ChangeLog
2007-11-08 22:31 tan2
* lib/Instructions.c, lib/Pan_problem_misc_functions.c: Replaced a
system call by std C library remove() and disabled another system
call (backup input file). Partially fixed issue130. All remaining
system calls are in lib/Output_gzdir.c.
2007-11-08 21:38 tan2
* ChangeLog: Updated file ChangeLog to r8242
2007-11-08 21:36 tan2
* examples/Makefile.am: Removed binary checkpoint files from
makefile, as the file size is too big for distribution.
2007-11-08 21:17 tan2
* ChangeLog: Updated file ChangeLog to r8240
2007-11-08 19:19 tan2
* configure.ac: Update the version number
2007-11-08 19:18 tan2
* NEWS: Update NEWS
2007-11-08 19:18 tan2
* examples/Cookbook5/cookbook5.cfg: Dereased the timestep size to
reduce artifacts in advection
2007-11-07 19:52 tan2
* examples/Cookbook4/cookbook4.cfg: Decreased the # of processors.
This is the only way I can reproduce single-cell convection as in
the manual.
2007-11-07 19:52 tan2
* CitcomS/Components/Output.py, lib/Output.c: Removed comp_el from
default output, since it is not required for restart anymore.
2007-11-07 19:51 tan2
* lib/Stokes_flow_Incomp.c: Print a warning when matrix eqn solver
not converging
2007-11-06 23:18 tan2
* examples/Cookbook7/cookbook7.cfg: Added cgrad solver convergence
parameters, increased buoyancy_ratio and lower the # of steps
2007-11-06 23:18 tan2
* examples/Cookbook6/cookbook6.cfg: Removed unused multigrid
parameters
2007-11-06 23:18 tan2
* examples/Full/input.sample, examples/Regional/input.sample:
Increase vlowstep to match the default value in pyre
2007-11-06 23:17 tan2
* visual/project_geoid.c: Fixed a few memory errors
2007-11-06 01:04 tan2
* lib/Output.c: Init'd some variables about vtk_io, which might be
accessed with uninit'd values in output_finalize()
2007-11-06 01:04 tan2
* lib/Full_obsolete.c, lib/Global_operations.c, lib/Obsolete.c,
lib/Sphere_harmonics.c, lib/Topo_gravity.c: Shrank the size of
sph. harm arrays
2007-11-06 01:03 tan2
* lib/Regional_obsolete.c: Removed functions related sph. harm in
lib/Regional_obsolete.c
2007-11-06 01:03 tan2
* lib/Topo_gravity.c: Scaled topo with variable gravity. Fixed an
error in comment. Rearranged computation.
2007-11-01 23:33 tan2
* lib/Full_version_dependent.c: Fixed an error in comment
2007-11-01 23:33 tan2
* lib/Stokes_flow_Incomp.c: Print dv/v=dp/p=1.0 for the 1st Uzawa
iteraion
2007-10-30 22:29 tan2
* visual/Makefile.am: Minor modification
2007-10-30 21:54 tan2
* visual/Makefile.am: Added the C program project_geoid to the
makefile
2007-10-30 21:53 tan2
* visual/project_geoid.c: A post-processing program to project
geoid coefficents onto a regular (longitude, latitude) mesh
2007-10-30 21:50 tan2
* lib/Topo_gravity.c: Fixed a bug in dimensionalizing density.
Provided the formula of geoid calculation in the comments.
Rearranged the order of functions.
2007-10-30 21:49 tan2
* lib/Element_calculations.c, lib/Instructions.c: Compute
d(rho)/dr/rho from rho(r)
2007-10-22 20:57 tan2
* ChangeLog: Updated file ChangeLog to r8170
2007-10-22 20:26 tan2
* NEWS: Updated NEWS
2007-10-22 19:46 tan2
* AUTHORS, configure.ac: Minor update
2007-10-22 19:44 tan2
* INSTALL, README: Simpilify INSTALL
2007-10-22 19:03 tan2
* lib/Advection_diffusion.c: Eliminated unnecessary computation
2007-10-22 19:03 tan2
* lib/Advection_diffusion.c: Variable material properties in latent
heat correction on adiabatic cooling
2007-10-22 19:02 tan2
* lib/Advection_diffusion.c, lib/Phase_change.c: Added some
comments
2007-10-19 19:24 tan2
* lib/Advection_diffusion.c, lib/Phase_change.c, lib/global_defs.h,
module/setProperties.c: Renamed control.width* ->
control.inv_width* for clarity
2007-10-18 18:53 tan2
* CitcomS/Coupler/Coupler.py, module/Exchanger/Convertor.cc,
module/Exchanger/Convertor.h, module/Exchanger/exchangers.cc:
Renamed coupler inventory: dimensional -> si_unit and
transformational -> cartesian
2007-10-17 22:44 tan2
* examples/Cookbook5/cookbook5.cfg,
examples/Cookbook9/cookbook9.cfg: Minor change in the examples
2007-10-17 20:56 tan2
* bin/Citcom.c: Added comments on where C code is replaced by
python code in Citcom.c
2007-10-17 20:55 tan2
* lib/Determine_net_rotation.c, lib/Drive_solvers.c,
lib/Output_gzdir.c, lib/Stokes_flow_Incomp.c,
lib/Viscosity_structures.c, lib/viscosity_descriptions.h: Put the
rest of r8111 back
2007-10-17 20:33 tan2
* examples/Full/input.sample, examples/Regional/input.sample: Fixed
input diffusivity parameter in the examples, from r8111.
2007-10-17 20:32 tan2
* lib/Drive_solvers.c, lib/Global_operations.c,
lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c:
Added back minor modification from r8111
2007-10-17 18:40 tan2
* examples/Cookbook9/cookbook9.cfg: Fixed a typo in the example
2007-10-17 18:36 tan2
* lib/Global_operations.c: Fixed a bug in remove_rigid_rot()
2007-10-17 18:35 tan2
* bin/Citcom.c, examples/Full/input.sample,
lib/Determine_net_rotation.c, lib/Drive_solvers.c,
lib/Full_version_dependent.c, lib/Global_operations.c,
lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c,
lib/Output_gzdir.c, lib/Stokes_flow_Incomp.c,
lib/Viscosity_structures.c, lib/viscosity_descriptions.h: Roll
back r8111, reading velo files for init. temperature stays as
tic_method=-1. Other changes in r8111 will be put back later.
2007-10-13 19:07 becker
* bin/Citcom.c, examples/Full/input.sample,
lib/Determine_net_rotation.c, lib/Drive_solvers.c,
lib/Full_version_dependent.c, lib/Global_operations.c,
lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c,
lib/Output_gzdir.c, lib/Stokes_flow_Incomp.c,
lib/Viscosity_structures.c, lib/viscosity_descriptions.h: Fixed
rigid rotation code bug. Added restart=2 option which will not
use checkpoints, but tic_method=-1 style temperature input
(formally realized via tic_method=-1, but this should be cleaner)
fixed input diffusivity parameter in full example file.
2007-10-12 20:24 tan2
* tests/coupled.cfg: Turn off monitor_max_T in the test
2007-10-12 20:23 tan2
* module/Exchanger/Boundary.cc: Boundary class is for regional
model only, add a checking for it.
2007-10-11 01:23 tan2
* examples/Cookbook9, examples/Cookbook9/cookbook9.cfg,
examples/Cookbook9/ic, examples/Cookbook9/ic/cntn.velo.0.0,
examples/Cookbook9/ic/cntn.velo.1.0,
examples/Cookbook9/ic/embd.velo.0.0,
examples/Cookbook9/ic/embd.velo.1.0, examples/Cookbook9/velocity,
examples/Cookbook9/velocity/bvel.dat0,
examples/Cookbook9/velocity/bvel.dat1, examples/Makefile.am:
Cookbook 9: nested solver coupling + coor_refine + tsolver tuning
2007-10-11 00:03 becker
* lib/Process_buoyancy.c: Wiser now, commented in the E->fp output
2007-10-10 23:40 becker
* bin/Citcom.c, lib/Construct_arrays.c,
lib/Full_version_dependent.c, lib/Ggrd_handling.c,
lib/Initial_temperature.c, lib/Instructions.c,
lib/Pan_problem_misc_functions.c, lib/Process_buoyancy.c,
lib/Regional_sphere_related.c, lib/Regional_version_dependent.c,
lib/Viscosity_structures.c, lib/convection_variables.h,
lib/global_defs.h: Added coor=3 option for radial node spacing a
la CitcomCU. Streamlined ggrd temperature init. Added file flush
to heat flow output.
2007-10-10 21:00 tan2
* CitcomS/Coupler/Coupler.py: Add an assertion
2007-10-10 20:11 tan2
* CitcomS/Components/Stokes_solver/Incompressible.py,
examples/Cookbook8/cookbook8.cfg, examples/Full/input.sample,
examples/Regional/input.sample, lib/Drive_solvers.c,
lib/Global_operations.c, lib/Instructions.c, lib/global_defs.h,
module/setProperties.c: Remove rigid body rotation from the
velocity solution from global model.
A input parameter 'solver.vsolver.remove_rigid_rotation', default
to on, indicate whether to remove the rigid body rotation. For
free-slip model, this parameter should be on. For model with
imposed plate velocity, it is advised to turn off this parameter.
2007-10-05 20:02 tan2
* CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py,
CitcomS/Coupler/EmbeddedCoupler.py,
CitcomS/Solver/CoupledSolver.py: Renamed excludeTop ->
exclude_top, and excludeBottom -> exclude_bottom. (No other
CitcomS parameter uses CamelCase.)
Reworked the interaction of initial temperature and coupling.
Created a new parameter exchange_initial_temperature.
2007-10-05 20:00 tan2
* CitcomS/Components/Stokes_solver/Incompressible.py: Strengthen
the default convergence criterion for the 3rd iteration in
compressible cg solver
2007-10-05 19:58 tan2
* lib/Regional_read_input_from_files.c: Disable a debugging output
2007-10-05 19:58 tan2
* CitcomS/Coupler/MultiC_Coupler.py,
CitcomS/Coupler/MultiE_Coupler.py: Add licence text to the
multi-couplers
2007-10-05 19:57 tan2
* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
lib/Advection_diffusion.c: Turn off filter_temp by default since
it's not in the energy equation
2007-10-04 19:35 becker
* lib/Viscosity_structures.c: Fxied material assignment bug in
PDEPV (0 vs. 1 array issue...)
2007-10-01 20:38 tan2
* examples/Cookbook1/cookbook1.cfg,
examples/Cookbook2/cookbook2.cfg,
examples/Cookbook4/cookbook4.cfg,
examples/Cookbook5/cookbook5.cfg, examples/Cookbook5/ic,
examples/Cookbook5/restart_files,
examples/Cookbook6/cookbook6.cfg,
examples/Cookbook7/cookbook7.cfg, examples/Makefile.am,
examples/example1.cfg: Updated the cookbook scripts
2007-10-01 19:26 tan2
* examples/Cookbook8, examples/Cookbook8/cookbook8.cfg,
examples/Cookbook8/coord.dat, examples/Cookbook8/restart,
examples/Cookbook8/restart/cookbook8.chkpt.0.9000,
examples/Cookbook8/restart/cookbook8.chkpt.1.9000,
examples/Cookbook8/restart/cookbook8.chkpt.10.9000,
examples/Cookbook8/restart/cookbook8.chkpt.11.9000,
examples/Cookbook8/restart/cookbook8.chkpt.2.9000,
examples/Cookbook8/restart/cookbook8.chkpt.3.9000,
examples/Cookbook8/restart/cookbook8.chkpt.4.9000,
examples/Cookbook8/restart/cookbook8.chkpt.5.9000,
examples/Cookbook8/restart/cookbook8.chkpt.6.9000,
examples/Cookbook8/restart/cookbook8.chkpt.7.9000,
examples/Cookbook8/restart/cookbook8.chkpt.8.9000,
examples/Cookbook8/restart/cookbook8.chkpt.9.9000,
examples/Makefile.am: Added Cookbook8 for compressible model +
geoid + checkpoint + vsolver tuning
2007-09-28 23:36 becker
* lib/Full_version_dependent.c, lib/Initial_temperature.c,
lib/Output_gzdir.c: Fixed restart I/O bug in Output_gzdir.
2007-09-27 19:33 tan2
* bin/Citcom.c, lib/Output_gzdir.c: Added function prototype and
fixed a few errors
2007-09-27 19:07 tan2
* lib/Checkpoints.c, lib/Composition_related.c, lib/Tracer_setup.c,
lib/composition_related.h: Shrink the size of checkpoint files
2007-09-27 19:07 tan2
* CitcomS/Components/Sphere/Sphere.py,
lib/Regional_sphere_related.c, module/setProperties.c: Enable
coor_refine for regional model, only radial coordinate is refined
2007-09-25 19:40 tan2
* lib/Instructions.c: Fixed a bug in vtkio
2007-09-25 01:31 tan2
* CitcomS/Components/Param.py, lib/Instructions.c,
lib/Material_properties.c, lib/global_defs.h,
module/setProperties.c: Introducing choice of reference state:
When solver.param.reference_state=0, the reference state is read
from a file (solver.param.refstate_file)
When solver.param.reference_state=1 (default), the reference
state is calculated using Adams-Williamson equation of state.
2007-09-24 21:29 tan2
* configure.ac, lib/Output_gzdir.c: Detect the presence of libz and
enable ascii-gz at configure time
2007-09-24 21:28 tan2
* lib/Instructions.c, lib/Material_properties.c, lib/global_defs.h:
Comment out varialbe thermal conductivity. Removed unused struct
members.
2007-09-24 21:28 tan2
* lib/Advection_diffusion.c: Multiply rho*cp to DT/dt
2007-09-19 20:34 tan2
* lib/Material_properties.c: Don't write to log file, since only
rank-0 proc can access it
2007-09-19 20:34 tan2
* lib/Composition_related.c, lib/Instructions.c: Set default value
for tracer/composition flags earlier
2007-09-19 20:33 tan2
* lib/Checkpoints.c: Shrink the size of arrays
2007-09-19 20:31 tan2
* lib/Instructions.c: Shrink the size of arrays
2007-09-19 20:30 tan2
* lib/Output.c, lib/Output_gzdir.c, lib/Output_h5.c,
lib/Topo_gravity.c: Fixed uninit'd heat flux and geoid arrays
bugs, as reported by valgrind
2007-09-19 00:28 becker
* lib/Advection_diffusion.c, lib/Output_gzdir.c: Minor bug fix in
Output_gzidir, output_heating function didn't work.
2007-09-18 23:08 tan2
* lib/Checkpoints.c: Fixed a memory bug in checkpoint
2007-09-18 23:07 tan2
* lib/Regional_tracer_advection.c: Setup composition for regional
model
2007-09-18 01:52 leif
* configure.ac, setup.py: Fix for Issue129: "CitcomS configured
without exchanger still links with -lExchanger". Also, use
CIT_HEADER_MPI so that configuring --with-exchanger using MPICH2
works (see Issue14 and Issue57).
2007-09-17 20:30 tan2
* lib/Composition_related.c: Generalized init. composition from
neighbors for multi-component composition
2007-09-17 19:07 tan2
* lib/Composition_related.c: Using neighboring elements to
determine the initial composition, if only a few elements are
empty.
2007-09-15 00:17 tan2
* lib/Tracer_setup.c: Revert accidental commit in part of r7957
2007-09-14 23:39 tan2
* lib/Advection_diffusion.c, lib/Phase_change.c: Rearranged
computation of latent heat and the test condition of phase change
2007-09-14 23:11 tan2
* lib/Advection_diffusion.c: Added the contribution of latent heat
to the diffusion term
2007-09-14 23:11 tan2
* lib/Obsolete.c, lib/Phase_change.c: Replace abs() by fabs()
2007-09-14 23:10 tan2
* lib/Advection_diffusion.c: Consevert energy (sum of rho*cp*T)
instead of temperature (sum of T) in the Lenardic filter, also
fixed a long-standing bug (abs -> fabs)
2007-09-14 23:09 tan2
* lib/Advection_diffusion.c: Changed the magic numbers (0.0 and
1.0) to const variables, reindent the code.
2007-09-13 22:36 tan2
* CitcomS/Solver/Solver.py, lib/Instructions.c,
lib/Material_properties.c, lib/global_defs.h,
module/setProperties.c: Comment out adiabatic temperature profile
for now, since it is not used in the code.
2007-09-12 19:24 tan2
* visual/parser.py: Fixed a problem when the input string is empty
2007-09-12 19:24 tan2
* lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c,
lib/Tracer_setup.c, lib/global_defs.h: Added heating file to
optional output
2007-09-12 19:24 tan2
* lib/Stokes_flow_Incomp.c: Keep the load vector intact in the bicg
solver
2007-09-12 19:23 tan2
* lib/Composition_related.c, lib/Full_tracer_advection.c,
lib/Tracer_setup.c: Using drand48() instead of rand() to improve
the quality of random tracers. Added some debugging output if the
tracer count is low.
2007-09-12 19:22 tan2
* CitcomS/Components/Tracer.py, lib/Composition_related.c,
lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c,
lib/Tracer_setup.c, module/setProperties.c: Add new input boolean
parameter 'itracer_warnings'. Default to on. When it is off, the
exit condition of tracer is relaxed.
2007-09-12 19:19 tan2
* lib/Stokes_flow_Incomp.c: Removed the test for F=0 load vector
bug. The bug was fixed in r7940.
2007-09-07 22:53 tan2
* lib/Advection_diffusion.c, lib/Size_does_matter.c: Fixed tsolver.
Fixed a bug in TMass and another in convert element # to nz.
2007-09-05 22:35 tan2
* lib/Checkpoints.c, lib/Construct_arrays.c, lib/Drive_solvers.c,
lib/Element_calculations.c, lib/Full_obsolete.c,
lib/Full_parallel_related.c, lib/General_matrix_functions.c,
lib/Instructions.c, lib/Obsolete.c, lib/Regional_obsolete.c,
lib/Regional_parallel_related.c, lib/Solver_multigrid.c,
lib/Stokes_flow_Incomp.c: Fixed a few memory problems.
Shrink the size of several arrays related to Stokes eqn.
Moved jacobi() to Obsolete.c
2007-09-05 22:21 tan2
* module/Exchanger/SIUnit.cc: Forgot to update surfacee_tem
2007-09-05 22:20 tan2
* lib/Viscosity_structures.c: Set the min of 2nd strain rate
invariant to 1e-16 to prevent infinite viscosity when SDEPV=on
2007-09-05 22:20 tan2
* lib/Convection.c: Init'd timestep variables
2007-09-04 23:09 becker
* lib/Full_tracer_advection.c, lib/Instructions.c,
lib/Stokes_flow_Incomp.c: Added test for F=0 load vector bug,
moved open_qfiles to after set_elapsed time.
2007-08-29 23:50 tan2
* examples/Makefile.am: Forgot to update the makefile
2007-08-29 23:39 tan2
* examples/Cookbook5/velocity/bvel.dat57,
examples/Cookbook5/velocity/bvel.dat58,
examples/Cookbook5/velocity/bvel.dat59,
examples/Cookbook5/velocity/bvel.dat60,
examples/Cookbook5/velocity/bvel.dat61,
examples/Cookbook5/velocity/bvel.dat62,
examples/Cookbook5/velocity/bvel.dat63,
examples/Cookbook5/velocity/bvel.dat64,
examples/Cookbook5/velocity/bvel.dat65,
examples/Cookbook5/velocity/bvel.dat66,
examples/Cookbook5/velocity/bvel.dat67,
examples/Cookbook5/velocity/bvel.dat68,
examples/Cookbook5/velocity/bvel.dat69,
examples/Cookbook5/velocity/bvel.dat70,
examples/Cookbook5/velocity/bvel.dat71: Removed unused velocity
bc files
2007-08-29 23:18 tan2
* doc/CitcomS, doc: Restructing the repository layout for CitcomS
documentation
2007-08-29 20:55 tan2
* lib/Instructions.c: Forgot to update r7902
2007-08-29 20:48 tan2
* lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c,
lib/Regional_obsolete.c, lib/Viscosity_structures.c,
lib/output.h: Replaced output_open() with output_open_mode()
Append the log and time files if restarting
2007-08-29 20:47 tan2
* lib/Advection_diffusion.c: Minor fix
2007-08-29 01:46 becker
* lib/Instructions.c: Missed to merge one modification after the
conflict.
2007-08-29 00:51 becker
* bin/Citcom.c, lib/Full_version_dependent.c, lib/Ggrd_handling.c,
lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c,
lib/Output_gzdir.c, lib/Output_h5.c, lib/Process_buoyancy.c,
lib/Regional_version_dependent.c, lib/Viscosity_structures.c,
lib/convection_variables.h, lib/global_defs.h: When checking in
my changes, I had to resolve a conflict for lib/Instructions.c by
hand, which I hope I did properly. Here are my changes:
- renamed CONTOL structure members ORTHO and ORTHOZ to
CITCOM_ORTHO and CITCOM_ORTHOZ Those were never used and
conflicted with definitions in GMT gmt.h
- Added a higher frequency heat flow output option like so:
write_q_files=1 # option to write heat flux to files qt.dat and
qb.dat # at intervals smaller than storage_spacing (0)
- Added the capability to read in initial temperatures from
netcdf grd files, if -USE_GGRD is used. Lot of options, like so:
# # read initial temperature conditions from grd files (default
values in parentheses) # tic_method=4 # read initial temperature
from netcdf GRD files (off)
ggrd_tinit_scale_with_prem=off # scale the temperature with PREM
densities (off)
ggrd_tinit_scale=1.0 # scaling factor to apply to read in scalars
f (1.0)
ggrd_tinit_offset=-0.5 # offset, T = f * scale + offset + tm
(0.0) # where tm is the mean between top and bottom TBC values #
if the bottom is flux, will use 1 for bottom TBC value
ggrd_tinit_gfile="../../data/tomography/s20a_smean_new_age/t" #
prefix of grd files, will # try to read t.1.grd, t.2.grd ...
t.n.grd # where n is the number of layers in the depth file
ggrd_tinit_dfile="../../data/tomography/s20a_smean_new_age/tdepth.dat"
# file with layer depths in km from bottom up
ggrd_tinit_prem_file="../../progs/src/hc-svn/prem/prem.dat" #
PREM data file ggrd_tinit_override_tbc=on # override temperature
boundary conditions (off)
2007-08-28 01:10 tan2
* CitcomS/Solver/Solver.py, lib/Instructions.c: Defaulting
datadir_old to the current directory
2007-08-28 01:09 tan2
* CitcomS/Components/Const.py, CitcomS/Solver/Solver.py,
lib/Advection_diffusion.c, lib/Instructions.c,
lib/Material_properties.c, lib/Output_h5.c, lib/global_defs.h,
module/setProperties.c: Added various heating term to the energy
equation.
A new input parameter: solver.surfaceT for non-dimensional
surface temperature.
Removed old (and unused) input parameter: solver.const.surf_temp.
2007-08-27 19:34 tan2
* lib/Stokes_flow_Incomp.c: Fixed a index bug in stokes solver
2007-08-27 19:34 tan2
* CitcomS/Components/Output.py, CitcomS/Components/Tracer.py,
CitcomS/Components/Visc.py, lib/Advection_diffusion.c,
module/setProperties.c: Add pyre input for new parameters
introduced by TWB
2007-08-27 19:34 tan2
* lib/Advection_diffusion.c, lib/Checkpoints.c,
lib/Construct_arrays.c, lib/Determine_net_rotation.c,
lib/Drive_solvers.c, lib/Full_geometry_cartesian.c,
lib/Full_lith_age_read_files.c, lib/Full_tracer_advection.c,
lib/General_matrix_functions.c, lib/Instructions.c,
lib/Lith_age.c, lib/Pan_problem_misc_functions.c, lib/Parsing.c,
lib/Regional_lith_age_read_files.c,
lib/Regional_sphere_related.c, lib/Regional_tracer_advection.c,
lib/Regional_version_dependent.c, lib/Tracer_setup.c,
lib/Viscosity_structures.c, lib/output.h, module/setProperties.c:
Clean up the code and declared function prototypes to avoid
compiler warnings
2007-08-23 20:20 tan2
* lib/Advection_diffusion.c: Compute total visc and adi heating
2007-08-23 20:19 tan2
* lib/Advection_diffusion.c, lib/Parsing.c: Minor refactoring
2007-08-23 20:18 tan2
* lib/Pan_problem_misc_functions.c, lib/Phase_change.c: Compute
phase change wrt reference density and gravity profiles.
2007-08-23 20:18 tan2
* lib/Composition_related.c, lib/Tracer_setup.c,
module/setProperties.c: Avoid reading unused input parameters
2007-08-23 20:17 tan2
* CitcomS/Controller.py, CitcomS/Coupler/Coupler.py,
CitcomS/Coupler/EmbeddedCoupler.py,
CitcomS/Coupler/MultiC_Coupler.py,
CitcomS/Solver/CoupledSolver.py: assert
solver.tsolver.monitor_max_T is off in coupled run and remove
debugging output
2007-08-23 20:16 tan2
* lib/Advection_diffusion.c, lib/Instructions.c, lib/Output_h5.c,
lib/advection.h, lib/global_defs.h, module/setProperties.c:
Renamed E->control.filter_temperature to
E->advection.filter_temperature
2007-08-23 20:16 tan2
* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
lib/Advection_diffusion.c, lib/advection.h,
module/setProperties.c: Added new input parameter
solver.tsolver.monitor_max_T
When it is on (default), if the max temperature changes too much
between timestep, the temperature field is restored at the
tsolver is called using half of the timestep size.
2007-08-23 20:15 tan2
* lib/Advection_diffusion.c, lib/advection.h: Removed unused var.
in struct advection
2007-08-23 20:14 tan2
* lib/Size_does_matter.c: A new way to compute TMass
2007-08-23 20:14 tan2
* lib/Advection_diffusion.c, lib/Material_properties.c,
lib/Pan_problem_misc_functions.c, lib/Process_buoyancy.c,
lib/Size_does_matter.c, lib/global_defs.h, module/mesher.c: Minor
refactoring: add comments, rename variables
2007-08-22 01:00 becker
* lib/Advection_diffusion.c, lib/Determine_net_rotation.c,
lib/Instructions.c, lib/Makefile.am, lib/Output.c,
lib/Output_gzdir.c, lib/Pan_problem_misc_functions.c,
lib/Tracer_setup.c, lib/global_defs.h: Added an option to remove
net rotations of the whole model before ascii-gz output. This
might be something of interest for other output options as well,
but is still experimental. Obvisouly, NR motions could be removed
in a post-processing step, but it is useful to monitor how those
develop during a model run. (Particularly pronounced for strong
lateral viscosity variations based on composition.)
2007-08-21 22:42 tan2
* lib/Stokes_flow_Incomp.c: Removed the 2nd exit condition for bicg
solver because the convergence criterion is hard to determine.
2007-08-21 22:41 tan2
* lib/Topo_gravity.c: Fixed the scaling constants in geoid
calculation with reference state
2007-08-21 22:41 tan2
* lib/Pan_problem_misc_functions.c, lib/Phase_change.c: Disable
phase change in compressible flow
2007-08-21 20:28 tan2
* AUTHORS: Added Wei Leng to author list
2007-08-21 20:27 tan2
* CitcomS/Components/Stokes_solver/Incompressible.py,
lib/Instructions.c, lib/Stokes_flow_Incomp.c, lib/global_defs.h,
module/setProperties.c: A new input parameter to specify which
compressible solver
If solver.vsolver.uzawa == "cg", Wei Leng's implementation is
used. If solver.vsolver.uzawa == "bicg", Eh Tan's implementation
is used.
2007-08-21 20:26 tan2
* lib/Stokes_flow_Incomp.c: Refactored non-newtonian stokes solver
and iter-CG compressible stokes solver
2007-08-20 19:44 becker
* lib/Viscosity_structures.c: Forgot this file.
2007-08-20 18:11 tan2
* lib/Instructions.c: Added #ifdef block around vtk_io in
output_finalize()
2007-08-20 00:11 becker
* lib/Advection_diffusion.c, lib/Tracer_setup.c: Made CDEPV and
Q0.enriched work only with ncomp=1 for now.
2007-08-19 23:54 becker
* lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c,
lib/Output_h5.c, lib/Parsing.c: - merged changes with Eh's
additions
- added coor=2 option (for full citcom) to assign finer radial
node spacing to top and lower layers of shell. The
coor_refine=0.1,0.15,0.1,0.2 parameter specifies the radius
fraction of the bottom layer [0], the fraction of the nodes in
this layer [1], the top layer fraction [2], and the top layer
node fraction [3]. I.e. the defaults will put 15% of all nz nodes
into the 10% lower layer, 20% in the top 10% upper layer, and the
rest in between.
- renamed gzipped output option ascii-gz
- built in restart facilities for temperature and tracers when
using gzdir I/O
- added a composition viscosity function, CDEPV, based on two
tracer flavors
- for this to work, I had to move viscosity_input() *behind*
tic_input() and tracer_input() in instructions
- added tracer_enriched option. If tracer = on and
tracer_enriched = on, will reader Q0_enriched and vary the
element heat production between Q0 for C = 0 and Q0_enriched for
C = 1. I.e. this only works if C varies between 0 and 1.
- added an experimental option to write to a single VTK file
(note caveats!) if ascii-gz is activated
gzdir_vtkio = 2, will try to write VTK straight (experimental)
the VTK output is of the "legacy", serial type, and requires that
all processors see the same filesystem. This will likely lead to
a bottleneck for larg CPU computations as each processor has to
wait til the previous is done.
2007-08-17 21:41 tan2
* tests/checkpoint/run.sh: Added excutable permission to testing
shell script
2007-08-17 21:39 tan2
* tests/checkpoint/restart.cfg: Added comments to restart example
2007-08-17 18:35 tan2
* lib/Advection_diffusion.c, lib/Output.c, lib/Output_gzdir.c,
lib/Viscosity_structures.c: Converting TWB's ascii-gz and vtkio
output and CDEPV and tracer_enriched for multi-component chemical
convection.
2007-08-17 18:33 tan2
* CitcomS/Components/Tracer.py, lib/Checkpoints.c,
lib/Composition_related.c, lib/Full_tracer_advection.c,
lib/Output.c, lib/Pan_problem_misc_functions.c,
lib/Regional_tracer_advection.c, lib/Tracer_setup.c,
lib/global_defs.h, lib/tracer_defs.h, module/setProperties.c,
tests/checkpoint/tracer.cfg, visual/autocombine.py,
visual/batchcombine.py, visual/dxgeneral.py: Multi-component
chemical convection.
By setting tracer_flavors > 2, one can enable multi-component
chemical convection. See tests/checkpoint/tracer.cfg for example
input.
2007-08-16 21:36 tan2
* CitcomS/Components/IC.py, CitcomS/Components/Tracer.py,
CitcomS/Controller.py, CitcomS/Solver/CoupledSolver.py,
CitcomS/Solver/Solver.py, bin/Citcom.c,
examples/Cookbook5/cookbook5.cfg, lib/Checkpoints.c,
lib/Composition_related.c, lib/Full_tracer_advection.c,
lib/Initial_temperature.c, lib/Instructions.c, lib/Lith_age.c,
lib/Makefile.am, lib/Output.c, lib/Problem_related.c,
lib/Regional_tracer_advection.c, lib/Tracer_setup.c,
lib/Viscosity_structures.c, lib/checkpoints.h, lib/global_defs.h,
lib/initial_temperature.h, lib/lith_age.h, module/bindings.c,
module/initial_conditions.c, module/initial_conditions.h,
module/outputs.c, module/outputs.h, module/setProperties.c,
tests/checkpoint, tests/checkpoint/restart.cfg,
tests/checkpoint/run.sh, tests/checkpoint/tracer.cfg: Merging the
checkpoint branch to trunk.
The checkpoint file is called [datafile].chkpt.[rank].[step] and
is outputed with an interval of controller.checkpointFrequency.
To read back the checkpoint file, set solver.ic.restart=on. The
old checkpoint file,
[datafile_old].chkpt.[rank].[solution_cycles_init] will be read
in.
The old way of restarting (read in temperature from the velo
files) will still be available through solver.ic.tic_method=-1.
Setting solver.tracer.ic_method=2 will read the old *.tracer.*
files as before, but the composition field will be calculated
according to the tracers, not read from the *.comp_el.* files.
The parameter solver.tracer.reset_initial_composition becomes
obsolete.
2007-08-16 20:10 tan2
* lib/Element_calculations.c, lib/Viscosity_structures.c: When the
element is close to the poles, use a more precise method to
compute the strain rate.
2007-08-16 19:38 tan2
* lib/Material_properties.c, lib/material_properties.h: Forgot to
add two files to the repository
2007-08-16 19:28 tan2
* CitcomS/Components/Stokes_solver/Incompressible.py,
lib/Construct_arrays.c, lib/Element_calculations.c,
lib/Instructions.c, lib/Output_h5.c,
lib/Pan_problem_misc_functions.c, lib/Stokes_flow_Incomp.c,
lib/Topo_gravity.c, lib/Viscosity_structures.c,
lib/global_defs.h, module/setProperties.c,
visual/pasteCitcomData.py: Merging compressible branch to trunk.
The TALA solver is working. Two new input parameters:
dissipation_number and gruneisen.
2007-08-16 01:42 tan2
* examples/Cookbook5/cookbook5.cfg,
examples/Cookbook5/restart_files/cookbook5.velo.0.0,
examples/Cookbook5/restart_files/cookbook5.velo.1.0,
examples/Cookbook5/restart_files/cookbook5.velo.10.0,
examples/Cookbook5/restart_files/cookbook5.velo.11.0,
examples/Cookbook5/restart_files/cookbook5.velo.12.0,
examples/Cookbook5/restart_files/cookbook5.velo.13.0,
examples/Cookbook5/restart_files/cookbook5.velo.14.0,
examples/Cookbook5/restart_files/cookbook5.velo.15.0,
examples/Cookbook5/restart_files/cookbook5.velo.16.0,
examples/Cookbook5/restart_files/cookbook5.velo.17.0,
examples/Cookbook5/restart_files/cookbook5.velo.18.0,
examples/Cookbook5/restart_files/cookbook5.velo.19.0,
examples/Cookbook5/restart_files/cookbook5.velo.2.0,
examples/Cookbook5/restart_files/cookbook5.velo.20.0,
examples/Cookbook5/restart_files/cookbook5.velo.21.0,
examples/Cookbook5/restart_files/cookbook5.velo.22.0,
examples/Cookbook5/restart_files/cookbook5.velo.23.0,
examples/Cookbook5/restart_files/cookbook5.velo.24.0,
examples/Cookbook5/restart_files/cookbook5.velo.25.0,
examples/Cookbook5/restart_files/cookbook5.velo.26.0,
examples/Cookbook5/restart_files/cookbook5.velo.27.0,
examples/Cookbook5/restart_files/cookbook5.velo.28.0,
examples/Cookbook5/restart_files/cookbook5.velo.29.0,
examples/Cookbook5/restart_files/cookbook5.velo.3.0,
examples/Cookbook5/restart_files/cookbook5.velo.30.0,
examples/Cookbook5/restart_files/cookbook5.velo.31.0,
examples/Cookbook5/restart_files/cookbook5.velo.32.0,
examples/Cookbook5/restart_files/cookbook5.velo.33.0,
examples/Cookbook5/restart_files/cookbook5.velo.34.0,
examples/Cookbook5/restart_files/cookbook5.velo.35.0,
examples/Cookbook5/restart_files/cookbook5.velo.36.0,
examples/Cookbook5/restart_files/cookbook5.velo.37.0,
examples/Cookbook5/restart_files/cookbook5.velo.38.0,
examples/Cookbook5/restart_files/cookbook5.velo.39.0,
examples/Cookbook5/restart_files/cookbook5.velo.4.0,
examples/Cookbook5/restart_files/cookbook5.velo.40.0,
examples/Cookbook5/restart_files/cookbook5.velo.41.0,
examples/Cookbook5/restart_files/cookbook5.velo.42.0,
examples/Cookbook5/restart_files/cookbook5.velo.43.0,
examples/Cookbook5/restart_files/cookbook5.velo.44.0,
examples/Cookbook5/restart_files/cookbook5.velo.45.0,
examples/Cookbook5/restart_files/cookbook5.velo.46.0,
examples/Cookbook5/restart_files/cookbook5.velo.47.0,
examples/Cookbook5/restart_files/cookbook5.velo.48.0,
examples/Cookbook5/restart_files/cookbook5.velo.49.0,
examples/Cookbook5/restart_files/cookbook5.velo.5.0,
examples/Cookbook5/restart_files/cookbook5.velo.50.0,
examples/Cookbook5/restart_files/cookbook5.velo.51.0,
examples/Cookbook5/restart_files/cookbook5.velo.52.0,
examples/Cookbook5/restart_files/cookbook5.velo.53.0,
examples/Cookbook5/restart_files/cookbook5.velo.54.0,
examples/Cookbook5/restart_files/cookbook5.velo.55.0,
examples/Cookbook5/restart_files/cookbook5.velo.56.0,
examples/Cookbook5/restart_files/cookbook5.velo.57.0,
examples/Cookbook5/restart_files/cookbook5.velo.58.0,
examples/Cookbook5/restart_files/cookbook5.velo.59.0,
examples/Cookbook5/restart_files/cookbook5.velo.6.0,
examples/Cookbook5/restart_files/cookbook5.velo.60.0,
examples/Cookbook5/restart_files/cookbook5.velo.61.0,
examples/Cookbook5/restart_files/cookbook5.velo.62.0,
examples/Cookbook5/restart_files/cookbook5.velo.63.0,
examples/Cookbook5/restart_files/cookbook5.velo.7.0,
examples/Cookbook5/restart_files/cookbook5.velo.8.0,
examples/Cookbook5/restart_files/cookbook5.velo.9.0,
examples/Makefile.am: Updated Cookbook5 so that it uses only 2
processors.
