drive_solvers.c,
	  lib/Common/General_matrix_functions.c,
	  lib/Common/Stokes_flow_Incomp.c,
	  lib/Common/advection_diffusion.h, lib/Common/drive_solvers.h:
	  Fixed a bug related to deciding the validity of velocity solution
	  in General_matrix_functions.c
	  
	  Functions reorganized for PG_timestep class.

2003-05-23 11:22  ces74

	* pyre/Components/Advection_diffusion/Advection_diffusion.py: class
	  PG_timestep now has only two methods: .init and .solve

2003-05-23 09:41  tan2

	* module/Regional/outputs.cc, pyre/CitcomSRegional.py,
	  pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: add class
	  OutputVisc and its bindings

2003-05-23 07:46  ces74

	* lib/Common/Advection_diffusion.c, lib/Common/Make.mm,
	  lib/Common/advection_diffusion.h: bug in Make.mm fixed.
	  advection_diffusion.h is now included in Advection_diffusion.c

2003-05-23 06:18  tan2

	* lib/Common/output.h, lib/Regional/Output.c,
	  lib/Regional/output.h: *** empty log message ***

2003-05-23 06:10  tan2

	* module/Regional/bindings.cc: *** empty log message ***

2003-05-23 06:08  tan2

	* module/Regional/outputs.cc, module/Regional/outputs.h: add
	  bindings to class OutputVisc

2003-05-23 05:41  ces74

	* module/Regional/outputs.cc: bug fixed: include outputs.h, not
	  output_binding.h

2003-05-23 05:39  ces74

	* module/Regional/advdiffu.cc: bug fixed: PG_timestep_Init to
	  ..._init PG_timestep_Fini to ..._fini

2003-05-23 05:37  ces74

	* lib/Common/advection_diffusion.h, lib/Regional/Output.c: Bugs
	  fixed.

2003-05-23 05:27  ces74

	* pyre/Components/Advection_diffusion/Advection_diffusion.py:
	  Changed class name from Advection_diffusion to PG_timestep

2003-05-23 01:32  ces74

	* module/Regional/Make.mm, module/Regional/advdiffu.cc,
	  module/Regional/advdiffu.h, module/Regional/bindings.cc,
	  module/Regional/misc.cc, module/Regional/misc.h: Inconsistency
	  caused by adding advdiffu modules has been fixed.

2003-05-23 01:21  tan2

	* lib/Regional/Output.c, module/Regional/Make.mm,
	  module/Regional/bindings.cc: 1. change filename from
	  'output_bindings.*' to 'outputs.*' 2. delete
	  OutputCoord.writeheader() method 3. fix a typo in Output.py

2003-05-23 01:20  ces74

	* pyre/CitcomSRegional.py, pyre/Components/Advection_diffusion,
	  pyre/Components/Advection_diffusion/Advection_diffusion.py,
	  pyre/Components/Advection_diffusion/Make.mm,
	  pyre/Components/Advection_diffusion/__init__.py,
	  pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: A new package
	  Advection_diffusion created. This package includes a new class,
	  PG_timestep.

2003-05-23 01:17  ces74

	* lib/Common/Advection_diffusion.c, lib/Common/Make.mm,
	  lib/Common/advection_diffusion.h: Functions added and modified
	  for PG_timestep class

2003-05-22 04:28  tan2

	* lib/Common/output.h, lib/Regional/Output.c,
	  lib/Regional/output.h, module/Regional/Make.mm,
	  module/Regional/bindings.cc, module/Regional/misc.cc,
	  module/Regional/misc.h, module/Regional/outputs.cc,
	  module/Regional/outputs.h, pyre/CitcomSRegional.py,
	  pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: 1. add class
	  CitcomOutput 2. add classes OutputCoord and OutputVelo, which
	  write out coordinate and velocity output 3. add some functions in
	  lib/Regional/Output.c for bindings 4. add python bindings to all
	  above

2003-05-21 01:56  tan2

	* pyre/Components/Stokes_solver/Imcompressible.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Stokes_solver/Stokes_solver.py: 1. change
	  implementation of Stokes_solver 2. change ImcompressibleNewtonian
	  and ImcompressibleNonNewtonian accordingly

2003-05-21 01:55  tan2

	* lib/Common/Drive_solvers.c: initialize
	  'monitor.elapsed_time_vsoln'

