[cig-commits] r15268 - mc/3D/CitcomS/trunk
tan2 at geodynamics.org
tan2 at geodynamics.org
Mon Jun 15 11:21:42 PDT 2009
Author: tan2
Date: 2009-06-15 11:21:41 -0700 (Mon, 15 Jun 2009)
New Revision: 15268
Modified:
mc/3D/CitcomS/trunk/ChangeLog
Log:
Update ChangeLog to r15180
Modified: mc/3D/CitcomS/trunk/ChangeLog
===================================================================
--- mc/3D/CitcomS/trunk/ChangeLog 2009-06-15 18:04:20 UTC (rev 15267)
+++ mc/3D/CitcomS/trunk/ChangeLog 2009-06-15 18:21:41 UTC (rev 15268)
@@ -1,3 +1,1452 @@
+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
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