2007-08-16 00:27 tan2
* CitcomS/Solver/Solver.py, lib/Advection_diffusion.c,
lib/Construct_arrays.c, lib/Convection.c, lib/Drive_solvers.c,
lib/Element_calculations.c, lib/Full_version_dependent.c,
lib/Instructions.c, lib/Makefile.am, lib/Obsolete.c,
lib/Output.c, lib/Output_h5.c, lib/Pan_problem_misc_functions.c,
lib/Process_buoyancy.c, lib/Regional_obsolete.c,
lib/Regional_version_dependent.c, lib/Size_does_matter.c,
lib/Stokes_flow_Incomp.c, lib/Topo_gravity.c,
lib/Viscosity_structures.c, lib/global_defs.h, module/mesher.c,
module/setProperties.c: Merging compressible branch (up to r6584)
to trunk.
2007-08-14 03:33 becker
* lib/Advection_diffusion.c, lib/Full_version_dependent.c,
lib/Instructions.c, lib/Output.c, lib/Output_gzdir.c,
lib/Pan_problem_misc_functions.c, lib/Problem_related.c,
lib/Process_buoyancy.c, lib/Regional_sphere_related.c,
lib/Regional_version_dependent.c, lib/Tracer_setup.c,
lib/global_defs.h: - added coor=2 option (for full citcom) to
assign finer radial node spacing to top and lower layers of
shell. The coor_refine=0.1,0.15,0.1,0.2 parameters specify the
radius fraction of the bottom layer [0], the fraction of the
nodes in this layer [1], the top layer fraction [2], and the top
layer node fraction [3]. I.e. the defaults will put 15% of all nz
nodes into the 10% lower layer, 20% in the top 10% upper layer,
and the rest in between.
- renamed gzipped output version with sub-directory storage
ascii-gz
- built in restart facilities for temperature and tracers when
using ascii-gz I/O with vtkio != 2
- added a composition viscosity function, CDEPV, based on two
tracer flavors
- for this to work, I had to move viscosity_input() *behind*
tic_input() and tracer_input() in instructions
- added tracer_enriched option for internal heating. If tracer =
on and tracer_enriched = on, will reader Q0_enriched and vary the
element heat production between Q0 for C = 0 and Q0_enriched for
C = 1. I.e. this only works if C varies between 0 and 1.
- added an option to write from all processros to a single VTK
file, if ascii-gz is activated, and vtkio = 2. The VTK output is
of the "legacy", serial, single-file type, and requires that all
processors see the same filesystem.
This will lead to a bottleneck for large # of CPU computations as
each processor has to wait til the previous is done.
More efficient I/O should be possible by using the distributed
storage version of VTK, but I have no clue how this works.
Anyone?
2007-08-13 22:55 tan2
* lib/Global_operations.c, lib/Nodal_mesh.c, lib/Obsolete.c,
lib/Pan_problem_misc_functions.c, lib/Stokes_flow_Incomp.c: Minor
refactoring, clean-up and moving functions between files
2007-08-13 21:43 tan2
* lib/Obsolete.c, lib/Phase_change.c: Moved obsolete functions
phae_change_* from Phase_change.c to Obsolete.c and declared
private functions to be static
2007-08-10 23:56 tan2
* AUTHORS: Update the author list
2007-08-10 23:56 sue
* doc/manual/citcoms.lyx: additions per becker, tan2
2007-08-10 23:44 tan2
* lib/Drive_solvers.c, lib/Global_operations.c: Fixed two
type-mismatch errors. Issue127 is fixed by this change and r7802.
2007-08-10 23:43 tan2
* lib/Stokes_flow_Incomp.c: Prevent the original force vector being
modified by Uzawa solver. This is needed for the non-Newtonian
iterations.
2007-08-10 20:51 becker
* lib/Initial_temperature.c, lib/Instructions.c, lib/Output.c,
lib/Problem_related.c, lib/Tracer_setup.c: - renamed gzipped
output option ascii-gz
- built in restart facilities for temperature and tracers when
using gzdir I/O
- added a composition viscosity function, CDEPV, based on two
tracer flavors
- for this to work, I had to move viscosity_input() *behind*
tic_input() and tracer_input() in instructions
2007-08-09 01:27 becker
* lib/Initial_temperature.c, lib/Instructions.c,
lib/Output_gzdir.c, lib/Problem_related.c, lib/Tracer_setup.c,
lib/Viscosity_structures.c, lib/viscosity_descriptions.h: - added
a compositional viscosity function, CDEPV, based on two tracer
flavors
- for this to work, I had to move viscosity_input() *behind*
tic_input() and tracer_input() in Instructions.c
- built in restart facilities for temperature and tracers when
using gzdir I/O
2007-08-08 22:55 becker
* doc/manual/citcoms.lyx, lib/Composition_related.c,
lib/Construct_arrays.c, lib/Full_tracer_advection.c,
lib/General_matrix_functions.c, lib/Ggrd_handling.c,
lib/Instructions.c, lib/Makefile.am, lib/Output.c,
lib/Output_gzdir.c, lib/Pan_problem_misc_functions.c,
lib/Tracer_setup.c, lib/Viscosity_structures.c,
lib/global_defs.h, lib/tracer_defs.h: - added new routine
Ggrd_handling which will take care of netcdf grd input. For now,
only the tracer innitial conditions can be set by using, for
example,
ictracer_grd_layers=2 ictracer_grd_file="tmask.grd"
for this to work, the ggrd libraries from HC, as well as the
-lgmt and -lnetcdf need to be linked, and -DUSE_GGRD needs to be
defined on compile time.
- rewrote TDEPV viscosity options 3 and 4 slightly to make them
more efficient
- added TDEPV viscosity option 6
eta = N_0 exp(E(T_0-T) + (1-z) Z_0 )
- took layers subroutine in Construct_arrays.c apart to allow
calling the same function in a more flexible from other
subroutines
- addded error handling routine "myerror" to
Pan_problem_misc_functions
- made the output behavior of the multigrid solver convergence
parameters consisent with verbosity setting (ie. use report
instead of always stderr output)
- changed tracer input parameter "tracer" and "chemical_buoyancy"
to boolean routine for added flexibility (I hope)
- made check_initial_composition consistent with tracer
advection, exits after warning only for
E->trace.itracer_warnings==1
- debugging output in Full_tracer_advection.c and Tracer_setup
only gets printed to file for E->control.verbose == 1
- fixed some typos in Output_gzdir (that might have been
introduced by asynchronous svn updating or something like that)
2007-08-08 16:41 becker
* lib/Output_gzdir.c: Forgot to actually add the new file that is
needed for gzipped and "vtk" I/O.
2007-08-08 05:58 becker
* lib/Advection_diffusion.c, lib/Drive_solvers.c,
lib/Instructions.c, lib/Makefile.am, lib/Output.c,
lib/Pan_problem_misc_functions.c, lib/Stokes_flow_Incomp.c,
lib/Viscosity_structures.c, lib/global_defs.h, lib/output.h,
lib/viscosity_descriptions.h: - added functions rtp2xyz,
calc_cbase_at_tp, and convert_pvec_to_cvec for spherical to
Cartesian vector conversion to Pan_problem_functions.c
Added "safe_malloc" to the same file because I didn't like the
way Malloc1 uses int as arguments (64 bit issues).
- added support for gzipped ascii output into subdirectories of
data_dir, option gzdir. To use, need to compile with USE_GZDIR
and link with the -lz zlib libraries. Within gzdir output mode,
selected by
output_format=gzdir user can define vtk I/O (gzdir_vtkio=1) to
write Cartesian coordinates and velocities that are easy to
combine to a single vtk file in a post-processing step.
If gzlib_vtkio=0 the gzdir output option is meant to be identical
to the original ascii output, but files are all gzipped on the
fly, and the output that changes with each cycle is placed into
subdirectories of data_dir/ called data_dir/cycles/ For gzdir
I/O, data_name is not used at all, all single output files are
placed in the data_dir/ directory without prefix.
- added a new rheology option, PDEPV, for pseudo-plasticity and
added a corresponding description to the manual.
- Modified Drive_solver stderr output to show v.v, and not only
dv.dv/v.v
2007-08-02 22:44 luis
* .gitignore: Ignore most files generated by build system
2007-07-27 23:33 hlin
* module/Exchanger/Boundary.cc: M Boundary.cc fixed a bug on topbc
2007-07-26 00:20 tan2
* examples/Cookbook5/cookbook5.cfg: Fixed a typo, which was
introduced in svn r5399
2007-07-26 00:13 tan2
* visual/batchcombine.py, visual/combine.py: Fixed a bug that
*opt*.general files are mistakenly named. This bug is introduced
by svn r7236
2007-07-25 23:19 tan2
* visual/dxgeneral.py: Fixed a bug in ordering of mesh nodes. The
bug was introduced in svn r6510.
2007-07-23 19:50 hlin
* tests/coupled.cfg, tests/multicoupled.cfg: M
tests/multicoupled.cfg M tests/coupled.cfg
The code has passed a test on a regional containing solver.
Timestep will sync and initial condition will match.
Going to use a full containing solver with embedded solvers at
Hawaii and Reunion in next revision.
2007-07-20 21:52 hlin
* tests/coupled.cfg: M coupled.cfg alligned nodes in the solvers
for comparing velocity directly.
2007-07-19 18:51 tan2
* module/advdiffu.c: Fixed a bug in setting stable timestep
2007-07-19 18:51 tan2
* CitcomS/CoupledApp.py, CitcomS/MultiCoupledApp.py,
tests/coupled.cfg, tests/multicoupled.cfg: Changed the name
attribute of all application classes to 'CitcomS'. This allows
the users to specify the same launcher parameters for all
application in their ~/.pyre/CitcomS/CitcomS.cfg.
2007-07-19 18:37 hlin
* CitcomS/Controller.py, CitcomS/Coupler/EmbeddedCoupler.py,
CitcomS/Coupler/MultiC_Coupler.py,
CitcomS/Coupler/MultiE_Coupler.py, CitcomS/Coupler/__init__.py,
CitcomS/MultiCoupledApp.py, CitcomS/Solver/CoupledSolver.py: M
trunk/CitcomS/Coupler/MultiE_Coupler.py M
trunk/CitcomS/Coupler/__init__.py M
trunk/CitcomS/Coupler/EmbeddedCoupler.py M
trunk/CitcomS/Coupler/MultiC_Coupler.py M
trunk/CitcomS/Solver/CoupledSolver.py M
trunk/CitcomS/Controller.py M trunk/CitcomS/MultiCoupledApp.py
solved the synchronization issue. There are some bugs in the log
of time.
2007-07-18 23:06 hlin
* CitcomS/Coupler/MultiC_Coupler.py,
CitcomS/Coupler/MultiE_Coupler.py: A Coupler/MultiE_Coupler.py M
Coupler/MultiC_Coupler.py
Fixed the synchronization part. Need to test on it. Now Embedded
Couplers will wait until containing coupler make a decision.
2007-07-18 21:01 tan2
* bin/Makefile.am, bin/citcoms.in, bin/coupledcitcoms.in: Unify
bin/citcoms with bin/coupledcitcoms scripts. Users can run
'bin/citcoms --coupled' to launch a coupled run and 'bin/citcoms
--multicoupled' to launch a multicoupled run.
2007-07-17 22:49 tan2
* tests/multicoupled.cfg: An input file for multicoupled run
2007-07-17 22:48 tan2
* CitcomS/Coupler/MultiC_Coupler.py, CitcomS/Coupler/__init__.py,
CitcomS/MultiCoupledApp.py: Fixed a few typos and attached
MultiC_Coupler as the default factory for the ccoupler facility
2007-07-17 22:48 tan2
* CitcomS/Solver/MultiC_FullSolver.py,
CitcomS/Solver/MultiC_RegionalSolver.py,
CitcomS/Solver/MultiC_Solver.py, CitcomS/Solver/__init__.py:
Simplified the MultiC_*Solver classes
2007-07-16 23:45 hlin
* CitcomS/Solver/MultiC_FullSolver.py,
CitcomS/Solver/MultiC_RegionalSolver.py,
CitcomS/Solver/MultiC_Solver.py: A
Solver/MultiC_RegionalSolver.py A Solver/MultiC_FullSolver.py A
Solver/MultiC_Solver.py
ideally these files works as the solvers I needed for the
project.
2007-07-16 21:21 hlin
* CitcomS/Coupler/MultiC_Coupler.py, CitcomS/MultiLayout.py: M
CitcomS/MultiLayout.py trivial comment change
M CitcomS/Coupler/MultiC_Coupler.py a nearly complete version.
Although I am not sure how most of the things works , I managed
to create a copy of everything.initTemperature,
restartTemperature , and modifyT not defined.
2007-07-13 23:24 hlin
* CitcomS/Coupler/ContainingCoupler.py: M
Coupler/ContainingCoupler.py trivial modification on comments
2007-07-13 23:23 hlin
* CitcomS/Coupler/MultiC_Coupler.py: M Coupler/MultiC_Coupler.py
add __init__, initialize, createMesh some of createMesh are
commented out because I do not understand it.
2007-07-13 21:09 hlin
* CitcomS/Coupler/MultiC_Coupler.py: A Coupler/MultiC_Coupler.py
It's a child of Containing Coupler It has nothing now.
2007-07-11 20:17 tan2
* module/Exchanger/Boundary.cc,
module/Exchanger/CitcomInterpolator.cc,
module/Exchanger/CitcomSource.cc, module/Exchanger/SVTInlet.cc,
module/Exchanger/SVTOutlet.cc: Added some comments
2007-07-10 20:08 tan2
* CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py,
CitcomS/Coupler/EmbeddedCoupler.py: Renamed variables for
clarification
2007-07-09 22:03 tan2
* CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py,
CitcomS/Coupler/EmbeddedCoupler.py: Small changes in *Coupler
class. * consolidated __init__() and initialize() * renamed
numSrc -> remoteSize, boundary -> remoteBdryList, interior ->
remoteIntrList * defaulted the dimensional and transformational
properties to False
2007-07-06 20:48 tan2
* CitcomS/MultiCoupledApp.py, CitcomS/MultiLayout.py: Added
svn:keywords Id
2007-07-06 20:46 tan2
* CitcomS/MultiCoupledApp.py, CitcomS/MultiLayout.py: Debugged
MultiLayout.initialize() and MultiCoupledApp.findLayout(). Fixed
some typos.
2007-07-06 18:00 tan2
* CitcomS/CoupledApp.py: Using log() instead of line() to flush the
journal buffer, otherwise no output at all.
2007-07-06 17:50 hlin
* CitcomS/MultiCoupledApp.py, CitcomS/MultiLayout.py: fix myPlus
and remotePlus and report in MultiCoupledApp edit some comments
in MultiLayout
2007-07-05 23:45 hlin
* CitcomS/MultiCoupledApp.py, CitcomS/MultiLayout.py: add
MultiLayout not sure about number of processor, currently assign
1-10 for ccom 11 for ecom1, and 12 for ecom2
2007-07-05 22:36 hlin
* CitcomS/MultiCoupledApp.py:
2007-07-05 20:49 hlin
* CitcomS/MultiCoupledApp.py:
2007-07-04 00:02 hlin
* CitcomS/MultiCoupledApp.py: a draft for multicoupled application
2007-07-02 22:21 tan2
* doc/manual/citcoms.lyx: Removing outdated and redundant
documentation
2007-07-02 22:21 tan2
* CitcomS/SimpleApp.py: Using log() instead of line() to flush the
journal buffer, otherwise no output at all.
2007-06-28 19:35 tan2
* CitcomS/Layout.py, tests/coupled.cfg: Renamed ccomm ->
containing_group and ecomm -> embedded_group. Added more checks
to the groups
2007-06-27 01:04 tan2
* CitcomS/BaseApplication.py, CitcomS/Controller.py,
CitcomS/CoupledApp.py, CitcomS/Coupler/ContainingCoupler.py,
CitcomS/Coupler/Coupler.py, CitcomS/Coupler/EmbeddedCoupler.py,
CitcomS/Layout.py, CitcomS/SimpleApp.py,
CitcomS/Solver/CoupledSolver.py: Added/updated a bunch of
comments, renamed variables
2007-06-26 00:37 tan2
* doc/manual/graphics/citcoms_cover-layers.pdf,
doc/manual/graphics/citcoms_cover.pdf: Added mime-type property
to the PDF files
2007-06-23 00:33 tan2
* CitcomS/CoupledApp.py, CitcomS/Coupler/ContainingCoupler.py,
CitcomS/Coupler/Coupler.py, CitcomS/Coupler/EmbeddedCoupler.py,
CitcomS/SimpleApp.py, CitcomS/Solver/CoupledSolver.py,
module/Exchanger/BoundaryVTInlet.cc,
module/Exchanger/CitcomSource.cc, module/Exchanger/SVTOutlet.cc,
module/Exchanger/exchangers.cc, module/Exchanger/misc.cc,
tests/array2d.cc, tests/coupled.cfg: Giving
Exchanger/Coupler/CoupledApp as new life. The testing script
tests/coupled.cfg finished successfully.
2007-06-23 00:30 tan2
* lib/Citcom_init.c: Useful debuggin output, but disabled
2007-06-23 00:29 tan2
* configure.ac: Print CXX and CXXFLAGS after finishing configure
2007-06-23 00:28 tan2
* lib/Viscosity_structures.c: Removed the back-and-forth
interpolation of viscosity, which smoothes the viscosity field
unnecessarily
2007-06-22 23:43 tan2
* module/setProperties.c: Forgot to commit module/setProperties.c
in r7289. This should fix issue115 in the pyre version also.
2007-06-22 04:36 leif
* .: Added BuildBot config.
2007-06-21 22:35 hlin
* tests/test1.sh: Resolved the conflict
2007-06-21 22:25 tan2
* tests/test1.sh: Preparing a conflict test, again
2007-06-21 22:22 tan2
* tests/test1.sh: Preparing a conflict test, again
2007-06-21 22:19 tan2
* tests/test1.sh: Preparing a conflict test
2007-06-18 23:21 tan2
* CitcomS/CoupledApp.py, CitcomS/Coupler/Coupler.py,
CitcomS/Layout.py, etc/full.odb, etc/regional.odb: Renamed 'XXX1'
-> 'cXXX' and 'XXX2' -> 'eXXX'
2007-06-18 23:06 tan2
* lib/Instructions.c, lib/Tracer_setup.c: Fixing issue115:
interference between restart=1 & tracer_ic_method
Previously, when "restart" is set, tracer_ic_method will be set
to 2 (restart tracers) by the code. Now, these two options are
independent.
2007-06-15 18:01 leif
* bin/dummy.cc: Fix for problem with GCC 3.4.5 (observed on
CITerra):
mv: cannot stat `.deps/dummy.Tpo': No such file or directory
2007-06-14 21:38 tan2
* lib/Topo_gravity.c: Zeroing geoid arrays before every geoid
calculation. This fixes issue114
2007-06-14 17:55 tan2
* visual/autocombine.py, visual/batchcombine.py,
visual/pasteCitcomData.py: A better fix for issue110
2007-06-14 01:36 tan2
* visual/pasteCitcomData.py: Fixing issue111: Expanding %RANK in
autocombine.py
2007-06-13 17:55 hlin
* tests/test1.sh: A trivial change
2007-06-12 00:05 tan2
* module/setProperties.c: Fixing issue112
2007-05-11 20:19 leif
* bin/Makefile.am: Fixed LINK problem w/Automake.
2007-05-11 02:02 leif
* CitcomS/CoupledApp.py, bin/Makefile.am, bin/coupledcitcoms.in,
bin/dummy.cc, bin/pycitcoms.c, configure.ac,
module/Exchanger/AreaWeightedNormal.cc,
module/Exchanger/Boundary.cc,
module/Exchanger/BoundaryVTInlet.cc,
module/Exchanger/CitcomInterpolator.cc,
module/Exchanger/CitcomSource.cc, module/Exchanger/Convertor.cc,
module/Exchanger/Exchangermodule.cc,
module/Exchanger/Exchangermodule.h, module/Exchanger/Interior.cc,
module/Exchanger/Makefile.am, module/Exchanger/SIUnit.cc,
module/Exchanger/SInlet.cc, module/Exchanger/SVTInlet.cc,
module/Exchanger/SVTOutlet.cc, module/Exchanger/TInlet.cc,
module/Exchanger/TOutlet.cc, module/Exchanger/VOutlet.cc,
module/Exchanger/VTInlet.cc, module/Exchanger/VTOutlet.cc,
module/Exchanger/bindings.cc, module/Exchanger/exceptions.cc,
module/Exchanger/exchangers.cc, module/Exchanger/global_bbox.cc,
module/Exchanger/initTemperature.cc,
module/Exchanger/inlets_outlets.cc, module/Exchanger/misc.cc,
module/Makefile.am, setup.py: Build with Exchanger, if available.
The Exchanger package will be automatically detected if it is
installed on your PYTHONPATH. The preprocessor & link flags for
compiling/linking with Exchanger are handled automatically.
To my chagrin, this change increases the CitcomS language count
back up to 3 again (C, C++, Python). Even with the aid of the
'cproto' tool, it would take many hours of work to make the C
code in 'lib' compile using a C++ compiler.
2007-04-11 00:40 tan2
* tests/Makefile.am: Forgot to update the makefile in r6541
2007-04-10 21:59 tan2
* lib/Tracer_setup.c: Finding the min/max of the Cartesian
coordinates. The min/max values provide the bounding box for
random tracer generation. This will speed up the tracer
generation, and should avoid a potential problem of "too many
tries?" error when the domain size of a processor is much smaller
(<1%) than the size of the whole sphere.
2007-04-10 21:58 tan2
* tests/asap.py, tests/hrothgar.py: Removed obsolete pyre
components in tests/
2007-04-05 22:21 tan2
* visual/Makefile.am, visual/autocombine.py,
visual/batchcombine.py, visual/batchpaste.sh, visual/combine.py,
visual/dxgeneral.py, visual/dxgeneral.sh, visual/execpaste.py,
visual/pasteCitcomData.py, visual/pasteCitcomData.sh: Adding the
ability to combine optional fields to the post-processing
scripts.
autocombine.py will read the parameter 'output_optional' from the
cfg file and combine the optional fields (can be pressure,
stress, comp_nd, or a combination of the three) into a file. The
file is named similar to the cap file, with 'cap' replaced by
'opt'. A .general file is also created, which describes the
content, shape, and structure of the opt file.
2007-03-27 20:54 sue
* doc/manual/graphics/citcoms_cover-layers.pdf: standardized
typefaces on cover
2007-03-27 06:51 sue
* doc/manual/citcoms.pdf,
doc/manual/graphics/citcoms_cover-layers.pdf,
doc/manual/graphics/citcoms_cover.pdf: changed version to 2.2.1
per tan2
2007-03-27 04:39 tan2
* ChangeLog: Regenerated ChangeLog upto r6417
2007-03-27 04:37 tan2
* NEWS, configure.ac, doc/manual/citcoms.lyx: Updated NEWS for the
upcoming 2.2.1
2007-03-27 04:20 tan2
* examples/Makefile.am: Forgot to add cookbook7.cfg to the file
list
2007-03-26 18:48 tan2
* ChangeLog: Regenerated ChangeLog upto r6409
2007-03-26 18:45 tan2
* lib/Makefile.am: Forgot to add a header file to the file list
2007-03-26 18:25 tan2
* ChangeLog: Regenerated ChangeLog upto r6403
2007-03-26 18:20 tan2
* visual/plot_annulus.py: Set the length unit to cm to fit within
the page
2007-03-26 18:11 tan2
* visual/plot_layer.py: Changed the size of gmt plots to fit within
the page
2007-03-26 18:05 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: restored edits to
stable copy; regen pdf, images showing
2007-03-26 06:01 tan2
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: Enlarged the
figure of cookbook7. Rephrased the description of the
low-viscosity-zone parameters, per Sue's suggestion.
2007-03-26 00:23 sue
* doc/manual/citcoms.pdf: chasing down image problem
2007-03-25 23:07 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: changed verbage
in History 1.2, paragraphs on version 2.1, to past tense, since
notes on 2.2 should be only ones in present tense \c
2007-03-25 22:55 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: edits of new
copy; attempt to fix an image that is not displaying, still
unresolved
2007-03-24 23:05 tan2
* doc/manual/citcoms.lyx: Finished Cookbook7
2007-03-24 23:03 tan2
* README, configure.ac, setup.py: Changed the version number to 2.2
2007-03-24 00:02 tan2
* examples/Cookbook7, examples/Cookbook7/cookbook7.cfg: Added new
cookbook7
2007-03-23 22:21 tan2
* NEWS, doc/manual/citcoms.lyx: Updated the NEWS for v2.2.0
2007-03-23 22:21 tan2
* doc/manual/citcoms.lyx, examples/Full/input.sample,
examples/Regional/input.sample: Added new parameter 'adv_gamme'
to the manual and input samples. Documented a new tic_method=3
2007-03-23 21:06 tan2
* doc/manual/citcoms.lyx: Added description to the tracer and
composition input/output files
2007-03-23 20:40 tan2
* doc/manual/citcoms.lyx, examples/Full/input.sample,
examples/Regional/input.sample: Added the tracer parameters to
the manual and sample input files
2007-03-23 20:39 tan2
* CitcomS/Components/Tracer.py, lib/Full_tracer_advection.c,
module/setProperties.c: Disable the parameter
"analytical_tracer_test", and make "chemical_buoyancy" a boolean
2007-03-23 19:37 tan2
* doc/manual/citcoms.lyx, examples/Full/input.sample,
examples/Regional/input.sample: Added the low-visc-zone
parameters to the manual and the sample input files
2007-03-23 05:31 tan2
* doc/manual/graphics/cookbook7.jpg: Added the image for cookbook7
(thermo-chemical convection
2007-03-23 05:30 tan2
* doc/manual/citcoms.lyx, doc/manual/graphics/cookbook6.eps,
doc/manual/graphics/cookbook7.eps: When I renamed the old
Cookbook7/ directory to Cookbook6/, I forgot to rename
cookbook7.eps to cookbook6.eps. Now it is done.
2007-03-23 05:25 tan2
* doc/manual/graphics/cookbook6.2.eps,
doc/manual/graphics/cookbook6.eps: These two EPS files are the
leftover of an old cookbook
2007-03-23 05:22 tan2
* lib/Tracer_setup.c: Gather theta and phi only in
get_neighboring_caps()
2007-03-23 05:21 tan2
* lib/Composition_related.c, lib/Output.c: Changed the header
format of comp_* output to be consistent with other data files
2007-03-22 22:11 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf,
doc/manual/graphics/citcoms_cover-layers.pdf,
doc/manual/graphics/citcoms_cover.pdf: added bib entry per eh,
changed cover to citcoms (rem .py), changed to 2.2.0, todo
notation removed; regen pdf
2007-03-22 19:58 tan2
* lib/Stokes_flow_Incomp.c: Make the output of 1st iteration
consistent with later iterations
2007-03-22 19:57 tan2
* lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c,
lib/Tracer_setup.c: Calling find_tracers() and
count_tracers_of_flavors() in initialize_tracers(), so that the
former two functions can become static/private
2007-03-22 19:55 tan2
* lib/Tracer_setup.c: Renamed initialize_tracer_arrays() to
allocate_tracer_arrays()
2007-03-21 22:46 tan2
* doc/manual/citcoms.lyx: Updated the version number to 2.2.0
2007-03-21 22:46 tan2
* doc/manual/citcoms.lyx: Updated the dependency information
2007-03-21 22:46 tan2
* doc/manual/citcoms.lyx: Added chemical Rayleigh number to the
equations
2007-03-21 22:45 tan2
* doc/manual/citcoms.lyx: Added history of v2.2 release
2007-03-21 22:45 tan2
* doc/manual/citcoms.lyx: Added citation to McNamara & Zhong 2004
2007-03-21 19:30 tan2
* lib/Full_tracer_advection.c: Added a safeguard against nprocx or
nprocy greater than 1
2007-03-20 06:34 tan2
* lib/Full_tracer_advection.c: full_lost_souls() now works for
nprocz>1 as well
2007-03-20 06:27 tan2
* CitcomS/Components/Tracer.py, lib/Full_tracer_advection.c,
lib/Regional_tracer_advection.c, lib/Tracer_setup.c,
lib/tracer_defs.h, module/setProperties.c: Removed the
'tracer_interpolation_scheme' and 'tracer_advection_scheme'
parameters
2007-03-20 06:26 tan2
* lib/Viscosity_structures.c: Reporting error if low viscosity
channel/wedge is turned on, but tracer is turned off
2007-03-19 23:49 tan2
* lib/Full_tracer_advection.c, lib/Global_operations.c,
lib/Regional_parallel_related.c, lib/Regional_tracer_advection.c,
lib/Tracer_setup.c, lib/tracer_defs.h: lost_souls() cannot be
shared by both versions. The parallel communications of both
versions are too different. So, the original lost_souls() is
renamed to full_lost_souls(). A new regional_lost_souls() is
implemented. This code has been tested in 3x3x3 processors,
running over 100 timesteps. The number of total tracers is
conserved.
2007-03-19 23:44 tan2
* module/setProperties.c: Init'd
E->composition.icompositional_rheology to 0
2007-03-19 23:42 tan2
* lib/Composition_related.c, lib/composition_related.h: * Init'd
E->composition.icompositional_rheology to 0 * Write composition
instruction only if it is turned on * Clean up the code a bit
2007-03-19 23:29 tan2
* lib/Composition_related.c: Removing read_comp(), which is not
used anymore
2007-03-19 23:25 tan2
* CitcomS/Solver/Solver.py: Advect the tracers right after
temperature advection, before solving velocity
2007-03-19 23:08 tan2
* lib/Regional_parallel_related.c: Replaced for-loop by an if,
which matchs the intention better
2007-03-19 22:53 tan2
* lib/Advection_diffusion.c, lib/Convection.c: Init'd
advection.timestep and advection.timesteps earlier. The time
output uses these parameters.
2007-03-19 22:51 tan2
* lib/Viscosity_structures.c: Reimplemented my version of
low_viscosity_channel_factor() and low_viscosity_wedge_factor()
2007-03-19 22:50 tan2
* lib/Full_tracer_advection.c, lib/Tracer_setup.c: Clean up the
function prototype declaration
2007-03-19 22:48 tan2
* lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c,
lib/Tracer_setup.c: Moving tracer initialization code to a
function
2007-03-19 22:45 tan2
* lib/Full_tracer_advection.c, lib/Regional_tracer_advection.c,
lib/Size_does_matter.c, lib/Tracer_setup.c, lib/global_defs.h:
Compute the volume of the mesh, use it to estimate the # of
tracers in the proc. make_tracer_array() now works for both
versions
2007-03-17 00:38 tan2
* lib/Pan_problem_misc_functions.c: Apply chemical buoyancy only
when using tracer
2007-03-17 00:21 tan2
* bin/Citcom.c, lib/Full_obsolete.c, lib/Full_tracer_advection.c,
lib/Output.c, lib/Output_h5.c, lib/Regional_tracer_advection.c,
lib/Tracer_setup.c, lib/Viscosity_structures.c,
lib/global_defs.h, lib/tracer_defs.h, module/misc.c,
module/setProperties.c: Merged the regional and global tracer
codes.
Basically, Vlad's code is mostly gone and is replaced by Allen's
and mine code. A few functions, eg. analytical_test(),
low_viscosity_*_factor(), are disabled, need to work on them
later.
2007-03-15 02:51 leif
* CitcomS/BaseApplication.py: Removed broken usage() method.
(Pythia v0.8.1.3 will have a reasonable default for this method.)
2007-03-13 00:56 gurnis
* lib/Full_read_input_from_files.c,
lib/Regional_lith_age_read_files.c,
lib/Regional_read_input_from_files.c: Refactored the regional
parts of the code so that the age grids are read in from the same
code as are the velocity and material files. Moved the guts of
Regional_lith_age_read_files.c to
Regional_read_input_from_files.c. This nearly makes the structure
of Full and Regional the same -- refactoring that Leif initiated
last year
2007-03-12 23:27 tan2
* CitcomS/Components/Tracer.py, lib/Composition_related.c,
module/setProperties.c: Commented out code about
compositional_rheology, which is not implemented
2007-03-12 23:11 tan2
* lib/Composition_related.c, lib/Full_tracer_advection.c: Removed
static variables, added some code documentation
2007-03-12 22:14 tan2
* CitcomS/Components/Tracer.py, lib/Composition_related.c,
lib/Full_tracer_advection.c, lib/composition_related.h,
lib/global_defs.h, lib/tracer_defs.h, module/setProperties.c: A
new input parameter "ic_method_for_flavors", to specify which way
to initialize the flavors when the tracers are init'd randomly
Currrently, only ic_method_for_flavors=0 is allowed, which
produces a layered structure, any tracer above z_interface is of
flavor 0, below z_interface is of flavor 1.
2007-03-12 22:07 tan2
* lib/Composition_related.c, lib/Full_tracer_advection.c,
lib/composition_related.h: Initial bulk composition
2007-03-12 22:06 tan2
* lib/Full_tracer_advection.c, lib/Output.c, lib/tracer_defs.h:
Output the total composition information to the log file, get rid
of extra file handles in trace struct
2007-03-12 22:05 tan2
* lib/Full_tracer_advection.c, lib/Stokes_flow_Incomp.c,
lib/tracer_defs.h: Compute the Cartesian velocity on the fly, not
storing it in a seperated array
2007-03-12 20:08 gurnis
* lib/Advection_diffusion.c, lib/Lith_age.c,
lib/Regional_lith_age_read_files.c,
lib/Regional_read_input_from_files.c: Modified
Regional_read_input_from_files.c so that it now opens and reads
in material files. Material files are organized by elements.
Previsouly only worked for Full
2007-03-11 05:27 tan2
* CitcomS/Components/Tracer.py, lib/Composition_related.c,
lib/Full_tracer_advection.c, lib/Output.c, lib/global_defs.h,
lib/tracer_defs.h, module/setProperties.c: A new way to compute
composition.