2003-05-17 04:11  tan2

	* lib/Common/Drive_solvers.c, lib/Common/drive_solvers.h,
	  module/Regional/bindings.cc, module/Regional/misc.cc,
	  module/Regional/misc.h, pyre/CitcomSRegional.py,
	  pyre/Components/Stokes_solver/Imcompressible.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Stokes_solver/Make.mm,
	  pyre/Components/Stokes_solver/Stokes_solver.py,
	  pyre/Components/Stokes_solver/__init__.py, pyre/RegionalApp.py,
	  pyre/Solver/RegionalSolver.py, tests/citcomsregional.py,
	  tests/signon.py: 1. add python class Stokes_solver 2. add python
	  classes ImcompressibleNewtonian and ImcompressibleNonNewtonian,
	  derived from Stokes_solver 3. add python binding to methods of
	  ImcompressibleNewtonian 4. modify tests accordingly

2003-05-15 07:07  tan2

	* pyre/Components, pyre/Components/Stokes_solver,
	  pyre/Components/Stokes_solver/Imcompressible.py,
	  pyre/Components/Stokes_solver/Incompressible.py,
	  pyre/Components/Stokes_solver/Make.mm,
	  pyre/Components/Stokes_solver/Stokes_solver.py,
	  pyre/Components/Stokes_solver/__init__.py: Initial revision

2003-05-15 01:31  tan2

	* lib/Common/Instructions.c, lib/Common/Viscosity_structures.c,
	  lib/Regional/Version_dependent.c, module/Regional/misc.cc,
	  tests/signon.py: seperate viscosity input and computation into
	  different functions

2003-05-14 02:51  tan2

	* drivers/Citcom.c, lib/Common/Citcom_init.c,
	  lib/Common/Global_operations.c, lib/Common/citcom_init.h,
	  lib/Common/global_defs.h, lib/Common/parallel_related.h,
	  lib/Regional/Global_operations.c,
	  lib/Regional/Parallel_related.c, lib/Regional/global_defs.h,
	  lib/Regional/parallel_related.h, module/Regional/misc.cc,
	  tests/signon.py: 1. creat a new global variable E->parallel.world
	  2. replace all MPI_COMM_WORLD by E->parallel.world

2003-04-30 03:14  tan2

	* lib/Common/phase_change.h: add function prototypes

2003-04-30 03:13  tan2

	* lib/Regional/Version_dependent.c: fix bugs when input
	  'control.coor_file', 'control.reset_startage', and
	  'control.zero_elapsed_time'

2003-04-29 01:55  tan2

	* lib/Common/Instructions.c,
	  lib/Common/Pan_problem_misc_functions.c,
	  lib/Common/Phase_change.c, lib/Regional/Version_dependent.c: 1.
	  move everything about phase change to 'Phase_change.c' 2.
	  restructure phase change functions

2003-04-26 07:59  tan2

	* lib/Common/Problem_related.c, lib/Common/global_defs.h,
	  lib/Regional/Boundary_conditions.c,
	  lib/Regional/Problem_related.c, lib/Regional/Version_dependent.c,
	  lib/Regional/global_defs.h: 1. change 'control.mantle_temp' to
	  'control.lith_age_mantle_temp' 2. move functions deal with
	  'lith_age' to a 'Lith_age.c' (complete)

2003-04-26 07:36  tan2

	* lib/Common/Element_calculations.c, lib/Common/Sphere_harmonics.c:
	  bug fix in original code

2003-04-26 05:58  tan2

	* drivers/Make.mm, lib/Make.mm, module/Make.mm, pyre/Make.mm:
	  diable build on 'Full' version

2003-04-26 05:29  tan2

	* lib/Common/Initial_temperature.c, lib/Common/global_defs.h,
	  lib/Common/initial_temperature.h, lib/Common/lith_age.h,
	  lib/Common/parsing.h, lib/Regional/Initial_temperature.c,
	  lib/Regional/Lith_age.c, lib/Regional/Make.mm,
	  lib/Regional/global_defs.h, lib/Regional/initial_temperature.h,
	  lib/Regional/lith_age.h: 1. add parsing.h 2. modularize
	  convection_initial_temperature() 3. move functions deal with
	  'lith_age' to a 'Lith_age.c' (not finished)

2003-04-26 05:12  tan2

	* drivers/Citcom.c, lib/Common/Citcom_init.c: 1. more
	  initialization done in Citcom_Init() 2. fix bug from previous
	  commit in main()

2003-04-25 02:07  tan2

	* lib/Common/Element_calculations.c,
	  lib/Common/General_matrix_functions.c: bug fix

2003-04-11 08:31  tan2

	* lib/Common/Citcom_init.c, module/Regional/misc.cc: clean up debug
	  message

2003-04-11 08:27  ces74

	* pyre/CitcomSRegional.py, pyre/RegionalApp.py,
	  pyre/Solver/RegionalSolver.py: class name changed to RegionalApp

2003-04-11 06:40  tan2

	* tests/citcomsregional.py, tests/signon.py: change module name
	  from CitcomSRegional to Regional

