2009-06-25 17:47 tan2 * NEWS, README, configure.ac: Change version number 2009-06-25 17:38 tan2 * examples/Cookbook10/cmt-solution.cookbook10, examples/Cookbook10/stations.cookbook10: forgot to add these files 2009-06-10 20:42 tan2 * configure.ac: Added COND_GGRD flags; removed redundant LIBS 2009-06-10 20:41 tan2 * configure.ac: Checking malloc.h earlier to initialize even when not using pyre 2009-06-10 17:49 tan2 * configure.ac: checking netcdf header and library 2009-06-10 04:11 tan2 * configure.ac: Append GMTHOME/lib to LD path 2009-06-09 23:47 tan2 * configure.ac: Adding ggrd compilation support 2009-06-08 21:03 tan2 * NEWS: One more feature and mention where to find the features in the cookbooks. 2009-06-08 18:11 tan2 * CitcomS/Coupler/EmbeddedCoupler.py: Added a safe guard 2009-06-04 21:04 tan2 * examples/Cookbook9/cookbook9.cfg: Reordering parameter 2009-06-03 21:08 tan2 * module/Exchanger/BoundarySVTInlet.cc, module/Exchanger/SVTInlet.cc, module/Exchanger/SVTInlet.h: Update SVTInlet to inherit from BaseSVTInlet 2009-06-03 21:07 tan2 * module/Exchanger/Makefile.am: adding files to makefile 2009-06-02 22:58 tan2 * tests/coupled.cfg, tests/exchange.py: update to current coupler 2009-06-02 22:58 tan2 * examples/Cookbook9/cookbook9.cfg: reducing the accuracy of solvers, otherwise, they will converge to the wrong result 2009-06-02 22:56 tan2 * CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py, CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/Coupler/Inlet.py, CitcomS/Coupler/Outlet.py, CitcomS/Solver/CoupledSolver.py, module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/AreaWeightedNormal.h, module/Exchanger/BaseSVTInlet.cc, module/Exchanger/BaseSVTInlet.h, module/Exchanger/BoundarySVTInlet.cc, module/Exchanger/BoundarySVTInlet.h, module/Exchanger/BoundaryVTInlet.cc, module/Exchanger/CitcomInterpolator.cc, module/Exchanger/Makefile.am, module/Exchanger/PInlet.cc, module/Exchanger/PInlet.h, module/Exchanger/PInterior.cc, module/Exchanger/PInterior.h, module/Exchanger/POutlet.cc, module/Exchanger/POutlet.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h, module/Exchanger/inlets_outlets.cc, module/Exchanger/inlets_outlets.h: Added parameters 'amending_outflow' and 'exchange_pressure' to help the convergence of esolver When 'amending_outflow' is set to true, the imposed velocity BC will be amended slightly to be divergence-free. (The divergence, e.g. outflow, is caused by the combination of solver inaccuracy and interpolation inaccuracy.) When 'exchange_pressure' is set to true, the initial pressure (at element level) of the embedded solver is taken from the pressure solution of the containing solver. 2009-06-02 22:09 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: Boundary for global mesh, not sure whether it works with interpolator or not 2009-06-02 21:58 tan2 * lib/Instructions.c: init'd E->output.seismic and E->output.coord_bin 2009-06-02 21:58 tan2 * examples/Cookbook10/cookbook10.cfg: refining cookbook10 2009-05-28 01:50 leif * configure.ac, lib/General_matrix_functions.c, lib/Makefile.am, lib/cgrad_kernel.cu: CUDA-ized e_assemble_del2_u(), and ran it successfully -- and slowly! -- under the device emulator. Added a new 'configure' option: "--with-cuda". 2009-05-27 02:32 leif * lib/cgrad_kernel.cu: Parallelized strip_bcs_from_residual(). 2009-05-27 01:28 leif * lib/cgrad_kernel.cu: Sketched data-parallel version of e_assemble_del2_u(). 2009-05-26 15:21 becker * lib/Initial_temperature.c, lib/convection_variables.h: Added blob_bc_persist parameter (default = off) to allow assigning blob-like temperature anomalies to BCs. 2009-05-26 15:03 becker * lib/Initial_temperature.c, lib/Pan_problem_misc_functions.c: Fixed typo in blob temperature assignment. Changed conversion of coordinates, now assignment works. 2009-05-21 23:16 tan2 * NEWS: add changes in r14999 2009-05-15 22:32 tan2 * visual/project_geoid.c: ignoring the degree-0 and degree-1 components of geoid 2009-05-10 23:18 tan2 * NEWS: add more chaanges in v3.1.0 2009-05-10 16:37 tan2 * configure.ac, setup.py: Change version number for v3.1.0 alpha release 2009-05-10 16:35 tan2 * NEWS: Summary of changes in this release 2009-05-01 22:19 tan2 * examples/Cookbook10, examples/Cookbook10/cookbook10.cfg: Adding cookbook for synthetic seismogram, mostly copied from cookbook7 2009-05-01 22:18 tan2 * lib/Mineral_physics_models.c: Depth is measured from r=1.0, not outer radius, because in coupled model, the outer radius can be < 1.0. 2009-05-01 22:17 tan2 * lib/Instructions.c: Printing a big warning when plate velocity is imposed but remove_angular_momentum or remove_rigid_rotation is on. 2009-05-01 22:15 tan2 * lib/Drive_solvers.c: Removing angular momentum in pseudo free surface case 2009-05-01 22:14 tan2 * visual/parser.py: ignore anything after ';' 2009-05-01 22:13 tan2 * INSTALL: explicitly add Python.h to requirement 2009-04-28 22:53 leif * lib/cgrad_kernel.cu: For my own sanity, simplified code assuming the following: E->sphere.caps_per_proc == 1 E->parallel.nproc == 1 E->mesh.levmax == 0 E->mesh.nsd == 3 2009-04-27 20:15 leif * lib/cgrad_kernel.cu: Moved malloc/free calls outside of kernel. (The amount of memory allocated appears to be invariant.) 2009-04-27 18:39 leif * lib/cgrad_kernel.cu: Consolidated calls to malloc/free. 2009-04-24 18:37 becker * lib/Instructions.c, lib/Viscosity_structures.c, lib/global_defs.h: Added flag to allow using the more precise method of computing strain-rates throughout the globe, and not just close to the poles. precise_strain_rate=on will select this, default is "odd", i.e. poles only as before. 2009-04-23 02:32 leif * lib/cgrad_kernel.cu: Don't call through function pointers -- otherwise, 'nvcc' crashes! 2009-04-23 02:22 leif * lib/cgrad_kernel.cu: Proposed CUDA kernel for conjugate gradient solver. 2009-04-22 00:59 leif * lib/Instructions.c: Avoid core dump in record() when E->fp hasn't been set yet. 2009-04-21 22:29 leif * configure.ac: The new Python.h header check reorders this script somewhat. CIT_CHECK_PYTHON_HEADER must follow AC_PROG_CC, and precede CIT_PYTHON_EGG_SETUP. 2009-04-21 19:33 leif * configure.ac: Issue45: Check for Python.h. 2009-04-17 03:37 becker * lib/Viscosity_structures.c: Added viscosity options 9 and 10 for TDPEPV which are identical to 3 and 8 but temperature is not limited to [0;1]. This is cumbersome, but perhaps needed for backward compatibility. 2009-04-16 18:24 tan2 * CitcomS/Components/IC.py, CitcomS/Components/Param.py, examples/Cookbook6/cookbook6.cfg, lib/Initial_temperature.c, lib/Lith_age.c, lib/Output_h5.c, lib/global_defs.h, module/Exchanger/initTemperature.cc, module/setProperties.c: Move parameter "mantle_temp" from CitcomS.solver.param to CitcomS.solver.ic. Renamed E->control.lith_age_mantle_temp to E->control.mantle_temp. 2009-04-16 18:23 tan2 * examples/Cookbook8/cookbook8.cfg: update cookbook8 with the manual 2009-04-16 18:22 tan2 * module/Exchanger/Makefile.am: Add -DUSE_HDF5 to CPPFLAGS in module/Exchanger 2009-04-16 18:21 tan2 * examples/Cookbook7/cookbook7.cfg: change the viscosity section to be the same as that in cookbook3. 2009-04-16 18:20 tan2 * examples/Cookbook4/cookbook4.cfg, examples/Cookbook5/cookbook5.cfg: Removed domain extents, since they are determined by coor_file. 2009-04-16 18:07 tan2 * INSTALL: Removed instructions to 'make install', 'make clean' and 'make distclean'. Added dependencies. 2009-04-09 20:53 tan2 * lib/Instructions.c, module/setProperties.c: Fixed a bug in cgrad solver introduced in r13270. 2009-04-09 20:39 becker * lib/Output.c: Left debugging output in, now cleaned up 2009-04-09 20:37 becker * bin/Citcom.c, lib/Instructions.c, lib/Output.c: Fixed file output issue which caused vtk log file I/O to bomb during Citcom finalize. 2009-04-08 23:39 tan2 * CitcomS/BaseApplication.py, CitcomS/Controller.py, CitcomS/Solver/CoupledFullSolver.py, CitcomS/Solver/CoupledRegionalSolver.py, CitcomS/Solver/FullSolver.py, CitcomS/Solver/RegionalSolver.py, CitcomS/Solver/Solver.py, bin/Citcom.c, lib/Instructions.c, lib/Viscosity_structures.c, lib/citcom_init.h, module/initial_conditions.c: Sync'ing C and Pyre and adding comments 2009-04-08 23:38 tan2 * CitcomS/Controller.py, CitcomS/Solver/CoupledSolver.py, CitcomS/Solver/Solver.py, bin/Citcom.c, lib/Citcom_init.c, lib/Parallel_util.c, lib/citcom_init.h, lib/parallel_related.h, module/bindings.c, module/initial_conditions.c, module/misc.c, module/misc.h, module/outputs.c, module/outputs.h: Added a function citcom_finalize() to close files and MPI before exit. Return 0 when the code is finished normally. Rearrang post_processing and stokes_flow_only. 2009-04-08 23:34 tan2 * examples/Full/input.sample, examples/Regional/input.sample, lib/Convection.c, lib/Instructions.c, lib/Viscosity_structures.c, lib/global_defs.h, module/advdiffu.c, module/bindings.c, module/misc.c, module/misc.h: Clean up. 2009-04-08 23:31 tan2 * CitcomS/Components/Stokes_solver/Incompressible.py, lib/Construct_arrays.c, lib/Full_parallel_related.c, lib/Full_version_dependent.c, lib/General_matrix_functions.c, lib/Instructions.c, lib/Regional_parallel_related.c, lib/Regional_sphere_related.c, lib/Regional_version_dependent.c, lib/Size_does_matter.c, lib/Solver_conj_grad.c, lib/Solver_multigrid.c, lib/global_defs.h, module/bindings.c, module/stokes_solver.c, module/stokes_solver.h: Removed multigrid-el option of stokes solver, which is broken for a long time and not used by anyone. 2009-04-08 23:27 tan2 * lib/Instructions.c: Moved where to call read_rayleigh_from_file() earlier. I hope this doesn't break the ray_control stuff. 2009-04-08 20:24 becker * lib/Ggrd_handling.c: Fixed bug in vtop assignment. 2009-04-07 22:50 tan2 * examples/Makefile.am: Revert the unintended modification of examples/Makefile.am 2009-04-07 22:45 tan2 * examples/Cookbook3/cookbook3.cfg, examples/Cookbook4/cookbook4.cfg, examples/Makefile.am: Change the viscosity option in cookbook3 and cookbook4 2009-04-07 22:44 tan2 * examples/Cookbook2/cookbook2.cfg: Change the mesh size in cookbook2 2009-04-04 00:59 tan2 * lib/Makefile.am, lib/Mineral_physics_models.c, lib/Seismic_model.c: Renamed Seismic_model.c to Mineral_physics_models.c 2009-04-04 00:57 tan2 * lib/Output.c, lib/Seismic_model.c: Fixed a few bugs in seismic output * fixed errors in the coefficient table * fixed typos * normalized drho by reference density profile * more digits in the prem radius table * added two specfem flags in PREM calculation. * "dv" output for debugging purpose, disabled. 2009-04-04 00:52 tan2 * examples/example0.cfg: Inconsisent parameters with the manual 2009-03-28 02:29 becker * lib/Full_tracer_advection.c, lib/Ggrd_handling.c, lib/Tracer_setup.c: Modified the way the compositional init with ggrd tracer can now select either a range of layers (>0) or a specific layer (<0). 2009-03-20 23:36 tan2 * CitcomS/Components/Stokes_solver/Incompressible.py, lib/General_matrix_functions.c, lib/Instructions.c, lib/global_defs.h, module/setProperties.c: limiting the number of multigrid cycles in solve_del2_u(). A new input parameter solver.vsolver.max_mg_cycles (default to 50) controls the max. number of multigrid cycles when solving the velocity. Without this parameter, when the stiffness matrix is near singular, the the multigrid solver may become an infinite loop. 2009-03-18 19:39 tan2 * CitcomS/Components/Sphere/Sphere.py, module/setProperties.c: Remove mgunitx etc from pyre input. This restores the behavior in v3.0 and earlier version. In pyre version, the mesh size is always specified by nodex etc. In C version, the mesh size is specified by nodex if Solver=cgrad, and by mgunitx and levels if Solver=multigrid. 2009-03-17 23:42 tan2 * lib/Output.c: Rollback the unintended change in velo output. 2009-03-17 00:18 tan2 * lib/Full_read_input_from_files.c, lib/Full_version_dependent.c, lib/Initial_temperature.c, lib/Lith_age.c, lib/Material_properties.c, lib/Output_gzdir.c, lib/Problem_related.c, lib/Regional_read_input_from_files.c, lib/Regional_sphere_related.c, lib/Regional_version_dependent.c: Check return values of sscanf/fscanf. This fixs issue265. 2009-03-17 00:17 tan2 * lib/Obsolete.c, lib/Pan_problem_misc_functions.c: Removed obsolete function read_previous_field() 2009-03-17 00:16 tan2 * CitcomS/Components/Stokes_solver/Incompressible.py, examples/Cookbook8/cookbook8.cfg, lib/Drive_solvers.c, lib/Global_operations.c, lib/Instructions.c, lib/Output_gzdir.c, lib/Tracer_setup.c, lib/global_defs.h, module/setProperties.c: remove angular momentum from stokes solution by setting solver.vsolver.remove_angular_mementum=1 2009-03-16 23:17 tan2 * CitcomS/Components/Param.py, lib/Instructions.c, lib/Makefile.am, lib/Output.c, lib/Output_gzdir.c, lib/Output_h5.c, lib/Seismic_model.c, lib/global_defs.h, lib/output.h, module/setProperties.c: Converting temperature/composition fields to seismic velocities, in a format that specfem3d portal and v4.1 can understand. * solver.param.mineral_physics_mode: default to 3, the model of Tramper, Vacher and Vlaar's PEPI 2001. * output_optional=seismic will write coordinates and seismic velocities in binary files for specfem comsumption. * domain bounds file "datafile.domain": binary file with nproc * 10 doubles. The 10 doubles are (rmin, rmax) and four (theta, phi) pairs for the four bottom corner nodes. This file is written by rank-0 processor only. 2009-03-16 22:52 tan2 * lib/Initial_temperature.c, tests/stokes, tests/stokes/bousinessq.cfg, tests/stokes/tala.cfg: add test cases for the stokes solver under bousinessq approximation and truncated anelastic liquid approximation 2009-03-16 22:50 tan2 * CitcomS/Components/Sphere/Sphere.py, CitcomS/Solver/Solver.py, lib/Full_geometry_cartesian.c, lib/Full_sphere_related.c, lib/Instructions.c, lib/Regional_geometry_cartesian.c, lib/Regional_sphere_related.c, module/bindings.c, module/mesher.c, module/mesher.h, module/setProperties.c: seperate initialization and parameter input 2009-03-16 22:44 tan2 * CitcomS/Components/Sphere/Sphere.py: change the default of mgunit 2009-03-16 22:43 tan2 * CitcomS/Components/Advection_diffusion/Advection_diffusion.py, CitcomS/Components/Sphere/Sphere.py, CitcomS/Components/Stokes_solver/Incompressible.py, CitcomS/Solver/Solver.py: Make the initialization step in pyre conforms to C version. This fixs a bug in r13270. 2009-03-10 00:58 tan2 * lib/Determine_net_rotation.c: Disable HC related stuff if USE_GGRD is not set 2009-03-04 23:45 becker * bin/Citcom.c, lib/Checkpoints.c, lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c, lib/Tracer_setup.c: Changed ic flavors from 100 to 99 as per Eh's request 2009-03-04 23:00 becker * bin/Citcom.c, lib/Checkpoints.c, lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c, lib/Tracer_setup.c: Changed ggrd flavor init for tracers with checkpoint override from 2 to 100 as per Eh's request. 2009-02-28 21:23 becker * bin/Citcom.c, lib/Checkpoints.c, lib/Composition_related.c, lib/Determine_net_rotation.c, lib/Full_tracer_advection.c, lib/Instructions.c, lib/Tracer_setup.c: Added ic_method_for_flavors=2, which works like the ggrd based tracer flavor init method ic_method_for_flavors=1 but overrides restart settings for tracers. This allows a compositional restart of a purely thermal run. 2009-02-20 00:09 tan2 * CitcomS/Components/Tracer.py, lib/Full_tracer_advection.c, lib/Process_buoyancy.c, lib/Tracer_setup.c, lib/tracer_defs.h, module/setProperties.c: Partially back out r19268,r9272,r11215, since the AVM stuff is redesigned. 2009-02-19 23:46 tan2 * lib/Full_tracer_advection.c, lib/Process_buoyancy.c, lib/Tracer_setup.c: Partially back out r11218, since the AVM stuff is redesigned. 2009-02-19 23:41 tan2 * CitcomS/BaseApplication.py, CitcomS/Controller.py, lib/Process_buoyancy.c, module/initial_conditions.c: Partially back out r11221, since the AVM stuff is redesigned. 2009-02-19 23:35 tan2 * lib/Process_buoyancy.c: Back out r11279, since the AVM stuff is redesigned. 2009-02-13 03:46 leif * lib/Checkpoints.c: Fixed minor bug exposed by C-to-C++ translation (r14045). 2009-02-06 19:51 tan2 * lib/Instructions.c, lib/Stokes_flow_Incomp.c: Emit the warning message from a different place to get rid of static variables. Also, the macros TRUE and FALSE are undefined unless configured with GMT. 2008-12-22 18:48 tan2 * lib/Viscosity_structures.c: Fixed a bug in viscosity rheol=7. Bug reported by Laura Alisic. 2008-11-19 06:49 tan2 * lib/General_matrix_functions.c: Fixed two bugs in lg_pow(a, n), which computes a^n. One bug is when n=0, it returned a, instead of 1 Another bug is a^(n-1) was returned 2008-11-18 23:56 tan2 * lib/Topo_gravity.c: One more fix to zero geoid arrays 2008-11-18 22:58 tan2 * lib/Topo_gravity.c: Zero'ed geoid arrays. 2008-11-18 06:55 becker * lib/Ggrd_handling.c, lib/Instructions.c, lib/Stokes_flow_Incomp.c, lib/global_defs.h: Patched up Ggrd_handling for velocity grids close to pole. Addded flag to suppress check of incompressibility and pressure convergence. Partially, this is because for kinematic BCs pressure will only be constrained up to a constant, partially because mixed density/plate flow models show very poor convergence, still to be checked. 2008-11-11 02:55 becker * lib/Initial_temperature.c: blob parameters were required even if tic_method != 2, changed such that the parameters were only read in if tic_method == 2 2008-11-11 02:48 becker * lib/Initial_temperature.c: Minor fix to allow compilation with USE_GGRD 2008-11-07 23:35 tan2 * module/setProperties.c: forget to check in module/setProperties.c 2008-11-07 23:32 tan2 * CitcomS/Components/IC.py, examples/Cookbook6/cookbook6.cfg, lib/Full_solver.c, lib/Full_version_dependent.c, lib/Initial_temperature.c, lib/Regional_solver.c, lib/Regional_version_dependent.c, lib/solver.h: * Reserved 'tic_method=100' for user-defined initial temperature. * Read all parameters related to initial temperature regardless which tic_method is used. This will make the life easier when adding new tic_method. * Fixed a bug in 'tic_method=0' for regional model. The bug causes that the sinosoidal temperature perturbation is applied at 0th processor only. * Fixed a bug in 'tic_method=1' for regional model. 'tic_method=1' should generate a top TBL according to the input parameter 'half_space_age'. However, the code effectively multiply 25x to the age. Cookbook6 is using this tic_method, so its half_space_age needs to become 2500 to get the original temperature. * In 'tic_method=2', compute distance in Cartesian coordinate, instead of spherical coordinate. * Refactoring codes for temperature initial conditions. * Merged regional_construct_tic_from_input() and full_construct_tic_from_input() to construct_tic_from_input(). 2008-11-07 23:32 tan2 * lib/Viscosity_structures.c: Reserved 'rheol=100' for user-defined viscosity law. 2008-11-07 23:31 tan2 * CitcomS/Components/Output.py, module/setProperties.c: Added parameter 'use_cbf_topo' to pyre binding, default to off. 2008-11-07 23:14 tan2 * CitcomS/Components/Sphere/Sphere.py, CitcomS/Solver/Solver.py, examples/Full/input.sample, examples/Regional/input.sample, lib/Full_solver.c, lib/Full_version_dependent.c, lib/Instructions.c, lib/Regional_solver.c, lib/Regional_version_dependent.c, lib/solver.h, module/setProperties.c: * Added back parameters mgunitx/mgunity/mgunitz. This partly reverts r13256. * Under pyre, uses mgunitx/mgunity/mgunitz and levels to compute nodex/nodey/nodez in multigrid solver. * Merged regional_global_derived_values() and full_global_derived_values() to global_derived_values(). 2008-11-05 00:19 tan2 * lib/Full_version_dependent.c: Minor fix on node counting 2008-11-04 22:50 tan2 * visual/pasteCitcomData.py: Added a missing import 2008-11-04 21:02 tan2 * visual/zslice.py: zslice.py will slice opt files if present 2008-11-04 21:01 tan2 * CitcomS/Solver/Solver.py, examples/Full/input.sample, examples/Regional/input.sample, lib/Instructions.c, module/bindings.c, module/misc.c, module/misc.h: Removed input parameters "mgunitx", "mgunity" and "mgunitz". Their values are inferred from other parameters. Also, the code checks that "levels" > 1 when multigrid solver is used. 2008-11-04 21:00 tan2 * lib/Output.c: Fixed a bug in outputting comp_el 2008-11-01 18:37 becker * lib/Full_sphere_related.c, lib/Full_version_dependent.c, lib/Instructions.c, lib/Stokes_flow_Incomp.c: Fixed two typos, velocity norm function was called where pressure norm should have been called. This leads to core dumps, all seems to be working now. 2008-10-31 20:18 tan2 * lib/Full_version_dependent.c, lib/Regional_version_dependent.c: Reporting correct nno and nel (number of nodes and elements) 2008-10-29 23:22 tan2 * lib/global_defs.h: (for r13196) Fixing convergence criterion for Stokes solver. * New functions global_v_norm2(), global_p_norm2(), global_div_norm2() compute the L2 norm of velocity, pressure, and divergence. * The L2 norm of the vector f is defined as: \sum_{all elements} ( \int_{element} (f*f dA) ) / A where A is the volume of the domain. * The convergence criterion is controlled by parameter "accuracy" under "[CitcomS.solver.vsolver]". The iteration stops if (norm(div(rho*V))/norm(V) < accuracy) or ( (norm(dV)/norm(V) < accuracy) and (norm(dP)/norm(P) < accuracy) for the last two iterations ) * The default value of "accuracy" becomes 1e-4. * The input parameters "tole_compressibility" and "relative_err_accuracy" under "[CitcomS.solver.vsolver]" are gone. * The mass matrix E->MASS becomes double precision (was single precision). 2008-10-29 23:17 tan2 * CitcomS/Components/Stokes_solver/Incompressible.py, examples/Cookbook6/cookbook6.cfg, examples/Cookbook7/cookbook7.cfg, examples/Cookbook8/cookbook8.cfg, examples/Cookbook9/cookbook9.cfg, examples/Full/input.sample, examples/Regional/input.sample, lib/Checkpoints.c, lib/Element_calculations.c, lib/General_matrix_functions.c, lib/Global_operations.c, lib/Instructions.c, lib/Output_h5.c, lib/Output_vtk.c, lib/Size_does_matter.c, lib/Stokes_flow_Incomp.c, lib/global_defs.h, module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/misc.cc, module/setProperties.c, tests/coupled.cfg, tests/multicoupled.cfg, tests/test2.sh, tests/test5.sh: Fixed two bugs in vtk velocity output 2008-10-23 23:35 becker * lib/Ggrd_handling.c, lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c, lib/Topo_gravity.c, lib/Viscosity_structures.c, lib/global_defs.h: Initial test implementation of netcdf grd based assignment of designated Euler vectors based on a code grd. 2008-09-04 22:46 tan2 * lib/Viscosity_structures.c: multi-component chemical viscosity 2008-09-04 20:18 tan2 * lib/Regional_sphere_related.c: Fixed issue 158: incorrect E->control.fi_max with coor=1 2008-09-04 00:20 tan2 * lib/Instructions.c, lib/Makefile.am, lib/Output_vtk.c: Some basic VTK parallel XML output * output in vts/pvts Structured VTK XML format * only these fields are available: coordinate, temperature, velocity and viscosity * coordinate and velocity are in Cartesian coordinates Some notes for future tasks: * adding other node- or element-based fields (pressure, stress, comp_nd, comp_el) is easy * tracer output should be in vtp format * surf, botm, and horiz_avg will be in vts format * geoid will still be as an ascii table 2008-09-04 00:12 tan2 * lib/global_defs.h: forgot to checkin this change in r12799 2008-09-04 00:11 tan2 * CitcomS/Components/Output.py, module/setProperties.c: pyre input for "self_gravitation" 2008-09-04 00:10 tan2 * lib/Sphere_harmonics.c, lib/Topo_gravity.c: self-gravitation geoid stuff * compute geoid due to internal buoyancy at the bottom * get rid of stress arrays * seperating topo effect on surface geoid into two part: surface topo and CMB topo. 2008-07-24 18:42 tan2 * module/setProperties.c: E->viscosity.zbase_layer is not init'd in pyre version. This fixes issue 155. 2008-07-24 18:21 becker * lib/Instructions.c: Both Eh and I were right and now the z_layer check should be finally fixed. 2008-07-24 18:13 becker * lib/Instructions.c, lib/Viscosity_structures.c: Fixed typo that provided assignment of zbase_layer thanks to Eh. 2008-07-24 01:00 becker * bin/Citcom.c, lib/Ggrd_handling.c, lib/Instructions.c, lib/Pan_problem_misc_functions.c, lib/Viscosity_structures.c, lib/viscosity_descriptions.h: Added rheology option eight. The other merges are surprising. 2008-06-30 15:49 becker * lib/Output.c, lib/Output_gzdir.c, lib/Output_h5.c: Moved the stress computation into stress output subroutine, for consistency with the style of the Output...c files. 2008-06-30 02:12 becker * lib/Construct_arrays.c, lib/Ggrd_handling.c, lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c, lib/Output_h5.c, lib/Topo_gravity.c, lib/Viscosity_structures.c, lib/global_defs.h, lib/viscosity_descriptions.h: Made CBF topography method and call to E->solver.parallel_communication_routs_s contingent on a "use_cbf_topo" parameter which is for now, by default, off, until the potential remaining memory bug (?) is tracked down. Made sure the stress tensor is computed before stress output, as CBF topo does not require the computation of the stress tensor. Added a z_layer input flag for zbase_layer other than the four layers used for the control of phase boundary depth. (Default is backward compatible.) 2008-06-27 00:53 becker * lib/Global_operations.c: Check in of proper version for elliptical net rotation correction. 2008-06-26 23:56 becker * lib/Global_operations.c, lib/Instructions.c, lib/Pan_problem_misc_functions.c, lib/global_defs.h: Reordered loop in get_buoyancy to speed up array access. Fixed omission of one elliptical correction, added a flag. 2008-06-26 23:04 becker * lib/Determine_net_rotation.c, lib/Drive_solvers.c, lib/Full_sphere_related.c, lib/Full_version_dependent.c, lib/Global_operations.c, lib/Instructions.c, lib/Nodal_mesh.c, lib/Output_gzdir.c, lib/Pan_problem_misc_functions.c, lib/Regional_version_dependent.c, lib/Size_does_matter.c, lib/global_defs.h: Replaced several trig function evaluations in Size_does_matter.c witht he precomputed SinCos arrays for speedup. Experimental ellipticity implementation has been improved somewhat, and made accessible only when -DALLOW_ELLIPTICAL is set. This was necessary to not slow the spherical version of the code down with if statements. 2008-06-25 01:13 becker * lib/Determine_net_rotation.c, lib/Element_calculations.c, lib/Ggrd_handling.c, lib/Global_operations.c, lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c, lib/Pan_problem_misc_functions.c, lib/Size_does_matter.c, lib/Topo_gravity.c, lib/Tracer_setup.c: Modified net rotation computation for ellipticity. Minor additions (prototypes) to make the code compile smoothly under PGI. 2008-06-24 21:18 tan2 * lib/Construct_arrays.c, lib/Full_parallel_related.c: Modified routs_s for lines. Added some debugging output and updated comments. 2008-06-24 21:11 tan2 * lib/Topo_gravity.c: Only top/bottom processors need to communicate 2008-06-21 22:28 becker * lib/Full_boundary_conditions.c, lib/Full_parallel_related.c, lib/Full_read_input_from_files.c, lib/Full_version_dependent.c, lib/Ggrd_handling.c, lib/Initial_temperature.c, lib/Instructions.c, lib/Regional_boundary_conditions.c, lib/Regional_read_input_from_files.c, lib/global_defs.h: Assignment of velocity boundary condition only called once at the top multigrid level during boundary condition assignment. Experimental implementation of mixed velocity/free slip boundary condition based on netcdf grids, in Ggrd_handling. 2008-06-20 23:01 tan2 * lib/Output.c, lib/Output_gzdir.c, lib/Output_h5.c: Enable CBF topography 2008-06-20 22:51 tan2 * lib/Topo_gravity.c: Added back get_CBF_topo(), from Shijie Zhong, with some minor modifications. Minor modifications: * some double arrays -> float arrays * calling exchange_snode_d() -> calling *_exchange_snode_f() 2008-06-20 22:50 tan2 * lib/Full_parallel_related.c, lib/Regional_parallel_related.c: Resurrected full_parallel_communication_routs_s(), which is needed by CBF topo. Renamed exchange_snode_f() to full_exchange_snode_f() and regional_exchange_snode_f(). 2008-06-20 22:42 tan2 * lib/Size_does_matter.c: Added get_global_1d_shape_fn_L() from Shijie Zhong 2008-06-20 22:41 tan2 * lib/Shape_functions.c: Compute E->L and E->Lx 1d shape functions (1d is a misnomer, they are 2d actually). 2008-06-20 19:08 tan2 * lib/Full_version_dependent.c: The function declaration was put at a wrong place. 2008-06-19 22:20 tan2 * visual/project_geoid.c: Change back the order of input arguments to match the manual. 2008-06-19 21:43 tan2 * lib/Viscosity_structures.c: The comment in rheol=4 doesn't match the code and is removed. Added option rheol=7, with a complete temperature- and pressure-dependent Arrhenius law. This fixed issue152. 2008-06-19 21:42 tan2 * lib/Full_version_dependent.c, lib/Sphere_harmonics.c: Added debugging (but disabled) function for spherical harmonics expansion. 2008-06-19 01:05 tan2 * lib/Global_operations.c, lib/Topo_gravity.c: Send geoid arrays to vertical columns of processors. After this fix, the geoid output is the same for nprocz=1 and nprocz>1. 2008-06-19 01:04 tan2 * lib/Size_does_matter.c, lib/Sphere_harmonics.c: Compute E->surf_det (top surface area, ie. surface jacobian, of an element) on a unit sphere. Use E->surf_det, instead of the surface jacobian returned by get_global_1d_shape_fn(), to expand spherical harmonics. The surface jacobian returned by get_global_1d_shape_fn() is defined at the top radius of the current mesh. When nprocz>1, the top radius is not the same as the outer radius of the sphere for processors. As a result, the spherical harmonics expansion gave incorrect result when nprocz>1 in the previous revisions. 2008-06-18 22:35 becker * lib/Global_operations.c: Speed up of computation by precomputing constants. 2008-06-17 21:23 tan2 * lib/General_matrix_functions.c, lib/Output.c, lib/Output_gzdir.c, lib/Output_h5.c, lib/Sphere_harmonics.c, lib/Topo_gravity.c, lib/global_defs.h: Compute geoid with self gravitation. Code contributed by Shijie Zhong. 2008-06-17 20:31 becker * lib/Drive_solvers.c, lib/General_matrix_functions.c, lib/Instructions.c, lib/Output.c, lib/Size_does_matter.c, lib/Solver_conj_grad.c, lib/Solver_multigrid.c, lib/Sphere_harmonics.c, lib/Topo_gravity.c, lib/global_defs.h: Added a few more comments and made a few loops more efficient. 2008-06-14 00:00 becker * bin/Citcom.c, lib/Full_read_input_from_files.c, lib/Ggrd_handling.c, lib/Instructions.c, lib/Pan_problem_misc_functions.c, lib/Problem_related.c, lib/global_defs.h: Added a few comments on Rayleigh number netcdf control. 2008-06-13 23:36 tan2 * NEWS: update NEWS item 2008-06-13 23:35 tan2 * lib/Ggrd_handling.c, lib/Global_operations.c, lib/Output_gzdir.c: Replaced MPI_COMM_WORLD by E->parallel.world. MPI_COMM_WORLD is the global communicator. E->parallel.world is the communicator for the current solver. These two are different in a coupled run. Before this fix, full-regional coupling will dead lock. 2008-06-13 23:34 tan2 * bin/Citcom.c: Added some comments 2008-06-13 23:33 tan2 * CitcomS/Controller.py: To be consistent with C version, disable checkpoint point output at 0th step if restarting. 2008-06-13 23:32 tan2 * lib/Construct_arrays.c, lib/Drive_solvers.c, lib/Full_parallel_related.c, lib/Full_version_dependent.c, lib/General_matrix_functions.c, lib/Regional_parallel_related.c, lib/Regional_version_dependent.c, lib/Stokes_flow_Incomp.c: Correctly counting the global number of equations. This will slightly affect the results of the stokes solver. This avoid double counting the overlapping nodes between processors and the global norm of velocity vector. 2008-06-13 23:25 tan2 * module/Exchanger/Boundary.cc: Using firewall channel, since error channel doesn't stop the code. 2008-06-13 23:24 tan2 * lib/Stokes_flow_Incomp.c: Decalred variables as double to avoid float-double conversion later in the loop. 2008-06-13 19:14 tan2 * visual/project_geoid.c: update the help message 2008-06-12 21:22 becker * bin/Citcom.c, lib/Checkpoints.c, lib/Construct_arrays.c, lib/Determine_net_rotation.c, lib/Drive_solvers.c, lib/Full_boundary_conditions.c, lib/Full_read_input_from_files.c, lib/Full_sphere_related.c, lib/Full_version_dependent.c, lib/Ggrd_handling.c, lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c, lib/Pan_problem_misc_functions.c, lib/Process_buoyancy.c, lib/Regional_boundary_conditions.c, lib/Size_does_matter.c, lib/Topo_gravity.c, lib/Tracer_setup.c, lib/global_defs.h, visual/project_geoid.c: Added tentative implementation of a rotating, elliptical Earth. Made restart for constant viscosity cases possible. Added alternative geoid computation place holder for self-gravitating mantle, to be filled out by Shijie's old code. 2008-05-30 18:42 becker * visual/project_geoid.c: Fixed typo in memory allocation procedure that led to core dump. 2008-05-12 21:22 gurnis * NEWS: fixed typo 2008-05-12 21:16 gurnis * NEWS: Just a place holder for the next release 2008-05-05 19:17 gurnis * lib/Regional_read_input_from_files.c: Bug Fix 2008-05-01 22:59 tan2 * CitcomS/Components/BC.py, CitcomS/Solver/Solver.py, module/bindings.c, module/misc.c, module/misc.h: Add python binding to update top surface temperatures 2008-05-01 22:56 gurnis * bin/Citcom.c, lib/Full_boundary_conditions.c, lib/Full_read_input_from_files.c, lib/Problem_related.c, lib/Regional_boundary_conditions.c, lib/Regional_read_input_from_files.c, lib/Viscosity_structures.c: More additions to allow top surface temperatures to be read in a each time step. Should read in every time step for C only version. Additional changes for Pyre version to follow; will test more once these changes are made. Small changes to viscosity structures when reading in materials for each element. More documentation to follow. 2008-05-01 00:51 tan2 * CitcomS/Components/Param.py, lib/Instructions.c, lib/Output_h5.c, module/setProperties.c: Inputing tbcs_file & temperature_boundary_file 2008-04-30 23:11 gurnis * lib/global_defs.h: Start to add new features for reading surface temperature for all top surface node points Added new variables to the CONTROL structure vbcs_file & temperature_boundary_fi le 2008-04-06 21:58 becker * bin/Citcom.c, lib/Advection_diffusion.c, lib/Full_read_input_from_files.c, lib/Ggrd_handling.c, lib/Instructions.c, lib/Pan_problem_misc_functions.c, lib/Problem_related.c, lib/Regional_read_input_from_files.c, lib/ggrd_handling.h, lib/global_defs.h, lib/viscosity_descriptions.h: GMT/Netcdf grd input can now deal with velocity boundary conditions, material dependence, and local Rayleigh number in surface layers. 2008-03-05 21:15 tan2 * lib/Instructions.c: Close trace_log files when finalizing 2008-03-05 21:07 tan2 * lib/Full_sphere_related.c, lib/Full_version_dependent.c, lib/General_matrix_functions.c, lib/Instructions.c, lib/Obsolete.c, lib/Regional_version_dependent.c, lib/global_defs.h: Clean up unused arrays and functions 2008-03-05 21:06 tan2 * lib/Tracer_setup.c: Write exclusive tracer time every 20 steps 2008-03-05 21:04 tan2 * examples/Makefile.am, lib/Full_sphere_related.c, lib/Full_version_dependent.c, lib/General_matrix_functions.c, lib/Instructions.c, lib/Obsolete.c, lib/Regional_version_dependent.c, lib/Tracer_setup.c, lib/global_defs.h, visual/Makefile.am: Revert r11328 2008-03-05 20:50 tan2 * examples/Makefile.am, lib/Full_sphere_related.c, lib/Full_version_dependent.c, lib/General_matrix_functions.c, lib/Instructions.c, lib/Obsolete.c, lib/Regional_version_dependent.c, lib/Tracer_setup.c, lib/global_defs.h, visual/Makefile.am: Write exclusive tracer time every 20 steps 2008-02-28 01:03 tan2 * lib/Composition_related.c: Removed artificial tolerance of empty elements. This greatly decreases the minimal number of tracers per element required for a given mesh. This fixed issue140. 2008-02-28 01:00 tan2 * lib/Process_buoyancy.c: Minor tweak 2008-02-27 07:42 becker * lib/Full_read_input_from_files.c, lib/Ggrd_handling.c, lib/Initial_temperature.c, lib/Instructions.c, lib/Lith_age.c, lib/Output_gzdir.c, lib/Pan_problem_misc_functions.c, lib/Regional_read_input_from_files.c, lib/Tracer_setup.c, lib/ggrd_handling.h: Built surface velocity BC support via Netcdf grd files back in. This needs more testing, but it would be good to have the framework in place before new additions are made. Also, age control is not yet implemented, but will be soon. 2008-02-21 01:25 tan2 * bin/Citcom.c: Removed unnecessary call to construct_mat_group() 2008-02-21 01:03 tan2 * CitcomS/BaseApplication.py, CitcomS/Controller.py, lib/Full_tracer_advection.c, lib/Process_buoyancy.c, module/initial_conditions.c: Finished interpolating fields onto tracers 2008-02-21 01:02 tan2 * lib/Full_tracer_advection.c: Renamed fix_phi() to fix_angle() 2008-02-21 01:01 tan2 * lib/Full_tracer_advection.c: Fixed issue139. Bug for tracers near South pole. 2008-02-21 01:00 tan2 * lib/Full_tracer_advection.c, lib/Process_buoyancy.c, lib/Tracer_setup.c: Get new tracers in post processing stage 2008-02-21 00:56 tan2 * lib/Pan_problem_misc_functions.c, lib/Tracer_setup.c: Read multiple extraq 2008-02-21 00:55 tan2 * lib/Composition_related.c, lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c: Write averaged composition in horiz_avg output. The HDF5 part of output is not implemented... 2008-02-21 00:54 tan2 * lib/Process_buoyancy.c: Removed horizontal average from output_interpolated_fields() 2008-02-21 00:53 tan2 * lib/Instructions.c, lib/Process_buoyancy.c, lib/global_defs.h: Compute horizontal average for composition fields 2008-02-17 00:14 becker * bin/Citcom.c, lib/Full_read_input_from_files.c, lib/Ggrd_handling.c, lib/Initial_temperature.c, lib/Instructions.c, lib/Regional_read_input_from_files.c, lib/Viscosity_structures.c, lib/convection_variables.h, lib/global_defs.h: Modified Citcom.c such that E->mat gets assigned based on element depth (as was default before), even if mat_control is not selected. Added (back in?) ggrd netcdf type VIP prefactor material control via ggrd_mat_control flags (as documented in Instructions.c) Renamed some of the ggrd stuff to make it more modular. 2008-02-09 00:14 tan2 * lib/Process_buoyancy.c: Interpolate fields in post_processing() * The parameter "itracer_interpolate_fields" is the same as "model_type" in the AVM code. * If itracer_interpolate_fields is 1, 2, or 3, it interpolates temperature and compositions. The horizonal average is not removed yet. 2008-02-08 23:58 tan2 * lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c: Refactored the functions. * get shape functions on tracer location * interpolate data using acquired shape functions 2008-02-08 23:56 tan2 * CitcomS/Solver/Solver.py, bin/Citcom.c, module/bindings.c, module/initial_conditions.c, module/initial_conditions.h: Added binding for post_processing(). Exit program after post processing and saving results. 2008-02-08 23:54 tan2 * lib/Full_tracer_advection.c, lib/global_defs.h: * Using a different reference point for uv space. This fixed a nasty bug when some cap extends over ~pi/2. * A bunch of debugging output (disabled) * Disable more debugging output 2008-02-08 23:50 tan2 * CitcomS/Components/Tracer.py, lib/Full_tracer_advection.c, lib/Tracer_setup.c, lib/tracer_defs.h, module/setProperties.c: Added new parameter: itracer_interpolate_fields When it is 0 (default), nothing is done. Otherwise, the convection fields are interpolated onto the location of tracers. 2008-02-04 23:23 tan2 * examples/Makefile.am, visual/Makefile.am: Reverted part of unwannted change 2008-02-04 23:21 tan2 * examples/Makefile.am, module/misc.c, visual/Makefile.am: Fixed potential memory leak 2008-02-04 23:13 tan2 * module/Exchanger/exchangers.cc: Fixed bugs in managing reference counts and potential double-free 2008-02-04 20:40 tan2 * lib/Initial_temperature.c: Fixed a regression reported by Lydia Dicaprio. The initial temperature should be constructured in this order: 1. if tic_method=-1, read from velo files. 2. if lith_age=1, read/constructed from lith_age files. 3. otherwise, call {full,regional}_construct_tic_from_input() 2008-01-22 19:52 tan2 * lib/Advection_diffusion.c, lib/Element_calculations.c, lib/Size_does_matter.c, lib/Topo_gravity.c, lib/Viscosity_structures.c: Renamed functions 2008-01-22 19:38 tan2 * lib/Advection_diffusion.c, lib/Element_calculations.c, lib/Global_operations.c, lib/Instructions.c, lib/Obsolete.c, lib/Process_buoyancy.c, lib/Size_does_matter.c, lib/Topo_gravity.c, lib/Viscosity_structures.c, lib/global_defs.h: Computes the derivatives of shape functions and jacobians only once and stores them for later use. This reduces the total cpu time of cookbook8 by 13%. - get_global_shape_fn_sph() computes and stores the derivatives of shape functions and jacobians. - Moved get_global_shape_fn() to Obsolete.c - Calling construct_shape_function_derivatives() in initial_mesh_solver_setup(). This function call get_global_shape_fn_sph() for each element. - get_rtf_at_vpts() and get_rtf_at_ppts() are for coord. transformation matrix at vpts and ppts respectively - Passed arguments by references in PG solvers instead of by values to avoid copying. 2008-01-17 02:06 becker * lib/Full_tracer_advection.c, lib/global_defs.h: Changed GNOMONIC to CITCOM_GNOMONIC to avoid namespace conflict with GMT gmt.h 2008-01-16 20:53 tan2 * lib/Tracer_setup.c: Forgot to checkin this file 2008-01-16 20:34 tan2 * lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c, lib/tracer_defs.h: Added timing information for tracer module. The timing is reported in *.tracer_log.* files. 2008-01-16 20:30 tan2 * lib/Full_tracer_advection.c, lib/global_defs.h, lib/tracer_defs.h: A more memory efficient way to find shape function for tracers. - Migrated E->tracer.UV to E->gnomonic. The reference point is the 1st node of the local mesh. The 0th element of E->gnomonic stores the sine of cosine of reference theta. - Convertd shape_coefs array from size of nel to size of snel to save memory. 2008-01-15 23:36 tan2 * AUTHORS: Added Luis Armendariz to the author list 2008-01-15 23:11 tan2 * lib/Full_sphere_related.c: Simplified loop over levels 2008-01-15 23:05 tan2 * examples/Makefile.am, lib/Full_sphere_related.c, lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c, lib/Tracer_setup.c, lib/global_defs.h, lib/tracer_defs.h, visual/Makefile.am: Reverted previous checkin 2008-01-15 23:01 tan2 * examples/Makefile.am, lib/Full_sphere_related.c, lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c, lib/Tracer_setup.c, lib/global_defs.h, lib/tracer_defs.h, visual/Makefile.am: Simplified loop over levels 2008-01-15 00:29 tan2 * lib/Full_sphere_related.c: Forgot to rename variables 2008-01-14 23:03 tan2 * lib/Full_sphere_related.c: Fixed 2 bugs in full_coord_of_cap(). 1. x and y arrays were overridden in the loop of level. 2. Choice of reference point was not optimal and may cause round off problem. 2008-01-03 19:51 tan2 * lib/Construct_arrays.c, lib/Full_geometry_cartesian.c, lib/Full_sphere_related.c, lib/Full_tracer_advection.c, lib/Full_version_dependent.c, lib/Output_h5.c, lib/Regional_version_dependent.c, lib/Sphere_harmonics.c, lib/Sphere_util.c, lib/global_defs.h: Re-applied patches that got reverted in r8973 2007-12-29 07:02 becker * lib/Construct_arrays.c, lib/Full_geometry_cartesian.c, lib/Full_sphere_related.c, lib/Full_tracer_advection.c, lib/Full_version_dependent.c, lib/Instructions.c, lib/Output_h5.c, lib/Regional_version_dependent.c, lib/Sphere_harmonics.c, lib/Sphere_util.c, lib/global_defs.h: Trying to sync back up, those should be old changes, I hope. 2007-12-20 20:30 tan2 * lib/Full_sphere_related.c, lib/Full_tracer_advection.c, lib/Full_version_dependent.c, lib/Sphere_harmonics.c, lib/Sphere_util.c, lib/global_defs.h, tests/gnomonic.c: Generated global mesh by great circles. Tracer module can split the cap in the map view now. 2007-12-20 20:27 tan2 * lib/Full_geometry_cartesian.c: Fine tune the mesh so that each cap has the same surface area 2007-12-20 20:26 tan2 * lib/Regional_version_dependent.c: Removed obsolete code 2007-12-20 20:25 tan2 * lib/Construct_arrays.c: Fixed a redundant cast 2007-12-17 22:06 tan2 * lib/Output_h5.c: Fixed phase change width 2007-11-12 22:42 tan2 * NEWS, configure.ac: Updated the version number and file NEWS 2007-11-12 22:38 tan2 * module/Exchanger/Makefile.am: Added mishing header file to the makefile, also avoided compiling unused code. 2007-11-11 20:37 becker * lib/Construct_arrays.c, lib/Full_obsolete.c, lib/Ggrd_handling.c, lib/Material_properties.c, lib/global_defs.h: Synching with the new release, none of those changes should be relevant. 2007-11-08 22:41 tan2 * ChangeLog: Updated file ChangeLog to r8244 2007-11-08 22:31 tan2 * lib/Instructions.c, lib/Pan_problem_misc_functions.c: Replaced a system call by std C library remove() and disabled another system call (backup input file). Partially fixed issue130. All remaining system calls are in lib/Output_gzdir.c. 2007-11-08 21:38 tan2 * ChangeLog: Updated file ChangeLog to r8242 2007-11-08 21:36 tan2 * examples/Makefile.am: Removed binary checkpoint files from makefile, as the file size is too big for distribution. 2007-11-08 21:17 tan2 * ChangeLog: Updated file ChangeLog to r8240 2007-11-08 19:19 tan2 * configure.ac: Update the version number 2007-11-08 19:18 tan2 * NEWS: Update NEWS 2007-11-08 19:18 tan2 * examples/Cookbook5/cookbook5.cfg: Dereased the timestep size to reduce artifacts in advection 2007-11-07 19:52 tan2 * examples/Cookbook4/cookbook4.cfg: Decreased the # of processors. This is the only way I can reproduce single-cell convection as in the manual. 2007-11-07 19:52 tan2 * CitcomS/Components/Output.py, lib/Output.c: Removed comp_el from default output, since it is not required for restart anymore. 2007-11-07 19:51 tan2 * lib/Stokes_flow_Incomp.c: Print a warning when matrix eqn solver not converging 2007-11-06 23:18 tan2 * examples/Cookbook7/cookbook7.cfg: Added cgrad solver convergence parameters, increased buoyancy_ratio and lower the # of steps 2007-11-06 23:18 tan2 * examples/Cookbook6/cookbook6.cfg: Removed unused multigrid parameters 2007-11-06 23:18 tan2 * examples/Full/input.sample, examples/Regional/input.sample: Increase vlowstep to match the default value in pyre 2007-11-06 23:17 tan2 * visual/project_geoid.c: Fixed a few memory errors 2007-11-06 01:04 tan2 * lib/Output.c: Init'd some variables about vtk_io, which might be accessed with uninit'd values in output_finalize() 2007-11-06 01:04 tan2 * lib/Full_obsolete.c, lib/Global_operations.c, lib/Obsolete.c, lib/Sphere_harmonics.c, lib/Topo_gravity.c: Shrank the size of sph. harm arrays 2007-11-06 01:03 tan2 * lib/Regional_obsolete.c: Removed functions related sph. harm in lib/Regional_obsolete.c 2007-11-06 01:03 tan2 * lib/Topo_gravity.c: Scaled topo with variable gravity. Fixed an error in comment. Rearranged computation. 2007-11-01 23:33 tan2 * lib/Full_version_dependent.c: Fixed an error in comment 2007-11-01 23:33 tan2 * lib/Stokes_flow_Incomp.c: Print dv/v=dp/p=1.0 for the 1st Uzawa iteraion 2007-10-30 22:29 tan2 * visual/Makefile.am: Minor modification 2007-10-30 21:54 tan2 * visual/Makefile.am: Added the C program project_geoid to the makefile 2007-10-30 21:53 tan2 * visual/project_geoid.c: A post-processing program to project geoid coefficents onto a regular (longitude, latitude) mesh 2007-10-30 21:50 tan2 * lib/Topo_gravity.c: Fixed a bug in dimensionalizing density. Provided the formula of geoid calculation in the comments. Rearranged the order of functions. 2007-10-30 21:49 tan2 * lib/Element_calculations.c, lib/Instructions.c: Compute d(rho)/dr/rho from rho(r) 2007-10-22 20:57 tan2 * ChangeLog: Updated file ChangeLog to r8170 2007-10-22 20:26 tan2 * NEWS: Updated NEWS 2007-10-22 19:46 tan2 * AUTHORS, configure.ac: Minor update 2007-10-22 19:44 tan2 * INSTALL, README: Simpilify INSTALL 2007-10-22 19:03 tan2 * lib/Advection_diffusion.c: Eliminated unnecessary computation 2007-10-22 19:03 tan2 * lib/Advection_diffusion.c: Variable material properties in latent heat correction on adiabatic cooling 2007-10-22 19:02 tan2 * lib/Advection_diffusion.c, lib/Phase_change.c: Added some comments 2007-10-19 19:24 tan2 * lib/Advection_diffusion.c, lib/Phase_change.c, lib/global_defs.h, module/setProperties.c: Renamed control.width* -> control.inv_width* for clarity 2007-10-18 18:53 tan2 * CitcomS/Coupler/Coupler.py, module/Exchanger/Convertor.cc, module/Exchanger/Convertor.h, module/Exchanger/exchangers.cc: Renamed coupler inventory: dimensional -> si_unit and transformational -> cartesian 2007-10-17 22:44 tan2 * examples/Cookbook5/cookbook5.cfg, examples/Cookbook9/cookbook9.cfg: Minor change in the examples 2007-10-17 20:56 tan2 * bin/Citcom.c: Added comments on where C code is replaced by python code in Citcom.c 2007-10-17 20:55 tan2 * lib/Determine_net_rotation.c, lib/Drive_solvers.c, lib/Output_gzdir.c, lib/Stokes_flow_Incomp.c, lib/Viscosity_structures.c, lib/viscosity_descriptions.h: Put the rest of r8111 back 2007-10-17 20:33 tan2 * examples/Full/input.sample, examples/Regional/input.sample: Fixed input diffusivity parameter in the examples, from r8111. 2007-10-17 20:32 tan2 * lib/Drive_solvers.c, lib/Global_operations.c, lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c: Added back minor modification from r8111 2007-10-17 18:40 tan2 * examples/Cookbook9/cookbook9.cfg: Fixed a typo in the example 2007-10-17 18:36 tan2 * lib/Global_operations.c: Fixed a bug in remove_rigid_rot() 2007-10-17 18:35 tan2 * bin/Citcom.c, examples/Full/input.sample, lib/Determine_net_rotation.c, lib/Drive_solvers.c, lib/Full_version_dependent.c, lib/Global_operations.c, lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c, lib/Stokes_flow_Incomp.c, lib/Viscosity_structures.c, lib/viscosity_descriptions.h: Roll back r8111, reading velo files for init. temperature stays as tic_method=-1. Other changes in r8111 will be put back later. 