Each tracer has a "flavor" (can only be either 0 or 1 currently).
In the ratio method, the composition of an element is determined
by: (# of tracers of flavor i)/(# of total tracers)
2007-03-11 05:20 tan2
* CitcomS/Components/Tracer.py, lib/Composition_related.c,
lib/Full_obsolete.c, lib/Full_tracer_advection.c, lib/Output.c,
lib/Pan_problem_misc_functions.c, lib/global_defs.h,
lib/tracer_defs.h, module/setProperties.c: * Unifying output for
extra tracer quantities * Renamed rtrac to basicq, etrac to
extraq, to match the basic/extra quantities for advection *
Renamed itrac to ielement, itracsize to ielementsize,
ielementsize to max_ntracers * A new member for the # of tracers
* Removed some unused members in trace struct * Untabify and
indent the code
2007-03-09 00:26 tan2
* AUTHORS: Add Vlad to the author list
2007-03-09 00:25 tan2
* AUTHORS, CitcomS/Components/Output.py,
CitcomS/Components/Tracer.py, lib/Composition_related.c,
lib/Element_calculations.c, lib/Full_obsolete.c,
lib/Full_tracer_advection.c, lib/Global_operations.c,
lib/Instructions.c, lib/Makefile.am, lib/Output.c,
lib/Pan_problem_misc_functions.c, lib/Stokes_flow_Incomp.c,
lib/Viscosity_structures.c, lib/composition_related.h,
lib/global_defs.h, lib/tracer_defs.h, module/setProperties.c: A
big patch for tracers and composition:
* Seperating composition codes from tracer codes, several struct
members in E->trace are moved to E->composition * Add chemical
buoyancy term * Renamed thermal_buoyancy() to get_buoyancy() to
reflect the fact that this function computes buoyancy according
to temperature/composition/phase * Fix and optimize the fix_*()
functions * Remove some static variables, or converte them to
const * Change the type of E->SinCos from float to double, and
replace E->trace.DSinCos * Provide default values for "required"
input parameters * Renamed tracer_restart to tracer_ic_method,
also remapped the options * Removed option for Cartesian tracer
input and trace.iwrite_tracers_every * Replaced
trace.itracer_type by composition.ichemical_buoyancy * Optionally
output tracers and composition fields
2007-03-08 00:35 leif
* bin/Makefile.am: Minor Makefile fix I made while working on
Nemesis (i.e. with embedding disabled).
2007-03-02 00:09 tan2
* lib/Full_tracer_advection.c, lib/tracer_defs.h: * Simplified
checking in the radial direction * Removed obsolete variables in
trace struct
2007-03-01 21:23 tan2
* lib/Full_tracer_advection.c: Finally, exchanging tracers between
processors works, at least in 12-proc cases
2007-03-01 21:21 tan2
* lib/Full_tracer_advection.c, lib/Output.c, lib/tracer_defs.h: *
Communicate cap boundary information with neighboring processors.
This information will be used in icheck_cap() later * Update
icheck_cap() for our paralleism * Disable composition-related
output
2007-03-01 21:17 tan2
* lib/Full_tracer_advection.c: Fixed two errors reported by icc
2007-03-01 21:16 tan2
* CitcomS/Components/Tracer.py, lib/Full_tracer_advection.c,
module/setProperties.c: * Create pyre inventory for tracer input
* Changed the default values of some tracer parameters to be
consistent with pyre inventory
2007-03-01 21:15 tan2
* bin/Citcom.c, lib/Full_tracer_advection.c,
lib/Full_version_dependent.c, lib/Global_operations.c,
lib/Instructions.c, lib/Tracer_setup.c,
lib/Viscosity_structures.c, lib/global_defs.h, lib/tracer_defs.h,
module/initial_conditions.c: Migrating the tracer code (not
finished)
2007-03-01 21:02 tan2
* lib/Full_tracer_advection.c, lib/Global_operations.c,
lib/Makefile.am, lib/global_defs.h, lib/tracer_defs.h: Copied
from Allen McNamara's tracer code. The code will fail to compile
2007-02-16 17:44 leif
* module/Exchanger: Resurrected Exchanger source.
2007-02-08 00:15 tan2
* lib/Advection_diffusion.c: Spherical version of the temperature
solver
2007-02-08 00:14 tan2
* visual/execpaste.py: Removed the use of a new feature in python
2.4 ("substring" in "string")
2007-02-06 02:23 tan2
* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
lib/Advection_diffusion.c, lib/Convection.c,
module/setProperties.c: Added input parameters that controlling
the predictor-corrector scheme
2007-02-06 02:22 tan2
* lib/Full_version_dependent.c: Fixed a bug when reading coor_file
in full CitcomS
2007-02-06 02:22 tan2
* lib/Solver_multigrid.c: Changed smoothing method for viscosity to
be consistent with CitcomCU
2007-02-02 23:30 tan2
* CitcomS/Components/IC.py, lib/Full_version_dependent.c,
lib/Initial_temperature.c, lib/Regional_version_dependent.c,
module/setProperties.c: A new option for initial temperature,
which is used in Shijie's benchmark
When tic_method==3, the initial temperature is a linear profile
plus mag * modified_plgndr_a(ll, mm, theta) * (cos(mm*phi) +
sin(mm*phi)) * sin(M_PI * (r - E->sphere.ri) / (E->sphere.ro -
E->sphere.ri))
2007-02-02 20:10 tan2
* CitcomS/Solver/Solver.py: Disable pid output for processors of
rank>0
2007-01-31 20:46 tan2
* CitcomS/Solver/Solver.py: Removed spaces around the equal sign
when writing pid file, which confused parser.py
2007-01-30 21:16 leif
* configure.ac: Moved Python egg stuff into our Autoconf macro
library.
2007-01-30 19:29 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: added spaces
after = in sec b.2; redid table in c.4.9 prev updated by eh;
regen pdf
2007-01-30 19:04 tan2
* lib/Viscosity_structures.c: Compute the 2nd invariant of strain
rate tensor in spherical coordinate
2007-01-29 20:51 gurnis
* lib/Full_read_input_from_files.c: The functionality of this
routine is now expanded so that for evey time step the element
materials are read in. The code for determining the material file
names and opening the file name and then reading in the element
files is placed in the same code that the age grids and velocity
files are processed. Obviously, reading in materials currently
only works for Full; fill be working on Regional next.
2007-01-29 20:46 gurnis
* lib/Advection_diffusion.c, lib/BC_util.c, lib/Instructions.c,
lib/Problem_related.c: Changed the seequence placement in the
time step when the age grids are assimilated into the temperature
field. Previously, going back to the original code contributed by
CC, the assimilation occurred avery time the temperature BCs were
set (meaning multiple times in a PC loop). Now assimilation
happens only once at the end of the time step. This is placed at
the end of the routine PG_time_step_solve. Once we have worked
with this some more, we will want to expose this code at a higher
level so that assimulation will work properly from either plain C
code or the Pyre version. Currently only tested with Full.
2007-01-29 20:37 gurnis
* lib/Lith_age.c: A minor change so that restart now works properly
when lith_age=1. Now restart from old temperature fields appear
to work without any obvious corruption of the Temp field. Only
tested with Full.
2007-01-29 20:32 gurnis
* lib/Viscosity_structures.c: Small change for rheol=5 to use
harmonic mean when element materials are read in. Also, this
involved a minor conflict resolution with Eh s recent change to
this file
2007-01-26 21:32 tan2
* CitcomS/Solver/Solver.py: Write controller inventory to pid file.
This is a heck!
2007-01-25 23:30 tan2
* lib/Stokes_flow_Incomp.c: Compute the velocity in Cartesian coord
on the fly.
The previous code computed and stored the Cartesian velocity in
E->temp in v_from_vector() and accessed E->temp in
velo_from_element. This is bug prone. E->temp is a temporary
array and should be used for storage.
Also, in previous code, if E->sphere.cap[m].V is modified, one
has to recompute E->temp. Otherwise, the Cartesian velocity will
be incorrect.
2007-01-25 01:38 tan2
* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
bin/Citcom.c, lib/Advection_diffusion.c, lib/Convection.c,
lib/Solver_multigrid.c, lib/global_defs.h: Get rid of static
variables
2007-01-25 00:57 tan2
* CitcomS/Solver/Solver.py, bin/Citcom.c,
lib/Advection_diffusion.c, lib/Convection.c,
lib/Full_geometry_cartesian.c, lib/Instructions.c,
lib/Regional_geometry_cartesian.c, module/advdiffu.c,
module/mesher.c, module/setProperties.c: Refactoring various
functions to simplify their pyre counterpart
2007-01-17 20:02 tan2
* lib/Viscosity_structures.c: Fixed a bug in locating elements
right above tracers
2007-01-17 01:54 tan2
* lib/Instructions.c, lib/Pan_problem_misc_functions.c: Replaced
'exit(0)' with correct MPI exit, related to issue69
2007-01-16 20:37 tan2
* lib/Full_read_input_from_files.c,
lib/Regional_read_input_from_files.c: Fixed issue77 - velocity
b.c not scaled correctly when age becomes negative
2007-01-16 19:49 tan2
* CitcomS/Components/IC.py, module/setProperties.c: Read input
parameter 'half_space_age' when tic_method=1
2007-01-16 18:50 tan2
* lib/Regional_tracer_advection.c: Fixed incorrect prototype
2007-01-16 18:43 tan2
* lib/Regional_version_dependent.c: When "tic_method=1", the
temperature is isothermal (== bottom b.c.) with a uniformly cold
plate (thickness specified by 'half_space_age')
2007-01-16 17:41 tan2
* CitcomS/Components/Visc.py, lib/Regional_tracer_advection.c,
lib/Viscosity_structures.c, lib/viscosity_descriptions.h,
module/setProperties.c: Tracer-defined rheology -- low viscosity
channel/wedge
2007-01-15 21:42 tan2
* lib/Makefile.am, lib/Regional_tracer_advection.c,
lib/Tracer_advection.c, lib/Tracer_setup.c, lib/tracer_defs.h,
module/misc.c: Added regional (passive) tracers
2007-01-09 21:11 tan2
* lib/Problem_related.c: Fix for time-invariant velocity boundary
conditions, issue75
2007-01-08 23:09 tan2
* doc/manual/citcoms.lyx: Another document fix for issue75, related
to "how to specify time-invariant velocity boundary conditions?"
2007-01-08 22:19 tan2
* doc/manual/citcoms.lyx: 1. Fixed a reference error, "Section 1.6"
should be "Equation 1.6" 2. Velocity BC input and geoid output
are dimensional. The units were undocumented in previous release.
This fix the issue75. 3. More information about geoid output: the
meaning of each column and how to compute the geoid field.
2007-01-08 22:19 tan2
* visual/plot_annulus.py, visual/plot_layer.py: Truncate the
temperature grd file at specified min/max
Sometimes the temperature field has overshoot/undershoot, which
would be leave a blank area in the contour plot. This is a simple
workaround.
2007-01-05 22:33 tan2
* visual/batchpaste.sh: Fix for issue73 "problems with
autocombine.py in single workstation mode"
$HOSTNAME is not defined in the non-interactive shell in Ubuntu
6.10. Need to put a quote around it.
2007-01-05 00:06 leif
* Makefile.am: Fix for issue72: "'make install' broken for
non-pyred CitcomS".
2006-12-20 22:13 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: added note about
updating to 2.10.3
2006-12-09 00:26 tan2
* ChangeLog: Regenerated ChangeLog upto r5565
2006-12-09 00:22 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: gurnis final
changes; image resize; ready for release
2006-12-08 23:50 sue
* doc/manual/citcoms.lyx: small text changes; image resize
2006-12-08 23:45 tan2
* doc/manual/citcoms.lyx: Added "created by OpenDX" on several
figure captions
2006-12-08 23:36 tan2
* doc/manual/citcoms.lyx, doc/manual/graphics/mayavi2.png: Updated
MayaVi2 section
2006-12-08 23:30 tan2
* visual/Makefile.am,
visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py,
visual/mayavi2_citcoms_display.py: Renamed the MayaVi launching
script and move it to visual/
2006-12-08 23:26 tan2
* visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py: Added
executable bit to file permission
2006-12-08 22:44 luis
* visual/Makefile.am: Add plugins for MayaVi2 to installation
2006-12-08 22:27 luis
* visual/Mayavi2/README, visual/Mayavi2/citcoms_display/README,
visual/Mayavi2/citcoms_plugins/README: Added README files
2006-12-08 22:00 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: fixed image size,
text size and other small text changes
2006-12-08 21:16 luis
* visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py: Removing
reduce filter from comments, as it is currently obsolete.
2006-12-08 21:15 luis
* doc/manual/citcoms.lyx: Added MayaVi screenshot to manual, along
with a couple of other fixes.
2006-12-08 20:03 luis
* visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py,
visual/Mayavi2/citcoms_plugins/plugins/OpenCitcomSFILES.py: Last
set of patches to citcoms_plugins * Display filename in mayavi
pipeline * Changed glob pattern so that only HDF5 timestep files
can be selected
2006-12-08 19:47 luis
* visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py,
visual/Mayavi2/citcoms_plugins/custom_ui.py,
visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py,
visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSFilterActions.py,
visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSreduce.py,
visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSshowCaps.py,
visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomsCapFilter.py,
visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomsReduceFilter.py:
Forgot to rename data filters.
2006-12-08 17:53 luis
* doc/manual/graphics/mayavi2.png: Added MayaVi2 screenshot for the
manual.
2006-12-08 17:44 luis
* visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py,
visual/Mayavi2/citcoms_plugins/custom_ui.py,
visual/Mayavi2/citcoms_plugins/plugins/CitcomSHDFUgrid.py,
visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py,
visual/Mayavi2/citcoms_plugins/plugins/OpenCitcomSFILES.py,
visual/Mayavi2/citcoms_plugins/utils.py: Various patches.
2006-12-08 17:40 luis
* visual/Mayavi2/citcoms_plugins,
visual/Mayavi2/citcoms_plugins/Citcoms_HdfDisplay.py,
visual/Mayavi2/citcoms_plugins/__init__.py,
visual/Mayavi2/citcoms_plugins/plugins,
visual/Mayavi2/citcoms_plugins/plugins/CitcomSHDFUgrid.py,
visual/Mayavi2/citcoms_plugins/plugins/CitcomS_hdf_file_reader.py,
visual/Mayavi2/citcoms_plugins/plugins/OpenCitcomSFILES.py,
visual/Mayavi2/citcoms_plugins/plugins/__init__.py,
visual/Mayavi2/citcoms_plugins/plugins/filter,
visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSFilterActions.py,
visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSSphere.py,
visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSreduce.py,
visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSshowCaps.py,
visual/Mayavi2/citcoms_plugins/plugins/filter/CitcomSshowSurface.py,
visual/Mayavi2/citcoms_plugins/plugins/filter/__init__.py:
Forking original plugins
2006-12-08 17:32 luis
* visual/Mayavi2/Martin, visual/Mayavi2/original_plugins,
visual/Mayavi2/original_plugins/README: Archiving original
plugins.
2006-12-08 17:31 luis
* visual/Mayavi2/mayavi_custom_ui.py: Modify plugins directory
2006-12-08 17:29 luis
* visual/Mayavi2/Martin/README: Explain contents of each directory.
2006-12-08 02:29 leif
* configure.ac: Made 'install_deps' actually do what 'configure'
says it's doing (*missing* deps, not *all*).
2006-12-07 23:26 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf,
doc/manual/graphics/regtest.100.z005.jpg: reinstated a few lost
changes; changed caption position on fig 5.3 on request; enlarged
fig 5.4; regen pdf
2006-12-07 22:34 tan2
* doc/manual/citcoms.lyx: chapter 5 * Added MayaVi2 in the
introduction * Added links to MayaVi2 installation
2006-12-07 22:19 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: fixed image size;
regen pdf
2006-12-07 22:09 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: text fixes to
recent additions
2006-12-07 21:30 tan2
* doc/manual/citcoms.lyx, doc/manual/graphics/hdfview.png: * Put
back the HDFView sections * Added a screenshot of HDFView * Added
a warning on "-O3" compiler flag
2006-12-07 05:03 sue
* doc/manual/citcoms.lyx: text edits to appendices and bib
2006-12-07 00:12 sue
* doc/manual/citcoms.lyx: small changes to chapt 6; standardized
cross refference style; sstandardized code spacing
2006-12-06 23:31 sue
* doc/manual/citcoms.lyx: enumerating several sections of the
instructions in chap 5 for clarity, and a few minor text fixes
2006-12-06 20:59 sue
* doc/manual/citcoms.lyx: a few text fixes in chapter 3
2006-12-06 20:33 sue
* doc/manual/citcoms.lyx: a few text fixes, preface to end of chapt
2
2006-12-06 18:59 sue
* doc/manual/citcoms.lyx: gurnis corrections and some other fixes
2006-12-06 08:52 luis
* visual/Makefile.am: Temporarily removing Mayavi2 files from
Makefile.am
2006-12-06 08:23 luis
* visual/Mayavi2/Citcoms_Hdf2Vtk.c,
visual/Mayavi2/Citcoms_Hdf2Vtk.py,
visual/Mayavi2/Citcoms_HdfDisplay.py,
visual/Mayavi2/Citcoms_VtkDisplay.py, visual/Mayavi2/Martin,
visual/Mayavi2/Martin/Citcoms_Hdf2Vtk.c,
visual/Mayavi2/Martin/Citcoms_Hdf2Vtk.py,
visual/Mayavi2/Martin/Citcoms_HdfDisplay.py,
visual/Mayavi2/Martin/Citcoms_VtkDisplay.py,
visual/Mayavi2/Martin/README, visual/Mayavi2/Martin/__init__.py,
visual/Mayavi2/Martin/plugins, visual/Mayavi2/README,
visual/Mayavi2/__init__.py, visual/Mayavi2/plugins: Archive files
created during Martin Weier's internship
2006-12-06 08:16 luis
* visual/Mayavi2/citcoms_display/plugins,
visual/Mayavi2/citcoms_display/plugins/HDF5FileReader.py,
visual/Mayavi2/citcoms_display/plugins/HDF5UGrid.py,
visual/Mayavi2/citcoms_display/plugins/ReduceFilter.py,
visual/Mayavi2/citcoms_display/plugins/ShowCapsFilter.py,
visual/Mayavi2/citcoms_display/plugins/ShowSurfaceFilter.py,
visual/Mayavi2/citcoms_display/plugins/Sphere.py,
visual/Mayavi2/citcoms_display/plugins/UGridThread.py,
visual/Mayavi2/citcoms_display/plugins/VTKFileReader.py,
visual/Mayavi2/citcoms_display/plugins/__init__.py: Reorganized
structure of the Mayavi2 plugin modules
2006-12-06 08:13 luis
* visual/Mayavi2/citcoms_display/custom_ui.py,
visual/Mayavi2/citcoms_display/mayavi_custom_ui.py,
visual/Mayavi2/mayavi_custom_ui.py: Simplified the file that will
be be copied to user's ~/.mayavi2 directory.
2006-12-06 06:55 luis
* visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Group all
CitcomS options under a single menu group.
2006-12-06 05:58 luis
* doc/manual/citcoms.lyx: Quick fixes to manual.
2006-12-06 01:08 leif
* CitcomS/Makefile.am, module/Regionalmodule.c, visual/Makefile.am:
Adding missing files to tarball ("make dist"), including the
'Mayavi2' directory, which is now installed under share/CitcomS.
Also deleted 'Regionalmodule.c', which is no longer used.
2006-12-06 00:49 sue
* doc/manual/citcoms.lyx: small changes in one image caption and in
citation
2006-12-06 00:42 leif
* Makefile.am, bin/Makefile.am, configure.ac: Fix for eggs not
being installed by "make install" when builddir == srcdir. This
change also re-fixes the setup.py infinite regress in a cleaner
way.
2006-12-06 00:18 luis
* visual/Mayavi2/citcoms_display/actions.py,
visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Added actions
for ReduceFilter and ShowCapsFilter
2006-12-05 23:13 leif
* Makefile.am, setup.py: Require final release version of Pythia.
Include egg-related files in release tarball ("make dist").
2006-12-05 20:46 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: edited text and
images placement in 5.8
2006-12-05 20:34 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: slghtly widened
l. col in appendix a tables as using typewriter widened lines;
fixed other formatting issues in appendices
2006-12-05 20:11 sue
* doc/manual/citcoms.lyx: changing font style to typewriter small
in appendix a tablesi and a few typos
2006-12-05 19:19 sue
* doc/manual/citcoms.lyx: small fixes to chap 4, text and table
placement
2006-12-05 18:04 sue
* doc/manual/citcoms.lyx: making use of typewriter font and quotes
consistent in appendix a
2006-12-05 07:09 tan2
* doc/manual/citcoms.lyx: Updated Chapter 4
2006-12-05 06:17 tan2
* visual/samples/cookbook1.100.h5, visual/samples/cookbook1.h5:
Example h5 files including all optional output
2006-12-05 06:14 tan2
* visual/Makefile.am: Forgot to update the makefile
2006-12-05 05:04 tan2
* doc/manual/citcoms.lyx: Removed sections about HDFView.
HDFView by default displays the dataset in a 2D table, which can
be very confusing when working on multidimensional dataset.
"h5ls -r" is a better tool for discovering the group structure
and dataset dimension.
2006-12-05 04:19 tan2
* visual/estimate.py, visual/estimate_size.py: * Renamed
estimate.py to estimate_size.py * Added license text * Update for
new HDF5 layout
2006-12-05 00:46 luis
* doc/manual/citcoms.lyx: Changed code in A.1.1 and A.1.2 to use
small font with typewriter style.
2006-12-05 00:40 tan2
* NEWS: Mentioned change of naming scheme for capfiles in NEWS
2006-12-05 00:31 sue
* doc/manual/citcoms.lyx: fixed quotes; added degree symbols as
requested
2006-12-05 00:14 tan2
* doc/manual/citcoms.lyx,
doc/manual/graphics/fulltest.xsect.100.jpg,
doc/manual/graphics/regtest.100.z005.jpg: Finished the GMT script
section
2006-12-04 23:47 tan2
* visual/plot_annulus.py: Renamed "center" to "starting point"
2006-12-04 22:42 sue
* doc/manual/citcoms.lyx: minor sentence/word form changes in 5.1
and 5.2
2006-12-04 22:33 sue
* doc/manual/citcoms.lyx: reformatted column names in c.4.9
2006-12-04 22:19 tan2
* doc/manual/citcoms.lyx: Revised Chapter 5 and Appendix A * Minor
revision of post-processing * Update OpenDX section for new HDF5
layout * Briefly mentioned GMT scripts (unfinished) * Described
new viscosity laws * Using Greek letter eta in the viscosity
equations
2006-12-04 20:33 sue
* doc/manual/citcoms.lyx: fixed more quotes, fixed table breaks,
lines in table missing, other minor format problems
2006-12-04 19:48 luis
* visual/Mayavi2/citcoms_display/__init__.py,
visual/Mayavi2/citcoms_display/actions.py,
visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Added
OpenHDF5 and OpenVTK actions for mayavi2
2006-12-04 17:24 luis
* doc/manual/citcoms.lyx: Fixes to manual
2006-12-04 17:24 luis
* NEWS: Fixed typos
2006-12-04 16:54 luis
* visual/h5tocap.c: Added vim modeline
2006-12-04 14:21 luis
* visual/Mayavi2/citcoms_display/__init__.py,
visual/Mayavi2/citcoms_display/mayavi_custom_ui.py: Mayavi2 UI
customizations
2006-12-04 14:11 luis
* visual/Mayavi2/citcoms_display: Added python module namespace for
the citcoms mayavi2 plugins
2006-12-04 13:43 luis
* visual/Mayavi2/__init__.py,
visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py,
visual/Mayavi2/plugins/__init__.py,
visual/Mayavi2/plugins/filter/__init__.py: Removed executable
permissions
2006-12-02 07:41 tan2
* doc/manual/graphics/CitcomSImportHDF5.net.gif,
visual/OpenDXMacro/CitcomSImportHDF5.net.in: Update for new HDF5
layout
2006-12-02 07:14 tan2
* examples/Full/input.sample, examples/Regional/input.sample: *
Removed obsolete parameters * Added new parameters * Only one
"parameter=value" per line
2006-12-02 06:04 tan2
* visual/h5tocap.c: Updated for new HDF5 layout
2006-12-02 06:04 tan2
* visual/h5util.c, visual/h5util.h: Minor tweaks
2006-12-02 04:43 tan2
* visual/Makefile.am, visual/h5tovelo.c, visual/h5util.c,
visual/h5util.h: Moved utility functions to h5util.c
2006-12-02 04:15 tan2
* visual/h5tovelo.c: Fixed a bug of counting argc
2006-12-02 00:57 tan2
* lib/Viscosity_structures.c: Added more rheology options, which is
required for benchmarks
rheol=1: visc = visc0 * exp(viscE * (viscT - T)) rheol=2: visc =
visc0 * exp(-T / viscT)
2006-12-02 00:38 tan2
* visual/h5tocap.py: Updated h5tocap.py for new layout of HDF5
files
2006-12-02 00:03 tan2
* visual/Makefile.am, visual/h5tovelo.c: Added a program to convert
h5 file to velo files for restart
2006-12-01 23:34 sue
* doc/manual/citcoms.lyx: removed todo at 4.5.1, no issue there
2006-12-01 22:00 leif
* configure.ac: Fix for infinite regress when builddir == srcdir.
!@#$%*
The .pth/sitedir/sys.path/PYTHONPATH aspect of eggs is really
irritating. I hope setuptools becomes a part of the standard
Python distro, as the Python core developers are likely to accept
it uncritically and unmodified (as they are wont to do,
apparently -- judging by all the other crap that is in the
standard library). God willing, this will further accelerate the
death of the language.
2006-12-01 21:56 tan2
* visual/Makefile.am, visual/samples/cookbook1.100.h5,
visual/samples/cookbook1.h5: Added samples of HDF5 output
2006-12-01 21:33 leif
* bin/Makefile.am, configure.ac: builddir != srcdir works again.
The use of setup.py/distutils/setuptools forces the creation of
files in srcdir. This bugs me.
2006-12-01 04:40 leif
* Makefile.am, configure.ac: The "make install" command now works
again.
2006-11-30 23:38 sue
* doc/manual/citcoms.lyx: fixed sentence in A.1.2 last row
2006-11-30 23:08 tan2
* doc/manual/citcoms.lyx: Updated Chapter 6 * sync'd the manual
with the cookbook scripts * improving the resolution of
cookbook5.2.eps is left until the next release
Also, fixed table borders in Appendix A.
2006-11-30 22:55 tan2
* examples/Cookbook5/cookbook5.cfg: Moved path name of restart file
to "datadir_old"
2006-11-30 22:53 tan2
* examples/Cookbook1/cookbook1.cfg,
examples/Cookbook2/cookbook2.cfg,
examples/Cookbook3/cookbook3.cfg,
examples/Cookbook4/cookbook4.cfg,
examples/Cookbook5/cookbook5.cfg: Fixed issue63, Change
"monitoringfrequency" comment in citcoms cookbooks
2006-11-30 22:21 luis
* doc/manual/citcoms.lyx: Done with Chapter 4 references.
2006-11-30 21:16 tan2
* doc/manual/citcoms.lyx: The concept of caps is explained in
section 1.7
2006-11-30 21:10 luis
* visual/Makefile.am, visual/h5steps.c: Removing obsolete program
h5steps.c
2006-11-30 20:57 tan2
* doc/manual/citcoms.lyx: Updated Appendices
2006-11-30 20:26 tan2
* doc/manual/citcoms.lyx: Updated section 3.6.1
2006-11-28 23:28 leif
* CitcomS/Components/IC.py,
CitcomS/Components/Sphere/FullSphere.py,
CitcomS/Components/Sphere/RegionalSphere.py,
CitcomS/Solver/Solver.py, module/bindings.c,
module/getProperty.h, module/misc.c, module/misc.h,
module/setProperties.c: Fixed some bugs, some of which were
introduced during the C -> C++ transition.
Using a pidXXXX.cfg file as input should "work" now, although it
still doesn't reproduce the original simulation, since at least
one parameter is missing ('steps'). I maintain that dumping the
configuration is really the job of the framework (Pyre).
Unfortunately, Pyre's current capabilities in this area are buggy
in the case of '.pml' files, and non-existent in the case of
'.cfg' files.
Note: 'nproc_surf' is now a real inventory item, instead of a
fake one. It looks like it doesn't belong in the inventory at
all, though. (I left it there to avoid breakage.)
2006-11-28 21:08 leif
* doc/manual/citcoms.lyx: Checked-in a virus, a worm, a Trojan
horse, and some other malware. LyX doesn't support copy & paste
between applications, so this check-in may have introduced some
bugs as well.
2006-11-28 19:26 sue
* doc/manual/citcoms.lyx: various edits to 3.6.1 and 3.7
2006-11-28 07:33 leif
* lib/Instructions.c: Rewrote expand_str() in order to: 1) avoid
potential buffer overflow; 2) avoid the use of non-standard
strndup(); 3) avoid the use of the heap altogether. (Prompted by
unresolved strndup on Mac OS X.)
2006-11-28 05:00 tan2
* examples/Cookbook2/cookbook2.cfg: Clarified the comment
2006-11-28 04:42 tan2
* NEWS: Updated for new features
2006-11-28 04:41 tan2
* README: Added a reference to NEWS
2006-11-28 03:34 tan2
* doc/manual/citcoms.lyx: Chapter 3 updated
2006-11-28 03:01 leif
* CitcomS/CoupledApp.py, CitcomS/SimpleApp.py, bin/citcoms.in,
setup.py: Changes related to Pythia v0.8.1.0b7, which CitcomS now
requires: 'journal' is no longer a part of an application's
inventory, and pyre.applications.start() is now responsible for
calling run().
2006-11-28 02:57 tan2
* examples/Cookbook6/cookbook6.cfg, examples/Full/input.sample,
examples/Regional/input.sample: Updated the dimensional const
2006-11-28 02:55 tan2
* examples/example1.cfg: Updated to be consistent with the manual
2006-11-27 23:09 tan2
* CitcomS/Solver/Solver.py, lib/Instructions.c: Changed the default
value of "datadir" to "."
2006-11-27 22:37 tan2
* visual/Makefile.am, visual/autocombine.py,
visual/batchcombine.py, visual/batchpaste.sh,
visual/batchpaste2.sh, visual/execpaste.py: Changed
postprocessing scripts for the new "datadir" parameter
2006-11-27 21:27 tan2
* visual/pasteCitcomData.sh: Fix for POSIX-compliant arithmetic
expression
The "sh" shell on my Ubuntu 6.10 doesn't have the "let" command.
That's how I found that "let" is not in the POSIX standard. Use
"$((expression))" instead.
2006-11-27 20:05 tan2
* visual/citcoms_datadir: Added extern program to determine
"datadir"
2006-11-27 20:05 tan2
* CitcomS/Components/Output.py, CitcomS/Solver/Solver.py,
lib/Instructions.c, lib/Output.c, lib/global_defs.h,
module/setProperties.c: Changes how to specify output directory
* "output_format" must be either "ascii" (the default) or "hdf5",
the "ascii-local" option is gone * "datafile" becomes the prefix
of the filename and cannot contain "/" * "datadir" becomes
mandatory input parameters * If "datadir" is "%DATADIR", the
output directory is determined by an external program
"citcoms_datadir" * Special substrings "%RANK", "%HOSTNAME" in
datadir will be substituted by mpi rank, machine's hostname,
$DATADIR environment variable, respectively. * These special
strings start with "%", rather than "$", becuase it's very
difficult to input "$" from the command line.
2006-11-22 21:26 tan2
* lib/Stokes_flow_Incomp.c: Changed the convergence criterion of
Stokes solver: * stop iterations if delta(v) or delta(p) becomes
too small (i.e., v or p has converged) * this is suggested by
Shijie Zhong
2006-11-22 21:25 tan2
* lib/Full_parallel_related.c: Ignoring overlapping nodes when
counting # of global nodes
2006-11-22 20:25 sue
* doc/manual/citcoms.lyx: typo; made references into an itemized
list
2006-11-22 20:05 tan2
* lib/Full_parallel_related.c, lib/Full_version_dependent.c,
lib/Makefile.am, lib/Regional_parallel_related.c,
lib/Regional_version_dependent.c, lib/global_defs.h,
lib/temperature_descriptions.h: Removed unused codes and files
2006-11-22 19:41 tan2
* lib/Output.c, lib/Output_h5.c, lib/Sphere_harmonics.c,
lib/Topo_gravity.c, lib/global_defs.h: Refactored geoid
calculation
2006-11-21 23:03 luis
* doc/manual/citcoms.lyx: Expanded section on optimizing parallel
I/O.
2006-11-21 20:18 tan2
* visual/plot_annulus.py, visual/plot_layer.py, visual/zslice.py:
Added scripts for 2D temperature plots, using GMT commands
2006-11-20 19:24 tan2
* lib/Sphere_harmonics.c: Forgot to declare function prototype
2006-11-18 05:17 tan2
* lib/Sphere_harmonics.c: Disabled a debugging output, which is not
protected by a "if(E->control.verbose)" and caused Segmentation
Fault.
2006-11-18 01:29 leif
* bin/pycitcoms.c: The function loadObject() has been moved from
Pythia to Merlin.
2006-11-18 00:48 tan2
* examples/Full/input.sample, examples/Full/velbc/README,
examples/Full/velbc/velbc_full.tar.gz, examples/Makefile.am:
Updated the vbc files and input file
2006-11-18 00:41 tan2
* examples/Regional/input.sample, examples/Regional/velbc/README,
examples/Regional/velbc/velbc_regional.tar.gz,
examples/Regional/velbc/velbc_regional40,
examples/Regional/velbc/velbc_regional41: Updated the vbc files
and input file.
2006-11-18 00:20 tan2
* lib/Instructions.c, lib/Output_h5.c, lib/hdf5_related.h,
lib/output_h5.h: HDF5 output for geoid is working
2006-11-17 22:37 luis
* ., CitcomS, bin, etc, examples, lib, module, tests, visual,
visual/OpenDXMacro: Cleaned up 'svn status' by updating
svn:ignore property
2006-11-17 20:25 tan2
* lib/Output_h5.c: HDF5 output of surf, botm, horiz_avg are working
now.
* Time and timestep infomation is written as scalar attributes
"time" and "timestep" in / group. * Set MPI_Info according to
input parameters "cb_block_size" and "cb_buffer_size" * I decided
not to write surf, botm, and horiz_avg coordinates. This
coordinate can be retrieved from the 3D coordinate very easily by
this pseudo-code: surf_coord = coord[cap=all, x=all, y=all, z=1]
z_coord = coord[cap=1, x=1, y=1, z=all]
Remainging works: geoid for hdf5, update the manual
2006-11-17 06:26 tan2
* lib/Instructions.c, lib/Output_h5.c, lib/hdf5_related.h,
lib/output_h5.h: HDF5 output reloaded. See issue4 for reasoning.
Most data outputs are working. Remaining works: * How to deal
with time output? (Maybe not output at all? Time info is always
written in the .time file anyway.) * Where to put 2d and 1d
coordinate output? (Maybe output with the data? These datasets
are small and won't take too much space anyway.) * Geoid output
2006-11-17 05:34 leif
* CitcomS/Components/Output.py: Fixed a minor bug in Output.py.
2006-11-17 02:24 leif
* doc/manual/citcoms.lyx: Revised everything having to do with
runtime configuration: launcher.xxx, scheduler.xxx, and job.xxx.
Lowered the prominence/importance given to .pml files... and
resisted my temptation to delete all reference to them :-)
(I think I'm pretty much done with the v2.1 manual at this point.
