https://github.com/geodynamics/citcoms
Raw File
Tip revision: 304266d8447efe5ee990624f615b250c633079ef authored by Leif Strand on 14 February 2006, 23:27 UTC
Merged r2605, "Updated NEWS and ChangeLog".
Tip revision: 304266d
ChangeLog
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
	* 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
	* 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
	* 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
	* 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
	* 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()
	* 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
	* 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
	* 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
	* 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()
	* 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
	* 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
	* 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.
	* 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.
	* 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.
	* 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
	* 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()
	* 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
	* 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
	* 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
	* 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
	* 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_*()
	* 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 ***
	* 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
	* 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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