2007-10-13 19:07 becker * bin/Citcom.c, examples/Full/input.sample, lib/Determine_net_rotation.c, lib/Drive_solvers.c, lib/Full_version_dependent.c, lib/Global_operations.c, lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c, lib/Stokes_flow_Incomp.c, lib/Viscosity_structures.c, lib/viscosity_descriptions.h: Fixed rigid rotation code bug. Added restart=2 option which will not use checkpoints, but tic_method=-1 style temperature input (formally realized via tic_method=-1, but this should be cleaner) fixed input diffusivity parameter in full example file. 2007-10-12 20:24 tan2 * tests/coupled.cfg: Turn off monitor_max_T in the test 2007-10-12 20:23 tan2 * module/Exchanger/Boundary.cc: Boundary class is for regional model only, add a checking for it. 2007-10-11 01:23 tan2 * examples/Cookbook9, examples/Cookbook9/cookbook9.cfg, examples/Cookbook9/ic, examples/Cookbook9/ic/cntn.velo.0.0, examples/Cookbook9/ic/cntn.velo.1.0, examples/Cookbook9/ic/embd.velo.0.0, examples/Cookbook9/ic/embd.velo.1.0, examples/Cookbook9/velocity, examples/Cookbook9/velocity/bvel.dat0, examples/Cookbook9/velocity/bvel.dat1, examples/Makefile.am: Cookbook 9: nested solver coupling + coor_refine + tsolver tuning 2007-10-11 00:03 becker * lib/Process_buoyancy.c: Wiser now, commented in the E->fp output 2007-10-10 23:40 becker * bin/Citcom.c, lib/Construct_arrays.c, lib/Full_version_dependent.c, lib/Ggrd_handling.c, lib/Initial_temperature.c, lib/Instructions.c, lib/Pan_problem_misc_functions.c, lib/Process_buoyancy.c, lib/Regional_sphere_related.c, lib/Regional_version_dependent.c, lib/Viscosity_structures.c, lib/convection_variables.h, lib/global_defs.h: Added coor=3 option for radial node spacing a la CitcomCU. Streamlined ggrd temperature init. Added file flush to heat flow output. 2007-10-10 21:00 tan2 * CitcomS/Coupler/Coupler.py: Add an assertion 2007-10-10 20:11 tan2 * CitcomS/Components/Stokes_solver/Incompressible.py, examples/Cookbook8/cookbook8.cfg, examples/Full/input.sample, examples/Regional/input.sample, lib/Drive_solvers.c, lib/Global_operations.c, lib/Instructions.c, lib/global_defs.h, module/setProperties.c: Remove rigid body rotation from the velocity solution from global model. A input parameter 'solver.vsolver.remove_rigid_rotation', default to on, indicate whether to remove the rigid body rotation. For free-slip model, this parameter should be on. For model with imposed plate velocity, it is advised to turn off this parameter. 2007-10-05 20:02 tan2 * CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py, CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/Solver/CoupledSolver.py: Renamed excludeTop -> exclude_top, and excludeBottom -> exclude_bottom. (No other CitcomS parameter uses CamelCase.) Reworked the interaction of initial temperature and coupling. Created a new parameter exchange_initial_temperature. 2007-10-05 20:00 tan2 * CitcomS/Components/Stokes_solver/Incompressible.py: Strengthen the default convergence criterion for the 3rd iteration in compressible cg solver 2007-10-05 19:58 tan2 * lib/Regional_read_input_from_files.c: Disable a debugging output 2007-10-05 19:58 tan2 * CitcomS/Coupler/MultiC_Coupler.py, CitcomS/Coupler/MultiE_Coupler.py: Add licence text to the multi-couplers 2007-10-05 19:57 tan2 * CitcomS/Components/Advection_diffusion/Advection_diffusion.py, lib/Advection_diffusion.c: Turn off filter_temp by default since it's not in the energy equation 2007-10-04 19:35 becker * lib/Viscosity_structures.c: Fxied material assignment bug in PDEPV (0 vs. 1 array issue...) 2007-10-01 20:38 tan2 * examples/Cookbook1/cookbook1.cfg, examples/Cookbook2/cookbook2.cfg, examples/Cookbook4/cookbook4.cfg, examples/Cookbook5/cookbook5.cfg, examples/Cookbook5/ic, examples/Cookbook5/restart_files, examples/Cookbook6/cookbook6.cfg, examples/Cookbook7/cookbook7.cfg, examples/Makefile.am, examples/example1.cfg: Updated the cookbook scripts 2007-10-01 19:26 tan2 * examples/Cookbook8, examples/Cookbook8/cookbook8.cfg, examples/Cookbook8/coord.dat, examples/Cookbook8/restart, examples/Cookbook8/restart/cookbook8.chkpt.0.9000, examples/Cookbook8/restart/cookbook8.chkpt.1.9000, examples/Cookbook8/restart/cookbook8.chkpt.10.9000, examples/Cookbook8/restart/cookbook8.chkpt.11.9000, examples/Cookbook8/restart/cookbook8.chkpt.2.9000, examples/Cookbook8/restart/cookbook8.chkpt.3.9000, examples/Cookbook8/restart/cookbook8.chkpt.4.9000, examples/Cookbook8/restart/cookbook8.chkpt.5.9000, examples/Cookbook8/restart/cookbook8.chkpt.6.9000, examples/Cookbook8/restart/cookbook8.chkpt.7.9000, examples/Cookbook8/restart/cookbook8.chkpt.8.9000, examples/Cookbook8/restart/cookbook8.chkpt.9.9000, examples/Makefile.am: Added Cookbook8 for compressible model + geoid + checkpoint + vsolver tuning 2007-09-28 23:36 becker * lib/Full_version_dependent.c, lib/Initial_temperature.c, lib/Output_gzdir.c: Fixed restart I/O bug in Output_gzdir. 2007-09-27 19:33 tan2 * bin/Citcom.c, lib/Output_gzdir.c: Added function prototype and fixed a few errors 2007-09-27 19:07 tan2 * lib/Checkpoints.c, lib/Composition_related.c, lib/Tracer_setup.c, lib/composition_related.h: Shrink the size of checkpoint files 2007-09-27 19:07 tan2 * CitcomS/Components/Sphere/Sphere.py, lib/Regional_sphere_related.c, module/setProperties.c: Enable coor_refine for regional model, only radial coordinate is refined 2007-09-25 19:40 tan2 * lib/Instructions.c: Fixed a bug in vtkio 2007-09-25 01:31 tan2 * CitcomS/Components/Param.py, lib/Instructions.c, lib/Material_properties.c, lib/global_defs.h, module/setProperties.c: Introducing choice of reference state: When solver.param.reference_state=0, the reference state is read from a file (solver.param.refstate_file) When solver.param.reference_state=1 (default), the reference state is calculated using Adams-Williamson equation of state. 2007-09-24 21:29 tan2 * configure.ac, lib/Output_gzdir.c: Detect the presence of libz and enable ascii-gz at configure time 2007-09-24 21:28 tan2 * lib/Instructions.c, lib/Material_properties.c, lib/global_defs.h: Comment out varialbe thermal conductivity. Removed unused struct members. 2007-09-24 21:28 tan2 * lib/Advection_diffusion.c: Multiply rho*cp to DT/dt 2007-09-19 20:34 tan2 * lib/Material_properties.c: Don't write to log file, since only rank-0 proc can access it 2007-09-19 20:34 tan2 * lib/Composition_related.c, lib/Instructions.c: Set default value for tracer/composition flags earlier 2007-09-19 20:33 tan2 * lib/Checkpoints.c: Shrink the size of arrays 2007-09-19 20:31 tan2 * lib/Instructions.c: Shrink the size of arrays 2007-09-19 20:30 tan2 * lib/Output.c, lib/Output_gzdir.c, lib/Output_h5.c, lib/Topo_gravity.c: Fixed uninit'd heat flux and geoid arrays bugs, as reported by valgrind 2007-09-19 00:28 becker * lib/Advection_diffusion.c, lib/Output_gzdir.c: Minor bug fix in Output_gzidir, output_heating function didn't work. 2007-09-18 23:08 tan2 * lib/Checkpoints.c: Fixed a memory bug in checkpoint 2007-09-18 23:07 tan2 * lib/Regional_tracer_advection.c: Setup composition for regional model 2007-09-18 01:52 leif * configure.ac, setup.py: Fix for Issue129: "CitcomS configured without exchanger still links with -lExchanger". Also, use CIT_HEADER_MPI so that configuring --with-exchanger using MPICH2 works (see Issue14 and Issue57). 2007-09-17 20:30 tan2 * lib/Composition_related.c: Generalized init. composition from neighbors for multi-component composition 2007-09-17 19:07 tan2 * lib/Composition_related.c: Using neighboring elements to determine the initial composition, if only a few elements are empty. 2007-09-15 00:17 tan2 * lib/Tracer_setup.c: Revert accidental commit in part of r7957 2007-09-14 23:39 tan2 * lib/Advection_diffusion.c, lib/Phase_change.c: Rearranged computation of latent heat and the test condition of phase change 2007-09-14 23:11 tan2 * lib/Advection_diffusion.c: Added the contribution of latent heat to the diffusion term 2007-09-14 23:11 tan2 * lib/Obsolete.c, lib/Phase_change.c: Replace abs() by fabs() 2007-09-14 23:10 tan2 * lib/Advection_diffusion.c: Consevert energy (sum of rho*cp*T) instead of temperature (sum of T) in the Lenardic filter, also fixed a long-standing bug (abs -> fabs) 2007-09-14 23:09 tan2 * lib/Advection_diffusion.c: Changed the magic numbers (0.0 and 1.0) to const variables, reindent the code. 2007-09-13 22:36 tan2 * CitcomS/Solver/Solver.py, lib/Instructions.c, lib/Material_properties.c, lib/global_defs.h, module/setProperties.c: Comment out adiabatic temperature profile for now, since it is not used in the code. 2007-09-12 19:24 tan2 * visual/parser.py: Fixed a problem when the input string is empty 2007-09-12 19:24 tan2 * lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c, lib/Tracer_setup.c, lib/global_defs.h: Added heating file to optional output 2007-09-12 19:24 tan2 * lib/Stokes_flow_Incomp.c: Keep the load vector intact in the bicg solver 2007-09-12 19:23 tan2 * lib/Composition_related.c, lib/Full_tracer_advection.c, lib/Tracer_setup.c: Using drand48() instead of rand() to improve the quality of random tracers. Added some debugging output if the tracer count is low. 2007-09-12 19:22 tan2 * CitcomS/Components/Tracer.py, lib/Composition_related.c, lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c, lib/Tracer_setup.c, module/setProperties.c: Add new input boolean parameter 'itracer_warnings'. Default to on. When it is off, the exit condition of tracer is relaxed. 2007-09-12 19:19 tan2 * lib/Stokes_flow_Incomp.c: Removed the test for F=0 load vector bug. The bug was fixed in r7940. 2007-09-07 22:53 tan2 * lib/Advection_diffusion.c, lib/Size_does_matter.c: Fixed tsolver. Fixed a bug in TMass and another in convert element # to nz. 2007-09-05 22:35 tan2 * lib/Checkpoints.c, lib/Construct_arrays.c, lib/Drive_solvers.c, lib/Element_calculations.c, lib/Full_obsolete.c, lib/Full_parallel_related.c, lib/General_matrix_functions.c, lib/Instructions.c, lib/Obsolete.c, lib/Regional_obsolete.c, lib/Regional_parallel_related.c, lib/Solver_multigrid.c, lib/Stokes_flow_Incomp.c: Fixed a few memory problems. Shrink the size of several arrays related to Stokes eqn. Moved jacobi() to Obsolete.c 2007-09-05 22:21 tan2 * module/Exchanger/SIUnit.cc: Forgot to update surfacee_tem 2007-09-05 22:20 tan2 * lib/Viscosity_structures.c: Set the min of 2nd strain rate invariant to 1e-16 to prevent infinite viscosity when SDEPV=on 2007-09-05 22:20 tan2 * lib/Convection.c: Init'd timestep variables 2007-09-04 23:09 becker * lib/Full_tracer_advection.c, lib/Instructions.c, lib/Stokes_flow_Incomp.c: Added test for F=0 load vector bug, moved open_qfiles to after set_elapsed time. 2007-08-29 23:50 tan2 * examples/Makefile.am: Forgot to update the makefile 2007-08-29 23:39 tan2 * examples/Cookbook5/velocity/bvel.dat57, examples/Cookbook5/velocity/bvel.dat58, examples/Cookbook5/velocity/bvel.dat59, examples/Cookbook5/velocity/bvel.dat60, examples/Cookbook5/velocity/bvel.dat61, examples/Cookbook5/velocity/bvel.dat62, examples/Cookbook5/velocity/bvel.dat63, examples/Cookbook5/velocity/bvel.dat64, examples/Cookbook5/velocity/bvel.dat65, examples/Cookbook5/velocity/bvel.dat66, examples/Cookbook5/velocity/bvel.dat67, examples/Cookbook5/velocity/bvel.dat68, examples/Cookbook5/velocity/bvel.dat69, examples/Cookbook5/velocity/bvel.dat70, examples/Cookbook5/velocity/bvel.dat71: Removed unused velocity bc files 2007-08-29 23:18 tan2 * doc/CitcomS, doc: Restructing the repository layout for CitcomS documentation 2007-08-29 20:55 tan2 * lib/Instructions.c: Forgot to update r7902 2007-08-29 20:48 tan2 * lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c, lib/Regional_obsolete.c, lib/Viscosity_structures.c, lib/output.h: Replaced output_open() with output_open_mode() Append the log and time files if restarting 2007-08-29 20:47 tan2 * lib/Advection_diffusion.c: Minor fix 2007-08-29 01:46 becker * lib/Instructions.c: Missed to merge one modification after the conflict. 2007-08-29 00:51 becker * bin/Citcom.c, lib/Full_version_dependent.c, lib/Ggrd_handling.c, lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c, lib/Output_h5.c, lib/Process_buoyancy.c, lib/Regional_version_dependent.c, lib/Viscosity_structures.c, lib/convection_variables.h, lib/global_defs.h: When checking in my changes, I had to resolve a conflict for lib/Instructions.c by hand, which I hope I did properly. Here are my changes: - renamed CONTOL structure members ORTHO and ORTHOZ to CITCOM_ORTHO and CITCOM_ORTHOZ Those were never used and conflicted with definitions in GMT gmt.h - Added a higher frequency heat flow output option like so: write_q_files=1 # option to write heat flux to files qt.dat and qb.dat # at intervals smaller than storage_spacing (0) - Added the capability to read in initial temperatures from netcdf grd files, if -USE_GGRD is used. Lot of options, like so: # # read initial temperature conditions from grd files (default values in parentheses) # tic_method=4 # read initial temperature from netcdf GRD files (off) ggrd_tinit_scale_with_prem=off # scale the temperature with PREM densities (off) ggrd_tinit_scale=1.0 # scaling factor to apply to read in scalars f (1.0) ggrd_tinit_offset=-0.5 # offset, T = f * scale + offset + tm (0.0) # where tm is the mean between top and bottom TBC values # if the bottom is flux, will use 1 for bottom TBC value ggrd_tinit_gfile="../../data/tomography/s20a_smean_new_age/t" # prefix of grd files, will # try to read t.1.grd, t.2.grd ... t.n.grd # where n is the number of layers in the depth file ggrd_tinit_dfile="../../data/tomography/s20a_smean_new_age/tdepth.dat" # file with layer depths in km from bottom up ggrd_tinit_prem_file="../../progs/src/hc-svn/prem/prem.dat" # PREM data file ggrd_tinit_override_tbc=on # override temperature boundary conditions (off) 2007-08-28 01:10 tan2 * CitcomS/Solver/Solver.py, lib/Instructions.c: Defaulting datadir_old to the current directory 2007-08-28 01:09 tan2 * CitcomS/Components/Const.py, CitcomS/Solver/Solver.py, lib/Advection_diffusion.c, lib/Instructions.c, lib/Material_properties.c, lib/Output_h5.c, lib/global_defs.h, module/setProperties.c: Added various heating term to the energy equation. A new input parameter: solver.surfaceT for non-dimensional surface temperature. Removed old (and unused) input parameter: solver.const.surf_temp. 2007-08-27 19:34 tan2 * lib/Stokes_flow_Incomp.c: Fixed a index bug in stokes solver 2007-08-27 19:34 tan2 * CitcomS/Components/Output.py, CitcomS/Components/Tracer.py, CitcomS/Components/Visc.py, lib/Advection_diffusion.c, module/setProperties.c: Add pyre input for new parameters introduced by TWB 2007-08-27 19:34 tan2 * lib/Advection_diffusion.c, lib/Checkpoints.c, lib/Construct_arrays.c, lib/Determine_net_rotation.c, lib/Drive_solvers.c, lib/Full_geometry_cartesian.c, lib/Full_lith_age_read_files.c, lib/Full_tracer_advection.c, lib/General_matrix_functions.c, lib/Instructions.c, lib/Lith_age.c, lib/Pan_problem_misc_functions.c, lib/Parsing.c, lib/Regional_lith_age_read_files.c, lib/Regional_sphere_related.c, lib/Regional_tracer_advection.c, lib/Regional_version_dependent.c, lib/Tracer_setup.c, lib/Viscosity_structures.c, lib/output.h, module/setProperties.c: Clean up the code and declared function prototypes to avoid compiler warnings 2007-08-23 20:20 tan2 * lib/Advection_diffusion.c: Compute total visc and adi heating 2007-08-23 20:19 tan2 * lib/Advection_diffusion.c, lib/Parsing.c: Minor refactoring 2007-08-23 20:18 tan2 * lib/Pan_problem_misc_functions.c, lib/Phase_change.c: Compute phase change wrt reference density and gravity profiles. 2007-08-23 20:18 tan2 * lib/Composition_related.c, lib/Tracer_setup.c, module/setProperties.c: Avoid reading unused input parameters 2007-08-23 20:17 tan2 * CitcomS/Controller.py, CitcomS/Coupler/Coupler.py, CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/Coupler/MultiC_Coupler.py, CitcomS/Solver/CoupledSolver.py: assert solver.tsolver.monitor_max_T is off in coupled run and remove debugging output 2007-08-23 20:16 tan2 * lib/Advection_diffusion.c, lib/Instructions.c, lib/Output_h5.c, lib/advection.h, lib/global_defs.h, module/setProperties.c: Renamed E->control.filter_temperature to E->advection.filter_temperature 2007-08-23 20:16 tan2 * CitcomS/Components/Advection_diffusion/Advection_diffusion.py, lib/Advection_diffusion.c, lib/advection.h, module/setProperties.c: Added new input parameter solver.tsolver.monitor_max_T When it is on (default), if the max temperature changes too much between timestep, the temperature field is restored at the tsolver is called using half of the timestep size. 2007-08-23 20:15 tan2 * lib/Advection_diffusion.c, lib/advection.h: Removed unused var. in struct advection 2007-08-23 20:14 tan2 * lib/Size_does_matter.c: A new way to compute TMass 2007-08-23 20:14 tan2 * lib/Advection_diffusion.c, lib/Material_properties.c, lib/Pan_problem_misc_functions.c, lib/Process_buoyancy.c, lib/Size_does_matter.c, lib/global_defs.h, module/mesher.c: Minor refactoring: add comments, rename variables 2007-08-22 01:00 becker * lib/Advection_diffusion.c, lib/Determine_net_rotation.c, lib/Instructions.c, lib/Makefile.am, lib/Output.c, lib/Output_gzdir.c, lib/Pan_problem_misc_functions.c, lib/Tracer_setup.c, lib/global_defs.h: Added an option to remove net rotations of the whole model before ascii-gz output. This might be something of interest for other output options as well, but is still experimental. Obvisouly, NR motions could be removed in a post-processing step, but it is useful to monitor how those develop during a model run. (Particularly pronounced for strong lateral viscosity variations based on composition.) 2007-08-21 22:42 tan2 * lib/Stokes_flow_Incomp.c: Removed the 2nd exit condition for bicg solver because the convergence criterion is hard to determine. 2007-08-21 22:41 tan2 * lib/Topo_gravity.c: Fixed the scaling constants in geoid calculation with reference state 2007-08-21 22:41 tan2 * lib/Pan_problem_misc_functions.c, lib/Phase_change.c: Disable phase change in compressible flow 2007-08-21 20:28 tan2 * AUTHORS: Added Wei Leng to author list 2007-08-21 20:27 tan2 * CitcomS/Components/Stokes_solver/Incompressible.py, lib/Instructions.c, lib/Stokes_flow_Incomp.c, lib/global_defs.h, module/setProperties.c: A new input parameter to specify which compressible solver If solver.vsolver.uzawa == "cg", Wei Leng's implementation is used. If solver.vsolver.uzawa == "bicg", Eh Tan's implementation is used. 2007-08-21 20:26 tan2 * lib/Stokes_flow_Incomp.c: Refactored non-newtonian stokes solver and iter-CG compressible stokes solver 2007-08-20 19:44 becker * lib/Viscosity_structures.c: Forgot this file. 2007-08-20 18:11 tan2 * lib/Instructions.c: Added #ifdef block around vtk_io in output_finalize() 2007-08-20 00:11 becker * lib/Advection_diffusion.c, lib/Tracer_setup.c: Made CDEPV and Q0.enriched work only with ncomp=1 for now. 2007-08-19 23:54 becker * lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c, lib/Output_h5.c, lib/Parsing.c: - merged changes with Eh's additions - added coor=2 option (for full citcom) to assign finer radial node spacing to top and lower layers of shell. The coor_refine=0.1,0.15,0.1,0.2 parameter specifies the radius fraction of the bottom layer [0], the fraction of the nodes in this layer [1], the top layer fraction [2], and the top layer node fraction [3]. I.e. the defaults will put 15% of all nz nodes into the 10% lower layer, 20% in the top 10% upper layer, and the rest in between. - renamed gzipped output option ascii-gz - built in restart facilities for temperature and tracers when using gzdir I/O - added a composition viscosity function, CDEPV, based on two tracer flavors - for this to work, I had to move viscosity_input() *behind* tic_input() and tracer_input() in instructions - added tracer_enriched option. If tracer = on and tracer_enriched = on, will reader Q0_enriched and vary the element heat production between Q0 for C = 0 and Q0_enriched for C = 1. I.e. this only works if C varies between 0 and 1. - added an experimental option to write to a single VTK file (note caveats!) if ascii-gz is activated gzdir_vtkio = 2, will try to write VTK straight (experimental) the VTK output is of the "legacy", serial type, and requires that all processors see the same filesystem. This will likely lead to a bottleneck for larg CPU computations as each processor has to wait til the previous is done. 2007-08-17 21:41 tan2 * tests/checkpoint/run.sh: Added excutable permission to testing shell script 2007-08-17 21:39 tan2 * tests/checkpoint/restart.cfg: Added comments to restart example 2007-08-17 18:35 tan2 * lib/Advection_diffusion.c, lib/Output.c, lib/Output_gzdir.c, lib/Viscosity_structures.c: Converting TWB's ascii-gz and vtkio output and CDEPV and tracer_enriched for multi-component chemical convection. 2007-08-17 18:33 tan2 * CitcomS/Components/Tracer.py, lib/Checkpoints.c, lib/Composition_related.c, lib/Full_tracer_advection.c, lib/Output.c, lib/Pan_problem_misc_functions.c, lib/Regional_tracer_advection.c, lib/Tracer_setup.c, lib/global_defs.h, lib/tracer_defs.h, module/setProperties.c, tests/checkpoint/tracer.cfg, visual/autocombine.py, visual/batchcombine.py, visual/dxgeneral.py: Multi-component chemical convection. By setting tracer_flavors > 2, one can enable multi-component chemical convection. See tests/checkpoint/tracer.cfg for example input. 2007-08-16 21:36 tan2 * CitcomS/Components/IC.py, CitcomS/Components/Tracer.py, CitcomS/Controller.py, CitcomS/Solver/CoupledSolver.py, CitcomS/Solver/Solver.py, bin/Citcom.c, examples/Cookbook5/cookbook5.cfg, lib/Checkpoints.c, lib/Composition_related.c, lib/Full_tracer_advection.c, lib/Initial_temperature.c, lib/Instructions.c, lib/Lith_age.c, lib/Makefile.am, lib/Output.c, lib/Problem_related.c, lib/Regional_tracer_advection.c, lib/Tracer_setup.c, lib/Viscosity_structures.c, lib/checkpoints.h, lib/global_defs.h, lib/initial_temperature.h, lib/lith_age.h, module/bindings.c, module/initial_conditions.c, module/initial_conditions.h, module/outputs.c, module/outputs.h, module/setProperties.c, tests/checkpoint, tests/checkpoint/restart.cfg, tests/checkpoint/run.sh, tests/checkpoint/tracer.cfg: Merging the checkpoint branch to trunk. The checkpoint file is called [datafile].chkpt.[rank].[step] and is outputed with an interval of controller.checkpointFrequency. To read back the checkpoint file, set solver.ic.restart=on. The old checkpoint file, [datafile_old].chkpt.[rank].[solution_cycles_init] will be read in. The old way of restarting (read in temperature from the velo files) will still be available through solver.ic.tic_method=-1. Setting solver.tracer.ic_method=2 will read the old *.tracer.* files as before, but the composition field will be calculated according to the tracers, not read from the *.comp_el.* files. The parameter solver.tracer.reset_initial_composition becomes obsolete. 2007-08-16 20:10 tan2 * lib/Element_calculations.c, lib/Viscosity_structures.c: When the element is close to the poles, use a more precise method to compute the strain rate. 2007-08-16 19:38 tan2 * lib/Material_properties.c, lib/material_properties.h: Forgot to add two files to the repository 2007-08-16 19:28 tan2 * CitcomS/Components/Stokes_solver/Incompressible.py, lib/Construct_arrays.c, lib/Element_calculations.c, lib/Instructions.c, lib/Output_h5.c, lib/Pan_problem_misc_functions.c, lib/Stokes_flow_Incomp.c, lib/Topo_gravity.c, lib/Viscosity_structures.c, lib/global_defs.h, module/setProperties.c, visual/pasteCitcomData.py: Merging compressible branch to trunk. The TALA solver is working. Two new input parameters: dissipation_number and gruneisen. 2007-08-16 01:42 tan2 * examples/Cookbook5/cookbook5.cfg, examples/Cookbook5/restart_files/cookbook5.velo.0.0, examples/Cookbook5/restart_files/cookbook5.velo.1.0, examples/Cookbook5/restart_files/cookbook5.velo.10.0, examples/Cookbook5/restart_files/cookbook5.velo.11.0, examples/Cookbook5/restart_files/cookbook5.velo.12.0, examples/Cookbook5/restart_files/cookbook5.velo.13.0, examples/Cookbook5/restart_files/cookbook5.velo.14.0, examples/Cookbook5/restart_files/cookbook5.velo.15.0, examples/Cookbook5/restart_files/cookbook5.velo.16.0, examples/Cookbook5/restart_files/cookbook5.velo.17.0, examples/Cookbook5/restart_files/cookbook5.velo.18.0, examples/Cookbook5/restart_files/cookbook5.velo.19.0, examples/Cookbook5/restart_files/cookbook5.velo.2.0, examples/Cookbook5/restart_files/cookbook5.velo.20.0, examples/Cookbook5/restart_files/cookbook5.velo.21.0, examples/Cookbook5/restart_files/cookbook5.velo.22.0, examples/Cookbook5/restart_files/cookbook5.velo.23.0, examples/Cookbook5/restart_files/cookbook5.velo.24.0, examples/Cookbook5/restart_files/cookbook5.velo.25.0, examples/Cookbook5/restart_files/cookbook5.velo.26.0, examples/Cookbook5/restart_files/cookbook5.velo.27.0, examples/Cookbook5/restart_files/cookbook5.velo.28.0, examples/Cookbook5/restart_files/cookbook5.velo.29.0, examples/Cookbook5/restart_files/cookbook5.velo.3.0, examples/Cookbook5/restart_files/cookbook5.velo.30.0, examples/Cookbook5/restart_files/cookbook5.velo.31.0, examples/Cookbook5/restart_files/cookbook5.velo.32.0, examples/Cookbook5/restart_files/cookbook5.velo.33.0, examples/Cookbook5/restart_files/cookbook5.velo.34.0, examples/Cookbook5/restart_files/cookbook5.velo.35.0, examples/Cookbook5/restart_files/cookbook5.velo.36.0, examples/Cookbook5/restart_files/cookbook5.velo.37.0, examples/Cookbook5/restart_files/cookbook5.velo.38.0, examples/Cookbook5/restart_files/cookbook5.velo.39.0, examples/Cookbook5/restart_files/cookbook5.velo.4.0, examples/Cookbook5/restart_files/cookbook5.velo.40.0, examples/Cookbook5/restart_files/cookbook5.velo.41.0, examples/Cookbook5/restart_files/cookbook5.velo.42.0, examples/Cookbook5/restart_files/cookbook5.velo.43.0, examples/Cookbook5/restart_files/cookbook5.velo.44.0, examples/Cookbook5/restart_files/cookbook5.velo.45.0, examples/Cookbook5/restart_files/cookbook5.velo.46.0, examples/Cookbook5/restart_files/cookbook5.velo.47.0, examples/Cookbook5/restart_files/cookbook5.velo.48.0, examples/Cookbook5/restart_files/cookbook5.velo.49.0, examples/Cookbook5/restart_files/cookbook5.velo.5.0, examples/Cookbook5/restart_files/cookbook5.velo.50.0, examples/Cookbook5/restart_files/cookbook5.velo.51.0, examples/Cookbook5/restart_files/cookbook5.velo.52.0, examples/Cookbook5/restart_files/cookbook5.velo.53.0, examples/Cookbook5/restart_files/cookbook5.velo.54.0, examples/Cookbook5/restart_files/cookbook5.velo.55.0, examples/Cookbook5/restart_files/cookbook5.velo.56.0, examples/Cookbook5/restart_files/cookbook5.velo.57.0, examples/Cookbook5/restart_files/cookbook5.velo.58.0, examples/Cookbook5/restart_files/cookbook5.velo.59.0, examples/Cookbook5/restart_files/cookbook5.velo.6.0, examples/Cookbook5/restart_files/cookbook5.velo.60.0, examples/Cookbook5/restart_files/cookbook5.velo.61.0, examples/Cookbook5/restart_files/cookbook5.velo.62.0, examples/Cookbook5/restart_files/cookbook5.velo.63.0, examples/Cookbook5/restart_files/cookbook5.velo.7.0, examples/Cookbook5/restart_files/cookbook5.velo.8.0, examples/Cookbook5/restart_files/cookbook5.velo.9.0, examples/Makefile.am: Updated Cookbook5 so that it uses only 2 processors. 2007-08-16 00:27 tan2 * CitcomS/Solver/Solver.py, lib/Advection_diffusion.c, lib/Construct_arrays.c, lib/Convection.c, lib/Drive_solvers.c, lib/Element_calculations.c, lib/Full_version_dependent.c, lib/Instructions.c, lib/Makefile.am, lib/Obsolete.c, lib/Output.c, lib/Output_h5.c, lib/Pan_problem_misc_functions.c, lib/Process_buoyancy.c, lib/Regional_obsolete.c, lib/Regional_version_dependent.c, lib/Size_does_matter.c, lib/Stokes_flow_Incomp.c, lib/Topo_gravity.c, lib/Viscosity_structures.c, lib/global_defs.h, module/mesher.c, module/setProperties.c: Merging compressible branch (up to r6584) to trunk. 2007-08-14 03:33 becker * lib/Advection_diffusion.c, lib/Full_version_dependent.c, lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c, lib/Pan_problem_misc_functions.c, lib/Problem_related.c, lib/Process_buoyancy.c, lib/Regional_sphere_related.c, lib/Regional_version_dependent.c, lib/Tracer_setup.c, lib/global_defs.h: - added coor=2 option (for full citcom) to assign finer radial node spacing to top and lower layers of shell. The coor_refine=0.1,0.15,0.1,0.2 parameters specify the radius fraction of the bottom layer [0], the fraction of the nodes in this layer [1], the top layer fraction [2], and the top layer node fraction [3]. I.e. the defaults will put 15% of all nz nodes into the 10% lower layer, 20% in the top 10% upper layer, and the rest in between. - renamed gzipped output version with sub-directory storage ascii-gz - built in restart facilities for temperature and tracers when using ascii-gz I/O with vtkio != 2 - added a composition viscosity function, CDEPV, based on two tracer flavors - for this to work, I had to move viscosity_input() *behind* tic_input() and tracer_input() in instructions - added tracer_enriched option for internal heating. If tracer = on and tracer_enriched = on, will reader Q0_enriched and vary the element heat production between Q0 for C = 0 and Q0_enriched for C = 1. I.e. this only works if C varies between 0 and 1. - added an option to write from all processros to a single VTK file, if ascii-gz is activated, and vtkio = 2. The VTK output is of the "legacy", serial, single-file type, and requires that all processors see the same filesystem. This will lead to a bottleneck for large # of CPU computations as each processor has to wait til the previous is done. More efficient I/O should be possible by using the distributed storage version of VTK, but I have no clue how this works. Anyone? 2007-08-13 22:55 tan2 * lib/Global_operations.c, lib/Nodal_mesh.c, lib/Obsolete.c, lib/Pan_problem_misc_functions.c, lib/Stokes_flow_Incomp.c: Minor refactoring, clean-up and moving functions between files 2007-08-13 21:43 tan2 * lib/Obsolete.c, lib/Phase_change.c: Moved obsolete functions phae_change_* from Phase_change.c to Obsolete.c and declared private functions to be static 2007-08-10 23:56 tan2 * AUTHORS: Update the author list 2007-08-10 23:56 sue * doc/manual/citcoms.lyx: additions per becker, tan2 2007-08-10 23:44 tan2 * lib/Drive_solvers.c, lib/Global_operations.c: Fixed two type-mismatch errors. Issue127 is fixed by this change and r7802. 2007-08-10 23:43 tan2 * lib/Stokes_flow_Incomp.c: Prevent the original force vector being modified by Uzawa solver. This is needed for the non-Newtonian iterations. 2007-08-10 20:51 becker * lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c, lib/Problem_related.c, lib/Tracer_setup.c: - renamed gzipped output option ascii-gz - built in restart facilities for temperature and tracers when using gzdir I/O - added a composition viscosity function, CDEPV, based on two tracer flavors - for this to work, I had to move viscosity_input() *behind* tic_input() and tracer_input() in instructions 2007-08-09 01:27 becker * lib/Initial_temperature.c, lib/Instructions.c, lib/Output_gzdir.c, lib/Problem_related.c, lib/Tracer_setup.c, lib/Viscosity_structures.c, lib/viscosity_descriptions.h: - added a compositional viscosity function, CDEPV, based on two tracer flavors - for this to work, I had to move viscosity_input() *behind* tic_input() and tracer_input() in Instructions.c - built in restart facilities for temperature and tracers when using gzdir I/O 2007-08-08 22:55 becker * doc/manual/citcoms.lyx, lib/Composition_related.c, lib/Construct_arrays.c, lib/Full_tracer_advection.c, lib/General_matrix_functions.c, lib/Ggrd_handling.c, lib/Instructions.c, lib/Makefile.am, lib/Output.c, lib/Output_gzdir.c, lib/Pan_problem_misc_functions.c, lib/Tracer_setup.c, lib/Viscosity_structures.c, lib/global_defs.h, lib/tracer_defs.h: - added new routine Ggrd_handling which will take care of netcdf grd input. For now, only the tracer innitial conditions can be set by using, for example, ictracer_grd_layers=2 ictracer_grd_file="tmask.grd" for this to work, the ggrd libraries from HC, as well as the -lgmt and -lnetcdf need to be linked, and -DUSE_GGRD needs to be defined on compile time. - rewrote TDEPV viscosity options 3 and 4 slightly to make them more efficient - added TDEPV viscosity option 6 eta = N_0 exp(E(T_0-T) + (1-z) Z_0 ) - took layers subroutine in Construct_arrays.c apart to allow calling the same function in a more flexible from other subroutines - addded error handling routine "myerror" to Pan_problem_misc_functions - made the output behavior of the multigrid solver convergence parameters consisent with verbosity setting (ie. use report instead of always stderr output) - changed tracer input parameter "tracer" and "chemical_buoyancy" to boolean routine for added flexibility (I hope) - made check_initial_composition consistent with tracer advection, exits after warning only for E->trace.itracer_warnings==1 - debugging output in Full_tracer_advection.c and Tracer_setup only gets printed to file for E->control.verbose == 1 - fixed some typos in Output_gzdir (that might have been introduced by asynchronous svn updating or something like that) 2007-08-08 16:41 becker * lib/Output_gzdir.c: Forgot to actually add the new file that is needed for gzipped and "vtk" I/O. 2007-08-08 05:58 becker * lib/Advection_diffusion.c, lib/Drive_solvers.c, lib/Instructions.c, lib/Makefile.am, lib/Output.c, lib/Pan_problem_misc_functions.c, lib/Stokes_flow_Incomp.c, lib/Viscosity_structures.c, lib/global_defs.h, lib/output.h, lib/viscosity_descriptions.h: - added functions rtp2xyz, calc_cbase_at_tp, and convert_pvec_to_cvec for spherical to Cartesian vector conversion to Pan_problem_functions.c Added "safe_malloc" to the same file because I didn't like the way Malloc1 uses int as arguments (64 bit issues). - added support for gzipped ascii output into subdirectories of data_dir, option gzdir. To use, need to compile with USE_GZDIR and link with the -lz zlib libraries. Within gzdir output mode, selected by output_format=gzdir user can define vtk I/O (gzdir_vtkio=1) to write Cartesian coordinates and velocities that are easy to combine to a single vtk file in a post-processing step. If gzlib_vtkio=0 the gzdir output option is meant to be identical to the original ascii output, but files are all gzipped on the fly, and the output that changes with each cycle is placed into subdirectories of data_dir/ called data_dir/cycles/ For gzdir I/O, data_name is not used at all, all single output files are placed in the data_dir/ directory without prefix. - added a new rheology option, PDEPV, for pseudo-plasticity and added a corresponding description to the manual. - Modified Drive_solver stderr output to show v.v, and not only dv.dv/v.v 2007-08-02 22:44 luis * .gitignore: Ignore most files generated by build system 2007-07-27 23:33 hlin * module/Exchanger/Boundary.cc: M Boundary.cc fixed a bug on topbc 2007-07-26 00:20 tan2 * examples/Cookbook5/cookbook5.cfg: Fixed a typo, which was introduced in svn r5399 2007-07-26 00:13 tan2 * visual/batchcombine.py, visual/combine.py: Fixed a bug that *opt*.general files are mistakenly named. This bug is introduced by svn r7236 2007-07-25 23:19 tan2 * visual/dxgeneral.py: Fixed a bug in ordering of mesh nodes. The bug was introduced in svn r6510. 2007-07-23 19:50 hlin * tests/coupled.cfg, tests/multicoupled.cfg: M tests/multicoupled.cfg M tests/coupled.cfg The code has passed a test on a regional containing solver. Timestep will sync and initial condition will match. Going to use a full containing solver with embedded solvers at Hawaii and Reunion in next revision. 2007-07-20 21:52 hlin * tests/coupled.cfg: M coupled.cfg alligned nodes in the solvers for comparing velocity directly. 2007-07-19 18:51 tan2 * module/advdiffu.c: Fixed a bug in setting stable timestep 2007-07-19 18:51 tan2 * CitcomS/CoupledApp.py, CitcomS/MultiCoupledApp.py, tests/coupled.cfg, tests/multicoupled.cfg: Changed the name attribute of all application classes to 'CitcomS'. This allows the users to specify the same launcher parameters for all application in their ~/.pyre/CitcomS/CitcomS.cfg. 2007-07-19 18:37 hlin * CitcomS/Controller.py, CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/Coupler/MultiC_Coupler.py, CitcomS/Coupler/MultiE_Coupler.py, CitcomS/Coupler/__init__.py, CitcomS/MultiCoupledApp.py, CitcomS/Solver/CoupledSolver.py: M trunk/CitcomS/Coupler/MultiE_Coupler.py M trunk/CitcomS/Coupler/__init__.py M trunk/CitcomS/Coupler/EmbeddedCoupler.py M trunk/CitcomS/Coupler/MultiC_Coupler.py M trunk/CitcomS/Solver/CoupledSolver.py M trunk/CitcomS/Controller.py M trunk/CitcomS/MultiCoupledApp.py solved the synchronization issue. There are some bugs in the log of time. 2007-07-18 23:06 hlin * CitcomS/Coupler/MultiC_Coupler.py, CitcomS/Coupler/MultiE_Coupler.py: A Coupler/MultiE_Coupler.py M Coupler/MultiC_Coupler.py Fixed the synchronization part. Need to test on it. Now Embedded Couplers will wait until containing coupler make a decision. 2007-07-18 21:01 tan2 * bin/Makefile.am, bin/citcoms.in, bin/coupledcitcoms.in: Unify bin/citcoms with bin/coupledcitcoms scripts. Users can run 'bin/citcoms --coupled' to launch a coupled run and 'bin/citcoms --multicoupled' to launch a multicoupled run. 2007-07-17 22:49 tan2 * tests/multicoupled.cfg: An input file for multicoupled run 2007-07-17 22:48 tan2 * CitcomS/Coupler/MultiC_Coupler.py, CitcomS/Coupler/__init__.py, CitcomS/MultiCoupledApp.py: Fixed a few typos and attached MultiC_Coupler as the default factory for the ccoupler facility 2007-07-17 22:48 tan2 * CitcomS/Solver/MultiC_FullSolver.py, CitcomS/Solver/MultiC_RegionalSolver.py, CitcomS/Solver/MultiC_Solver.py, CitcomS/Solver/__init__.py: Simplified the MultiC_*Solver classes 2007-07-16 23:45 hlin * CitcomS/Solver/MultiC_FullSolver.py, CitcomS/Solver/MultiC_RegionalSolver.py, CitcomS/Solver/MultiC_Solver.py: A Solver/MultiC_RegionalSolver.py A Solver/MultiC_FullSolver.py A Solver/MultiC_Solver.py ideally these files works as the solvers I needed for the project. 2007-07-16 21:21 hlin * CitcomS/Coupler/MultiC_Coupler.py, CitcomS/MultiLayout.py: M CitcomS/MultiLayout.py trivial comment change M CitcomS/Coupler/MultiC_Coupler.py a nearly complete version. Although I am not sure how most of the things works , I managed to create a copy of everything.initTemperature, restartTemperature , and modifyT not defined. 2007-07-13 23:24 hlin * CitcomS/Coupler/ContainingCoupler.py: M Coupler/ContainingCoupler.py trivial modification on comments 2007-07-13 23:23 hlin * CitcomS/Coupler/MultiC_Coupler.py: M Coupler/MultiC_Coupler.py add __init__, initialize, createMesh some of createMesh are commented out because I do not understand it. 2007-07-13 21:09 hlin * CitcomS/Coupler/MultiC_Coupler.py: A Coupler/MultiC_Coupler.py It's a child of Containing Coupler It has nothing now. 2007-07-11 20:17 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/CitcomInterpolator.cc, module/Exchanger/CitcomSource.cc, module/Exchanger/SVTInlet.cc, module/Exchanger/SVTOutlet.cc: Added some comments 2007-07-10 20:08 tan2 * CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py, CitcomS/Coupler/EmbeddedCoupler.py: Renamed variables for clarification 2007-07-09 22:03 tan2 * CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py, CitcomS/Coupler/EmbeddedCoupler.py: Small changes in *Coupler class. * consolidated __init__() and initialize() * renamed numSrc -> remoteSize, boundary -> remoteBdryList, interior -> remoteIntrList * defaulted the dimensional and transformational properties to False 2007-07-06 20:48 tan2 * CitcomS/MultiCoupledApp.py, CitcomS/MultiLayout.py: Added svn:keywords Id 2007-07-06 20:46 tan2 * CitcomS/MultiCoupledApp.py, CitcomS/MultiLayout.py: Debugged MultiLayout.initialize() and MultiCoupledApp.findLayout(). Fixed some typos. 2007-07-06 18:00 tan2 * CitcomS/CoupledApp.py: Using log() instead of line() to flush the journal buffer, otherwise no output at all. 2007-07-06 17:50 hlin * CitcomS/MultiCoupledApp.py, CitcomS/MultiLayout.py: fix myPlus and remotePlus and report in MultiCoupledApp edit some comments in MultiLayout 2007-07-05 23:45 hlin * CitcomS/MultiCoupledApp.py, CitcomS/MultiLayout.py: add MultiLayout not sure about number of processor, currently assign 1-10 for ccom 11 for ecom1, and 12 for ecom2 2007-07-05 22:36 hlin * CitcomS/MultiCoupledApp.py: 2007-07-05 20:49 hlin * CitcomS/MultiCoupledApp.py: 2007-07-04 00:02 hlin * CitcomS/MultiCoupledApp.py: a draft for multicoupled application 2007-07-02 22:21 tan2 * doc/manual/citcoms.lyx: Removing outdated and redundant documentation 2007-07-02 22:21 tan2 * CitcomS/SimpleApp.py: Using log() instead of line() to flush the journal buffer, otherwise no output at all. 2007-06-28 19:35 tan2 * CitcomS/Layout.py, tests/coupled.cfg: Renamed ccomm -> containing_group and ecomm -> embedded_group. Added more checks to the groups 2007-06-27 01:04 tan2 * CitcomS/BaseApplication.py, CitcomS/Controller.py, CitcomS/CoupledApp.py, CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py, CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/Layout.py, CitcomS/SimpleApp.py, CitcomS/Solver/CoupledSolver.py: Added/updated a bunch of comments, renamed variables 2007-06-26 00:37 tan2 * doc/manual/graphics/citcoms_cover-layers.pdf, doc/manual/graphics/citcoms_cover.pdf: Added mime-type property to the PDF files 2007-06-23 00:33 tan2 * CitcomS/CoupledApp.py, CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py, CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/SimpleApp.py, CitcomS/Solver/CoupledSolver.py, module/Exchanger/BoundaryVTInlet.cc, module/Exchanger/CitcomSource.cc, module/Exchanger/SVTOutlet.cc, module/Exchanger/exchangers.cc, module/Exchanger/misc.cc, tests/array2d.cc, tests/coupled.cfg: Giving Exchanger/Coupler/CoupledApp as new life. The testing script tests/coupled.cfg finished successfully. 2007-06-23 00:30 tan2 * lib/Citcom_init.c: Useful debuggin output, but disabled 2007-06-23 00:29 tan2 * configure.ac: Print CXX and CXXFLAGS after finishing configure 2007-06-23 00:28 tan2 * lib/Viscosity_structures.c: Removed the back-and-forth interpolation of viscosity, which smoothes the viscosity field unnecessarily 2007-06-22 23:43 tan2 * module/setProperties.c: Forgot to commit module/setProperties.c in r7289. This should fix issue115 in the pyre version also. 2007-06-22 04:36 leif * .: Added BuildBot config. 2007-06-21 22:35 hlin * tests/test1.sh: Resolved the conflict 2007-06-21 22:25 tan2 * tests/test1.sh: Preparing a conflict test, again 2007-06-21 22:22 tan2 * tests/test1.sh: Preparing a conflict test, again 2007-06-21 22:19 tan2 * tests/test1.sh: Preparing a conflict test 2007-06-18 23:21 tan2 * CitcomS/CoupledApp.py, CitcomS/Coupler/Coupler.py, CitcomS/Layout.py, etc/full.odb, etc/regional.odb: Renamed 'XXX1' -> 'cXXX' and 'XXX2' -> 'eXXX' 2007-06-18 23:06 tan2 * lib/Instructions.c, lib/Tracer_setup.c: Fixing issue115: interference between restart=1 & tracer_ic_method Previously, when "restart" is set, tracer_ic_method will be set to 2 (restart tracers) by the code. Now, these two options are independent. 2007-06-15 18:01 leif * bin/dummy.cc: Fix for problem with GCC 3.4.5 (observed on CITerra): mv: cannot stat `.deps/dummy.Tpo': No such file or directory 2007-06-14 21:38 tan2 * lib/Topo_gravity.c: Zeroing geoid arrays before every geoid calculation. This fixes issue114 2007-06-14 17:55 tan2 * visual/autocombine.py, visual/batchcombine.py, visual/pasteCitcomData.py: A better fix for issue110 2007-06-14 01:36 tan2 * visual/pasteCitcomData.py: Fixing issue111: Expanding %RANK in autocombine.py 2007-06-13 17:55 hlin * tests/test1.sh: A trivial change 2007-06-12 00:05 tan2 * module/setProperties.c: Fixing issue112 2007-05-11 20:19 leif * bin/Makefile.am: Fixed LINK problem w/Automake. 2007-05-11 02:02 leif * CitcomS/CoupledApp.py, bin/Makefile.am, bin/coupledcitcoms.in, bin/dummy.cc, bin/pycitcoms.c, configure.ac, module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/Boundary.cc, module/Exchanger/BoundaryVTInlet.cc, module/Exchanger/CitcomInterpolator.cc, module/Exchanger/CitcomSource.cc, module/Exchanger/Convertor.cc, module/Exchanger/Exchangermodule.cc, module/Exchanger/Exchangermodule.h, module/Exchanger/Interior.cc, module/Exchanger/Makefile.am, module/Exchanger/SIUnit.cc, module/Exchanger/SInlet.cc, module/Exchanger/SVTInlet.cc, module/Exchanger/SVTOutlet.cc, module/Exchanger/TInlet.cc, module/Exchanger/TOutlet.cc, module/Exchanger/VOutlet.cc, module/Exchanger/VTInlet.cc, module/Exchanger/VTOutlet.cc, module/Exchanger/bindings.cc, module/Exchanger/exceptions.cc, module/Exchanger/exchangers.cc, module/Exchanger/global_bbox.cc, module/Exchanger/initTemperature.cc, module/Exchanger/inlets_outlets.cc, module/Exchanger/misc.cc, module/Makefile.am, setup.py: Build with Exchanger, if available. The Exchanger package will be automatically detected if it is installed on your PYTHONPATH. The preprocessor & link flags for compiling/linking with Exchanger are handled automatically. To my chagrin, this change increases the CitcomS language count back up to 3 again (C, C++, Python). Even with the aid of the 'cproto' tool, it would take many hours of work to make the C code in 'lib' compile using a C++ compiler. 2007-04-11 00:40 tan2 * tests/Makefile.am: Forgot to update the makefile in r6541 2007-04-10 21:59 tan2 * lib/Tracer_setup.c: Finding the min/max of the Cartesian coordinates. The min/max values provide the bounding box for random tracer generation. This will speed up the tracer generation, and should avoid a potential problem of "too many tries?" error when the domain size of a processor is much smaller (<1%) than the size of the whole sphere. 2007-04-10 21:58 tan2 * tests/asap.py, tests/hrothgar.py: Removed obsolete pyre components in tests/ 2007-04-05 22:21 tan2 * visual/Makefile.am, visual/autocombine.py, visual/batchcombine.py, visual/batchpaste.sh, visual/combine.py, visual/dxgeneral.py, visual/dxgeneral.sh, visual/execpaste.py, visual/pasteCitcomData.py, visual/pasteCitcomData.sh: Adding the ability to combine optional fields to the post-processing scripts. autocombine.py will read the parameter 'output_optional' from the cfg file and combine the optional fields (can be pressure, stress, comp_nd, or a combination of the three) into a file. The file is named similar to the cap file, with 'cap' replaced by 'opt'. A .general file is also created, which describes the content, shape, and structure of the opt file. 2007-03-27 20:54 sue * doc/manual/graphics/citcoms_cover-layers.pdf: standardized typefaces on cover 2007-03-27 06:51 sue * doc/manual/citcoms.pdf, doc/manual/graphics/citcoms_cover-layers.pdf, doc/manual/graphics/citcoms_cover.pdf: changed version to 2.2.1 per tan2 2007-03-27 04:39 tan2 * ChangeLog: Regenerated ChangeLog upto r6417 2007-03-27 04:37 tan2 * NEWS, configure.ac, doc/manual/citcoms.lyx: Updated NEWS for the upcoming 2.2.1 2007-03-27 04:20 tan2 * examples/Makefile.am: Forgot to add cookbook7.cfg to the file list 2007-03-26 18:48 tan2 * ChangeLog: Regenerated ChangeLog upto r6409 2007-03-26 18:45 tan2 * lib/Makefile.am: Forgot to add a header file to the file list 2007-03-26 18:25 tan2 * ChangeLog: Regenerated ChangeLog upto r6403 2007-03-26 18:20 tan2 * visual/plot_annulus.py: Set the length unit to cm to fit within the page 2007-03-26 18:11 tan2 * visual/plot_layer.py: Changed the size of gmt plots to fit within the page 2007-03-26 18:05 sue * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: restored edits to stable copy; regen pdf, images showing 2007-03-26 06:01 tan2 * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: Enlarged the figure of cookbook7. Rephrased the description of the low-viscosity-zone parameters, per Sue's suggestion. 