Reading the manual makes me tired, because it reminds me of how
much work remains to be done on the code itself. Ease-of-use
could be substantially improved...)
2006-11-16 21:58 leif
* bin/Makefile.am: Reverted another recent decision of mine: Always
build the legacy drivers, 'CitcomSFull' and 'CitcomSRegional'. I
took these out of the Pyre build to avoid confusion; but now --
thinking of shared installations of CitcomS on clusters -- I
think they should always be built (as they were before) so that
users have the option.
2006-11-16 21:36 leif
* examples/Makefile.am: Install examples under
PREFIX/share/CitcomS/examples, as now documented in the manual.
This is for the benefit of users of shared installations of
CitcomS. I also sync'd the file list in examples/Makefile.am.
Note: the file velbc_regional.tar.gz seems to be corrupt!!!
2006-11-16 21:25 leif
* doc/manual/citcoms.lyx: Corrections with respect to r5302: the
binaries/scripts are now once again built under the 'bin'
subdirectory.
Also reviewed all references to PREFIX.
2006-11-16 14:40 leif
* Citcom.c, CitcomSFull.c, CitcomSRegional.c, Makefile.am, bin,
bin/Citcom.c, bin/CitcomSFull.c, bin/CitcomSRegional.c,
bin/Makefile.am, bin/citcoms.in, bin/pycitcoms.c, citcoms.in,
configure.ac, pycitcoms.c: Re-created 'bin' subdirectory to avoid
filename conflict on case-sensitive filesystems (Mac, Windows):
"CitcomS" == "citcoms".
Fixed egg-related bugs which prevented 'configure' from
succeeding when buildir != srcdir (another BuildBot test vector).
Call addsitedir() in the 'citcoms' script. I guess this is now
necessary since "site.py" is no longer in the same directory as
"citcoms". (*)
Note that there is currently a bug in Merlin which prevents
'citcoms' from running ("No module named pkg_resources"). The
work-around is to manually add the merlin egg to the
merlin-install.pth file.
There are more bugs which prevent running on Mac OS X at all
(still investigating).
(*) I'm becoming annoyed with setuptools' use of .pth files as a
sys.path/PYTHONPATH persistence mechanism, mainly because of the
accompanying hacks which are used to turn ordinary directories
into "site" directories (i.e., directories where .pth files work)
-- these ugly, confusing hacks include the fake site.py, "virtual
python", etc. I think Merlin will only use .pth files in real
site directories. It will use clear, straitforward, direct
sys.path manipulation everywhere else.
2006-11-16 03:04 tan2
* module/setProperties.c: Forgot to commit module/ directory
2006-11-16 03:01 tan2
* lib/Topo_gravity.c: Declared function prototype at the top
2006-11-16 02:07 tan2
* CitcomS/Components/Const.py, CitcomS/Components/Output.py,
CitcomS/Components/Sphere/Sphere.py: Forgot to commit python
files
2006-11-16 02:07 tan2
* lib/Sphere_harmonics.c: Declared function prototype at the top
2006-11-16 01:52 tan2
* lib/Element_calculations.c, lib/Full_obsolete.c,
lib/Full_parallel_related.c, lib/Full_version_dependent.c,
lib/General_matrix_functions.c, lib/Global_operations.c,
lib/Instructions.c, lib/Obsolete.c, lib/Output.c,
lib/Output_h5.c, lib/Regional_obsolete.c,
lib/Regional_parallel_related.c,
lib/Regional_version_dependent.c, lib/Sphere_harmonics.c,
lib/Topo_gravity.c, lib/global_defs.h: Implemented geoid
calculation, see issue64. User visible changes include: *
"output_optional" can include string "geoid", which will enable
geoid output * new input parameters: radius, density_above,
density_below * removed input parameters: layerd, wdensity,
llmax, nlong, nlati * moved input parameter "output_ll_max" from
Sphere.py to Output.py * sync'd the defalut values of input
parameters in Const.py and Instructions.c
TODO: h5output_geoid() not finished
2006-11-15 22:01 leif
* doc/manual/citcoms.lyx: Elaborated a bit on .egg download, and
clarified that CitcomS needs Pythia v0.8.1.x (instead of 0.8).
2006-11-15 21:18 leif
* doc/manual/citcoms.lyx: Re-read the stuff I worked on yesterday,
making minor corrections: "is in your PATH" -> "is on your PATH",
inserted the word "Section" before section references, other
minor changes.
2006-11-15 20:40 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms.pdf: a few typos
fixed, http removed from htmlurl tags (not needed and lengthen
name in line); pdf regen
2006-11-15 02:06 leif
* doc/manual/citcoms.lyx: Corrections to the section, "Changing
Parameters".
2006-11-15 01:14 leif
* doc/manual/citcoms.lyx: Updated the installation chapter.
2006-11-14 03:25 leif
* Makefile.am, citcoms.in, pycitcoms.c, setup.py: Pythia
v0.8.1.0b4: Fixed bugs relating to MPI launching: Fix
sys.path/PYTHONPATH automatically; don't touch 'argv' until after
MPI_Init().
Next, I may try to slurp 'pycitcoms.c' into the framework... it
contains a lot of implementation details which have everything to
do with Pyre and nothing to do with CitcomS.
2006-11-11 03:34 leif
* ., configure.ac, ez_setup.py, setup.py: Use the new merlin (the
setuptools clone). Download Python dependencies automatically
during 'configure' (This doesn't work for "make install" yet.)
The Dynamo BuildBot might even succeed after this check-in...
fingers crossed...
2006-11-10 19:20 sue
* doc/manual/citcoms.lyx: created formulas for sec a.1.11
2006-11-10 18:54 sue
* doc/manual/citcoms.lyx, doc/manual/graphics/cookbook7.eps:
cookbook 6 graphic edited, various small tweaks
2006-11-10 01:59 sue
* doc/manual/citcoms.lyx: finished various typos and fixes after
checking with Luis on questions
2006-11-09 19:37 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms_cover-layers.pdf,
doc/manual/citcoms_cover.pdf, doc/manual/graphics/c_fig1.eps:
various typos and fixes
2006-11-07 19:33 tan2
* doc/manual/citcoms.lyx: * Fixed a few typos * Added "TODO" in
front of all unfinished text.
2006-11-07 02:30 leif
* Makefile.am, configure.ac, lib/Makefile.am, visual/Makefile.am:
Moved CitcomS HDF5 macros to cs/autoconf.
2006-11-07 01:33 leif
* ., CitcomS/Makefile.am, Makefile.am, bin, citcoms.in,
configure.ac, etc/Makefile.am, lib/Makefile.am, module/Exchanger,
module/Makefile.am, project.cfg, pycitcoms.c, setup.py,
visual/Makefile.am: Took a step backwards so that I can take a
more conservative approach to build/install. Also, temporarily
deleted 'Exchanger' and all references to it, to avoid confusion.
We can always go back in time and retrieve it later.
2006-11-07 00:49 sue
* doc/manual/citcoms.pdf: pdf generated
2006-11-07 00:49 sue
* doc/manual/citcoms.lyx, doc/manual/graphics/c_fig1.eps,
doc/manual/graphics/cookbook1.eps,
doc/manual/graphics/cookbook2.eps: gurnis edits, new pdf
2006-11-06 18:53 sue
* doc/manual/citcoms.lyx,
doc/manual/graphics/citcoms_cover-layers.pdf,
doc/manual/graphics/citcoms_cover.pdf: added authors to cover
2006-11-06 18:33 sue
* doc/manual/citcoms.lyx, doc/manual/graphics/proc_mesh.eps: added
new section 1.7 per gurnis and supporting graphic
2006-11-01 20:47 luis
* doc/manual/citcoms.lyx: Re-typed most of the changes from my copy
of the citcoms.lyx file
2006-10-27 21:26 tan2
* tests/.cvsignore: Removed legacy file .cvsignore
2006-10-27 21:25 tan2
* doc/.cvsignore: Removed legary file .cvsignore
2006-10-20 19:36 tan2
* examples/.reset-temporary: This file (examples/.reset-temporary)
was checked into svn at the initial import by me. I don't
remember what this file was used for.
2006-10-20 19:00 tan2
* CitcomS/Solver/Solver.py: * Removed extra output_time(), which
was used for profiling * Converted tab to 4 spaces
2006-10-20 08:19 leif
* configure.ac: Fail if MPI lib/header is not found.
2006-10-17 11:00 leif
* CitcomS/Makefile.am, Makefile.am, bin/Makefile.am,
etc/Makefile.am, lib/Makefile.am, module/Makefile.am: Fixed
legacy build.
2006-10-17 09:18 leif
* ., Citcom.c, CitcomSFull.c, CitcomSRegional.c, Makefile.am,
bin/Citcom.c, configure.ac, doc/CitComS.doxyconf,
lib/Pan_problem_misc_functions.c, lib/Tracer_advection.c,
module/CitcomSmodule.c, module/Makefile.am,
module/Regionalmodule.c, module/advdiffu.c, module/bindings.c,
module/exceptions.c, module/initial_conditions.c,
module/mesher.c, module/misc.c, module/outputs.c,
module/setProperties.c, module/stokes_solver.c, project.cfg,
setup.py, tests/Makefile.am, visual/Makefile.am: Transitioning to
Merlin. (Warning: still under construction.)
2006-10-14 00:29 tan2
* CitcomS/Solver/CoupledSolver.py: Undid the accidental checkin at
r4998
2006-10-14 00:27 tan2
* CitcomS/Solver/Solver.py, doc/manual/citcoms.lyx,
lib/Instructions.c, lib/Output.c, lib/Output_h5.c,
lib/global_defs.h, visual/estimate.py: Renamed reference of
"average" to "horiz_avg"
2006-10-14 00:06 tan2
* NEWS: Added description on new features and bug fixes for v2.1.0
2006-10-13 23:59 luis
* lib/Output_h5.c: Settled on /horiz_avg/ instead of /have/
2006-10-13 23:46 sue
* doc/manual/citcoms.lyx: updated url handling
2006-10-13 23:18 tan2
* visual/h5tocap.c: * Updated for the new layout of HDF5 group *
Changed the order of nodes, so that the output is the same as the
cap file from autocombine.py
2006-10-13 07:39 tan2
* doc/manual/citcoms.lyx: * Fixed a typo "PHDF HOME" -> "PHDF_HOME"
* Added a section on using none-pyre version * Undid a xref in
section 3.1, which should link to (not-checked-in-yet) "Working
with HDF5" chapter * Updated Appendix A and changed the title *
Added description on new output files (stress, pressure, average)
2006-10-13 06:43 tan2
* lib/Full_geometry_cartesian.c, lib/Regional_geometry_cartesian.c,
lib/Viscosity_structures.c: Gave default values to several
parameters
2006-10-13 04:15 tan2
* examples/Full/input.sample, examples/Regional/input.sample:
Removed obsolete input parameter "maxadvtime" from the input
samples
2006-10-13 04:10 tan2
* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
CitcomS/Components/Stokes_solver/Incompressible.py,
lib/Output_h5.c, module/setProperties.c: Moved input parameters
"aug_lagr" and "aug_number" from tsolver to vsolver, where they
really should belong to. These parameters are for augmented
lagragian stiffness matrix (I have no idea on what it is...), as
indicated in Element_calculations.c.
2006-10-12 21:43 tan2
* CitcomS/Components/IC.py, module/setProperties.c:
'half_space_age' was not used when 'tic_method'=1. So, fixed the
comment and removed the conditional input
2006-10-12 14:48 leif
* CitcomS/BaseApplication.py,
CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
CitcomS/Components/BC.py, CitcomS/Components/CitcomComponent.py,
CitcomS/Components/CodecConfig.py, CitcomS/Components/Const.py,
CitcomS/Components/HackedConfigParser.py,
CitcomS/Components/IC.py, CitcomS/Components/Launchers.py,
CitcomS/Components/Output.py, CitcomS/Components/Param.py,
CitcomS/Components/Phase.py, CitcomS/Components/Sphere/Sphere.py,
CitcomS/Components/Stokes_solver/Incompressible.py,
CitcomS/Components/Tracer.py, CitcomS/Components/Visc.py,
CitcomS/CoupledApp.py, CitcomS/SimpleApp.py,
CitcomS/Solver/Solver.py, bin/Citcom.c, bin/Makefile.am,
bin/citcoms.in, bin/coupledcitcoms.in, bin/pycitcoms.c,
bin/pycitcoms.cc, bin/pycppcitcoms.cc, configure.ac,
doc/manual/citcoms.lyx, etc/CitcomS.pml.in, etc/Makefile.am,
etc/globus.odb, etc/lam-mpi.odb, etc/lsf.odb, etc/mpich.odb,
etc/pbs.odb, lib/Advection_diffusion.c, lib/Citcom_init.c,
lib/Drive_solvers.c, lib/Full_parallel_related.c,
lib/Full_version_dependent.c, lib/Global_operations.c,
lib/Instructions.c, lib/Lith_age.c, lib/Output.c,
lib/Output_h5.c, lib/Parsing.c, lib/Process_buoyancy.c,
lib/Regional_parallel_related.c,
lib/Regional_version_dependent.c, lib/Topo_gravity.c,
lib/Tracer_advection.c, lib/global_defs.h,
lib/sphere_communication.h, module/CitcomSmodule.c,
module/CitcomSmodule.cc, module/CitcomSmodule.h,
module/Makefile.am, module/PyxMPI, module/Regionalmodule.c,
module/Regionalmodule.cc, module/advdiffu.c, module/advdiffu.cc,
module/advdiffu.h, module/bindings.c, module/bindings.cc,
module/bindings.h, module/exceptions.c, module/exceptions.cc,
module/exceptions.h, module/getProperty.h,
module/initial_conditions.c, module/initial_conditions.cc,
module/initial_conditions.h, module/mesher.c, module/mesher.cc,
module/mesher.h, module/misc.c, module/misc.cc, module/misc.h,
module/outputs.c, module/outputs.cc, module/outputs.h,
module/setProperties.c, module/setProperties.cc,
module/setProperties.h, module/stokes_solver.c,
module/stokes_solver.cc, module/stokes_solver.h, setup.py: Moved
'launcher' and '.cfg' support out of CitcomS and into the
framework.
As I was revising the "Installation" chapter of the manual (still
in progress), I got frustrated with how complicated everything
was -- and how difficult it was to document that complexity -- so
I did something slightly violent:
Converted the CitcomS extension module, 'CitcomSLib', from C++ to
C. This is made possible by Pythia 0.8.1.0b2, which replaces
_mpimodule with _mpi.pyx, which has a C interface.
It is now possible to build CitcomS -- and all its prerequisites
(e.g. Python) -- entirely from source, starting with nothing but
a C compiler. Exchanger still requires C++, of course. I have yet
to test these changes with Exchanger enabled, but I don't
anticipate any serious problems.
This may have been overkill, but I also cleaned the source of
C++-style comments (even though most modern C compilers probably
accept them... it became standard in C99 or something).
I'll bet you can install CitcomS with GCC 2.x now :-)
2006-10-11 20:01 sue
* doc/manual/citcoms.lyx: took care of some todo items
2006-10-10 23:48 tan2
* doc/manual/citcoms.lyx: * Added subsection on installing
OpenDXutils package * Aligned figures to the center * Changed the
layout of the Appendices
2006-10-10 20:37 sue
* doc/manual/citcoms.lyx: added hdf5 install and addt tools
chapters
2006-10-10 18:42 luis
* doc/manual/citcoms.lyx: Inserted a few TODO items
2006-10-10 13:00 luis
* lib/Makefile.am, lib/Output_h5.c, lib/PyTables.c, lib/pytables.h:
1. Reorganized routines in a more logical order. 2. Consolidated
routines from PyTables.[ch] into Output_h5.c
2006-10-10 11:54 luis
* lib/Instructions.c, lib/Output_h5.c, lib/output_h5.h: Renamed
local function to conform with h5 prefix.
2006-10-10 07:29 luis
* lib/Output_h5.c, lib/PyTables.c, lib/pytables.h: 1. Added PID to
metadata to make it easier to identify the corresponding .cfg
file 2. Wrapped most calls to set_attribute() to avoid using
addresses as arguments 3. Added
set_attribute_{int,float,double}_vector() functions
2006-10-10 00:52 luis
* lib/Output_h5.c: Forgot to delete reference to obsolete
data_group.
2006-10-10 00:52 tan2
* doc/manual/citcoms_cover-layers.pdf,
doc/manual/citcoms_cover.pdf: Set MIME type to pdf
2006-10-10 00:51 tan2
* doc/manual/graphics/CitcomSImportHDF5.net.gif: Set MIME type to
image
2006-10-10 00:48 tan2
* doc/manual/graphics/c_fig1.eps, doc/manual/graphics/c_fig10.eps,
doc/manual/graphics/c_fig2.eps, doc/manual/graphics/c_fig3.jpg,
doc/manual/graphics/c_fig4.eps, doc/manual/graphics/c_fig5.eps,
doc/manual/graphics/c_fig6.jpg, doc/manual/graphics/c_fig7.eps,
doc/manual/graphics/c_fig8.eps, doc/manual/graphics/c_fig9.eps,
doc/manual/graphics/cookbook1.2.jpg,
doc/manual/graphics/cookbook1.eps,
doc/manual/graphics/cookbook1.png,
doc/manual/graphics/cookbook2.2.eps,
doc/manual/graphics/cookbook2.2eps,
doc/manual/graphics/cookbook2.eps,
doc/manual/graphics/cookbook3.eps,
doc/manual/graphics/cookbook4.eps,
doc/manual/graphics/cookbook5.2.eps,
doc/manual/graphics/cookbook5.eps,
doc/manual/graphics/cookbook6.2.eps,
doc/manual/graphics/cookbook6.eps,
doc/manual/graphics/cookbook7.eps: Set MIME type to image
2006-10-10 00:45 luis
* lib/Output_h5.c: Shortened /average/ group into /have/
2006-10-10 00:42 tan2
* doc/manual/graphics/CitcomSImportHDF5.net.gif: Figure for HDF5
visualization
2006-10-10 00:41 tan2
* doc/manual/citcoms.lyx: Added section on visualizing HDF5 output
2006-10-10 00:38 luis
* lib/Output_h5.c: Fix mispelling in input parameters (allignment
options).
2006-10-09 23:25 tan2
* doc/manual/citcoms.lyx: * Added documentaion of .pml file, which
comes from DANSE FAQ * Added section on visualization of full
version * Moved the discussion on .log and .time files from
Section 4.2 to Section 3.5.3 * Updated links to equations
2006-10-09 23:14 sue
* doc/manual/citcoms.lyx: change equation numbering
2006-10-09 20:41 tan2
* visual/OpenDXMacro/CitcomSImportHDF5.net.in: Changed the order of
input parameters
2006-10-09 19:58 tan2
* visual/OpenDXMacro/CitcomSImportHDF5.net.in: Updated for the new
layout of hdf5 output
2006-10-09 00:14 gurnis
* lib/Full_read_input_from_files.c, lib/Problem_related.c,
lib/Viscosity_structures.c: For Viscosity_structures.c, added a
new rheology, rheol=5, that is a variant of rheol=3. The
difference lay in the way that plate boundaries are weakened.
Must set mat_control=1 and enter materials into the VIP array.
Removed debug statements from Problem_related.c in preparation of
new release.
2006-10-08 12:04 leif
* configure.ac, setup.py: Pointed CitcomS egg-downloading at the
new "Eggs" section on the web site, to insulate CitcomS from the
imminent chaos in pythia-dev.
2006-10-07 01:15 tan2
* visual/h5tocap.py: Updated for the new layout in the h5 file
2006-10-07 00:01 luis
* lib/Output_h5.c: Eliminated data group in HDF5 file. Main
datasets are now on the root-level.
2006-10-06 21:10 tan2
* lib/Obsolete.c: The type of elt_g should be "higher_precision"
instead of "double".
2006-10-06 20:18 tan2
* lib/Interuption.c: Changed the signature of the signal handler
from (void)(interuption(void)) to (void)(interuption(int)) to
conform with the C standard
2006-10-06 20:02 tan2
* lib/element_definitions.h: Missing braces around initializers for
array structs node_point[] and offset[]
2006-10-06 17:17 tan2
* doc/manual/citcoms.lyx: Some minor edits
2006-10-05 20:07 tan2
* visual/combine.py: Using 2-digit number for the cap filename, eg.
prefix.cap00.step
2006-10-05 00:38 tan2
* visual/visFull.cfg, visual/visFull.net.in,
visual/visRegional.cfg, visual/visRegional.net.in: Updated macros
to use new samples files and fixed a few stylus issues
2006-10-05 00:15 tan2
* visual/Makefile.am: Rearranged file list
2006-10-05 00:15 tan2
* visual/Makefile.am: Updated file list
2006-10-05 00:04 tan2
* visual/samples/fulltest.cap0.0,
visual/samples/fulltest.cap0.0.general,
visual/samples/fulltest.cap00.100,
visual/samples/fulltest.cap00.100.general,
visual/samples/fulltest.cap01.100,
visual/samples/fulltest.cap01.100.general,
visual/samples/fulltest.cap02.100,
visual/samples/fulltest.cap02.100.general,
visual/samples/fulltest.cap03.100,
visual/samples/fulltest.cap03.100.general,
visual/samples/fulltest.cap04.100,
visual/samples/fulltest.cap04.100.general,
visual/samples/fulltest.cap05.100,
visual/samples/fulltest.cap05.100.general,
visual/samples/fulltest.cap06.100,
visual/samples/fulltest.cap06.100.general,
visual/samples/fulltest.cap07.100,
visual/samples/fulltest.cap07.100.general,
visual/samples/fulltest.cap08.100,
visual/samples/fulltest.cap08.100.general,
visual/samples/fulltest.cap09.100,
visual/samples/fulltest.cap09.100.general,
visual/samples/fulltest.cap1.0,
visual/samples/fulltest.cap1.0.general,
visual/samples/fulltest.cap10.0,
visual/samples/fulltest.cap10.0.general,
visual/samples/fulltest.cap10.100,
visual/samples/fulltest.cap10.100.general,
visual/samples/fulltest.cap11.0,
visual/samples/fulltest.cap11.0.general,
visual/samples/fulltest.cap11.100,
visual/samples/fulltest.cap11.100.general,
visual/samples/fulltest.cap2.0,
visual/samples/fulltest.cap2.0.general,
visual/samples/fulltest.cap3.0,
visual/samples/fulltest.cap3.0.general,
visual/samples/fulltest.cap4.0,
visual/samples/fulltest.cap4.0.general,
visual/samples/fulltest.cap5.0,
visual/samples/fulltest.cap5.0.general,
visual/samples/fulltest.cap6.0,
visual/samples/fulltest.cap6.0.general,
visual/samples/fulltest.cap7.0,
visual/samples/fulltest.cap7.0.general,
visual/samples/fulltest.cap8.0,
visual/samples/fulltest.cap8.0.general,
visual/samples/fulltest.cap9.0,
visual/samples/fulltest.cap9.0.general,
visual/samples/regtest.cap0.0,
visual/samples/regtest.cap0.0.general,
visual/samples/regtest.cap00.100,
visual/samples/regtest.cap00.100.general: Replaced sample files
at 0th time step with sample files at 100th time step, which have
more interesting features in the visualization,
2006-10-04 18:34 tan2
* examples/Cookbook1/cookbook1.cfg,
examples/Cookbook2/cookbook2.cfg,
examples/Cookbook3/cookbook3.cfg,
examples/Cookbook4/cookbook4.cfg,
examples/Cookbook5/cookbook5.cfg,
examples/Cookbook6/cookbook6.cfg: * Removed some unnecessary
parameters * Changed the layout slightly * Updated the cookbook
scripts to be consistent with the manual
2006-10-04 18:32 tan2
* doc/manual/citcoms.lyx: Updated the Cookbook chapter
2006-10-04 18:24 tan2
* doc/manual/graphics/cookbook1.jpg, doc/manual/graphics/eq1.eps,
doc/manual/graphics/eq10.eps, doc/manual/graphics/eq11.eps,
doc/manual/graphics/eq12.eps, doc/manual/graphics/eq13.eps,
doc/manual/graphics/eq14.eps, doc/manual/graphics/eq15.eps,
doc/manual/graphics/eq16.eps, doc/manual/graphics/eq17.eps,
doc/manual/graphics/eq18.eps, doc/manual/graphics/eq19.eps,
doc/manual/graphics/eq2.eps, doc/manual/graphics/eq20.2.eps,
doc/manual/graphics/eq20.eps, doc/manual/graphics/eq21.eps,
doc/manual/graphics/eq3.eps, doc/manual/graphics/eq4.eps,
doc/manual/graphics/eq5.eps, doc/manual/graphics/eq6.eps,
doc/manual/graphics/eq7.eps, doc/manual/graphics/eq8.eps,
doc/manual/graphics/eq9.eps, doc/manual/graphics/exp1.eps,
doc/manual/graphics/exp10.eps, doc/manual/graphics/exp11.eps,
doc/manual/graphics/exp12.eps, doc/manual/graphics/exp2.eps,
doc/manual/graphics/exp3.eps, doc/manual/graphics/exp4.eps,
doc/manual/graphics/exp5.eps, doc/manual/graphics/exp6.eps,
doc/manual/graphics/exp7.eps, doc/manual/graphics/exp8.eps,
doc/manual/graphics/exp9.eps: Removed unused figures
2006-10-04 01:56 tan2
* examples/Cookbook6/cookbook6.cfg,
examples/Cookbook6/cookbook7.cfg: Renamed file to be consistent
with the manual
2006-10-04 01:54 tan2
* examples/Cookbook6, examples/Cookbook7: Renamed directory to be
consistent with the manual
2006-10-02 22:46 tan2
* examples/Cookbook1/cookbook1.cfg: Using default Rayleigh number,
which is stated in the manual. Also updated the comment to be
consistent with the manual.
2006-10-02 22:43 tan2
* doc/manual/citcoms.lyx: Slightly updated postprocessing chapter.
Revised Cookbook 1.
2006-09-30 00:56 tan2
* doc/manual/citcoms.lyx: Updated Chapter 3 "Running CitComS.py"
for the .cfg input format, also explained how to launch a
parallel job. Some TODO items left.
2006-09-29 23:14 gurnis
* lib/Full_read_input_from_files.c, lib/Problem_related.c,
lib/Regional_lith_age_read_files.c: Fixed age bug in Regional. In
Regional_lith_age_read_files.c, find_age_in_MY() was not being
converted to a float
2006-09-29 21:50 sue
* doc/manual/citcoms_cover-layers.pdf,
doc/manual/citcoms_cover.pdf: updated version on pdf cover and
added pdf layered file
2006-09-28 14:56 luis
* lib/Output_h5.c, lib/hdf5_related.h: 1. Added a cap dimension for
efficient parallel I/O 2. Bulk of data write operations now done
in collective mode. 4. Passing various parallel I/O tuning
parameters to HDF5 and MPI-IO. 5. Consolidated all data buffers
into one (only largest size allocated).
2006-09-28 14:30 luis
* CitcomS/Components/Output.py, module/setProperties.cc: Fixed typo
in names
2006-09-27 23:33 tan2
* CitcomS/Components/Output.py: * Removed debugging output * Added
svn:keywords and svn:mime-type attributes
2006-09-27 20:37 leif
* setup.py: Relaxed setuptools version requirement to 0.6b1.
2006-09-27 00:24 tan2
* CitcomS/Components/Output.py, CitcomS/Makefile.am,
CitcomS/Solver/Solver.py, lib/Instructions.c, lib/Output.c,
lib/Output_h5.c, lib/global_defs.h, lib/output.h,
lib/output_h5.h, module/bindings.cc, module/setProperties.cc,
module/setProperties.h: * Created new component 'Output.py' for
storing output-related properties * Added several input
parameters for HDF5 output performance tuning * Moved
'output_format' and 'output_optional' form Solver.py to Output.py
2006-09-26 12:20 luis
* bin/Makefile.am, examples/Makefile.am, lib/Makefile.am,
module/Makefile.am, visual/OpenDXMacro/Makefile.am: Fixed broken
'make dist'
2006-09-26 01:09 leif
* bin/Makefile.am, bin/pycitcoms.cc, configure.ac, ez_setup.py,
module/Exchanger/Makefile.am, module/Makefile.am, setup.py: Made
'Exchanger' optional. Give "--with-exchanger=[yes|no]" as an
argument to 'configure' to manually specify whether you want
Exchanger; the default is "auto", which means to use Exchanger if
it's installed (and on your PYTHONPATH).
Egg-ified 'configure' checks for Python packages. This means that
CitcomS now requires the egg-ified CIG version of Pythia -- and
(optionally) the egg-ified Exchanger. Old Pythia/Exchanger
installations will not work, as they lack the egg-metadata
('configure' will act as if they are not installed).
Added 'setup.py', which will automatically download and install
the egg version of Pythia -- as well as the egg system itself
('setuptools'). If you want Exchanger, you still must install it
manually (the way C++ is used prevents complete egg-ification of
Exchanger). Note that 'setup.py' actually checks-out the latest
Pythia from the SVN repository. The release version of CitcomS
will download a packaged Pythia from the website instead.
2006-09-25 19:13 tan2
* lib/Output.c, lib/Output_h5.c: Disabled material output, since
material control is not working (yet)
2006-09-24 07:28 tan2
* CitcomS/Solver/Solver.py, lib/Instructions.c, lib/Output_h5.c,
lib/global_defs.h, module/setProperties.cc: Added new input
parameter 'datadir_old' in CitcomS.solver. If output_format=ascii
and restart=1, the restart files will be read from
${datadir_old}/${rank}/${datafile_old}.velo.${rank}.${step}. In
this case, 'datafile_old' cannot contain '/'. See issue56.
2006-09-22 23:26 tan2
* CitcomS/Solver/Solver.py, lib/Instructions.c: Write surf and botm
output by default (but can be disabled by setting
output_optional=''), which is compatible with v2.0.x.
2006-09-22 22:58 tan2
* lib/Instructions.c: Removed debugging output
2006-09-22 22:29 tan2
* visual/batchsurf.py: * Fixed issue55 "surf files got deleted by
batchsurf.py" * Refactored the codes on machinefile -> nodelist
2006-09-22 22:14 tan2
* visual/getcoord.sh, visual/getsurf.sh: These scripts accept
'localhost' as a valid machine name now
2006-09-22 22:01 luis
* lib/Output_h5.c: Bug fix: maxdims[0] is set to H5S_UNLIMITED in
extendible datasets, so it should never be incremented.
2006-09-22 20:37 tan2
* visual/autocombine.py, visual/estimate.py, visual/h5tocap.py,
visual/miff2avi, visual/miff2mpg, visual/parser.py,
visual/zslice.py: Added 'Id' keyword to the files
2006-09-22 19:19 tan2
* visual/batchpaste.sh, visual/batchpaste2.sh: Fixed two bugs in
post-processing scripts
2006-09-21 23:03 tan2
* visual/autocombine.py, visual/batchcombine.py,
visual/batchpaste.sh, visual/batchpaste2.sh: Updated
post-processing script for new output_format options. See
issue53.
2006-09-21 21:25 luis
* lib/Output_h5.c: Allow for optional fields when extending
datasets.
2006-09-21 21:17 tan2
* lib/Output.c, lib/Output_h5.c, lib/Process_buoyancy.c: Refactored
out the code computing horizontal average of temperature and rms
velocity into a function. This fixes the bug in issue46.
2006-09-21 20:08 tan2
* lib/Instructions.c: Forgot to change the default value in C
2006-09-21 19:57 tan2
* CitcomS/Solver/Solver.py, lib/Instructions.c, lib/Output.c,
lib/Output_h5.c, lib/global_defs.h: Added new option for
"output_format". The current behavior is: * If
output_format=="ascii-local" (the default), CitcomS will write
ascii files to the directory and prefix specified by "datafile",
ie., the same behavior as in v2.0 * If output_format=="ascii",
CitcomS will write ascii files to the directory specified by
"datadir" with the prefix specified by "datafile". In the case,
"datafile" cannot contains the '/' (path seperator) character. *
If output_format=="hdf5", CitcomS will write singe HDf5 file to
the directory and prefix specified by "datafile".
2006-09-21 17:51 tan2
* visual/parser.py: Parser will skip lines starting with '[', so
that it can parse .cfg file correctly
2006-09-21 17:49 tan2
* module/setProperties.cc: Removed quotes from output string
2006-09-21 00:18 tan2
* CitcomS/CoupledApp.py, CitcomS/SimpleApp.py,
examples/Cookbook1/cookbook1.cfg,
examples/Cookbook2/cookbook2.cfg,
examples/Cookbook3/cookbook3.cfg,
examples/Cookbook4/cookbook4.cfg,
examples/Cookbook5/cookbook5.cfg,
examples/Cookbook7/cookbook7.cfg, examples/example0.cfg,
examples/example1.cfg: Calculate the needed # of cpu according to
mesher properties. There is no longer a need to set
launcher.nodes.
2006-09-20 22:51 tan2
* CitcomS/BaseApplication.py, CitcomS/Solver/CoupledFullSolver.py,
CitcomS/Solver/CoupledRegionalSolver.py,
CitcomS/Solver/CoupledSolver.py: Added svn:keywprds = Id
2006-09-20 20:47 tan2
* lib/Output_h5.c: Sync'd h5output_meta() with setProperties
2006-09-20 20:45 tan2
* CitcomS/Components/IC.py: Fixed the comment
2006-09-20 20:34 tan2
* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
lib/Advection_diffusion.c, lib/Output_h5.c,
module/setProperties.cc: Removed unused parameter 'maxadvtime'
2006-09-20 20:30 tan2
* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
CitcomS/Components/Const.py, CitcomS/Components/IC.py,
CitcomS/Components/Visc.py, module/setProperties.cc: Print out
all pyre properties to the pid file
2006-09-20 19:54 tan2
* lib/Citcom_init.c, lib/Instructions.c, module/mesher.cc,
module/setProperties.cc: Saving the input parameters to a unique
file 'pidXXXXX.cfg' for archives.
2006-09-19 19:50 luis
* lib/Output_h5.c: Allocate tensor field buffer only when
necessary.
2006-09-19 18:44 tan2
* citcoms_profile: Since the opendx scripts have the macro path
built in the file, there is no need to define $DXMACROS env. var.
2006-09-17 17:32 tan2
* CitcomS/Solver/Solver.py, examples/Cookbook5/cookbook5.cfg,
examples/Full/input.sample, examples/Regional/input.sample,
lib/Instructions.c, lib/Output.c, lib/Output_h5.c,
lib/global_defs.h, module/setProperties.cc,
visual/autocombine.py, visual/batchcombine.py,
visual/batchpaste.sh, visual/combine.py,
visual/pasteCitcomData.sh: * Added new input parameter 'datadir'
in Solver * All outputs are done in 'datadir' directory *
Processors write its own ascii output in 'datadir/rank' directory
* Post-processing codes and cookbook examples were updated
accordingly
2006-09-14 18:14 maweier
* visual/Mayavi2/Citcoms_Hdf2Vtk.c: added help on usage.
2006-09-13 19:04 maweier
* visual/Mayavi2/plugins/filter/CitcomSreduce.py: Changed range
trait.
2006-09-12 20:50 tan2
* lib/global_defs.h: Fixed the bug of negative CPU time, which is
caused by storing the walltime in insufficient precision
2006-09-11 17:25 maweier
* visual/Mayavi2/Citcoms_Hdf2Vtk.c: added latest version of file
converter in c.
2006-09-11 17:24 maweier
* visual/Mayavi2/Citcoms_HdfDisplay.py,
visual/Mayavi2/Citcoms_VtkDisplay.py,
visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
visual/Mayavi2/plugins/filter/CitcomSFilterActions.py,
visual/Mayavi2/plugins/filter/CitcomSSphere.py,
visual/Mayavi2/plugins/filter/CitcomSreduce.py,
visual/Mayavi2/plugins/filter/CitcomSshowCaps.py,
visual/Mayavi2/plugins/filter/CitcomSshowSurface.py,
visual/Mayavi2/plugins/plugin_defs/mayavi_ui_plugin_definition.py:
Updated licenses.