2003-04-11 06:34  tan2

	* pyre/CitcomSRegional.py, pyre/RegionalApp.py,
	  pyre/Solver/RegionalSolver.py: 1. add preInit() and postInit() 2.
	  change EarthModelGrid to SimulationGrid

2003-04-11 06:25  tan2

	* module/Full/Fullmodule.cc, module/Full/Make.mm,
	  module/Full/bindings.cc, module/Full/bindings.h,
	  module/Full/exceptions.cc, module/Full/exceptions.h,
	  module/Full/misc.cc, module/Full/misc.h: change module name from
	  CitcomSFull to Full

2003-04-11 06:18  tan2

	* module/Regional/Make.mm, module/Regional/Regionalmodule.cc,
	  module/Regional/bindings.cc, module/Regional/bindings.h,
	  module/Regional/exceptions.cc, module/Regional/exceptions.h,
	  module/Regional/misc.cc, module/Regional/misc.h: change module
	  name from CitcomSRegional to Regional

2003-04-11 03:15  tan2

	* tests/signon.py: test for new Citcom_Init(), which takes 2
	  arguments now.

2003-04-11 02:07  tan2

	* drivers/Citcom.c, lib/Common/Citcom_init.c,
	  lib/Common/citcom_init.h, module/Regional/misc.cc: 1. Pass rank
	  and size to Citcom_Init(). 2. Disable
	  parallel_process_initilization(). Its functionality is performed
	  by Citcom_Init().

2003-04-10 01:59  ces74

	* pyre/CitcomSRegional.py, pyre/RegionalApp.py, pyre/Solver,
	  pyre/Solver/RegionalSolver.py: Modified to reflect changes in
	  moduels in pyre/Common

2003-04-06 07:51  tan2

	* drivers/Citcom.c, lib/Common/Citcom_init.c,
	  lib/Common/Instructions.c, lib/Common/Parsing.c,
	  module/Regional/bindings.cc, module/Regional/misc.cc,
	  module/Regional/misc.h, tests/signon.py: 1. pass input filename,
	  rather than argc and argv, to read_instructions() 2. pass input
	  filename, rather than argc and argv, to setup_parser() 3. more
	  initialization done in Citcom_Init() 4. add python binding to
	  read_instructions()

2003-04-06 04:57  tan2

	* drivers/Citcom.c, lib/Common/Citcom_init.c,
	  lib/Common/citcom_init.h, module/Regional/misc.cc: binding of
	  Citcom_Init(), finished

2003-04-06 04:25  tan2

	* drivers/Full/Make.mm, drivers/Make.mm, drivers/Regional/Make.mm,
	  examples/Full/Make.mm, examples/Make.mm,
	  examples/Regional/Make.mm, lib/Common/Make.mm, lib/Full/Make.mm,
	  lib/Make.mm, lib/Regional/Make.mm, module/Full/Make.mm,
	  module/Make.mm, module/Regional/Make.mm, pyre/Make.mm,
	  tests/Make.mm: PROJ_TMPDIR is specified by PACKAGE too

2003-04-04 08:42  tan2

	* module/Regional/Make.mm, module/Regional/bindings.cc,
	  module/Regional/misc.cc, module/Regional/misc.h, tests/signon.py:
	  trial on binding of Citcom_Init(), not finished.

2003-04-04 08:41  tan2

	* lib/Full/Make.mm, lib/Regional/Make.mm: export header files

2003-04-04 08:40  tan2

	* drivers/Citcom.c: 1. declare "struct All_variables *E" as global
	  in read_instruction() 2. allocate *E in Citcom_Init()

2003-04-04 08:39  tan2

	* lib/Common/Citcom.c: redundant file

2003-04-04 08:37  tan2

	* lib/Common/Citcom_init.c, lib/Common/Instructions.c,
	  lib/Common/Make.mm, lib/Common/citcom_init.h: 1. declare "struct
	  All_variables *E" as global in read_instruction() 2. allocate *E
	  in Citcom_Init()

2003-04-04 03:40  tan2

	* lib/Make.mm, module/Make.mm, pyre/RadiusDepth.py: cosmetics

2003-04-04 03:38  tan2

	* drivers/Full/Make.mm, drivers/Make.mm, drivers/Regional/Make.mm:
	  fix bugs caused by symlink to Citcom.c

2003-03-26 08:49  ces74

	* tests/citcomsregional.py: for testing EarthModel properties

2003-03-25 05:48  tan2

	* pyre/RadiusDepth.py: 1. change attribute 'R0' to 'outer_radius'
	  2. outer_radius, inRadius, and inDepth are read-only now 3. add
	  self-test section

2003-03-25 03:48  tan2

	* pyre/RadiusDepth.py: Add RadiusDepth.py, which defines two
	  classed converting depth to radius, and vise versa.