2007-03-26 00:23 sue * doc/manual/citcoms.pdf: chasing down image problem 2007-03-25 23:07 sue * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: changed verbage in History 1.2, paragraphs on version 2.1, to past tense, since notes on 2.2 should be only ones in present tense \c 2007-03-25 22:55 sue * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: edits of new copy; attempt to fix an image that is not displaying, still unresolved 2007-03-24 23:05 tan2 * doc/manual/citcoms.lyx: Finished Cookbook7 2007-03-24 23:03 tan2 * README, configure.ac, setup.py: Changed the version number to 2.2 2007-03-24 00:02 tan2 * examples/Cookbook7, examples/Cookbook7/cookbook7.cfg: Added new cookbook7 2007-03-23 22:21 tan2 * NEWS, doc/manual/citcoms.lyx: Updated the NEWS for v2.2.0 2007-03-23 22:21 tan2 * doc/manual/citcoms.lyx, examples/Full/input.sample, examples/Regional/input.sample: Added new parameter 'adv_gamme' to the manual and input samples. Documented a new tic_method=3 2007-03-23 21:06 tan2 * doc/manual/citcoms.lyx: Added description to the tracer and composition input/output files 2007-03-23 20:40 tan2 * doc/manual/citcoms.lyx, examples/Full/input.sample, examples/Regional/input.sample: Added the tracer parameters to the manual and sample input files 2007-03-23 20:39 tan2 * CitcomS/Components/Tracer.py, lib/Full_tracer_advection.c, module/setProperties.c: Disable the parameter "analytical_tracer_test", and make "chemical_buoyancy" a boolean 2007-03-23 19:37 tan2 * doc/manual/citcoms.lyx, examples/Full/input.sample, examples/Regional/input.sample: Added the low-visc-zone parameters to the manual and the sample input files 2007-03-23 05:31 tan2 * doc/manual/graphics/cookbook7.jpg: Added the image for cookbook7 (thermo-chemical convection 2007-03-23 05:30 tan2 * doc/manual/citcoms.lyx, doc/manual/graphics/cookbook6.eps, doc/manual/graphics/cookbook7.eps: When I renamed the old Cookbook7/ directory to Cookbook6/, I forgot to rename cookbook7.eps to cookbook6.eps. Now it is done. 2007-03-23 05:25 tan2 * doc/manual/graphics/cookbook6.2.eps, doc/manual/graphics/cookbook6.eps: These two EPS files are the leftover of an old cookbook 2007-03-23 05:22 tan2 * lib/Tracer_setup.c: Gather theta and phi only in get_neighboring_caps() 2007-03-23 05:21 tan2 * lib/Composition_related.c, lib/Output.c: Changed the header format of comp_* output to be consistent with other data files 2007-03-22 22:11 sue * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf, doc/manual/graphics/citcoms_cover-layers.pdf, doc/manual/graphics/citcoms_cover.pdf: added bib entry per eh, changed cover to citcoms (rem .py), changed to 2.2.0, todo notation removed; regen pdf 2007-03-22 19:58 tan2 * lib/Stokes_flow_Incomp.c: Make the output of 1st iteration consistent with later iterations 2007-03-22 19:57 tan2 * lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c, lib/Tracer_setup.c: Calling find_tracers() and count_tracers_of_flavors() in initialize_tracers(), so that the former two functions can become static/private 2007-03-22 19:55 tan2 * lib/Tracer_setup.c: Renamed initialize_tracer_arrays() to allocate_tracer_arrays() 2007-03-21 22:46 tan2 * doc/manual/citcoms.lyx: Updated the version number to 2.2.0 2007-03-21 22:46 tan2 * doc/manual/citcoms.lyx: Updated the dependency information 2007-03-21 22:46 tan2 * doc/manual/citcoms.lyx: Added chemical Rayleigh number to the equations 2007-03-21 22:45 tan2 * doc/manual/citcoms.lyx: Added history of v2.2 release 2007-03-21 22:45 tan2 * doc/manual/citcoms.lyx: Added citation to McNamara & Zhong 2004 2007-03-21 19:30 tan2 * lib/Full_tracer_advection.c: Added a safeguard against nprocx or nprocy greater than 1 2007-03-20 06:34 tan2 * lib/Full_tracer_advection.c: full_lost_souls() now works for nprocz>1 as well 2007-03-20 06:27 tan2 * CitcomS/Components/Tracer.py, lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c, lib/Tracer_setup.c, lib/tracer_defs.h, module/setProperties.c: Removed the 'tracer_interpolation_scheme' and 'tracer_advection_scheme' parameters 2007-03-20 06:26 tan2 * lib/Viscosity_structures.c: Reporting error if low viscosity channel/wedge is turned on, but tracer is turned off 2007-03-19 23:49 tan2 * lib/Full_tracer_advection.c, lib/Global_operations.c, lib/Regional_parallel_related.c, lib/Regional_tracer_advection.c, lib/Tracer_setup.c, lib/tracer_defs.h: lost_souls() cannot be shared by both versions. The parallel communications of both versions are too different. So, the original lost_souls() is renamed to full_lost_souls(). A new regional_lost_souls() is implemented. This code has been tested in 3x3x3 processors, running over 100 timesteps. The number of total tracers is conserved. 2007-03-19 23:44 tan2 * module/setProperties.c: Init'd E->composition.icompositional_rheology to 0 2007-03-19 23:42 tan2 * lib/Composition_related.c, lib/composition_related.h: * Init'd E->composition.icompositional_rheology to 0 * Write composition instruction only if it is turned on * Clean up the code a bit 2007-03-19 23:29 tan2 * lib/Composition_related.c: Removing read_comp(), which is not used anymore 2007-03-19 23:25 tan2 * CitcomS/Solver/Solver.py: Advect the tracers right after temperature advection, before solving velocity 2007-03-19 23:08 tan2 * lib/Regional_parallel_related.c: Replaced for-loop by an if, which matchs the intention better 2007-03-19 22:53 tan2 * lib/Advection_diffusion.c, lib/Convection.c: Init'd advection.timestep and advection.timesteps earlier. The time output uses these parameters. 2007-03-19 22:51 tan2 * lib/Viscosity_structures.c: Reimplemented my version of low_viscosity_channel_factor() and low_viscosity_wedge_factor() 2007-03-19 22:50 tan2 * lib/Full_tracer_advection.c, lib/Tracer_setup.c: Clean up the function prototype declaration 2007-03-19 22:48 tan2 * lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c, lib/Tracer_setup.c: Moving tracer initialization code to a function 2007-03-19 22:45 tan2 * lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c, lib/Size_does_matter.c, lib/Tracer_setup.c, lib/global_defs.h: Compute the volume of the mesh, use it to estimate the # of tracers in the proc. make_tracer_array() now works for both versions 2007-03-17 00:38 tan2 * lib/Pan_problem_misc_functions.c: Apply chemical buoyancy only when using tracer 2007-03-17 00:21 tan2 * bin/Citcom.c, lib/Full_obsolete.c, lib/Full_tracer_advection.c, lib/Output.c, lib/Output_h5.c, lib/Regional_tracer_advection.c, lib/Tracer_setup.c, lib/Viscosity_structures.c, lib/global_defs.h, lib/tracer_defs.h, module/misc.c, module/setProperties.c: Merged the regional and global tracer codes. Basically, Vlad's code is mostly gone and is replaced by Allen's and mine code. A few functions, eg. analytical_test(), low_viscosity_*_factor(), are disabled, need to work on them later. 2007-03-15 02:51 leif * CitcomS/BaseApplication.py: Removed broken usage() method. (Pythia v0.8.1.3 will have a reasonable default for this method.) 2007-03-13 00:56 gurnis * lib/Full_read_input_from_files.c, lib/Regional_lith_age_read_files.c, lib/Regional_read_input_from_files.c: Refactored the regional parts of the code so that the age grids are read in from the same code as are the velocity and material files. Moved the guts of Regional_lith_age_read_files.c to Regional_read_input_from_files.c. This nearly makes the structure of Full and Regional the same -- refactoring that Leif initiated last year 2007-03-12 23:27 tan2 * CitcomS/Components/Tracer.py, lib/Composition_related.c, module/setProperties.c: Commented out code about compositional_rheology, which is not implemented 2007-03-12 23:11 tan2 * lib/Composition_related.c, lib/Full_tracer_advection.c: Removed static variables, added some code documentation 2007-03-12 22:14 tan2 * CitcomS/Components/Tracer.py, lib/Composition_related.c, lib/Full_tracer_advection.c, lib/composition_related.h, lib/global_defs.h, lib/tracer_defs.h, module/setProperties.c: A new input parameter "ic_method_for_flavors", to specify which way to initialize the flavors when the tracers are init'd randomly Currrently, only ic_method_for_flavors=0 is allowed, which produces a layered structure, any tracer above z_interface is of flavor 0, below z_interface is of flavor 1. 2007-03-12 22:07 tan2 * lib/Composition_related.c, lib/Full_tracer_advection.c, lib/composition_related.h: Initial bulk composition 2007-03-12 22:06 tan2 * lib/Full_tracer_advection.c, lib/Output.c, lib/tracer_defs.h: Output the total composition information to the log file, get rid of extra file handles in trace struct 2007-03-12 22:05 tan2 * lib/Full_tracer_advection.c, lib/Stokes_flow_Incomp.c, lib/tracer_defs.h: Compute the Cartesian velocity on the fly, not storing it in a seperated array 2007-03-12 20:08 gurnis * lib/Advection_diffusion.c, lib/Lith_age.c, lib/Regional_lith_age_read_files.c, lib/Regional_read_input_from_files.c: Modified Regional_read_input_from_files.c so that it now opens and reads in material files. Material files are organized by elements. Previsouly only worked for Full 2007-03-11 05:27 tan2 * CitcomS/Components/Tracer.py, lib/Composition_related.c, lib/Full_tracer_advection.c, lib/Output.c, lib/global_defs.h, lib/tracer_defs.h, module/setProperties.c: A new way to compute composition. Each tracer has a "flavor" (can only be either 0 or 1 currently). In the ratio method, the composition of an element is determined by: (# of tracers of flavor i)/(# of total tracers) 2007-03-11 05:20 tan2 * CitcomS/Components/Tracer.py, lib/Composition_related.c, lib/Full_obsolete.c, lib/Full_tracer_advection.c, lib/Output.c, lib/Pan_problem_misc_functions.c, lib/global_defs.h, lib/tracer_defs.h, module/setProperties.c: * Unifying output for extra tracer quantities * Renamed rtrac to basicq, etrac to extraq, to match the basic/extra quantities for advection * Renamed itrac to ielement, itracsize to ielementsize, ielementsize to max_ntracers * A new member for the # of tracers * Removed some unused members in trace struct * Untabify and indent the code 2007-03-09 00:26 tan2 * AUTHORS: Add Vlad to the author list 2007-03-09 00:25 tan2 * AUTHORS, CitcomS/Components/Output.py, CitcomS/Components/Tracer.py, lib/Composition_related.c, lib/Element_calculations.c, lib/Full_obsolete.c, lib/Full_tracer_advection.c, lib/Global_operations.c, lib/Instructions.c, lib/Makefile.am, lib/Output.c, lib/Pan_problem_misc_functions.c, lib/Stokes_flow_Incomp.c, lib/Viscosity_structures.c, lib/composition_related.h, lib/global_defs.h, lib/tracer_defs.h, module/setProperties.c: A big patch for tracers and composition: * Seperating composition codes from tracer codes, several struct members in E->trace are moved to E->composition * Add chemical buoyancy term * Renamed thermal_buoyancy() to get_buoyancy() to reflect the fact that this function computes buoyancy according to temperature/composition/phase * Fix and optimize the fix_*() functions * Remove some static variables, or converte them to const * Change the type of E->SinCos from float to double, and replace E->trace.DSinCos * Provide default values for "required" input parameters * Renamed tracer_restart to tracer_ic_method, also remapped the options * Removed option for Cartesian tracer input and trace.iwrite_tracers_every * Replaced trace.itracer_type by composition.ichemical_buoyancy * Optionally output tracers and composition fields 2007-03-08 00:35 leif * bin/Makefile.am: Minor Makefile fix I made while working on Nemesis (i.e. with embedding disabled). 2007-03-02 00:09 tan2 * lib/Full_tracer_advection.c, lib/tracer_defs.h: * Simplified checking in the radial direction * Removed obsolete variables in trace struct 2007-03-01 21:23 tan2 * lib/Full_tracer_advection.c: Finally, exchanging tracers between processors works, at least in 12-proc cases 2007-03-01 21:21 tan2 * lib/Full_tracer_advection.c, lib/Output.c, lib/tracer_defs.h: * Communicate cap boundary information with neighboring processors. This information will be used in icheck_cap() later * Update icheck_cap() for our paralleism * Disable composition-related output 2007-03-01 21:17 tan2 * lib/Full_tracer_advection.c: Fixed two errors reported by icc 2007-03-01 21:16 tan2 * CitcomS/Components/Tracer.py, lib/Full_tracer_advection.c, module/setProperties.c: * Create pyre inventory for tracer input * Changed the default values of some tracer parameters to be consistent with pyre inventory 2007-03-01 21:15 tan2 * bin/Citcom.c, lib/Full_tracer_advection.c, lib/Full_version_dependent.c, lib/Global_operations.c, lib/Instructions.c, lib/Tracer_setup.c, lib/Viscosity_structures.c, lib/global_defs.h, lib/tracer_defs.h, module/initial_conditions.c: Migrating the tracer code (not finished) 2007-03-01 21:02 tan2 * lib/Full_tracer_advection.c, lib/Global_operations.c, lib/Makefile.am, lib/global_defs.h, lib/tracer_defs.h: Copied from Allen McNamara's tracer code. The code will fail to compile 2007-02-16 17:44 leif * module/Exchanger: Resurrected Exchanger source. 2007-02-08 00:15 tan2 * lib/Advection_diffusion.c: Spherical version of the temperature solver 2007-02-08 00:14 tan2 * visual/execpaste.py: Removed the use of a new feature in python 2.4 ("substring" in "string") 2007-02-06 02:23 tan2 * CitcomS/Components/Advection_diffusion/Advection_diffusion.py, lib/Advection_diffusion.c, lib/Convection.c, module/setProperties.c: Added input parameters that controlling the predictor-corrector scheme 2007-02-06 02:22 tan2 * lib/Full_version_dependent.c: Fixed a bug when reading coor_file in full CitcomS 2007-02-06 02:22 tan2 * lib/Solver_multigrid.c: Changed smoothing method for viscosity to be consistent with CitcomCU 2007-02-02 23:30 tan2 * CitcomS/Components/IC.py, lib/Full_version_dependent.c, lib/Initial_temperature.c, lib/Regional_version_dependent.c, module/setProperties.c: A new option for initial temperature, which is used in Shijie's benchmark When tic_method==3, the initial temperature is a linear profile plus mag * modified_plgndr_a(ll, mm, theta) * (cos(mm*phi) + sin(mm*phi)) * sin(M_PI * (r - E->sphere.ri) / (E->sphere.ro - E->sphere.ri)) 2007-02-02 20:10 tan2 * CitcomS/Solver/Solver.py: Disable pid output for processors of rank>0 2007-01-31 20:46 tan2 * CitcomS/Solver/Solver.py: Removed spaces around the equal sign when writing pid file, which confused parser.py 2007-01-30 21:16 leif * configure.ac: Moved Python egg stuff into our Autoconf macro library. 2007-01-30 19:29 sue * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: added spaces after = in sec b.2; redid table in c.4.9 prev updated by eh; regen pdf 2007-01-30 19:04 tan2 * lib/Viscosity_structures.c: Compute the 2nd invariant of strain rate tensor in spherical coordinate 2007-01-29 20:51 gurnis * lib/Full_read_input_from_files.c: The functionality of this routine is now expanded so that for evey time step the element materials are read in. The code for determining the material file names and opening the file name and then reading in the element files is placed in the same code that the age grids and velocity files are processed. Obviously, reading in materials currently only works for Full; fill be working on Regional next. 2007-01-29 20:46 gurnis * lib/Advection_diffusion.c, lib/BC_util.c, lib/Instructions.c, lib/Problem_related.c: Changed the seequence placement in the time step when the age grids are assimilated into the temperature field. Previously, going back to the original code contributed by CC, the assimilation occurred avery time the temperature BCs were set (meaning multiple times in a PC loop). Now assimilation happens only once at the end of the time step. This is placed at the end of the routine PG_time_step_solve. Once we have worked with this some more, we will want to expose this code at a higher level so that assimulation will work properly from either plain C code or the Pyre version. Currently only tested with Full. 2007-01-29 20:37 gurnis * lib/Lith_age.c: A minor change so that restart now works properly when lith_age=1. Now restart from old temperature fields appear to work without any obvious corruption of the Temp field. Only tested with Full. 2007-01-29 20:32 gurnis * lib/Viscosity_structures.c: Small change for rheol=5 to use harmonic mean when element materials are read in. Also, this involved a minor conflict resolution with Eh s recent change to this file 2007-01-26 21:32 tan2 * CitcomS/Solver/Solver.py: Write controller inventory to pid file. This is a heck! 2007-01-25 23:30 tan2 * lib/Stokes_flow_Incomp.c: Compute the velocity in Cartesian coord on the fly. The previous code computed and stored the Cartesian velocity in E->temp in v_from_vector() and accessed E->temp in velo_from_element. This is bug prone. E->temp is a temporary array and should be used for storage. Also, in previous code, if E->sphere.cap[m].V is modified, one has to recompute E->temp. Otherwise, the Cartesian velocity will be incorrect. 2007-01-25 01:38 tan2 * CitcomS/Components/Advection_diffusion/Advection_diffusion.py, bin/Citcom.c, lib/Advection_diffusion.c, lib/Convection.c, lib/Solver_multigrid.c, lib/global_defs.h: Get rid of static variables 2007-01-25 00:57 tan2 * CitcomS/Solver/Solver.py, bin/Citcom.c, lib/Advection_diffusion.c, lib/Convection.c, lib/Full_geometry_cartesian.c, lib/Instructions.c, lib/Regional_geometry_cartesian.c, module/advdiffu.c, module/mesher.c, module/setProperties.c: Refactoring various functions to simplify their pyre counterpart 2007-01-17 20:02 tan2 * lib/Viscosity_structures.c: Fixed a bug in locating elements right above tracers 2007-01-17 01:54 tan2 * lib/Instructions.c, lib/Pan_problem_misc_functions.c: Replaced 'exit(0)' with correct MPI exit, related to issue69 2007-01-16 20:37 tan2 * lib/Full_read_input_from_files.c, lib/Regional_read_input_from_files.c: Fixed issue77 - velocity b.c not scaled correctly when age becomes negative 2007-01-16 19:49 tan2 * CitcomS/Components/IC.py, module/setProperties.c: Read input parameter 'half_space_age' when tic_method=1 2007-01-16 18:50 tan2 * lib/Regional_tracer_advection.c: Fixed incorrect prototype 2007-01-16 18:43 tan2 * lib/Regional_version_dependent.c: When "tic_method=1", the temperature is isothermal (== bottom b.c.) with a uniformly cold plate (thickness specified by 'half_space_age') 2007-01-16 17:41 tan2 * CitcomS/Components/Visc.py, lib/Regional_tracer_advection.c, lib/Viscosity_structures.c, lib/viscosity_descriptions.h, module/setProperties.c: Tracer-defined rheology -- low viscosity channel/wedge 2007-01-15 21:42 tan2 * lib/Makefile.am, lib/Regional_tracer_advection.c, lib/Tracer_advection.c, lib/Tracer_setup.c, lib/tracer_defs.h, module/misc.c: Added regional (passive) tracers 2007-01-09 21:11 tan2 * lib/Problem_related.c: Fix for time-invariant velocity boundary conditions, issue75 2007-01-08 23:09 tan2 * doc/manual/citcoms.lyx: Another document fix for issue75, related to "how to specify time-invariant velocity boundary conditions?" 2007-01-08 22:19 tan2 * doc/manual/citcoms.lyx: 1. Fixed a reference error, "Section 1.6" should be "Equation 1.6" 2. Velocity BC input and geoid output are dimensional. The units were undocumented in previous release. This fix the issue75. 3. More information about geoid output: the meaning of each column and how to compute the geoid field. 2007-01-08 22:19 tan2 * visual/plot_annulus.py, visual/plot_layer.py: Truncate the temperature grd file at specified min/max Sometimes the temperature field has overshoot/undershoot, which would be leave a blank area in the contour plot. This is a simple workaround. 2007-01-05 22:33 tan2 * visual/batchpaste.sh: Fix for issue73 "problems with autocombine.py in single workstation mode" $HOSTNAME is not defined in the non-interactive shell in Ubuntu 6.10. Need to put a quote around it. 2007-01-05 00:06 leif * Makefile.am: Fix for issue72: "'make install' broken for non-pyred CitcomS". 2006-12-20 22:13 sue * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: added note about updating to 2.10.3 2006-12-09 00:26 tan2 * ChangeLog: Regenerated ChangeLog upto r5565 2006-12-09 00:22 sue * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: gurnis final changes; image resize; ready for release 2006-12-08 23:50 sue * doc/manual/citcoms.lyx: small text changes; image resize 2006-12-08 23:45 tan2 * doc/manual/citcoms.lyx: Added "created by OpenDX" on several figure captions 2006-12-08 23:36 tan2 * doc/manual/citcoms.lyx, doc/manual/graphics/mayavi2.png: Updated MayaVi2 section 2006-12-08 23:30 tan2 * visual/Makefile.am, visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py, visual/mayavi2_citcoms_display.py: Renamed the MayaVi launching script and move it to visual/ 2006-12-08 23:26 tan2 * visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py: Added executable bit to file permission 2006-12-08 22:44 luis * visual/Makefile.am: Add plugins for MayaVi2 to installation 2006-12-08 22:27 luis * visual/Mayavi2/README, visual/Mayavi2/citcoms_display/README, visual/Mayavi2/citcoms_plugins/README: Added README files 2006-12-08 22:00 sue * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: fixed image size, text size and other small text changes 2006-12-08 21:16 luis * visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py: Removing reduce filter from comments, as it is currently obsolete. 2006-12-08 21:15 luis * doc/manual/citcoms.lyx: Added MayaVi screenshot to manual, along with a couple of other fixes. 2006-12-08 20:03 luis * visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py, visual/Mayavi2/citcoms_plugins/plugins/OpenCitcomSFILES.py: Last set of patches to citcoms_plugins * Display filename in mayavi pipeline * Changed glob pattern so that only HDF5 timestep files can be selected 2006-12-08 19:47 luis * visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py, visual/Mayavi2/citcoms_plugins/custom_ui.py, visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py, visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSFilterActions.py, visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSreduce.py, visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSshowCaps.py, visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomsCapFilter.py, visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomsReduceFilter.py: Forgot to rename data filters. 2006-12-08 17:53 luis * doc/manual/graphics/mayavi2.png: Added MayaVi2 screenshot for the manual. 2006-12-08 17:44 luis * visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py, visual/Mayavi2/citcoms_plugins/custom_ui.py, visual/Mayavi2/citcoms_plugins/plugins/CitcomSHDFUgrid.py, visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py, visual/Mayavi2/citcoms_plugins/plugins/OpenCitcomSFILES.py, visual/Mayavi2/citcoms_plugins/utils.py: Various patches. 2006-12-08 17:40 luis * visual/Mayavi2/citcoms_plugins, visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py, visual/Mayavi2/citcoms_plugins/__init__.py, visual/Mayavi2/citcoms_plugins/plugins, visual/Mayavi2/citcoms_plugins/plugins/CitcomSHDFUgrid.py, visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py, visual/Mayavi2/citcoms_plugins/plugins/OpenCitcomSFILES.py, visual/Mayavi2/citcoms_plugins/plugins/__init__.py, visual/Mayavi2/citcoms_plugins/plugins/filter, visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSFilterActions.py, visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSSphere.py, visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSreduce.py, visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSshowCaps.py, visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSshowSurface.py, visual/Mayavi2/citcoms_plugins/plugins/filter/__init__.py: Forking original plugins 2006-12-08 17:32 luis * visual/Mayavi2/Martin, visual/Mayavi2/original_plugins, visual/Mayavi2/original_plugins/README: Archiving original plugins. 2006-12-08 17:31 luis * visual/Mayavi2/mayavi_custom_ui.py: Modify plugins directory 2006-12-08 17:29 luis * visual/Mayavi2/Martin/README: Explain contents of each directory. 2006-12-08 02:29 leif * configure.ac: Made 'install_deps' actually do what 'configure' says it's doing (*missing* deps, not *all*). 2006-12-07 23:26 sue * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf, doc/manual/graphics/regtest.100.z005.jpg: reinstated a few lost changes; changed caption position on fig 5.3 on request; enlarged fig 5.4; regen pdf 2006-12-07 22:34 tan2 * doc/manual/citcoms.lyx: chapter 5 * Added MayaVi2 in the introduction * Added links to MayaVi2 installation 2006-12-07 22:19 sue * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: fixed image size; regen pdf 2006-12-07 22:09 sue * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: text fixes to recent additions 2006-12-07 21:30 tan2 * doc/manual/citcoms.lyx, doc/manual/graphics/hdfview.png: * Put back the HDFView sections * Added a screenshot of HDFView * Added a warning on "-O3" compiler flag 2006-12-07 05:03 sue * doc/manual/citcoms.lyx: text edits to appendices and bib 2006-12-07 00:12 sue * doc/manual/citcoms.lyx: small changes to chapt 6; standardized cross refference style; sstandardized code spacing 2006-12-06 23:31 sue * doc/manual/citcoms.lyx: enumerating several sections of the instructions in chap 5 for clarity, and a few minor text fixes 2006-12-06 20:59 sue * doc/manual/citcoms.lyx: a few text fixes in chapter 3 2006-12-06 20:33 sue * doc/manual/citcoms.lyx: a few text fixes, preface to end of chapt 2 2006-12-06 18:59 sue * doc/manual/citcoms.lyx: gurnis corrections and some other fixes 2006-12-06 08:52 luis * visual/Makefile.am: Temporarily removing Mayavi2 files from Makefile.am 2006-12-06 08:23 luis * visual/Mayavi2/Citcoms_Hdf2Vtk.c, visual/Mayavi2/Citcoms_Hdf2Vtk.py, visual/Mayavi2/Citcoms_HdfDisplay.py, visual/Mayavi2/Citcoms_VtkDisplay.py, visual/Mayavi2/Martin, visual/Mayavi2/Martin/Citcoms_Hdf2Vtk.c, visual/Mayavi2/Martin/Citcoms_Hdf2Vtk.py, visual/Mayavi2/Martin/Citcoms_HdfDisplay.py, visual/Mayavi2/Martin/Citcoms_VtkDisplay.py, visual/Mayavi2/Martin/README, visual/Mayavi2/Martin/__init__.py, visual/Mayavi2/Martin/plugins, visual/Mayavi2/README, visual/Mayavi2/__init__.py, visual/Mayavi2/plugins: Archive files created during Martin Weier's internship 2006-12-06 08:16 luis * visual/Mayavi2/citcoms_display/plugins, visual/Mayavi2/citcoms_display/plugins/HDF5FileReader.py, visual/Mayavi2/citcoms_display/plugins/HDF5UGrid.py, visual/Mayavi2/citcoms_display/plugins/ReduceFilter.py, visual/Mayavi2/citcoms_display/plugins/ShowCapsFilter.py, visual/Mayavi2/citcoms_display/plugins/ShowSurfaceFilter.py, visual/Mayavi2/citcoms_display/plugins/Sphere.py, visual/Mayavi2/citcoms_display/plugins/UGridThread.py, visual/Mayavi2/citcoms_display/plugins/VTKFileReader.py, visual/Mayavi2/citcoms_display/plugins/__init__.py: Reorganized structure of the Mayavi2 plugin modules 2006-12-06 08:13 luis * visual/Mayavi2/citcoms_display/custom_ui.py, visual/Mayavi2/citcoms_display/mayavi_custom_ui.py, visual/Mayavi2/mayavi_custom_ui.py: Simplified the file that will be be copied to user's ~/.mayavi2 directory. 2006-12-06 06:55 luis * visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Group all CitcomS options under a single menu group. 2006-12-06 05:58 luis * doc/manual/citcoms.lyx: Quick fixes to manual. 2006-12-06 01:08 leif * CitcomS/Makefile.am, module/Regionalmodule.c, visual/Makefile.am: Adding missing files to tarball ("make dist"), including the 'Mayavi2' directory, which is now installed under share/CitcomS. Also deleted 'Regionalmodule.c', which is no longer used. 2006-12-06 00:49 sue * doc/manual/citcoms.lyx: small changes in one image caption and in citation 2006-12-06 00:42 leif * Makefile.am, bin/Makefile.am, configure.ac: Fix for eggs not being installed by "make install" when builddir == srcdir. This change also re-fixes the setup.py infinite regress in a cleaner way. 2006-12-06 00:18 luis * visual/Mayavi2/citcoms_display/actions.py, visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Added actions for ReduceFilter and ShowCapsFilter 2006-12-05 23:13 leif * Makefile.am, setup.py: Require final release version of Pythia. Include egg-related files in release tarball ("make dist"). 2006-12-05 20:46 sue * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: edited text and images placement in 5.8 2006-12-05 20:34 sue * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: slghtly widened l. col in appendix a tables as using typewriter widened lines; fixed other formatting issues in appendices 2006-12-05 20:11 sue * doc/manual/citcoms.lyx: changing font style to typewriter small in appendix a tablesi and a few typos 2006-12-05 19:19 sue * doc/manual/citcoms.lyx: small fixes to chap 4, text and table placement 2006-12-05 18:04 sue * doc/manual/citcoms.lyx: making use of typewriter font and quotes consistent in appendix a 2006-12-05 07:09 tan2 * doc/manual/citcoms.lyx: Updated Chapter 4 2006-12-05 06:17 tan2 * visual/samples/cookbook1.100.h5, visual/samples/cookbook1.h5: Example h5 files including all optional output 2006-12-05 06:14 tan2 * visual/Makefile.am: Forgot to update the makefile 2006-12-05 05:04 tan2 * doc/manual/citcoms.lyx: Removed sections about HDFView. HDFView by default displays the dataset in a 2D table, which can be very confusing when working on multidimensional dataset. "h5ls -r" is a better tool for discovering the group structure and dataset dimension. 2006-12-05 04:19 tan2 * visual/estimate.py, visual/estimate_size.py: * Renamed estimate.py to estimate_size.py * Added license text * Update for new HDF5 layout 2006-12-05 00:46 luis * doc/manual/citcoms.lyx: Changed code in A.1.1 and A.1.2 to use small font with typewriter style. 2006-12-05 00:40 tan2 * NEWS: Mentioned change of naming scheme for capfiles in NEWS 2006-12-05 00:31 sue * doc/manual/citcoms.lyx: fixed quotes; added degree symbols as requested 2006-12-05 00:14 tan2 * doc/manual/citcoms.lyx, doc/manual/graphics/fulltest.xsect.100.jpg, doc/manual/graphics/regtest.100.z005.jpg: Finished the GMT script section 2006-12-04 23:47 tan2 * visual/plot_annulus.py: Renamed "center" to "starting point" 2006-12-04 22:42 sue * doc/manual/citcoms.lyx: minor sentence/word form changes in 5.1 and 5.2 2006-12-04 22:33 sue * doc/manual/citcoms.lyx: reformatted column names in c.4.9 2006-12-04 22:19 tan2 * doc/manual/citcoms.lyx: Revised Chapter 5 and Appendix A * Minor revision of post-processing * Update OpenDX section for new HDF5 layout * Briefly mentioned GMT scripts (unfinished) * Described new viscosity laws * Using Greek letter eta in the viscosity equations 2006-12-04 20:33 sue * doc/manual/citcoms.lyx: fixed more quotes, fixed table breaks, lines in table missing, other minor format problems 2006-12-04 19:48 luis * visual/Mayavi2/citcoms_display/__init__.py, visual/Mayavi2/citcoms_display/actions.py, visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Added OpenHDF5 and OpenVTK actions for mayavi2 2006-12-04 17:24 luis * doc/manual/citcoms.lyx: Fixes to manual 2006-12-04 17:24 luis * NEWS: Fixed typos 2006-12-04 16:54 luis * visual/h5tocap.c: Added vim modeline 2006-12-04 14:21 luis * visual/Mayavi2/citcoms_display/__init__.py, visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Mayavi2 UI customizations 2006-12-04 14:11 luis * visual/Mayavi2/citcoms_display: Added python module namespace for the citcoms mayavi2 plugins 2006-12-04 13:43 luis * visual/Mayavi2/__init__.py, visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py, visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py, visual/Mayavi2/plugins/__init__.py, visual/Mayavi2/plugins/filter/__init__.py: Removed executable permissions 2006-12-02 07:41 tan2 * doc/manual/graphics/CitcomSImportHDF5.net.gif, visual/OpenDXMacro/CitcomSImportHDF5.net.in: Update for new HDF5 layout 2006-12-02 07:14 tan2 * examples/Full/input.sample, examples/Regional/input.sample: * Removed obsolete parameters * Added new parameters * Only one "parameter=value" per line 2006-12-02 06:04 tan2 * visual/h5tocap.c: Updated for new HDF5 layout 2006-12-02 06:04 tan2 * visual/h5util.c, visual/h5util.h: Minor tweaks 2006-12-02 04:43 tan2 * visual/Makefile.am, visual/h5tovelo.c, visual/h5util.c, visual/h5util.h: Moved utility functions to h5util.c 2006-12-02 04:15 tan2 * visual/h5tovelo.c: Fixed a bug of counting argc 2006-12-02 00:57 tan2 * lib/Viscosity_structures.c: Added more rheology options, which is required for benchmarks rheol=1: visc = visc0 * exp(viscE * (viscT - T)) rheol=2: visc = visc0 * exp(-T / viscT) 2006-12-02 00:38 tan2 * visual/h5tocap.py: Updated h5tocap.py for new layout of HDF5 files 2006-12-02 00:03 tan2 * visual/Makefile.am, visual/h5tovelo.c: Added a program to convert h5 file to velo files for restart 2006-12-01 23:34 sue * doc/manual/citcoms.lyx: removed todo at 4.5.1, no issue there 2006-12-01 22:00 leif * configure.ac: Fix for infinite regress when builddir == srcdir. !@#$%* The .pth/sitedir/sys.path/PYTHONPATH aspect of eggs is really irritating. I hope setuptools becomes a part of the standard Python distro, as the Python core developers are likely to accept it uncritically and unmodified (as they are wont to do, apparently -- judging by all the other crap that is in the standard library). God willing, this will further accelerate the death of the language. 2006-12-01 21:56 tan2 * visual/Makefile.am, visual/samples/cookbook1.100.h5, visual/samples/cookbook1.h5: Added samples of HDF5 output 2006-12-01 21:33 leif * bin/Makefile.am, configure.ac: builddir != srcdir works again. The use of setup.py/distutils/setuptools forces the creation of files in srcdir. This bugs me. 2006-12-01 04:40 leif * Makefile.am, configure.ac: The "make install" command now works again. 2006-11-30 23:38 sue * doc/manual/citcoms.lyx: fixed sentence in A.1.2 last row 2006-11-30 23:08 tan2 * doc/manual/citcoms.lyx: Updated Chapter 6 * sync'd the manual with the cookbook scripts * improving the resolution of cookbook5.2.eps is left until the next release Also, fixed table borders in Appendix A. 2006-11-30 22:55 tan2 * examples/Cookbook5/cookbook5.cfg: Moved path name of restart file to "datadir_old" 2006-11-30 22:53 tan2 * examples/Cookbook1/cookbook1.cfg, examples/Cookbook2/cookbook2.cfg, examples/Cookbook3/cookbook3.cfg, examples/Cookbook4/cookbook4.cfg, examples/Cookbook5/cookbook5.cfg: Fixed issue63, Change "monitoringfrequency" comment in citcoms cookbooks 2006-11-30 22:21 luis * doc/manual/citcoms.lyx: Done with Chapter 4 references. 2006-11-30 21:16 tan2 * doc/manual/citcoms.lyx: The concept of caps is explained in section 1.7 2006-11-30 21:10 luis * visual/Makefile.am, visual/h5steps.c: Removing obsolete program h5steps.c 2006-11-30 20:57 tan2 * doc/manual/citcoms.lyx: Updated Appendices 2006-11-30 20:26 tan2 * doc/manual/citcoms.lyx: Updated section 3.6.1 2006-11-28 23:28 leif * CitcomS/Components/IC.py, CitcomS/Components/Sphere/FullSphere.py, CitcomS/Components/Sphere/RegionalSphere.py, CitcomS/Solver/Solver.py, module/bindings.c, module/getProperty.h, module/misc.c, module/misc.h, module/setProperties.c: Fixed some bugs, some of which were introduced during the C -> C++ transition. Using a pidXXXX.cfg file as input should "work" now, although it still doesn't reproduce the original simulation, since at least one parameter is missing ('steps'). I maintain that dumping the configuration is really the job of the framework (Pyre). Unfortunately, Pyre's current capabilities in this area are buggy in the case of '.pml' files, and non-existent in the case of '.cfg' files. Note: 'nproc_surf' is now a real inventory item, instead of a fake one. It looks like it doesn't belong in the inventory at all, though. (I left it there to avoid breakage.) 2006-11-28 21:08 leif * doc/manual/citcoms.lyx: Checked-in a virus, a worm, a Trojan horse, and some other malware. LyX doesn't support copy & paste between applications, so this check-in may have introduced some bugs as well. 2006-11-28 19:26 sue * doc/manual/citcoms.lyx: various edits to 3.6.1 and 3.7 2006-11-28 07:33 leif * lib/Instructions.c: Rewrote expand_str() in order to: 1) avoid potential buffer overflow; 2) avoid the use of non-standard strndup(); 3) avoid the use of the heap altogether. (Prompted by unresolved strndup on Mac OS X.) 2006-11-28 05:00 tan2 * examples/Cookbook2/cookbook2.cfg: Clarified the comment 2006-11-28 04:42 tan2 * NEWS: Updated for new features 2006-11-28 04:41 tan2 * README: Added a reference to NEWS 2006-11-28 03:34 tan2 * doc/manual/citcoms.lyx: Chapter 3 updated 2006-11-28 03:01 leif * CitcomS/CoupledApp.py, CitcomS/SimpleApp.py, bin/citcoms.in, setup.py: Changes related to Pythia v0.8.1.0b7, which CitcomS now requires: 'journal' is no longer a part of an application's inventory, and pyre.applications.start() is now responsible for calling run(). 2006-11-28 02:57 tan2 * examples/Cookbook6/cookbook6.cfg, examples/Full/input.sample, examples/Regional/input.sample: Updated the dimensional const 2006-11-28 02:55 tan2 * examples/example1.cfg: Updated to be consistent with the manual 2006-11-27 23:09 tan2 * CitcomS/Solver/Solver.py, lib/Instructions.c: Changed the default value of "datadir" to "." 2006-11-27 22:37 tan2 * visual/Makefile.am, visual/autocombine.py, visual/batchcombine.py, visual/batchpaste.sh, visual/batchpaste2.sh, visual/execpaste.py: Changed postprocessing scripts for the new "datadir" parameter 2006-11-27 21:27 tan2 * visual/pasteCitcomData.sh: Fix for POSIX-compliant arithmetic expression The "sh" shell on my Ubuntu 6.10 doesn't have the "let" command. That's how I found that "let" is not in the POSIX standard. Use "$((expression))" instead. 2006-11-27 20:05 tan2 * visual/citcoms_datadir: Added extern program to determine "datadir" 2006-11-27 20:05 tan2 * CitcomS/Components/Output.py, CitcomS/Solver/Solver.py, lib/Instructions.c, lib/Output.c, lib/global_defs.h, module/setProperties.c: Changes how to specify output directory * "output_format" must be either "ascii" (the default) or "hdf5", the "ascii-local" option is gone * "datafile" becomes the prefix of the filename and cannot contain "/" * "datadir" becomes mandatory input parameters * If "datadir" is "%DATADIR", the output directory is determined by an external program "citcoms_datadir" * Special substrings "%RANK", "%HOSTNAME" in datadir will be substituted by mpi rank, machine's hostname, $DATADIR environment variable, respectively. * These special strings start with "%", rather than "$", becuase it's very difficult to input "$" from the command line. 2006-11-22 21:26 tan2 * lib/Stokes_flow_Incomp.c: Changed the convergence criterion of Stokes solver: * stop iterations if delta(v) or delta(p) becomes too small (i.e., v or p has converged) * this is suggested by Shijie Zhong 2006-11-22 21:25 tan2 * lib/Full_parallel_related.c: Ignoring overlapping nodes when counting # of global nodes 2006-11-22 20:25 sue * doc/manual/citcoms.lyx: typo; made references into an itemized list 2006-11-22 20:05 tan2 * lib/Full_parallel_related.c, lib/Full_version_dependent.c, lib/Makefile.am, lib/Regional_parallel_related.c, lib/Regional_version_dependent.c, lib/global_defs.h, lib/temperature_descriptions.h: Removed unused codes and files 2006-11-22 19:41 tan2 * lib/Output.c, lib/Output_h5.c, lib/Sphere_harmonics.c, lib/Topo_gravity.c, lib/global_defs.h: Refactored geoid calculation 2006-11-21 23:03 luis * doc/manual/citcoms.lyx: Expanded section on optimizing parallel I/O. 2006-11-21 20:18 tan2 * visual/plot_annulus.py, visual/plot_layer.py, visual/zslice.py: Added scripts for 2D temperature plots, using GMT commands 2006-11-20 19:24 tan2 * lib/Sphere_harmonics.c: Forgot to declare function prototype 2006-11-18 05:17 tan2 * lib/Sphere_harmonics.c: Disabled a debugging output, which is not protected by a "if(E->control.verbose)" and caused Segmentation Fault. 2006-11-18 01:29 leif * bin/pycitcoms.c: The function loadObject() has been moved from Pythia to Merlin. 2006-11-18 00:48 tan2 * examples/Full/input.sample, examples/Full/velbc/README, examples/Full/velbc/velbc_full.tar.gz, examples/Makefile.am: Updated the vbc files and input file 2006-11-18 00:41 tan2 * examples/Regional/input.sample, examples/Regional/velbc/README, examples/Regional/velbc/velbc_regional.tar.gz, examples/Regional/velbc/velbc_regional40, examples/Regional/velbc/velbc_regional41: Updated the vbc files and input file. 2006-11-18 00:20 tan2 * lib/Instructions.c, lib/Output_h5.c, lib/hdf5_related.h, lib/output_h5.h: HDF5 output for geoid is working 2006-11-17 22:37 luis * ., CitcomS, bin, etc, examples, lib, module, tests, visual, visual/OpenDXMacro: Cleaned up 'svn status' by updating svn:ignore property 2006-11-17 20:25 tan2 * lib/Output_h5.c: HDF5 output of surf, botm, horiz_avg are working now. * Time and timestep infomation is written as scalar attributes "time" and "timestep" in / group. * Set MPI_Info according to input parameters "cb_block_size" and "cb_buffer_size" * I decided not to write surf, botm, and horiz_avg coordinates. This coordinate can be retrieved from the 3D coordinate very easily by this pseudo-code: surf_coord = coord[cap=all, x=all, y=all, z=1] z_coord = coord[cap=1, x=1, y=1, z=all] Remainging works: geoid for hdf5, update the manual 2006-11-17 06:26 tan2 * lib/Instructions.c, lib/Output_h5.c, lib/hdf5_related.h, lib/output_h5.h: HDF5 output reloaded. See issue4 for reasoning. Most data outputs are working. Remaining works: * How to deal with time output? (Maybe not output at all? Time info is always written in the .time file anyway.) * Where to put 2d and 1d coordinate output? (Maybe output with the data? These datasets are small and won't take too much space anyway.) * Geoid output 2006-11-17 05:34 leif * CitcomS/Components/Output.py: Fixed a minor bug in Output.py. 2006-11-17 02:24 leif * doc/manual/citcoms.lyx: Revised everything having to do with runtime configuration: launcher.xxx, scheduler.xxx, and job.xxx. Lowered the prominence/importance given to .pml files... and resisted my temptation to delete all reference to them :-) (I think I'm pretty much done with the v2.1 manual at this point. Reading the manual makes me tired, because it reminds me of how much work remains to be done on the code itself. Ease-of-use could be substantially improved...) 2006-11-16 21:58 leif * bin/Makefile.am: Reverted another recent decision of mine: Always build the legacy drivers, 'CitcomSFull' and 'CitcomSRegional'. I took these out of the Pyre build to avoid confusion; but now -- thinking of shared installations of CitcomS on clusters -- I think they should always be built (as they were before) so that users have the option. 2006-11-16 21:36 leif * examples/Makefile.am: Install examples under PREFIX/share/CitcomS/examples, as now documented in the manual. This is for the benefit of users of shared installations of CitcomS. I also sync'd the file list in examples/Makefile.am. Note: the file velbc_regional.tar.gz seems to be corrupt!!! 2006-11-16 21:25 leif * doc/manual/citcoms.lyx: Corrections with respect to r5302: the binaries/scripts are now once again built under the 'bin' subdirectory. Also reviewed all references to PREFIX. 2006-11-16 14:40 leif * Citcom.c, CitcomSFull.c, CitcomSRegional.c, Makefile.am, bin, bin/Citcom.c, bin/CitcomSFull.c, bin/CitcomSRegional.c, bin/Makefile.am, bin/citcoms.in, bin/pycitcoms.c, citcoms.in, configure.ac, pycitcoms.c: Re-created 'bin' subdirectory to avoid filename conflict on case-sensitive filesystems (Mac, Windows): "CitcomS" == "citcoms". Fixed egg-related bugs which prevented 'configure' from succeeding when buildir != srcdir (another BuildBot test vector). Call addsitedir() in the 'citcoms' script. I guess this is now necessary since "site.py" is no longer in the same directory as "citcoms". (*) Note that there is currently a bug in Merlin which prevents 'citcoms' from running ("No module named pkg_resources"). The work-around is to manually add the merlin egg to the merlin-install.pth file. There are more bugs which prevent running on Mac OS X at all (still investigating). (*) I'm becoming annoyed with setuptools' use of .pth files as a sys.path/PYTHONPATH persistence mechanism, mainly because of the accompanying hacks which are used to turn ordinary directories into "site" directories (i.e., directories where .pth files work) -- these ugly, confusing hacks include the fake site.py, "virtual python", etc. I think Merlin will only use .pth files in real site directories. It will use clear, straitforward, direct sys.path manipulation everywhere else. 2006-11-16 03:04 tan2 * module/setProperties.c: Forgot to commit module/ directory 2006-11-16 03:01 tan2 * lib/Topo_gravity.c: Declared function prototype at the top 2006-11-16 02:07 tan2 * CitcomS/Components/Const.py, CitcomS/Components/Output.py, CitcomS/Components/Sphere/Sphere.py: Forgot to commit python files 2006-11-16 02:07 tan2 * lib/Sphere_harmonics.c: Declared function prototype at the top 2006-11-16 01:52 tan2 * lib/Element_calculations.c, lib/Full_obsolete.c, lib/Full_parallel_related.c, lib/Full_version_dependent.c, lib/General_matrix_functions.c, lib/Global_operations.c, lib/Instructions.c, lib/Obsolete.c, lib/Output.c, lib/Output_h5.c, lib/Regional_obsolete.c, lib/Regional_parallel_related.c, lib/Regional_version_dependent.c, lib/Sphere_harmonics.c, lib/Topo_gravity.c, lib/global_defs.h: Implemented geoid calculation, see issue64. User visible changes include: * "output_optional" can include string "geoid", which will enable geoid output * new input parameters: radius, density_above, density_below * removed input parameters: layerd, wdensity, llmax, nlong, nlati * moved input parameter "output_ll_max" from Sphere.py to Output.py * sync'd the defalut values of input parameters in Const.py and Instructions.c TODO: h5output_geoid() not finished 2006-11-15 22:01 leif * doc/manual/citcoms.lyx: Elaborated a bit on .egg download, and clarified that CitcomS needs Pythia v0.8.1.x (instead of 0.8). 2006-11-15 21:18 leif * doc/manual/citcoms.lyx: Re-read the stuff I worked on yesterday, making minor corrections: "is in your PATH" -> "is on your PATH", inserted the word "Section" before section references, other minor changes. 2006-11-15 20:40 sue * doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: a few typos fixed, http removed from htmlurl tags (not needed and lengthen name in line); pdf regen 2006-11-15 02:06 leif * doc/manual/citcoms.lyx: Corrections to the section, "Changing Parameters". 2006-11-15 01:14 leif * doc/manual/citcoms.lyx: Updated the installation chapter. 2006-11-14 03:25 leif * Makefile.am, citcoms.in, pycitcoms.c, setup.py: Pythia v0.8.1.0b4: Fixed bugs relating to MPI launching: Fix sys.path/PYTHONPATH automatically; don't touch 'argv' until after MPI_Init(). Next, I may try to slurp 'pycitcoms.c' into the framework... it contains a lot of implementation details which have everything to do with Pyre and nothing to do with CitcomS. 2006-11-11 03:34 leif * ., configure.ac, ez_setup.py, setup.py: Use the new merlin (the setuptools clone). Download Python dependencies automatically during 'configure' (This doesn't work for "make install" yet.) The Dynamo BuildBot might even succeed after this check-in... fingers crossed... 2006-11-10 19:20 sue * doc/manual/citcoms.lyx: created formulas for sec a.1.11 2006-11-10 18:54 sue * doc/manual/citcoms.lyx, doc/manual/graphics/cookbook7.eps: cookbook 6 graphic edited, various small tweaks 2006-11-10 01:59 sue * doc/manual/citcoms.lyx: finished various typos and fixes after checking with Luis on questions 2006-11-09 19:37 sue * doc/manual/citcoms.lyx, doc/manual/citcoms_cover-layers.pdf, doc/manual/citcoms_cover.pdf, doc/manual/graphics/c_fig1.eps: various typos and fixes 2006-11-07 19:33 tan2 * doc/manual/citcoms.lyx: * Fixed a few typos * Added "TODO" in front of all unfinished text. 2006-11-07 02:30 leif * Makefile.am, configure.ac, lib/Makefile.am, visual/Makefile.am: Moved CitcomS HDF5 macros to cs/autoconf. 2006-11-07 01:33 leif * ., CitcomS/Makefile.am, Makefile.am, bin, citcoms.in, configure.ac, etc/Makefile.am, lib/Makefile.am, module/Exchanger, module/Makefile.am, project.cfg, pycitcoms.c, setup.py, visual/Makefile.am: Took a step backwards so that I can take a more conservative approach to build/install. Also, temporarily deleted 'Exchanger' and all references to it, to avoid confusion. We can always go back in time and retrieve it later. 2006-11-07 00:49 sue * doc/manual/citcoms.pdf: pdf generated 2006-11-07 00:49 sue * doc/manual/citcoms.lyx, doc/manual/graphics/c_fig1.eps, doc/manual/graphics/cookbook1.eps, doc/manual/graphics/cookbook2.eps: gurnis edits, new pdf 2006-11-06 18:53 sue * doc/manual/citcoms.lyx, doc/manual/graphics/citcoms_cover-layers.pdf, doc/manual/graphics/citcoms_cover.pdf: added authors to cover 2006-11-06 18:33 sue * doc/manual/citcoms.lyx, doc/manual/graphics/proc_mesh.eps: added new section 1.7 per gurnis and supporting graphic 2006-11-01 20:47 luis * doc/manual/citcoms.lyx: Re-typed most of the changes from my copy of the citcoms.lyx file 2006-10-27 21:26 tan2 * tests/.cvsignore: Removed legacy file .cvsignore 2006-10-27 21:25 tan2 * doc/.cvsignore: Removed legary file .cvsignore 2006-10-20 19:36 tan2 * examples/.reset-temporary: This file (examples/.reset-temporary) was checked into svn at the initial import by me. I don't remember what this file was used for. 2006-10-20 19:00 tan2 * CitcomS/Solver/Solver.py: * Removed extra output_time(), which was used for profiling * Converted tab to 4 spaces 2006-10-20 08:19 leif * configure.ac: Fail if MPI lib/header is not found. 2006-10-17 11:00 leif * CitcomS/Makefile.am, Makefile.am, bin/Makefile.am, etc/Makefile.am, lib/Makefile.am, module/Makefile.am: Fixed legacy build. 2006-10-17 09:18 leif * ., Citcom.c, CitcomSFull.c, CitcomSRegional.c, Makefile.am, bin/Citcom.c, configure.ac, doc/CitComS.doxyconf, lib/Pan_problem_misc_functions.c, lib/Tracer_advection.c, module/CitcomSmodule.c, module/Makefile.am, module/Regionalmodule.c, module/advdiffu.c, module/bindings.c, module/exceptions.c, module/initial_conditions.c, module/mesher.c, module/misc.c, module/outputs.c, module/setProperties.c, module/stokes_solver.c, project.cfg, setup.py, tests/Makefile.am, visual/Makefile.am: Transitioning to Merlin. (Warning: still under construction.) 