2006-09-11 17:23 maweier
* visual/Mayavi2/Citcoms_Hdf2Vtk.c: Update
2006-09-11 00:17 luis
* visual/Makefile.am, visual/h5steps.c, visual/h5tocap.c: 1. Added
utility to extract steps from CitcomS HDF5 file. 2. Changed
h5tocombined.c to h5tocap.c in copyright header.
2006-09-11 00:09 luis
* visual/h5tocap.c: When no frames are specified, print number of
available frames.
2006-09-10 09:50 luis
* visual/Makefile.am, visual/h5tocap.c: 1. Added h5tocap to build
procedure 2. Changed h5tocap to read frames from command-line
(instead of steps)
2006-09-10 07:36 luis
* lib/Output_h5.c, visual/estimate.py: Moved connectivity dataset
to root group.
2006-09-09 01:45 tan2
* configure.ac: * set --with-hdf5=auto as default, which will try
to detect HDF5 library, if not found, HDF5 support will be
disabled * Reported summary at the end of configure
2006-09-09 00:24 tan2
* configure.ac: Added $PHDF5_HOME env. variables for the home
directory of parallel HDF5 lib
2006-09-08 20:59 tan2
* visual/Makefile.am: Forgot to rename file
2006-09-08 20:27 luis
* visual/h5tocap.c, visual/h5tocombined.c: Changed name to
h5tocap.c
2006-09-08 19:20 tan2
* visual/h5tocap.py: Added a comment
2006-09-08 19:18 tan2
* visual/visRegional.cfg: Reverted the accidental check-in at r4498
2006-09-08 19:14 tan2
* visual/h52combined.py, visual/h5tocap.py, visual/visRegional.cfg:
Renamed the conversion script
2006-09-08 19:14 tan2
* visual/h52combined.py: * Using 'caps' attribute in the input
group * frame -> timestep conversion * Cleaned up the code
2006-09-08 15:53 luis
* lib/Output_h5.c, lib/pytables.h: Removing unnecessary HDF5
attribute.
2006-09-08 15:46 luis
* lib/Output_h5.c: Fix allocation of buffer for connectivity (done
per cap, not globally).
2006-09-07 21:07 maweier
* visual/Mayavi2/Citcoms_Hdf2Vtk.py,
visual/Mayavi2/Citcoms_HdfDisplay.py,
visual/Mayavi2/plugins/CitcomSHDFUgrid.py: Fixed connectivity
issues. Fixed HdfDisplays wrong status output.
2006-09-06 22:33 maweier
* visual/Mayavi2/Citcoms_Hdf2Vtk.py,
visual/Mayavi2/plugins/CitcomSHDFUgrid.py: Got rid of the
iterator to change the order.
2006-09-06 21:01 luis
* visual/Mayavi2/Citcoms_Hdf2Vtk.c: Added function to retrieve
float attributes from HDF5 file.
2006-09-06 20:18 tan2
* visual/OpenDXMacro/CitcomSImportHDF5.net.in,
visual/OpenDXMacro/Makefile.am: * Made CitcomSImportHDF5 accept
NULL (default) input for the caplist * Added CitcomSImportHDF5 to
the install list
2006-09-06 19:06 tan2
* CitcomS/Makefile.am: Forgot backslash (line continuation) after
Solver/__init__.py. See issue48.
2006-09-06 18:39 tan2
* visual/OpenDXMacro/CitcomSImportHDF5.net.in: Added an dx macro to
import HDF5 output, this module depends on the Cactus OpenDXutils
project (http://www.cactuscode.org/Visualization/openDX)
2006-09-06 16:41 maweier
* visual/Mayavi2/Citcoms_Hdf2Vtk.c: New C version of the Hdf to Vtk
converter.
2006-09-05 22:41 maweier
* visual/Mayavi2/Citcoms_Hdf2Vtk.py, visual/Mayavi2/README:
Bugfixes and a new README on how to use the code.
2006-09-05 21:10 maweier
* visual/Mayavi2/Citcoms_Hdf2Vtk.py,
visual/Mayavi2/Citcoms_hdf2vtk.py: Consistency
2006-09-05 20:53 maweier
* visual/Mayavi2/Citcoms_HdfDisplay.py,
visual/Mayavi2/Citcoms_hdf2vtk.py, visual/Mayavi2/__init__.py,
visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py,
visual/Mayavi2/plugins/filter/CitcomSFilterActions.py,
visual/Mayavi2/plugins/filter/CitcomSshowCaps.py,
visual/Mayavi2/plugins/filter/CitcomSshowSurface.py,
visual/Mayavi2/plugins/filter/__init__.py: Some minor bugfixes
2006-09-05 20:49 maweier
* visual/Mayavi2/Citcoms_hdf2vtk.py,
visual/Mayavi2/citcoms_hdf2vtk.py: Rename for consistence.
2006-09-02 10:11 luis
* lib/Instructions.c, lib/Output_h5.c, lib/global_defs.h,
visual/estimate.py: Added connectivity datasets (per cap) to HDF5
optional output.
2006-09-02 09:31 luis
* visual/h5tocombined.c: Opened all available cap groups outside
the main loop.
2006-08-31 23:06 maweier
* visual/Mayavi2, visual/Mayavi2/Citcoms_HdfDisplay.py,
visual/Mayavi2/Citcoms_VtkDisplay.py, visual/Mayavi2/__init__.py,
visual/Mayavi2/citcoms_hdf2vtk.py, visual/Mayavi2/plugins,
visual/Mayavi2/plugins/CitcomHDFThread.py,
visual/Mayavi2/plugins/CitcomSHDFUgrid.py,
visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py,
visual/Mayavi2/plugins/OpenCitcomSFILES.py,
visual/Mayavi2/plugins/__init__.py,
visual/Mayavi2/plugins/filter,
visual/Mayavi2/plugins/filter/CitcomSFilterActions.py,
visual/Mayavi2/plugins/filter/CitcomSSphere.py,
visual/Mayavi2/plugins/filter/CitcomSreduce.py,
visual/Mayavi2/plugins/filter/CitcomSshowCaps.py,
visual/Mayavi2/plugins/filter/CitcomSshowSurface.py,
visual/Mayavi2/plugins/filter/__init__.py,
visual/Mayavi2/plugins/plugin_defs,
visual/Mayavi2/plugins/plugin_defs/mayavi_ui_plugin_definition.py:
New folder structure.
2006-08-31 23:05 maweier
* visual/Mayavi2: Complete update to new Folder structure.
2006-08-31 14:56 luis
* visual/h5tocombined.c: Added ability to output multiple timesteps
(specified on command-line).
2006-08-31 13:28 luis
* visual/h5tocombined.c: 1. Cleaned up code in general. 2. Fixed
bug in reading coord dataset (need to do it for each cap!).
2006-08-29 23:44 maweier
* visual/Mayavi2/citcoms_hdf2vtk.py,
visual/Mayavi2/plugins/CitcomSHDFUgrid.py,
visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
visual/Mayavi2/plugins/filter/CitcomSshowCaps.py: More stable
versions. Some performance enhancements.
2006-08-28 23:19 maweier
* visual/Mayavi2/core/CitcomSHDFUgrid.pyc,
visual/Mayavi2/core/__init__.pyc,
visual/Mayavi2/filter/CitcomSFilterActions.pyc,
visual/Mayavi2/filter/CitcomSSphere.pyc,
visual/Mayavi2/filter/CitcomSreduce.pyc,
visual/Mayavi2/filter/CitcomSshowCaps.pyc,
visual/Mayavi2/filter/__init__.pyc,
visual/Mayavi2/plugins/CitcomSHDFUgrid.pyc,
visual/Mayavi2/plugins/CitcomS_hdf_file_reader.pyc,
visual/Mayavi2/plugins/CitcomS_vtk_file_reader.pyc,
visual/Mayavi2/plugins/OpenCitcomSFILES.pyc,
visual/Mayavi2/plugins/__init__.pyc,
visual/Mayavi2/plugins/filter/CitcomSFilterActions.pyc,
visual/Mayavi2/plugins/filter/CitcomSSphere.pyc,
visual/Mayavi2/plugins/filter/CitcomSreduce.pyc,
visual/Mayavi2/plugins/filter/CitcomSshowCaps.pyc,
visual/Mayavi2/plugins/filter/__init__.pyc,
visual/Mayavi2/plugins/filter/showcaps.pyc: Deleting Bytecode
Files
2006-08-28 23:17 maweier
* visual/Mayavi2, visual/Mayavi2/HdfDisplay.py,
visual/Mayavi2/VtkDisplay.py, visual/Mayavi2/__init__.py,
visual/Mayavi2/citcoms_hdf2vtk.py, visual/Mayavi2/core,
visual/Mayavi2/core/CitcomSHDFUgrid.py,
visual/Mayavi2/core/CitcomSHDFUgrid.pyc,
visual/Mayavi2/core/__init__.py,
visual/Mayavi2/core/__init__.pyc, visual/Mayavi2/filter,
visual/Mayavi2/filter/CitcomSFilterActions.py,
visual/Mayavi2/filter/CitcomSFilterActions.pyc,
visual/Mayavi2/filter/CitcomSSphere.py,
visual/Mayavi2/filter/CitcomSSphere.pyc,
visual/Mayavi2/filter/CitcomSreduce.py,
visual/Mayavi2/filter/CitcomSreduce.pyc,
visual/Mayavi2/filter/CitcomSshowCaps.py,
visual/Mayavi2/filter/CitcomSshowCaps.pyc,
visual/Mayavi2/filter/CitcomSshowSurface.py,
visual/Mayavi2/filter/__init__.py,
visual/Mayavi2/filter/__init__.pyc, visual/Mayavi2/plugins,
visual/Mayavi2/plugins/CitcomSHDFUgrid.py,
visual/Mayavi2/plugins/CitcomSHDFUgrid.pyc,
visual/Mayavi2/plugins/CitcomS_hdf_file_reader.py,
visual/Mayavi2/plugins/CitcomS_hdf_file_reader.pyc,
visual/Mayavi2/plugins/CitcomS_vtk_file_reader.py,
visual/Mayavi2/plugins/CitcomS_vtk_file_reader.pyc,
visual/Mayavi2/plugins/OpenCitcomSFILES.py,
visual/Mayavi2/plugins/OpenCitcomSFILES.pyc,
visual/Mayavi2/plugins/__init__.py,
visual/Mayavi2/plugins/__init__.pyc,
visual/Mayavi2/plugins/filter,
visual/Mayavi2/plugins/filter/CitcomSFilterActions.py,
visual/Mayavi2/plugins/filter/CitcomSFilterActions.pyc,
visual/Mayavi2/plugins/filter/CitcomSSphere.py,
visual/Mayavi2/plugins/filter/CitcomSSphere.pyc,
visual/Mayavi2/plugins/filter/CitcomSreduce.py,
visual/Mayavi2/plugins/filter/CitcomSreduce.pyc,
visual/Mayavi2/plugins/filter/CitcomSshowCaps.py,
visual/Mayavi2/plugins/filter/CitcomSshowCaps.pyc,
visual/Mayavi2/plugins/filter/CitcomSshowSurface.py,
visual/Mayavi2/plugins/filter/__init__.py,
visual/Mayavi2/plugins/filter/__init__.pyc,
visual/Mayavi2/plugins/filter/showcaps.pyc,
visual/Mayavi2/plugins/plugin_defs,
visual/Mayavi2/plugins/plugin_defs/mayavi_ui_plugin_definition.py:
Files for Mayavi2 plugins
2006-08-28 21:20 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms_cover.pdf: fixed man
cover, removed pg no., fixed date, added table of figures,
enabled URL hotlinks
2006-08-26 00:49 tan2
* lib/Full_boundary_conditions.c, lib/Full_parallel_related.c,
lib/Full_version_dependent.c, lib/Phase_change.c,
lib/Process_buoyancy.c, lib/Regional_boundary_conditions.c,
lib/Regional_parallel_related.c,
lib/Regional_version_dependent.c, lib/Size_does_matter.c,
lib/Viscosity_structures.c: Flushed debugging output
2006-08-25 23:15 tan2
* doc/manual/citcoms.lyx: Improved the section of full CitcomS
visualization. Fixed issue44
2006-08-24 23:46 luis
* visual/estimate.py: Added script to estimate the size of the
output from CitcomS.
2006-08-24 20:08 tan2
* CitcomS/CoupledApp.py, CitcomS/Layout.py: Renamed some attributes
2006-08-24 20:08 tan2
* CitcomS/Makefile.am: Updated file list
2006-08-24 19:40 tan2
* CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py,
CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/Coupler/__init__.py:
Changed the class names
2006-08-24 19:34 tan2
* CitcomS/Coupler/CoarseGridExchanger.py,
CitcomS/Coupler/ContainingCoupler.py, CitcomS/Coupler/Coupler.py,
CitcomS/Coupler/EmbeddedCoupler.py, CitcomS/Coupler/Exchanger.py,
CitcomS/Coupler/FineGridExchanger.py: Renamed *Exchanger.py to
*Coupler.py
2006-08-24 19:31 tan2
* CitcomS/Components/Exchanger, CitcomS/Coupler,
CitcomS/Coupler.py: Started refactoring Coupler and Exchanger ...
2006-08-24 19:27 tan2
* CitcomS/BaseApplication.py, CitcomS/CoupledApp.py,
CitcomS/SimpleApp.py, CitcomS/Solver/CoupledFullSolver.py,
CitcomS/Solver/CoupledRegionalSolver.py,
CitcomS/Solver/CoupledSolver.py, CitcomS/Solver/Solver.py,
CitcomS/Solver/__init__.py, bin/Makefile.am, bin/citcoms.in,
bin/coupledcitcoms.in: * Refactored coupler-related codes from
Solver.py to CoupledSolver.py * Created CoupledFullSolver.py and
CoupledRegionalSolver.py * Refactored common codes between
CoupledApp.py and SimpleApp.py to BaseApplication.py * Changed
the facility names in CoupledApp.py * Created a coupledcitcoms
script
2006-08-24 02:47 luis
* lib/Output_h5.c, lib/hdf5_related.h: Added /cap/average/coord
dataset
2006-08-23 23:24 luis
* lib/Output_h5.c: Fixed silly typos.
2006-08-23 23:16 luis
* lib/Output_h5.c, lib/hdf5_related.h: 1. Grouped horizontal
average data into its own HDF5 group. 2. All datasets are
referenced using relative paths (to its own cap group).
2006-08-22 18:24 luis
* lib/Output_h5.c, lib/hdf5_related.h: Data buffer in field_t
struct should be a float.
2006-08-22 13:08 luis
* lib/Output_h5.c: 1. Fixed PyTables attributes for time dataset
(bugfix) 2. Added surf and botm data (optional output) 3. Added
horizontal averages (optional output)
2006-08-21 22:42 tan2
* lib/Output_h5.c: Added two attributes to /input group * 'scalev'
: velocity scale, in cm/yr * 'scalet' : time scale, in Myrs
2006-08-21 21:38 luis
* visual/h5tocombined.c: Added program to convert the HDF5 output
file to the ASCII combined file, using the HDF5 C-API.
2006-08-18 18:43 tan2
* bin/Citcom.c, lib/Output.c, lib/Output_h5.c, lib/output.h,
lib/output_h5.h, module/outputs.cc: Refactored and Merged
output_pseudo_surf with output
2006-08-18 04:59 tan2
* CitcomS/Solver/Solver.py, bin/Citcom.c, lib/Instructions.c,
lib/Output.c, lib/Output_h5.c, lib/global_defs.h,
module/outputs.cc, module/setProperties.cc: * Closed E->fp_out
properly * Fixed a bug when output_format is illegal * Added new
input parameter "output_optional", which is a comma seperated
list of fields to output. Currently, supported outputs are
"pressure", "stress", "surf", "botm", and "average". * Changed
the format of stress output to be consistent with other output
2006-08-15 21:50 sue
* doc/manual/citcoms2.0.2.lyx, doc/manual/citcoms2.0.2.pdf,
doc/manual/citcoms_cover2-0-2.pdf: deleted versioned files
2006-08-15 20:48 tan2
* lib/Citcom_init.c, lib/Instructions.c: Added 'output_format'
input for stand-alone version
2006-08-15 20:46 tan2
* lib/global_defs.h: Commented out an unused include file
2006-08-15 20:14 sue
* doc/manual/citcoms.lyx: one more cross-reference fix
2006-08-15 19:46 sue
* doc/manual/citcoms.lyx: fixed tan's requests and recoded tables
to use space better
2006-08-15 18:43 tan2
* doc/manual/citcoms.lyx: Fixed various typos/inconsistency/errors
Added some comments (started with 'tan2:')
2006-08-15 14:02 luis
* lib/Output_h5.c, lib/PyTables.c, lib/pytables.h: Fixed issues
with time dataset.
2006-08-15 12:09 luis
* lib/Output_h5.c, lib/hdf5_related.h: 1. Introduced field_t
object, and updated the appropriate functions to use it. 2.
Changed to independent parallel I/O for dataset writes. 3. Using
collective calls to extend time-varying datasets (bugfix).
2006-08-15 06:26 tan2
* doc/manual/citcoms.lyx: Updated the status of multi-grid solver
2006-08-14 22:24 sue
* doc/manual/citcoms.lyx: restored 2-sided page setting
2006-08-14 19:52 sue
* doc/manual/citcoms.lyx: got appendices into toc
2006-08-14 19:29 sue
* doc/manual/citcoms.lyx: changed margins and doc settings as
requested
2006-08-14 11:52 luis
* lib/Output_h5.c: 1. Switching default data transfer property to
use independent parallel I/O. 2. Time-varying fields are now
created without an extent along time-dimension. 3. Consolidated
some debug statements into a single printf.
2006-08-14 11:22 luis
* lib/Output_h5.c, lib/hdf5_related.h: Added step column to the
/time table dataset.
2006-08-14 11:01 luis
* lib/Output_h5.c: Determine hyperslab block size based on mpi
process coordinates, not mpi process rank (bugfix).
2006-08-14 08:38 luis
* lib/Output_h5.c, lib/PyTables.c, lib/pytables.h: Added some
useful set_attribute*() functions.
2006-08-12 22:47 gurnis
* lib/Full_boundary_conditions.c, lib/Lith_age.c: Fix bug
associated with assimilating age grids in global models. Only
relevant change was made in the subroutine
full_temperature_boundary_condition() in which I now make a call
to lith_age_temperature_bound_adj() if lith_age_time is on.
2006-08-12 02:37 luis
* visual/h52combined.py: Rearranged (i,j,k) indices for
consistency, i.e. to correspond to (x,y,z) coords instead of
(y,x,z). Also, moved constant format string outside of the loop
body.
2006-08-11 21:36 tan2
* doc/manual/citcoms.lyx: Fixed the status of CitcomS.py on
TeraGrid
2006-08-11 20:28 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms_cover.pdf: added
leif's gnu build sys additions
2006-08-11 20:05 sue
* doc/manual/citcoms.lyx: incorporated tan2 changes/comments
2006-08-11 06:11 leif
* visual/Makefile.am: Whoops -- macro references from visual/*.net
must refer to subdirectory 'OpenDXMacro'.
2006-08-11 01:55 leif
* bin/Makefile.am, bin/citcoms.in, configure.ac,
visual/Makefile.am, visual/OpenDXMacro,
visual/OpenDXMacro/Makefile.am: Build OpenDX macros in-place
during 'make'. Remove 'citcoms' script during 'uninstall'. Also,
partial fixes for MPICH2... one still needs to add
-DMPICH_SKIP_MPICXX to CPPFLAGS, however; see issue14.
2006-08-10 20:48 sue
* doc/manual/citcoms2.0.2.lyx, doc/manual/citcoms2.0.2.pdf,
doc/manual/citcoms_cover2-0-2.pdf: added 2.0.2 manual draft and
cover
2006-08-08 21:24 tan2
* lib/Output_h5.c, lib/PyTables.c: Made the code compile when
configured --with-hdf5=no
2006-08-08 20:47 luis
* configure.ac: Fix checks for hdf5.h and for parallel HDF5. Should
now be performed only if --with-hdf5 is specified.
2006-08-08 04:55 ces74
* examples/Cookbook7/cookbook7.cfg: * fixed a bug in the module
specification: - vsolver --> solver.vsolver - tsolver -->
solver.tsolver.
2006-08-07 21:24 luis
* lib/Output_h5.c, lib/hdf5_related.h: Added time dataset
2006-08-07 06:47 luis
* configure.ac: Added configure check for Parallel-HDF5
2006-08-07 06:38 luis
* lib/Makefile.am: Removed reference to nonexistent directory
2006-08-07 06:10 luis
* bin/Makefile.am, configure.ac, lib/Citcom_init.c,
lib/Makefile.am, lib/hdf5_related.h, module/Makefile.am: Changed
configure script to compile everything with -DUSE_HDF5 when HDF5
support is enabled (--with-hdf5)
2006-08-07 04:56 luis
* lib/Makefile.am, lib/global_defs.h, lib/hdf5_info.h,
lib/hdf5_related.h: Need to maintain multiple structs in header
file, so renaming hdf5_info.h to hdf5_related.h
2006-08-07 00:46 luis
* lib/Output_h5.c: Commented out debug statements
2006-08-05 12:48 luis
* lib/Output_h5.c: Added h5output_meta(), and saved to the HDF5
input group the same input parameters that are used in
pyCitcom_*_set_properties().
2006-08-05 12:43 luis
* lib/PyTables.c, lib/pytables.h: Added set_attribute_numerical*()
functions for creating numerical attributes (int, float, double,
...) on a specified HDF5 object.
2006-08-05 00:26 tan2
* visual/Makefile.am: Added h52combined.py to the install list
2006-08-05 00:14 tan2
* visual/h52combined.py: Added a script to convert the HDF5 output
file to the ASCII combined file, using PyTables extension
package.
2006-08-04 23:37 tan2
* lib/Advection_diffusion.c: Added some comments for filter()
2006-08-04 23:20 luis
* lib/Output_h5.c: Output viscosity.
2006-08-04 23:13 luis
* lib/Output_h5.c, lib/hdf5_info.h: Renamed E->hdf5.step to
something less confusing: E->hdf5.count
2006-08-04 21:46 tan2
* CitcomS/Solver/Solver.py, bin/Citcom.c, lib/Output.c,
lib/output.h, module/bindings.cc, module/outputs.cc,
module/outputs.h: * Fixed skipped time output when
monitoringFrequency > 1, which was introduced in r4118 * Forgot
to change to the E->output function pointer in r4126
2006-08-03 14:14 luis
* lib/Output_h5.c: Changed h5output() so that it prints an error if
the C macro USE_HDF5 is not defined (and similarly for
h5output_pseudo_surf())
2006-08-03 14:03 luis
* lib/Output_h5.c, lib/hdf5_info.h: Fix bug in behavior for values
of monitoringFrequency > 1 by keeping an internal count of steps
(Python does not pass monitoringFrequency to C code).
2006-08-03 11:17 luis
* module/PyxMPI/PyxMPI.c: Regenerated PyxMPI.c with Pyrex 0.9.4 to
fix GCC4 lvalue-casting error.
2006-08-03 11:14 luis
* configure.ac: Fixed typo in configure.ac and added conditional
check for hdf5.h header.
2006-08-03 04:22 luis
* lib/Output_h5.c: 1. Disabled creation of surf & botm (temporary)
2. Only outputs (per cap) are currently coord, velocity &
temperature fields 3. For clarity, added indentation to the
debugging output
2006-08-03 03:05 luis
* lib/Output_h5.c: Rewrote h5write_field().
2006-08-03 02:31 luis
* lib/Output_h5.c: Renamed h5write_array_hyperslab() to
h5write_dataset() and fixed the comment describing the usage of
h5create_field().
2006-08-03 02:15 luis
* lib/Output_h5.c: Rewrote h5create_field() to use indices instead
of if-else branches when building the arguments (dims, maxdims,
chunkdims) for dataset creation.
2006-08-03 01:43 luis
* lib/Output_h5.c: In h5create_dataset(), renamed local variable
filespace into dataspace.
2006-08-03 01:42 luis
* lib/Output_h5.c: Renamed h5create_array() to h5create_dataset()
and made sure that the datasets created by that function are
compatibles with PyTables.
2006-08-03 01:30 luis
* lib/Output_h5.c: Updated debug statements.
2006-08-03 01:05 luis
* lib/Output_h5.c: Added h5create_file() and modified
h5create_group() so that the files and groups created with these
functions are compatible with PyTables.
2006-08-03 01:04 luis
* lib/Makefile.am, lib/PyTables.c: Fixed typo in PyTables.c and
added it to the sources in Makefile.am
2006-08-02 23:38 sue
* doc/manual/citcoms.lyx: added cover image
2006-08-02 19:42 sue
* doc/manual/citcoms.lyx, doc/manual/citcoms_book.xml,
doc/manual/graphics.tar.gz: replace manual with lyx manual
2006-08-02 00:17 tan2
* lib/Instructions.c, lib/Output_h5.c: Open and close HDF5 output
properly
2006-08-01 23:25 luis
* lib/Output_h5.c: Added debug statements.
2006-08-01 23:17 luis
* lib/pytables.h: Updated prototypes for the pytables-derived
functions.
2006-08-01 23:09 luis
* lib/global_defs.h: Added flags to control which data
(viscosity,stress,pressure) gets written to output.
2006-08-01 22:50 luis
* lib/hdf5_info.h: Consolidated buffers by size instead of by type.
2006-08-01 22:47 luis
* lib/PyTables.c: Use strings as default HDF5 attribute type.
2006-08-01 19:21 tan2
* CitcomS/Solver/Solver.py, module/bindings.cc, module/outputs.cc,
module/outputs.h: Closing output files in Solver.py
2006-08-01 19:06 tan2
* CitcomS/Components/Param.py, CitcomS/Solver/Solver.py,
module/setProperties.cc: Moved the 'output_format' property from
Param.py to Solver.py
2006-08-01 05:57 tan2
* CitcomS/Components/Param.py, module/outputs.cc,
module/setProperties.cc: * Created pyre property for
'output_format' * Changed the output function pointer in the
python binding
2006-08-01 00:54 luis
* bin/Makefile.am, configure.ac, lib/Makefile.am: Added --with-hdf5
options to configure.ac. Also, modified Makefile.am so that
Output_h5.o is compiled.
2006-08-01 00:23 tan2
* CitcomS/Controller.py, CitcomS/Solver/Solver.py,
module/bindings.cc, module/misc.cc, module/misc.h: Completely
fixed issue35 (inconsistent times) and related problems * t, dt,
step are modified only in the C code. Their python counterparts
are read-only * Changed the ancestor of the Controller from
Pyre's SimulationController to Pyre's Component, as the
SimulationController hinders the use of read-only properties *
Changed the ancestor of the Solver from Pyre's Solver to Pyre's
Component, as Pyre's Solver hinders the use of read-only
properties
2006-07-31 23:07 tan2
* lib/Instructions.c: Changed the default value of 'layerd' from
2800 km (the depth of the mantle) to 6371 km (the radius of the
Earth), which is necessary to dimensionalize the time
2006-07-31 23:04 tan2
* bin/Citcom.c, lib/Instructions.c, lib/global_defs.h,
module/mesher.cc: Added logic to switch the E->output function
pointer
2006-07-29 00:08 luis
* lib/Output_h5.c: Added two methods for writing to HDF5 arrays
(refactored from CitcomCU).
2006-07-28 22:12 luis
* lib/Output_h5.c: Fixed typos in h5output_coord()
2006-07-28 22:06 tan2
* CitcomS/Solver/Solver.py: Removed unused variables due to
refactoring of time output
2006-07-28 18:37 tan2
* lib/Output.c: Flushed the E->fptime stream after each output
2006-07-28 18:36 tan2
* lib/Instructions.c: Added missing function declaration
2006-07-27 22:02 tan2
* CitcomS/Controller.py, CitcomS/Solver/Solver.py, bin/Citcom.c,
lib/Instructions.c, lib/Output.c, lib/global_defs.h,
module/mesher.cc: Moved the responsibility of time output from
Citcom.c and Solver.py to Output.c, which includes the following
changes * open .time file at either mesher.cc (for pyre run) or
Instructions.c (for C run) * .time file is opened and closed only
by the rank-0 processor. This will avoid multiple processors
opening/writing/closing on the same file. Similar modification is
necessary for the .log file. * created two variables
E->monitor.cpu_time_at_start and
E->monitor.cpu_time_at_last_cycles for storing the wall clock
time at startup and last timestep, respectively * output .time
file in output_time() in Output.c
2006-07-27 21:06 luis
* lib/Output_h5.c: Refactored code for array creation.
2006-07-27 21:04 luis
* lib/hdf5_info.h: Eliminated unecessary buffer arrays.
2006-07-27 19:57 tan2
* examples/example0.cfg: forgot to change the 'datafile' parameter
2006-07-24 11:22 luis
* lib/Output_h5.c: Prepare output functions for optional HDF5
configuration with autoconf.
2006-07-24 11:18 luis
* lib/global_defs.h: Added output function pointer to All_variables
struct.
2006-07-19 20:19 tan2
* examples/example0.cfg: example script of single-processor run
2006-07-19 18:42 luis
* lib/global_defs.h, lib/hdf5_info.h: Created new hdf5 struct
member within the All_variables struct.
2006-07-18 23:42 sue
* doc/manual/graphics, doc/manual/graphics/c_fig1.eps,
doc/manual/graphics/c_fig10.eps, doc/manual/graphics/c_fig2.eps,
doc/manual/graphics/c_fig3.jpg, doc/manual/graphics/c_fig4.eps,
doc/manual/graphics/c_fig5.eps, doc/manual/graphics/c_fig6.jpg,
doc/manual/graphics/c_fig7.eps, doc/manual/graphics/c_fig8.eps,
doc/manual/graphics/c_fig9.eps,
doc/manual/graphics/cookbook1.2.jpg,
doc/manual/graphics/cookbook1.eps,
doc/manual/graphics/cookbook1.jpg,
doc/manual/graphics/cookbook1.png,
doc/manual/graphics/cookbook2.2.eps,
doc/manual/graphics/cookbook2.2eps,
doc/manual/graphics/cookbook2.eps,
doc/manual/graphics/cookbook3.eps,
doc/manual/graphics/cookbook4.eps,
doc/manual/graphics/cookbook5.2.eps,
doc/manual/graphics/cookbook5.eps,
doc/manual/graphics/cookbook6.2.eps,
doc/manual/graphics/cookbook6.eps,
doc/manual/graphics/cookbook7.eps, doc/manual/graphics/eq1.eps,
doc/manual/graphics/eq10.eps, doc/manual/graphics/eq11.eps,
doc/manual/graphics/eq12.eps, doc/manual/graphics/eq13.eps,
doc/manual/graphics/eq14.eps, doc/manual/graphics/eq15.eps,
doc/manual/graphics/eq16.eps, doc/manual/graphics/eq17.eps,
doc/manual/graphics/eq18.eps, doc/manual/graphics/eq19.eps,
doc/manual/graphics/eq2.eps, doc/manual/graphics/eq20.2.eps,
doc/manual/graphics/eq20.eps, doc/manual/graphics/eq21.eps,
doc/manual/graphics/eq3.eps, doc/manual/graphics/eq4.eps,
doc/manual/graphics/eq5.eps, doc/manual/graphics/eq6.eps,
doc/manual/graphics/eq7.eps, doc/manual/graphics/eq8.eps,
doc/manual/graphics/eq9.eps, doc/manual/graphics/exp1.eps,
doc/manual/graphics/exp10.eps, doc/manual/graphics/exp11.eps,
doc/manual/graphics/exp12.eps, doc/manual/graphics/exp2.eps,
doc/manual/graphics/exp3.eps, doc/manual/graphics/exp4.eps,
doc/manual/graphics/exp5.eps, doc/manual/graphics/exp6.eps,
doc/manual/graphics/exp7.eps, doc/manual/graphics/exp8.eps,
doc/manual/graphics/exp9.eps: adding graphics directory
2006-07-18 23:05 sue
* doc/manual/citcoms_book.xml: updated dtd address
2006-07-18 01:00 luis
* lib/PyTables.c, lib/pytables.h: Provide an API for creating
PyTables-compatible HDF5 files.
2006-07-17 23:31 luis
* lib/Output_h5.c, lib/output_h5.h: For the new HDF5 output format,
use a similar API as in Output.c Copying the bodies from the old
functions for now, but prefixing the function name with 'h5'.
2006-07-15 02:14 leif
* CitcomS/SimpleApp.py: Bug fix in
_getPrivateDepositoryLocations(); updated usage().
2006-07-13 23:41 leif
* examples/Cookbook1/cookbook1.cfg,
examples/Cookbook1/cookbook1.sh,
examples/Cookbook2/cookbook2.cfg,
examples/Cookbook2/cookbook2.sh,
examples/Cookbook3/cookbook3.cfg,
examples/Cookbook3/cookbook3.sh,
examples/Cookbook4/cookbook4.cfg,
examples/Cookbook4/cookbook4.sh,
examples/Cookbook5/cookbook5.cfg,
examples/Cookbook5/cookbook5.sh,
examples/Cookbook7/cookbook7.cfg,
examples/Cookbook7/cookbook7.sh, examples/example1.sh,
tests/Makefile.am, tests/citcomsfull.sh.in,
tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Nuked
citcoms{full,regional}.sh, coupledcitcoms.sh. Converted cookbook
*.sh files to *.cfg files, and sprinkled-in some comments derived
from the manual.
2006-07-13 20:06 leif
* configure.ac: Fix for broken "make install" on Pangu (discovered
by Lydia): add both 'pythondir' and 'pyexecdir' to
PYTHONPATH/sys.path.
2006-07-07 23:54 leif
* bin/pycitcoms.cc: Temporary work-around for broken _mpimodule on
Pangu.
2006-07-07 23:07 tan2
* CitcomS/Controller.py: Renamed extension module (see r3983)
2006-07-07 22:35 leif
* CitcomS/Components/Advection_diffusion/Advection_diffusion.py,
CitcomS/Components/BC.py, CitcomS/Components/Const.py,
CitcomS/Components/Exchanger/Exchanger.py,
CitcomS/Components/Exchanger/Inlet.py,
CitcomS/Components/Exchanger/Outlet.py, CitcomS/Components/IC.py,
CitcomS/Components/Param.py, CitcomS/Components/Phase.py,
CitcomS/Components/Sphere/FullSphere.py,
CitcomS/Components/Sphere/RegionalSphere.py,
CitcomS/Components/Sphere/Sphere.py,
CitcomS/Components/Stokes_solver/Incompressible.py,
CitcomS/Components/Tracer.py, CitcomS/Components/Visc.py,
CitcomS/Makefile.am, CitcomS/SimpleApp.py,
CitcomS/Solver/FullSolver.py, CitcomS/Solver/RegionalSolver.py,
CitcomS/Solver/Solver.py, bin/Makefile.am, bin/citcoms.in,
bin/pycitcoms.cc, module/CitcomSmodule.cc,
module/CitcomSmodule.h, module/Exchanger/Exchangermodule.cc,
module/Exchanger/Exchangermodule.h, module/Exchanger/Makefile.am,
module/Full, module/Makefile.am, module/Regional,
module/Regionalmodule.cc, module/advdiffu.cc, module/advdiffu.h,
module/bindings.cc, module/bindings.h, module/exceptions.cc,
module/exceptions.h, module/initial_conditions.cc,
module/initial_conditions.h, module/mesher.cc, module/mesher.h,
module/misc.cc, module/misc.h, module/outputs.cc,
module/outputs.h, module/setProperties.cc,
module/setProperties.h, module/stokes_solver.cc,
module/stokes_solver.h, tests/exchange.py: Moved & renamed
extension modules:
CitcomS.CitcomS -> CitcomsLib CitcomS.Exchanger -> ExchangerLib
Top-level modules allow easy toggling between embedding &
extending without any special hacks in the embedding case. Also,
it allows the Python scripts to be installed under 'libdir'
instead of 'libexecdir', although this is a minor issue.