2003-03-25 01:38  tan2

	* drivers/Make.mm, module/Make.mm, pyre/Make.mm: add
	  BLD_ACTION="all"

2003-03-24 09:46  tan2

	* Make.mm, drivers, drivers/Citcom.c, drivers/Full,
	  drivers/Full/Make.mm, drivers/Full/local.def, drivers/Make.mm,
	  drivers/Regional, drivers/Regional/Make.mm,
	  drivers/Regional/local.def, drivers/local.def, examples,
	  examples/.reset-temporary, examples/Full, examples/Full/Make.mm,
	  examples/Full/input.sample, examples/Full/local.def,
	  examples/Full/machine.sample, examples/Make.mm,
	  examples/Regional, examples/Regional/Make.mm,
	  examples/Regional/input.sample, examples/Regional/local.def,
	  examples/Regional/machines.sample, examples/local.def, lib,
	  lib/Common, lib/Common/Advection_diffusion.c,
	  lib/Common/Citcom.c, lib/Common/Construct_arrays.c,
	  lib/Common/Convection.c, lib/Common/Drive_solvers.c,
	  lib/Common/Element_calculations.c,
	  lib/Common/General_matrix_functions.c,
	  lib/Common/Global_operations.c, lib/Common/Initial_temperature.c,
	  lib/Common/Instructions.c, lib/Common/Make.mm,
	  lib/Common/Nodal_mesh.c, lib/Common/Output.c,
	  lib/Common/Pan_problem_misc_functions.c, lib/Common/Parsing.c,
	  lib/Common/Phase_change.c, lib/Common/Problem_related.c,
	  lib/Common/Process_buoyancy.c, lib/Common/Process_velocity.c,
	  lib/Common/Shape_functions.c, lib/Common/Size_does_matter.c,
	  lib/Common/Solver_conj_grad.c, lib/Common/Solver_multigrid.c,
	  lib/Common/Sphere_harmonics.c, lib/Common/Stokes_flow_Incomp.c,
	  lib/Common/Topo_gravity.c, lib/Common/Tracer_advection.c,
	  lib/Common/Viscosity_structures.c, lib/Common/advection.h,
	  lib/Common/convection_variables.h,
	  lib/Common/element_definitions.h, lib/Common/global_defs.h,
	  lib/Common/local.def, lib/Common/sphere_communication.h,
	  lib/Common/temperature_descriptions.h, lib/Common/tracer_defs.h,
	  lib/Common/viscosity_descriptions.h, lib/Full,
	  lib/Full/Boundary_conditions.c, lib/Full/Geometry_cartesian.c,
	  lib/Full/Global_operations.c, lib/Full/Initial_temperature.c,
	  lib/Full/Make.mm, lib/Full/Output.c, lib/Full/Parallel_related.c,
	  lib/Full/Problem_related.c, lib/Full/Process_buoyancy.c,
	  lib/Full/Sphere_related.c, lib/Full/Version_dependent.c,
	  lib/Full/global_defs.h, lib/Full/local.def, lib/Make.mm,
	  lib/Regional, lib/Regional/Boundary_conditions.c,
	  lib/Regional/Geometry_cartesian.c,
	  lib/Regional/Global_operations.c,
	  lib/Regional/Initial_temperature.c, lib/Regional/Make.mm,
	  lib/Regional/Output.c, lib/Regional/Parallel_related.c,
	  lib/Regional/Problem_related.c, lib/Regional/Process_buoyancy.c,
	  lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c,
	  lib/Regional/global_defs.h, lib/Regional/local.def,
	  lib/local.def, local.def, module, module/Full,
	  module/Full/Fullmodule.cc, module/Full/Make.mm,
	  module/Full/bindings.cc, module/Full/bindings.h,
	  module/Full/exceptions.cc, module/Full/exceptions.h,
	  module/Full/local.def, module/Full/misc.cc, module/Full/misc.h,
	  module/Make.mm, module/Regional, module/Regional/Make.mm,
	  module/Regional/Regionalmodule.cc, module/Regional/bindings.cc,
	  module/Regional/bindings.h, module/Regional/exceptions.cc,
	  module/Regional/exceptions.h, module/Regional/local.def,
	  module/Regional/misc.cc, module/Regional/misc.h,
	  module/local.def, pyre, pyre/Make.mm, pyre/__init__.py,
	  pyre/local.def, tests, tests/Make.mm, tests/local.def,
	  tests/signon.py: Initial revision

2005-08-23 02:43  boo

	* .: [vcp] select <> as trunk

2005-08-23 02:42  VCP

	* mc/3D/CitcomS/branches, .: VCP: initializing layout

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