2006-10-14 00:29 tan2 * CitcomS/Solver/CoupledSolver.py: Undid the accidental checkin at r4998 2006-10-14 00:27 tan2 * CitcomS/Solver/Solver.py, doc/manual/citcoms.lyx, lib/Instructions.c, lib/Output.c, lib/Output_h5.c, lib/global_defs.h, visual/estimate.py: Renamed reference of "average" to "horiz_avg" 2006-10-14 00:06 tan2 * NEWS: Added description on new features and bug fixes for v2.1.0 2006-10-13 23:59 luis * lib/Output_h5.c: Settled on /horiz_avg/ instead of /have/ 2006-10-13 23:46 sue * doc/manual/citcoms.lyx: updated url handling 2006-10-13 23:18 tan2 * visual/h5tocap.c: * Updated for the new layout of HDF5 group * Changed the order of nodes, so that the output is the same as the cap file from autocombine.py 2006-10-13 07:39 tan2 * doc/manual/citcoms.lyx: * Fixed a typo "PHDF HOME" -> "PHDF_HOME" * Added a section on using none-pyre version * Undid a xref in section 3.1, which should link to (not-checked-in-yet) "Working with HDF5" chapter * Updated Appendix A and changed the title * Added description on new output files (stress, pressure, average) 2006-10-13 06:43 tan2 * lib/Full_geometry_cartesian.c, lib/Regional_geometry_cartesian.c, lib/Viscosity_structures.c: Gave default values to several parameters 2006-10-13 04:15 tan2 * examples/Full/input.sample, examples/Regional/input.sample: Removed obsolete input parameter "maxadvtime" from the input samples 2006-10-13 04:10 tan2 * CitcomS/Components/Advection_diffusion/Advection_diffusion.py, CitcomS/Components/Stokes_solver/Incompressible.py, lib/Output_h5.c, module/setProperties.c: Moved input parameters "aug_lagr" and "aug_number" from tsolver to vsolver, where they really should belong to. These parameters are for augmented lagragian stiffness matrix (I have no idea on what it is...), as indicated in Element_calculations.c. 2006-10-12 21:43 tan2 * CitcomS/Components/IC.py, module/setProperties.c: 'half_space_age' was not used when 'tic_method'=1. So, fixed the comment and removed the conditional input 2006-10-12 14:48 leif * CitcomS/BaseApplication.py, CitcomS/Components/Advection_diffusion/Advection_diffusion.py, CitcomS/Components/BC.py, CitcomS/Components/CitcomComponent.py, CitcomS/Components/CodecConfig.py, CitcomS/Components/Const.py, CitcomS/Components/HackedConfigParser.py, CitcomS/Components/IC.py, CitcomS/Components/Launchers.py, CitcomS/Components/Output.py, CitcomS/Components/Param.py, CitcomS/Components/Phase.py, CitcomS/Components/Sphere/Sphere.py, CitcomS/Components/Stokes_solver/Incompressible.py, CitcomS/Components/Tracer.py, CitcomS/Components/Visc.py, CitcomS/CoupledApp.py, CitcomS/SimpleApp.py, CitcomS/Solver/Solver.py, bin/Citcom.c, bin/Makefile.am, bin/citcoms.in, bin/coupledcitcoms.in, bin/pycitcoms.c, bin/pycitcoms.cc, bin/pycppcitcoms.cc, configure.ac, doc/manual/citcoms.lyx, etc/CitcomS.pml.in, etc/Makefile.am, etc/globus.odb, etc/lam-mpi.odb, etc/lsf.odb, etc/mpich.odb, etc/pbs.odb, lib/Advection_diffusion.c, lib/Citcom_init.c, lib/Drive_solvers.c, lib/Full_parallel_related.c, lib/Full_version_dependent.c, lib/Global_operations.c, lib/Instructions.c, lib/Lith_age.c, lib/Output.c, lib/Output_h5.c, lib/Parsing.c, lib/Process_buoyancy.c, lib/Regional_parallel_related.c, lib/Regional_version_dependent.c, lib/Topo_gravity.c, lib/Tracer_advection.c, lib/global_defs.h, lib/sphere_communication.h, module/CitcomSmodule.c, module/CitcomSmodule.cc, module/CitcomSmodule.h, module/Makefile.am, module/PyxMPI, module/Regionalmodule.c, module/Regionalmodule.cc, module/advdiffu.c, module/advdiffu.cc, module/advdiffu.h, module/bindings.c, module/bindings.cc, module/bindings.h, module/exceptions.c, module/exceptions.cc, module/exceptions.h, module/getProperty.h, module/initial_conditions.c, module/initial_conditions.cc, module/initial_conditions.h, module/mesher.c, module/mesher.cc, module/mesher.h, module/misc.c, module/misc.cc, module/misc.h, module/outputs.c, module/outputs.cc, module/outputs.h, module/setProperties.c, module/setProperties.cc, module/setProperties.h, module/stokes_solver.c, module/stokes_solver.cc, module/stokes_solver.h, setup.py: Moved 'launcher' and '.cfg' support out of CitcomS and into the framework. As I was revising the "Installation" chapter of the manual (still in progress), I got frustrated with how complicated everything was -- and how difficult it was to document that complexity -- so I did something slightly violent: Converted the CitcomS extension module, 'CitcomSLib', from C++ to C. This is made possible by Pythia 0.8.1.0b2, which replaces _mpimodule with _mpi.pyx, which has a C interface. It is now possible to build CitcomS -- and all its prerequisites (e.g. Python) -- entirely from source, starting with nothing but a C compiler. Exchanger still requires C++, of course. I have yet to test these changes with Exchanger enabled, but I don't anticipate any serious problems. This may have been overkill, but I also cleaned the source of C++-style comments (even though most modern C compilers probably accept them... it became standard in C99 or something). I'll bet you can install CitcomS with GCC 2.x now :-) 2006-10-11 20:01 sue * doc/manual/citcoms.lyx: took care of some todo items 2006-10-10 23:48 tan2 * doc/manual/citcoms.lyx: * Added subsection on installing OpenDXutils package * Aligned figures to the center * Changed the layout of the Appendices 2006-10-10 20:37 sue * doc/manual/citcoms.lyx: added hdf5 install and addt tools chapters 2006-10-10 18:42 luis * doc/manual/citcoms.lyx: Inserted a few TODO items 2006-10-10 13:00 luis * lib/Makefile.am, lib/Output_h5.c, lib/PyTables.c, lib/pytables.h: 1. Reorganized routines in a more logical order. 2. Consolidated routines from PyTables.[ch] into Output_h5.c 2006-10-10 11:54 luis * lib/Instructions.c, lib/Output_h5.c, lib/output_h5.h: Renamed local function to conform with h5 prefix. 2006-10-10 07:29 luis * lib/Output_h5.c, lib/PyTables.c, lib/pytables.h: 1. Added PID to metadata to make it easier to identify the corresponding .cfg file 2. Wrapped most calls to set_attribute() to avoid using addresses as arguments 3. Added set_attribute_{int,float,double}_vector() functions 2006-10-10 00:52 luis * lib/Output_h5.c: Forgot to delete reference to obsolete data_group. 2006-10-10 00:52 tan2 * doc/manual/citcoms_cover-layers.pdf, doc/manual/citcoms_cover.pdf: Set MIME type to pdf 2006-10-10 00:51 tan2 * doc/manual/graphics/CitcomSImportHDF5.net.gif: Set MIME type to image 2006-10-10 00:48 tan2 * doc/manual/graphics/c_fig1.eps, doc/manual/graphics/c_fig10.eps, doc/manual/graphics/c_fig2.eps, doc/manual/graphics/c_fig3.jpg, doc/manual/graphics/c_fig4.eps, doc/manual/graphics/c_fig5.eps, doc/manual/graphics/c_fig6.jpg, doc/manual/graphics/c_fig7.eps, doc/manual/graphics/c_fig8.eps, doc/manual/graphics/c_fig9.eps, doc/manual/graphics/cookbook1.2.jpg, doc/manual/graphics/cookbook1.eps, doc/manual/graphics/cookbook1.png, doc/manual/graphics/cookbook2.2.eps, doc/manual/graphics/cookbook2.2eps, doc/manual/graphics/cookbook2.eps, doc/manual/graphics/cookbook3.eps, doc/manual/graphics/cookbook4.eps, doc/manual/graphics/cookbook5.2.eps, doc/manual/graphics/cookbook5.eps, doc/manual/graphics/cookbook6.2.eps, doc/manual/graphics/cookbook6.eps, doc/manual/graphics/cookbook7.eps: Set MIME type to image 2006-10-10 00:45 luis * lib/Output_h5.c: Shortened /average/ group into /have/ 2006-10-10 00:42 tan2 * doc/manual/graphics/CitcomSImportHDF5.net.gif: Figure for HDF5 visualization 2006-10-10 00:41 tan2 * doc/manual/citcoms.lyx: Added section on visualizing HDF5 output 2006-10-10 00:38 luis * lib/Output_h5.c: Fix mispelling in input parameters (allignment options). 2006-10-09 23:25 tan2 * doc/manual/citcoms.lyx: * Added documentaion of .pml file, which comes from DANSE FAQ * Added section on visualization of full version * Moved the discussion on .log and .time files from Section 4.2 to Section 3.5.3 * Updated links to equations 2006-10-09 23:14 sue * doc/manual/citcoms.lyx: change equation numbering 2006-10-09 20:41 tan2 * visual/OpenDXMacro/CitcomSImportHDF5.net.in: Changed the order of input parameters 2006-10-09 19:58 tan2 * visual/OpenDXMacro/CitcomSImportHDF5.net.in: Updated for the new layout of hdf5 output 2006-10-09 00:14 gurnis * lib/Full_read_input_from_files.c, lib/Problem_related.c, lib/Viscosity_structures.c: For Viscosity_structures.c, added a new rheology, rheol=5, that is a variant of rheol=3. The difference lay in the way that plate boundaries are weakened. Must set mat_control=1 and enter materials into the VIP array. Removed debug statements from Problem_related.c in preparation of new release. 2006-10-08 12:04 leif * configure.ac, setup.py: Pointed CitcomS egg-downloading at the new "Eggs" section on the web site, to insulate CitcomS from the imminent chaos in pythia-dev. 2006-10-07 01:15 tan2 * visual/h5tocap.py: Updated for the new layout in the h5 file 2006-10-07 00:01 luis * lib/Output_h5.c: Eliminated data group in HDF5 file. Main datasets are now on the root-level. 2006-10-06 21:10 tan2 * lib/Obsolete.c: The type of elt_g should be "higher_precision" instead of "double". 2006-10-06 20:18 tan2 * lib/Interuption.c: Changed the signature of the signal handler from (void)(interuption(void)) to (void)(interuption(int)) to conform with the C standard 2006-10-06 20:02 tan2 * lib/element_definitions.h: Missing braces around initializers for array structs node_point[] and offset[] 2006-10-06 17:17 tan2 * doc/manual/citcoms.lyx: Some minor edits 2006-10-05 20:07 tan2 * visual/combine.py: Using 2-digit number for the cap filename, eg. prefix.cap00.step 2006-10-05 00:38 tan2 * visual/visFull.cfg, visual/visFull.net.in, visual/visRegional.cfg, visual/visRegional.net.in: Updated macros to use new samples files and fixed a few stylus issues 2006-10-05 00:15 tan2 * visual/Makefile.am: Rearranged file list 2006-10-05 00:15 tan2 * visual/Makefile.am: Updated file list 2006-10-05 00:04 tan2 * visual/samples/fulltest.cap0.0, visual/samples/fulltest.cap0.0.general, visual/samples/fulltest.cap00.100, visual/samples/fulltest.cap00.100.general, visual/samples/fulltest.cap01.100, visual/samples/fulltest.cap01.100.general, visual/samples/fulltest.cap02.100, visual/samples/fulltest.cap02.100.general, visual/samples/fulltest.cap03.100, visual/samples/fulltest.cap03.100.general, visual/samples/fulltest.cap04.100, visual/samples/fulltest.cap04.100.general, visual/samples/fulltest.cap05.100, visual/samples/fulltest.cap05.100.general, visual/samples/fulltest.cap06.100, visual/samples/fulltest.cap06.100.general, visual/samples/fulltest.cap07.100, visual/samples/fulltest.cap07.100.general, visual/samples/fulltest.cap08.100, visual/samples/fulltest.cap08.100.general, visual/samples/fulltest.cap09.100, visual/samples/fulltest.cap09.100.general, visual/samples/fulltest.cap1.0, visual/samples/fulltest.cap1.0.general, visual/samples/fulltest.cap10.0, visual/samples/fulltest.cap10.0.general, visual/samples/fulltest.cap10.100, visual/samples/fulltest.cap10.100.general, visual/samples/fulltest.cap11.0, visual/samples/fulltest.cap11.0.general, visual/samples/fulltest.cap11.100, visual/samples/fulltest.cap11.100.general, visual/samples/fulltest.cap2.0, visual/samples/fulltest.cap2.0.general, visual/samples/fulltest.cap3.0, visual/samples/fulltest.cap3.0.general, visual/samples/fulltest.cap4.0, visual/samples/fulltest.cap4.0.general, visual/samples/fulltest.cap5.0, visual/samples/fulltest.cap5.0.general, visual/samples/fulltest.cap6.0, visual/samples/fulltest.cap6.0.general, visual/samples/fulltest.cap7.0, visual/samples/fulltest.cap7.0.general, visual/samples/fulltest.cap8.0, visual/samples/fulltest.cap8.0.general, visual/samples/fulltest.cap9.0, visual/samples/fulltest.cap9.0.general, visual/samples/regtest.cap0.0, visual/samples/regtest.cap0.0.general, visual/samples/regtest.cap00.100, visual/samples/regtest.cap00.100.general: Replaced sample files at 0th time step with sample files at 100th time step, which have more interesting features in the visualization, 2006-10-04 18:34 tan2 * examples/Cookbook1/cookbook1.cfg, examples/Cookbook2/cookbook2.cfg, examples/Cookbook3/cookbook3.cfg, examples/Cookbook4/cookbook4.cfg, examples/Cookbook5/cookbook5.cfg, examples/Cookbook6/cookbook6.cfg: * Removed some unnecessary parameters * Changed the layout slightly * Updated the cookbook scripts to be consistent with the manual 2006-10-04 18:32 tan2 * doc/manual/citcoms.lyx: Updated the Cookbook chapter 2006-10-04 18:24 tan2 * doc/manual/graphics/cookbook1.jpg, doc/manual/graphics/eq1.eps, doc/manual/graphics/eq10.eps, doc/manual/graphics/eq11.eps, doc/manual/graphics/eq12.eps, doc/manual/graphics/eq13.eps, doc/manual/graphics/eq14.eps, doc/manual/graphics/eq15.eps, doc/manual/graphics/eq16.eps, doc/manual/graphics/eq17.eps, doc/manual/graphics/eq18.eps, doc/manual/graphics/eq19.eps, doc/manual/graphics/eq2.eps, doc/manual/graphics/eq20.2.eps, doc/manual/graphics/eq20.eps, doc/manual/graphics/eq21.eps, doc/manual/graphics/eq3.eps, doc/manual/graphics/eq4.eps, doc/manual/graphics/eq5.eps, doc/manual/graphics/eq6.eps, doc/manual/graphics/eq7.eps, doc/manual/graphics/eq8.eps, doc/manual/graphics/eq9.eps, doc/manual/graphics/exp1.eps, doc/manual/graphics/exp10.eps, doc/manual/graphics/exp11.eps, doc/manual/graphics/exp12.eps, doc/manual/graphics/exp2.eps, doc/manual/graphics/exp3.eps, doc/manual/graphics/exp4.eps, doc/manual/graphics/exp5.eps, doc/manual/graphics/exp6.eps, doc/manual/graphics/exp7.eps, doc/manual/graphics/exp8.eps, doc/manual/graphics/exp9.eps: Removed unused figures 2006-10-04 01:56 tan2 * examples/Cookbook6/cookbook6.cfg, examples/Cookbook6/cookbook7.cfg: Renamed file to be consistent with the manual 2006-10-04 01:54 tan2 * examples/Cookbook6, examples/Cookbook7: Renamed directory to be consistent with the manual 2006-10-02 22:46 tan2 * examples/Cookbook1/cookbook1.cfg: Using default Rayleigh number, which is stated in the manual. Also updated the comment to be consistent with the manual. 2006-10-02 22:43 tan2 * doc/manual/citcoms.lyx: Slightly updated postprocessing chapter. Revised Cookbook 1. 2006-09-30 00:56 tan2 * doc/manual/citcoms.lyx: Updated Chapter 3 "Running CitComS.py" for the .cfg input format, also explained how to launch a parallel job. Some TODO items left. 2006-09-29 23:14 gurnis * lib/Full_read_input_from_files.c, lib/Problem_related.c, lib/Regional_lith_age_read_files.c: Fixed age bug in Regional. In Regional_lith_age_read_files.c, find_age_in_MY() was not being converted to a float 2006-09-29 21:50 sue * doc/manual/citcoms_cover-layers.pdf, doc/manual/citcoms_cover.pdf: updated version on pdf cover and added pdf layered file 2006-09-28 14:56 luis * lib/Output_h5.c, lib/hdf5_related.h: 1. Added a cap dimension for efficient parallel I/O 2. Bulk of data write operations now done in collective mode. 4. Passing various parallel I/O tuning parameters to HDF5 and MPI-IO. 5. Consolidated all data buffers into one (only largest size allocated). 2006-09-28 14:30 luis * CitcomS/Components/Output.py, module/setProperties.cc: Fixed typo in names 2006-09-27 23:33 tan2 * CitcomS/Components/Output.py: * Removed debugging output * Added svn:keywords and svn:mime-type attributes 2006-09-27 20:37 leif * setup.py: Relaxed setuptools version requirement to 0.6b1. 2006-09-27 00:24 tan2 * CitcomS/Components/Output.py, CitcomS/Makefile.am, CitcomS/Solver/Solver.py, lib/Instructions.c, lib/Output.c, lib/Output_h5.c, lib/global_defs.h, lib/output.h, lib/output_h5.h, module/bindings.cc, module/setProperties.cc, module/setProperties.h: * Created new component 'Output.py' for storing output-related properties * Added several input parameters for HDF5 output performance tuning * Moved 'output_format' and 'output_optional' form Solver.py to Output.py 2006-09-26 12:20 luis * bin/Makefile.am, examples/Makefile.am, lib/Makefile.am, module/Makefile.am, visual/OpenDXMacro/Makefile.am: Fixed broken 'make dist' 2006-09-26 01:09 leif * bin/Makefile.am, bin/pycitcoms.cc, configure.ac, ez_setup.py, module/Exchanger/Makefile.am, module/Makefile.am, setup.py: Made 'Exchanger' optional. Give "--with-exchanger=[yes|no]" as an argument to 'configure' to manually specify whether you want Exchanger; the default is "auto", which means to use Exchanger if it's installed (and on your PYTHONPATH). Egg-ified 'configure' checks for Python packages. This means that CitcomS now requires the egg-ified CIG version of Pythia -- and (optionally) the egg-ified Exchanger. Old Pythia/Exchanger installations will not work, as they lack the egg-metadata ('configure' will act as if they are not installed). Added 'setup.py', which will automatically download and install the egg version of Pythia -- as well as the egg system itself ('setuptools'). If you want Exchanger, you still must install it manually (the way C++ is used prevents complete egg-ification of Exchanger). Note that 'setup.py' actually checks-out the latest Pythia from the SVN repository. The release version of CitcomS will download a packaged Pythia from the website instead. 2006-09-25 19:13 tan2 * lib/Output.c, lib/Output_h5.c: Disabled material output, since material control is not working (yet) 2006-09-24 07:28 tan2 * CitcomS/Solver/Solver.py, lib/Instructions.c, lib/Output_h5.c, lib/global_defs.h, module/setProperties.cc: Added new input parameter 'datadir_old' in CitcomS.solver. If output_format=ascii and restart=1, the restart files will be read from ${datadir_old}/${rank}/${datafile_old}.velo.${rank}.${step}. In this case, 'datafile_old' cannot contain '/'. See issue56. 2006-09-22 23:26 tan2 * CitcomS/Solver/Solver.py, lib/Instructions.c: Write surf and botm output by default (but can be disabled by setting output_optional=''), which is compatible with v2.0.x. 2006-09-22 22:58 tan2 * lib/Instructions.c: Removed debugging output 2006-09-22 22:29 tan2 * visual/batchsurf.py: * Fixed issue55 "surf files got deleted by batchsurf.py" * Refactored the codes on machinefile -> nodelist 2006-09-22 22:14 tan2 * visual/getcoord.sh, visual/getsurf.sh: These scripts accept 'localhost' as a valid machine name now 2006-09-22 22:01 luis * lib/Output_h5.c: Bug fix: maxdims[0] is set to H5S_UNLIMITED in extendible datasets, so it should never be incremented. 2006-09-22 20:37 tan2 * visual/autocombine.py, visual/estimate.py, visual/h5tocap.py, visual/miff2avi, visual/miff2mpg, visual/parser.py, visual/zslice.py: Added 'Id' keyword to the files 2006-09-22 19:19 tan2 * visual/batchpaste.sh, visual/batchpaste2.sh: Fixed two bugs in post-processing scripts 2006-09-21 23:03 tan2 * visual/autocombine.py, visual/batchcombine.py, visual/batchpaste.sh, visual/batchpaste2.sh: Updated post-processing script for new output_format options. See issue53. 2006-09-21 21:25 luis * lib/Output_h5.c: Allow for optional fields when extending datasets. 2006-09-21 21:17 tan2 * lib/Output.c, lib/Output_h5.c, lib/Process_buoyancy.c: Refactored out the code computing horizontal average of temperature and rms velocity into a function. This fixes the bug in issue46. 2006-09-21 20:08 tan2 * lib/Instructions.c: Forgot to change the default value in C 2006-09-21 19:57 tan2 * CitcomS/Solver/Solver.py, lib/Instructions.c, lib/Output.c, lib/Output_h5.c, lib/global_defs.h: Added new option for "output_format". The current behavior is: * If output_format=="ascii-local" (the default), CitcomS will write ascii files to the directory and prefix specified by "datafile", ie., the same behavior as in v2.0 * If output_format=="ascii", CitcomS will write ascii files to the directory specified by "datadir" with the prefix specified by "datafile". In the case, "datafile" cannot contains the '/' (path seperator) character. * If output_format=="hdf5", CitcomS will write singe HDf5 file to the directory and prefix specified by "datafile". 2006-09-21 17:51 tan2 * visual/parser.py: Parser will skip lines starting with '[', so that it can parse .cfg file correctly 2006-09-21 17:49 tan2 * module/setProperties.cc: Removed quotes from output string 2006-09-21 00:18 tan2 * CitcomS/CoupledApp.py, CitcomS/SimpleApp.py, examples/Cookbook1/cookbook1.cfg, examples/Cookbook2/cookbook2.cfg, examples/Cookbook3/cookbook3.cfg, examples/Cookbook4/cookbook4.cfg, examples/Cookbook5/cookbook5.cfg, examples/Cookbook7/cookbook7.cfg, examples/example0.cfg, examples/example1.cfg: Calculate the needed # of cpu according to mesher properties. There is no longer a need to set launcher.nodes. 2006-09-20 22:51 tan2 * CitcomS/BaseApplication.py, CitcomS/Solver/CoupledFullSolver.py, CitcomS/Solver/CoupledRegionalSolver.py, CitcomS/Solver/CoupledSolver.py: Added svn:keywprds = Id 2006-09-20 20:47 tan2 * lib/Output_h5.c: Sync'd h5output_meta() with setProperties 2006-09-20 20:45 tan2 * CitcomS/Components/IC.py: Fixed the comment 2006-09-20 20:34 tan2 * CitcomS/Components/Advection_diffusion/Advection_diffusion.py, lib/Advection_diffusion.c, lib/Output_h5.c, module/setProperties.cc: Removed unused parameter 'maxadvtime' 2006-09-20 20:30 tan2 * CitcomS/Components/Advection_diffusion/Advection_diffusion.py, CitcomS/Components/Const.py, CitcomS/Components/IC.py, CitcomS/Components/Visc.py, module/setProperties.cc: Print out all pyre properties to the pid file 2006-09-20 19:54 tan2 * lib/Citcom_init.c, lib/Instructions.c, module/mesher.cc, module/setProperties.cc: Saving the input parameters to a unique file 'pidXXXXX.cfg' for archives. 2006-09-19 19:50 luis * lib/Output_h5.c: Allocate tensor field buffer only when necessary. 2006-09-19 18:44 tan2 * citcoms_profile: Since the opendx scripts have the macro path built in the file, there is no need to define $DXMACROS env. var. 2006-09-17 17:32 tan2 * CitcomS/Solver/Solver.py, examples/Cookbook5/cookbook5.cfg, examples/Full/input.sample, examples/Regional/input.sample, lib/Instructions.c, lib/Output.c, lib/Output_h5.c, lib/global_defs.h, module/setProperties.cc, visual/autocombine.py, visual/batchcombine.py, visual/batchpaste.sh, visual/combine.py, visual/pasteCitcomData.sh: * Added new input parameter 'datadir' in Solver * All outputs are done in 'datadir' directory * Processors write its own ascii output in 'datadir/rank' directory * Post-processing codes and cookbook examples were updated accordingly 2006-09-14 18:14 maweier * visual/Mayavi2/Citcoms_Hdf2Vtk.c: added help on usage. 2006-09-13 19:04 maweier * visual/Mayavi2/plugins/filter/CitcomSreduce.py: Changed range trait. 2006-09-12 20:50 tan2 * lib/global_defs.h: Fixed the bug of negative CPU time, which is caused by storing the walltime in insufficient precision 2006-09-11 17:25 maweier * visual/Mayavi2/Citcoms_Hdf2Vtk.c: added latest version of file converter in c. 2006-09-11 17:24 maweier * visual/Mayavi2/Citcoms_HdfDisplay.py, visual/Mayavi2/Citcoms_VtkDisplay.py, visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py, visual/Mayavi2/plugins/filter/CitcomSFilterActions.py, visual/Mayavi2/plugins/filter/CitcomSSphere.py, visual/Mayavi2/plugins/filter/CitcomSreduce.py, visual/Mayavi2/plugins/filter/CitcomSshowCaps.py, visual/Mayavi2/plugins/filter/CitcomSshowSurface.py, visual/Mayavi2/plugins/plugin_defs/mayavi_ui_plugin_definition.py: Updated licenses. 2006-09-11 17:23 maweier * visual/Mayavi2/Citcoms_Hdf2Vtk.c: Update 2006-09-11 00:17 luis * visual/Makefile.am, visual/h5steps.c, visual/h5tocap.c: 1. Added utility to extract steps from CitcomS HDF5 file. 2. Changed h5tocombined.c to h5tocap.c in copyright header. 2006-09-11 00:09 luis * visual/h5tocap.c: When no frames are specified, print number of available frames. 2006-09-10 09:50 luis * visual/Makefile.am, visual/h5tocap.c: 1. Added h5tocap to build procedure 2. Changed h5tocap to read frames from command-line (instead of steps) 2006-09-10 07:36 luis * lib/Output_h5.c, visual/estimate.py: Moved connectivity dataset to root group. 2006-09-09 01:45 tan2 * configure.ac: * set --with-hdf5=auto as default, which will try to detect HDF5 library, if not found, HDF5 support will be disabled * Reported summary at the end of configure 2006-09-09 00:24 tan2 * configure.ac: Added $PHDF5_HOME env. variables for the home directory of parallel HDF5 lib 2006-09-08 20:59 tan2 * visual/Makefile.am: Forgot to rename file 2006-09-08 20:27 luis * visual/h5tocap.c, visual/h5tocombined.c: Changed name to h5tocap.c 2006-09-08 19:20 tan2 * visual/h5tocap.py: Added a comment 2006-09-08 19:18 tan2 * visual/visRegional.cfg: Reverted the accidental check-in at r4498 2006-09-08 19:14 tan2 * visual/h52combined.py, visual/h5tocap.py, visual/visRegional.cfg: Renamed the conversion script 2006-09-08 19:14 tan2 * visual/h52combined.py: * Using 'caps' attribute in the input group * frame -> timestep conversion * Cleaned up the code 2006-09-08 15:53 luis * lib/Output_h5.c, lib/pytables.h: Removing unnecessary HDF5 attribute. 2006-09-08 15:46 luis * lib/Output_h5.c: Fix allocation of buffer for connectivity (done per cap, not globally). 2006-09-07 21:07 maweier * visual/Mayavi2/Citcoms_Hdf2Vtk.py, visual/Mayavi2/Citcoms_HdfDisplay.py, visual/Mayavi2/plugins/CitcomSHDFUgrid.py: Fixed connectivity issues. Fixed HdfDisplays wrong status output. 2006-09-06 22:33 maweier * visual/Mayavi2/Citcoms_Hdf2Vtk.py, visual/Mayavi2/plugins/CitcomSHDFUgrid.py: Got rid of the iterator to change the order. 2006-09-06 21:01 luis * visual/Mayavi2/Citcoms_Hdf2Vtk.c: Added function to retrieve float attributes from HDF5 file. 2006-09-06 20:18 tan2 * visual/OpenDXMacro/CitcomSImportHDF5.net.in, visual/OpenDXMacro/Makefile.am: * Made CitcomSImportHDF5 accept NULL (default) input for the caplist * Added CitcomSImportHDF5 to the install list 2006-09-06 19:06 tan2 * CitcomS/Makefile.am: Forgot backslash (line continuation) after Solver/__init__.py. See issue48. 2006-09-06 18:39 tan2 * visual/OpenDXMacro/CitcomSImportHDF5.net.in: Added an dx macro to import HDF5 output, this module depends on the Cactus OpenDXutils project (http://www.cactuscode.org/Visualization/openDX) 2006-09-06 16:41 maweier * visual/Mayavi2/Citcoms_Hdf2Vtk.c: New C version of the Hdf to Vtk converter. 2006-09-05 22:41 maweier * visual/Mayavi2/Citcoms_Hdf2Vtk.py, visual/Mayavi2/README: Bugfixes and a new README on how to use the code. 2006-09-05 21:10 maweier * visual/Mayavi2/Citcoms_Hdf2Vtk.py, visual/Mayavi2/Citcoms_hdf2vtk.py: Consistency 2006-09-05 20:53 maweier * visual/Mayavi2/Citcoms_HdfDisplay.py, visual/Mayavi2/Citcoms_hdf2vtk.py, visual/Mayavi2/__init__.py, visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py, visual/Mayavi2/plugins/filter/CitcomSFilterActions.py, visual/Mayavi2/plugins/filter/CitcomSshowCaps.py, visual/Mayavi2/plugins/filter/CitcomSshowSurface.py, visual/Mayavi2/plugins/filter/__init__.py: Some minor bugfixes 2006-09-05 20:49 maweier * visual/Mayavi2/Citcoms_hdf2vtk.py, visual/Mayavi2/citcoms_hdf2vtk.py: Rename for consistence. 2006-09-02 10:11 luis * lib/Instructions.c, lib/Output_h5.c, lib/global_defs.h, visual/estimate.py: Added connectivity datasets (per cap) to HDF5 optional output. 2006-09-02 09:31 luis * visual/h5tocombined.c: Opened all available cap groups outside the main loop. 2006-08-31 23:06 maweier * visual/Mayavi2, visual/Mayavi2/Citcoms_HdfDisplay.py, visual/Mayavi2/Citcoms_VtkDisplay.py, visual/Mayavi2/__init__.py, visual/Mayavi2/citcoms_hdf2vtk.py, visual/Mayavi2/plugins, visual/Mayavi2/plugins/CitcomHDFThread.py, visual/Mayavi2/plugins/CitcomSHDFUgrid.py, visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py, visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py, visual/Mayavi2/plugins/OpenCitcomSFILES.py, visual/Mayavi2/plugins/__init__.py, visual/Mayavi2/plugins/filter, visual/Mayavi2/plugins/filter/CitcomSFilterActions.py, visual/Mayavi2/plugins/filter/CitcomSSphere.py, visual/Mayavi2/plugins/filter/CitcomSreduce.py, visual/Mayavi2/plugins/filter/CitcomSshowCaps.py, visual/Mayavi2/plugins/filter/CitcomSshowSurface.py, visual/Mayavi2/plugins/filter/__init__.py, visual/Mayavi2/plugins/plugin_defs, visual/Mayavi2/plugins/plugin_defs/mayavi_ui_plugin_definition.py: New folder structure. 2006-08-31 23:05 maweier * visual/Mayavi2: Complete update to new Folder structure. 2006-08-31 14:56 luis * visual/h5tocombined.c: Added ability to output multiple timesteps (specified on command-line). 2006-08-31 13:28 luis * visual/h5tocombined.c: 1. Cleaned up code in general. 2. Fixed bug in reading coord dataset (need to do it for each cap!). 2006-08-29 23:44 maweier * visual/Mayavi2/citcoms_hdf2vtk.py, visual/Mayavi2/plugins/CitcomSHDFUgrid.py, visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py, visual/Mayavi2/plugins/filter/CitcomSshowCaps.py: More stable versions. Some performance enhancements. 2006-08-28 23:19 maweier * visual/Mayavi2/core/CitcomSHDFUgrid.pyc, visual/Mayavi2/core/__init__.pyc, visual/Mayavi2/filter/CitcomSFilterActions.pyc, visual/Mayavi2/filter/CitcomSSphere.pyc, visual/Mayavi2/filter/CitcomSreduce.pyc, visual/Mayavi2/filter/CitcomSshowCaps.pyc, visual/Mayavi2/filter/__init__.pyc, visual/Mayavi2/plugins/CitcomSHDFUgrid.pyc, visual/Mayavi2/plugins/CitcomS_hdf_file_reader.pyc, visual/Mayavi2/plugins/CitcomS_vtk_file_reader.pyc, visual/Mayavi2/plugins/OpenCitcomSFILES.pyc, visual/Mayavi2/plugins/__init__.pyc, visual/Mayavi2/plugins/filter/CitcomSFilterActions.pyc, visual/Mayavi2/plugins/filter/CitcomSSphere.pyc, visual/Mayavi2/plugins/filter/CitcomSreduce.pyc, visual/Mayavi2/plugins/filter/CitcomSshowCaps.pyc, visual/Mayavi2/plugins/filter/__init__.pyc, visual/Mayavi2/plugins/filter/showcaps.pyc: Deleting Bytecode Files 2006-08-28 23:17 maweier * visual/Mayavi2, visual/Mayavi2/HdfDisplay.py, visual/Mayavi2/VtkDisplay.py, visual/Mayavi2/__init__.py, visual/Mayavi2/citcoms_hdf2vtk.py, visual/Mayavi2/core, visual/Mayavi2/core/CitcomSHDFUgrid.py, visual/Mayavi2/core/CitcomSHDFUgrid.pyc, visual/Mayavi2/core/__init__.py, visual/Mayavi2/core/__init__.pyc, visual/Mayavi2/filter, visual/Mayavi2/filter/CitcomSFilterActions.py, visual/Mayavi2/filter/CitcomSFilterActions.pyc, visual/Mayavi2/filter/CitcomSSphere.py, visual/Mayavi2/filter/CitcomSSphere.pyc, visual/Mayavi2/filter/CitcomSreduce.py, visual/Mayavi2/filter/CitcomSreduce.pyc, visual/Mayavi2/filter/CitcomSshowCaps.py, visual/Mayavi2/filter/CitcomSshowCaps.pyc, visual/Mayavi2/filter/CitcomSshowSurface.py, visual/Mayavi2/filter/__init__.py, visual/Mayavi2/filter/__init__.pyc, visual/Mayavi2/plugins, visual/Mayavi2/plugins/CitcomSHDFUgrid.py, visual/Mayavi2/plugins/CitcomSHDFUgrid.pyc, visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py, visual/Mayavi2/plugins/CitcomS_hdf_file_reader.pyc, visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py, visual/Mayavi2/plugins/CitcomS_vtk_file_reader.pyc, visual/Mayavi2/plugins/OpenCitcomSFILES.py, visual/Mayavi2/plugins/OpenCitcomSFILES.pyc, visual/Mayavi2/plugins/__init__.py, visual/Mayavi2/plugins/__init__.pyc, visual/Mayavi2/plugins/filter, visual/Mayavi2/plugins/filter/CitcomSFilterActions.py, visual/Mayavi2/plugins/filter/CitcomSFilterActions.pyc, visual/Mayavi2/plugins/filter/CitcomSSphere.py, visual/Mayavi2/plugins/filter/CitcomSSphere.pyc, visual/Mayavi2/plugins/filter/CitcomSreduce.py, visual/Mayavi2/plugins/filter/CitcomSreduce.pyc, visual/Mayavi2/plugins/filter/CitcomSshowCaps.py, visual/Mayavi2/plugins/filter/CitcomSshowCaps.pyc, visual/Mayavi2/plugins/filter/CitcomSshowSurface.py, visual/Mayavi2/plugins/filter/__init__.py, visual/Mayavi2/plugins/filter/__init__.pyc, visual/Mayavi2/plugins/filter/showcaps.pyc, visual/Mayavi2/plugins/plugin_defs, visual/Mayavi2/plugins/plugin_defs/mayavi_ui_plugin_definition.py: Files for Mayavi2 plugins 2006-08-28 21:20 sue * doc/manual/citcoms.lyx, doc/manual/citcoms_cover.pdf: fixed man cover, removed pg no., fixed date, added table of figures, enabled URL hotlinks 2006-08-26 00:49 tan2 * lib/Full_boundary_conditions.c, lib/Full_parallel_related.c, lib/Full_version_dependent.c, lib/Phase_change.c, lib/Process_buoyancy.c, lib/Regional_boundary_conditions.c, lib/Regional_parallel_related.c, lib/Regional_version_dependent.c, lib/Size_does_matter.c, lib/Viscosity_structures.c: Flushed debugging output 2006-08-25 23:15 tan2 * doc/manual/citcoms.lyx: Improved the section of full CitcomS visualization. Fixed issue44 2006-08-24 23:46 luis * visual/estimate.py: Added script to estimate the size of the output from CitcomS. 2006-08-24 20:08 tan2 * CitcomS/CoupledApp.py, CitcomS/Layout.py: Renamed some attributes 2006-08-24 20:08 tan2 * CitcomS/Makefile.am: Updated file list 2006-08-24 19:40 tan2 * CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py, CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/Coupler/__init__.py: Changed the class names 2006-08-24 19:34 tan2 * CitcomS/Coupler/CoarseGridExchanger.py, CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py, CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/Coupler/Exchanger.py, CitcomS/Coupler/FineGridExchanger.py: Renamed *Exchanger.py to *Coupler.py 2006-08-24 19:31 tan2 * CitcomS/Components/Exchanger, CitcomS/Coupler, CitcomS/Coupler.py: Started refactoring Coupler and Exchanger ... 2006-08-24 19:27 tan2 * CitcomS/BaseApplication.py, CitcomS/CoupledApp.py, CitcomS/SimpleApp.py, CitcomS/Solver/CoupledFullSolver.py, CitcomS/Solver/CoupledRegionalSolver.py, CitcomS/Solver/CoupledSolver.py, CitcomS/Solver/Solver.py, CitcomS/Solver/__init__.py, bin/Makefile.am, bin/citcoms.in, bin/coupledcitcoms.in: * Refactored coupler-related codes from Solver.py to CoupledSolver.py * Created CoupledFullSolver.py and CoupledRegionalSolver.py * Refactored common codes between CoupledApp.py and SimpleApp.py to BaseApplication.py * Changed the facility names in CoupledApp.py * Created a coupledcitcoms script 2006-08-24 02:47 luis * lib/Output_h5.c, lib/hdf5_related.h: Added /cap/average/coord dataset 2006-08-23 23:24 luis * lib/Output_h5.c: Fixed silly typos. 2006-08-23 23:16 luis * lib/Output_h5.c, lib/hdf5_related.h: 1. Grouped horizontal average data into its own HDF5 group. 2. All datasets are referenced using relative paths (to its own cap group). 2006-08-22 18:24 luis * lib/Output_h5.c, lib/hdf5_related.h: Data buffer in field_t struct should be a float. 2006-08-22 13:08 luis * lib/Output_h5.c: 1. Fixed PyTables attributes for time dataset (bugfix) 2. Added surf and botm data (optional output) 3. Added horizontal averages (optional output) 2006-08-21 22:42 tan2 * lib/Output_h5.c: Added two attributes to /input group * 'scalev' : velocity scale, in cm/yr * 'scalet' : time scale, in Myrs 2006-08-21 21:38 luis * visual/h5tocombined.c: Added program to convert the HDF5 output file to the ASCII combined file, using the HDF5 C-API. 2006-08-18 18:43 tan2 * bin/Citcom.c, lib/Output.c, lib/Output_h5.c, lib/output.h, lib/output_h5.h, module/outputs.cc: Refactored and Merged output_pseudo_surf with output 2006-08-18 04:59 tan2 * CitcomS/Solver/Solver.py, bin/Citcom.c, lib/Instructions.c, lib/Output.c, lib/Output_h5.c, lib/global_defs.h, module/outputs.cc, module/setProperties.cc: * Closed E->fp_out properly * Fixed a bug when output_format is illegal * Added new input parameter "output_optional", which is a comma seperated list of fields to output. Currently, supported outputs are "pressure", "stress", "surf", "botm", and "average". * Changed the format of stress output to be consistent with other output 2006-08-15 21:50 sue * doc/manual/citcoms2.0.2.lyx, doc/manual/citcoms2.0.2.pdf, doc/manual/citcoms_cover2-0-2.pdf: deleted versioned files 2006-08-15 20:48 tan2 * lib/Citcom_init.c, lib/Instructions.c: Added 'output_format' input for stand-alone version 2006-08-15 20:46 tan2 * lib/global_defs.h: Commented out an unused include file 2006-08-15 20:14 sue * doc/manual/citcoms.lyx: one more cross-reference fix 2006-08-15 19:46 sue * doc/manual/citcoms.lyx: fixed tan's requests and recoded tables to use space better 2006-08-15 18:43 tan2 * doc/manual/citcoms.lyx: Fixed various typos/inconsistency/errors Added some comments (started with 'tan2:') 2006-08-15 14:02 luis * lib/Output_h5.c, lib/PyTables.c, lib/pytables.h: Fixed issues with time dataset. 2006-08-15 12:09 luis * lib/Output_h5.c, lib/hdf5_related.h: 1. Introduced field_t object, and updated the appropriate functions to use it. 2. Changed to independent parallel I/O for dataset writes. 3. Using collective calls to extend time-varying datasets (bugfix). 2006-08-15 06:26 tan2 * doc/manual/citcoms.lyx: Updated the status of multi-grid solver 2006-08-14 22:24 sue * doc/manual/citcoms.lyx: restored 2-sided page setting 2006-08-14 19:52 sue * doc/manual/citcoms.lyx: got appendices into toc 2006-08-14 19:29 sue * doc/manual/citcoms.lyx: changed margins and doc settings as requested 2006-08-14 11:52 luis * lib/Output_h5.c: 1. Switching default data transfer property to use independent parallel I/O. 2. Time-varying fields are now created without an extent along time-dimension. 3. Consolidated some debug statements into a single printf. 2006-08-14 11:22 luis * lib/Output_h5.c, lib/hdf5_related.h: Added step column to the /time table dataset. 2006-08-14 11:01 luis * lib/Output_h5.c: Determine hyperslab block size based on mpi process coordinates, not mpi process rank (bugfix). 2006-08-14 08:38 luis * lib/Output_h5.c, lib/PyTables.c, lib/pytables.h: Added some useful set_attribute*() functions. 2006-08-12 22:47 gurnis * lib/Full_boundary_conditions.c, lib/Lith_age.c: Fix bug associated with assimilating age grids in global models. Only relevant change was made in the subroutine full_temperature_boundary_condition() in which I now make a call to lith_age_temperature_bound_adj() if lith_age_time is on. 2006-08-12 02:37 luis * visual/h52combined.py: Rearranged (i,j,k) indices for consistency, i.e. to correspond to (x,y,z) coords instead of (y,x,z). Also, moved constant format string outside of the loop body. 2006-08-11 21:36 tan2 * doc/manual/citcoms.lyx: Fixed the status of CitcomS.py on TeraGrid 2006-08-11 20:28 sue * doc/manual/citcoms.lyx, doc/manual/citcoms_cover.pdf: added leif's gnu build sys additions 2006-08-11 20:05 sue * doc/manual/citcoms.lyx: incorporated tan2 changes/comments 2006-08-11 06:11 leif * visual/Makefile.am: Whoops -- macro references from visual/*.net must refer to subdirectory 'OpenDXMacro'. 2006-08-11 01:55 leif * bin/Makefile.am, bin/citcoms.in, configure.ac, visual/Makefile.am, visual/OpenDXMacro, visual/OpenDXMacro/Makefile.am: Build OpenDX macros in-place during 'make'. Remove 'citcoms' script during 'uninstall'. Also, partial fixes for MPICH2... one still needs to add -DMPICH_SKIP_MPICXX to CPPFLAGS, however; see issue14. 2006-08-10 20:48 sue * doc/manual/citcoms2.0.2.lyx, doc/manual/citcoms2.0.2.pdf, doc/manual/citcoms_cover2-0-2.pdf: added 2.0.2 manual draft and cover 2006-08-08 21:24 tan2 * lib/Output_h5.c, lib/PyTables.c: Made the code compile when configured --with-hdf5=no 2006-08-08 20:47 luis * configure.ac: Fix checks for hdf5.h and for parallel HDF5. Should now be performed only if --with-hdf5 is specified. 2006-08-08 04:55 ces74 * examples/Cookbook7/cookbook7.cfg: * fixed a bug in the module specification: - vsolver --> solver.vsolver - tsolver --> solver.tsolver. 2006-08-07 21:24 luis * lib/Output_h5.c, lib/hdf5_related.h: Added time dataset 2006-08-07 06:47 luis * configure.ac: Added configure check for Parallel-HDF5 2006-08-07 06:38 luis * lib/Makefile.am: Removed reference to nonexistent directory 2006-08-07 06:10 luis * bin/Makefile.am, configure.ac, lib/Citcom_init.c, lib/Makefile.am, lib/hdf5_related.h, module/Makefile.am: Changed configure script to compile everything with -DUSE_HDF5 when HDF5 support is enabled (--with-hdf5) 2006-08-07 04:56 luis * lib/Makefile.am, lib/global_defs.h, lib/hdf5_info.h, lib/hdf5_related.h: Need to maintain multiple structs in header file, so renaming hdf5_info.h to hdf5_related.h 2006-08-07 00:46 luis * lib/Output_h5.c: Commented out debug statements 2006-08-05 12:48 luis * lib/Output_h5.c: Added h5output_meta(), and saved to the HDF5 input group the same input parameters that are used in pyCitcom_*_set_properties(). 2006-08-05 12:43 luis * lib/PyTables.c, lib/pytables.h: Added set_attribute_numerical*() functions for creating numerical attributes (int, float, double, ...) on a specified HDF5 object. 2006-08-05 00:26 tan2 * visual/Makefile.am: Added h52combined.py to the install list 2006-08-05 00:14 tan2 * visual/h52combined.py: Added a script to convert the HDF5 output file to the ASCII combined file, using PyTables extension package. 2006-08-04 23:37 tan2 * lib/Advection_diffusion.c: Added some comments for filter() 2006-08-04 23:20 luis * lib/Output_h5.c: Output viscosity. 2006-08-04 23:13 luis * lib/Output_h5.c, lib/hdf5_info.h: Renamed E->hdf5.step to something less confusing: E->hdf5.count 2006-08-04 21:46 tan2 * CitcomS/Solver/Solver.py, bin/Citcom.c, lib/Output.c, lib/output.h, module/bindings.cc, module/outputs.cc, module/outputs.h: * Fixed skipped time output when monitoringFrequency > 1, which was introduced in r4118 * Forgot to change to the E->output function pointer in r4126 2006-08-03 14:14 luis * lib/Output_h5.c: Changed h5output() so that it prints an error if the C macro USE_HDF5 is not defined (and similarly for h5output_pseudo_surf()) 2006-08-03 14:03 luis * lib/Output_h5.c, lib/hdf5_info.h: Fix bug in behavior for values of monitoringFrequency > 1 by keeping an internal count of steps (Python does not pass monitoringFrequency to C code). 2006-08-03 11:17 luis * module/PyxMPI/PyxMPI.c: Regenerated PyxMPI.c with Pyrex 0.9.4 to fix GCC4 lvalue-casting error. 2006-08-03 11:14 luis * configure.ac: Fixed typo in configure.ac and added conditional check for hdf5.h header. 2006-08-03 04:22 luis * lib/Output_h5.c: 1. Disabled creation of surf & botm (temporary) 2. Only outputs (per cap) are currently coord, velocity & temperature fields 3. For clarity, added indentation to the debugging output 2006-08-03 03:05 luis * lib/Output_h5.c: Rewrote h5write_field(). 2006-08-03 02:31 luis * lib/Output_h5.c: Renamed h5write_array_hyperslab() to h5write_dataset() and fixed the comment describing the usage of h5create_field(). 2006-08-03 02:15 luis * lib/Output_h5.c: Rewrote h5create_field() to use indices instead of if-else branches when building the arguments (dims, maxdims, chunkdims) for dataset creation. 2006-08-03 01:43 luis * lib/Output_h5.c: In h5create_dataset(), renamed local variable filespace into dataspace. 2006-08-03 01:42 luis * lib/Output_h5.c: Renamed h5create_array() to h5create_dataset() and made sure that the datasets created by that function are compatibles with PyTables. 2006-08-03 01:30 luis * lib/Output_h5.c: Updated debug statements. 2006-08-03 01:05 luis * lib/Output_h5.c: Added h5create_file() and modified h5create_group() so that the files and groups created with these functions are compatible with PyTables. 2006-08-03 01:04 luis * lib/Makefile.am, lib/PyTables.c: Fixed typo in PyTables.c and added it to the sources in Makefile.am 2006-08-02 23:38 sue * doc/manual/citcoms.lyx: added cover image 2006-08-02 19:42 sue * doc/manual/citcoms.lyx, doc/manual/citcoms_book.xml, doc/manual/graphics.tar.gz: replace manual with lyx manual 2006-08-02 00:17 tan2 * lib/Instructions.c, lib/Output_h5.c: Open and close HDF5 output properly 2006-08-01 23:25 luis * lib/Output_h5.c: Added debug statements. 2006-08-01 23:17 luis * lib/pytables.h: Updated prototypes for the pytables-derived functions. 2006-08-01 23:09 luis * lib/global_defs.h: Added flags to control which data (viscosity,stress,pressure) gets written to output. 2006-08-01 22:50 luis * lib/hdf5_info.h: Consolidated buffers by size instead of by type. 2006-08-01 22:47 luis * lib/PyTables.c: Use strings as default HDF5 attribute type. 2006-08-01 19:21 tan2 * CitcomS/Solver/Solver.py, module/bindings.cc, module/outputs.cc, module/outputs.h: Closing output files in Solver.py 2006-08-01 19:06 tan2 * CitcomS/Components/Param.py, CitcomS/Solver/Solver.py, module/setProperties.cc: Moved the 'output_format' property from Param.py to Solver.py 2006-08-01 05:57 tan2 * CitcomS/Components/Param.py, module/outputs.cc, module/setProperties.cc: * Created pyre property for 'output_format' * Changed the output function pointer in the python binding 2006-08-01 00:54 luis * bin/Makefile.am, configure.ac, lib/Makefile.am: Added --with-hdf5 options to configure.ac. Also, modified Makefile.am so that Output_h5.o is compiled. 2006-08-01 00:23 tan2 * CitcomS/Controller.py, CitcomS/Solver/Solver.py, module/bindings.cc, module/misc.cc, module/misc.h: Completely fixed issue35 (inconsistent times) and related problems * t, dt, step are modified only in the C code. Their python counterparts are read-only * Changed the ancestor of the Controller from Pyre's SimulationController to Pyre's Component, as the SimulationController hinders the use of read-only properties * Changed the ancestor of the Solver from Pyre's Solver to Pyre's Component, as Pyre's Solver hinders the use of read-only properties 2006-07-31 23:07 tan2 * lib/Instructions.c: Changed the default value of 'layerd' from 2800 km (the depth of the mantle) to 6371 km (the radius of the Earth), which is necessary to dimensionalize the time 2006-07-31 23:04 tan2 * bin/Citcom.c, lib/Instructions.c, lib/global_defs.h, module/mesher.cc: Added logic to switch the E->output function pointer 2006-07-29 00:08 luis * lib/Output_h5.c: Added two methods for writing to HDF5 arrays (refactored from CitcomCU). 2006-07-28 22:12 luis * lib/Output_h5.c: Fixed typos in h5output_coord() 2006-07-28 22:06 tan2 * CitcomS/Solver/Solver.py: Removed unused variables due to refactoring of time output 2006-07-28 18:37 tan2 * lib/Output.c: Flushed the E->fptime stream after each output 2006-07-28 18:36 tan2 * lib/Instructions.c: Added missing function declaration 2006-07-27 22:02 tan2 * CitcomS/Controller.py, CitcomS/Solver/Solver.py, bin/Citcom.c, lib/Instructions.c, lib/Output.c, lib/global_defs.h, module/mesher.cc: Moved the responsibility of time output from Citcom.c and Solver.py to Output.c, which includes the following changes * open .time file at either mesher.cc (for pyre run) or Instructions.c (for C run) * .time file is opened and closed only by the rank-0 processor. This will avoid multiple processors opening/writing/closing on the same file. Similar modification is necessary for the .log file. * created two variables E->monitor.cpu_time_at_start and E->monitor.cpu_time_at_last_cycles for storing the wall clock time at startup and last timestep, respectively * output .time file in output_time() in Output.c 2006-07-27 21:06 luis * lib/Output_h5.c: Refactored code for array creation. 2006-07-27 21:04 luis * lib/hdf5_info.h: Eliminated unecessary buffer arrays. 2006-07-27 19:57 tan2 * examples/example0.cfg: forgot to change the 'datafile' parameter 2006-07-24 11:22 luis * lib/Output_h5.c: Prepare output functions for optional HDF5 configuration with autoconf. 2006-07-24 11:18 luis * lib/global_defs.h: Added output function pointer to All_variables struct. 2006-07-19 20:19 tan2 * examples/example0.cfg: example script of single-processor run 2006-07-19 18:42 luis * lib/global_defs.h, lib/hdf5_info.h: Created new hdf5 struct member within the All_variables struct. 2006-07-18 23:42 sue * doc/manual/graphics, doc/manual/graphics/c_fig1.eps, doc/manual/graphics/c_fig10.eps, doc/manual/graphics/c_fig2.eps, doc/manual/graphics/c_fig3.jpg, doc/manual/graphics/c_fig4.eps, doc/manual/graphics/c_fig5.eps, doc/manual/graphics/c_fig6.jpg, doc/manual/graphics/c_fig7.eps, doc/manual/graphics/c_fig8.eps, doc/manual/graphics/c_fig9.eps, doc/manual/graphics/cookbook1.2.jpg, doc/manual/graphics/cookbook1.eps, doc/manual/graphics/cookbook1.jpg, doc/manual/graphics/cookbook1.png, doc/manual/graphics/cookbook2.2.eps, doc/manual/graphics/cookbook2.2eps, doc/manual/graphics/cookbook2.eps, doc/manual/graphics/cookbook3.eps, doc/manual/graphics/cookbook4.eps, doc/manual/graphics/cookbook5.2.eps, doc/manual/graphics/cookbook5.eps, doc/manual/graphics/cookbook6.2.eps, doc/manual/graphics/cookbook6.eps, doc/manual/graphics/cookbook7.eps, doc/manual/graphics/eq1.eps, doc/manual/graphics/eq10.eps, doc/manual/graphics/eq11.eps, doc/manual/graphics/eq12.eps, doc/manual/graphics/eq13.eps, doc/manual/graphics/eq14.eps, doc/manual/graphics/eq15.eps, doc/manual/graphics/eq16.eps, doc/manual/graphics/eq17.eps, doc/manual/graphics/eq18.eps, doc/manual/graphics/eq19.eps, doc/manual/graphics/eq2.eps, doc/manual/graphics/eq20.2.eps, doc/manual/graphics/eq20.eps, doc/manual/graphics/eq21.eps, doc/manual/graphics/eq3.eps, doc/manual/graphics/eq4.eps, doc/manual/graphics/eq5.eps, doc/manual/graphics/eq6.eps, doc/manual/graphics/eq7.eps, doc/manual/graphics/eq8.eps, doc/manual/graphics/eq9.eps, doc/manual/graphics/exp1.eps, doc/manual/graphics/exp10.eps, doc/manual/graphics/exp11.eps, doc/manual/graphics/exp12.eps, doc/manual/graphics/exp2.eps, doc/manual/graphics/exp3.eps, doc/manual/graphics/exp4.eps, doc/manual/graphics/exp5.eps, doc/manual/graphics/exp6.eps, doc/manual/graphics/exp7.eps, doc/manual/graphics/exp8.eps, doc/manual/graphics/exp9.eps: adding graphics directory 2006-07-18 23:05 sue * doc/manual/citcoms_book.xml: updated dtd address 2006-07-18 01:00 luis * lib/PyTables.c, lib/pytables.h: Provide an API for creating PyTables-compatible HDF5 files. 2006-07-17 23:31 luis * lib/Output_h5.c, lib/output_h5.h: For the new HDF5 output format, use a similar API as in Output.c Copying the bodies from the old functions for now, but prefixing the function name with 'h5'. 2006-07-15 02:14 leif * CitcomS/SimpleApp.py: Bug fix in _getPrivateDepositoryLocations(); updated usage(). 2006-07-13 23:41 leif * examples/Cookbook1/cookbook1.cfg, examples/Cookbook1/cookbook1.sh, examples/Cookbook2/cookbook2.cfg, examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.cfg, examples/Cookbook3/cookbook3.sh, examples/Cookbook4/cookbook4.cfg, examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.cfg, examples/Cookbook5/cookbook5.sh, examples/Cookbook7/cookbook7.cfg, examples/Cookbook7/cookbook7.sh, examples/example1.sh, tests/Makefile.am, tests/citcomsfull.sh.in, tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Nuked citcoms{full,regional}.sh, coupledcitcoms.sh. Converted cookbook *.sh files to *.cfg files, and sprinkled-in some comments derived from the manual. 2006-07-13 20:06 leif * configure.ac: Fix for broken "make install" on Pangu (discovered by Lydia): add both 'pythondir' and 'pyexecdir' to PYTHONPATH/sys.path. 2006-07-07 23:54 leif * bin/pycitcoms.cc: Temporary work-around for broken _mpimodule on Pangu. 