Also: moved module/Regional/* source to module/* to really
complete the Full/Regional merge (there is only one CitcomS
extension module now). Plus, a bug fix in collectUserInput.
2006-07-07 21:36 tan2
* CitcomS/Controller.py, CitcomS/Solver/Solver.py,
module/Regional/bindings.cc, module/Regional/misc.cc,
module/Regional/misc.h: A quick fix to issue35 "inconsistent
times in C and Pyre"
2006-07-07 00:54 leif
* bin/Makefile.am, configure.ac, lib/Advection_diffusion.c,
lib/BC_util.c, lib/Citcom_init.c, lib/Common,
lib/Construct_arrays.c, lib/Convection.c, lib/Drive_solvers.c,
lib/Element_calculations.c, lib/Full,
lib/Full_boundary_conditions.c, lib/Full_geometry_cartesian.c,
lib/Full_lith_age_read_files.c, lib/Full_obsolete.c,
lib/Full_parallel_related.c, lib/Full_read_input_from_files.c,
lib/Full_solver.c, lib/Full_sphere_related.c,
lib/Full_version_dependent.c, lib/General_matrix_functions.c,
lib/Global_operations.c, lib/Initial_temperature.c,
lib/Instructions.c, lib/Interuption.c, lib/Lith_age.c,
lib/Makefile.am, lib/Nodal_mesh.c, lib/Obsolete.c, lib/Output.c,
lib/Pan_problem_misc_functions.c, lib/Parallel_util.c,
lib/Parsing.c, lib/Phase_change.c, lib/Problem_related.c,
lib/Process_buoyancy.c, lib/Regional,
lib/Regional_boundary_conditions.c,
lib/Regional_geometry_cartesian.c,
lib/Regional_lith_age_read_files.c, lib/Regional_obsolete.c,
lib/Regional_parallel_related.c,
lib/Regional_read_input_from_files.c, lib/Regional_solver.c,
lib/Regional_sphere_related.c, lib/Regional_version_dependent.c,
lib/Shape_functions.c, lib/Size_does_matter.c,
lib/Solver_conj_grad.c, lib/Solver_multigrid.c,
lib/Sphere_harmonics.c, lib/Sphere_util.c,
lib/Stokes_flow_Incomp.c, lib/Topo_gravity.c,
lib/Tracer_advection.c, lib/Viscosity_structures.c,
lib/advection.h, lib/advection_diffusion.h, lib/citcom_init.h,
lib/convection_variables.h, lib/drive_solvers.h,
lib/element_definitions.h, lib/global_defs.h,
lib/initial_temperature.h, lib/interuption.h, lib/lith_age.h,
lib/output.h, lib/parallel_related.h, lib/parsing.h,
lib/phase_change.h, lib/solver.h, lib/sphere_communication.h,
lib/temperature_descriptions.h, lib/tracer_defs.h,
lib/viscosity_descriptions.h, module/Exchanger/Makefile.am,
module/Makefile.am: Avoid shared libraries altogether when
embedding. Shared libs are very likely to fail with static
MPICH... this was confirmed when the link failed on Eh's iBook.
Also completed the Full/Regional merge by flatting the directory
structure under 'lib'.
2006-07-06 23:20 leif
* CitcomS, CitcomS/Components,
CitcomS/Components/Advection_diffusion,
CitcomS/Components/Exchanger, CitcomS/Components/Sphere,
CitcomS/Components/Stokes_solver, CitcomS/Makefile.am,
CitcomS/SimpleApp.py, CitcomS/Solver, CitcomS/__init__.py,
CitcomS/__init__.py.in, Makefile.am, bin/Makefile.am,
configure.ac: Issue32: "make install" is now optional. Users can
now simply "configure", "make", and then add the "bin"
subdirectory of the source/build directory to their PATH.
In this mode, changes to C/C++ simply require a "make" from the
top-level directory ("make" from a subdirectory will not work in
the near future). Changes to the Python code do not require you
to run "make" at all -- simply re-run 'citcoms'.
2006-07-06 22:22 leif
* CitcomS, bin, drivers, pyre: Renamed directories in preparation
for next check-in:
pyre -> CitcomS drivers -> bin
This is to work-around this error message from 'svn':
"new node revision ID without delete".
I am not loving Subversion right now. Wasn't the whole point that
it handles renames gracefully?
2006-07-06 18:16 leif
* Make.mm, drivers/Full, drivers/Make.mm, drivers/Regional,
drivers/local.def, etc/Make.mm, lib/Common/Make.mm,
lib/Common/local.def, lib/Full/Make.mm, lib/Full/local.def,
lib/Make.mm, lib/Regional/Make.mm, lib/Regional/local.def,
lib/local.def, local.def, module/Exchanger/Make.mm,
module/Full/Make.mm, module/Full/local.def, module/Make.mm,
module/Regional/Make.mm, module/Regional/local.def,
pyre/Components/Advection_diffusion/Make.mm,
pyre/Components/Exchanger/Make.mm, pyre/Components/Make.mm,
pyre/Components/Sphere/Make.mm,
pyre/Components/Stokes_solver/Make.mm, pyre/Make.mm,
pyre/Solver/Make.mm, pyre/local.def, tests/Make.mm,
tests/local.def, visual/Make.mm: Nuked "Make.mm" files, which are
no longer used.
2006-07-06 02:53 leif
* examples/example1.cfg, pyre/Components/CodecConfig.py,
pyre/Components/HackedConfigParser.py, pyre/Makefile.am,
pyre/SimpleApp.py: Added the ability to use ".cfg" files instead
of clumsy shell scripts for specifying parameters.
Example usage:
citcoms example1.cfg
(The file 'example1.cfg' is checked-in under 'examples'.)
The code which made this possible was copied & pasted from
Specfem project; it will be factored-out into a shared package at
some point...
2006-07-06 02:16 leif
* Makefile.am, configure.ac, drivers/Citcom.c, drivers/Makefile.am,
drivers/citcoms.in, drivers/pycitcoms.cc, etc/CitcomS.pml.in,
etc/Makefile.am, lib/Common/Advection_diffusion.c,
lib/Common/BC_util.c, lib/Common/Construct_arrays.c,
lib/Common/Convection.c, lib/Common/Element_calculations.c,
lib/Common/General_matrix_functions.c,
lib/Common/Initial_temperature.c, lib/Common/Instructions.c,
lib/Common/Lith_age.c, lib/Common/Makefile.am,
lib/Common/Nodal_mesh.c, lib/Common/Parallel_util.c,
lib/Common/Problem_related.c, lib/Common/Process_buoyancy.c,
lib/Common/Size_does_matter.c, lib/Common/Solver_multigrid.c,
lib/Common/Sphere_util.c, lib/Common/global_defs.h,
lib/Common/lith_age.h, lib/Common/parallel_related.h,
lib/Common/solver.h, lib/Full/Boundary_conditions.c,
lib/Full/Geometry_cartesian.c, lib/Full/Lith_age.c,
lib/Full/Lith_age_read_files.c, lib/Full/Makefile.am,
lib/Full/Parallel_related.c, lib/Full/Read_input_from_files.c,
lib/Full/Solver.c, lib/Full/Sphere_related.c,
lib/Full/Version_dependent.c, lib/Makefile.am,
lib/Regional/Boundary_conditions.c,
lib/Regional/Geometry_cartesian.c, lib/Regional/Lith_age.c,
lib/Regional/Lith_age_read_files.c, lib/Regional/Makefile.am,
lib/Regional/Parallel_related.c,
lib/Regional/Read_input_from_files.c, lib/Regional/Solver.c,
lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c,
module/CitcomSmodule.cc, module/CitcomSmodule.h,
module/Exchanger/Exchangermodule.cc,
module/Exchanger/Exchangermodule.h, module/Exchanger/Makefile.am,
module/Full/Makefile.am, module/Makefile.am, module/PyxMPI,
module/PyxMPI/PyxMPI.c, module/PyxMPI/PyxMPI.pyx,
module/PyxMPI/cmpi.pxd, module/Regional/Makefile.am,
module/Regional/bindings.cc, module/Regional/mesher.cc,
module/Regional/misc.cc, module/Regional/misc.h,
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/BC.py, pyre/Components/CitcomComponent.py,
pyre/Components/Const.py, pyre/Components/IC.py,
pyre/Components/Launchers.py, pyre/Components/Param.py,
pyre/Components/Phase.py, pyre/Components/Sphere/FullSphere.py,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Sphere/Sphere.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Tracer.py, pyre/Components/Visc.py,
pyre/SimpleApp.py, pyre/Solver/FullSolver.py,
pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py,
tests/Makefile.am, tests/citcomsfull.sh.in,
tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Added
the capability to embed Python instead of extending it. This
creates one, big monolithic executable, 'pycitcoms', which
contains all CitcomS code and an embedded Python interpreter.
Embedding works-around MPI portability issues. (See issue15 for
details.) Embed by default.
Configure with '--disable-embedding' to build the old way with
".so" extension modules. This is *NOT* guaranteed to work unless
you have a shared MPI library. The ugly hacks which made it work
in the past (even with a static "libmpich.a", for example) are no
longer supported.
Merged "Full" and "Regional" into a single library to cut down on
redundancy, both in the source code and in the amount of object
code which is produced. (I performed this merge so that I would
only need a single 'pycitcoms' intepreter, instead of two.)
2006-06-12 17:43 gurnis
* lib/Common/Advection_diffusion.c,
lib/Common/Initial_temperature.c, lib/Common/Problem_related.c,
lib/Full/Read_input_from_files.c, pyre/Solver/Solver.py: Fixed
restart_tic() in Initial_temperature.c so that time is correctly
read in while using the lith_ages
2006-06-02 23:38 gurnis
* lib/Full/Boundary_conditions.c, lib/Full/Lith_age.c,
lib/Regional/Boundary_conditions.c, lib/Regional/Lith_age.c:
Fixed bugs associated assimilating lith_age files into Full.
Slightly improved method of assimilating lith_age
2006-05-18 18:05 cassie
* doc/manual/citcoms_book.xml: typo in manual corrected
2006-05-16 19:50 cassie
* doc/manual/citcoms_book.xml: additional minor updates to manual
2006-05-16 18:36 cassie
* doc/manual/citcoms_book.xml: minor updates to manual
2006-04-18 23:34 luis
* lib/Full/Obsolete.c: Fixed typos.
2006-03-28 19:22 walter
* .: Changed externals from svn:// to http://
2006-02-14 23:24 leif
* ChangeLog, NEWS: Updated NEWS and ChangeLog.
2006-02-14 22:24 leif
* pyre/SimpleApp.py, tests/Makefile.am, tests/citcomsfull.sh.in,
tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Merged
r2600 (fix for issue13, "make PYTHONPATH automatic") from v2
branch to trunk.
2006-02-04 02:11 luis
* doc/manual/citcoms_book.xml: Fixed about 20 assorted typos.
2006-02-04 00:18 luis
* lib/Regional/Version_dependent.c: Eliminated the unused local
variables lx,ly,lz in global_derived_values().
2006-02-04 00:15 luis
* lib/Full/Version_dependent.c: The value of max_size needs to be
larger by 1, or else we access out-of-bound array elements in the
arrays E->boundary.element and E->boundary.normal.
Refer to issue10 in roundup for more details.
2006-02-04 00:11 luis
* lib/Common/global_defs.h: Adjusted size of arrays in struct
Shape_function_dA. This fixes a bug involving out-of-bounds array
access caused by use of fortran-style indexing.
Refer to issue10 in roundup for more information.
2006-02-04 00:04 luis
* lib/Common/Citcom_init.c: Need to initialize to zero the
following variables * E->control.total_iteration_cycles *
E->control.total_v_solver_calls
2006-01-31 23:16 leif
* pyre/Components/Launchers.py: Merged r2575 (fix for issue9, "need
a property for extra LSF options") from v2 branch to trunk.
2006-01-31 20:23 leif
* pyre/Components/Launchers.py: Merged r2573 (fix for issue8,
"eliminate CitcomS default time limit for batch jobs") from v2
branch to trunk.
2006-01-31 02:54 leif
* configure.ac, etc/Makefile.am, pyre/Makefile.am,
tests/Makefile.am, tests/citcomsfull.sh.in,
tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Merged
r2565 (fix for issue11, "broken install when 'pkgpyexecdir' is
distinct from 'pkgpythondir'") from v2 branch to trunk.
2006-01-31 00:07 leif
* configure.ac: Merged r2563 (fix for issue7, "CitcomS check_CXX
check is broken") from v2 branch to trunk.
2005-11-17 19:14 luis
* examples/Cookbook2/cookbook2.sh: Corrected typo. Should be:
--solver.bc.topvbyval=0
2005-11-17 00:35 luis
* doc/manual/citcoms_book.xml: boundition --> boundary condition
2005-11-16 02:23 leif
* pyre/Components/IC.py: Fixed a bug which Luis found
("--solver.ic.help-properties"): bad default values for
blob_radius and blob_dT.
2005-11-09 18:53 leif
* doc/manual/citcoms_book.xml: Regenerated PDF.
2005-11-09 12:15 luis
* doc/manual/citcoms_book.xml: Fixed example 5.6 in Cookbook 5
2005-11-09 11:45 luis
* doc/manual/citcoms_book.xml: Fixed a few more typos.
2005-11-09 11:31 luis
* doc/manual/citcoms_book.xml: Missed a stray =
2005-11-09 11:20 luis
* doc/manual/citcoms_book.xml: Corrected several typos and
mispelling errors.
2005-11-04 19:39 leif
* doc/manual/citcoms_book.xml: Regenerated PDF: updated date; minor
corrections, format tweaks.
2005-11-03 00:26 tan2
* doc/manual/citcoms_book.xml: fixed a bug in closing <filename>
tag
2005-11-01 01:10 tan2
* doc/manual/citcoms_book.xml: changes in Chapter 4
(post-processing) and Appendix C (output format)
2005-10-29 02:16 leif
* mc/3D/CitcomS/branches/v2/examples/Cookbook1/cookbook1.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook2/cookbook2.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook3/cookbook3.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook4/cookbook4.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook5/cookbook5.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook7/cookbook7.sh,
mc/3D/CitcomS/branches/v2/examples/example1.sh,
mc/3D/CitcomS/tags/v2.0.1/examples/Cookbook1/cookbook1.sh,
mc/3D/CitcomS/tags/v2.0.1/examples/Cookbook2/cookbook2.sh,
mc/3D/CitcomS/tags/v2.0.1/examples/Cookbook3/cookbook3.sh,
mc/3D/CitcomS/tags/v2.0.1/examples/Cookbook4/cookbook4.sh,
mc/3D/CitcomS/tags/v2.0.1/examples/Cookbook5/cookbook5.sh,
mc/3D/CitcomS/tags/v2.0.1/examples/Cookbook7/cookbook7.sh,
mc/3D/CitcomS/tags/v2.0.1/examples/example1.sh,
examples/Cookbook1/cookbook1.sh, examples/Cookbook2/cookbook2.sh:
Set svn:executable on all examples and cookbooks.
2005-10-29 02:07 leif
* doc/manual/citcoms_book.xml: Numerous minor corrections and
format tweaks.
2005-10-28 22:58 leif
* doc/manual/citcoms_book.xml: Minor corrections to Chapter 3,
"Running CitComS.py", and a major update to Chapter 4,
"Postprocessing and Graphics" (which still contained references
to the "regcitcom input file").
2005-10-28 20:06 leif
* doc/manual/citcoms_book.xml: Minor updates to Chapter 2 -- in
particular, removed reference to the separate, sync'd Pythia
repository. Also, removed reference to the Python installer.
2005-10-28 19:45 leif
* doc/manual, doc/manual/citcoms_book.xml,
doc/manual/citcoms_cover.pdf, doc/manual/graphics.tar.gz: Added
DocBook manual files from Cassie.
2005-10-21 19:35 leif
* mc/3D/CitcomS/branches/v2/examples/Cookbook1/cookbook1.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook2/cookbook2.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook3/cookbook3.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook4/cookbook4.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook5/cookbook5.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook7/cookbook7.sh,
mc/3D/CitcomS/branches/v2/examples/example1.sh,
mc/3D/CitcomS/branches/v2/visual/Makefile.am,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSFullImport.net,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSFullImport.net.in,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSImport.net,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSImport.net.in,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceHeatflux.net,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceHeatflux.net.in,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceImport.net,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceImport.net.in,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceTopo.net,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceTopo.net.in,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceVelocity.net,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSSurfaceVelocity.net.in,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSTemperature.net,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSTemperature.net.in,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSVelocity.net,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSVelocity.net.in,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSViscosity.net,
mc/3D/CitcomS/branches/v2/visual/OpenDXMacro/CitcomSViscosity.net.in,
mc/3D/CitcomS/branches/v2/visual/visFull.net,
mc/3D/CitcomS/branches/v2/visual/visFull.net.in,
mc/3D/CitcomS/branches/v2/visual/visRegional.net,
mc/3D/CitcomS/branches/v2/visual/visRegional.net.in,
mc/3D/CitcomS/branches/v2/visual/visRegionalSurface.net,
mc/3D/CitcomS/branches/v2/visual/visRegionalSurface.net.in,
examples/Cookbook1/cookbook1.sh, examples/Cookbook2/cookbook2.sh,
examples/Cookbook3/cookbook3.sh, examples/Cookbook4/cookbook4.sh,
examples/Cookbook5/cookbook5.sh, examples/Cookbook7/cookbook7.sh,
examples/example1.sh, visual/Makefile.am,
visual/OpenDXMacro/CitcomSFullImport.net,
visual/OpenDXMacro/CitcomSFullImport.net.in,
visual/OpenDXMacro/CitcomSImport.net,
visual/OpenDXMacro/CitcomSImport.net.in,
visual/OpenDXMacro/CitcomSSurfaceHeatflux.net,
visual/OpenDXMacro/CitcomSSurfaceHeatflux.net.in,
visual/OpenDXMacro/CitcomSSurfaceImport.net,
visual/OpenDXMacro/CitcomSSurfaceImport.net.in,
visual/OpenDXMacro/CitcomSSurfaceTopo.net,
visual/OpenDXMacro/CitcomSSurfaceTopo.net.in,
visual/OpenDXMacro/CitcomSSurfaceVelocity.net,
visual/OpenDXMacro/CitcomSSurfaceVelocity.net.in,
visual/OpenDXMacro/CitcomSTemperature.net,
visual/OpenDXMacro/CitcomSTemperature.net.in,
visual/OpenDXMacro/CitcomSVelocity.net,
visual/OpenDXMacro/CitcomSVelocity.net.in,
visual/OpenDXMacro/CitcomSViscosity.net,
visual/OpenDXMacro/CitcomSViscosity.net.in, visual/visFull.net,
visual/visFull.net.in, visual/visRegional.net,
visual/visRegional.net.in, visual/visRegionalSurface.net,
visual/visRegionalSurface.net.in: Merged revision 2466 from
CitcomS v2.0.1 to v2 branch and trunk.
2005-10-07 12:37 leif
* mc/3D/CitcomS/branches/v2/pyre/Solver/FullSolver.py,
mc/3D/CitcomS/branches/v2/pyre/Solver/RegionalSolver.py,
pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py: Don't
suppress errors loading Full/Regional module.
2005-10-04 23:58 tan2
* visual/dxgeneralsurf.sh, visual/pasteCitcomData.sh: changed the
argument style of 'head'/'tail' command to conform with the
standard
2005-10-04 23:56 tan2
* visual/dxgeneral.sh: changed 'head -1' to 'head -n 1' to conform
with the standard
2005-10-04 22:37 leif
* mc/3D/CitcomS/branches/v2/Make.mm,
mc/3D/CitcomS/branches/v2/Makefile.am,
mc/3D/CitcomS/branches/v2/configure.ac,
mc/3D/CitcomS/branches/v2/drivers/Citcom.c,
mc/3D/CitcomS/branches/v2/drivers/Full/Make.mm,
mc/3D/CitcomS/branches/v2/drivers/Full/local.def,
mc/3D/CitcomS/branches/v2/drivers/Make.mm,
mc/3D/CitcomS/branches/v2/drivers/Makefile.am,
mc/3D/CitcomS/branches/v2/drivers/Regional/Make.mm,
mc/3D/CitcomS/branches/v2/drivers/Regional/local.def,
mc/3D/CitcomS/branches/v2/drivers/local.def,
mc/3D/CitcomS/branches/v2/etc/Make.mm,
mc/3D/CitcomS/branches/v2/etc/Makefile.am,
mc/3D/CitcomS/branches/v2/etc/__vault__.odb,
mc/3D/CitcomS/branches/v2/etc/full-sphere.odb,
mc/3D/CitcomS/branches/v2/etc/full.odb,
mc/3D/CitcomS/branches/v2/etc/globus.odb,
mc/3D/CitcomS/branches/v2/etc/incomp-newtonian.odb,
mc/3D/CitcomS/branches/v2/etc/incomp-non-newtonian.odb,
mc/3D/CitcomS/branches/v2/etc/lam-mpi.odb,
mc/3D/CitcomS/branches/v2/etc/lsf.odb,
mc/3D/CitcomS/branches/v2/etc/mpich.odb,
mc/3D/CitcomS/branches/v2/etc/pbs.odb,
mc/3D/CitcomS/branches/v2/etc/regional-sphere.odb,
mc/3D/CitcomS/branches/v2/etc/regional.odb,
mc/3D/CitcomS/branches/v2/etc/temp.odb,
mc/3D/CitcomS/branches/v2/examples/Cookbook1/cookbook1.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook2/cookbook2.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook3/cookbook3.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook4/cookbook4.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook5/cookbook5.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook7/cookbook7.sh,
mc/3D/CitcomS/branches/v2/examples/Makefile.am,
mc/3D/CitcomS/branches/v2/examples/example1.sh,
mc/3D/CitcomS/branches/v2/lib/Common/Advection_diffusion.c,
mc/3D/CitcomS/branches/v2/lib/Common/Citcom_init.c,
mc/3D/CitcomS/branches/v2/lib/Common/Construct_arrays.c,
mc/3D/CitcomS/branches/v2/lib/Common/Convection.c,
mc/3D/CitcomS/branches/v2/lib/Common/Drive_solvers.c,
mc/3D/CitcomS/branches/v2/lib/Common/Element_calculations.c,
mc/3D/CitcomS/branches/v2/lib/Common/General_matrix_functions.c,
mc/3D/CitcomS/branches/v2/lib/Common/Global_operations.c,
mc/3D/CitcomS/branches/v2/lib/Common/Initial_temperature.c,
mc/3D/CitcomS/branches/v2/lib/Common/Instructions.c,
mc/3D/CitcomS/branches/v2/lib/Common/Interuption.c,
mc/3D/CitcomS/branches/v2/lib/Common/Make.mm,
mc/3D/CitcomS/branches/v2/lib/Common/Makefile.am,
mc/3D/CitcomS/branches/v2/lib/Common/Nodal_mesh.c,
mc/3D/CitcomS/branches/v2/lib/Common/Obsolete.c,
mc/3D/CitcomS/branches/v2/lib/Common/Output.c,
mc/3D/CitcomS/branches/v2/lib/Common/Pan_problem_misc_functions.c,
mc/3D/CitcomS/branches/v2/lib/Common/Parsing.c,
mc/3D/CitcomS/branches/v2/lib/Common/Phase_change.c,
mc/3D/CitcomS/branches/v2/lib/Common/Problem_related.c,
mc/3D/CitcomS/branches/v2/lib/Common/Process_buoyancy.c,
mc/3D/CitcomS/branches/v2/lib/Common/Shape_functions.c,
mc/3D/CitcomS/branches/v2/lib/Common/Size_does_matter.c,
mc/3D/CitcomS/branches/v2/lib/Common/Solver_conj_grad.c,
mc/3D/CitcomS/branches/v2/lib/Common/Solver_multigrid.c,
mc/3D/CitcomS/branches/v2/lib/Common/Sphere_harmonics.c,
mc/3D/CitcomS/branches/v2/lib/Common/Stokes_flow_Incomp.c,
mc/3D/CitcomS/branches/v2/lib/Common/Topo_gravity.c,
mc/3D/CitcomS/branches/v2/lib/Common/Tracer_advection.c,
mc/3D/CitcomS/branches/v2/lib/Common/Viscosity_structures.c,
mc/3D/CitcomS/branches/v2/lib/Common/advection.h,
mc/3D/CitcomS/branches/v2/lib/Common/advection_diffusion.h,
mc/3D/CitcomS/branches/v2/lib/Common/citcom_init.h,
mc/3D/CitcomS/branches/v2/lib/Common/convection_variables.h,
mc/3D/CitcomS/branches/v2/lib/Common/drive_solvers.h,
mc/3D/CitcomS/branches/v2/lib/Common/element_definitions.h,
mc/3D/CitcomS/branches/v2/lib/Common/global_defs.h,
mc/3D/CitcomS/branches/v2/lib/Common/initial_temperature.h,
mc/3D/CitcomS/branches/v2/lib/Common/interuption.h,
mc/3D/CitcomS/branches/v2/lib/Common/lith_age.h,
mc/3D/CitcomS/branches/v2/lib/Common/local.def,
mc/3D/CitcomS/branches/v2/lib/Common/output.h,
mc/3D/CitcomS/branches/v2/lib/Common/parallel_related.h,
mc/3D/CitcomS/branches/v2/lib/Common/parsing.h,
mc/3D/CitcomS/branches/v2/lib/Common/phase_change.h,
mc/3D/CitcomS/branches/v2/lib/Common/sphere_communication.h,
mc/3D/CitcomS/branches/v2/lib/Common/temperature_descriptions.h,
mc/3D/CitcomS/branches/v2/lib/Common/tracer_defs.h,
mc/3D/CitcomS/branches/v2/lib/Common/viscosity_descriptions.h,
mc/3D/CitcomS/branches/v2/lib/Full/Boundary_conditions.c,
mc/3D/CitcomS/branches/v2/lib/Full/Geometry_cartesian.c,
mc/3D/CitcomS/branches/v2/lib/Full/Lith_age.c,
mc/3D/CitcomS/branches/v2/lib/Full/Make.mm,
mc/3D/CitcomS/branches/v2/lib/Full/Makefile.am,
mc/3D/CitcomS/branches/v2/lib/Full/Obsolete.c,
mc/3D/CitcomS/branches/v2/lib/Full/Parallel_related.c,
mc/3D/CitcomS/branches/v2/lib/Full/Read_input_from_files.c,
mc/3D/CitcomS/branches/v2/lib/Full/Sphere_related.c,
mc/3D/CitcomS/branches/v2/lib/Full/Version_dependent.c,
mc/3D/CitcomS/branches/v2/lib/Full/local.def,
mc/3D/CitcomS/branches/v2/lib/Make.mm,
mc/3D/CitcomS/branches/v2/lib/Makefile.am,
mc/3D/CitcomS/branches/v2/lib/Regional/Boundary_conditions.c,
mc/3D/CitcomS/branches/v2/lib/Regional/Geometry_cartesian.c,
mc/3D/CitcomS/branches/v2/lib/Regional/Lith_age.c,
mc/3D/CitcomS/branches/v2/lib/Regional/Make.mm,
mc/3D/CitcomS/branches/v2/lib/Regional/Makefile.am,
mc/3D/CitcomS/branches/v2/lib/Regional/Obsolete.c,
mc/3D/CitcomS/branches/v2/lib/Regional/Parallel_related.c,
mc/3D/CitcomS/branches/v2/lib/Regional/Read_input_from_files.c,
mc/3D/CitcomS/branches/v2/lib/Regional/Sphere_related.c,
mc/3D/CitcomS/branches/v2/lib/Regional/Version_dependent.c,
mc/3D/CitcomS/branches/v2/lib/Regional/local.def,
mc/3D/CitcomS/branches/v2/lib/local.def,
mc/3D/CitcomS/branches/v2/local.def,
mc/3D/CitcomS/branches/v2/module/Full/Fullmodule.cc,
mc/3D/CitcomS/branches/v2/module/Full/Make.mm,
mc/3D/CitcomS/branches/v2/module/Full/Makefile.am,
mc/3D/CitcomS/branches/v2/module/Full/local.def,
mc/3D/CitcomS/branches/v2/module/Make.mm,
mc/3D/CitcomS/branches/v2/module/Makefile.am,
mc/3D/CitcomS/branches/v2/module/Regional/Make.mm,
mc/3D/CitcomS/branches/v2/module/Regional/Makefile.am,
mc/3D/CitcomS/branches/v2/module/Regional/Regionalmodule.cc,
mc/3D/CitcomS/branches/v2/module/Regional/advdiffu.cc,
mc/3D/CitcomS/branches/v2/module/Regional/advdiffu.h,
mc/3D/CitcomS/branches/v2/module/Regional/bindings.cc,
mc/3D/CitcomS/branches/v2/module/Regional/bindings.h,
mc/3D/CitcomS/branches/v2/module/Regional/exceptions.cc,
mc/3D/CitcomS/branches/v2/module/Regional/exceptions.h,
mc/3D/CitcomS/branches/v2/module/Regional/initial_conditions.cc,
mc/3D/CitcomS/branches/v2/module/Regional/initial_conditions.h,
mc/3D/CitcomS/branches/v2/module/Regional/local.def,
mc/3D/CitcomS/branches/v2/module/Regional/mesher.cc,
mc/3D/CitcomS/branches/v2/module/Regional/mesher.h,
mc/3D/CitcomS/branches/v2/module/Regional/misc.cc,
mc/3D/CitcomS/branches/v2/module/Regional/misc.h,
mc/3D/CitcomS/branches/v2/module/Regional/outputs.cc,
mc/3D/CitcomS/branches/v2/module/Regional/outputs.h,
mc/3D/CitcomS/branches/v2/module/Regional/setProperties.cc,
mc/3D/CitcomS/branches/v2/module/Regional/setProperties.h,
mc/3D/CitcomS/branches/v2/module/Regional/stokes_solver.cc,
mc/3D/CitcomS/branches/v2/module/Regional/stokes_solver.h,
mc/3D/CitcomS/branches/v2/pyre/Components/Advection_diffusion/Advection_diffusion.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Advection_diffusion/Make.mm,
mc/3D/CitcomS/branches/v2/pyre/Components/Advection_diffusion/__init__.py,
mc/3D/CitcomS/branches/v2/pyre/Components/BC.py,
mc/3D/CitcomS/branches/v2/pyre/Components/CitcomComponent.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Const.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/CoarseGridExchanger.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Exchanger.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/FineGridExchanger.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Inlet.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Make.mm,
mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Outlet.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/__init__.py,
mc/3D/CitcomS/branches/v2/pyre/Components/IC.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Launchers.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Make.mm,
mc/3D/CitcomS/branches/v2/pyre/Components/Param.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Phase.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/FullSphere.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/Make.mm,
mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/RegionalSphere.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/Sphere.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/__init__.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Stokes_solver/Incompressible.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Stokes_solver/Make.mm,
mc/3D/CitcomS/branches/v2/pyre/Components/Stokes_solver/__init__.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Tracer.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Visc.py,
mc/3D/CitcomS/branches/v2/pyre/Components/__init__.py,
mc/3D/CitcomS/branches/v2/pyre/Controller.py,
mc/3D/CitcomS/branches/v2/pyre/CoupledApp.py,
mc/3D/CitcomS/branches/v2/pyre/Coupler.py,
mc/3D/CitcomS/branches/v2/pyre/Layout.py,
mc/3D/CitcomS/branches/v2/pyre/Make.mm,
mc/3D/CitcomS/branches/v2/pyre/Makefile.am,
mc/3D/CitcomS/branches/v2/pyre/SimpleApp.py,
mc/3D/CitcomS/branches/v2/pyre/Solver/FullSolver.py,
mc/3D/CitcomS/branches/v2/pyre/Solver/Make.mm,
mc/3D/CitcomS/branches/v2/pyre/Solver/RegionalSolver.py,
mc/3D/CitcomS/branches/v2/pyre/Solver/Solver.py,
mc/3D/CitcomS/branches/v2/pyre/Solver/__init__.py,
mc/3D/CitcomS/branches/v2/pyre/__init__.py.in,
mc/3D/CitcomS/branches/v2/pyre/local.def,
mc/3D/CitcomS/branches/v2/tests/Make.mm,
mc/3D/CitcomS/branches/v2/tests/Makefile.am,
mc/3D/CitcomS/branches/v2/tests/asap.py,
mc/3D/CitcomS/branches/v2/tests/citcomsfull.sh.in,
mc/3D/CitcomS/branches/v2/tests/citcomsregional.sh.in,
mc/3D/CitcomS/branches/v2/tests/hrothgar.py,
mc/3D/CitcomS/branches/v2/tests/local.def,
mc/3D/CitcomS/branches/v2/tests/signon.py,
mc/3D/CitcomS/branches/v2/visual/Make.mm,
mc/3D/CitcomS/branches/v2/visual/Makefile.am,
mc/3D/CitcomS/branches/v2/visual/autocombine.py,
mc/3D/CitcomS/branches/v2/visual/batchcombine.py,
mc/3D/CitcomS/branches/v2/visual/batchpaste.sh,
mc/3D/CitcomS/branches/v2/visual/batchsurf.py,
mc/3D/CitcomS/branches/v2/visual/combine.py,
mc/3D/CitcomS/branches/v2/visual/combinesurf.py,
mc/3D/CitcomS/branches/v2/visual/dxgeneral.sh,
mc/3D/CitcomS/branches/v2/visual/dxgeneralsurf.sh,
mc/3D/CitcomS/branches/v2/visual/getcoord.sh,
mc/3D/CitcomS/branches/v2/visual/getlog.sh,
mc/3D/CitcomS/branches/v2/visual/getsurf.sh,
mc/3D/CitcomS/branches/v2/visual/parser.py,
mc/3D/CitcomS/branches/v2/visual/pasteCitcomData.sh,
mc/3D/CitcomS/branches/v2/visual/zslice.py, Make.mm, Makefile.am,
configure.ac, drivers/Citcom.c, drivers/Full/Make.mm,
drivers/Full/local.def, drivers/Make.mm, drivers/Makefile.am,
drivers/Regional/Make.mm, drivers/Regional/local.def,
drivers/local.def, etc/Make.mm, etc/Makefile.am,
etc/__vault__.odb, etc/full-sphere.odb, etc/full.odb,
etc/globus.odb, etc/incomp-newtonian.odb,
etc/incomp-non-newtonian.odb, etc/lam-mpi.odb, etc/lsf.odb,
etc/mpich.odb, etc/pbs.odb, etc/regional-sphere.odb,
etc/regional.odb, etc/temp.odb, examples/Cookbook1/cookbook1.sh,
examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh,
examples/Cookbook7/cookbook7.sh, examples/Makefile.am,
examples/example1.sh, lib/Common/Advection_diffusion.c,
lib/Common/Citcom_init.c, lib/Common/Construct_arrays.c,
lib/Common/Convection.c, lib/Common/Drive_solvers.c,
lib/Common/Element_calculations.c,
lib/Common/General_matrix_functions.c,
lib/Common/Global_operations.c, lib/Common/Initial_temperature.c,
lib/Common/Instructions.c, lib/Common/Interuption.c,
lib/Common/Make.mm, lib/Common/Makefile.am,
lib/Common/Nodal_mesh.c, lib/Common/Obsolete.c,
lib/Common/Output.c, lib/Common/Pan_problem_misc_functions.c,
lib/Common/Parsing.c, lib/Common/Phase_change.c,
lib/Common/Problem_related.c, lib/Common/Process_buoyancy.c,
lib/Common/Shape_functions.c, lib/Common/Size_does_matter.c,
lib/Common/Solver_conj_grad.c, lib/Common/Solver_multigrid.c,
lib/Common/Sphere_harmonics.c, lib/Common/Stokes_flow_Incomp.c,
lib/Common/Topo_gravity.c, lib/Common/Tracer_advection.c,
lib/Common/Viscosity_structures.c, lib/Common/advection.h,
lib/Common/advection_diffusion.h, lib/Common/citcom_init.h,
lib/Common/convection_variables.h, lib/Common/drive_solvers.h,
lib/Common/element_definitions.h, lib/Common/global_defs.h,
lib/Common/initial_temperature.h, lib/Common/interuption.h,
lib/Common/lith_age.h, lib/Common/local.def, lib/Common/output.h,
lib/Common/parallel_related.h, lib/Common/parsing.h,
lib/Common/phase_change.h, lib/Common/sphere_communication.h,
lib/Common/temperature_descriptions.h, lib/Common/tracer_defs.h,
lib/Common/viscosity_descriptions.h,
lib/Full/Boundary_conditions.c, lib/Full/Geometry_cartesian.c,
lib/Full/Lith_age.c, lib/Full/Make.mm, lib/Full/Makefile.am,
lib/Full/Obsolete.c, lib/Full/Parallel_related.c,
lib/Full/Read_input_from_files.c, lib/Full/Sphere_related.c,
lib/Full/Version_dependent.c, lib/Full/local.def, lib/Make.mm,
lib/Makefile.am, lib/Regional/Boundary_conditions.c,
lib/Regional/Geometry_cartesian.c, lib/Regional/Lith_age.c,
lib/Regional/Make.mm, lib/Regional/Makefile.am,
lib/Regional/Obsolete.c, lib/Regional/Parallel_related.c,
lib/Regional/Read_input_from_files.c,
lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c,
lib/Regional/local.def, lib/local.def, local.def,
module/Exchanger/AreaWeightedNormal.cc,
module/Exchanger/AreaWeightedNormal.h,
module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/BoundaryVTInlet.cc,
module/Exchanger/BoundaryVTInlet.h,
module/Exchanger/CitcomInterpolator.cc,
module/Exchanger/CitcomInterpolator.h,
module/Exchanger/CitcomSource.cc,
module/Exchanger/CitcomSource.h, module/Exchanger/Convertor.cc,
module/Exchanger/Convertor.h,
module/Exchanger/Exchangermodule.cc,
module/Exchanger/Interior.cc, module/Exchanger/Interior.h,
module/Exchanger/Make.mm, module/Exchanger/Makefile.am,
module/Exchanger/SIUnit.cc, module/Exchanger/SIUnit.h,
module/Exchanger/SInlet.cc, module/Exchanger/SInlet.h,
module/Exchanger/SVTInlet.cc, module/Exchanger/SVTInlet.h,
module/Exchanger/SVTOutlet.cc, module/Exchanger/SVTOutlet.h,
module/Exchanger/TInlet.cc, module/Exchanger/TInlet.h,
module/Exchanger/TOutlet.cc, module/Exchanger/TOutlet.h,
module/Exchanger/VOutlet.cc, module/Exchanger/VOutlet.h,
module/Exchanger/VTInlet.cc, module/Exchanger/VTInlet.h,
module/Exchanger/VTOutlet.cc, module/Exchanger/VTOutlet.h,
module/Exchanger/bindings.cc, module/Exchanger/bindings.h,
module/Exchanger/exceptions.cc, module/Exchanger/exceptions.h,
module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h,
module/Exchanger/global_bbox.cc, module/Exchanger/global_bbox.h,
module/Exchanger/initTemperature.cc,
module/Exchanger/initTemperature.h,
module/Exchanger/inlets_outlets.cc,
module/Exchanger/inlets_outlets.h, module/Exchanger/misc.cc,
module/Exchanger/misc.h, module/Full/Fullmodule.cc,
module/Full/Make.mm, module/Full/Makefile.am,
module/Full/local.def, module/Make.mm, module/Makefile.am,
module/Regional/Make.mm, module/Regional/Makefile.am,
module/Regional/Regionalmodule.cc, module/Regional/advdiffu.cc,
module/Regional/advdiffu.h, module/Regional/bindings.cc,
module/Regional/bindings.h, module/Regional/exceptions.cc,
module/Regional/exceptions.h,
module/Regional/initial_conditions.cc,
module/Regional/initial_conditions.h, module/Regional/local.def,
module/Regional/mesher.cc, module/Regional/mesher.h,
module/Regional/misc.cc, module/Regional/misc.h,
module/Regional/outputs.cc, module/Regional/outputs.h,
module/Regional/setProperties.cc,
module/Regional/setProperties.h,
module/Regional/stokes_solver.cc,
module/Regional/stokes_solver.h,
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/Advection_diffusion/Make.mm,
pyre/Components/Advection_diffusion/__init__.py,
pyre/Components/BC.py, pyre/Components/CitcomComponent.py,
pyre/Components/Const.py,
pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
pyre/Components/Exchanger/Inlet.py,
pyre/Components/Exchanger/Make.mm,
pyre/Components/Exchanger/Outlet.py,
pyre/Components/Exchanger/__init__.py, pyre/Components/IC.py,
pyre/Components/Launchers.py, pyre/Components/Make.mm,
pyre/Components/Param.py, pyre/Components/Phase.py,
pyre/Components/Sphere/FullSphere.py,
pyre/Components/Sphere/Make.mm,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Sphere/Sphere.py,
pyre/Components/Sphere/__init__.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Stokes_solver/Make.mm,
pyre/Components/Stokes_solver/__init__.py,
pyre/Components/Tracer.py, pyre/Components/Visc.py,
pyre/Components/__init__.py, pyre/Controller.py,
pyre/CoupledApp.py, pyre/Coupler.py, pyre/Layout.py,
pyre/Make.mm, pyre/Makefile.am, pyre/SimpleApp.py,
pyre/Solver/FullSolver.py, pyre/Solver/Make.mm,
pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py,
pyre/Solver/__init__.py, pyre/__init__.py.in, pyre/local.def,
tests/Make.mm, tests/Makefile.am, tests/array2d.cc,
tests/asap.py, tests/citcomsfull.sh.in,
tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in,
tests/exchange.py, tests/hrothgar.py, tests/local.def,
tests/signon.py, tests/test1.sh, tests/test2.sh, tests/test5.sh,
visual/Make.mm, visual/Makefile.am, visual/autocombine.py,
visual/batchcombine.py, visual/batchpaste.sh,
visual/batchsurf.py, visual/combine.py, visual/combinesurf.py,
visual/dxgeneral.sh, visual/dxgeneralsurf.sh, visual/getcoord.sh,
visual/getlog.sh, visual/getsurf.sh, visual/parser.py,
visual/pasteCitcomData.sh, visual/zslice.py: Changed CitcomS
license header text to GNU GPL.
2005-10-04 02:53 leif
* mc/3D/CitcomS/branches/v2/AUTHORS,
mc/3D/CitcomS/branches/v2/COPYING,
mc/3D/CitcomS/branches/v2/ChangeLog,
mc/3D/CitcomS/branches/v2/CitcomS.py-LICENSE.txt,
mc/3D/CitcomS/branches/v2/INSTALL,
mc/3D/CitcomS/branches/v2/Make.mm,
mc/3D/CitcomS/branches/v2/Makefile.am,
mc/3D/CitcomS/branches/v2/NEWS, mc/3D/CitcomS/branches/v2/README,
mc/3D/CitcomS/branches/v2/citcoms_profile,
mc/3D/CitcomS/branches/v2/configure.ac,
mc/3D/CitcomS/branches/v2/drivers/Full/Make.mm,
mc/3D/CitcomS/branches/v2/drivers/Full/local.def,
mc/3D/CitcomS/branches/v2/drivers/Make.mm,
mc/3D/CitcomS/branches/v2/drivers/Makefile.am,
mc/3D/CitcomS/branches/v2/drivers/Regional/Make.mm,
mc/3D/CitcomS/branches/v2/drivers/Regional/local.def,
mc/3D/CitcomS/branches/v2/drivers/local.def,
mc/3D/CitcomS/branches/v2/etc/CitcomS.pml.in,
mc/3D/CitcomS/branches/v2/etc/Make.mm,
mc/3D/CitcomS/branches/v2/etc/Makefile.am,
mc/3D/CitcomS/branches/v2/etc/__vault__.odb,
mc/3D/CitcomS/branches/v2/etc/full-sphere.odb,
mc/3D/CitcomS/branches/v2/etc/full.odb,
mc/3D/CitcomS/branches/v2/etc/globus.odb,
mc/3D/CitcomS/branches/v2/etc/incomp-newtonian.odb,
mc/3D/CitcomS/branches/v2/etc/incomp-non-newtonian.odb,
mc/3D/CitcomS/branches/v2/etc/lam-mpi.odb,
mc/3D/CitcomS/branches/v2/etc/lsf.odb,
mc/3D/CitcomS/branches/v2/etc/mpich.odb,
mc/3D/CitcomS/branches/v2/etc/pbs.odb,
mc/3D/CitcomS/branches/v2/etc/regional-sphere.odb,
mc/3D/CitcomS/branches/v2/etc/regional.odb,
mc/3D/CitcomS/branches/v2/etc/temp.odb,
mc/3D/CitcomS/branches/v2/examples/Cookbook2/cookbook2.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook3/cookbook3.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook4/cookbook4.sh,
mc/3D/CitcomS/branches/v2/examples/Cookbook5/cookbook5.sh,
mc/3D/CitcomS/branches/v2/examples/Makefile.am,
mc/3D/CitcomS/branches/v2/examples/example1.sh,
mc/3D/CitcomS/branches/v2/lib/Common/Element_calculations.c,
mc/3D/CitcomS/branches/v2/lib/Common/Make.mm,
mc/3D/CitcomS/branches/v2/lib/Common/Makefile.am,
mc/3D/CitcomS/branches/v2/lib/Common/Obsolete.c,
mc/3D/CitcomS/branches/v2/lib/Common/Pan_problem_misc_functions.c,
mc/3D/CitcomS/branches/v2/lib/Common/Size_does_matter.c,
mc/3D/CitcomS/branches/v2/lib/Common/Topo_gravity.c,
mc/3D/CitcomS/branches/v2/lib/Common/Tracer_advection.c,
mc/3D/CitcomS/branches/v2/lib/Common/advection_diffusion.h,
mc/3D/CitcomS/branches/v2/lib/Common/citcom_init.h,
mc/3D/CitcomS/branches/v2/lib/Common/drive_solvers.h,
mc/3D/CitcomS/branches/v2/lib/Common/global_defs.h,
mc/3D/CitcomS/branches/v2/lib/Common/local.def,
mc/3D/CitcomS/branches/v2/lib/Common/output.h,
mc/3D/CitcomS/branches/v2/lib/Common/parallel_related.h,
mc/3D/CitcomS/branches/v2/lib/Full/Boundary_conditions.c,
mc/3D/CitcomS/branches/v2/lib/Full/Make.mm,
mc/3D/CitcomS/branches/v2/lib/Full/Makefile.am,
mc/3D/CitcomS/branches/v2/lib/Full/local.def,
mc/3D/CitcomS/branches/v2/lib/Make.mm,
mc/3D/CitcomS/branches/v2/lib/Makefile.am,
mc/3D/CitcomS/branches/v2/lib/Regional/Boundary_conditions.c,
mc/3D/CitcomS/branches/v2/lib/Regional/Make.mm,
mc/3D/CitcomS/branches/v2/lib/Regional/Makefile.am,
mc/3D/CitcomS/branches/v2/lib/Regional/local.def,
mc/3D/CitcomS/branches/v2/lib/local.def,
mc/3D/CitcomS/branches/v2/local.def,
mc/3D/CitcomS/branches/v2/module/Full/Fullmodule.cc,
mc/3D/CitcomS/branches/v2/module/Full/Make.mm,
mc/3D/CitcomS/branches/v2/module/Full/Makefile.am,
mc/3D/CitcomS/branches/v2/module/Full/local.def,
mc/3D/CitcomS/branches/v2/module/Make.mm,
mc/3D/CitcomS/branches/v2/module/Makefile.am,
mc/3D/CitcomS/branches/v2/module/Regional/Make.mm,
mc/3D/CitcomS/branches/v2/module/Regional/Makefile.am,
mc/3D/CitcomS/branches/v2/module/Regional/Regionalmodule.cc,
mc/3D/CitcomS/branches/v2/module/Regional/advdiffu.cc,
mc/3D/CitcomS/branches/v2/module/Regional/advdiffu.h,
mc/3D/CitcomS/branches/v2/module/Regional/bindings.cc,
mc/3D/CitcomS/branches/v2/module/Regional/bindings.h,
mc/3D/CitcomS/branches/v2/module/Regional/exceptions.cc,
mc/3D/CitcomS/branches/v2/module/Regional/exceptions.h,
mc/3D/CitcomS/branches/v2/module/Regional/initial_conditions.cc,
mc/3D/CitcomS/branches/v2/module/Regional/initial_conditions.h,
mc/3D/CitcomS/branches/v2/module/Regional/local.def,
mc/3D/CitcomS/branches/v2/module/Regional/mesher.cc,
mc/3D/CitcomS/branches/v2/module/Regional/mesher.h,
mc/3D/CitcomS/branches/v2/module/Regional/misc.cc,
mc/3D/CitcomS/branches/v2/module/Regional/misc.h,
mc/3D/CitcomS/branches/v2/module/Regional/outputs.cc,
mc/3D/CitcomS/branches/v2/module/Regional/outputs.h,
mc/3D/CitcomS/branches/v2/module/Regional/setProperties.cc,
mc/3D/CitcomS/branches/v2/module/Regional/setProperties.h,
mc/3D/CitcomS/branches/v2/module/Regional/stokes_solver.cc,
mc/3D/CitcomS/branches/v2/module/Regional/stokes_solver.h,
mc/3D/CitcomS/branches/v2/pyre/Components/Advection_diffusion/Advection_diffusion.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Advection_diffusion/Make.mm,
mc/3D/CitcomS/branches/v2/pyre/Components/Advection_diffusion/__init__.py,
mc/3D/CitcomS/branches/v2/pyre/Components/BC.py,
mc/3D/CitcomS/branches/v2/pyre/Components/CitcomComponent.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Const.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/CoarseGridExchanger.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Exchanger.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/FineGridExchanger.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Inlet.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Make.mm,
mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/Outlet.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Exchanger/__init__.py,
mc/3D/CitcomS/branches/v2/pyre/Components/IC.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Launchers.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Make.mm,
mc/3D/CitcomS/branches/v2/pyre/Components/Param.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Phase.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/FullSphere.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/Make.mm,
mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/RegionalSphere.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/Sphere.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Sphere/__init__.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Stokes_solver/Incompressible.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Stokes_solver/Make.mm,
mc/3D/CitcomS/branches/v2/pyre/Components/Stokes_solver/__init__.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Tracer.py,
mc/3D/CitcomS/branches/v2/pyre/Components/Visc.py,
mc/3D/CitcomS/branches/v2/pyre/Components/__init__.py,
mc/3D/CitcomS/branches/v2/pyre/CoupledApp.py,
mc/3D/CitcomS/branches/v2/pyre/Coupler.py,
mc/3D/CitcomS/branches/v2/pyre/Layout.py,
mc/3D/CitcomS/branches/v2/pyre/Make.mm,
mc/3D/CitcomS/branches/v2/pyre/Makefile.am,
mc/3D/CitcomS/branches/v2/pyre/SimpleApp.py,
mc/3D/CitcomS/branches/v2/pyre/Solver/FullSolver.py,
mc/3D/CitcomS/branches/v2/pyre/Solver/Make.mm,
mc/3D/CitcomS/branches/v2/pyre/Solver/RegionalSolver.py,
mc/3D/CitcomS/branches/v2/pyre/Solver/Solver.py,
mc/3D/CitcomS/branches/v2/pyre/Solver/__init__.py,
mc/3D/CitcomS/branches/v2/pyre/__init__.py,
mc/3D/CitcomS/branches/v2/pyre/__init__.py.in,
mc/3D/CitcomS/branches/v2/pyre/local.def,
mc/3D/CitcomS/branches/v2/tests/Make.mm,
mc/3D/CitcomS/branches/v2/tests/Makefile.am,
mc/3D/CitcomS/branches/v2/tests/asap.py,
mc/3D/CitcomS/branches/v2/tests/citcomsfull.sh,
mc/3D/CitcomS/branches/v2/tests/citcomsfull.sh.in,
mc/3D/CitcomS/branches/v2/tests/citcomsregional.sh,
mc/3D/CitcomS/branches/v2/tests/citcomsregional.sh.in,
mc/3D/CitcomS/branches/v2/tests/hrothgar.py,
mc/3D/CitcomS/branches/v2/tests/local.def,
mc/3D/CitcomS/branches/v2/tests/signon.py,
mc/3D/CitcomS/branches/v2/visual/Make.mm,
mc/3D/CitcomS/branches/v2/visual/Makefile.am,
mc/3D/CitcomS/branches/v2/visual/batchcombine.py,
mc/3D/CitcomS/branches/v2/visual/batchpaste.sh,
mc/3D/CitcomS/branches/v2/visual/batchsurf.py,
mc/3D/CitcomS/branches/v2/visual/combine.py,
mc/3D/CitcomS/branches/v2/visual/combinesurf.py,
mc/3D/CitcomS/branches/v2/visual/dxgeneral.sh,
mc/3D/CitcomS/branches/v2/visual/dxgeneralsurf.sh,
mc/3D/CitcomS/branches/v2/visual/getcoord.sh,
mc/3D/CitcomS/branches/v2/visual/getlog.sh,
mc/3D/CitcomS/branches/v2/visual/getsurf.sh,
mc/3D/CitcomS/branches/v2/visual/pasteCitcomData.sh, Makefile.am,
tests/Make.mm: Ported GNU Build System from CitcomS trunk to v2
branch.
2005-10-04 00:34 leif
* pyre/Controller, pyre/Coupler, pyre/Facilities, pyre/Layout:
Nuked empty directories.
2005-10-01 01:17 leif
* ChangeLog: Strip "mc/3D/CitcomS/trunk" directory prefix. By the
way, this file is generated with svn2cl
(http://ch.tudelft.nl/~arthur/svn2cl/) using the command "svn log
--xml --verbose | xsltproc --stringparam strip-prefix
mc/3D/CitcomS/trunk svn2cl.xsl - > ChangeLog".
2005-10-01 01:01 leif
* AUTHORS, COPYING, ChangeLog, CitcomS.py-LICENSE.txt, INSTALL,
NEWS, README: Added various GNU standard files, including the
GPL.
2005-09-30 23:48 leif
* module/Full: Doh! Restored svn:ignore'ing of those ridiculous
symlinks used by Make.mm.
2005-09-30 22:39 leif
* ., drivers, etc, examples, lib, lib/Common, lib/Full,
lib/Regional, module, module/Exchanger, module/Full,
module/Regional, pyre, tests, visual: Ignore files generated by
Autoconf/Automake/Libtool.
2005-09-30 17:59 leif
* configure.ac: Push/pop C++ around MPI tests, which are now
sensitive to the current language. Made sure that
'--without-pyre' works in the absence of a C++ compiler (tested
on Hrothgar). When building with Pyre modules, fail if a C++
compiler is not found.
2005-09-28 23:26 leif
* configure.ac, etc/CitcomS.pml.in, etc/Make.mm, etc/Makefile.am,
pyre/Components/Launchers.py, pyre/CoupledApp.py, pyre/Make.mm,
pyre/Makefile.am, pyre/SimpleApp.py, pyre/__init__.py,
pyre/__init__.py.in, tests/Make.mm, tests/Makefile.am,
tests/citcomsfull.sh.in, tests/citcomsregional.sh.in,
tests/coupledcitcoms.sh.in: Add ${pythondir} to PYTHONPATH before
checking for Python modules, so that installing multiple packages
to a single PREFIX "just works". This also attempts to simulate
the final installation environment, which might make a difference
in unusual cases. Also, 'sed' the install-time PYTHONPATH into
CitComS scripts (instead of an explicit list of @pythondir@'s).
Added _getPrivateDepositoryLocations() and CitcomS.pml. Changed
"etc/citcoms" to "etc/CitcomS" for consistency with the Python
package name. Add PACKAGE_VERSION to __init__.py, and added
pyconfig-generated config.py. Freeze the full path to 'mpirun'
and 'mpipython.exe' at 'configure' time. First crack at batch
system configuration.
2005-09-21 00:03 leif
* Makefile.am, configure.ac,
lib/Common/Pan_problem_misc_functions.c,
lib/Common/Tracer_advection.c, module/Exchanger/Makefile.am,
module/Full/Makefile.am, module/Regional/Makefile.am,
tests/Make.mm, tests/Makefile.am, tests/citcomsfull.sh.in,
tests/citcomsregional.sh.in, tests/coupledcitcoms.sh.in: Utilize
my new 'pyconfig' facility to automatically slurp config info
from Pythia, Exchanger. Changed contact e-mail to cig-mc; other
misc. changes.
2005-09-09 19:49 leif
* Makefile.am, configure.ac, drivers/Makefile.am, etc/Makefile.am,
examples/Makefile.am, lib/Common/Makefile.am,
lib/Full/Makefile.am, lib/Makefile.am, lib/Regional/Makefile.am,
module/Exchanger/Makefile.am, module/Full/Makefile.am,
module/Makefile.am, module/Regional/Makefile.am,
pyre/Makefile.am, tests/Makefile.am, visual/Makefile.am: Added Id
keyword property to configure.ac, Makefile.am.
2005-09-09 19:41 leif
* ., Makefile.am, configure.ac, drivers/Makefile.am,
etc/Makefile.am, examples/Makefile.am, lib/Common/Makefile.am,
lib/Full/Makefile.am, lib/Makefile.am, lib/Regional/Makefile.am,
module/Exchanger/Makefile.am, module/Full, module/Full/Make.mm,
module/Full/Makefile.am, module/Make.mm, module/Makefile.am,
module/Regional/Makefile.am, pyre/Components/Launchers.py,
pyre/Makefile.am, pyre/Solver/FullSolver.py,
pyre/Solver/RegionalSolver.py, tests/Make.mm, tests/Makefile.am,
tests/citcomsfull.sh, tests/citcomsfull.sh.in,
tests/citcomsregional.sh, tests/citcomsregional.sh.in,
tests/coupledcitcoms.sh, tests/coupledcitcoms.sh.in,
visual/Makefile.am: Added files for the GNU Build System.
2005-08-29 19:28 leif
* Make.mm, citcoms_profile, drivers/Full/Make.mm,
drivers/Full/local.def, drivers/Make.mm,
drivers/Regional/Make.mm, drivers/Regional/local.def,
drivers/local.def, etc/Make.mm, etc/__vault__.odb,
etc/full-sphere.odb, etc/full.odb, etc/globus.odb,
etc/incomp-newtonian.odb, etc/incomp-non-newtonian.odb,
etc/lam-mpi.odb, etc/lsf.odb, etc/mpich.odb, etc/pbs.odb,
etc/regional-sphere.odb, etc/regional.odb, etc/temp.odb,
examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh,
examples/Cookbook7/cookbook7.sh, examples/example1.sh,
lib/Common/Element_calculations.c, lib/Common/Make.mm,
lib/Common/Obsolete.c, lib/Common/Size_does_matter.c,
lib/Common/Topo_gravity.c, lib/Common/local.def,
lib/Full/Boundary_conditions.c, lib/Full/Make.mm,
lib/Full/local.def, lib/Make.mm,
lib/Regional/Boundary_conditions.c, lib/Regional/Make.mm,
lib/Regional/local.def, lib/local.def, local.def,
module/Exchanger/AreaWeightedNormal.cc,
module/Exchanger/AreaWeightedNormal.h,
module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/BoundaryVTInlet.cc,
module/Exchanger/BoundaryVTInlet.h,
module/Exchanger/CitcomInterpolator.cc,
module/Exchanger/CitcomInterpolator.h,
module/Exchanger/CitcomSource.cc,
module/Exchanger/CitcomSource.h, module/Exchanger/Convertor.cc,
module/Exchanger/Convertor.h,
module/Exchanger/Exchangermodule.cc,
module/Exchanger/Interior.cc, module/Exchanger/Interior.h,
module/Exchanger/Make.mm, module/Exchanger/SIUnit.cc,
module/Exchanger/SIUnit.h, module/Exchanger/SInlet.cc,
module/Exchanger/SInlet.h, module/Exchanger/SVTInlet.cc,
module/Exchanger/SVTInlet.h, module/Exchanger/SVTOutlet.cc,
module/Exchanger/SVTOutlet.h, module/Exchanger/TInlet.cc,
module/Exchanger/TInlet.h, module/Exchanger/TOutlet.cc,
module/Exchanger/TOutlet.h, module/Exchanger/VOutlet.cc,
module/Exchanger/VOutlet.h, module/Exchanger/VTInlet.cc,
module/Exchanger/VTInlet.h, module/Exchanger/VTOutlet.cc,
module/Exchanger/VTOutlet.h, module/Exchanger/bindings.cc,
module/Exchanger/bindings.h, module/Exchanger/exceptions.cc,
module/Exchanger/exceptions.h, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h, module/Exchanger/global_bbox.cc,
module/Exchanger/global_bbox.h,
module/Exchanger/initTemperature.cc,
module/Exchanger/initTemperature.h,
module/Exchanger/inlets_outlets.cc,
module/Exchanger/inlets_outlets.h, module/Exchanger/misc.cc,
module/Exchanger/misc.h, module/Full/Fullmodule.cc,
module/Full/Make.mm, module/Full/local.def, module/Make.mm,
module/Regional/Make.mm, module/Regional/Regionalmodule.cc,
module/Regional/advdiffu.cc, module/Regional/advdiffu.h,
module/Regional/bindings.cc, module/Regional/bindings.h,
module/Regional/exceptions.cc, module/Regional/exceptions.h,
module/Regional/initial_conditions.cc,
module/Regional/initial_conditions.h, module/Regional/local.def,
module/Regional/mesher.cc, module/Regional/mesher.h,
module/Regional/misc.cc, module/Regional/misc.h,
module/Regional/outputs.cc, module/Regional/outputs.h,
module/Regional/setProperties.cc,
module/Regional/setProperties.h,
module/Regional/stokes_solver.cc,
module/Regional/stokes_solver.h,
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/Advection_diffusion/Make.mm,
pyre/Components/Advection_diffusion/__init__.py,
pyre/Components/BC.py, pyre/Components/CitcomComponent.py,
pyre/Components/Const.py,
pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
pyre/Components/Exchanger/Inlet.py,
pyre/Components/Exchanger/Make.mm,
pyre/Components/Exchanger/Outlet.py,
pyre/Components/Exchanger/__init__.py, pyre/Components/IC.py,
pyre/Components/Launchers.py, pyre/Components/Make.mm,
pyre/Components/Param.py, pyre/Components/Phase.py,
pyre/Components/Sphere/FullSphere.py,
pyre/Components/Sphere/Make.mm,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Sphere/Sphere.py,
pyre/Components/Sphere/__init__.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Stokes_solver/Make.mm,
pyre/Components/Stokes_solver/__init__.py,
pyre/Components/Tracer.py, pyre/Components/Visc.py,
pyre/Components/__init__.py, pyre/CoupledApp.py, pyre/Coupler.py,
pyre/Layout.py, pyre/Make.mm, pyre/SimpleApp.py,
pyre/Solver/FullSolver.py, pyre/Solver/Make.mm,
pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py,
pyre/Solver/__init__.py, pyre/__init__.py, pyre/local.def,
tests/Make.mm, tests/array2d.cc, tests/asap.py,
tests/citcomsfull.sh, tests/citcomsregional.sh,
tests/coupledcitcoms.sh, tests/exchange.py, tests/hrothgar.py,
tests/local.def, tests/signon.py, tests/test1.sh, tests/test2.sh,
tests/test5.sh, visual/Make.mm, visual/autocombine.py,
visual/batchcombine.py, visual/batchpaste.sh,
visual/batchsurf.py, visual/combine.py, visual/combinesurf.py,
visual/dxgeneral.sh, visual/dxgeneralsurf.sh, visual/getcoord.sh,
visual/getlog.sh, visual/getsurf.sh, visual/miff2avi,
visual/miff2mpg, visual/parser.py, visual/pasteCitcomData.sh,
visual/zslice.py: Added executable property and 'Id' keyword
expansion.
2005-08-27 03:04 leif
* lib/Common/advection_diffusion.h, lib/Common/citcom_init.h,
lib/Common/drive_solvers.h, lib/Common/global_defs.h,
lib/Common/output.h, lib/Common/parallel_related.h,
module/Regional/advdiffu.cc,
module/Regional/initial_conditions.cc, module/Regional/mesher.cc,
module/Regional/misc.cc, module/Regional/outputs.cc,
module/Regional/stokes_solver.cc: Avoid 'extern "C" { #include
... }'; it causes problems with mpi++.h/mpicxx.h.
2005-07-27 08:58 leif
* etc/mpich.odb, pyre/Components/Launchers.py, pyre/SimpleApp.py:
Fixed it so that the uniprocessor examples work again. This
invovled creating CitcomS's own version of LauncherMPICH, and
tweaking the MPI launchers so that CitcomS re-execs itself under
'mpipython.exe' when it is run under plain old 'python'. Also:
made "--launcher.dry" work; ignore 'nodegen' in LauncherBatch (so
that the examples "just work" on the TeraGrid); added some 'tips'
("--launcher.help-properties"); added SimpleApp.usage().
2005-07-23 08:35 leif
* Make.mm, examples/Cookbook1/cookbook1.sh,
examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh,
examples/example1.sh, tests/Make.mm, tests/array2d.cc,
visual/Make.mm: General build clean-up: 'export' all the various
scripts to $EXPORT_ROOT/bin, so that goofy relative paths are not
needed (e.g., "../tests/citcomsregional.sh"); and so that the
'visual' directory doesn't have to be added to the PATH. I also
dusted-off 'array2d' -- it compiles and links now.
2005-07-23 08:00 leif
* module/Regional/misc.cc: Raise an exception -- instead of
crashing -- when pyCitcom_citcom_init() is passed a null
"mpi::Communicator *" argument.
2005-07-22 10:03 leif
* pyre/Components/Launchers.py: Switched from Python's '%' operator
to pyre.util.expandMacros(), so that I don't have to escape '%'
(e.g., --launcher.nodegen="n%03d"). Also, export key environment
variables to LAM/MPI jobs.
2005-07-22 05:55 leif
* lib/Common/Make.mm, lib/Common/local.def, lib/Full/Make.mm,
lib/Full/local.def, lib/Regional/Make.mm, lib/Regional/local.def:
Build with soflags to produce position-independent code. 'Export'
the resulting shared libraries.
2005-07-20 04:23 leif
* tests/citcomsfull.sh, tests/citcomsregional.sh,
tests/coupledcitcoms.sh: Use 'python' instead of 'mpipython.exe'
-- on some TeraGrid clusters, MPI programs cannot be run
directly.
2005-07-20 04:12 leif
* examples/ncsa.sh, examples/tacc.sh: Removed sample batch scripts,
which are obsoleted by my new launchers. Use "--launcher=pbs" or
"--launcher=lsf" on NCSA and TACC, respectively.
2005-07-20 04:07 leif
* etc/Make.mm, etc/globus.odb, etc/lam-mpi.odb, etc/lsf.odb,
etc/mpich.odb, etc/pbs.odb, pyre/Components/Launchers.py,
pyre/Components/Make.mm: Added Pyre launchers for LAM/MPI,
Globus, LSF, and PBS. This is their temporary home; they should
be incorporated into Pyre eventually.
2005-07-20 03:55 leif
* visual/batchpaste.sh: Merged revision 1.5.2.1 from CitcomS-2_x
branch to trunk: tan2: "a fix for single-processor (eg. laptop)".
2005-06-30 08:31 leif
* lib/Common/global_defs.h, module/Exchanger/Make.mm,
module/Full/Make.mm, module/Regional/Make.mm: Changes for Mac OS
X build.
2005-08-23 03:42 unknown_user
* pyre/Facilities/Make.mm, pyre/Facilities/Mesher.py,
pyre/Facilities/Solver.py, pyre/Facilities/TSolver.py,
pyre/Facilities/VSolver.py, pyre/Facilities/__init__.py: [vcp]
delete of edited revision with dead state
2005-06-18 04:24 leif
* pyre/Facilities/Make.mm, pyre/Facilities/Mesher.py,
pyre/Facilities/Solver.py, pyre/Facilities/TSolver.py,
pyre/Facilities/VSolver.py, pyre/Facilities/__init__.py,
pyre/Make.mm: Removed 'Facilities' directory -- no longer needed
under Pythia v0.8.
2005-06-18 04:20 leif
* examples/ncsa.sh, examples/tacc.sh: Added example batch scripts
for NCSA and TACC TeraGrid clusters.
2005-06-18 02:07 ces74
* visual/visFull.cfg, visual/visFull.net, visual/visRegional.cfg,
visual/visRegional.net, visual/visRegionalSurface.cfg,
visual/visRegionalSurface.net: * removed default paths to
input/output files. * removed absolute paths to macros.
2005-06-16 02:33 tan2
* visual/autocombine.py: script to automatically read input
parameters from input file and call batchcombine.py
2005-06-16 02:33 tan2
* visual/batchcombine.py: 1. moved parts of the script into
functions so that other scripts can import them. 2. raise
ValueError when the length of machinefile is not right
2005-06-16 02:30 tan2
* visual/parser.py: using new-style class
2005-06-16 01:27 tan2
* pyre/Components/Sphere/Sphere.py, pyre/Solver/Solver.py: print
messages to stderr instead of stdout
2005-06-14 23:47 leif
* module/Full/Make.mm, module/Regional/Make.mm: Corrected use of
-Xlinker.