2006-07-07 23:07 tan2 * CitcomS/Controller.py: Renamed extension module (see r3983) 2006-07-07 22:35 leif * CitcomS/Components/Advection_diffusion/Advection_diffusion.py, CitcomS/Components/BC.py, CitcomS/Components/Const.py, CitcomS/Components/Exchanger/Exchanger.py, CitcomS/Components/Exchanger/Inlet.py, CitcomS/Components/Exchanger/Outlet.py, CitcomS/Components/IC.py, CitcomS/Components/Param.py, CitcomS/Components/Phase.py, CitcomS/Components/Sphere/FullSphere.py, CitcomS/Components/Sphere/RegionalSphere.py, CitcomS/Components/Sphere/Sphere.py, CitcomS/Components/Stokes_solver/Incompressible.py, CitcomS/Components/Tracer.py, CitcomS/Components/Visc.py, CitcomS/Makefile.am, CitcomS/SimpleApp.py, CitcomS/Solver/FullSolver.py, CitcomS/Solver/RegionalSolver.py, CitcomS/Solver/Solver.py, bin/Makefile.am, bin/citcoms.in, bin/pycitcoms.cc, module/CitcomSmodule.cc, module/CitcomSmodule.h, module/Exchanger/Exchangermodule.cc, module/Exchanger/Exchangermodule.h, module/Exchanger/Makefile.am, module/Full, module/Makefile.am, module/Regional, module/Regionalmodule.cc, module/advdiffu.cc, module/advdiffu.h, module/bindings.cc, module/bindings.h, module/exceptions.cc, module/exceptions.h, module/initial_conditions.cc, module/initial_conditions.h, module/mesher.cc, module/mesher.h, module/misc.cc, module/misc.h, module/outputs.cc, module/outputs.h, module/setProperties.cc, module/setProperties.h, module/stokes_solver.cc, module/stokes_solver.h, tests/exchange.py: Moved & renamed extension modules: CitcomS.CitcomS -> CitcomsLib CitcomS.Exchanger -> ExchangerLib Top-level modules allow easy toggling between embedding & extending without any special hacks in the embedding case. Also, it allows the Python scripts to be installed under 'libdir' instead of 'libexecdir', although this is a minor issue. Also: moved module/Regional/* source to module/* to really complete the Full/Regional merge (there is only one CitcomS extension module now). Plus, a bug fix in collectUserInput. 2006-07-07 21:36 tan2 * CitcomS/Controller.py, CitcomS/Solver/Solver.py, module/Regional/bindings.cc, module/Regional/misc.cc, module/Regional/misc.h: A quick fix to issue35 "inconsistent times in C and Pyre" 2006-07-07 00:54 leif * bin/Makefile.am, configure.ac, lib/Advection_diffusion.c, lib/BC_util.c, lib/Citcom_init.c, lib/Common, lib/Construct_arrays.c, lib/Convection.c, lib/Drive_solvers.c, lib/Element_calculations.c, lib/Full, lib/Full_boundary_conditions.c, lib/Full_geometry_cartesian.c, lib/Full_lith_age_read_files.c, lib/Full_obsolete.c, lib/Full_parallel_related.c, lib/Full_read_input_from_files.c, lib/Full_solver.c, lib/Full_sphere_related.c, lib/Full_version_dependent.c, lib/General_matrix_functions.c, lib/Global_operations.c, lib/Initial_temperature.c, lib/Instructions.c, lib/Interuption.c, lib/Lith_age.c, lib/Makefile.am, lib/Nodal_mesh.c, lib/Obsolete.c, lib/Output.c, lib/Pan_problem_misc_functions.c, lib/Parallel_util.c, lib/Parsing.c, lib/Phase_change.c, lib/Problem_related.c, lib/Process_buoyancy.c, lib/Regional, lib/Regional_boundary_conditions.c, lib/Regional_geometry_cartesian.c, lib/Regional_lith_age_read_files.c, lib/Regional_obsolete.c, lib/Regional_parallel_related.c, lib/Regional_read_input_from_files.c, lib/Regional_solver.c, lib/Regional_sphere_related.c, lib/Regional_version_dependent.c, lib/Shape_functions.c, lib/Size_does_matter.c, lib/Solver_conj_grad.c, lib/Solver_multigrid.c, lib/Sphere_harmonics.c, lib/Sphere_util.c, lib/Stokes_flow_Incomp.c, lib/Topo_gravity.c, lib/Tracer_advection.c, lib/Viscosity_structures.c, lib/advection.h, lib/advection_diffusion.h, lib/citcom_init.h, lib/convection_variables.h, lib/drive_solvers.h, lib/element_definitions.h, lib/global_defs.h, lib/initial_temperature.h, lib/interuption.h, lib/lith_age.h, lib/output.h, lib/parallel_related.h, lib/parsing.h, lib/phase_change.h, lib/solver.h, lib/sphere_communication.h, lib/temperature_descriptions.h, lib/tracer_defs.h, lib/viscosity_descriptions.h, module/Exchanger/Makefile.am, module/Makefile.am: Avoid shared libraries altogether when embedding. Shared libs are very likely to fail with static MPICH... this was confirmed when the link failed on Eh's iBook. Also completed the Full/Regional merge by flatting the directory structure under 'lib'. 2006-07-06 23:20 leif * CitcomS, CitcomS/Components, CitcomS/Components/Advection_diffusion, CitcomS/Components/Exchanger, CitcomS/Components/Sphere, CitcomS/Components/Stokes_solver, CitcomS/Makefile.am, CitcomS/SimpleApp.py, CitcomS/Solver, CitcomS/__init__.py, CitcomS/__init__.py.in, Makefile.am, bin/Makefile.am, configure.ac: Issue32: "make install" is now optional. Users can now simply "configure", "make", and then add the "bin" subdirectory of the source/build directory to their PATH. In this mode, changes to C/C++ simply require a "make" from the top-level directory ("make" from a subdirectory will not work in the near future). Changes to the Python code do not require you to run "make" at all -- simply re-run 'citcoms'. 2006-07-06 22:22 leif * CitcomS, bin, drivers, pyre: Renamed directories in preparation for next check-in: pyre -> CitcomS drivers -> bin This is to work-around this error message from 'svn': "new node revision ID without delete". I am not loving Subversion right now. Wasn't the whole point that it handles renames gracefully? 2006-07-06 18:16 leif * Make.mm, drivers/Full, drivers/Make.mm, drivers/Regional, drivers/local.def, etc/Make.mm, lib/Common/Make.mm, lib/Common/local.def, lib/Full/Make.mm, lib/Full/local.def, lib/Make.mm, lib/Regional/Make.mm, lib/Regional/local.def, lib/local.def, local.def, module/Exchanger/Make.mm, module/Full/Make.mm, module/Full/local.def, module/Make.mm, module/Regional/Make.mm, module/Regional/local.def, pyre/Components/Advection_diffusion/Make.mm, pyre/Components/Exchanger/Make.mm, pyre/Components/Make.mm, pyre/Components/Sphere/Make.mm, pyre/Components/Stokes_solver/Make.mm, pyre/Make.mm, pyre/Solver/Make.mm, pyre/local.def, tests/Make.mm, tests/local.def, visual/Make.mm: Nuked "Make.mm" files, which are no longer used. 2006-07-06 02:53 leif * examples/example1.cfg, pyre/Components/CodecConfig.py, pyre/Components/HackedConfigParser.py, pyre/Makefile.am, pyre/SimpleApp.py: Added the ability to use ".cfg" files instead of clumsy shell scripts for specifying parameters. Example usage: citcoms example1.cfg (The file 'example1.cfg' is checked-in under 'examples'.) The code which made this possible was copied & pasted from Specfem project; it will be factored-out into a shared package at some point... 2006-07-06 02:16 leif * Makefile.am, configure.ac, drivers/Citcom.c, drivers/Makefile.am, drivers/citcoms.in, drivers/pycitcoms.cc, etc/CitcomS.pml.in, etc/Makefile.am, lib/Common/Advection_diffusion.c, lib/Common/BC_util.c, lib/Common/Construct_arrays.c, lib/Common/Convection.c, lib/Common/Element_calculations.c, lib/Common/General_matrix_functions.c, lib/Common/Initial_temperature.c, lib/Common/Instructions.c, lib/Common/Lith_age.c, lib/Common/Makefile.am, lib/Common/Nodal_mesh.c, lib/Common/Parallel_util.c, lib/Common/Problem_related.c, lib/Common/Process_buoyancy.c, lib/Common/Size_does_matter.c, lib/Common/Solver_multigrid.c, lib/Common/Sphere_util.c, lib/Common/global_defs.h, lib/Common/lith_age.h, lib/Common/parallel_related.h, lib/Common/solver.h, lib/Full/Boundary_conditions.c, lib/Full/Geometry_cartesian.c, lib/Full/Lith_age.c, lib/Full/Lith_age_read_files.c, lib/Full/Makefile.am, lib/Full/Parallel_related.c, lib/Full/Read_input_from_files.c, lib/Full/Solver.c, lib/Full/Sphere_related.c, lib/Full/Version_dependent.c, lib/Makefile.am, lib/Regional/Boundary_conditions.c, lib/Regional/Geometry_cartesian.c, lib/Regional/Lith_age.c, lib/Regional/Lith_age_read_files.c, lib/Regional/Makefile.am, lib/Regional/Parallel_related.c, lib/Regional/Read_input_from_files.c, lib/Regional/Solver.c, lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c, module/CitcomSmodule.cc, module/CitcomSmodule.h, module/Exchanger/Exchangermodule.cc, module/Exchanger/Exchangermodule.h, module/Exchanger/Makefile.am, module/Full/Makefile.am, module/Makefile.am, module/PyxMPI, module/PyxMPI/PyxMPI.c, module/PyxMPI/PyxMPI.pyx, module/PyxMPI/cmpi.pxd, module/Regional/Makefile.am, module/Regional/bindings.cc, module/Regional/mesher.cc, module/Regional/misc.cc, module/Regional/misc.h, pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/BC.py, pyre/Components/CitcomComponent.py, pyre/Components/Const.py, pyre/Components/IC.py, pyre/Components/Launchers.py, pyre/Components/Param.py, pyre/Components/Phase.py, pyre/Components/Sphere/FullSphere.py, pyre/Components/Sphere/RegionalSphere.py, pyre/Components/Sphere/Sphere.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Components/Tracer.py, pyre/Components/Visc.py, pyre/SimpleApp.py, pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py, tests/Makefile.am, tests/citcomsfull.sh.in, tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Added the capability to embed Python instead of extending it. This creates one, big monolithic executable, 'pycitcoms', which contains all CitcomS code and an embedded Python interpreter. Embedding works-around MPI portability issues. (See issue15 for details.) Embed by default. Configure with '--disable-embedding' to build the old way with ".so" extension modules. This is *NOT* guaranteed to work unless you have a shared MPI library. The ugly hacks which made it work in the past (even with a static "libmpich.a", for example) are no longer supported. Merged "Full" and "Regional" into a single library to cut down on redundancy, both in the source code and in the amount of object code which is produced. (I performed this merge so that I would only need a single 'pycitcoms' intepreter, instead of two.) 2006-06-12 17:43 gurnis * lib/Common/Advection_diffusion.c, lib/Common/Initial_temperature.c, lib/Common/Problem_related.c, lib/Full/Read_input_from_files.c, pyre/Solver/Solver.py: Fixed restart_tic() in Initial_temperature.c so that time is correctly read in while using the lith_ages 2006-06-02 23:38 gurnis * lib/Full/Boundary_conditions.c, lib/Full/Lith_age.c, lib/Regional/Boundary_conditions.c, lib/Regional/Lith_age.c: Fixed bugs associated assimilating lith_age files into Full. Slightly improved method of assimilating lith_age 2006-05-18 18:05 cassie * doc/manual/citcoms_book.xml: typo in manual corrected 2006-05-16 19:50 cassie * doc/manual/citcoms_book.xml: additional minor updates to manual 2006-05-16 18:36 cassie * doc/manual/citcoms_book.xml: minor updates to manual 2006-04-18 23:34 luis * lib/Full/Obsolete.c: Fixed typos. 2006-03-28 19:22 walter * .: Changed externals from svn:// to http:// 2006-02-14 23:24 leif * ChangeLog, NEWS: Updated NEWS and ChangeLog. 2006-02-14 22:24 leif * pyre/SimpleApp.py, tests/Makefile.am, tests/citcomsfull.sh.in, tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Merged r2600 (fix for issue13, "make PYTHONPATH automatic") from v2 branch to trunk. 2006-02-04 02:11 luis * doc/manual/citcoms_book.xml: Fixed about 20 assorted typos. 2006-02-04 00:18 luis * lib/Regional/Version_dependent.c: Eliminated the unused local variables lx,ly,lz in global_derived_values(). 2006-02-04 00:15 luis * lib/Full/Version_dependent.c: The value of max_size needs to be larger by 1, or else we access out-of-bound array elements in the arrays E->boundary.element and E->boundary.normal. Refer to issue10 in roundup for more details. 2006-02-04 00:11 luis * lib/Common/global_defs.h: Adjusted size of arrays in struct Shape_function_dA. This fixes a bug involving out-of-bounds array access caused by use of fortran-style indexing. Refer to issue10 in roundup for more information. 2006-02-04 00:04 luis * lib/Common/Citcom_init.c: Need to initialize to zero the following variables * E->control.total_iteration_cycles * E->control.total_v_solver_calls 2006-01-31 23:16 leif * pyre/Components/Launchers.py: Merged r2575 (fix for issue9, "need a property for extra LSF options") from v2 branch to trunk. 2006-01-31 20:23 leif * pyre/Components/Launchers.py: Merged r2573 (fix for issue8, "eliminate CitcomS default time limit for batch jobs") from v2 branch to trunk. 2006-01-31 02:54 leif * configure.ac, etc/Makefile.am, pyre/Makefile.am, tests/Makefile.am, tests/citcomsfull.sh.in, tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Merged r2565 (fix for issue11, "broken install when 'pkgpyexecdir' is distinct from 'pkgpythondir'") from v2 branch to trunk. 2006-01-31 00:07 leif * configure.ac: Merged r2563 (fix for issue7, "CitcomS check_CXX check is broken") from v2 branch to trunk. 2005-11-17 19:14 luis * examples/Cookbook2/cookbook2.sh: Corrected typo. Should be: --solver.bc.topvbyval=0 2005-11-17 00:35 luis * doc/manual/citcoms_book.xml: boundition --> boundary condition 2005-11-16 02:23 leif * pyre/Components/IC.py: Fixed a bug which Luis found ("--solver.ic.help-properties"): bad default values for blob_radius and blob_dT. 2005-11-09 18:53 leif * doc/manual/citcoms_book.xml: Regenerated PDF. 2005-11-09 12:15 luis * doc/manual/citcoms_book.xml: Fixed example 5.6 in Cookbook 5 2005-11-09 11:45 luis * doc/manual/citcoms_book.xml: Fixed a few more typos. 2005-11-09 11:31 luis * doc/manual/citcoms_book.xml: Missed a stray = 2005-11-09 11:20 luis * doc/manual/citcoms_book.xml: Corrected several typos and mispelling errors. 2005-11-04 19:39 leif * doc/manual/citcoms_book.xml: Regenerated PDF: updated date; minor corrections, format tweaks. 2005-11-03 00:26 tan2 * doc/manual/citcoms_book.xml: fixed a bug in closing 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, 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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, 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mc/3D/CitcomS/branches/v2/tests/citcomsregional.sh, mc/3D/CitcomS/branches/v2/tests/citcomsregional.sh.in, mc/3D/CitcomS/branches/v2/tests/hrothgar.py, mc/3D/CitcomS/branches/v2/tests/local.def, mc/3D/CitcomS/branches/v2/tests/signon.py, mc/3D/CitcomS/branches/v2/visual/Make.mm, mc/3D/CitcomS/branches/v2/visual/Makefile.am, mc/3D/CitcomS/branches/v2/visual/batchcombine.py, mc/3D/CitcomS/branches/v2/visual/batchpaste.sh, mc/3D/CitcomS/branches/v2/visual/batchsurf.py, mc/3D/CitcomS/branches/v2/visual/combine.py, mc/3D/CitcomS/branches/v2/visual/combinesurf.py, mc/3D/CitcomS/branches/v2/visual/dxgeneral.sh, mc/3D/CitcomS/branches/v2/visual/dxgeneralsurf.sh, mc/3D/CitcomS/branches/v2/visual/getcoord.sh, mc/3D/CitcomS/branches/v2/visual/getlog.sh, mc/3D/CitcomS/branches/v2/visual/getsurf.sh, mc/3D/CitcomS/branches/v2/visual/pasteCitcomData.sh, Makefile.am, tests/Make.mm: Ported GNU Build System from CitcomS trunk to v2 branch. 2005-10-04 00:34 leif * pyre/Controller, pyre/Coupler, pyre/Facilities, pyre/Layout: Nuked empty directories. 2005-10-01 01:17 leif * ChangeLog: Strip "mc/3D/CitcomS/trunk" directory prefix. By the way, this file is generated with svn2cl (http://ch.tudelft.nl/~arthur/svn2cl/) using the command "svn log --xml --verbose | xsltproc --stringparam strip-prefix mc/3D/CitcomS/trunk svn2cl.xsl - > ChangeLog". 2005-10-01 01:01 leif * AUTHORS, COPYING, ChangeLog, CitcomS.py-LICENSE.txt, INSTALL, NEWS, README: Added various GNU standard files, including the GPL. 2005-09-30 23:48 leif * module/Full: Doh! Restored svn:ignore'ing of those ridiculous symlinks used by Make.mm. 2005-09-30 22:39 leif * ., drivers, etc, examples, lib, lib/Common, lib/Full, lib/Regional, module, module/Exchanger, module/Full, module/Regional, pyre, tests, visual: Ignore files generated by Autoconf/Automake/Libtool. 2005-09-30 17:59 leif * configure.ac: Push/pop C++ around MPI tests, which are now sensitive to the current language. Made sure that '--without-pyre' works in the absence of a C++ compiler (tested on Hrothgar). When building with Pyre modules, fail if a C++ compiler is not found. 2005-09-28 23:26 leif * configure.ac, etc/CitcomS.pml.in, etc/Make.mm, etc/Makefile.am, pyre/Components/Launchers.py, pyre/CoupledApp.py, pyre/Make.mm, pyre/Makefile.am, pyre/SimpleApp.py, pyre/__init__.py, pyre/__init__.py.in, tests/Make.mm, tests/Makefile.am, tests/citcomsfull.sh.in, tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Add ${pythondir} to PYTHONPATH before checking for Python modules, so that installing multiple packages to a single PREFIX "just works". This also attempts to simulate the final installation environment, which might make a difference in unusual cases. Also, 'sed' the install-time PYTHONPATH into CitComS scripts (instead of an explicit list of @pythondir@'s). Added _getPrivateDepositoryLocations() and CitcomS.pml. Changed "etc/citcoms" to "etc/CitcomS" for consistency with the Python package name. Add PACKAGE_VERSION to __init__.py, and added pyconfig-generated config.py. Freeze the full path to 'mpirun' and 'mpipython.exe' at 'configure' time. First crack at batch system configuration. 2005-09-21 00:03 leif * Makefile.am, configure.ac, lib/Common/Pan_problem_misc_functions.c, lib/Common/Tracer_advection.c, module/Exchanger/Makefile.am, module/Full/Makefile.am, module/Regional/Makefile.am, tests/Make.mm, tests/Makefile.am, tests/citcomsfull.sh.in, tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Utilize my new 'pyconfig' facility to automatically slurp config info from Pythia, Exchanger. Changed contact e-mail to cig-mc; other misc. changes. 2005-09-09 19:49 leif * Makefile.am, configure.ac, drivers/Makefile.am, etc/Makefile.am, examples/Makefile.am, lib/Common/Makefile.am, lib/Full/Makefile.am, lib/Makefile.am, lib/Regional/Makefile.am, module/Exchanger/Makefile.am, module/Full/Makefile.am, module/Makefile.am, module/Regional/Makefile.am, pyre/Makefile.am, tests/Makefile.am, visual/Makefile.am: Added Id keyword property to configure.ac, Makefile.am. 2005-09-09 19:41 leif * ., Makefile.am, configure.ac, drivers/Makefile.am, etc/Makefile.am, examples/Makefile.am, lib/Common/Makefile.am, lib/Full/Makefile.am, lib/Makefile.am, lib/Regional/Makefile.am, module/Exchanger/Makefile.am, module/Full, module/Full/Make.mm, module/Full/Makefile.am, module/Make.mm, module/Makefile.am, module/Regional/Makefile.am, pyre/Components/Launchers.py, pyre/Makefile.am, pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py, tests/Make.mm, tests/Makefile.am, tests/citcomsfull.sh, tests/citcomsfull.sh.in, tests/citcomsregional.sh, tests/citcomsregional.sh.in, tests/coupledcitcoms.sh, tests/coupledcitcoms.sh.in, visual/Makefile.am: Added files for the GNU Build System. 2005-08-29 19:28 leif * Make.mm, citcoms_profile, drivers/Full/Make.mm, drivers/Full/local.def, drivers/Make.mm, drivers/Regional/Make.mm, drivers/Regional/local.def, drivers/local.def, etc/Make.mm, etc/__vault__.odb, etc/full-sphere.odb, etc/full.odb, etc/globus.odb, etc/incomp-newtonian.odb, etc/incomp-non-newtonian.odb, etc/lam-mpi.odb, etc/lsf.odb, etc/mpich.odb, etc/pbs.odb, etc/regional-sphere.odb, etc/regional.odb, etc/temp.odb, examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh, examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh, examples/Cookbook7/cookbook7.sh, examples/example1.sh, lib/Common/Element_calculations.c, lib/Common/Make.mm, lib/Common/Obsolete.c, lib/Common/Size_does_matter.c, lib/Common/Topo_gravity.c, lib/Common/local.def, lib/Full/Boundary_conditions.c, lib/Full/Make.mm, lib/Full/local.def, lib/Make.mm, lib/Regional/Boundary_conditions.c, lib/Regional/Make.mm, lib/Regional/local.def, lib/local.def, local.def, module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/AreaWeightedNormal.h, module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/BoundaryVTInlet.cc, module/Exchanger/BoundaryVTInlet.h, module/Exchanger/CitcomInterpolator.cc, module/Exchanger/CitcomInterpolator.h, module/Exchanger/CitcomSource.cc, module/Exchanger/CitcomSource.h, module/Exchanger/Convertor.cc, module/Exchanger/Convertor.h, module/Exchanger/Exchangermodule.cc, module/Exchanger/Interior.cc, module/Exchanger/Interior.h, module/Exchanger/Make.mm, module/Exchanger/SIUnit.cc, module/Exchanger/SIUnit.h, module/Exchanger/SInlet.cc, module/Exchanger/SInlet.h, module/Exchanger/SVTInlet.cc, module/Exchanger/SVTInlet.h, module/Exchanger/SVTOutlet.cc, module/Exchanger/SVTOutlet.h, module/Exchanger/TInlet.cc, module/Exchanger/TInlet.h, module/Exchanger/TOutlet.cc, module/Exchanger/TOutlet.h, module/Exchanger/VOutlet.cc, module/Exchanger/VOutlet.h, module/Exchanger/VTInlet.cc, module/Exchanger/VTInlet.h, module/Exchanger/VTOutlet.cc, module/Exchanger/VTOutlet.h, module/Exchanger/bindings.cc, module/Exchanger/bindings.h, module/Exchanger/exceptions.cc, module/Exchanger/exceptions.h, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h, module/Exchanger/global_bbox.cc, module/Exchanger/global_bbox.h, module/Exchanger/initTemperature.cc, module/Exchanger/initTemperature.h, module/Exchanger/inlets_outlets.cc, module/Exchanger/inlets_outlets.h, module/Exchanger/misc.cc, module/Exchanger/misc.h, module/Full/Fullmodule.cc, module/Full/Make.mm, module/Full/local.def, module/Make.mm, module/Regional/Make.mm, module/Regional/Regionalmodule.cc, module/Regional/advdiffu.cc, module/Regional/advdiffu.h, module/Regional/bindings.cc, module/Regional/bindings.h, module/Regional/exceptions.cc, module/Regional/exceptions.h, module/Regional/initial_conditions.cc, module/Regional/initial_conditions.h, module/Regional/local.def, module/Regional/mesher.cc, module/Regional/mesher.h, module/Regional/misc.cc, module/Regional/misc.h, module/Regional/outputs.cc, module/Regional/outputs.h, module/Regional/setProperties.cc, module/Regional/setProperties.h, module/Regional/stokes_solver.cc, module/Regional/stokes_solver.h, pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/Advection_diffusion/Make.mm, pyre/Components/Advection_diffusion/__init__.py, pyre/Components/BC.py, pyre/Components/CitcomComponent.py, pyre/Components/Const.py, pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, pyre/Components/Exchanger/Inlet.py, pyre/Components/Exchanger/Make.mm, pyre/Components/Exchanger/Outlet.py, pyre/Components/Exchanger/__init__.py, pyre/Components/IC.py, pyre/Components/Launchers.py, pyre/Components/Make.mm, pyre/Components/Param.py, pyre/Components/Phase.py, pyre/Components/Sphere/FullSphere.py, pyre/Components/Sphere/Make.mm, pyre/Components/Sphere/RegionalSphere.py, pyre/Components/Sphere/Sphere.py, pyre/Components/Sphere/__init__.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Components/Stokes_solver/Make.mm, pyre/Components/Stokes_solver/__init__.py, pyre/Components/Tracer.py, pyre/Components/Visc.py, pyre/Components/__init__.py, pyre/CoupledApp.py, pyre/Coupler.py, pyre/Layout.py, pyre/Make.mm, pyre/SimpleApp.py, pyre/Solver/FullSolver.py, pyre/Solver/Make.mm, pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py, pyre/Solver/__init__.py, pyre/__init__.py, pyre/local.def, tests/Make.mm, tests/array2d.cc, tests/asap.py, tests/citcomsfull.sh, tests/citcomsregional.sh, tests/coupledcitcoms.sh, tests/exchange.py, tests/hrothgar.py, tests/local.def, tests/signon.py, tests/test1.sh, tests/test2.sh, tests/test5.sh, visual/Make.mm, visual/autocombine.py, visual/batchcombine.py, visual/batchpaste.sh, visual/batchsurf.py, visual/combine.py, visual/combinesurf.py, visual/dxgeneral.sh, visual/dxgeneralsurf.sh, visual/getcoord.sh, visual/getlog.sh, visual/getsurf.sh, visual/miff2avi, visual/miff2mpg, visual/parser.py, visual/pasteCitcomData.sh, visual/zslice.py: Added executable property and 'Id' keyword expansion. 2005-08-27 03:04 leif * lib/Common/advection_diffusion.h, lib/Common/citcom_init.h, lib/Common/drive_solvers.h, lib/Common/global_defs.h, lib/Common/output.h, lib/Common/parallel_related.h, module/Regional/advdiffu.cc, module/Regional/initial_conditions.cc, module/Regional/mesher.cc, module/Regional/misc.cc, module/Regional/outputs.cc, module/Regional/stokes_solver.cc: Avoid 'extern "C" { #include ... }'; it causes problems with mpi++.h/mpicxx.h. 2005-07-27 08:58 leif * etc/mpich.odb, pyre/Components/Launchers.py, pyre/SimpleApp.py: Fixed it so that the uniprocessor examples work again. This invovled creating CitcomS's own version of LauncherMPICH, and tweaking the MPI launchers so that CitcomS re-execs itself under 'mpipython.exe' when it is run under plain old 'python'. Also: made "--launcher.dry" work; ignore 'nodegen' in LauncherBatch (so that the examples "just work" on the TeraGrid); added some 'tips' ("--launcher.help-properties"); added SimpleApp.usage(). 2005-07-23 08:35 leif * Make.mm, examples/Cookbook1/cookbook1.sh, examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh, examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh, examples/example1.sh, tests/Make.mm, tests/array2d.cc, visual/Make.mm: General build clean-up: 'export' all the various scripts to $EXPORT_ROOT/bin, so that goofy relative paths are not needed (e.g., "../tests/citcomsregional.sh"); and so that the 'visual' directory doesn't have to be added to the PATH. I also dusted-off 'array2d' -- it compiles and links now. 2005-07-23 08:00 leif * module/Regional/misc.cc: Raise an exception -- instead of crashing -- when pyCitcom_citcom_init() is passed a null "mpi::Communicator *" argument. 2005-07-22 10:03 leif * pyre/Components/Launchers.py: Switched from Python's '%' operator to pyre.util.expandMacros(), so that I don't have to escape '%' (e.g., --launcher.nodegen="n%03d"). Also, export key environment variables to LAM/MPI jobs. 2005-07-22 05:55 leif * lib/Common/Make.mm, lib/Common/local.def, lib/Full/Make.mm, lib/Full/local.def, lib/Regional/Make.mm, lib/Regional/local.def: Build with soflags to produce position-independent code. 'Export' the resulting shared libraries. 2005-07-20 04:23 leif * tests/citcomsfull.sh, tests/citcomsregional.sh, tests/coupledcitcoms.sh: Use 'python' instead of 'mpipython.exe' -- on some TeraGrid clusters, MPI programs cannot be run directly. 2005-07-20 04:12 leif * examples/ncsa.sh, examples/tacc.sh: Removed sample batch scripts, which are obsoleted by my new launchers. Use "--launcher=pbs" or "--launcher=lsf" on NCSA and TACC, respectively. 2005-07-20 04:07 leif * etc/Make.mm, etc/globus.odb, etc/lam-mpi.odb, etc/lsf.odb, etc/mpich.odb, etc/pbs.odb, pyre/Components/Launchers.py, pyre/Components/Make.mm: Added Pyre launchers for LAM/MPI, Globus, LSF, and PBS. This is their temporary home; they should be incorporated into Pyre eventually. 2005-07-20 03:55 leif * visual/batchpaste.sh: Merged revision 1.5.2.1 from CitcomS-2_x branch to trunk: tan2: "a fix for single-processor (eg. laptop)". 2005-06-30 08:31 leif * lib/Common/global_defs.h, module/Exchanger/Make.mm, module/Full/Make.mm, module/Regional/Make.mm: Changes for Mac OS X build. 2005-08-23 03:42 unknown_user * pyre/Facilities/Make.mm, pyre/Facilities/Mesher.py, pyre/Facilities/Solver.py, pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py, pyre/Facilities/__init__.py: [vcp] delete of edited revision with dead state 2005-06-18 04:24 leif * pyre/Facilities/Make.mm, pyre/Facilities/Mesher.py, pyre/Facilities/Solver.py, pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py, pyre/Facilities/__init__.py, pyre/Make.mm: Removed 'Facilities' directory -- no longer needed under Pythia v0.8. 2005-06-18 04:20 leif * examples/ncsa.sh, examples/tacc.sh: Added example batch scripts for NCSA and TACC TeraGrid clusters. 2005-06-18 02:07 ces74 * visual/visFull.cfg, visual/visFull.net, visual/visRegional.cfg, visual/visRegional.net, visual/visRegionalSurface.cfg, visual/visRegionalSurface.net: * removed default paths to input/output files. * removed absolute paths to macros. 2005-06-16 02:33 tan2 * visual/autocombine.py: script to automatically read input parameters from input file and call batchcombine.py 2005-06-16 02:33 tan2 * visual/batchcombine.py: 1. moved parts of the script into functions so that other scripts can import them. 2. raise ValueError when the length of machinefile is not right 2005-06-16 02:30 tan2 * visual/parser.py: using new-style class 2005-06-16 01:27 tan2 * pyre/Components/Sphere/Sphere.py, pyre/Solver/Solver.py: print messages to stderr instead of stdout 2005-06-14 23:47 leif * module/Full/Make.mm, module/Regional/Make.mm: Corrected use of -Xlinker. 2005-06-10 09:23 leif * CitcomS.py-LICENSE.txt, drivers/Citcom.c, drivers/Full/Make.mm, drivers/Full/local.def, drivers/Make.mm, drivers/Regional/Make.mm, drivers/Regional/local.def, drivers/local.def, etc/Make.mm, etc/__vault__.odb, etc/full-sphere.odb, etc/full.odb, etc/incomp-newtonian.odb, etc/incomp-non-newtonian.odb, etc/regional-sphere.odb, etc/regional.odb, etc/temp.odb, examples/Cookbook1/cookbook1.sh, examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh, examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh, examples/Cookbook7/cookbook7.sh, examples/example1.sh, lib/Common/Advection_diffusion.c, lib/Common/Citcom_init.c, lib/Common/Construct_arrays.c, lib/Common/Convection.c, lib/Common/Drive_solvers.c, lib/Common/Element_calculations.c, lib/Common/General_matrix_functions.c, lib/Common/Global_operations.c, lib/Common/Initial_temperature.c, lib/Common/Instructions.c, lib/Common/Interuption.c, lib/Common/Make.mm, lib/Common/Nodal_mesh.c, lib/Common/Obsolete.c, lib/Common/Output.c, lib/Common/Pan_problem_misc_functions.c, lib/Common/Parsing.c, lib/Common/Phase_change.c, lib/Common/Problem_related.c, lib/Common/Process_buoyancy.c, lib/Common/Shape_functions.c, lib/Common/Size_does_matter.c, lib/Common/Solver_conj_grad.c, lib/Common/Solver_multigrid.c, lib/Common/Sphere_harmonics.c, lib/Common/Stokes_flow_Incomp.c, lib/Common/Topo_gravity.c, lib/Common/Tracer_advection.c, lib/Common/Viscosity_structures.c, lib/Common/advection.h, lib/Common/advection_diffusion.h, lib/Common/citcom_init.h, lib/Common/convection_variables.h, lib/Common/drive_solvers.h, lib/Common/element_definitions.h, lib/Common/global_defs.h, lib/Common/initial_temperature.h, lib/Common/interuption.h, lib/Common/lith_age.h, lib/Common/local.def, lib/Common/output.h, lib/Common/parallel_related.h, lib/Common/parsing.h, lib/Common/phase_change.h, lib/Common/sphere_communication.h, lib/Common/temperature_descriptions.h, lib/Common/tracer_defs.h, lib/Common/viscosity_descriptions.h, lib/Full/Boundary_conditions.c, lib/Full/Geometry_cartesian.c, lib/Full/Lith_age.c, lib/Full/Make.mm, lib/Full/Obsolete.c, lib/Full/Parallel_related.c, lib/Full/Read_input_from_files.c, lib/Full/Sphere_related.c, lib/Full/Version_dependent.c, lib/Full/local.def, lib/Make.mm, lib/Regional/Boundary_conditions.c, lib/Regional/Geometry_cartesian.c, lib/Regional/Lith_age.c, lib/Regional/Make.mm, lib/Regional/Obsolete.c, lib/Regional/Parallel_related.c, lib/Regional/Read_input_from_files.c, lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c, lib/Regional/local.def, lib/local.def, module/Full/Fullmodule.cc, module/Full/Make.mm, module/Full/local.def, module/Make.mm, module/Regional/Make.mm, module/Regional/Regionalmodule.cc, module/Regional/advdiffu.cc, module/Regional/advdiffu.h, module/Regional/bindings.cc, module/Regional/bindings.h, module/Regional/exceptions.cc, module/Regional/exceptions.h, module/Regional/initial_conditions.cc, module/Regional/initial_conditions.h, module/Regional/local.def, module/Regional/mesher.cc, module/Regional/mesher.h, module/Regional/misc.cc, module/Regional/misc.h, module/Regional/outputs.cc, module/Regional/outputs.h, module/Regional/setProperties.cc, module/Regional/setProperties.h, module/Regional/stokes_solver.cc, module/Regional/stokes_solver.h, pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/Advection_diffusion/Make.mm, pyre/Components/Advection_diffusion/__init__.py, pyre/Components/BC.py, pyre/Components/CitcomComponent.py, pyre/Components/Const.py, pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, pyre/Components/Exchanger/Inlet.py, pyre/Components/Exchanger/Make.mm, pyre/Components/Exchanger/Outlet.py, pyre/Components/Exchanger/__init__.py, pyre/Components/IC.py, pyre/Components/Make.mm, pyre/Components/Param.py, pyre/Components/Phase.py, pyre/Components/Sphere/FullSphere.py, pyre/Components/Sphere/Make.mm, pyre/Components/Sphere/RegionalSphere.py, pyre/Components/Sphere/Sphere.py, pyre/Components/Sphere/__init__.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Components/Stokes_solver/Make.mm, pyre/Components/Stokes_solver/__init__.py, pyre/Components/Tracer.py, pyre/Components/Visc.py, pyre/Components/__init__.py, pyre/Controller.py, pyre/CoupledApp.py, pyre/Coupler.py, pyre/Facilities/Make.mm, pyre/Facilities/Mesher.py, pyre/Facilities/Solver.py, pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py, pyre/Facilities/__init__.py, pyre/Layout.py, pyre/Make.mm, pyre/SimpleApp.py, pyre/Solver/FullSolver.py, pyre/Solver/Make.mm, pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py, pyre/Solver/__init__.py, pyre/__init__.py, pyre/local.def, tests/Make.mm, tests/array2d.cc, tests/asap.py, tests/citcomsfull.sh, tests/citcomsregional.sh, tests/coupledcitcoms.sh, tests/exchange.py, tests/hrothgar.py, tests/local.def, tests/signon.py, tests/test1.sh, tests/test2.sh, tests/test5.sh, visual/batchcombine.py, visual/batchpaste.sh, visual/batchsurf.py, visual/combine.py, visual/combinesurf.py, visual/dxgeneral.sh, visual/dxgeneralsurf.sh, visual/getcoord.sh, visual/getlog.sh, visual/getsurf.sh, visual/parser.py, visual/pasteCitcomData.sh, visual/zslice.py: Added license text. 2005-06-08 11:02 tan2 * examples/Cookbook5/cookbook5.sh: 1. subsitute 'staging' with 'launcher' as required by pythia-0.8 2. removed unneccesary input parameters 2005-06-08 08:55 leif * pyre/CoupledApp.py, pyre/SimpleApp.py, pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: Port from pythia-0.4 to pythia-0.8, continued: use "factory=" instead of "default=" in facilities where appropriate. The scripts example1.sh and test5.sh seem to work now. 2005-06-06 06:41 tan2 * visual/parser.py: Parser class to parse CitcomS input file 2005-06-06 06:13 tan2 * visual/batchpaste.sh: execute 'cmd_copy' only if 'cmd_paste' was finished without error 2005-06-04 04:51 leif * Make.mm, etc, etc/Make.mm, etc/__vault__.odb, etc/full-sphere.odb, etc/full.odb, etc/incomp-newtonian.odb, etc/incomp-non-newtonian.odb, etc/regional-sphere.odb, etc/regional.odb, etc/temp.odb, examples/Cookbook1/cookbook1.sh, examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh, examples/Cookbook4/cookbook4.sh, examples/Cookbook7/cookbook7.sh, examples/example1.sh, module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/Boundary.cc, module/Exchanger/CitcomInterpolator.cc, module/Exchanger/CitcomSource.cc, module/Exchanger/Convertor.cc, module/Exchanger/Interior.cc, module/Exchanger/Make.mm, module/Exchanger/SInlet.cc, module/Exchanger/SVTInlet.cc, module/Exchanger/SVTOutlet.cc, module/Exchanger/TInlet.cc, module/Exchanger/TOutlet.cc, module/Exchanger/VOutlet.cc, module/Exchanger/VTInlet.cc, module/Exchanger/VTOutlet.cc, module/Exchanger/initTemperature.cc, module/Full/Make.mm, module/Regional/Make.mm, pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/BC.py, pyre/Components/Const.py, pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, pyre/Components/IC.py, pyre/Components/Param.py, pyre/Components/Phase.py, pyre/Components/Sphere/RegionalSphere.py, pyre/Components/Sphere/Sphere.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Components/Tracer.py, pyre/Components/Visc.py, pyre/Controller.py, pyre/CoupledApp.py, pyre/Facilities/Mesher.py, pyre/Facilities/Solver.py, pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py, pyre/Layout.py, pyre/SimpleApp.py, pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py, tests/exchange.py, tests/test1.sh, tests/test2.sh, tests/test5.sh: Initial port from pythia-0.4 to pythia-0.8. 2005-05-28 12:27 ces74 * lib/Regional/Version_dependent.c, module/Regional/setProperties.cc, pyre/Components/IC.py: * If a user doesn't specify "blob_center", assign [-999.,-999.,-999] as a default values in IC.py. * The real default values are assigned in setProperties.cc * The distance calculation in "construct_tic_from_input" modified. * A bug in non-dimensionalizing half_space_age fixed. 2005-05-28 04:41 vlad * examples/example1.sh: *** empty log message *** 2005-05-28 04:11 gurnis * examples/Cookbook1/cookbook1.sh: *** empty log message *** 2005-05-28 01:39 vlad * examples/Cookbook5/velocity, examples/Cookbook5/velocity/bvel.dat0, examples/Cookbook5/velocity/bvel.dat1, examples/Cookbook5/velocity/bvel.dat10, examples/Cookbook5/velocity/bvel.dat11, examples/Cookbook5/velocity/bvel.dat12, examples/Cookbook5/velocity/bvel.dat13, examples/Cookbook5/velocity/bvel.dat14, examples/Cookbook5/velocity/bvel.dat15, examples/Cookbook5/velocity/bvel.dat16, examples/Cookbook5/velocity/bvel.dat17, examples/Cookbook5/velocity/bvel.dat18, examples/Cookbook5/velocity/bvel.dat19, examples/Cookbook5/velocity/bvel.dat2, examples/Cookbook5/velocity/bvel.dat20, examples/Cookbook5/velocity/bvel.dat21, examples/Cookbook5/velocity/bvel.dat22, examples/Cookbook5/velocity/bvel.dat23, examples/Cookbook5/velocity/bvel.dat24, examples/Cookbook5/velocity/bvel.dat25, examples/Cookbook5/velocity/bvel.dat26, examples/Cookbook5/velocity/bvel.dat27, examples/Cookbook5/velocity/bvel.dat28, examples/Cookbook5/velocity/bvel.dat29, examples/Cookbook5/velocity/bvel.dat3, examples/Cookbook5/velocity/bvel.dat30, examples/Cookbook5/velocity/bvel.dat31, examples/Cookbook5/velocity/bvel.dat32, examples/Cookbook5/velocity/bvel.dat33, examples/Cookbook5/velocity/bvel.dat34, examples/Cookbook5/velocity/bvel.dat35, examples/Cookbook5/velocity/bvel.dat36, examples/Cookbook5/velocity/bvel.dat37, examples/Cookbook5/velocity/bvel.dat38, examples/Cookbook5/velocity/bvel.dat39, examples/Cookbook5/velocity/bvel.dat4, examples/Cookbook5/velocity/bvel.dat40, examples/Cookbook5/velocity/bvel.dat41, examples/Cookbook5/velocity/bvel.dat42, examples/Cookbook5/velocity/bvel.dat43, examples/Cookbook5/velocity/bvel.dat44, examples/Cookbook5/velocity/bvel.dat45, examples/Cookbook5/velocity/bvel.dat46, examples/Cookbook5/velocity/bvel.dat47, examples/Cookbook5/velocity/bvel.dat48, examples/Cookbook5/velocity/bvel.dat49, examples/Cookbook5/velocity/bvel.dat5, examples/Cookbook5/velocity/bvel.dat50, examples/Cookbook5/velocity/bvel.dat51, examples/Cookbook5/velocity/bvel.dat52, examples/Cookbook5/velocity/bvel.dat53, examples/Cookbook5/velocity/bvel.dat54, examples/Cookbook5/velocity/bvel.dat55, examples/Cookbook5/velocity/bvel.dat56, examples/Cookbook5/velocity/bvel.dat57, examples/Cookbook5/velocity/bvel.dat58, examples/Cookbook5/velocity/bvel.dat59, examples/Cookbook5/velocity/bvel.dat6, examples/Cookbook5/velocity/bvel.dat60, examples/Cookbook5/velocity/bvel.dat61, examples/Cookbook5/velocity/bvel.dat62, examples/Cookbook5/velocity/bvel.dat63, examples/Cookbook5/velocity/bvel.dat64, examples/Cookbook5/velocity/bvel.dat65, examples/Cookbook5/velocity/bvel.dat66, examples/Cookbook5/velocity/bvel.dat67, examples/Cookbook5/velocity/bvel.dat68, examples/Cookbook5/velocity/bvel.dat69, examples/Cookbook5/velocity/bvel.dat7, examples/Cookbook5/velocity/bvel.dat70, examples/Cookbook5/velocity/bvel.dat71, examples/Cookbook5/velocity/bvel.dat8, examples/Cookbook5/velocity/bvel.dat9: Velocity files 2005-05-28 01:38 vlad * examples/Cookbook5/restart_files, examples/Cookbook5/restart_files/cookbook5.velo.0.0, examples/Cookbook5/restart_files/cookbook5.velo.1.0, examples/Cookbook5/restart_files/cookbook5.velo.10.0, examples/Cookbook5/restart_files/cookbook5.velo.11.0, examples/Cookbook5/restart_files/cookbook5.velo.12.0, examples/Cookbook5/restart_files/cookbook5.velo.13.0, examples/Cookbook5/restart_files/cookbook5.velo.14.0, examples/Cookbook5/restart_files/cookbook5.velo.15.0, examples/Cookbook5/restart_files/cookbook5.velo.16.0, examples/Cookbook5/restart_files/cookbook5.velo.17.0, examples/Cookbook5/restart_files/cookbook5.velo.18.0, examples/Cookbook5/restart_files/cookbook5.velo.19.0, examples/Cookbook5/restart_files/cookbook5.velo.2.0, examples/Cookbook5/restart_files/cookbook5.velo.20.0, examples/Cookbook5/restart_files/cookbook5.velo.21.0, examples/Cookbook5/restart_files/cookbook5.velo.22.0, examples/Cookbook5/restart_files/cookbook5.velo.23.0, examples/Cookbook5/restart_files/cookbook5.velo.24.0, examples/Cookbook5/restart_files/cookbook5.velo.25.0, examples/Cookbook5/restart_files/cookbook5.velo.26.0, examples/Cookbook5/restart_files/cookbook5.velo.27.0, examples/Cookbook5/restart_files/cookbook5.velo.28.0, examples/Cookbook5/restart_files/cookbook5.velo.29.0, examples/Cookbook5/restart_files/cookbook5.velo.3.0, examples/Cookbook5/restart_files/cookbook5.velo.30.0, examples/Cookbook5/restart_files/cookbook5.velo.31.0, examples/Cookbook5/restart_files/cookbook5.velo.32.0, examples/Cookbook5/restart_files/cookbook5.velo.33.0, examples/Cookbook5/restart_files/cookbook5.velo.34.0, examples/Cookbook5/restart_files/cookbook5.velo.35.0, examples/Cookbook5/restart_files/cookbook5.velo.36.0, examples/Cookbook5/restart_files/cookbook5.velo.37.0, examples/Cookbook5/restart_files/cookbook5.velo.38.0, examples/Cookbook5/restart_files/cookbook5.velo.39.0, examples/Cookbook5/restart_files/cookbook5.velo.4.0, examples/Cookbook5/restart_files/cookbook5.velo.40.0, examples/Cookbook5/restart_files/cookbook5.velo.41.0, examples/Cookbook5/restart_files/cookbook5.velo.42.0, examples/Cookbook5/restart_files/cookbook5.velo.43.0, examples/Cookbook5/restart_files/cookbook5.velo.44.0, examples/Cookbook5/restart_files/cookbook5.velo.45.0, examples/Cookbook5/restart_files/cookbook5.velo.46.0, examples/Cookbook5/restart_files/cookbook5.velo.47.0, examples/Cookbook5/restart_files/cookbook5.velo.48.0, examples/Cookbook5/restart_files/cookbook5.velo.49.0, examples/Cookbook5/restart_files/cookbook5.velo.5.0, examples/Cookbook5/restart_files/cookbook5.velo.50.0, examples/Cookbook5/restart_files/cookbook5.velo.51.0, examples/Cookbook5/restart_files/cookbook5.velo.52.0, examples/Cookbook5/restart_files/cookbook5.velo.53.0, examples/Cookbook5/restart_files/cookbook5.velo.54.0, examples/Cookbook5/restart_files/cookbook5.velo.55.0, examples/Cookbook5/restart_files/cookbook5.velo.56.0, examples/Cookbook5/restart_files/cookbook5.velo.57.0, examples/Cookbook5/restart_files/cookbook5.velo.58.0, examples/Cookbook5/restart_files/cookbook5.velo.59.0, examples/Cookbook5/restart_files/cookbook5.velo.6.0, examples/Cookbook5/restart_files/cookbook5.velo.60.0, examples/Cookbook5/restart_files/cookbook5.velo.61.0, examples/Cookbook5/restart_files/cookbook5.velo.62.0, examples/Cookbook5/restart_files/cookbook5.velo.63.0, examples/Cookbook5/restart_files/cookbook5.velo.7.0, examples/Cookbook5/restart_files/cookbook5.velo.8.0, examples/Cookbook5/restart_files/cookbook5.velo.9.0: Restart files 2005-05-28 01:35 vlad * examples/Cookbook5, examples/Cookbook5/cookbook5.sh, examples/Cookbook5/coor.dat: Cookbook5 and coordinate files 2005-05-25 08:22 tan2 * visual/zslice.py: changed the hard-wire path (/usr/bin/python) to run-time dep. path 2005-05-25 04:28 tan2 * visual/zslice.py: a utility script to slize horizontal layers from CitcomS output. See docstring for usage. 2005-05-25 01:12 leif * module/Make.mm: Prefer "$(MM)" to "mm". 2005-05-24 05:15 ces74 * examples/Cookbook7, examples/Cookbook7/README, examples/Cookbook7/cookbook7.sh, examples/Cookbook7/coord.dat: * adding a script to run the Cookbook7 example and coord.dat file. * README for some additional information. 2005-05-24 05:00 ces74 * lib/Common/Initial_temperature.c, lib/Common/convection_variables.h, lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c, module/Regional/setProperties.cc, pyre/Components/IC.py: * added new parameters to control a hot blob as temperature IC. - One can specify three parameters: 1. Coordinates(theta,fi,r) of the center. 2. Radius. 3. The amount of temperature increase/decrease within the blob. - Currently works only for the Regional version. - CitcomS variable name: convection.blob_center, convection.blob_radius, convection.blob_dT - Pyre parameter name: solver.ic.blob_center, solver.ic.blob_radius, solver.ic.blob_dT - it is required to set "solver.ic.tic_method=2" * the format of coordinates file has been modified. - "nsd=1" is not recognized as "%s%d" on some machine. - now it should be "nsd= 1" to be read as "%s %d". 2005-05-20 05:39 leif * module/Exchanger/CitcomInterpolator.cc, module/Exchanger/global_bbox.cc, module/Regional/setProperties.cc: Include in various files. Fixes compilation errors with GCC v3.4.3. 2005-05-20 05:01 ces74 * module/Exchanger/initTemperature.cc: * added a new function for the initial temperature field. - called "hot_blob_lith" - Thermal boudnary layer on top + one hot bloc at the center. 2005-05-19 01:27 leif * lib/Regional/Boundary_conditions.c: Added a prototype for temperatures_conform_bcs() -- fixes compilation failure with GCC v3.4.3. 2005-05-18 08:57 tan2 * tests/test5.sh: test for coupled run 2005-05-18 03:54 tan2 * module/Exchanger/Make.mm: using rpath to specify runtime library path 2005-05-18 02:45 tan2 * module/Full/Make.mm, module/Regional/Make.mm: using rpath to specify runtime library path 2005-05-17 07:35 tan2 * module/Full/Make.mm, module/Regional/Make.mm: the full path of shared library is given, otherwise g++ can compile but the program couldn't find the shared library at the run time 2005-05-17 06:53 vlad * lib/Common/Output.c, lib/Common/Tracer_advection.c, lib/Common/tracer_defs.h: 3D MPI tracer-advection code 2005-04-11 19:09 steve * lib/Common/Make.mm, lib/Full/Make.mm, lib/Regional/Make.mm: facelifted to work with new "config" repository (cvs -d :pserver:config@cvs.cacr.caltech.edu:/config co config). I think this will still work with the old config... Eh you may want to check. 2005-03-30 10:34 vlad * lib/Common/Output.c, lib/Common/Tracer_advection.c, lib/Common/tracer_defs.h: *** empty log message *** 2005-03-30 10:27 vlad * lib/Common/Output.c, lib/Common/Tracer_advection.c, lib/Common/tracer_defs.h: *** empty log message *** 2005-03-11 12:23 steve * module/Exchanger/Make.mm: Added EXCHANGER_INCDIR and EXCHANGER_LIBDIR, as in my case, I do not build exchanger into either pythia's or citcom's build root (but into its own) 2005-03-11 08:24 vlad * lib/Common/Output.c, lib/Common/Phase_change.c: *** empty log message *** 2005-03-09 06:24 vlad * lib/Common/Tracer_advection.c: The tracer code only works in root processor 2005-02-18 08:13 tan2 * pyre/Components/IC.py: fixed a bug in the validator of 'tic_method' 2005-02-18 07:15 tan2 * module/Regional/setProperties.cc: added new parameter 'tic_method' and 'half_space_age' 2005-02-18 06:57 tan2 * pyre/Components/IC.py: 1. added validator to some of the input. 2. added new parameter 'tic_method' and 'half_space_age'. 2005-02-18 06:14 tan2 * lib/Full/Version_dependent.c, lib/Regional/Version_dependent.c: implementation of cooling plate temperature is pending. 2005-02-18 06:12 tan2 * lib/Common/Initial_temperature.c, lib/Common/convection_variables.h: Added new input parameter: tic_method. When it is 0 (default), the temperature is a linear profile + perturbation at some layers. When it is 1, the temperature is isothermal (== bottom b.c.) + uniformly cold plate (thickness specified by 'half_space_age'). 2005-02-05 02:51 ces74 * module/Exchanger/SInlet.cc, module/Exchanger/SInlet.h, module/Exchanger/bindings.cc, module/Exchanger/inlets_outlets.cc, module/Exchanger/inlets_outlets.h: * bindings for the SInlet class added. * setSBCFlag() method added to SInlet. 2005-02-03 05:49 tan2 * module/Exchanger/Boundary.cc: fixed a bug in finding boundary nodes and rearraged code 2005-01-29 08:23 ces74 * pyre/Components/Exchanger/Inlet.py: * SInlet class added 2005-01-29 08:15 ces74 * module/Exchanger/Make.mm, module/Exchanger/SIUnit.cc, module/Exchanger/SInlet.cc, module/Exchanger/SInlet.h: * added a new class SInlet to receive stress from the coupled solver. * "stress_factor" defined in SIUnit.cc 2005-01-29 03:20 tan2 * module/Exchanger/Make.mm: removed redudant include and library path. PYTHIA_INCDIR and PYTHIA_LIBDIR must be defined. 2005-01-27 06:10 tan2 * lib/Common/Tracer_advection.c: removed tracer_output(), which is replaced by output_tracer() in Output.c 2005-01-27 06:05 tan2 * drivers/Citcom.c: removed calls to tracer_output(), which is replaced by output_tracer() in Output.c 2005-01-26 07:01 ces74 * lib/Common/Instructions.c: * removed a useless block of code 2005-01-26 04:05 tan2 * lib/Common/Tracer_advection.c: 1. Commented out part of the code that use itcolor, which is the starting age of the tracer. 2. Added a few comments about the code. This should help people to read the code. 2005-01-24 05:20 tan2 * pyre/Components/Exchanger/Exchanger.py: commented out debugging output 2005-01-21 06:29 tan2 * module/Regional/setProperties.cc, pyre/Components/Param.py: removed 'tracer' and 'tracer_file' properties from Param class (these properties are moved to Tracer class) 2005-01-21 06:25 tan2 * pyre/Components/Visc.py: fixed a bug in reading viscZ property 2005-01-20 03:02 ces74 * pyre/Components/BC.py: * A BC property, "pseudo_free_surf", added. Its default value is False. 2005-01-20 02:55 tan2 * module/Regional/setProperties.cc, pyre/Components/Visc.py: added new properties visc.viscZ and visc.rheol 2005-01-20 02:35 vlad * lib/Common/Viscosity_structures.c: a new viscosity law was added (case 4) 2005-01-19 10:19 tan2 * lib/Common/Output.c: added function output_tracer() 2005-01-19 10:02 tan2 * pyre/Components/Tracer.py, pyre/Solver/Solver.py: added Tracer module into Solver 2005-01-19 10:01 tan2 * module/Regional/bindings.cc, module/Regional/misc.cc, module/Regional/misc.h: added binding to tracer_advection() 2005-01-19 09:05 tan2 * module/Regional/bindings.cc, module/Regional/setProperties.cc, module/Regional/setProperties.h: added bindings to tracer input 2005-01-19 08:57 tan2 * pyre/Components/Make.mm: added Tracer.py to file list 2005-01-19 08:44 tan2 * pyre/Components/Tracer.py: added Tracer module 2005-01-19 08:43 tan2 * lib/Common/Tracer_advection.c: changed the default value of E->control.tracer_file 2005-01-19 08:38 tan2 * module/Regional/mesher.cc: modified according to changes in lib/Common/Instructions.c (add tracer module) 2005-01-19 08:36 tan2 * lib/Common/Instructions.c: fixed a syntax error 2005-01-19 08:35 tan2 * lib/Common/Instructions.c, lib/Common/Tracer_advection.c: 1. moved input of tracer-related parameters to tracer_input() 2. changed where tracer_initial_settings() is called 2005-01-19 07:19 tan2 * lib/Common/global_defs.h: fixed a problem in function pointer declaration 2005-01-19 07:19 tan2 * drivers/Citcom.c: uncommented tracer module 2005-01-19 06:30 vlad * examples/Cookbook4, examples/Cookbook4/cookbook4.sh, examples/Cookbook4/coor.dat: new cookbook with a refined mesh 2005-01-19 06:24 tan2 * tests/signon.py: *** empty log message *** 2005-01-08 11:24 ces74 * lib/Common/Element_calculations.c: * removed unnecessary debugging output from get_elt_tr() 2005-01-08 11:20 ces74 * module/Regional/bindings.cc, module/Regional/outputs.cc, module/Regional/outputs.h, module/Regional/stokes_solver.cc, module/Regional/stokes_solver.h: * call Citcom's functions in output, general_stokes_solver, respectively, instead of creating pseudo_surf bindings for each 2005-01-08 11:02 ces74 * module/Regional/bindings.cc, module/Regional/outputs.cc, module/Regional/outputs.h, module/Regional/setProperties.cc, module/Regional/stokes_solver.cc, module/Regional/stokes_solver.h: * added bindings for new functions for the "pseudo free surface" formulation 2005-01-08 10:57 ces74 * lib/Common/Instructions.c: * always assign memory for free_surf and Vprev for now. - in the future, need to save memory when pseudo_free_surf is off. 2005-01-08 10:16 ces74 * drivers/Citcom.c: * modified to enable the "pseudo free surface" mode. 2005-01-08 10:15 ces74 * lib/Common/Drive_solvers.c, lib/Common/Element_calculations.c, lib/Common/Instructions.c, lib/Common/Output.c, lib/Common/Stokes_flow_Incomp.c, lib/Common/Topo_gravity.c, lib/Common/global_defs.h, lib/Common/output.h: * functions added to track pseudo free surface and compute normal traction from it. 2005-01-05 06:58 tan2 * module/Exchanger/SVTInlet.cc: removed the declaration of my_tbc() 2005-01-05 06:57 tan2 * module/Exchanger/SVTInlet.cc: 1. uncommented the journal output 2. removed codes about 'upwind bc', as it is proved not accurate. 3. removed a call to my_tbc(), which is specific to my Hawaii plume model and sliped through the repository 2005-01-01 03:00 tan2 * lib/Common/Advection_diffusion.c, lib/Common/Convection.c: move parameter input from Convection.c to Advection_diffusion.c 2004-12-31 09:03 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: fixed a bug when nprocz>1 and excludeTop or/add excludeBottom is turned on 2004-12-28 09:38 tan2 * module/Exchanger/Boundary.cc: fixed a bug, which causes some nodes being excluded from Boundary when excludeTop or excludeBottom are turned off 2004-12-28 03:49 tan2 * visual/combine.py: renamed some variables and changed the doc_string 2004-12-03 04:23 tan2 * pyre/CoupledApp.py, pyre/SimpleApp.py: 1. In findLayput(), assing self.controller 2. In CoupledApp, two controllers are created. So, two controllers can have different output interval (monitoringFrequency). 2004-11-25 05:47 ces74 * lib/Common/Advection_diffusion.c, lib/Common/Instructions.c, lib/Common/global_defs.h, module/Regional/setProperties.cc, pyre/Components/Advection_diffusion/Advection_diffusion.py: * a new parameter, "filter_temperature" created as a memeber of the "Control" structure. - if it's 1, the function filter() is called to reduce artifical diffusioin. - it's 1 by default. * The command line option for this parameter is "filter_temp" - it belongs to the "Advection_diffusion" class, which is instantiated as "tsolver" in Solver.py. - Usage: --solver.tsolver.filter_temp=True/False 2004-11-16 19:43 steve * module/Exchanger/Make.mm, module/Full/Make.mm, module/Regional/Make.mm: made where to find pyre, etc a little more generic 2004-11-09 07:21 ces74 * visual/miff2avi, visual/miff2mpg: * added appropriate credits for these scripts. 2004-11-07 08:41 ces74 * visual/miff2avi, visual/miff2mpg: * scripts to make a movie out of images generated by OpenDX -- mjpeg tools are necessary to run. 2004-10-08 07:28 tan2 * pyre/Solver/Solver.py: don't use exchanger.initTemperature() when restart (use disk file for IC) 2004-10-08 07:25 tan2 * lib/Common/Process_buoyancy.c: disable writing out surface hear flux information, for processor on the surface usually don't have E->fp ready to use. 2004-10-08 07:21 tan2 * lib/Common/Construct_arrays.c: get_bcs_id_for_residual() is version independent. Move from Boundary_conditions.c to Common/Construct_arrays.c 2004-10-08 07:20 tan2 * lib/Common/global_defs.h: temperatures_conform_bcs() is version (Full/Regional) dependent. Make a function pointer for it. 2004-10-08 07:18 tan2 * lib/Full/Boundary_conditions.c, lib/Regional/Boundary_conditions.c: 1. temperatures_conform_bcs() is version (Full/Regional) dependent. Make a function pointer for it. 2. get_bcs_id_for_residual() is version independent. Move to Common/Construct_arrays.c 2004-10-08 07:11 tan2 * module/Exchanger/SVTInlet.cc, module/Exchanger/TInlet.cc, module/Exchanger/VTInlet.cc, module/Exchanger/initTemperature.cc: 1. temperatures_conform_bcs() is version (Full/Regional) dependent. Make a function pointer for it. 2. in initTemperature.cc, add several new functions of different IC. 2004-10-08 07:08 tan2 * module/Exchanger/Boundary.cc: 1. fixed a bug: normalFlag was not init'd correctly 2. when excludeBottom is true, bottome edge nodes are still included 2004-09-23 04:31 ces74 * visual/OpenDXMacro/CitcomSSurfaceHeatflux.net, visual/OpenDXMacro/CitcomSSurfaceImport.net, visual/OpenDXMacro/CitcomSSurfaceTopo.net, visual/OpenDXMacro/CitcomSSurfaceVelocity.net, visual/OpenDXMacro/RTFtoXYZ2D.net, visual/OpenDXMacro/VelocityRTFtoXYZ2D.net, visual/visRegionalSurface.cfg, visual/visRegionalSurface.net: * OpenDX macros and a new visual program for surface data. 2004-09-22 07:16 ces74 * visual/combinesurf.py: * fixed a bug related to the loop over the surface procs for each cap. 2004-09-22 06:44 ces74 * visual/batchsurf.py, visual/getcoord.sh: * fixed bugs related to generating a list of surface processors. 2004-08-10 07:22 tan2 * lib/Common/Initial_temperature.c: Print restart filename to logfile 2004-08-08 05:08 tan2 * pyre/Components/Exchanger/Exchanger.py, pyre/Controller.py, pyre/Coupler.py, pyre/Solver/Solver.py: Synchronized when to save the result. During a coupled run, when one solver saves the result, the other solver will save too. 2004-08-07 06:25 tan2 * visual/batchsurf.py: the 1st argument can be either the name of machine file or a quoted machine list(eg. 'n101 n102'). 2004-08-07 06:24 tan2 * visual/combinesurf.py: fixed quite a few bugs. this script is working correctly. 2004-08-07 05:47 tan2 * pyre/Components/Exchanger/FineGridExchanger.py: VTOutlet was used in creatII, TOutlet is used now. 2004-08-07 03:22 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py: nailed down a big bug. VTInlet was used in creatII, which set temperature bc flag for all interior nodes. TInlet is used now. 2004-08-05 01:29 tan2 * visual/OpenDXMacro/CitcomSFullImport.net: fixed a bug which incorrectly set cap_start=0 2004-08-04 03:11 tan2 * module/Regional/setProperties.cc, pyre/Components/Const.py: changed the units of depth parameters to be nondimensional, so that they are consistent with original CitcomS input format 2004-08-02 23:34 ces74 * pyre/Components/Stokes_solver/Incompressible.py: * some parameters that were hardwired can have user-defined values now. 2004-07-29 00:39 tan2 * visual/visFull.cfg, visual/visFull.net, visual/visRegional.cfg, visual/visRegional.net: * use the same colormap for temperature cross-section and isosurfaces. 2004-07-28 01:19 tan2 * module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/AreaWeightedNormal.h: * Change of implementation. Now the weighted normal vectors are taken from CitcomS' internal data (from boundary determinant E->boundary.det, this array has been throughly tested), no needto compute them again. Havn't tested. 2004-07-28 01:14 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: * Fixed a problem in initBBox(). It used to returned a tight boundingbox. So, when excludeTop or excludeBottom is set, the outer and inner radii are not the correct outer and inner radii of the mesh. This can cause confusion and problem in other part of program. * Added a new attribute, bnode. It is the index mapping from CitcomS' node # to Boundary's node #. 2004-07-27 06:56 tan2 * visual/batchcombine.py: * the 1st argument can be either the name of machine file or a quoted machine list(eg. 'n101 n102'). * modified the doc string 2004-07-09 01:15 tan2 * lib/Common/Problem_related.c, lib/Full/Lith_age.c, lib/Full/Read_input_from_files.c, lib/Regional/Lith_age.c, lib/Regional/Read_input_from_files.c: Previousely, CitcomS would abort running when age < -1 Ma. This behavior is not desirable. The following fixes change the behavior so that CitcomS will assume age=0 when time has passed present day. 1. find_age_in_MY() returns negative age when time has passed present day 2. changed how age is manipulated before reading age-dependet files 2004-07-06 13:32 patrick * doc/CitComS.doxyconf, doc/Exchanger.doxyconf: * Renamed Exchanger.doxyconf to CitComS.doxyconf * Set the tags to work properly 2004-07-03 03:47 tan2 * module/Exchanger/global_bbox.cc: Fixed a bug in fullGlobalBoundedBox(). The first and second dimension of bbox are swapped. This bug makes the interpolator skip some nodes. 2004-06-30 03:25 tan2 * examples/Cookbook3, examples/Cookbook3/cookbook3.sh: example of temperature-dependent viscosity 2004-06-30 00:25 tan2 * examples/Cookbook1, examples/Cookbook1/cookbook1.sh, examples/Cookbook2, examples/Cookbook2/cookbook2.sh, examples/example1.sh: more example scripts 2004-06-29 06:04 tan2 * tests/.cvsignore: tell cvs to ignore output files of test scripts 2004-06-29 05:58 tan2 * lib/Full/Lith_age.c, lib/Regional/Lith_age.c: calling temperatures_conform_bcs() after init'ed restarted temperature field 2004-06-29 05:29 tan2 * lib/Full/Lith_age.c: similar changes as in Regional/Lith_age.c 2004-06-29 04:20 tan2 * lib/Regional/Lith_age.c: 1. fix a bug when init'ing temperature 2. read lith_age_file in lith_age_init() 2004-06-29 02:56 tan2 * drivers/Full/Make.mm, drivers/Regional/Make.mm: changed export rule so that mm will create symbolic links of binary executables in $EXPORT_ROOT/bin 2004-06-29 02:54 tan2 * module/Regional/mesher.cc: calling lith_age_init() in mehser_init() 2004-06-29 02:53 tan2 * lib/Common/Instructions.c, lib/Common/lith_age.h, lib/Regional/Lith_age.c: 1. moved initialization of lith_age to lith_age_init() 2. calling lith_age_init() in read_instructions() 2004-06-29 02:49 tan2 * lib/Regional/Boundary_conditions.c: called temperatures_conform_bcs() after setting tbc 2004-06-29 01:36 tan2 * lib/Common/Pan_problem_misc_functions.c: bug fix 2004-06-29 01:10 tan2 * examples/example1.sh: typos fixed 2004-06-27 08:04 tan2 * module/Regional/initial_conditions.cc: enable lith_age support 2004-06-27 08:03 tan2 * lib/Regional/Lith_age.c: fixed a 'access unallocated memory' bug 2004-06-27 07:59 tan2 * lib/Common/Initial_temperature.c, lib/Common/initial_temperature.h: added declaration of restart_tic() and restart_tic() in header 2004-06-26 03:06 tan2 * visual/visFull.cfg, visual/visFull.net: 1. show (reduced) surface grid 2. make rotating the Plane easier 2004-06-26 01:50 tan2 * visual/visFull.cfg, visual/visFull.net: new OpenDX network for CitcomS Full 2004-06-26 01:49 tan2 * visual/visRegional.cfg, visual/visRegional.net: 1. import viscosity 2. changed names of transmitters/receivers 2004-06-26 01:48 tan2 * visual/OpenDXMacro/CitcomSFullImport.net, visual/OpenDXMacro/CitcomSImport.net, visual/OpenDXMacro/CitcomSViscosity.net: added viscosity import 2004-06-26 01:28 tan2 * visual/samples/fulltest.cap0.0, visual/samples/fulltest.cap0.0.general, visual/samples/fulltest.cap1.0, visual/samples/fulltest.cap1.0.general, visual/samples/fulltest.cap10.0, visual/samples/fulltest.cap10.0.general, visual/samples/fulltest.cap11.0, visual/samples/fulltest.cap11.0.general, visual/samples/fulltest.cap2.0, visual/samples/fulltest.cap2.0.general, visual/samples/fulltest.cap3.0, visual/samples/fulltest.cap3.0.general, visual/samples/fulltest.cap4.0, visual/samples/fulltest.cap4.0.general, visual/samples/fulltest.cap5.0, visual/samples/fulltest.cap5.0.general, visual/samples/fulltest.cap6.0, visual/samples/fulltest.cap6.0.general, visual/samples/fulltest.cap7.0, visual/samples/fulltest.cap7.0.general, visual/samples/fulltest.cap8.0, visual/samples/fulltest.cap8.0.general, visual/samples/fulltest.cap9.0, visual/samples/fulltest.cap9.0.general: added sample data file of CitcomS Full 2004-06-25 02:38 tan2 * examples/example1.sh: first example for Cookbook 2005-08-23 03:32 unknown_user * examples/Full/Make.mm, examples/Full/local.def, examples/Make.mm, examples/Regional/Make.mm, examples/Regional/local.def, examples/local.def: [vcp] delete of edited revision with dead state 2004-06-25 02:31 tan2 * Make.mm, examples/Full/Make.mm, examples/Full/local.def, examples/Make.mm, examples/Regional/Make.mm, examples/Regional/local.def, examples/local.def: removed makefiles in examples/ 2004-06-25 02:26 tan2 * pyre/Solver/Solver.py: new default value for Rayleight number 2004-06-25 02:25 tan2 * pyre/Components/Sphere/RegionalSphere.py: new default values for domain size 2004-06-25 02:24 tan2 * pyre/Components/IC.py: new default values, number of initial temperature perturbation is default to 1, perturbl and perturbm to 1, perturblayer to 5. 2004-06-12 03:14 tan2 * module/Exchanger/Make.mm, module/Full/Make.mm, module/Regional/Make.mm: modified library and include pathes 2004-06-11 06:07 tan2 * visual/visRegional.cfg, visual/visRegional.net: 1. added integer interactor to control the cutting dimension of Slab 2. made the names of interactor more descriptive 3. set the min of slab cutting position to 0 4. set the min and max of slab Autocolor to 0 and 1, respectively 2004-06-09 00:40 tan2 * module/Full/.cvsignore: tell cvs to ignore linked source codes in this directory 2004-06-09 00:32 tan2 * lib/Common/Output.c: disable pressure and stress output 2004-06-08 08:35 tan2 * visual/batchsurf.py, visual/combinesurf.py, visual/dxgeneralsurf.sh, visual/getsurf.sh: scripts to get back and combine the surf file (containing x, y, topography, heatflux, vx, vy) 2004-06-08 08:32 tan2 * visual/getcoord.sh: script to get the coord file 2004-06-08 05:29 tan2 * visual/batchcombine.py: changed the way to generate machine list 2004-06-08 04:51 tan2 * visual/batchpaste.sh: Removed hard-wired path. Users have to set CitcomS/visual in their path. 2004-06-08 02:54 tan2 * visual/batchcombine.py: removed debugging output 2004-06-08 02:45 tan2 * visual/batchcombine.py: When the length of machinefile mismatch the number of processors, the script will give a warging and try to match number of processors by applying machinefile multiple times. 2004-06-03 04:49 tan2 * citcoms_profile: environment variables for Pyre-ized CitcomS package. Users need to modify $GEOFRAMEWORK to the installation path 2004-06-03 03:30 tan2 * module/Exchanger/misc.cc: remove unused header file 2004-06-03 03:28 tan2 * module/Exchanger/exchangers.cc: fixed a bug in passing int when *int is expected 2004-06-03 03:27 tan2 * module/Exchanger/Boundary.cc: enable journal output 2004-06-03 03:23 tan2 * module/Exchanger/CitcomInterpolator.cc: throw an exception if selfTest() is failed 2004-06-02 06:59 tan2 * Make.mm, local.def: remove incorrect copyright listing 2004-05-29 08:19 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: 1. added new boolean property 'two_way_communication' in Exchanger.py. If it is false, communication is only one way (coarse to fine). 2. added new boolean properties 'excludeTop' and 'excludeBottom' in FineGridExchanger.py. These two are new construtor arguments of Boundary class. 2004-05-29 04:26 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/exchangers.cc: 1. Boundary can be constucted without top or bottom surfaces. This is done through two c'tor argument 'bool excludeTop, excludeBottom'. 2. disable journal 2004-05-27 06:56 tan2 * module/Regional/bindings.cc, module/Regional/misc.cc, module/Regional/misc.h: split 'BC_update_bc()' into 'Visc_update_material()' and 'BC_update_plate_velocity()' 2004-05-27 06:55 tan2 * pyre/Components/BC.py, pyre/Components/Visc.py, pyre/Solver/Solver.py: split 'BC.updateBC()' into 'Visc.updateMaterial()' and 'BC.updatePlateVelocity()' 2004-05-27 06:53 tan2 * pyre/Components/Advection_diffusion/Advection_diffusion.py: made "fixed_timestep" and "finetunedt" an inventory property (they were ordinary class member). 2004-05-26 05:41 tan2 * visual/visRegional.net: using relative path to the data files 2004-05-26 05:34 tan2 * visual/visRegional.cfg, visual/visRegional.net: basic OpenDX network script to visualize result from regional version of CitcomS 2004-05-26 05:24 tan2 * visual/samples, visual/samples/regtest.cap0.0, visual/samples/regtest.cap0.0.general: added new sample files for visualization 2004-05-25 07:29 tan2 * module/Exchanger/CitcomSource.cc, module/Exchanger/SVTInlet.cc, module/Exchanger/SVTOutlet.cc: journal is known to leak memory. Commented out journal output before the leak is fixed. 2004-05-25 03:32 tan2 * module/Regional/bindings.cc, module/Regional/misc.cc, module/Regional/misc.h, pyre/Components/BC.py, pyre/Solver/Solver.py: added support to read vel_bc files at every timestep 2004-05-25 03:30 tan2 * module/Regional/stokes_solver.cc: added function name in the argument to PyArg_ParseTuple() 2004-05-25 03:27 tan2 * tests/.cvsignore: tell cvs to ignore files generated by citcoms output 2004-05-25 02:59 tan2 * module/Exchanger/SVTInlet.cc: Two types of temperature b.c: upwind/normal. In upwind bc, bc can be either fixed temperature/heatflux depending on the direction of flow. In normal bc, bc is always fixed temperature. After more testing, I found normal bc works better than upwind bc. 2004-05-24 02:13 tan2 * lib/Common/Pan_problem_misc_functions.c: 'side_sbc' is applicable in regional version only. add a sanity check here. also remove some (incorrect) conditional #include 2004-05-24 02:10 tan2 * lib/Common/Topo_gravity.c, lib/Full/Boundary_conditions.c, lib/Regional/Boundary_conditions.c: fully implemented stress_conform_bcs() and moved it from Boundary_conditions.c to Topo_gravity.c 2004-05-24 01:45 tan2 * examples/Regional/input.sample: add missing parameter 'perturblayer' 2004-05-19 04:21 ces74 * module/Exchanger/Make.mm, module/Exchanger/bindings.cc, module/Exchanger/inlets_outlets.cc: * bindings for VOutlet, which sends only the velocity to a sink. 2004-05-19 04:18 ces74 * module/Exchanger/VOutlet.cc, module/Exchanger/VOutlet.h, module/Exchanger/inlets_outlets.h: * Binding for VOutlet created: this send only the velocity to a sink. 2004-05-19 04:15 ces74 * pyre/Components/Exchanger/Outlet.py: * a class added for exchanging only the velocity. 2004-05-19 03:40 tan2 * visual/OpenDXMacro/ScaledGlyphs.net: macro that takes two data and plot them as two glyphs that has the same size (eg. length of arrow) scale. The shape (eg. the thickness of arrow) cannot be scaled automaticly though. 2004-05-19 03:38 tan2 * visual/OpenDXMacro/ShowSphere.net: input1: origin of sphere; default=[0 0 0] input2: radius of sphere; default=0.5 output: sphere object 2004-05-13 02:10 patrick * doc/Exchanger.doxyconf: * Updated the package name in the Doxygen docs 2004-05-13 02:05 tan2 * visual/OpenDXMacro/CitcomSFullImport.net: Added two more inputs. One is an integer indicating the starting cap number. The other is an integer indicating the ending cap number. The default is 0-11, ie. all caps. If you wanna plot some specific caps only, change these two values. 2004-05-13 02:01 tan2 * visual/dxgeneral.sh: Changed the order of 'grid'. Now it is YXZ. Don't know why, but the old XYZ ordering doesn't work. 2004-05-12 02:32 tan2 * visual/OpenDXMacro, visual/OpenDXMacro/CitcomSFullImport.net, visual/OpenDXMacro/CitcomSImport.net, visual/OpenDXMacro/CitcomSTemperature.net, visual/OpenDXMacro/CitcomSVelocity.net, visual/OpenDXMacro/RTFtoXYZ.net, visual/OpenDXMacro/VelocityRTFtoXYZ.net: * OpenDX macros for importing CitcomS data file * how to use: 1. create the 'cap' files and '.general' files using scripts in CitcomS/visual/ directory. 2. use CitcomSImport to import single cap-file. use CitcomSFullImport to import 12 cap-files. 2005-08-23 03:30 unknown_user * module/Exchanger/TractionInlet.cc, module/Exchanger/TractionInlet.h, module/Exchanger/TractionOutlet.cc, module/Exchanger/TractionOutlet.h: [vcp] delete of edited revision with dead state 2004-05-12 01:36 tan2 * module/Exchanger/TractionInlet.cc, module/Exchanger/TractionInlet.h, module/Exchanger/TractionOutlet.cc, module/Exchanger/TractionOutlet.h: obsolete classes 2004-05-12 01:35 tan2 * module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/AreaWeightedNormal.h, module/Exchanger/BoundaryVTInlet.cc, module/Exchanger/BoundaryVTInlet.h: modified these classes using new base exchanger. these classes are not used currently and I didn't write any binding for them. 2004-05-11 14:59 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, pyre/Components/Exchanger/Inlet.py, pyre/Components/Exchanger/Outlet.py: * using new c++ class hierarchy 2005-08-23 03:30 unknown_user * module/Exchanger/AbstractSource.cc, module/Exchanger/AbstractSource.h, module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h, module/Exchanger/BoundedBox.cc, module/Exchanger/BoundedBox.h, module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h, module/Exchanger/CartesianCoord.cc, module/Exchanger/CartesianCoord.h, module/Exchanger/DIM.h, module/Exchanger/FEMInterpolator.cc, module/Exchanger/FEMInterpolator.h, module/Exchanger/Inlet.cc, module/Exchanger/Inlet.h, module/Exchanger/Outlet.cc, module/Exchanger/Outlet.h, module/Exchanger/Sink.cc, module/Exchanger/Sink.h, module/Exchanger/TractionInterpolator.cc, module/Exchanger/TractionInterpolator.h, module/Exchanger/TractionSource.cc, module/Exchanger/TractionSource.h, module/Exchanger/VTInterpolator.cc, module/Exchanger/VTInterpolator.h, module/Exchanger/VTSource.cc, module/Exchanger/VTSource.h, module/Exchanger/utilTemplate.cc, module/Exchanger/utilTemplate.h, module/Exchanger/utility.cc, module/Exchanger/utility.h: [vcp] delete of edited revision with dead state 2004-05-11 14:55 tan2 * module/Exchanger/AbstractSource.cc, module/Exchanger/AbstractSource.h, module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h, module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/BoundedBox.cc, module/Exchanger/BoundedBox.h, module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h, module/Exchanger/CartesianCoord.cc, module/Exchanger/CartesianCoord.h, module/Exchanger/CitcomInterpolator.cc, module/Exchanger/CitcomInterpolator.h, module/Exchanger/CitcomSource.cc, module/Exchanger/CitcomSource.h, module/Exchanger/Convertor.cc, module/Exchanger/Convertor.h, module/Exchanger/DIM.h, module/Exchanger/FEMInterpolator.cc, module/Exchanger/FEMInterpolator.h, module/Exchanger/Inlet.cc, module/Exchanger/Inlet.h, module/Exchanger/Interior.cc, module/Exchanger/Interior.h, module/Exchanger/Make.mm, module/Exchanger/Outlet.cc, module/Exchanger/Outlet.h, module/Exchanger/SIUnit.cc, module/Exchanger/SIUnit.h, module/Exchanger/SVTInlet.cc, module/Exchanger/SVTInlet.h, module/Exchanger/SVTOutlet.cc, module/Exchanger/SVTOutlet.h, module/Exchanger/Sink.cc, module/Exchanger/Sink.h, module/Exchanger/TInlet.cc, module/Exchanger/TInlet.h, module/Exchanger/TOutlet.cc, module/Exchanger/TOutlet.h, module/Exchanger/TractionInterpolator.cc, module/Exchanger/TractionInterpolator.h, module/Exchanger/TractionSource.cc, module/Exchanger/TractionSource.h, module/Exchanger/VTInlet.cc, module/Exchanger/VTInlet.h, module/Exchanger/VTInterpolator.cc, module/Exchanger/VTInterpolator.h, module/Exchanger/VTOutlet.cc, module/Exchanger/VTOutlet.h, module/Exchanger/VTSource.cc, module/Exchanger/VTSource.h, module/Exchanger/bindings.cc, module/Exchanger/bindings.h, module/Exchanger/exceptions.h, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h, module/Exchanger/global_bbox.cc, module/Exchanger/global_bbox.h, module/Exchanger/initTemperature.cc, module/Exchanger/initTemperature.h, module/Exchanger/inlets_outlets.cc, module/Exchanger/inlets_outlets.h, module/Exchanger/misc.cc, module/Exchanger/misc.h, module/Exchanger/utilTemplate.cc, module/Exchanger/utilTemplate.h, module/Exchanger/utility.cc, module/Exchanger/utility.h: * New class hierarchy. All base classes are moved to packages/Exchanger, so does non-CitcomS-specific utility classes. * Removed 'mode' argument in VTInlet and VTOutlet c'tors. Every Inlet and Outlet class is reponsible for only one job. * Merged all Interpolator into CitcomInterpolator * Merged all Source into CitcomSource 2004-05-08 01:44 tan2 * module/Exchanger/SVTInlet.cc: impose temperature b.c. when flow is toward into my domain. Otherwise, impose no-heatflux b.c. 2004-05-08 01:41 tan2 * module/Exchanger/misc.cc: changed default initial temperature field -- a hot spherical blob below the fine mesh 2004-05-01 01:41 tan2 * module/Exchanger/Sink.cc: added another self test. This test will make sure that every mesh node is interpolated. 2004-04-30 05:19 tan2 * lib/Common/Instructions.c: remove debug print out 2004-04-30 04:41 tan2 * module/Exchanger/SVTInlet.cc: implemented imposeSV(), passed benchmark. 2004-04-30 04:36 tan2 * module/Exchanger/VTInterpolator.cc: fixed a bug in accessing E->gstress array 2004-04-30 04:35 tan2 * lib/Common/Topo_gravity.c, lib/Full/Boundary_conditions.c, lib/Regional/Boundary_conditions.c: After stress is calculated, replace stress of boundary nodes with boundary conditions (if stress BC is specified). This is partially done in Regional version (if E->control.side_sbcs is on, should use different bc arrays). Not implemented in Full version. 2004-04-30 03:40 patrick * doc, doc/.cvsignore, doc/Exchanger.doxyconf: Commiting Doxygen config file to build the documents for the exchanger 2004-04-29 07:23 tan2 * pyre/Components/BC.py: side_sbcs default to False 2004-04-29 07:23 tan2 * lib/Common/Instructions.c: E->control.side_sbcs default to 0 2004-04-29 07:21 tan2 * lib/Common/Output.c: added new function output_stress() 2004-04-29 07:13 tan2 * lib/Regional/Version_dependent.c: added some comment for initial temperature in spherical harmonic for future reference 2005-08-23 03:29 unknown_user * tests/citcomsfull.py, tests/citcomsregional.py, tests/coupledcitcoms.py: [vcp] delete of edited revision with dead state 2004-04-24 05:15 tan2 * tests/citcomsfull.py, tests/citcomsfull.sh, tests/citcomsregional.py, tests/citcomsregional.sh, tests/coupledcitcoms.py, tests/coupledcitcoms.sh: update the scripts that executes pyreized versions 2004-04-24 04:15 tan2 * drivers/Regional/Make.mm: export binary executable 2004-04-23 03:52 tan2 * drivers/Full/Make.mm: export binary 2004-04-17 02:12 tan2 * lib/Common/Pan_problem_misc_functions.c: bug fix 2004-04-16 08:17 tan2 * module/Regional/setProperties.cc, pyre/Components/BC.py: add 'side_sbcs' to property list 2004-04-16 07:08 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: use SVTInlet and SVTOutlet as BC 2004-04-16 07:05 tan2 * pyre/Components/Exchanger/Inlet.py, pyre/Components/Exchanger/Outlet.py: add SVTOutlet and SVTInlet classes and their bindings. These classes are for CitcomS-CitcomS coupling, b.c. with temperature, normal velocity and shear traction 2004-04-16 07:03 tan2 * module/Exchanger/Make.mm, module/Exchanger/SVTInlet.cc, module/Exchanger/SVTInlet.h, module/Exchanger/SVTOutlet.cc, module/Exchanger/SVTOutlet.h, module/Exchanger/bindings.cc, module/Exchanger/inlets_outlets.cc, module/Exchanger/inlets_outlets.h: add SVTOutlet and SVTInlet classes and their bindings. These classes are for CitcomS-CitcomS coupling, b.c. with temperature, normal velocity and shear traction 2004-04-16 07:01 tan2 * module/Exchanger/VTSource.cc: add some journal debug output 2004-04-16 01:39 tan2 * lib/Common/Topo_gravity.c, module/Exchanger/TractionInterpolator.cc: rearranged the order of stress vector so that it conforms with Hugh's convention | 1 4 5 | stress =| 4 2 6 | | 5 6 3 | 2004-04-16 01:35 tan2 * lib/Common/Make.mm, lib/Common/Process_velocity.c: remove the empty file, Process_velocity.c, from the repository 2004-04-16 01:33 tan2 * lib/Common/Obsolete.c, lib/Common/Process_velocity.c, lib/Common/Topo_gravity.c: 1. move get_surf_stress() from Process_velocity.c to Topo_gravity.c 2. move get_ele_visc() from Process_velocity.c to Obsolete.c 2004-04-15 03:12 tan2 * module/Exchanger/VTSource.cc, module/Exchanger/VTSource.h: implement interpolateStress() 2004-04-15 03:06 tan2 * module/Exchanger/VTInterpolator.cc, module/Exchanger/VTInterpolator.h: implement interpolateStress() 2004-04-15 02:41 tan2 * module/Exchanger/AbstractSource.h, module/Exchanger/DIM.h, module/Exchanger/FEMInterpolator.h, module/Exchanger/TractionInterpolator.h, module/Exchanger/TractionSource.h, module/Exchanger/VTInterpolator.h, module/Exchanger/VTSource.h: 1. add a new constant, 'STRESS_DIM', for the dimension of stress (=6 in 3D) 2. in Interpolator and Source, stress has correct dimension now 3. add virtual function 'interpolateDisplacement' in Source 2004-04-15 01:29 tan2 * lib/Common/Element_calculations.c, lib/Common/Instructions.c, lib/Common/Pan_problem_misc_functions.c, lib/Common/global_defs.h, lib/Full/Boundary_conditions.c, lib/Regional/Boundary_conditions.c: convert b.c. data structure to support traction b.c. on all sides of a element 2004-04-13 06:30 tan2 * lib/Common/Element_calculations.c: bug fix 2004-04-13 06:23 tan2 * lib/Common/Element_calculations.c: modify get_elt_tr() so that it computes traction per side, not per element. Also, some minor speed improvement. 2004-04-10 08:05 tan2 * module/Exchanger/TractionInterpolator.cc: changes in interfaces of construct_side_c3x3matrix_el() and get_global_side_1d_shape_fn() 2004-04-10 08:03 tan2 * lib/Common/Size_does_matter.c: change the interface of get_global_side_1d_shape_fn(): NS and far is replaced by side 2004-04-10 07:49 tan2 * lib/Common/Element_calculations.c, lib/Common/Size_does_matter.c: 1. change interface of construct_side_c3x3matrix_el(): NS, far is replaced by side 2. in get_elt_tr(), traction is only imposed on top/bottom sides (will relax this constraint later) 2004-04-10 07:00 tan2 * lib/Common/Element_calculations.c: bug fix 2004-04-10 06:56 tan2 * lib/Common/Element_calculations.c, lib/Common/Obsolete.c: move get_elt_h() from Element_calculations.c to Obsolete.c 2004-04-10 06:31 tan2 * lib/Common/Element_calculations.c: 1. finished get_elt_tr(), which computes RHS vector contributed to traction b.c. 2. remove declaration of unused variables 2004-04-10 06:20 tan2 * lib/Common/Size_does_matter.c: 1. finished construct_bdry_det() 2. modify other functions related to sides 3. remove declaration unused variables 2004-04-10 06:19 tan2 * lib/Common/element_definitions.h: add/change side definition 2004-04-10 02:05 tan2 * lib/Common/Element_calculations.c: fixed a bug in calculating RHS force vector due to boundary velocity 2004-04-10 01:39 tan2 * lib/Common/Element_calculations.c: undo previous (uninit'd memory) bug fix -- it is not a bug 2004-04-09 07:13 tan2 * lib/Common/Element_calculations.c: fixed a bug in initializing array 2004-04-06 02:36 tan2 * module/Exchanger/FEMInterpolator.cc: minor modification to previous check-in 2004-04-05 06:03 tan2 * module/Exchanger/FEMInterpolator.cc: sometimes after coordinate conversion, surface nodes of different solvers won't line up, need this special treatment -- if x is a little bit above my top surface, move it back to the surface 2004-03-29 07:31 tan2 * module/Regional/mesher.cc: in sphere_launch(), call construct_bdry_det() to compute (6-side) surface determinants of boundary elements 2004-03-29 07:22 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: usage of VTOutlet and VTInlet is replaced by TractionInlet and TractionOutlet. Goal: impose normal velocity and shear traction as bounary conditions 2004-03-29 07:20 tan2 * pyre/Components/Exchanger/Inlet.py: bug fix 2004-03-29 07:19 tan2 * module/Exchanger/TractionInterpolator.cc, module/Exchanger/TractionInterpolator.h, module/Exchanger/TractionOutlet.cc, module/Exchanger/TractionOutlet.h, module/Exchanger/TractionSource.cc, module/Exchanger/TractionSource.h, module/Exchanger/exchangers.cc: 1. TractionOutlet c'tor has a new argument to specify 'mode'. Avaiable modes are: 'F': send traction only 'V": send velocity only (this is somewhat duplicated with VTOutlet) 'FV": send both traction and velocity 2. TractionSource and TractionInterpolateor have to know how to interpolate velocity (because of 1) 3. remove domian_cutout() 4. restructure TractionInterpolateor class to reuse CitcomS library 2004-03-29 07:05 tan2 * module/Exchanger/bindings.cc: add bindings to TractionOutlet and TractionInlet 2004-03-29 07:05 tan2 * module/Exchanger/Make.mm, module/Exchanger/TractionInlet.cc, module/Exchanger/TractionInlet.h, module/Exchanger/inlets_outlets.cc, module/Exchanger/inlets_outlets.h: add new class TractionInlet and its bindings 2004-03-29 07:01 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: send/recv/broadcast normal array as well 2004-03-27 08:10 steve * module/Exchanger/Make.mm: changed from $TOOLS_DIR/lib to $TOOL_LIBDIR 2004-03-27 08:04 tan2 * lib/Common/Element_calculations.c: 1. extract repeated codes to a new function add_force() 2. remove unused variables 3. add new function to compute RHS of momemtum eqn due to traction b.c. (not finished yet) 2004-03-27 07:42 tan2 * lib/Common/Size_does_matter.c: 1. move get_global_1d_shape_fn_1() form Size_does_matter.c to Obsolete.c 2. add new function construct_bdry_det() to compute (6-side) surface determinant of boundary element 3. isolate some repeated codes to new function get_x_cart() 2004-03-27 07:41 tan2 * lib/Common/Obsolete.c: move get_global_1d_shape_fn_1() form Size_does_matter.c to Obsolete.c 2004-03-27 07:39 tan2 * lib/Common/element_definitions.h: add a section defines the ordering of the 6 surfaces of a element and the ordering of 4 nodes within each surface 2004-03-27 07:39 tan2 * lib/Common/global_defs.h: add definition of new structure Bdry and declaration of E->boundary. This structure is used to mark boundary element and store its (6-side) surface determinants 2004-03-27 07:36 tan2 * lib/Full/Version_dependent.c, lib/Regional/Version_dependent.c: 1. add new function construct_boundary() to find boundary elements 2. fix bug in using fscanf() 3. remove unused variables 2004-03-27 01:53 tan2 * lib/Common/Instructions.c: 'read uninitialized value' bug fixed 2004-03-26 06:45 tan2 * lib/Common/Tracer_advection.c: minor bug fixed 2004-03-26 06:42 tan2 * lib/Regional/Sphere_related.c: minor bug fixed 2004-03-25 04:14 tan2 * lib/Common/Instructions.c: *** empty log message *** 2004-03-25 04:13 tan2 * lib/Common/Convection.c, lib/Common/Instructions.c: input of Rayleigh number is moved 2004-03-17 07:17 tan2 * lib/Common/Topo_gravity.c, lib/Common/global_defs.h, lib/Full/Parallel_related.c, lib/Regional/Parallel_related.c: 1. add function pointers void (* exchange_node_d) and void (* exchange_node_f) in struct All_variables 2. replace calls to exchange_node_d() by void (* exchange_node_d) in Topo_gravity.c. Because exchange_node_d() is version dependent and can't be called from Exchanger. 2004-03-17 05:07 tan2 * module/Regional/mesher.cc: construct surface arrays and compute surface determinant 2004-03-17 05:03 tan2 * lib/Common/Construct_arrays.c, lib/Common/Instructions.c, lib/Common/Size_does_matter.c: 1. construct surface node and element array for bookkeeping 2. compute surface determinant 2004-03-14 07:11 tan2 * lib/Common/Size_does_matter.c: remove debugging print out 2004-03-13 07:13 tan2 * lib/Common/Topo_gravity.c: another bug fix 2004-03-13 07:05 tan2 * lib/Common/Topo_gravity.c: restructure function get_STD_topo() 2004-03-13 07:05 tan2 * lib/Common/Output.c: bug fix 2004-03-13 07:01 tan2 * lib/Common/Output.c: isolate calculation and output of horizontal average into one function 2004-03-12 07:25 tan2 * pyre/Components/Exchanger/Inlet.py, pyre/Components/Exchanger/Outlet.py: 1. add TractionInlet class 2. simplified bindings for inlets and outlets 2004-03-12 07:23 tan2 * module/Exchanger/bindings.cc, module/Exchanger/inlets_outlets.cc, module/Exchanger/inlets_outlets.h: simplified bindings to inlets and outlets 2004-03-12 06:50 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: add attribute 'normal_' to indicate the direction of outward normal on each node. 2004-03-12 06:46 tan2 * module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: remove obsolete bindings 2004-03-12 06:42 tan2 * module/Exchanger/Sink.cc, module/Exchanger/VTInlet.cc: bug fixed 2004-03-12 06:36 tan2 * module/Exchanger/Sink.h, module/Exchanger/VTInlet.cc: change method name: 'recvArray2D' --> 'recv' 2005-08-23 03:27 unknown_user * module/Exchanger/BoundaryCondition.cc, module/Exchanger/BoundaryCondition.h, module/Exchanger/InteriorImposing.cc, module/Exchanger/InteriorImposing.h, module/Exchanger/Source.cc, module/Exchanger/Source.h, module/Exchanger/TractionBC.cc, module/Exchanger/TractionBC.h: [vcp] delete of edited revision with dead state 2004-03-12 06:22 tan2 * module/Exchanger/BoundaryCondition.cc, module/Exchanger/BoundaryCondition.h, module/Exchanger/InteriorImposing.cc, module/Exchanger/InteriorImposing.h, module/Exchanger/Make.mm, module/Exchanger/Source.cc, module/Exchanger/Source.h, module/Exchanger/TractionBC.cc, module/Exchanger/TractionBC.h: remove obsolete files 2004-03-11 09:07 tan2 * pyre/Components/Exchanger/Inlet.py: method 'storeTimestep' is moved up to the parent class 2004-03-11 09:06 tan2 * module/Exchanger/Inlet.cc, module/Exchanger/Inlet.h, module/Exchanger/VTInlet.cc, module/Exchanger/VTInlet.h, module/Exchanger/bindings.cc, module/Exchanger/inlets_outlets.cc, module/Exchanger/inlets_outlets.h: 1. move attributes 'fge_t' and 'cge_t', methods 'storeTimestep' and 'getFactor' from VTInlet to Inlet. 2. change the binding accordingly 2004-02-27 07:04 tan2 * module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/initTemperature.cc, module/Exchanger/initTemperature.h: delete initTemperatureSource(), initTemperatureSink() and their bindings. 2004-02-27 06:29 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: use Inlet and Outlet 2004-02-27 06:29 tan2 * pyre/Components/Exchanger/Inlet.py, pyre/Components/Exchanger/Make.mm, pyre/Components/Exchanger/Outlet.py: add various classes for exchanger 2004-02-27 03:27 tan2 * module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h: 1. remove "before_send_bbox" and "converted_bbox" journal log 2. add 'send' and 'recv' methods 2005-08-23 03:27 unknown_user * module/Exchanger/InformationSourceSink.h: [vcp] delete of edited revision with dead state 2004-02-26 07:29 tan2 * module/Exchanger/InformationSourceSink.h: obsolete (actually never used), replaced by Inlet and Outlet classes. 2004-02-26 07:25 tan2 * pyre/Components/Exchanger/FineGridExchanger.py: activate journal.info("incompressibility") 2004-02-26 07:24 tan2 * module/Exchanger/AreaWeightedNormal.cc: outputing outflow information is moved to journal.info category 2004-02-26 07:07 tan2 * module/Exchanger/Make.mm: add AbstractSource.cc 2004-02-26 07:07 tan2 * module/Exchanger/AbstractSource.cc, module/Exchanger/AbstractSource.h, module/Exchanger/TractionSource.cc, module/Exchanger/TractionSource.h, module/Exchanger/VTSource.cc, module/Exchanger/VTSource.h: 1. add AbstractSource.cc 2. move initialization of TractionSource and VTSource to AbstractSource 2004-02-25 08:54 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: new Exchanger, using inlets and outlets. 2004-02-25 04:40 tan2 * module/Exchanger/Make.mm: add new source files 2004-02-25 04:39 tan2 * module/Exchanger/bindings.cc: add bindings to various inlet and outlet classes in method table 2004-02-25 04:37 tan2 * module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: move 'createVTSource' function to inlets_outlets.cc 2004-02-25 04:35 tan2 * module/Exchanger/inlets_outlets.cc, module/Exchanger/inlets_outlets.h: bindings for various inlets and outlets classes 2004-02-25 04:34 tan2 * module/Exchanger/BoundaryVTInlet.cc, module/Exchanger/BoundaryVTInlet.h: class which consumes nodal velocities and temperature and enforce imcompressibility constraint, replacing BoundaryConditionSink class. 2004-02-25 04:26 tan2 * module/Exchanger/VTInlet.cc, module/Exchanger/VTInlet.h: class which consuming nodal velocities and temperature, replacing (part of) BoundaryConditionSink class. 2004-02-25 04:24 tan2 * module/Exchanger/VTOutlet.cc, module/Exchanger/VTOutlet.h: class which provides nodal velocities and temperature, replacing (part of) BoundaryConditionSource class. 2004-02-25 04:20 tan2 * module/Exchanger/VTSource.cc, module/Exchanger/VTSource.h: class which sends velocity and temperature across the network, replacing Source class. 2004-02-25 04:14 tan2 * module/Exchanger/TractionOutlet.cc, module/Exchanger/TractionOutlet.h: class which provides nodal traction, replacing TractionBC class. 2004-02-25 04:09 tan2 * module/Exchanger/FEMInterpolator.cc: small modification on convergence criterion 2004-02-25 04:03 tan2 * module/Exchanger/Inlet.cc, module/Exchanger/Inlet.h, module/Exchanger/Outlet.cc, module/Exchanger/Outlet.h: base classes for send/receive/impose exchanged information 2004-02-12 07:34 ces74 * lib/Common/Output.c: Pressure output added 2004-02-07 07:28 tan2 * lib/Common/Output.c: increase number of digits for coordinate and viscosity output 2004-02-06 04:17 tan2 * lib/Common/Initial_temperature.c, lib/Common/convection_variables.h, module/Regional/setProperties.cc: increase max. allowed # of perturbations to 255 2004-02-06 03:56 tan2 * module/Regional/setProperties.cc: change echo format of get*Property 2004-02-06 03:46 tan2 * module/Exchanger/misc.cc: allocate and init temperature boundary condition flags 2004-02-06 03:45 tan2 * module/Exchanger/FEMInterpolator.cc, module/Exchanger/Sink.cc: changes in journal log 2004-02-06 03:06 tan2 * pyre/Components/IC.py, pyre/Components/Visc.py: use pyre.properties.list instead of pyre.properties.sequence for several component properties because: 1. sequence only accepts integer from command line input 2. list doesn't require '[]' around command line input 2004-02-05 08:46 tan2 * visual/pasteCitcomData.sh: use space char. as field delimiter instead of tab char. 2004-01-23 04:06 puru * module/Exchanger/InteriorImposing.cc, module/Exchanger/InteriorImposing.h: Temporarily setVBCFlag is called inside recvV, which is computationally inefficient for testing purpose. 2004-01-22 11:38 puru * module/Exchanger/BoundedBox.cc: Corrected to include the case when one bounded box completely subsumes the other boundedbox 2004-01-22 04:46 tan2 * module/Exchanger/AreaWeightedNormal.h: #include mpi.h in the header 2004-01-22 02:09 tan2 * module/Exchanger/Source.h: #include BoundedBox.h in the header 2004-01-22 01:40 tan2 * module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/AreaWeightedNormal.h: remove Sink from the arguement list of computeWeightedNormal() 2004-01-21 08:13 puru * module/Exchanger/InteriorImposing.cc: A typo has been corrected 2004-01-21 08:13 puru * module/Exchanger/exchangers.cc: Corrected a typo 2004-01-21 06:57 tan2 * module/Exchanger/misc.cc: 1. seperate codes that is in original initTemperatureTest() to new functions: hot_blob(), add_hot_blob() and debug_output() 2. add new function five_hot_blob(), which put a hot blob in the center of bbox, and 4 hot blobs outside and around bbox. 2004-01-19 05:07 tan2 * module/Exchanger/FEMInterpolator.cc: add comments 2004-01-18 06:22 ces74 * module/Exchanger/TractionInterpolator.cc: a bug fixed in traction calculation. 2004-01-17 10:10 puru * module/Exchanger/InteriorImposing.cc, module/Exchanger/InteriorImposing.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: Facility to impose velocity from Snac to Citcom has been added. 2004-01-16 10:05 tan2 * module/Exchanger/FEMInterpolator.cc: revert to previous version 2004-01-16 09:50 tan2 * module/Exchanger/FEMInterpolator.cc: changes to make floating point comparison friendly 2004-01-15 11:00 ces74 * module/Exchanger/TractionInterpolator.h: header file for TractionInterpolator.cc 2004-01-15 10:59 ces74 * module/Exchanger/TractionBC.cc: converted fbc can be printed out for debugging. 2004-01-15 09:04 ces74 * module/Exchanger/TractionInterpolator.cc: 1. in initComputeTraction, bbox is now boundedMesh.tightBBox(). 2. domain_cutout() causes a problem in Citcom. Until fixed, it's not called. 2004-01-15 08:48 tan2 * visual/batchcombine.py: script to retrieve/combine Citcom data in OpenDX-friendly format 2004-01-15 08:47 tan2 * visual/batchpaste.sh: run 'rsh ...' in the foreground 2004-01-15 08:17 tan2 * visual/dxgeneral.sh: can have multiple input files now 2004-01-15 07:22 tan2 * visual, visual/batchpaste.sh, visual/combine.py, visual/dxgeneral.sh, visual/getlog.sh, visual/pasteCitcomData.sh: add scripts to combine/retrieve Citcom data 2004-01-15 03:07 tan2 * module/Exchanger/BoundedMesh.cc: small improvement 2004-01-15 02:52 tan2 * module/Exchanger/Boundary.cc: call tightBBox() to init bbox_ 2004-01-15 02:49 tan2 * module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h: add new method tightBBox() which returns a tight bounding box for current X_ 2005-08-23 03:26 unknown_user * module/Exchanger/TractionBC.cc~, module/Exchanger/TractionBC.h~: [vcp] delete of edited revision with dead state 2004-01-15 00:52 puru * module/Exchanger/TractionBC.cc~, module/Exchanger/TractionBC.h~: TractionBC.cc~ and Traction.h~ have been removed from repository 2004-01-14 10:40 ces74 * module/Exchanger/TractionBC.cc, module/Exchanger/TractionInterpolator.cc, module/Exchanger/bindings.cc, module/Exchanger/exchangers.h: bug fixed. The changes in the name of classes are corrected. 2004-01-14 10:11 ces74 * module/Exchanger/Make.mm, module/Exchanger/TractionBC.cc, module/Exchanger/TractionBC.cc~, module/Exchanger/TractionBC.h, module/Exchanger/TractionBC.h~, module/Exchanger/TractionSource.cc, module/Exchanger/TractionSource.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1) New files TractionBC.cc TractionBC.h have been added. 2) sendTraction is now a method of TractionSource. 2004-01-14 08:34 tan2 * module/Exchanger/initTemperature.cc: add function basal_tbl_central_hot_blob() 2004-01-14 08:34 tan2 * module/Exchanger/Source.cc, module/Exchanger/Source.h: definition of destructor is moved from Source.h to Source.cc 2004-01-14 02:53 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, pyre/Solver/Solver.py: change Solver attributes so that Exchangers don't access Solver.inventory.IC.inventory directly 2004-01-13 11:55 tan2 * module/Exchanger/FEMInterpolator.cc, module/Exchanger/FEMInterpolator.h, module/Exchanger/misc.cc: new FEMInterpolator using every element nodes to do interpolation (was using 4 element nodes) 2004-01-13 11:01 ces74 * pyre/Solver/Solver.py: initialization was improper. 2004-01-13 09:32 tan2 * drivers/Full/Make.mm, drivers/Regional/Make.mm: when linking binary file, will check dependency on object file 2004-01-13 09:21 ces74 * module/Exchanger/BoundaryCondition.cc, module/Exchanger/BoundedMesh.cc, module/Exchanger/Interior.cc, module/Exchanger/InteriorImposing.cc, module/Exchanger/Make.mm, module/Exchanger/SIUnit.cc, module/Exchanger/Sink.cc, module/Exchanger/Source.cc, module/Exchanger/exchangers.cc: bugs fixed. For synchronization between users. 2004-01-10 06:42 ces74 * module/Exchanger/FEMInterpolator.cc: Added a comment line 2004-01-09 14:10 ces74 * module/Exchanger/CartesianCoord.cc: fixed bugs in degenerate cases. 2004-01-09 09:25 tan2 * module/Exchanger/Convertor.cc: when unconverting, un-transformate first, then non-dimensionalize next. 2004-01-09 08:38 ces74 * module/Exchanger/CartesianCoord.cc: fixed bug in degenerate case 2004-01-09 07:43 tan2 * pyre/Solver/Solver.py: coupler get init'ed after setProperties() is called 2005-08-23 03:25 unknown_user * module/Exchanger/Dimensional.cc, module/Exchanger/Dimensional.h: [vcp] delete of edited revision with dead state 2004-01-09 07:31 tan2 * module/Exchanger/Dimensional.cc, module/Exchanger/Dimensional.h: renamed to SIUnit 2004-01-09 05:19 tan2 * module/Exchanger/CartesianCoord.cc: 'Array2D: second index out of range' bug fixed 2005-08-23 03:25 unknown_user * module/Exchanger/Interpolator.cc, module/Exchanger/Interpolator.h: [vcp] delete of edited revision with dead state 2004-01-09 04:42 tan2 * module/Exchanger/FEMInterpolator.cc, module/Exchanger/FEMInterpolator.h, module/Exchanger/Interpolator.cc, module/Exchanger/Interpolator.h, module/Exchanger/Make.mm, module/Exchanger/Source.cc, module/Exchanger/Source.h, module/Exchanger/TractionInterpolator.cc, module/Exchanger/TractionInterpolator.h, module/Exchanger/TractionSource.cc, module/Exchanger/VTInterpolator.cc, module/Exchanger/VTInterpolator.h: 1. Interpolator is renamed to VTInterpolator 2. Calculation of shape function is moved to FEMInterpolator 3. VTInterpolator and TractionInterpolatore inherit from FEMInterpolator 4. change Source and TractionSource accordingly 2004-01-09 02:40 tan2 * module/Exchanger/dimensionalization.h: obsolete 2004-01-09 02:38 tan2 * module/Exchanger/SIUnit.cc, module/Exchanger/SIUnit.h: dimensionalize temperature is done 2004-01-09 02:37 tan2 * module/Regional/setProperties.cc: bug fix 2004-01-09 02:26 tan2 * lib/Common/Instructions.c, module/Regional/setProperties.cc, pyre/Components/Const.py: 1. Const class has new property 'surftemp' 2. Instruction.c and setProperties.cc readin E->data.surf_temp and calculate temperature scale from Rayleigh number and other dimensional constants 2004-01-09 02:04 tan2 * module/Exchanger/Convertor.cc, module/Exchanger/Convertor.h: use plain pointer instead of auto_ptr 2004-01-09 00:28 puru * module/Exchanger/CartesianCoord.cc: Bounded box has been transformed while accounting for degenerate cases 2004-01-08 10:29 tan2 * module/Exchanger/AbstractSource.h, module/Exchanger/BoundaryCondition.cc, module/Exchanger/Convertor.cc, module/Exchanger/Interpolator.cc, module/Exchanger/Sink.cc, module/Exchanger/Sink.h, module/Exchanger/Source.cc, module/Exchanger/Source.h, module/Exchanger/TractionInterpolator.cc, module/Exchanger/TractionSource.cc, module/Exchanger/TractionSource.h: convert (dimensionalization + coordinate transformation) of exchanged velocity/temperature is done 2004-01-08 09:50 tan2 * module/Exchanger/exchangers.cc: bug fixed 2004-01-08 09:50 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: typo fixed 2004-01-08 07:54 tan2 * module/Exchanger/InteriorImposing.cc, module/Exchanger/InteriorImposing.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1. remove unnecessary functions in InteriorImposingSink and their bindings 2. convert/unconvert temperature to standard/internal representation 2004-01-08 06:01 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: changes in dimensionalization and coordinate transformation scheme 2004-01-08 05:54 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h, module/Exchanger/CartesianCoord.cc, module/Exchanger/CartesianCoord.h, module/Exchanger/Convertor.cc, module/Exchanger/Convertor.h, module/Exchanger/Interior.cc, module/Exchanger/Interior.h, module/Exchanger/Interpolator.cc, module/Exchanger/Make.mm, module/Exchanger/SIUnit.cc, module/Exchanger/SIUnit.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1. Convertor class will convert coordinate/velocity/traction/time/... from CitcomS' internal representation to some standard representation (currently in SI unit and Cartesian coordinate) 2. change other parts of code accordingly 2004-01-07 16:12 tan2 * module/Exchanger/exchangers.cc: remove calls to Transformation class 2005-08-23 03:24 unknown_user * module/Exchanger/Transformational.h: [vcp] delete of edited revision with dead state 2004-01-07 15:41 tan2 * module/Exchanger/Transformational.cc, module/Exchanger/Transformational.h: renamed to CartesianCoord 2004-01-07 09:07 tan2 * module/Exchanger/Interpolator.cc, module/Exchanger/Interpolator.h: remove obsolete function findMaxGridSpacing() 2004-01-07 06:40 puru * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h, module/Exchanger/Interior.cc, module/Exchanger/Interior.h, module/Exchanger/exchangers.cc: Transformation from Spherical coordinate system to Euclidean coordinate is done at citcom end 2004-01-07 06:38 puru * module/Exchanger/CartesianCoord.cc, module/Exchanger/CartesianCoord.h, module/Exchanger/Transformational.cc, module/Exchanger/Transformational.h: Added a new cleass Transformational for transforming from one coordinate system to another coordinate system 2003-12-31 05:46 tan2 * module/Exchanger/BoundaryCondition.cc: temporary fix 2003-12-31 05:46 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/BoundedBox.cc, module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h, module/Exchanger/Interior.cc, module/Exchanger/Interior.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: optional dimensionalization 2003-12-31 05:44 tan2 * module/Exchanger/Dimensional.cc, module/Exchanger/Dimensional.h, module/Exchanger/Make.mm, module/Exchanger/SIUnit.cc, module/Exchanger/SIUnit.h: add Dimensional class 2003-12-31 05:42 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: 1. add new property 'dimensional': if it is true, quantities exchanged are dimensional 2. (optional) dimensional BoundedBox, Boundary, Interior and timestep 2003-12-30 08:31 ces74 * module/Exchanger/BoundedBox.cc: dimensional_len was being used without a value assigned. --> temporarily, not used in regionalGlobalBoundedBox(). 2003-12-25 06:46 ces74 * pyre/Solver/Solver.py: a bug fixed: initTemperature is an attribute of exchanger, not coupler. 2003-12-23 15:02 puru * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: Initial condition initialization has been done at a higher level 2003-12-23 08:42 puru * module/Exchanger/Boundary.cc, module/Exchanger/InteriorImposing.cc, module/Exchanger/dimensionalization.h: fixed dimensionalization 2003-12-23 01:47 puru * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: all_variables has been moved from Exchanger to Finegrid and Coarsegrid Exchangers (for CitcomS-Snac Coupling) 2003-12-20 02:21 tan2 * module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: add bindings to functions initTemperatureSink(), initTemperatureSource() and modifyT() for exchange initial temperature field between CitcomS-CitcomS 2003-12-19 16:05 tan2 * module/Exchanger/initTemperature.h: add functions initTemperatureSink(), initTemperatureSource() and modifyT() for exchange initial temperature field between CitcomS-CitcomS 2003-12-19 06:30 puru * pyre/Components/Exchanger/__init__.py: Changed __init__.py to export Exchange class 2003-12-17 12:27 puru * module/Exchanger/Boundary.cc, module/Exchanger/BoundaryCondition.cc, module/Exchanger/BoundedBox.cc, module/Exchanger/Interior.cc, module/Exchanger/InteriorImposing.cc, module/Exchanger/Interpolator.cc, module/Exchanger/TractionInterpolator.cc, module/Exchanger/dimensionalization.h: 1) Added dimensionalize.h which contains variables for dimensionalizing CitcomS variables 2) All variables sent out by Citcom exchanger are dimensionalized 3) All variables received in by Citcom exchanger are non-dimensionalized 2003-12-17 09:35 puru * module/Exchanger/Interpolator.cc: fixed bug 2003-12-17 03:09 tan2 * module/Exchanger/Make.mm: add compilation for TractionInterpolator.cc and TractionSource.cc 2003-12-17 03:08 tan2 * module/Exchanger/Source.cc, module/Exchanger/Source.h: remove functions about traction interpolation (moved to TractionSource) 2003-12-17 02:50 tan2 * module/Exchanger/TractionSource.cc, module/Exchanger/TractionSource.h: source for CitcomS-Snac coupling 2003-12-16 11:01 puru * module/Exchanger/Boundary.cc, module/Exchanger/BoundedBox.cc, module/Exchanger/Interior.cc, module/Exchanger/Interpolator.cc: Dimensionalized exchanger part for the ease of interaction with Snac 2003-12-16 10:14 tan2 * module/Exchanger/FEMInterpolator.h, module/Exchanger/TractionInterpolator.cc, module/Exchanger/TractionInterpolator.h: 1. remove const-ness in Interpolate*() functions 2. remove passing E in TractionInterpolator 3. remove static qualifier of some local var. in TractionInterpolator 2003-12-04 08:28 puru * module/Exchanger/InteriorImposing.cc, module/Exchanger/TractionInterpolator.cc: Conevrsion from dimensional to non-dimensional and vice-versa 1) Forces have been dimensionalized in TractioInterpolator before sent to Snac 2) Velocities have been non-dimensionalized in InteriorImposing after receiving from Snac 2003-11-30 09:22 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: add restartTemperature() for read/send/receive/modify restarted temperature 2003-11-30 09:21 tan2 * module/Exchanger/initTemperature.cc: add comments and call temperatures_conform_bcs() 2003-11-30 08:12 tan2 * lib/Common/Process_buoyancy.c: fix a bug of flushing (maybe) non-existing file handle 2003-11-29 06:34 ces74 * module/Exchanger/TractionInterpolator.cc, module/Exchanger/TractionInterpolator.h: a new class added, but not being used yet. 2003-11-29 06:32 ces74 * module/Exchanger/Interpolator.cc: interpolateF removed. 2003-11-29 06:32 ces74 * module/Exchanger/Interpolator.h: interpolateF removed 2003-11-29 06:25 ces74 * module/Exchanger/exchangers.h: new definitions added for domain_cutout and sendTraction 2003-11-29 06:23 ces74 * module/Exchanger/exchangers.cc: new bindings added: PyObject * pyExchanger_sendTraction(PyObject *, PyObject *args) PyObject * pyExchanger_domain_cutout(PyObject *, PyObject *args) 2003-11-29 06:21 ces74 * module/Exchanger/bindings.cc: two entries added: sendTraction and domain_cutout 2003-11-29 06:20 ces74 * module/Exchanger/BoundaryCondition.h: new functions added: void sendTraction() void domain_cutout() 2003-11-29 06:20 tan2 * module/Regional/bindings.cc, module/Regional/initial_conditions.cc, module/Regional/initial_conditions.h: add bindings to 'restartTemperature()' and 'constructTemperature()', which are used for temperature initial condition 2003-11-29 06:19 ces74 * module/Exchanger/Source.h: new functions defined: void interpolateF(Array2D& F, All_variables* E) const; void domain_cutout(const All_variables* E) const; 2003-11-29 06:18 ces74 * module/Exchanger/Source.cc: new functions added: void Source::interpolateF() void Source::domain_cutout() 2003-11-29 06:18 tan2 * module/Regional/setProperties.cc: *** empty log message *** 2003-11-29 06:17 tan2 * pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/IC.py, pyre/Solver/Solver.py: move properties 'inputdiffusivity' from Solver to Advecton_diffusion; 'restart', 'post_p', 'solution_cycles_init', and 'zero_elapsed_time' from Solver to IC 2003-11-29 06:16 ces74 * module/Exchanger/BoundaryCondition.cc: The body of the following functions are commented out: void BoundaryConditionSource::sendTraction() void BoundaryConditionSource::domain_cutout() 2003-11-29 06:14 tan2 * pyre/CoupledApp.py, pyre/SimpleApp.py: add factory functions 2003-11-29 05:42 ces74 * lib/Common/Size_does_matter.c: two new functions added: 1. void construct_side_c3x3matrix_el() 2. void get_global_side_1d_shape_fn() 2003-11-27 07:27 tan2 * drivers/Full/Make.mm, drivers/Regional/Make.mm: modify Make.mm so that it always make a new binary file 2003-11-27 07:25 tan2 * lib/Regional/Parallel_related.c: fix a bug of memory leak 2003-11-27 06:31 tan2 * lib/Regional/Geometry_cartesian.c: fix a bug when reading input parameters 2003-11-27 05:26 tan2 * lib/Common/Initial_temperature.c, lib/Full/Version_dependent.c, lib/Regional/Version_dependent.c: 1. combine and move 'restart_tic_from_file()' from Version_dependent.c to Initial_temperature.c 2. fix bug in calculating dimensional information: E->data.layer_km is in kilometers, not in meters. 2003-11-27 05:24 tan2 * lib/Full/Make.mm, lib/Regional/Make.mm: remove options related to library linking 2003-11-26 02:41 puru * module/Exchanger/InteriorImposing.cc: fixed a bug 2003-11-26 01:58 puru * module/Exchanger/InteriorImposing.cc, module/Exchanger/InteriorImposing.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: Added facility (recvV) for CitcomS to receive velocity boundary condition in Snac-Citcom coupling 2003-11-25 10:59 tan2 * module/Exchanger/AbstractSource.h, module/Exchanger/FEMInterpolator.h, module/Exchanger/InformationSourceSink.h: base classes for exchanger 2003-11-25 05:38 ces74 * lib/Common/Instructions.c: The line for assigning memory to E->traction[] has been removed. 2003-11-25 05:37 ces74 * lib/Common/global_defs.h: traction[] array removed. 2003-11-25 05:37 ces74 * lib/Common/Topo_gravity.c: populate E->gstress in get_STD_topo. 2003-11-25 05:26 ces74 * lib/Common/Instructions.c: memory allocation to "E->gstress" and "E->traction[j]". 2003-11-25 05:25 ces74 * lib/Common/global_defs.h: new data members, "gstress" and "traction", added to the "All_variables" structure. 2003-11-25 05:22 ces74 * module/Exchanger/Interpolator.cc: a typo fixed 2003-11-25 05:03 ces74 * module/Exchanger/Interpolator.h: The prototype of "interpolateF" added to the class "Interpolator" as a public member function. 2003-11-25 05:03 ces74 * module/Exchanger/Source.h: The prototype of "interpolateF" added to the class "Source" as a public member function. 2003-11-24 03:08 ces74 * module/Exchanger/exchangers.h: the definition of "pyExchanger_sendTraction" added. 2003-11-24 03:06 ces74 * module/Exchanger/exchangers.cc: Python binding for sendTraction implemented. 2003-11-24 03:04 ces74 * module/Exchanger/bindings.cc: "sendTraction" added to Exchanger's method table 2003-11-24 02:25 ces74 * module/Exchanger/BoundaryCondition.cc: a typo fixed 2003-11-24 02:25 ces74 * module/Exchanger/BoundaryCondition.cc: BoundaryConditionSource::sendTraction() has been implemented. This is for sending CitcomS' traction to other app as force BC. 2003-11-24 02:21 ces74 * module/Exchanger/BoundaryCondition.h: 1. A datamember, "fbc", added to the class, "BoundaryConditionSource". 2. A public memberfunction, "sendTraction()" added to "BoundaryConditionSource". These are for sending CitcomS' traction to other app. as force BC. 2003-11-24 02:11 ces74 * module/Exchanger/Source.cc: a typo fixed 2003-11-24 02:10 ces74 * module/Exchanger/Source.cc: Source::interpolateF added. This is for sending CitcomS' traction to other app's as force BC. 2003-11-24 02:05 ces74 * module/Exchanger/Interpolator.cc: a typo fixed 2003-11-24 02:02 ces74 * module/Exchanger/Interpolator.cc: interpolateF added. This is for sending CitcomS' traction to other app's force BC. 2003-11-23 16:33 steve * module/Regional/Make.mm: changed from $(TOOLS_DIR)/lib to $(TOOLS_LIBDIR) as the former is not always true (if you let pyre choose the export dir it will be in .../lib/Linux...) 2003-11-23 16:31 steve * module/Full/Make.mm: changed from $(TOOLS_DIR)/lib to $(TOOLS_LIBDIR) as the former is not always true (if you let pyre choose the export dir it will be in .../lib/Linux...) 2003-11-22 07:15 tan2 * module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/Boundary.cc, module/Exchanger/BoundaryCondition.cc, module/Exchanger/BoundedMesh.h, module/Exchanger/Interior.cc, module/Exchanger/InteriorImposing.cc: 1. attribute name changed: BoundedMesh.meshID ==> BounedMesh.nodeID 2. in BoundaryConditionSink::imposeTBC, call 'temperatures_conform_bcs' 2003-11-20 03:06 tan2 * lib/Full/Read_input_from_files.c: restart file has cap number 0~11 (was 1~12) 2003-11-12 03:45 ces74 * module/Exchanger/BoundaryCondition.cc: setTBCFlag and imposeTBC completed. 2003-11-12 03:29 tan2 * module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h, module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/Interior.cc, module/Exchanger/Interior.h, module/Exchanger/InteriorImposing.cc, module/Exchanger/InteriorImposing.h, module/Exchanger/Interpolator.cc, module/Exchanger/Sink.cc, module/Exchanger/Sink.h, module/Exchanger/Source.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h, module/Exchanger/misc.cc, pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: 2-way communication 2003-11-11 05:59 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: change in BoundaryConditionSink c'tor 2003-11-11 05:55 tan2 * module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/AreaWeightedNormal.h, module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h, module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/BoundaryCondition.cc, module/Exchanger/BoundaryCondition.h, module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h, module/Exchanger/Interior.h, module/Exchanger/Make.mm, module/Exchanger/Sink.h, module/Exchanger/Source.h, module/Exchanger/exchangers.cc, module/Exchanger/utilTemplate.cc, module/Exchanger/utilTemplate.h, module/Exchanger/utility.cc, module/Exchanger/utility.h: 1. multi-processor AreaWeightedNormal 2. small improvements 2003-11-08 05:43 puru * module/Exchanger/InteriorImposing.cc, module/Exchanger/InteriorImposing.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: added bindings for two way communication 2003-11-08 04:41 puru * module/Exchanger/Interior.cc: Made it easier to read and initialized bbox_ 2003-11-08 04:39 puru * module/Exchanger/InteriorImposing.cc, module/Exchanger/InteriorImposing.h: Added InteriorImposing for two-way communication 2003-11-07 13:47 puru * module/Exchanger/Interior.cc: fixed the bug 2003-11-07 13:14 puru * module/Exchanger/Interior.cc: Set interior nodes for two way communication 2003-11-07 09:20 tan2 * module/Exchanger/BoundaryCondition.cc, module/Exchanger/BoundaryCondition.h: remove unnecessary base class BoundaryCondition 2005-08-23 03:21 unknown_user * module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h, module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h, module/Exchanger/auto_array_ptr.h: [vcp] delete of edited revision with dead state 2003-11-07 09:08 tan2 * module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/AreaWeightedNormal.h, module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h, module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/BoundaryCondition.cc, module/Exchanger/BoundaryCondition.h, module/Exchanger/BoundedBox.cc, module/Exchanger/BoundedBox.h, module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/DIM.h, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/Exchangermodule.cc, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h, module/Exchanger/Interior.cc, module/Exchanger/Interior.h, module/Exchanger/Interpolator.cc, module/Exchanger/Interpolator.h, module/Exchanger/Make.mm, module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h, module/Exchanger/Sink.cc, module/Exchanger/Sink.h, module/Exchanger/Source.cc, module/Exchanger/Source.h, module/Exchanger/auto_array_ptr.h, module/Exchanger/bindings.cc, module/Exchanger/bindings.h, module/Exchanger/exceptions.cc, module/Exchanger/exceptions.h, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h, module/Exchanger/initTemperature.cc, module/Exchanger/initTemperature.h, module/Exchanger/misc.cc, module/Exchanger/misc.h, module/Exchanger/utilTemplate.cc, module/Exchanger/utilTemplate.h, pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, pyre/CoupledApp.py, pyre/Coupler.py, pyre/Layout.py, pyre/Solver/Solver.py: point-to-point communication 2003-10-31 07:36 tan2 * module/Exchanger/ExchangerClass.cc, module/Exchanger/Mapping.cc: replace c functions/macros (fabs, min, max) with c++ functions 2003-10-31 07:28 tan2 * lib/Common/global_defs.h: add "#if defined(__cplusplus)" clause to skip macro (max, min, SWAP) definition when included in C++ 2003-10-31 06:45 tan2 * module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: fixed a bug that send/receive used different tag. 2003-10-31 06:25 tan2 * tests/Make.mm, tests/array2d.cc: add tests for Array2D class 2003-10-31 06:21 tan2 * module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: 1. add non-blocking version of send/receive 2. move inlined function definition from .h to .cc file 2003-10-30 02:40 tan2 * module/Full/Make.mm, module/Regional/Make.mm, module/Regional/bindings.cc, module/Regional/initial_conditions.cc, module/Regional/initial_conditions.h, module/Regional/mesher.cc, module/Regional/stokes_solver.cc, module/Regional/stokes_solver.h, pyre/Components/IC.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Solver/Solver.py: 1. let IC initialize temperature, pressure, velocity, and viscosity fields 2. let Incompressible call general_stokes_solver_setup() 3. coupler.initTemperature replaces ic.initTemperature 2003-10-30 01:18 tan2 * module/Exchanger/Array2D.h: index range check when debugging 2003-10-29 09:13 tan2 * pyre/CoupledApp.py, pyre/Coupler.py, pyre/Solver/Solver.py: bug fix and small improvement 2003-10-29 07:52 tan2 * module/Regional/bindings.cc, module/Regional/setProperties.cc, module/Regional/setProperties.h: add Solver_set_properties() and its binding 2005-08-23 03:20 unknown_user * pyre/Components/Stokes_solver/Stokes_solver.py: [vcp] delete of edited revision with dead state 2003-10-29 07:51 tan2 * pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/Advection_diffusion/__init__.py, pyre/Components/BC.py, pyre/Components/Const.py, pyre/Components/Exchanger/__init__.py, pyre/Components/IC.py, pyre/Components/Param.py, pyre/Components/Phase.py, pyre/Components/Sphere/RegionalSphere.py, pyre/Components/Sphere/Sphere.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Components/Stokes_solver/Stokes_solver.py, pyre/Components/Stokes_solver/__init__.py, pyre/Components/Visc.py, pyre/CoupledApp.py, pyre/SimpleApp.py, pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: 1. move properties around 2. provide default argurments to all constructors or factories 2003-10-29 03:57 tan2 * module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: 1. add sendSize(), receiveSize(), broadcastSize() and empty() methods 2. send(), receive(), and broadcast() will send/recieve size information and adjust its memory accordingly 2003-10-29 01:24 tan2 * pyre/Controller.py: *** empty log message *** 2003-10-28 10:34 puru * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h, module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: Two way communication between Coarse and Fine Grid has been incorporated 2003-10-28 09:56 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Solver/Solver.py: fixed bugs in time marching and output 2003-10-28 09:55 tan2 * pyre/Components/Sphere/__init__.py: add default component name 2003-10-28 09:52 tan2 * module/Make.mm: change the order of complilation: Exchanger/ is done last 2003-10-28 09:51 tan2 * module/Exchanger/ExchangerClass.cc: change to Array2D.swap() 2003-10-28 09:51 tan2 * module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: 1. implementation changed: using vector as internal representation 2. swap() becomes a member function 2003-10-25 07:45 ces74 * lib/Full/Version_dependent.c: a bug fixed in global_derived_values(): nox = E->mesh.mgunitx * (int) pow(2.0,(double)i), etc. ===> nox = E->mesh.mgunitx * (int) pow(2.0,(double)i)*E->parallel.nprocx, etc. 2003-10-24 12:23 tan2 * tests/coupledcitcoms.py, tests/exchange.py, tests/test1.sh, tests/test2.sh: update tests according to changes in module/ and pyre/ 2003-10-24 12:04 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, pyre/Components/Exchanger/__init__.py: 1. remove unsed attributes 'localLeader' 2. in __init__.py, factory methods now doesn't need any argument 2005-08-23 03:19 unknown_user * pyre/Controller/Make.mm, pyre/Controller/__init__.py, pyre/Coupler/Coupler.py, pyre/Coupler/Make.mm, pyre/Coupler/__init__.py, pyre/Layout/Layout.py, pyre/Layout/Make.mm, pyre/Layout/__init__.py: [vcp] delete of edited revision with dead state 2003-10-24 11:55 tan2 * pyre/Controller.py, pyre/Controller/Controller.py, pyre/Controller/Make.mm, pyre/Controller/__init__.py, pyre/CoupledApp.py, pyre/Coupler.py, pyre/Coupler/Coupler.py, pyre/Coupler/Make.mm, pyre/Coupler/__init__.py, pyre/Layout.py, pyre/Layout/Layout.py, pyre/Layout/Make.mm, pyre/Layout/__init__.py, pyre/Make.mm, pyre/Solver/Solver.py: 1. move Controller.py, Coupler.py, and Layout.py to pyre/ directory 2. change Make.mm accordingly 3. remove unused attributes 'self.localLeader' in Layout, CoupledApp, and Solver 2003-10-24 11:51 tan2 * module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h, module/Exchanger/Boundary.cc, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h, module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h, module/Exchanger/exchangers.cc: 1. add shrink() in Array2D 2. add shrinksize() in Boundary and Mapping 3. write (most) output via journal 4. remove unused attribute 'localLeader' in Exchanger 2003-10-24 02:06 puru * module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: fixed bugs 2003-10-24 01:26 puru * module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: added FindInteriorNodes 2003-10-23 03:33 ces74 * module/Exchanger/AreaWeightedNormal.cc: a bug fixed: in AreaWeightedNormal::imposeConstraint() if(outflow > toleranceOutflow_) ==> if (fabs(outflow) > toleranceOutflow_) 2003-10-22 08:15 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: add resize() method 2003-10-22 08:13 tan2 * module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: 1. resize() will copy the old data to new memory location 2. make reset() private (because its syntax in error-prone) 2003-10-22 00:32 tan2 * tests/test2.sh: with correction on outflow 2003-10-22 00:31 tan2 * tests/test2.sh: coupled citcoms test (4-proc coarse-grid solver, 1-proc fine-grid solver, no correction on outflow) 2003-10-22 00:26 tan2 * tests/test1.sh: functional test of exchanger 2003-10-21 00:13 tan2 * module/Exchanger/AreaWeightedNormal.cc, module/Exchanger/AreaWeightedNormal.h, module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm: more small improvements 2003-10-21 00:12 tan2 * module/Exchanger/Array2D.cc: bug in memory allocation fixed 2003-10-20 02:54 tan2 * module/Exchanger/Array2D.h, module/Exchanger/Mapping.h: fixed a bug in declaration 2003-10-19 08:01 tan2 * module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h, module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h, module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: many many small improvements 2003-10-18 03:18 ces74 * lib/Common/General_matrix_functions.c: A bug fixed in solve_del2_u(): now multigrid method can be used. 2003-10-17 03:06 tan2 * module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: 1. generalize template Array2D, 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', replace 'incoming' and 'outgoing' by 'incomingV', 'outgoingV', 'incomingT' and 'outgoingT' 2. decompose 'imposeConstraint()' into 'computeWeightedNormal()', 'computeOutflow()', and 'reduceOutflow()' 2003-10-06 11:31 tan2 * lib/Common/global_defs.h: header guard #define directive is added 2003-10-06 11:30 tan2 * lib/Common/Viscosity_structures.c: bug preventing viscosity initialization is fixed 2003-10-06 08:09 puru * module/Exchanger/Boundary.cc: Bug associated with round off error of degenerate case in fine grid node to Coarse grid element map has been fixed. 2003-10-06 07:53 puru * module/Exchanger/ExchangerClass.cc: bug associated switching of indices of theta and of theta fi has been fixed 2003-10-06 01:55 tan2 * module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h: 1. smoother temperature field in initTemperature() 2. remove obsolete functions 2003-10-05 06:37 puru * module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h: added method imposeConstraint to correct velocities which are consistent with incompressibility of the fluid. 2003-10-04 21:24 puru * module/Exchanger/ExchangerClass.cc: Boundary conditions for fine mesh have been modified to satisfy incompressiblility constraint in receiveVelocities 2003-10-04 04:50 puru * module/Exchanger/ExchangerClass.cc: net outflow corresponding to velocity boundary conditions has been added. 2003-10-04 02:20 tan2 * module/Exchanger/Boundary.cc: bug fix 2003-10-04 01:36 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: 1. decompose init() to two functions initBound() and findBoundaryNodes() 2. remove init(), all of its functionality is done in mapFindGrid() 3. in mapCoarseGrid(), extend the domain when searching for node mapping 4. use auto_array_ptr for all member arrays to improve exception safety 2003-10-04 01:25 tan2 * module/Exchanger/auto_array_ptr.h: first import, modified from Jack W. Reeves' code on March 1996 issue of the C++ Report. 2003-10-04 01:18 tan2 * pyre/Solver/Solver.py: call coupler.launch() right after mesher.run() to set BC flag and reconstruct ID array 2003-10-04 01:17 tan2 * pyre/Components/Exchanger/FineGridExchanger.py: 1. add call to self.module.setBCFlag() 2. call mapBoundary() before sendBoundary() to reflect change in module/Exchanger/Boundary.cc 2003-10-04 01:12 tan2 * module/Exchanger/FineGridExchanger.cc: 1. calculate boundary.size in a simplified way 2. remove call to boundary.init() (the job of init() is done in mapFindGrid() now) 2003-10-04 01:10 tan2 * module/Exchanger/misc.cc: init E->mesh.nno in commonE() 2003-10-02 08:14 tan2 * module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/Make.mm, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1. add Exchanger::setBCFlag() to set BC Flag and reconstruct E->ID 2. add binding to Exchanger::setBCFlag() 2003-10-02 05:21 tan2 * module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: add Exchanger::initTemperature() and its binding 2003-10-02 05:16 tan2 * pyre/Solver/Solver.py: 1. pass Solver.inventory.datafile to Param.inventory.datafile to get around a bug in pyre 2. add solveVelocities() and solverTemperature() 3. comment out applyBoundaryConditions(). BC is applied by FGE.preVSolverRun() or CGE.postVSolverRun() 4. fix a logical bug, exchanging velocities is done at the correct timestep 2003-10-02 05:07 tan2 * pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py: add property 'datafile' to get around a bug in pyre 2003-10-02 05:06 tan2 * pyre/Coupler.py, pyre/Coupler/Coupler.py: 1. remove solveVelocities() 2. add preVSolverRun() and postVSolverRun() 2003-10-02 05:04 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: 1. remove solverVelocities() 2. add preVSolverRun() and postVSolverRun() 3. add attribute 'toApplyBC' in FGE, which flags applying BC or not 4. print time marching information 2003-09-30 09:02 puru * module/Exchanger/ExchangerClass.cc: fixed degeneracy associated with cge=0 2003-09-30 08:50 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: add solveVelocities() and storeTimestep() 2003-09-30 08:49 tan2 * pyre/Controller.py, pyre/Controller/Controller.py: disable call to applyBoundaryConditions() 2003-09-30 08:48 tan2 * pyre/Coupler.py, pyre/Coupler/Coupler.py: add solveVelocities() 2003-09-30 08:47 tan2 * pyre/Solver/Solver.py: when coupled, call solveVelocities() instead of vsolver.run() 2003-09-30 08:45 puru * module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h: Interpolated Boundary conditions for fine mesh from coarse mesh has been added 2003-09-30 08:33 tan2 * module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1. add attributes 'fge_t' and 'cge_t' in Exchanger class 2. init 'fge_t' and 'cge_t' in constructor 3. add functions storeTimestep() in Exchanger class 4. add binding to storeTimestep() 2003-09-30 07:48 puru * module/Exchanger/Boundary.cc: Modified to account for multiple processes 2003-09-30 07:39 tan2 * module/Full/Make.mm, module/Regional/Make.mm: bug fixed 2003-09-30 05:31 puru * module/Exchanger/Boundary.cc, module/Exchanger/misc.cc: Modified to account for 2*PI crossover in spherical coordinates system 2003-09-30 03:25 tan2 * module/Full/Make.mm, module/Regional/Make.mm: update library and include path 2003-09-30 03:23 tan2 * pyre/Layout.py, pyre/Layout/Layout.py: cosmetics 2003-09-30 03:22 tan2 * pyre/Coupler.py, pyre/Coupler/Coupler.py: bug fix 2003-09-30 03:22 tan2 * module/Regional/setProperties.cc: bug in output fixed 2003-09-30 03:21 tan2 * drivers/Citcom.c, lib/Common/Instructions.c, module/Regional/mesher.cc, pyre/Controller.py, pyre/Controller/Controller.py, pyre/Solver/Solver.py: 1. open 'fptime' is moved to drivers/Citcom.c 2. rename open_log_and_time() to open_log() 3. add time ouput in pyre version 2003-09-30 01:34 puru * module/Exchanger/Boundary.cc: Implemented more efficient search of coarse element for fine mesh nodes 2003-09-30 01:06 tan2 * module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h: 1. add helper functions printDataT() and printDataV() 2. replace old debugging output by printDataV() 2003-09-30 01:03 tan2 * module/Exchanger/misc.cc: 1. allocate and initialize E->sphere.cap[].V 2. change debugging output accordingly 2003-09-29 09:52 puru * module/Exchanger/CoarseGridExchanger.cc: *** empty log message *** 2003-09-29 09:20 puru * module/Exchanger/misc.cc: fixed a bug 2003-09-29 09:09 puru * module/Exchanger/misc.cc: converted from cartesian to spherical coordinates 2003-09-29 09:04 puru * module/Exchanger/Boundary.cc: Converted from cartesian coordinates to spherical coordinates 2003-09-29 04:44 tan2 * pyre/CoupledApp.py: change default coarse solver to full version 2003-09-29 04:44 tan2 * pyre/Controller.py, pyre/Controller/Controller.py: pass 'totalTime' and 'steps' to endTimestep() 2003-09-29 04:43 tan2 * pyre/Coupler.py, pyre/Coupler/Coupler.py: 1. remove call to exchanger.mapBoundary() 2. comment out call to exchanger.initTemperature() 2003-09-29 03:45 tan2 * module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1. wait() and nowait() is replaced by exchangeSignal() 2. add helper functions exchangeInt(), exchangeDouble() and exchangeFloat() 2003-09-29 03:41 tan2 * module/Exchanger/misc.cc: cosmetics 2003-09-29 03:40 tan2 * pyre/Controller.py, pyre/Controller/Controller.py, pyre/Coupler.py, pyre/Coupler/Coupler.py, pyre/Solver/Solver.py: 1. add attribute 'self.done' in Controller indicating end of simulation 2. change argument list and return list of endTimestep() 3. Coupler can terminate the time marching by returning False at endTimestep() 4. synchronization between solvers is done in endTimestep 2003-09-29 03:36 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, tests/exchange.py: 1. synchronization between solvers is done in endTimestep() (was in NewStep()) 2. pass the test on synchronization 3. delete functions createDataArrays() and deleteDataArrays() 2003-09-28 22:47 tan2 * module/Exchanger/ExchangerClass.cc: check proc. rank in imposeBC() 2003-09-28 22:36 tan2 * module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/FineGridExchanger.cc: call createDataArrays() inside mapBoundary() 2003-09-28 13:03 tan2 * module/Exchanger/misc.cc: allocate and init E->node and E->cap.VB 2003-09-28 13:01 tan2 * pyre/Components/Exchanger/FineGridExchanger.py: finish test 2003-09-28 07:35 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, tests/exchange.py: 1. rename 'leaderRank' to 'leader' 2. remove unused functions 2003-09-28 07:34 tan2 * module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: remove unused bindings 2003-09-28 07:30 tan2 * pyre/Layout.py, pyre/Layout/Layout.py, pyre/Solver/Solver.py: rename attribute 'leaderRank' to 'leader' 2003-09-28 07:11 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h, module/Exchanger/exchangers.cc: 1. remove attribute 'lrank' in Exchanger class 2. 'rank' is processor rank in local communicator 3. modify Exchanger::createDataArray() and Exchanger::deleteDataArray() 4. gather() and distribute() become pure virtual functions 5. finish CGE::gather() 6. rename interpolate() to interpretate() 7. modify CGE::interpretate() 2003-09-28 04:04 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: 1. bid2proc contains current proc. rank (was current capid) 2. add sendBid2proc(), which send bid2proc array of each processor to localLeader 3. add printBid2proc() and printBid2elem() for debugging 2003-09-28 03:52 tan2 * module/Exchanger/exchangers.cc: change argument list of create*Exchanger() 2003-09-28 03:30 tan2 * module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h: 1. add attribute 'leaderRank' 2. change argument list of constructors 3. rewrite sendVelocities() and receiveVelocities() 2003-09-28 03:24 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, pyre/CoupledApp.py, pyre/Solver/Solver.py: 1. add attribute 'leaderRank' 2. pass 'leaderRank' to createExchanger() 2003-09-28 03:17 tan2 * pyre/Layout.py, pyre/Layout/Layout.py: add attribute 'leaderRank' 2003-09-28 03:16 tan2 * module/Exchanger/misc.cc: init E->parallel.nproc 2003-09-28 00:12 tan2 * module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h, module/Exchanger/exchangers.cc: 1. add new attributes 'lrank' 2. change arugment list of consturctors of all exchangers 3. cosmetics 2003-09-27 07:30 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py: remove getBid2crseelem() 2003-09-27 07:29 tan2 * module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h: add dummy definition of gather() and distribute() 2003-09-27 07:28 tan2 * module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1. remove binding to CoarseGridExchanger::getBid2crseelem() 2003-09-27 07:27 tan2 * module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h: 1. sendBoundary() and receiveBoundary() delegate most of their jobs to Boundary::send(), Boundary::receive() and Boundary::broadcast() 2. change return type of sendBoundary() from int to void 3. change argument list of mapFineGrid() and mapCoarseGrid() 4. remove CoarseGridExchanger::getBid2crseelem() 2003-09-27 07:09 tan2 * module/Exchanger/misc.cc: 1. init E->X according domain bound information in commonE() 2. add initialization of E->sphere.capid[] 3. change domain bound in FinereturnE() 2003-09-27 07:05 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: 1. delete attribute 'connectivity' 2. change argument list of mapFineGrid() and mapCoarseGrid() 3. add send(), receive() and broadcast() 4. add printBound() 5. move Tetrahedronvolume() and det3_sub() to private section 6. fix 'delete []' bug in mapFineGrid() 7. remove redundant initialization of X in mapFineGrid() 8. cosmetics 2003-09-27 05:04 puru * module/Exchanger/Boundary.cc: bug fixed 2003-09-27 04:54 ces74 * pyre/Solver/Solver.py: a typo fixed. 2003-09-27 04:11 tan2 * module/Exchanger/misc.cc: reduce repeated codes and do some cosmetics 2003-09-27 02:04 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, tests/exchange.py: replace self.fine_E and self.coarse_E by self.all_variables 2003-09-27 02:03 tan2 * pyre/Layout.py, pyre/Layout/Layout.py: change back: 'coarse' is full CitcomS 2003-09-27 01:24 puru * module/Exchanger/Boundary.h, module/Exchanger/CoarseGridExchanger.cc: bid2crseelem has been replaced with more obvious bid2elem and bid2proc 2003-09-27 01:23 puru * module/Exchanger/Boundary.cc: bid2crseelem with more obvious bid2elem and bid2proc have been introduced 2003-09-27 00:33 tan2 * module/Exchanger/Boundary.cc: uncomment self test 2003-09-27 00:01 ces74 * module/Exchanger/ExchangerClass.cc: Exchanger::imposeBC fixed. 2003-09-26 08:05 ces74 * module/Exchanger/ExchangerClass.cc: ImposeBC now changes flags of boundary nodes. 2003-09-26 05:47 ces74 * module/Exchanger/CoarseGridExchanger.cc: test output modified in CoarseGridExchanger::interpolate 2003-09-26 05:45 ces74 * module/Exchanger/Boundary.cc: an error fixed in Boundary::getBid2crseelem 2003-09-26 05:37 ces74 * module/Exchanger/Boundary.cc: Test part of Boundary::getBid2crseelem() is temporarily commented out. 2003-09-26 05:25 ces74 * module/Exchanger/CoarseGridExchanger.h, module/Exchanger/FineGridExchanger.h: gather and distribute are members of Exchanger Class. 2003-09-26 05:14 ces74 * module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: CoarseGridExchanger.interpolateTemperature added 2003-09-26 05:14 ces74 * module/Exchanger/bindings.cc: CoarseGridExchanger.interpolateTemperature addedcc 2003-09-26 02:17 ces74 * module/Exchanger/CoarseGridExchanger.cc: errors fixed in CoarseGridExchanger::interpolate. 2003-09-26 02:16 ces74 * module/Exchanger/FineGridExchanger.cc: boundary->bid2gid is transferred from Fine to Coarse Grid. 2003-09-25 10:37 ces74 * module/Exchanger/Boundary.cc: theta_max, theta_min, fi_max, fi_min, ro ,ri were being redeclared as local variables --> fixed so that they are used only as members of boundary class. 2003-09-25 09:51 ces74 * module/Exchanger/CoarseGridExchanger.cc: typo fixed. 2003-09-25 03:14 puru * module/Exchanger/Boundary.cc, module/Exchanger/CoarseGridExchanger.cc: Interpolation with arbitrary element shapes has been added 2003-09-25 02:42 puru * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/CoarseGridExchanger.cc: interpolation test added 2003-09-24 11:53 puru * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: interpolation from corase to fine has been added 2003-09-23 01:14 ces74 * lib/Common/global_defs.h, lib/Regional/Boundary_conditions.c, module/Exchanger/Boundary.cc, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h, module/Exchanger/misc.cc, pyre/Components/Exchanger/FineGridExchanger.py, tests/exchange.py: 1. in Boundary.cc, bid2gid is now generated in a consistent way with assigning boundary.X arrays. 2. in ExchangerClass.cc, imposeBC method is added and tested. 2003-09-22 05:24 ces74 * lib/Common/element_definitions.h, module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/ExchangerClass.cc, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h, module/Exchanger/misc.cc, pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, tests/exchange.py: All the functions needed by Exchanger are created and tested. 2003-09-20 08:32 ces74 * lib/Common/element_definitions.h, module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h, module/Exchanger/misc.cc, pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, tests/exchange.py: intermediate updates 2003-09-19 13:32 ces74 * module/Exchanger/Boundary.cc, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h, module/Exchanger/misc.cc, pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, tests/exchange.py: send/receive temperature between leader processors tested. 2003-09-19 05:37 ces74 * module/Exchanger/ExchangerClass.h: *** empty log message *** 2003-09-19 05:03 ces74 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/bindings.cc, module/Exchanger/misc.cc, module/Exchanger/misc.h, pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, tests/exchange.py: intermediate updates 2003-09-19 00:16 puru * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/ExchangerClass.h: Exchanger for Coarse grid has been introduced 2003-09-18 23:12 puru * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/FineGridExchanger.cc: New variables added to Boundary Class 2003-09-18 06:15 ces74 * module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, tests/exchange.py: two methods for exchanger added: 'gather' and 'distribute' 2003-09-12 23:25 tan2 * tests/citcomsfull.py, tests/citcomsregional.py, tests/coupledcitcoms.py: test 2003-09-12 05:10 tan2 * module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h: 1. change argument lists of createBoundary(), sendBoundary(), receiveBoundary() and mapBoundary() 2. createBoundary(), sendBoundary(), receiveBoundary() and mapBoundary() have passed test 2003-09-12 04:56 tan2 * module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h: 1. comment out send() and receive() declaration 2. change argument list of mapBoundary() 3. fix some bugs in sendVelocities() and receiveVelocities() 4. comment out reset_target() 5. add some output in constructor (commented out) 2003-09-12 04:50 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: add printX() and printBid2gid() methods 2003-09-12 04:43 tan2 * module/Exchanger/exchangers.cc: change the argument lists of createBoundary(), sendBoundary(), receiveBoundary(), and mapBoundary() 2003-09-12 04:41 tan2 * module/Exchanger/misc.cc: add All_variables data, which is required by Boundary object 2003-09-12 04:33 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: findBoundary will not return boundary object 2003-09-12 04:32 tan2 * tests/exchange.py: change output slightly 2003-09-11 11:07 puru * module/Exchanger/Boundary.cc: duplication of nodes on edges and vertices are removed 2003-09-11 06:40 puru * module/Exchanger/Boundary.cc: Duplication of nodes on edges and vertices has been fixed 2003-09-11 04:11 puru * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h: Boundary mapping completed 2003-09-11 01:51 ces74 * module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/ExchangerClass.cc: Added: functions to send/receive velocities between leader and workers 2003-09-10 11:03 tan2 * module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1. finish exchangeTimestep(), wait() and nowait() to Exchanger, test passed 2. add skeleton of sendTemperature() and receiveTemperature() to Exchanger 3. add bindings to the functions above 2003-09-10 11:01 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: finish stableTimestep() and NewStep() 2003-09-10 11:00 tan2 * tests/exchange.py: 1. add test for stableTimestep() and NewStep() 2003-09-10 04:08 tan2 * tests/exchange.py: reflecting changes in Exchanger.py 2003-09-10 04:04 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, pyre/Coupler.py, pyre/Coupler/Coupler.py, pyre/Solver/Solver.py: 1. remove exchanger.initialize() 2. change argument lists of initTemperature() and applyBoundaryConditions() 3. add more calls to Coupler in Solver 2003-09-10 03:57 tan2 * module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h, module/Exchanger/misc.cc, module/Exchanger/misc.h: 1. add boundary as a data member of Exchanger 2. assign boundary at sendBoundary and receiveBoundary 3. change argument list of gather, distribute, send and receive functions 2003-09-10 03:41 puru * module/Exchanger/FineGridExchanger.cc: global_defs.h has been included 2003-09-10 03:07 puru * module/Exchanger/FineGridExchanger.cc: fixed bug 2003-09-10 03:03 puru * module/Exchanger/FineGridExchanger.cc: size in FineGridExchanger::createBoundary has been set 2003-09-10 01:25 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1. declare map() in Boundary class 2. changer argument list of several Exchanger functions 2003-09-09 09:35 tan2 * module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h, module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1. move declartion and definition of Boundary class to seperated files (was in ExchangerClass.h) 2. add boundary creation and exchanging functions 3. add bindings to boundary creation and exchanging functions 2003-09-09 09:28 tan2 * tests/exchange.py: add test to Exchanger.findBoundary() 2003-09-09 09:27 tan2 * pyre/Layout.py, pyre/Layout/Layout.py: createIntercomm() returns mpi.world() 2005-08-23 03:11 unknown_user * module/Exchanger/Exchanger.cc, module/Exchanger/Exchanger.h: [vcp] delete of edited revision with dead state 2003-09-09 04:47 tan2 * module/Exchanger/CoarseGridExchanger.cc, module/Exchanger/CoarseGridExchanger.h, module/Exchanger/Exchanger.cc, module/Exchanger/Exchanger.h, module/Exchanger/ExchangerClass.cc, module/Exchanger/ExchangerClass.h, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm, module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h, module/Exchanger/misc.cc: 1. change filename Exchanger.* -> ExchangerClass.* to avoid import problem in python 2. add constructors to Exchanger and its child class 3. add bindings to constructors 2003-09-09 04:38 tan2 * module/Make.mm: add Exchanger module` 2003-09-09 04:37 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py: createExchanger() is done 2003-09-09 04:35 tan2 * tests/exchange.py: test for Exchanger component 2003-09-07 06:44 tan2 * module/Exchanger, module/Exchanger/Exchanger.cc, module/Exchanger/Exchanger.h, module/Exchanger/Exchangermodule.cc, module/Exchanger/FineGridExchanger.cc, module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm, module/Exchanger/bindings.cc, module/Exchanger/bindings.h, module/Exchanger/exceptions.cc, module/Exchanger/exceptions.h, module/Exchanger/misc.cc, module/Exchanger/misc.h: original source 2003-09-06 02:49 tan2 * pyre/Components/Exchanger/CoarseGridExchanger.py, pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/FineGridExchanger.py, pyre/Components/Exchanger/Make.mm, pyre/Components/Exchanger/__init__.py, pyre/CoupledApp.py, pyre/Coupler.py, pyre/Coupler/Coupler.py, pyre/Coupler/__init__.py, pyre/Layout.py, pyre/Layout/Layout.py, pyre/Layout/__init__.py, pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: add skeletons of coupler and exchanger, change application, layout, and solver accordingly. 2005-08-23 03:10 unknown_user * pyre/FullApp.py, pyre/RegionalApp.py: [vcp] delete of edited revision with dead state 2003-09-06 02:26 tan2 * pyre/FullApp.py, pyre/RegionalApp.py: obsolete 2005-08-23 03:10 unknown_user * pyre/CoupledRegionalApp.py: [vcp] delete of edited revision with dead state 2003-09-06 02:25 tan2 * pyre/CoupledRegionalApp.py: obsolete 2003-09-04 04:18 tan2 * pyre/CoupledApp.py, pyre/SimpleApp.py: 1. change layout() to findLayout() 2. change calling sequence in initialize() 2003-09-04 04:16 tan2 * pyre/Layout.py, pyre/Layout/Layout.py: 1. change layout() to initialize() 2. create intercommunicator (not finished) 2003-09-04 04:13 tan2 * pyre/Controller.py, pyre/Controller/Controller.py: add Controller.initialize() 2003-09-04 04:08 tan2 * pyre/Solver/Solver.py: Solver is now "coupler-awared". It will initialize/launch coupler and call coupler.stableTimestep() and coupler.applyBoundaryConditions() if necessary. 2003-09-03 11:02 ces74 * examples/Full/velbc/README: Typos fixed. 2003-09-03 11:01 ces74 * examples/Regional/velbc/README, examples/Regional/velbc/velbc_regional.tar.gz: 1. Velbc example files are now tarred and compressed. 2. README file explains how to untar the provided velbc archive and the naming scheme of the velbc files. 2003-09-03 10:57 ces74 * examples/Full/input.sample, examples/Full/velbc, examples/Full/velbc/README, examples/Full/velbc/velbc_full.tar.gz: 1. input.sample has been modified to show how to read in velocity b.c. from files. 2. The gzipped tar file, velbc_full.tar.gz, contains velbc files for each M.Y. and for each sphereical cap. 3. README explains how to untar the velbc files and their naming scheme. 2003-09-03 07:23 ces74 * examples/Regional/input.sample, examples/Regional/velbc, examples/Regional/velbc/velbc_regional40, examples/Regional/velbc/velbc_regional41: 1. The example input file is modified to show how to use velbc files. 2. velbc directory is added together with velbc examples. 2003-09-02 01:30 ces74 * lib/Common/Problem_related.c, lib/Full/Make.mm, lib/Full/Read_input_from_files.c, lib/Regional/Make.mm, lib/Regional/Read_input_from_files.c: 1. The function to read in velocity boundary conditions for every My is removed from Common/Problem_related.c. 2. A new file, Read_input_from_files.c is added to lib/Full/ and lib/Regional/. This file contains a sinlge function 'read_input_files_for_timesteps'. 3. Full/Make.mm and Regional/Make.mm have been changed accordingly. 2003-09-01 09:02 ces74 * drivers/Full/Make.mm, drivers/Regional/Make.mm: A bug fixed in the Makefiles: The rule for linking binaries, CitcomSFull and CitcomSRegional, had libCitcomSCommon.a and libCitcomSFull(or Regional).a as dependencies. --> now these are treated as libraries to which Citcom.o is linked. 2005-08-23 03:10 unknown_user * pyre/Components/Coupler.py, pyre/Components/Exchanger.py: [vcp] delete of edited revision with dead state 2003-08-30 07:45 tan2 * pyre/Components/Coupler.py, pyre/Components/Exchanger.py, pyre/Components/Make.mm, pyre/Make.mm: change directory structure 2003-08-30 07:44 tan2 * pyre/Components/Exchanger/Exchanger.py, pyre/Components/Exchanger/Make.mm, pyre/Components/Exchanger/__init__.py: original source 2003-08-30 07:39 tan2 * pyre/Components/Exchanger, pyre/Components/Exchanger/Exchanger.py, pyre/CoupledApp.py: original source 2003-08-30 07:37 tan2 * pyre/Coupler, pyre/Coupler/Make.mm, pyre/Coupler/__init__.py: original source 2003-08-30 07:35 tan2 * pyre/Layout, pyre/Layout.py, pyre/Layout/Layout.py, pyre/Layout/Make.mm, pyre/Layout/__init__.py: original source 2003-08-30 07:29 ces74 * pyre/Components/Advection_diffusion/Advection_diffusion.py: 'maxadvtime' is removed from Advection_diffusion.inventory. 2003-08-30 07:27 ces74 * pyre/Components/Param.py: The following five parameters are removed from the Param.inventory. minstep, maxstep, maxtotstep, storage_spacing, cpu_limits_in_seconds 2003-08-30 07:24 ces74 * drivers/Citcom.c: 1. A step is added to decide whether to proceed time-marching. 2. max_dimensionless_time is not a criterion for time-marching any more. 2003-08-30 07:19 ces74 * lib/Common/Advection_diffusion.c: The following parameters are no more used in PG_timestep_solve: minstep, maxstep, and maxtotstep 2003-08-30 03:41 tan2 * pyre/SimpleApp.py, pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: use new interface of Facilities 2003-08-30 03:40 tan2 * pyre/Facilities/Mesher.py, pyre/Facilities/Solver.py, pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py: change argument list of __init__() to be compatible with pyre facility 2003-08-30 02:46 tan2 * pyre/Facilities/Make.mm, pyre/Facilities/Solver.py, pyre/SimpleApp.py: add Solver facility and use it in SimpleApp.py 2003-08-30 01:33 tan2 * pyre/Controller.py, pyre/Controller/Controller.py: 1. change march() so that final step is saved 2. remove run_init_simulation() 3. change the argument list of save() 2003-08-30 01:31 tan2 * pyre/Solver/Solver.py: merge run_init_simulation() with launch() 2003-08-30 01:06 tan2 * pyre/SimpleApp.py, pyre/Solver/Solver.py: communicator is assigned in Application 2003-08-29 07:43 tan2 * pyre/Make.mm: add SimpleApp.py 2003-08-29 07:08 tan2 * pyre/SimpleApp.py, tests/citcomsregional.py: 1. add SimpleApp, which using Controller and Solver componets 2. change citcomsregional.py accordingly 2003-08-29 06:58 tan2 * pyre/Controller.py, pyre/Controller/Controller.py, pyre/Solver/Solver.py: fix typos 2003-08-29 06:18 ces74 * pyre/Solver/Solver.py: bug fixed in the 'advance' method: tsolver and vsolver are now defined before being used. 2003-08-29 06:12 ces74 * pyre/Controller/__init__.py: bug fixed: Controller is now imported before being used. 2003-08-29 06:10 ces74 * pyre/Make.mm: Controller is added to 'BLD_DIRS' 2003-08-29 06:04 ces74 * pyre/Controller.py, pyre/Controller/Controller.py, pyre/Controller/Make.mm, pyre/Controller/__init__.py, pyre/Solver/Solver.py: 1. Controller.py modified: self.solver.start_simulation --> self.solver.launch 2. Solver. py modified: self.start_simulation --> self.launch 3. Make.mm and __init__.py added to CitcomS/pyre/Controller/ 2003-08-29 05:53 ces74 * pyre/Controller, pyre/Controller.py, pyre/Controller/Controller.py: Controller.py newly added. It's a derivation from pyre/components/SimulationController.py. 2003-08-29 05:49 ces74 * pyre/Solver/Solver.py: method endSimulation modified: endSimulation(self) --> endSimulation(self,step) 2003-08-29 05:37 ces74 * pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Solver/Solver.py: 1. Solver.py modified to be consistent with 'Controller'. 2. Advection_diffusion.py A new method, 'launch', runs PG_timestep_init(). The '_solve' method now executes only PG_timestep_solve() 2005-08-23 03:09 unknown_user * pyre/Citcom.py, pyre/CitcomSFull.py, pyre/CitcomSRegional.py: [vcp] delete of edited revision with dead state 2003-08-28 05:24 tan2 * pyre/Citcom.py, pyre/CitcomSFull.py, pyre/CitcomSRegional.py, pyre/FullApp.py, pyre/Make.mm, pyre/RegionalApp.py, pyre/Solver/FullSolver.py, pyre/Solver/Make.mm, pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py, pyre/Solver/__init__.py: 1. move and rename files: Citcom.py -> Solver/Solver.py CitcomSFull.py -> Solver/FullSolver.py CitcomSRegional.py -> Solver/RegionalSolver.py 2. add Solver module 3. change Make.mm, FullApp.py and RegionalApp.py accordingly 2005-08-23 03:08 unknown_user * pyre/Components/Parallel.py: [vcp] delete of edited revision with dead state 2003-08-28 03:52 tan2 * pyre/Citcom.py, pyre/CitcomSFull.py, pyre/CitcomSRegional.py, pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/Advection_diffusion/__init__.py, pyre/Components/BC.py, pyre/Components/CitcomComponent.py, pyre/Components/Const.py, pyre/Components/IC.py, pyre/Components/Parallel.py, pyre/Components/Param.py, pyre/Components/Phase.py, pyre/Components/Sphere/FullSphere.py, pyre/Components/Sphere/RegionalSphere.py, pyre/Components/Sphere/Sphere.py, pyre/Components/Sphere/__init__.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Components/Stokes_solver/__init__.py, pyre/Components/Visc.py, pyre/CoupledRegionalApp.py, pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: simplified components layout 2003-08-27 03:58 tan2 * pyre/Components/Advection_diffusion/Advection_diffusion.py: add stable_timestep() method 2003-08-27 03:56 tan2 * lib/Common/Advection_diffusion.c, lib/Common/advection_diffusion.h, module/Regional/advdiffu.cc, module/Regional/advdiffu.h, module/Regional/bindings.cc: add stable_timestep() to lib/ and its binding to module/ 2003-08-26 02:34 tan2 * pyre/CitcomSFull.py, pyre/FullApp.py, pyre/Solver/FullSolver.py: add components CitcomSRegional and CitcomSFull 2005-08-23 03:08 unknown_user * pyre/CitcomApp.py: [vcp] delete of edited revision with dead state 2003-08-26 02:16 tan2 * pyre/Citcom.py, pyre/CitcomApp.py, pyre/CitcomSRegional.py, pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/Sphere/Sphere.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Make.mm, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: add components CitcomSRegional and CitcomSFull 2003-08-23 05:35 tan2 * pyre/Citcom.py, pyre/CitcomApp.py, pyre/CitcomSFull.py, pyre/CitcomSRegional.py, pyre/FullApp.py, pyre/RegionalApp.py, pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: fix bug introduced by previous check-in 2003-08-23 05:35 tan2 * module/Regional/bindings.cc, module/Regional/setProperties.cc, module/Regional/setProperties.h: fix typo 2005-08-23 03:07 unknown_user * pyre/Components/Stokes_solver/Imcompressible.py: [vcp] delete of edited revision with dead state 2003-08-23 05:24 tan2 * pyre/Components/Stokes_solver/Imcompressible.py: rename file 2003-08-23 05:21 tan2 * drivers/Citcom.c: output is performed every 'storage_spacing' time step 2003-08-23 05:19 tan2 * tests/citcomsfull.py, tests/citcomsregional.py, tests/coupledcitcoms.py: *** empty log message *** 2005-08-23 03:07 unknown_user * pyre/RadiusDepth.py: [vcp] delete of edited revision with dead state 2003-08-23 05:18 tan2 * pyre/Citcom.py, pyre/CitcomApp.py, pyre/CitcomSFull.py, pyre/CitcomSRegional.py, pyre/Components/Coupler.py, pyre/Components/Exchanger.py, pyre/Components/Make.mm, pyre/CoupledRegionalApp.py, pyre/FullApp.py, pyre/Make.mm, pyre/RadiusDepth.py, pyre/RegionalApp.py, pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: a small step toward coupled application 2003-08-23 05:16 tan2 * pyre/Facilities/VSolver.py: *** empty log message *** 2003-08-23 05:14 tan2 * pyre/Components/Stokes_solver/Imcompressible.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Components/Stokes_solver/Make.mm, pyre/Components/Stokes_solver/__init__.py: fix typo 2003-08-21 02:18 tan2 * lib/Common/Instructions.c, lib/Common/convection_variables.h, lib/Common/global_defs.h: remove several obsolelte variables 2003-08-21 01:54 tan2 * lib/Regional/Boundary_conditions.c: add open_top velocity boundary condition 2003-08-20 09:45 tan2 * tests/citcomsfull.py, tests/citcomsregional.py: determine staging.nodes from input parameters automatically 2003-08-20 04:24 tan2 * pyre/Citcom.py, pyre/CitcomApp.py, pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/CitcomComponent.py, pyre/Components/Sphere/FullSphere.py, pyre/Components/Sphere/RegionalSphere.py, pyre/Components/Stokes_solver/Imcompressible.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Solver/Solver.py: create a python variable CitcomApp.all_variables, which holds the C pointer "struct All_varialbes *E". CitcomApp.all_variables is passed as an argument to most CitcomModule functions. 2003-08-20 04:21 tan2 * module/Regional/advdiffu.cc, module/Regional/mesher.cc, module/Regional/misc.cc, module/Regional/outputs.cc, module/Regional/setProperties.cc, module/Regional/stokes_solver.cc: remove global declaration of "struct All_variables *E", E is passed as an argument to all functions. 2003-08-20 04:20 tan2 * drivers/Citcom.c, lib/Common/Citcom_init.c, lib/Common/Instructions.c, lib/Common/citcom_init.h: 1. remove declaration of "extern struct All_variables *E" in citcom_init.h 2. E is allocated in Citcom_init() and returned to main() 3. change other files accordingly. 2003-08-16 01:59 tan2 * lib/Common/Drive_solvers.c, lib/Common/drive_solvers.h: *** empty log message *** 2003-08-16 01:56 tan2 * module/Regional/bindings.cc, module/Regional/stokes_solver.cc, module/Regional/stokes_solver.h: remove obsolete bindings to general_stokes_solver_*() 2003-08-16 01:56 tan2 * module/Regional/setProperties.cc, module/Regional/setProperties.h: change function name: pyCitcom_Stokes_solver_set_properties() -> pyCitcom_Imcompressible_set_properties() 2003-08-16 01:47 tan2 * pyre/Components/Stokes_solver/Imcompressible.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Components/Stokes_solver/__init__.py: merge ImcompressibleNewtonian() and ImcompressibleNonNewtonian() to Imcompressible(), Stokes_solver() becomes obsolete. 2003-08-15 07:28 tan2 * lib/Common/Convection.c, lib/Common/Element_calculations.c, lib/Common/General_matrix_functions.c, lib/Common/global_defs.h, lib/Full/Lith_age.c, lib/Regional/Boundary_conditions.c, lib/Regional/Lith_age.c: eliminate static variables 2003-08-15 05:50 tan2 * module/Regional/bindings.cc, module/Regional/mesher.cc, module/Regional/stokes_solver.cc, module/Regional/stokes_solver.h, pyre/Components/Stokes_solver/Stokes_solver.py: reflect the change in general_stokes_solver() 2003-08-15 05:43 tan2 * lib/Common/Construct_arrays.c, lib/Common/Drive_solvers.c, lib/Common/Instructions.c: 1. change the flowline of general_stokes_solver() 2. eliminate static variables in construct_stiffness_B_matrix() 3. add call to general_stokes_solver_setup() in read_instructions() 2003-08-15 01:36 tan2 * lib/Full/Parallel_related.c: elimanate static variables. 2003-08-15 01:35 tan2 * module/Full/Make.mm, module/Regional/Make.mm: add $(TOOLS_DIR)/lib to library path 2003-08-13 08:22 tan2 * module/Full/Make.mm, module/Regional/Make.mm: change the library link paths 2003-08-13 03:43 ces74 * drivers/Full/Make.mm, drivers/Regional/Make.mm: Modified in order to use separate static libraries: libCitcomSCommon.a, libCitcomSFull.a, and libCitcomSRegional.a 2003-08-13 03:40 ces74 * lib/Common/Initial_temperature.c: Typo fixed: "Missing input parameter: 'perturbml' -> "Missing input parameter: 'perturbl' 2003-08-12 23:54 ces74 * lib/Full/Make.mm, lib/Regional/Make.mm: a bug fixed: lib/Common is now included in paths for header files. 2003-08-12 23:34 ces74 * lib/Common/Make.mm, lib/Full/Make.mm, lib/Make.mm, lib/Regional/Make.mm, module/Full/Make.mm, module/Regional/Make.mm: Makefiles in module/ and lib/ modified to create three separate static libraries: libCitcomSCommon.a, libCitcomSFull.a, and libCitcomSRegional.a These libraries are used when linking *.so objects. 2003-08-10 03:25 tan2 * lib/Common/Instructions.c, lib/Full/Version_dependent.c, lib/Regional/Version_dependent.c: unifying read_initial_settings() 2003-08-09 05:51 tan2 * lib/Common/Make.mm, lib/Full/Make.mm, lib/Full/Output.c, lib/Regional/Make.mm, lib/Regional/Obsolete.c, lib/Regional/Output.c: unifying 2003-08-09 05:34 tan2 * lib/Common/Make.mm, lib/Full/Make.mm, lib/Full/Process_buoyancy.c, lib/Regional/Make.mm, lib/Regional/Process_buoyancy.c: unifying 2005-08-23 03:05 unknown_user * pyre/Components/Advection_diffusion/Temperature_diffadv.py: [vcp] delete of edited revision with dead state 2003-08-09 05:13 tan2 * examples/Full/input.sample, examples/Full/machine.sample, pyre/Components/Advection_diffusion/Temperature_diffadv.py: obsolete 2003-08-09 05:03 tan2 * lib/Common/Output.c, lib/Common/Problem_related.c, lib/Common/Tracer_advection.c, lib/Common/global_defs.h, lib/Full/Output.c, lib/Full/Parallel_related.c, lib/Regional/Boundary_conditions.c, lib/Regional/Obsolete.c, lib/Regional/Output.c, lib/Regional/Parallel_related.c, lib/Regional/Process_buoyancy.c, lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c, module/Regional/bindings.cc, module/Regional/setProperties.cc, module/Regional/setProperties.h: 1. eliminate several global variables- parallel: mst, nproc[xyz]l, me_locl sphere: local_capid, pid_surf, cap.connection 2. change the way Regional/Parallel_related.c used to assign me_loc and PROCESSOR.pass 2003-08-08 05:05 tan2 * module/Make.mm: default action will link files from Regional/ to Full/ 2003-08-08 04:34 tan2 * module/Regional/setProperties.cc: only processor 0 can write to stderr now Note: device /dev/null and /dev/stderr are used, may not portable to non-unix platform 2003-08-08 02:49 tan2 * drivers/Citcom.c, lib/Common/Instructions.c, lib/Common/Sphere_harmonics.c, lib/Common/parallel_related.h, lib/Full/Obsolete.c, lib/Full/Parallel_related.c, lib/Regional/Obsolete.c, lib/Regional/Parallel_related.c, module/Regional/mesher.cc: *** empty log message *** 2003-08-08 01:41 tan2 * drivers/Full/Make.mm, drivers/Full/local.def, drivers/Make.mm, drivers/Regional/Make.mm, drivers/Regional/local.def, drivers/local.def, lib/Common/Output.c, lib/Common/global_defs.h, lib/Full/Output.c, lib/Full/global_defs.h, lib/Full/lith_age.h, lib/Full/output.h, lib/Full/parallel_related.h, lib/Make.mm, lib/Regional/global_defs.h, lib/Regional/lith_age.h, lib/Regional/output.h, lib/Regional/parallel_related.h, lib/local.def: move header files global_defs.h, lith_age.h, output.h, and parallel_related.h to Common/ 2003-08-07 04:09 tan2 * lib/Common/Make.mm, lib/Full/Make.mm, lib/Full/Problem_related.c, lib/Regional/Make.mm, lib/Regional/Problem_related.c: unify Problem_related.c 2003-08-07 04:00 tan2 * lib/Common/Initial_temperature.c, lib/Common/Make.mm, lib/Common/convection_variables.h, lib/Full/Initial_temperature.c, lib/Full/Make.mm, lib/Full/Version_dependent.c, lib/Full/initial_temperature.h, lib/Regional/Initial_temperature.c, lib/Regional/Make.mm, lib/Regional/Version_dependent.c, lib/Regional/initial_temperature.h, module/Regional/setProperties.cc: unify Initial_temperature.c and initial_temperature.h 2003-08-07 01:56 tan2 * lib/Common/Output.c, lib/Full/Obsolete.c, lib/Full/Output.c: move obsolete functions from Output.c to Obsolete.c 2003-08-07 01:47 tan2 * lib/Common/Global_operations.c, lib/Common/Make.mm, lib/Full/Global_operations.c, lib/Full/Make.mm, lib/Full/Obsolete.c, lib/Regional/Global_operations.c, lib/Regional/Make.mm, lib/Regional/Obsolete.c: unify two versions of Global_operations.c, and put it to Common/ 2003-08-03 07:43 tan2 * module/Regional/setProperties.cc: bug fixed, tests/citcomsfull.py now gives correct result 2003-08-02 05:57 tan2 * tests/citcomsfull.py, tests/hrothgar.py: to run a Full version of CitcomS, use the following command: ./citcomsfull.py --staging=hrothgar --param.datafile=/SOME_PATH/test 2005-08-23 03:02 unknown_user * module/local.def: [vcp] delete of edited revision with dead state 2003-08-02 05:53 tan2 * module/Make.mm, module/Regional/Regionalmodule.cc, module/Regional/advdiffu.cc, module/Regional/advdiffu.h, module/Regional/bindings.cc, module/Regional/bindings.h, module/Regional/exceptions.cc, module/Regional/exceptions.h, module/Regional/local.def, module/Regional/mesher.cc, module/Regional/mesher.h, module/Regional/misc.cc, module/Regional/misc.h, module/Regional/outputs.cc, module/Regional/outputs.h, module/Regional/setProperties.cc, module/Regional/setProperties.h, module/Regional/stokes_solver.cc, module/Regional/stokes_solver.h, module/local.def: make some changes in function names so that both Full and Regioanl versions can use the same source code. 2005-08-23 03:02 unknown_user * module/Full/bindings.cc, module/Full/bindings.h, module/Full/exceptions.cc, module/Full/exceptions.h, module/Full/misc.cc, module/Full/misc.h: [vcp] delete of edited revision with dead state 2003-08-02 05:52 tan2 * module/Full/Fullmodule.cc, module/Full/Make.mm, module/Full/bindings.cc, module/Full/bindings.h, module/Full/exceptions.cc, module/Full/exceptions.h, module/Full/local.def, module/Full/misc.cc, module/Full/misc.h: module/Full and module/Regional now use the same files, except $(TYPE)module.cc and Make.mm. ***** Important ***** When you check out this directory (module/Full) in the first time, do 'mm link' in this directory. This will hard-link every source files in module/Regional to this directory. 2003-08-02 05:25 tan2 * lib/Full/global_defs.h: add some variable declaration which are only used by regional version 2003-08-02 05:24 tan2 * pyre/Citcom.py, pyre/CitcomApp.py, pyre/CitcomSFull.py, pyre/CitcomSRegional.py, pyre/FullApp.py, pyre/Make.mm, pyre/RegionalApp.py, pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: 1. add base class CitcomApp 2. derive FullApp and RegionalApp form CitcomApp 2003-08-02 02:05 tan2 * pyre/Components/Sphere/FullSphere.py, pyre/Components/Sphere/Make.mm, pyre/Components/Sphere/RegionalSphere.py, pyre/Components/Sphere/Sphere.py, pyre/Components/Sphere/__init__.py, pyre/Facilities/Mesher.py: 1. add a base class Sphere for component Sphere 2. add a new component FullSphere for Full version 3. change Make.mm, __init__.py, and the binder of facility Mesher accordingly 2003-08-01 02:41 tan2 * lib/Common/General_matrix_functions.c, lib/Common/Initial_temperature.c, lib/Common/Instructions.c, lib/Full/Initial_temperature.c, lib/Full/Parallel_related.c, lib/Regional/Initial_temperature.c: bug fix 2003-08-01 02:40 tan2 * lib/Common/Process_buoyancy.c, lib/Full/Obsolete.c, lib/Full/Process_buoyancy.c: remove obsolete function 2003-07-30 03:54 tan2 * drivers/Make.mm, lib/Make.mm: *** empty log message *** 2003-07-30 03:54 tan2 * lib/Common/Output.c, lib/Common/Process_buoyancy.c, lib/Full/Boundary_conditions.c, lib/Full/Global_operations.c, lib/Full/Initial_temperature.c, lib/Full/Lith_age.c, lib/Full/Make.mm, lib/Full/Output.c, lib/Full/Parallel_related.c, lib/Full/Problem_related.c, lib/Full/Process_buoyancy.c, lib/Full/Version_dependent.c, lib/Full/global_defs.h, lib/Full/initial_temperature.h, lib/Full/lith_age.h, lib/Full/output.h, lib/Full/parallel_related.h: copy changes in Regional version to Full version 2003-07-29 06:03 tan2 * pyre/CitcomSRegional.py, pyre/Components/Advection_diffusion/Make.mm, pyre/Components/Make.mm, pyre/Components/Sphere/Make.mm, pyre/Components/Stokes_solver/Make.mm, pyre/Facilities/Mesher.py, pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py, pyre/Make.mm, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: change directory structures 2003-07-29 04:57 tan2 * lib/Common/Convection.c, lib/Common/Solver_multigrid.c, module/Regional/bindings.cc, module/Regional/outputs.cc, module/Regional/outputs.h, module/Regional/setProperties.cc, pyre/CitcomSRegional.py, pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/Sphere/RegionalSphere.py, pyre/Components/Stokes_solver/Stokes_solver.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: 1. RegionalApp._setProperties() is called before Component.init() 2. some cosmetics 2003-07-27 04:47 tan2 * drivers/Citcom.c, lib/Common/Instructions.c, lib/Common/Problem_related.c, lib/Common/Process_velocity.c, lib/Common/output.h, lib/Regional/Obsolete.c, lib/Regional/Output.c, lib/Regional/Problem_related.c, lib/Regional/Process_buoyancy.c, lib/Regional/Version_dependent.c, lib/Regional/output.h, module/Regional/bindings.cc, module/Regional/mesher.cc, module/Regional/misc.cc, module/Regional/misc.h, module/Regional/outputs.cc, module/Regional/outputs.h, pyre/CitcomSRegional.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: complete output part 2003-07-26 03:43 tan2 * drivers/Citcom.c, lib/Common/Advection_diffusion.c, lib/Common/Initial_temperature.c, lib/Regional/Initial_temperature.c, module/Regional/advdiffu.cc, module/Regional/bindings.cc, module/Regional/mesher.cc, module/Regional/misc.cc, module/Regional/misc.h, module/Regional/setProperties.cc, pyre/CitcomSRegional.py, pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/Advection_diffusion/__init__.py, pyre/Components/BC.py, pyre/Components/Const.py, pyre/Components/Param.py, pyre/Components/Phase.py, pyre/Components/Sphere/RegionalSphere.py, pyre/Components/Stokes_solver/Stokes_solver.py, pyre/Components/Visc.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: complete VSolver and TSolver 2003-07-26 02:17 tan2 * lib/Common/Parsing.c: bug fix 2003-07-26 02:13 tan2 * lib/Common/Parsing.c: cosmetic output 2003-07-25 03:10 tan2 * lib/Common/Global_operations.c, lib/Regional/Global_operations.c, lib/Regional/Parallel_related.c, module/Regional/bindings.cc, module/Regional/mesher.cc, module/Regional/mesher.h, module/Regional/setProperties.cc, pyre/CitcomSRegional.py, pyre/Components/Sphere/RegionalSphere.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: finish RegionalSphere.run(), it gives identical results as stand-alone CitcomSRegional 2003-07-25 00:46 tan2 * pyre/CitcomSRegional.py, pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/Advection_diffusion/__init__.py, pyre/Components/BC.py, pyre/Components/CitcomComponent.py, pyre/Components/Const.py, pyre/Components/IC.py, pyre/Components/Make.mm, pyre/Components/Parallel.py, pyre/Components/Param.py, pyre/Components/Phase.py, pyre/Components/Sphere/RegionalSphere.py, pyre/Components/Sphere/__init__.py, pyre/Components/Stokes_solver/Imcompressible.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Components/Stokes_solver/Stokes_solver.py, pyre/Components/Stokes_solver/__init__.py, pyre/Components/Visc.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py, tests/citcomsregional.py, tests/signon.py: 1. remove passing filename to RegionalApp.__init__() 2. add new base component CitcomComponent(), derive every component from CitcomComponent, the interface to __init__ and setProperties are changed 2003-07-24 07:04 tan2 * module/Regional/advdiffu.cc, module/Regional/advdiffu.h, module/Regional/bindings.cc, module/Regional/misc.cc, module/Regional/misc.h, pyre/Components/Advection_diffusion/Advection_diffusion.py: add binding of set_convection_defaults() 2003-07-24 06:00 tan2 * lib/Common/Initial_temperature.c, lib/Common/initial_temperature.h, lib/Regional/Initial_temperature.c, lib/Regional/Version_dependent.c, lib/Regional/initial_temperature.h: seperate input and init phases of temperature IC 2003-07-24 05:59 tan2 * lib/Common/global_defs.h, lib/Regional/global_defs.h, module/Regional/setProperties.cc: remove global variables VERBOSE, DESCRIBE, and BEGINNER 2003-07-24 05:00 tan2 * module/Regional/bindings.cc, module/Regional/setProperties.cc, module/Regional/setProperties.h, pyre/CitcomSRegional.py, pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/Const.py, pyre/Components/Parallel.py, pyre/Components/Param.py, pyre/Components/Sphere/RegionalSphere.py, pyre/Components/Stokes_solver/Stokes_solver.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: finished setting properties 2003-07-24 02:00 tan2 * pyre/Components/IC.py: typo fixed 2003-07-23 12:29 ces74 * pyre/Components/BC.py, pyre/Components/Const.py, pyre/Components/IC.py, pyre/Components/Parallel.py, pyre/Components/Param.py, pyre/Components/Phase.py, pyre/Components/Visc.py: '*_set_prop' methods of the 'Regioanl' module are now called '*_set_properties'. 2003-07-23 12:27 ces74 * lib/Common/global_defs.h, lib/Regional/global_defs.h: New members of the "CONTROL" and the "All_variables" structure added. 2003-07-23 12:26 ces74 * lib/Common/Initial_temperature.c, lib/Regional/Initial_temperature.c: Originally local variables, number_of_perturbations, perturb_ll, perturb_mm, load_depth, and perturb_mag, are now members of the global "All_variables" structure. 2003-07-23 12:22 ces74 * lib/Common/Parsing.c: Originally local variables, VERBOSE, DESCRIBE, and BEGINNER, are now global: members of the 'All_variables' structure. 2003-07-23 12:19 ces74 * module/Regional/bindings.cc, module/Regional/outputs.cc, module/Regional/stokes_solver.cc: function name changed from *_set_prop to *_set_properties. 2003-07-23 12:18 ces74 * module/Regional/setProperties.cc, module/Regional/setProperties.h: Properties for the following components added: IC, Const, Param, Phase, and Parallel. 2003-07-23 04:58 tan2 * module/Regional/bindings.cc, module/Regional/mesher.cc, module/Regional/misc.cc, module/Regional/misc.h, pyre/CitcomSRegional.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: 1. change Citcom_Init() to citcom_init() (finished) 2. add binding to open info_file 2003-07-23 02:52 tan2 * lib/Common/Advection_diffusion.c, lib/Common/advection.h: *** empty log message *** 2003-07-22 04:58 ces74 * lib/Common/Drive_solvers.c: Functions uncommented: void general_stokes_solver_init(struct All_variables *E) void general_stokes_solver_fini(struct All_variables *E) void general_stokes_solver_update_velo(struct All_variables *E) void general_stokes_solver_Unorm(struct All_variables *E, double *Udot_mag, double *dUdot_mag) void general_stokes_solver_log(struct All_variables *E, float Udot_mag, float dUdot_mag, int count) 2003-07-22 04:44 tan2 * lib/Common/output.h, lib/Regional/Boundary_conditions.c, lib/Regional/Obsolete.c, lib/Regional/Output.c, lib/Regional/Parallel_related.c, lib/Regional/output.h: partially eliminate use of static variables 2003-07-19 07:34 tan2 * lib/Common/Global_operations.c, lib/Common/global_defs.h, lib/Regional/Global_operations.c, lib/Regional/Parallel_related.c, lib/Regional/global_defs.h: add communicators E->parallel.horizontal_comm and E->parallel.vertical_comm and initialize them at set_horizontal_communicator() and set_vertical_communicator() 2003-07-19 05:15 tan2 * drivers/Citcom.c: change Citcom_Init() to citcom_init() 2003-07-18 07:10 tan2 * lib/Common/Citcom_init.c, lib/Common/Drive_solvers.c, lib/Common/Element_calculations.c, lib/Common/General_matrix_functions.c, lib/Common/Instructions.c, lib/Common/Interuption.c, lib/Common/Process_velocity.c, lib/Common/Solver_multigrid.c, lib/Common/Stokes_flow_Incomp.c, lib/Common/Tracer_advection.c, lib/Common/Viscosity_structures.c, lib/Common/citcom_init.h, lib/Common/interuption.h: 1. change Citcom_Init() to citcom_init() 2. add interuption.h, header file of Interuption.c 3. partially eliminate use of static variables 2003-07-18 06:31 tan2 * lib/Common/Global_operations.c, lib/Regional/Global_operations.c: vnorm_nonnewt() returned NaN if there was only one material type. bug? fixed. 2003-07-18 04:19 tan2 * lib/Regional/Sphere_related.c: memory-leak fixed 2003-07-17 04:52 tan2 * lib/Common/global_defs.h, lib/Regional/global_defs.h: add argument declaration for function pointers (necessarily when linking with C++) 2003-07-17 04:49 tan2 * module/Regional/Make.mm, module/Regional/bindings.cc, module/Regional/mesher.cc, module/Regional/mesher.h: add bindings of component RegionalSphere() 2005-08-23 02:55 unknown_user * pyre/Components/Mesh.py: [vcp] delete of edited revision with dead state 2003-07-16 04:53 tan2 * pyre/Components/Make.mm, pyre/Components/Mesh.py: component Mesh() is replaced by component RegionalSphere() 2003-07-16 04:50 tan2 * pyre/CitcomSRegional.py, pyre/Components/Sphere, pyre/Components/Sphere/Make.mm, pyre/Components/Sphere/RegionalSphere.py, pyre/Components/Sphere/__init__.py, pyre/Facilities/Make.mm, pyre/Facilities/Mesher.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: add new facility Mesher() and its default component RegionalSphere() 2003-07-16 04:47 tan2 * pyre/Components/Stokes_solver/Stokes_solver.py: typo fixed 2003-07-16 01:17 ces74 * module/Regional/bindings.cc: A missing part of the method talbe added: set_cg_defaults, set_mg_defaults, set_mg_el_defaults. 2005-08-23 02:55 unknown_user * pyre/Components/Adv_solver.py: [vcp] delete of edited revision with dead state 2003-07-16 01:06 ces74 * pyre/Components/Adv_solver.py: Binding for advection-diffusion solver is now in pyre/Regional/Facilities/TSolver.py 2003-07-16 01:04 ces74 * pyre/Facilities/TSolver.py: Binding of TSolver with a component (Temperature_diffadv.py) is implemented. 2003-07-16 01:03 ces74 * pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/Advection_diffusion/Temperature_diffadv.py, pyre/Components/Advection_diffusion/__init__.py: Temperature_diffadv now can call CitcomS subroutines to initialize and solve for the advection/diffusion of temperature field. 2003-07-16 01:01 ces74 * pyre/CitcomSRegional.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: modified to initialize the Advection_diffusion facility 2003-07-15 07:40 tan2 * module/Regional/Make.mm, module/Regional/bindings.cc, module/Regional/misc.cc, module/Regional/misc.h, module/Regional/stokes_solver.cc, module/Regional/stokes_solver.h, pyre/CitcomSRegional.py, pyre/Components/Stokes_solver/Stokes_solver.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: 1. move bindings related to Stokes_solver() to stokes_solver.cc 2. call set_cg_defaults()/set_mg_defaults() in Stokes_solver.init() 2003-07-15 04:08 tan2 * lib/Common/Instructions.c, lib/Common/Interuption.c, lib/Common/Make.mm: move everything related to System Signal to interuption.c 2003-07-15 02:44 tan2 * module/Regional/setProperties.cc: change helper functions to templates 2003-07-14 05:58 tan2 * module/Regional/bindings.cc, module/Regional/setProperties.cc, module/Regional/setProperties.h, pyre/CitcomSRegional.py, pyre/Components/Visc.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py, tests/signon.py: 1. more helper functions in setProperties.cc 2. Regional.BC_set_prop() and its binding 3. RegionalApp._setProperties() 4. some test in singon.py 2005-08-23 02:54 unknown_user * pyre/Components/Stokes_solver.py: [vcp] delete of edited revision with dead state 2003-07-10 02:42 tan2 * pyre/CitcomSRegional.py, pyre/Components/Adv_solver.py, pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/BC.py, pyre/Components/Const.py, pyre/Components/IC.py, pyre/Components/Mesh.py, pyre/Components/Parallel.py, pyre/Components/Param.py, pyre/Components/Phase.py, pyre/Components/Stokes_solver.py, pyre/Components/Stokes_solver/Imcompressible.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Components/Stokes_solver/Stokes_solver.py, pyre/Components/Visc.py, pyre/Facilities/VSolver.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: migrate toward pythia-0.4 2003-07-04 06:56 ces74 * pyre/CitcomSRegional.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: Typos corrected 2003-07-04 06:52 ces74 * pyre/CitcomSRegional.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: Modified to use the TSolver facility. 2003-07-04 06:43 ces74 * pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/Advection_diffusion/Make.mm, pyre/Components/Advection_diffusion/Temperature_diffadv.py, pyre/Components/Advection_diffusion/__init__.py: A component of "TSoler" facility added. Advection_diffusion.py is a general class of advection_diffusion solvers. Temperature_diffadv.py is a solver for temperature field. __init__.py exports temperature_diffadv under Advection_diffusion module. 2003-07-04 06:40 ces74 * pyre/Facilities/Make.mm, pyre/Facilities/TSolver.py: TSolver facility added. Make.mm modified accordingly. 2003-06-27 07:15 tan2 * module/Regional/Make.mm, module/Regional/bindings.cc, module/Regional/setProperties.cc, module/Regional/setProperties.h, pyre/CitcomSRegional.py, pyre/Components/BC.py, pyre/Components/Make.mm, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: passing properties of BC() to C variables 2003-06-27 06:14 tan2 * pyre/Components/Stokes_solver/Imcompressible.py, pyre/Components/Stokes_solver/Incompressible.py: ImcompressibleNonNewtonian() is inherited from ImcompressibleNewtonian() now 2003-06-27 06:14 tan2 * pyre/Components/Stokes_solver/Stokes_solver.py: remove properties related to viscosity 2003-06-24 04:01 tan2 * pyre/Facilities/VSolver.py: bug fix 2003-06-24 03:54 tan2 * pyre/Components/Stokes_solver/Imcompressible.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Components/Stokes_solver/Make.mm, pyre/Components/Stokes_solver/Stokes_solver.py, pyre/Components/Stokes_solver/__init__.py: 1. Stokes_solver() is a Component of new facility VSolver() 2. add properties to Stokes_solver(), including properties belong to (future) Viscosity component 3. change ImcompressibleNewtonian() and ImcompressibleNonNewtonian() accordingly 2003-06-24 03:43 tan2 * pyre/Facilities, pyre/Facilities/Make.mm, pyre/Facilities/VSolver.py, pyre/Facilities/__init__.py: add new facilities 2003-06-14 00:12 tan2 * pyre/CitcomSRegional.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: add facilities 2003-06-14 00:11 tan2 * tests/citcomsregional.py: tests for facilities 2003-06-13 01:25 tan2 * pyre/Components/__init__.py, pyre/__init__.py: 1. remove 'license_text' 2. add Common/Component/__init__.py 2003-06-12 06:02 tan2 * pyre/Components/Adv_solver.py, pyre/Components/BC.py, pyre/Components/Const.py, pyre/Components/IC.py, pyre/Components/Make.mm, pyre/Components/Mesh.py, pyre/Components/Parallel.py, pyre/Components/Param.py, pyre/Components/Phase.py, pyre/Components/Stokes_solver.py, pyre/Components/Visc.py: 1. move all components to new directory Component/ 2. all components have a new and shorter name 3. 'SimulationSolver' is splited into two components: 'Adv_solver' and 'Stokes_solver' 4. change Make.mm accordingly 2003-06-08 15:11 tan2 * module/Regional/Make.mm: fixed bug in linking with 'libmpimodule.a' (I don't like this solution though) 2003-06-07 02:04 tan2 * module/Regional/Make.mm, module/Regional/misc.cc: passing mpi communicator to Citcom_Init() 2003-05-24 00:58 tan2 * tests/asap.py, tests/hrothgar.py: add two staging classes (copied from specfem_globe/tests/) 2003-05-24 00:49 tan2 * module/Regional/misc.cc, module/Regional/outputs.cc: append function name to the argument of PyArg_ParseTuple() 2003-05-24 00:07 tan2 * module/Make.mm: fix a typo 2003-05-23 12:12 ces74 * module/Regional/advdiffu.cc, module/Regional/advdiffu.h, module/Regional/bindings.cc, module/Regional/misc.cc, module/Regional/misc.h: test methods are removed. class PG_timestep now has only two methods: init and solve 2003-05-23 12:11 ces74 * lib/Common/Drive_solvers.c, lib/Common/General_matrix_functions.c, lib/Common/Stokes_flow_Incomp.c, lib/Common/drive_solvers.h: test functions removed. 2003-05-23 11:47 ces74 * lib/Common/Advection_diffusion.c, lib/Common/Drive_solvers.c, lib/Common/General_matrix_functions.c, lib/Common/Stokes_flow_Incomp.c, lib/Common/advection_diffusion.h, lib/Common/drive_solvers.h: Fixed a bug related to deciding the validity of velocity solution in General_matrix_functions.c Functions reorganized for PG_timestep class. 2003-05-23 11:22 ces74 * pyre/Components/Advection_diffusion/Advection_diffusion.py: class PG_timestep now has only two methods: .init and .solve 2003-05-23 09:41 tan2 * module/Regional/outputs.cc, pyre/CitcomSRegional.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: add class OutputVisc and its bindings 2003-05-23 07:46 ces74 * lib/Common/Advection_diffusion.c, lib/Common/Make.mm, lib/Common/advection_diffusion.h: bug in Make.mm fixed. advection_diffusion.h is now included in Advection_diffusion.c 2003-05-23 06:18 tan2 * lib/Common/output.h, lib/Regional/Output.c, lib/Regional/output.h: *** empty log message *** 2003-05-23 06:10 tan2 * module/Regional/bindings.cc: *** empty log message *** 2003-05-23 06:08 tan2 * module/Regional/outputs.cc, module/Regional/outputs.h: add bindings to class OutputVisc 2003-05-23 05:41 ces74 * module/Regional/outputs.cc: bug fixed: include outputs.h, not output_binding.h 2003-05-23 05:39 ces74 * module/Regional/advdiffu.cc: bug fixed: PG_timestep_Init to ..._init PG_timestep_Fini to ..._fini 2003-05-23 05:37 ces74 * lib/Common/advection_diffusion.h, lib/Regional/Output.c: Bugs fixed. 2003-05-23 05:27 ces74 * pyre/Components/Advection_diffusion/Advection_diffusion.py: Changed class name from Advection_diffusion to PG_timestep 2003-05-23 01:32 ces74 * module/Regional/Make.mm, module/Regional/advdiffu.cc, module/Regional/advdiffu.h, module/Regional/bindings.cc, module/Regional/misc.cc, module/Regional/misc.h: Inconsistency caused by adding advdiffu modules has been fixed. 2003-05-23 01:21 tan2 * lib/Regional/Output.c, module/Regional/Make.mm, module/Regional/bindings.cc: 1. change filename from 'output_bindings.*' to 'outputs.*' 2. delete OutputCoord.writeheader() method 3. fix a typo in Output.py 2003-05-23 01:20 ces74 * pyre/CitcomSRegional.py, pyre/Components/Advection_diffusion, pyre/Components/Advection_diffusion/Advection_diffusion.py, pyre/Components/Advection_diffusion/Make.mm, pyre/Components/Advection_diffusion/__init__.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: A new package Advection_diffusion created. This package includes a new class, PG_timestep. 2003-05-23 01:17 ces74 * lib/Common/Advection_diffusion.c, lib/Common/Make.mm, lib/Common/advection_diffusion.h: Functions added and modified for PG_timestep class 2003-05-22 04:28 tan2 * lib/Common/output.h, lib/Regional/Output.c, lib/Regional/output.h, module/Regional/Make.mm, module/Regional/bindings.cc, module/Regional/misc.cc, module/Regional/misc.h, module/Regional/outputs.cc, module/Regional/outputs.h, pyre/CitcomSRegional.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: 1. add class CitcomOutput 2. add classes OutputCoord and OutputVelo, which write out coordinate and velocity output 3. add some functions in lib/Regional/Output.c for bindings 4. add python bindings to all above 2003-05-21 01:56 tan2 * pyre/Components/Stokes_solver/Imcompressible.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Components/Stokes_solver/Stokes_solver.py: 1. change implementation of Stokes_solver 2. change ImcompressibleNewtonian and ImcompressibleNonNewtonian accordingly 2003-05-21 01:55 tan2 * lib/Common/Drive_solvers.c: initialize 'monitor.elapsed_time_vsoln' 2003-05-17 04:11 tan2 * lib/Common/Drive_solvers.c, lib/Common/drive_solvers.h, module/Regional/bindings.cc, module/Regional/misc.cc, module/Regional/misc.h, pyre/CitcomSRegional.py, pyre/Components/Stokes_solver/Imcompressible.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Components/Stokes_solver/Make.mm, pyre/Components/Stokes_solver/Stokes_solver.py, pyre/Components/Stokes_solver/__init__.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py, tests/citcomsregional.py, tests/signon.py: 1. add python class Stokes_solver 2. add python classes ImcompressibleNewtonian and ImcompressibleNonNewtonian, derived from Stokes_solver 3. add python binding to methods of ImcompressibleNewtonian 4. modify tests accordingly 2003-05-15 07:07 tan2 * pyre/Components, pyre/Components/Stokes_solver, pyre/Components/Stokes_solver/Imcompressible.py, pyre/Components/Stokes_solver/Incompressible.py, pyre/Components/Stokes_solver/Make.mm, pyre/Components/Stokes_solver/Stokes_solver.py, pyre/Components/Stokes_solver/__init__.py: Initial revision 2003-05-15 01:31 tan2 * lib/Common/Instructions.c, lib/Common/Viscosity_structures.c, lib/Regional/Version_dependent.c, module/Regional/misc.cc, tests/signon.py: seperate viscosity input and computation into different functions 2003-05-14 02:51 tan2 * drivers/Citcom.c, lib/Common/Citcom_init.c, lib/Common/Global_operations.c, lib/Common/citcom_init.h, lib/Common/global_defs.h, lib/Common/parallel_related.h, lib/Regional/Global_operations.c, lib/Regional/Parallel_related.c, lib/Regional/global_defs.h, lib/Regional/parallel_related.h, module/Regional/misc.cc, tests/signon.py: 1. creat a new global variable E->parallel.world 2. replace all MPI_COMM_WORLD by E->parallel.world 2003-04-30 03:14 tan2 * lib/Common/phase_change.h: add function prototypes 2003-04-30 03:13 tan2 * lib/Regional/Version_dependent.c: fix bugs when input 'control.coor_file', 'control.reset_startage', and 'control.zero_elapsed_time' 2003-04-29 01:55 tan2 * lib/Common/Instructions.c, lib/Common/Pan_problem_misc_functions.c, lib/Common/Phase_change.c, lib/Regional/Version_dependent.c: 1. move everything about phase change to 'Phase_change.c' 2. restructure phase change functions 2003-04-26 07:59 tan2 * lib/Common/Problem_related.c, lib/Common/global_defs.h, lib/Regional/Boundary_conditions.c, lib/Regional/Problem_related.c, lib/Regional/Version_dependent.c, lib/Regional/global_defs.h: 1. change 'control.mantle_temp' to 'control.lith_age_mantle_temp' 2. move functions deal with 'lith_age' to a 'Lith_age.c' (complete) 2003-04-26 07:36 tan2 * lib/Common/Element_calculations.c, lib/Common/Sphere_harmonics.c: bug fix in original code 2003-04-26 05:58 tan2 * drivers/Make.mm, lib/Make.mm, module/Make.mm, pyre/Make.mm: diable build on 'Full' version 2003-04-26 05:29 tan2 * lib/Common/Initial_temperature.c, lib/Common/global_defs.h, lib/Common/initial_temperature.h, lib/Common/lith_age.h, lib/Common/parsing.h, lib/Regional/Initial_temperature.c, lib/Regional/Lith_age.c, lib/Regional/Make.mm, lib/Regional/global_defs.h, lib/Regional/initial_temperature.h, lib/Regional/lith_age.h: 1. add parsing.h 2. modularize convection_initial_temperature() 3. move functions deal with 'lith_age' to a 'Lith_age.c' (not finished) 2003-04-26 05:12 tan2 * drivers/Citcom.c, lib/Common/Citcom_init.c: 1. more initialization done in Citcom_Init() 2. fix bug from previous commit in main() 2003-04-25 02:07 tan2 * lib/Common/Element_calculations.c, lib/Common/General_matrix_functions.c: bug fix 2003-04-11 08:31 tan2 * lib/Common/Citcom_init.c, module/Regional/misc.cc: clean up debug message 2003-04-11 08:27 ces74 * pyre/CitcomSRegional.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: class name changed to RegionalApp 2003-04-11 06:40 tan2 * tests/citcomsregional.py, tests/signon.py: change module name from CitcomSRegional to Regional 2003-04-11 06:34 tan2 * pyre/CitcomSRegional.py, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: 1. add preInit() and postInit() 2. change EarthModelGrid to SimulationGrid 2003-04-11 06:25 tan2 * module/Full/Fullmodule.cc, module/Full/Make.mm, module/Full/bindings.cc, module/Full/bindings.h, module/Full/exceptions.cc, module/Full/exceptions.h, module/Full/misc.cc, module/Full/misc.h: change module name from CitcomSFull to Full 2003-04-11 06:18 tan2 * module/Regional/Make.mm, module/Regional/Regionalmodule.cc, module/Regional/bindings.cc, module/Regional/bindings.h, module/Regional/exceptions.cc, module/Regional/exceptions.h, module/Regional/misc.cc, module/Regional/misc.h: change module name from CitcomSRegional to Regional 2003-04-11 03:15 tan2 * tests/signon.py: test for new Citcom_Init(), which takes 2 arguments now. 2003-04-11 02:07 tan2 * drivers/Citcom.c, lib/Common/Citcom_init.c, lib/Common/citcom_init.h, module/Regional/misc.cc: 1. Pass rank and size to Citcom_Init(). 2. Disable parallel_process_initilization(). Its functionality is performed by Citcom_Init(). 2003-04-10 01:59 ces74 * pyre/CitcomSRegional.py, pyre/RegionalApp.py, pyre/Solver, pyre/Solver/RegionalSolver.py: Modified to reflect changes in moduels in pyre/Common 2003-04-06 07:51 tan2 * drivers/Citcom.c, lib/Common/Citcom_init.c, lib/Common/Instructions.c, lib/Common/Parsing.c, module/Regional/bindings.cc, module/Regional/misc.cc, module/Regional/misc.h, tests/signon.py: 1. pass input filename, rather than argc and argv, to read_instructions() 2. pass input filename, rather than argc and argv, to setup_parser() 3. more initialization done in Citcom_Init() 4. add python binding to read_instructions() 2003-04-06 04:57 tan2 * drivers/Citcom.c, lib/Common/Citcom_init.c, lib/Common/citcom_init.h, module/Regional/misc.cc: binding of Citcom_Init(), finished 2003-04-06 04:25 tan2 * drivers/Full/Make.mm, drivers/Make.mm, drivers/Regional/Make.mm, examples/Full/Make.mm, examples/Make.mm, examples/Regional/Make.mm, lib/Common/Make.mm, lib/Full/Make.mm, lib/Make.mm, lib/Regional/Make.mm, module/Full/Make.mm, module/Make.mm, module/Regional/Make.mm, pyre/Make.mm, tests/Make.mm: PROJ_TMPDIR is specified by PACKAGE too 2003-04-04 08:42 tan2 * module/Regional/Make.mm, module/Regional/bindings.cc, module/Regional/misc.cc, module/Regional/misc.h, tests/signon.py: trial on binding of Citcom_Init(), not finished. 2003-04-04 08:41 tan2 * lib/Full/Make.mm, lib/Regional/Make.mm: export header files 2003-04-04 08:40 tan2 * drivers/Citcom.c: 1. declare "struct All_variables *E" as global in read_instruction() 2. allocate *E in Citcom_Init() 2003-04-04 08:39 tan2 * lib/Common/Citcom.c: redundant file 2003-04-04 08:37 tan2 * lib/Common/Citcom_init.c, lib/Common/Instructions.c, lib/Common/Make.mm, lib/Common/citcom_init.h: 1. declare "struct All_variables *E" as global in read_instruction() 2. allocate *E in Citcom_Init() 2003-04-04 03:40 tan2 * lib/Make.mm, module/Make.mm, pyre/RadiusDepth.py: cosmetics 2003-04-04 03:38 tan2 * drivers/Full/Make.mm, drivers/Make.mm, drivers/Regional/Make.mm: fix bugs caused by symlink to Citcom.c 2003-03-26 08:49 ces74 * tests/citcomsregional.py: for testing EarthModel properties 2003-03-25 05:48 tan2 * pyre/RadiusDepth.py: 1. change attribute 'R0' to 'outer_radius' 2. outer_radius, inRadius, and inDepth are read-only now 3. add self-test section 2003-03-25 03:48 tan2 * pyre/RadiusDepth.py: Add RadiusDepth.py, which defines two classed converting depth to radius, and vise versa. 2003-03-25 01:38 tan2 * drivers/Make.mm, module/Make.mm, pyre/Make.mm: add BLD_ACTION="all" 2003-03-24 09:46 tan2 * Make.mm, drivers, drivers/Citcom.c, drivers/Full, drivers/Full/Make.mm, drivers/Full/local.def, drivers/Make.mm, drivers/Regional, drivers/Regional/Make.mm, drivers/Regional/local.def, drivers/local.def, examples, examples/.reset-temporary, examples/Full, examples/Full/Make.mm, examples/Full/input.sample, examples/Full/local.def, examples/Full/machine.sample, examples/Make.mm, examples/Regional, examples/Regional/Make.mm, examples/Regional/input.sample, examples/Regional/local.def, examples/Regional/machines.sample, examples/local.def, lib, lib/Common, lib/Common/Advection_diffusion.c, lib/Common/Citcom.c, lib/Common/Construct_arrays.c, lib/Common/Convection.c, lib/Common/Drive_solvers.c, lib/Common/Element_calculations.c, lib/Common/General_matrix_functions.c, lib/Common/Global_operations.c, lib/Common/Initial_temperature.c, lib/Common/Instructions.c, lib/Common/Make.mm, lib/Common/Nodal_mesh.c, lib/Common/Output.c, lib/Common/Pan_problem_misc_functions.c, lib/Common/Parsing.c, lib/Common/Phase_change.c, lib/Common/Problem_related.c, lib/Common/Process_buoyancy.c, lib/Common/Process_velocity.c, lib/Common/Shape_functions.c, lib/Common/Size_does_matter.c, lib/Common/Solver_conj_grad.c, lib/Common/Solver_multigrid.c, lib/Common/Sphere_harmonics.c, lib/Common/Stokes_flow_Incomp.c, lib/Common/Topo_gravity.c, lib/Common/Tracer_advection.c, lib/Common/Viscosity_structures.c, lib/Common/advection.h, lib/Common/convection_variables.h, lib/Common/element_definitions.h, lib/Common/global_defs.h, lib/Common/local.def, lib/Common/sphere_communication.h, lib/Common/temperature_descriptions.h, lib/Common/tracer_defs.h, lib/Common/viscosity_descriptions.h, lib/Full, lib/Full/Boundary_conditions.c, lib/Full/Geometry_cartesian.c, lib/Full/Global_operations.c, lib/Full/Initial_temperature.c, lib/Full/Make.mm, lib/Full/Output.c, lib/Full/Parallel_related.c, lib/Full/Problem_related.c, lib/Full/Process_buoyancy.c, lib/Full/Sphere_related.c, lib/Full/Version_dependent.c, lib/Full/global_defs.h, lib/Full/local.def, lib/Make.mm, lib/Regional, lib/Regional/Boundary_conditions.c, lib/Regional/Geometry_cartesian.c, lib/Regional/Global_operations.c, lib/Regional/Initial_temperature.c, lib/Regional/Make.mm, lib/Regional/Output.c, lib/Regional/Parallel_related.c, lib/Regional/Problem_related.c, lib/Regional/Process_buoyancy.c, lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c, lib/Regional/global_defs.h, lib/Regional/local.def, lib/local.def, local.def, module, module/Full, module/Full/Fullmodule.cc, module/Full/Make.mm, module/Full/bindings.cc, module/Full/bindings.h, module/Full/exceptions.cc, module/Full/exceptions.h, module/Full/local.def, module/Full/misc.cc, module/Full/misc.h, module/Make.mm, module/Regional, module/Regional/Make.mm, module/Regional/Regionalmodule.cc, module/Regional/bindings.cc, module/Regional/bindings.h, module/Regional/exceptions.cc, module/Regional/exceptions.h, module/Regional/local.def, module/Regional/misc.cc, module/Regional/misc.h, module/local.def, pyre, pyre/Make.mm, pyre/__init__.py, pyre/local.def, tests, tests/Make.mm, tests/local.def, tests/signon.py: Initial revision 2005-08-23 02:43 boo * .: [vcp] select <> as trunk 2005-08-23 02:42 VCP * mc/3D/CitcomS/branches, .: VCP: initializing layout