2005-06-10 09:23 leif
* CitcomS.py-LICENSE.txt, drivers/Citcom.c, drivers/Full/Make.mm,
drivers/Full/local.def, drivers/Make.mm,
drivers/Regional/Make.mm, drivers/Regional/local.def,
drivers/local.def, etc/Make.mm, etc/__vault__.odb,
etc/full-sphere.odb, etc/full.odb, etc/incomp-newtonian.odb,
etc/incomp-non-newtonian.odb, etc/regional-sphere.odb,
etc/regional.odb, etc/temp.odb, examples/Cookbook1/cookbook1.sh,
examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
examples/Cookbook4/cookbook4.sh, examples/Cookbook5/cookbook5.sh,
examples/Cookbook7/cookbook7.sh, examples/example1.sh,
lib/Common/Advection_diffusion.c, lib/Common/Citcom_init.c,
lib/Common/Construct_arrays.c, lib/Common/Convection.c,
lib/Common/Drive_solvers.c, lib/Common/Element_calculations.c,
lib/Common/General_matrix_functions.c,
lib/Common/Global_operations.c, lib/Common/Initial_temperature.c,
lib/Common/Instructions.c, lib/Common/Interuption.c,
lib/Common/Make.mm, lib/Common/Nodal_mesh.c,
lib/Common/Obsolete.c, lib/Common/Output.c,
lib/Common/Pan_problem_misc_functions.c, lib/Common/Parsing.c,
lib/Common/Phase_change.c, lib/Common/Problem_related.c,
lib/Common/Process_buoyancy.c, lib/Common/Shape_functions.c,
lib/Common/Size_does_matter.c, lib/Common/Solver_conj_grad.c,
lib/Common/Solver_multigrid.c, lib/Common/Sphere_harmonics.c,
lib/Common/Stokes_flow_Incomp.c, lib/Common/Topo_gravity.c,
lib/Common/Tracer_advection.c, lib/Common/Viscosity_structures.c,
lib/Common/advection.h, lib/Common/advection_diffusion.h,
lib/Common/citcom_init.h, lib/Common/convection_variables.h,
lib/Common/drive_solvers.h, lib/Common/element_definitions.h,
lib/Common/global_defs.h, lib/Common/initial_temperature.h,
lib/Common/interuption.h, lib/Common/lith_age.h,
lib/Common/local.def, lib/Common/output.h,
lib/Common/parallel_related.h, lib/Common/parsing.h,
lib/Common/phase_change.h, lib/Common/sphere_communication.h,
lib/Common/temperature_descriptions.h, lib/Common/tracer_defs.h,
lib/Common/viscosity_descriptions.h,
lib/Full/Boundary_conditions.c, lib/Full/Geometry_cartesian.c,
lib/Full/Lith_age.c, lib/Full/Make.mm, lib/Full/Obsolete.c,
lib/Full/Parallel_related.c, lib/Full/Read_input_from_files.c,
lib/Full/Sphere_related.c, lib/Full/Version_dependent.c,
lib/Full/local.def, lib/Make.mm,
lib/Regional/Boundary_conditions.c,
lib/Regional/Geometry_cartesian.c, lib/Regional/Lith_age.c,
lib/Regional/Make.mm, lib/Regional/Obsolete.c,
lib/Regional/Parallel_related.c,
lib/Regional/Read_input_from_files.c,
lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c,
lib/Regional/local.def, lib/local.def, module/Full/Fullmodule.cc,
module/Full/Make.mm, module/Full/local.def, module/Make.mm,
module/Regional/Make.mm, module/Regional/Regionalmodule.cc,
module/Regional/advdiffu.cc, module/Regional/advdiffu.h,
module/Regional/bindings.cc, module/Regional/bindings.h,
module/Regional/exceptions.cc, module/Regional/exceptions.h,
module/Regional/initial_conditions.cc,
module/Regional/initial_conditions.h, module/Regional/local.def,
module/Regional/mesher.cc, module/Regional/mesher.h,
module/Regional/misc.cc, module/Regional/misc.h,
module/Regional/outputs.cc, module/Regional/outputs.h,
module/Regional/setProperties.cc,
module/Regional/setProperties.h,
module/Regional/stokes_solver.cc,
module/Regional/stokes_solver.h,
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/Advection_diffusion/Make.mm,
pyre/Components/Advection_diffusion/__init__.py,
pyre/Components/BC.py, pyre/Components/CitcomComponent.py,
pyre/Components/Const.py,
pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
pyre/Components/Exchanger/Inlet.py,
pyre/Components/Exchanger/Make.mm,
pyre/Components/Exchanger/Outlet.py,
pyre/Components/Exchanger/__init__.py, pyre/Components/IC.py,
pyre/Components/Make.mm, pyre/Components/Param.py,
pyre/Components/Phase.py, pyre/Components/Sphere/FullSphere.py,
pyre/Components/Sphere/Make.mm,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Sphere/Sphere.py,
pyre/Components/Sphere/__init__.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Stokes_solver/Make.mm,
pyre/Components/Stokes_solver/__init__.py,
pyre/Components/Tracer.py, pyre/Components/Visc.py,
pyre/Components/__init__.py, pyre/Controller.py,
pyre/CoupledApp.py, pyre/Coupler.py, pyre/Facilities/Make.mm,
pyre/Facilities/Mesher.py, pyre/Facilities/Solver.py,
pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py,
pyre/Facilities/__init__.py, pyre/Layout.py, pyre/Make.mm,
pyre/SimpleApp.py, pyre/Solver/FullSolver.py,
pyre/Solver/Make.mm, pyre/Solver/RegionalSolver.py,
pyre/Solver/Solver.py, pyre/Solver/__init__.py, pyre/__init__.py,
pyre/local.def, tests/Make.mm, tests/array2d.cc, tests/asap.py,
tests/citcomsfull.sh, tests/citcomsregional.sh,
tests/coupledcitcoms.sh, tests/exchange.py, tests/hrothgar.py,
tests/local.def, tests/signon.py, tests/test1.sh, tests/test2.sh,
tests/test5.sh, visual/batchcombine.py, visual/batchpaste.sh,
visual/batchsurf.py, visual/combine.py, visual/combinesurf.py,
visual/dxgeneral.sh, visual/dxgeneralsurf.sh, visual/getcoord.sh,
visual/getlog.sh, visual/getsurf.sh, visual/parser.py,
visual/pasteCitcomData.sh, visual/zslice.py: Added license text.
2005-06-08 11:02 tan2
* examples/Cookbook5/cookbook5.sh: 1. subsitute 'staging' with
'launcher' as required by pythia-0.8 2. removed unneccesary input
parameters
2005-06-08 08:55 leif
* pyre/CoupledApp.py, pyre/SimpleApp.py, pyre/Solver/FullSolver.py,
pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: Port from
pythia-0.4 to pythia-0.8, continued: use "factory=" instead of
"default=" in facilities where appropriate. The scripts
example1.sh and test5.sh seem to work now.
2005-06-06 06:41 tan2
* visual/parser.py: Parser class to parse CitcomS input file
2005-06-06 06:13 tan2
* visual/batchpaste.sh: execute 'cmd_copy' only if 'cmd_paste' was
finished without error
2005-06-04 04:51 leif
* Make.mm, etc, etc/Make.mm, etc/__vault__.odb,
etc/full-sphere.odb, etc/full.odb, etc/incomp-newtonian.odb,
etc/incomp-non-newtonian.odb, etc/regional-sphere.odb,
etc/regional.odb, etc/temp.odb, examples/Cookbook1/cookbook1.sh,
examples/Cookbook2/cookbook2.sh, examples/Cookbook3/cookbook3.sh,
examples/Cookbook4/cookbook4.sh, examples/Cookbook7/cookbook7.sh,
examples/example1.sh, module/Exchanger/AreaWeightedNormal.cc,
module/Exchanger/Boundary.cc,
module/Exchanger/CitcomInterpolator.cc,
module/Exchanger/CitcomSource.cc, module/Exchanger/Convertor.cc,
module/Exchanger/Interior.cc, module/Exchanger/Make.mm,
module/Exchanger/SInlet.cc, module/Exchanger/SVTInlet.cc,
module/Exchanger/SVTOutlet.cc, module/Exchanger/TInlet.cc,
module/Exchanger/TOutlet.cc, module/Exchanger/VOutlet.cc,
module/Exchanger/VTInlet.cc, module/Exchanger/VTOutlet.cc,
module/Exchanger/initTemperature.cc, module/Full/Make.mm,
module/Regional/Make.mm,
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/BC.py, pyre/Components/Const.py,
pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
pyre/Components/IC.py, pyre/Components/Param.py,
pyre/Components/Phase.py,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Sphere/Sphere.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Tracer.py, pyre/Components/Visc.py,
pyre/Controller.py, pyre/CoupledApp.py,
pyre/Facilities/Mesher.py, pyre/Facilities/Solver.py,
pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py,
pyre/Layout.py, pyre/SimpleApp.py, pyre/Solver/FullSolver.py,
pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py,
tests/exchange.py, tests/test1.sh, tests/test2.sh,
tests/test5.sh: Initial port from pythia-0.4 to pythia-0.8.
2005-05-28 12:27 ces74
* lib/Regional/Version_dependent.c,
module/Regional/setProperties.cc, pyre/Components/IC.py: * If a
user doesn't specify "blob_center", assign [-999.,-999.,-999] as
a default values in IC.py. * The real default values are assigned
in setProperties.cc * The distance calculation in
"construct_tic_from_input" modified. * A bug in
non-dimensionalizing half_space_age fixed.
2005-05-28 04:41 vlad
* examples/example1.sh: *** empty log message ***
2005-05-28 04:11 gurnis
* examples/Cookbook1/cookbook1.sh: *** empty log message ***
2005-05-28 01:39 vlad
* examples/Cookbook5/velocity,
examples/Cookbook5/velocity/bvel.dat0,
examples/Cookbook5/velocity/bvel.dat1,
examples/Cookbook5/velocity/bvel.dat10,
examples/Cookbook5/velocity/bvel.dat11,
examples/Cookbook5/velocity/bvel.dat12,
examples/Cookbook5/velocity/bvel.dat13,
examples/Cookbook5/velocity/bvel.dat14,
examples/Cookbook5/velocity/bvel.dat15,
examples/Cookbook5/velocity/bvel.dat16,
examples/Cookbook5/velocity/bvel.dat17,
examples/Cookbook5/velocity/bvel.dat18,
examples/Cookbook5/velocity/bvel.dat19,
examples/Cookbook5/velocity/bvel.dat2,
examples/Cookbook5/velocity/bvel.dat20,
examples/Cookbook5/velocity/bvel.dat21,
examples/Cookbook5/velocity/bvel.dat22,
examples/Cookbook5/velocity/bvel.dat23,
examples/Cookbook5/velocity/bvel.dat24,
examples/Cookbook5/velocity/bvel.dat25,
examples/Cookbook5/velocity/bvel.dat26,
examples/Cookbook5/velocity/bvel.dat27,
examples/Cookbook5/velocity/bvel.dat28,
examples/Cookbook5/velocity/bvel.dat29,
examples/Cookbook5/velocity/bvel.dat3,
examples/Cookbook5/velocity/bvel.dat30,
examples/Cookbook5/velocity/bvel.dat31,
examples/Cookbook5/velocity/bvel.dat32,
examples/Cookbook5/velocity/bvel.dat33,
examples/Cookbook5/velocity/bvel.dat34,
examples/Cookbook5/velocity/bvel.dat35,
examples/Cookbook5/velocity/bvel.dat36,
examples/Cookbook5/velocity/bvel.dat37,
examples/Cookbook5/velocity/bvel.dat38,
examples/Cookbook5/velocity/bvel.dat39,
examples/Cookbook5/velocity/bvel.dat4,
examples/Cookbook5/velocity/bvel.dat40,
examples/Cookbook5/velocity/bvel.dat41,
examples/Cookbook5/velocity/bvel.dat42,
examples/Cookbook5/velocity/bvel.dat43,
examples/Cookbook5/velocity/bvel.dat44,
examples/Cookbook5/velocity/bvel.dat45,
examples/Cookbook5/velocity/bvel.dat46,
examples/Cookbook5/velocity/bvel.dat47,
examples/Cookbook5/velocity/bvel.dat48,
examples/Cookbook5/velocity/bvel.dat49,
examples/Cookbook5/velocity/bvel.dat5,
examples/Cookbook5/velocity/bvel.dat50,
examples/Cookbook5/velocity/bvel.dat51,
examples/Cookbook5/velocity/bvel.dat52,
examples/Cookbook5/velocity/bvel.dat53,
examples/Cookbook5/velocity/bvel.dat54,
examples/Cookbook5/velocity/bvel.dat55,
examples/Cookbook5/velocity/bvel.dat56,
examples/Cookbook5/velocity/bvel.dat57,
examples/Cookbook5/velocity/bvel.dat58,
examples/Cookbook5/velocity/bvel.dat59,
examples/Cookbook5/velocity/bvel.dat6,
examples/Cookbook5/velocity/bvel.dat60,
examples/Cookbook5/velocity/bvel.dat61,
examples/Cookbook5/velocity/bvel.dat62,
examples/Cookbook5/velocity/bvel.dat63,
examples/Cookbook5/velocity/bvel.dat64,
examples/Cookbook5/velocity/bvel.dat65,
examples/Cookbook5/velocity/bvel.dat66,
examples/Cookbook5/velocity/bvel.dat67,
examples/Cookbook5/velocity/bvel.dat68,
examples/Cookbook5/velocity/bvel.dat69,
examples/Cookbook5/velocity/bvel.dat7,
examples/Cookbook5/velocity/bvel.dat70,
examples/Cookbook5/velocity/bvel.dat71,
examples/Cookbook5/velocity/bvel.dat8,
examples/Cookbook5/velocity/bvel.dat9: Velocity files
2005-05-28 01:38 vlad
* examples/Cookbook5/restart_files,
examples/Cookbook5/restart_files/cookbook5.velo.0.0,
examples/Cookbook5/restart_files/cookbook5.velo.1.0,
examples/Cookbook5/restart_files/cookbook5.velo.10.0,
examples/Cookbook5/restart_files/cookbook5.velo.11.0,
examples/Cookbook5/restart_files/cookbook5.velo.12.0,
examples/Cookbook5/restart_files/cookbook5.velo.13.0,
examples/Cookbook5/restart_files/cookbook5.velo.14.0,
examples/Cookbook5/restart_files/cookbook5.velo.15.0,
examples/Cookbook5/restart_files/cookbook5.velo.16.0,
examples/Cookbook5/restart_files/cookbook5.velo.17.0,
examples/Cookbook5/restart_files/cookbook5.velo.18.0,
examples/Cookbook5/restart_files/cookbook5.velo.19.0,
examples/Cookbook5/restart_files/cookbook5.velo.2.0,
examples/Cookbook5/restart_files/cookbook5.velo.20.0,
examples/Cookbook5/restart_files/cookbook5.velo.21.0,
examples/Cookbook5/restart_files/cookbook5.velo.22.0,
examples/Cookbook5/restart_files/cookbook5.velo.23.0,
examples/Cookbook5/restart_files/cookbook5.velo.24.0,
examples/Cookbook5/restart_files/cookbook5.velo.25.0,
examples/Cookbook5/restart_files/cookbook5.velo.26.0,
examples/Cookbook5/restart_files/cookbook5.velo.27.0,
examples/Cookbook5/restart_files/cookbook5.velo.28.0,
examples/Cookbook5/restart_files/cookbook5.velo.29.0,
examples/Cookbook5/restart_files/cookbook5.velo.3.0,
examples/Cookbook5/restart_files/cookbook5.velo.30.0,
examples/Cookbook5/restart_files/cookbook5.velo.31.0,
examples/Cookbook5/restart_files/cookbook5.velo.32.0,
examples/Cookbook5/restart_files/cookbook5.velo.33.0,
examples/Cookbook5/restart_files/cookbook5.velo.34.0,
examples/Cookbook5/restart_files/cookbook5.velo.35.0,
examples/Cookbook5/restart_files/cookbook5.velo.36.0,
examples/Cookbook5/restart_files/cookbook5.velo.37.0,
examples/Cookbook5/restart_files/cookbook5.velo.38.0,
examples/Cookbook5/restart_files/cookbook5.velo.39.0,
examples/Cookbook5/restart_files/cookbook5.velo.4.0,
examples/Cookbook5/restart_files/cookbook5.velo.40.0,
examples/Cookbook5/restart_files/cookbook5.velo.41.0,
examples/Cookbook5/restart_files/cookbook5.velo.42.0,
examples/Cookbook5/restart_files/cookbook5.velo.43.0,
examples/Cookbook5/restart_files/cookbook5.velo.44.0,
examples/Cookbook5/restart_files/cookbook5.velo.45.0,
examples/Cookbook5/restart_files/cookbook5.velo.46.0,
examples/Cookbook5/restart_files/cookbook5.velo.47.0,
examples/Cookbook5/restart_files/cookbook5.velo.48.0,
examples/Cookbook5/restart_files/cookbook5.velo.49.0,
examples/Cookbook5/restart_files/cookbook5.velo.5.0,
examples/Cookbook5/restart_files/cookbook5.velo.50.0,
examples/Cookbook5/restart_files/cookbook5.velo.51.0,
examples/Cookbook5/restart_files/cookbook5.velo.52.0,
examples/Cookbook5/restart_files/cookbook5.velo.53.0,
examples/Cookbook5/restart_files/cookbook5.velo.54.0,
examples/Cookbook5/restart_files/cookbook5.velo.55.0,
examples/Cookbook5/restart_files/cookbook5.velo.56.0,
examples/Cookbook5/restart_files/cookbook5.velo.57.0,
examples/Cookbook5/restart_files/cookbook5.velo.58.0,
examples/Cookbook5/restart_files/cookbook5.velo.59.0,
examples/Cookbook5/restart_files/cookbook5.velo.6.0,
examples/Cookbook5/restart_files/cookbook5.velo.60.0,
examples/Cookbook5/restart_files/cookbook5.velo.61.0,
examples/Cookbook5/restart_files/cookbook5.velo.62.0,
examples/Cookbook5/restart_files/cookbook5.velo.63.0,
examples/Cookbook5/restart_files/cookbook5.velo.7.0,
examples/Cookbook5/restart_files/cookbook5.velo.8.0,
examples/Cookbook5/restart_files/cookbook5.velo.9.0: Restart
files
2005-05-28 01:35 vlad
* examples/Cookbook5, examples/Cookbook5/cookbook5.sh,
examples/Cookbook5/coor.dat: Cookbook5 and coordinate files
2005-05-25 08:22 tan2
* visual/zslice.py: changed the hard-wire path (/usr/bin/python) to
run-time dep. path
2005-05-25 04:28 tan2
* visual/zslice.py: a utility script to slize horizontal layers
from CitcomS output. See docstring for usage.
2005-05-25 01:12 leif
* module/Make.mm: Prefer "$(MM)" to "mm".
2005-05-24 05:15 ces74
* examples/Cookbook7, examples/Cookbook7/README,
examples/Cookbook7/cookbook7.sh, examples/Cookbook7/coord.dat: *
adding a script to run the Cookbook7 example and coord.dat file.
* README for some additional information.
2005-05-24 05:00 ces74
* lib/Common/Initial_temperature.c,
lib/Common/convection_variables.h, lib/Regional/Sphere_related.c,
lib/Regional/Version_dependent.c,
module/Regional/setProperties.cc, pyre/Components/IC.py: * added
new parameters to control a hot blob as temperature IC. - One can
specify three parameters: 1. Coordinates(theta,fi,r) of the
center. 2. Radius. 3. The amount of temperature increase/decrease
within the blob. - Currently works only for the Regional version.
- CitcomS variable name: convection.blob_center,
convection.blob_radius, convection.blob_dT - Pyre parameter name:
solver.ic.blob_center, solver.ic.blob_radius, solver.ic.blob_dT
- it is required to set "solver.ic.tic_method=2"
* the format of coordinates file has been modified. - "nsd=1" is
not recognized as "%s%d" on some machine. - now it should be
"nsd= 1" to be read as "%s %d".
2005-05-20 05:39 leif
* module/Exchanger/CitcomInterpolator.cc,
module/Exchanger/global_bbox.cc,
module/Regional/setProperties.cc: Include <cmath> in various
files. Fixes compilation errors with GCC v3.4.3.
2005-05-20 05:01 ces74
* module/Exchanger/initTemperature.cc: * added a new function for
the initial temperature field. - called "hot_blob_lith" - Thermal
boudnary layer on top + one hot bloc at the center.
2005-05-19 01:27 leif
* lib/Regional/Boundary_conditions.c: Added a prototype for
temperatures_conform_bcs() -- fixes compilation failure with GCC
v3.4.3.
2005-05-18 08:57 tan2
* tests/test5.sh: test for coupled run
2005-05-18 03:54 tan2
* module/Exchanger/Make.mm: using rpath to specify runtime library
path
2005-05-18 02:45 tan2
* module/Full/Make.mm, module/Regional/Make.mm: using rpath to
specify runtime library path
2005-05-17 07:35 tan2
* module/Full/Make.mm, module/Regional/Make.mm: the full path of
shared library is given, otherwise g++ can compile but the
program couldn't find the shared library at the run time
2005-05-17 06:53 vlad
* lib/Common/Output.c, lib/Common/Tracer_advection.c,
lib/Common/tracer_defs.h: 3D MPI tracer-advection code
2005-04-11 19:09 steve
* lib/Common/Make.mm, lib/Full/Make.mm, lib/Regional/Make.mm:
facelifted to work with new "config" repository (cvs -d
:pserver:config@cvs.cacr.caltech.edu:/config co config).
I think this will still work with the old config... Eh you may
want to check.
2005-03-30 10:34 vlad
* lib/Common/Output.c, lib/Common/Tracer_advection.c,
lib/Common/tracer_defs.h: *** empty log message ***
2005-03-30 10:27 vlad
* lib/Common/Output.c, lib/Common/Tracer_advection.c,
lib/Common/tracer_defs.h: *** empty log message ***
2005-03-11 12:23 steve
* module/Exchanger/Make.mm: Added EXCHANGER_INCDIR and
EXCHANGER_LIBDIR, as in my case, I do not build exchanger into
either pythia's or citcom's build root (but into its own)
2005-03-11 08:24 vlad
* lib/Common/Output.c, lib/Common/Phase_change.c: *** empty log
message ***
2005-03-09 06:24 vlad
* lib/Common/Tracer_advection.c: The tracer code only works in root
processor
2005-02-18 08:13 tan2
* pyre/Components/IC.py: fixed a bug in the validator of
'tic_method'
2005-02-18 07:15 tan2
* module/Regional/setProperties.cc: added new parameter
'tic_method' and 'half_space_age'
2005-02-18 06:57 tan2
* pyre/Components/IC.py: 1. added validator to some of the input.
2. added new parameter 'tic_method' and 'half_space_age'.
2005-02-18 06:14 tan2
* lib/Full/Version_dependent.c, lib/Regional/Version_dependent.c:
implementation of cooling plate temperature is pending.
2005-02-18 06:12 tan2
* lib/Common/Initial_temperature.c,
lib/Common/convection_variables.h: Added new input parameter:
tic_method. When it is 0 (default), the temperature is a linear
profile + perturbation at some layers. When it is 1, the
temperature is isothermal (== bottom b.c.) + uniformly cold plate
(thickness specified by 'half_space_age').
2005-02-05 02:51 ces74
* module/Exchanger/SInlet.cc, module/Exchanger/SInlet.h,
module/Exchanger/bindings.cc, module/Exchanger/inlets_outlets.cc,
module/Exchanger/inlets_outlets.h: * bindings for the SInlet
class added. * setSBCFlag() method added to SInlet.
2005-02-03 05:49 tan2
* module/Exchanger/Boundary.cc: fixed a bug in finding boundary
nodes and rearraged code
2005-01-29 08:23 ces74
* pyre/Components/Exchanger/Inlet.py: * SInlet class added
2005-01-29 08:15 ces74
* module/Exchanger/Make.mm, module/Exchanger/SIUnit.cc,
module/Exchanger/SInlet.cc, module/Exchanger/SInlet.h: * added a
new class SInlet to receive stress from the coupled solver. *
"stress_factor" defined in SIUnit.cc
2005-01-29 03:20 tan2
* module/Exchanger/Make.mm: removed redudant include and library
path. PYTHIA_INCDIR and PYTHIA_LIBDIR must be defined.
2005-01-27 06:10 tan2
* lib/Common/Tracer_advection.c: removed tracer_output(), which is
replaced by output_tracer() in Output.c
2005-01-27 06:05 tan2
* drivers/Citcom.c: removed calls to tracer_output(), which is
replaced by output_tracer() in Output.c
2005-01-26 07:01 ces74
* lib/Common/Instructions.c: * removed a useless block of code
2005-01-26 04:05 tan2
* lib/Common/Tracer_advection.c: 1. Commented out part of the code
that use itcolor, which is the starting age of the tracer. 2.
Added a few comments about the code. This should help people to
read the code.
2005-01-24 05:20 tan2
* pyre/Components/Exchanger/Exchanger.py: commented out debugging
output
2005-01-21 06:29 tan2
* module/Regional/setProperties.cc, pyre/Components/Param.py:
removed 'tracer' and 'tracer_file' properties from Param class
(these properties are moved to Tracer class)
2005-01-21 06:25 tan2
* pyre/Components/Visc.py: fixed a bug in reading viscZ property
2005-01-20 03:02 ces74
* pyre/Components/BC.py: * A BC property, "pseudo_free_surf",
added. Its default value is False.
2005-01-20 02:55 tan2
* module/Regional/setProperties.cc, pyre/Components/Visc.py: added
new properties visc.viscZ and visc.rheol
2005-01-20 02:35 vlad
* lib/Common/Viscosity_structures.c: a new viscosity law was added
(case 4)
2005-01-19 10:19 tan2
* lib/Common/Output.c: added function output_tracer()
2005-01-19 10:02 tan2
* pyre/Components/Tracer.py, pyre/Solver/Solver.py: added Tracer
module into Solver
2005-01-19 10:01 tan2
* module/Regional/bindings.cc, module/Regional/misc.cc,
module/Regional/misc.h: added binding to tracer_advection()
2005-01-19 09:05 tan2
* module/Regional/bindings.cc, module/Regional/setProperties.cc,
module/Regional/setProperties.h: added bindings to tracer input
2005-01-19 08:57 tan2
* pyre/Components/Make.mm: added Tracer.py to file list
2005-01-19 08:44 tan2
* pyre/Components/Tracer.py: added Tracer module
2005-01-19 08:43 tan2
* lib/Common/Tracer_advection.c: changed the default value of
E->control.tracer_file
2005-01-19 08:38 tan2
* module/Regional/mesher.cc: modified according to changes in
lib/Common/Instructions.c (add tracer module)
2005-01-19 08:36 tan2
* lib/Common/Instructions.c: fixed a syntax error
2005-01-19 08:35 tan2
* lib/Common/Instructions.c, lib/Common/Tracer_advection.c: 1.
moved input of tracer-related parameters to tracer_input() 2.
changed where tracer_initial_settings() is called
2005-01-19 07:19 tan2
* lib/Common/global_defs.h: fixed a problem in function pointer
declaration
2005-01-19 07:19 tan2
* drivers/Citcom.c: uncommented tracer module
2005-01-19 06:30 vlad
* examples/Cookbook4, examples/Cookbook4/cookbook4.sh,
examples/Cookbook4/coor.dat: new cookbook with a refined mesh
2005-01-19 06:24 tan2
* tests/signon.py: *** empty log message ***
2005-01-08 11:24 ces74
* lib/Common/Element_calculations.c: * removed unnecessary
debugging output from get_elt_tr()
2005-01-08 11:20 ces74
* module/Regional/bindings.cc, module/Regional/outputs.cc,
module/Regional/outputs.h, module/Regional/stokes_solver.cc,
module/Regional/stokes_solver.h: * call Citcom's functions in
output, general_stokes_solver, respectively, instead of creating
pseudo_surf bindings for each
2005-01-08 11:02 ces74
* module/Regional/bindings.cc, module/Regional/outputs.cc,
module/Regional/outputs.h, module/Regional/setProperties.cc,
module/Regional/stokes_solver.cc,
module/Regional/stokes_solver.h: * added bindings for new
functions for the "pseudo free surface" formulation
2005-01-08 10:57 ces74
* lib/Common/Instructions.c: * always assign memory for free_surf
and Vprev for now. - in the future, need to save memory when
pseudo_free_surf is off.
2005-01-08 10:16 ces74
* drivers/Citcom.c: * modified to enable the "pseudo free surface"
mode.
2005-01-08 10:15 ces74
* lib/Common/Drive_solvers.c, lib/Common/Element_calculations.c,
lib/Common/Instructions.c, lib/Common/Output.c,
lib/Common/Stokes_flow_Incomp.c, lib/Common/Topo_gravity.c,
lib/Common/global_defs.h, lib/Common/output.h: * functions added
to track pseudo free surface and compute normal traction from it.
2005-01-05 06:58 tan2
* module/Exchanger/SVTInlet.cc: removed the declaration of my_tbc()
2005-01-05 06:57 tan2
* module/Exchanger/SVTInlet.cc: 1. uncommented the journal output
2. removed codes about 'upwind bc', as it is proved not accurate.
3. removed a call to my_tbc(), which is specific to my Hawaii
plume model and sliped through the repository
2005-01-01 03:00 tan2
* lib/Common/Advection_diffusion.c, lib/Common/Convection.c: move
parameter input from Convection.c to Advection_diffusion.c
2004-12-31 09:03 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: fixed
a bug when nprocz>1 and excludeTop or/add excludeBottom is turned
on
2004-12-28 09:38 tan2
* module/Exchanger/Boundary.cc: fixed a bug, which causes some
nodes being excluded from Boundary when excludeTop or
excludeBottom are turned off
2004-12-28 03:49 tan2
* visual/combine.py: renamed some variables and changed the
doc_string
2004-12-03 04:23 tan2
* pyre/CoupledApp.py, pyre/SimpleApp.py: 1. In findLayput(), assing
self.controller 2. In CoupledApp, two controllers are created.
So, two controllers can have different output interval
(monitoringFrequency).
2004-11-25 05:47 ces74
* lib/Common/Advection_diffusion.c, lib/Common/Instructions.c,
lib/Common/global_defs.h, module/Regional/setProperties.cc,
pyre/Components/Advection_diffusion/Advection_diffusion.py: * a
new parameter, "filter_temperature" created as a memeber of the
"Control" structure. - if it's 1, the function filter() is called
to reduce artifical diffusioin. - it's 1 by default.
* The command line option for this parameter is "filter_temp" -
it belongs to the "Advection_diffusion" class, which is
instantiated as "tsolver" in Solver.py. - Usage:
--solver.tsolver.filter_temp=True/False
2004-11-16 19:43 steve
* module/Exchanger/Make.mm, module/Full/Make.mm,
module/Regional/Make.mm: made where to find pyre, etc a little
more generic
2004-11-09 07:21 ces74
* visual/miff2avi, visual/miff2mpg: * added appropriate credits for
these scripts.
2004-11-07 08:41 ces74
* visual/miff2avi, visual/miff2mpg: * scripts to make a movie out
of images generated by OpenDX -- mjpeg tools are necessary to
run.
2004-10-08 07:28 tan2
* pyre/Solver/Solver.py: don't use exchanger.initTemperature() when
restart (use disk file for IC)
2004-10-08 07:25 tan2
* lib/Common/Process_buoyancy.c: disable writing out surface hear
flux information, for processor on the surface usually don't have
E->fp ready to use.
2004-10-08 07:21 tan2
* lib/Common/Construct_arrays.c: get_bcs_id_for_residual() is
version independent. Move from Boundary_conditions.c to
Common/Construct_arrays.c
2004-10-08 07:20 tan2
* lib/Common/global_defs.h: temperatures_conform_bcs() is version
(Full/Regional) dependent. Make a function pointer for it.
2004-10-08 07:18 tan2
* lib/Full/Boundary_conditions.c,
lib/Regional/Boundary_conditions.c: 1. temperatures_conform_bcs()
is version (Full/Regional) dependent. Make a function pointer for
it. 2. get_bcs_id_for_residual() is version independent. Move to
Common/Construct_arrays.c
2004-10-08 07:11 tan2
* module/Exchanger/SVTInlet.cc, module/Exchanger/TInlet.cc,
module/Exchanger/VTInlet.cc, module/Exchanger/initTemperature.cc:
1. temperatures_conform_bcs() is version (Full/Regional)
dependent. Make a function pointer for it. 2. in
initTemperature.cc, add several new functions of different IC.
2004-10-08 07:08 tan2
* module/Exchanger/Boundary.cc: 1. fixed a bug: normalFlag was not
init'd correctly 2. when excludeBottom is true, bottome edge
nodes are still included
2004-09-23 04:31 ces74
* visual/OpenDXMacro/CitcomSSurfaceHeatflux.net,
visual/OpenDXMacro/CitcomSSurfaceImport.net,
visual/OpenDXMacro/CitcomSSurfaceTopo.net,
visual/OpenDXMacro/CitcomSSurfaceVelocity.net,
visual/OpenDXMacro/RTFtoXYZ2D.net,
visual/OpenDXMacro/VelocityRTFtoXYZ2D.net,
visual/visRegionalSurface.cfg, visual/visRegionalSurface.net: *
OpenDX macros and a new visual program for surface data.
2004-09-22 07:16 ces74
* visual/combinesurf.py: * fixed a bug related to the loop over the
surface procs for each cap.
2004-09-22 06:44 ces74
* visual/batchsurf.py, visual/getcoord.sh: * fixed bugs related to
generating a list of surface processors.
2004-08-10 07:22 tan2
* lib/Common/Initial_temperature.c: Print restart filename to
logfile
2004-08-08 05:08 tan2
* pyre/Components/Exchanger/Exchanger.py, pyre/Controller.py,
pyre/Coupler.py, pyre/Solver/Solver.py: Synchronized when to save
the result. During a coupled run, when one solver saves the
result, the other solver will save too.
2004-08-07 06:25 tan2
* visual/batchsurf.py: the 1st argument can be either the name of
machine file or a quoted machine list(eg. 'n101 n102').
2004-08-07 06:24 tan2
* visual/combinesurf.py: fixed quite a few bugs. this script is
working correctly.
2004-08-07 05:47 tan2
* pyre/Components/Exchanger/FineGridExchanger.py: VTOutlet was used
in creatII, TOutlet is used now.
2004-08-07 03:22 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py: nailed down a
big bug. VTInlet was used in creatII, which set temperature bc
flag for all interior nodes. TInlet is used now.
2004-08-05 01:29 tan2
* visual/OpenDXMacro/CitcomSFullImport.net: fixed a bug which
incorrectly set cap_start=0
2004-08-04 03:11 tan2
* module/Regional/setProperties.cc, pyre/Components/Const.py:
changed the units of depth parameters to be nondimensional, so
that they are consistent with original CitcomS input format
2004-08-02 23:34 ces74
* pyre/Components/Stokes_solver/Incompressible.py: * some
parameters that were hardwired can have user-defined values now.
2004-07-29 00:39 tan2
* visual/visFull.cfg, visual/visFull.net, visual/visRegional.cfg,
visual/visRegional.net: * use the same colormap for temperature
cross-section and isosurfaces.
2004-07-28 01:19 tan2
* module/Exchanger/AreaWeightedNormal.cc,
module/Exchanger/AreaWeightedNormal.h: * Change of
implementation. Now the weighted normal vectors are taken from
CitcomS' internal data (from boundary determinant
E->boundary.det, this array has been throughly tested), no needto
compute them again. Havn't tested.
2004-07-28 01:14 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: *
Fixed a problem in initBBox(). It used to returned a tight
boundingbox. So, when excludeTop or excludeBottom is set, the
outer and inner radii are not the correct outer and inner radii
of the mesh. This can cause confusion and problem in other part
of program. * Added a new attribute, bnode. It is the index
mapping from CitcomS' node # to Boundary's node #.
2004-07-27 06:56 tan2
* visual/batchcombine.py: * the 1st argument can be either the name
of machine file or a quoted machine list(eg. 'n101 n102'). *
modified the doc string
2004-07-09 01:15 tan2
* lib/Common/Problem_related.c, lib/Full/Lith_age.c,
lib/Full/Read_input_from_files.c, lib/Regional/Lith_age.c,
lib/Regional/Read_input_from_files.c: Previousely, CitcomS would
abort running when age < -1 Ma. This behavior is not desirable.
The following fixes change the behavior so that CitcomS will
assume age=0 when time has passed present day.
1. find_age_in_MY() returns negative age when time has passed
present day 2. changed how age is manipulated before reading
age-dependet files
2004-07-06 13:32 patrick
* doc/CitComS.doxyconf, doc/Exchanger.doxyconf: * Renamed
Exchanger.doxyconf to CitComS.doxyconf * Set the tags to work
properly
2004-07-03 03:47 tan2
* module/Exchanger/global_bbox.cc: Fixed a bug in
fullGlobalBoundedBox(). The first and second dimension of bbox
are swapped. This bug makes the interpolator skip some nodes.
2004-06-30 03:25 tan2
* examples/Cookbook3, examples/Cookbook3/cookbook3.sh: example of
temperature-dependent viscosity
2004-06-30 00:25 tan2
* examples/Cookbook1, examples/Cookbook1/cookbook1.sh,
examples/Cookbook2, examples/Cookbook2/cookbook2.sh,
examples/example1.sh: more example scripts
2004-06-29 06:04 tan2
* tests/.cvsignore: tell cvs to ignore output files of test scripts
2004-06-29 05:58 tan2
* lib/Full/Lith_age.c, lib/Regional/Lith_age.c: calling
temperatures_conform_bcs() after init'ed restarted temperature
field
2004-06-29 05:29 tan2
* lib/Full/Lith_age.c: similar changes as in Regional/Lith_age.c
2004-06-29 04:20 tan2
* lib/Regional/Lith_age.c: 1. fix a bug when init'ing temperature
2. read lith_age_file in lith_age_init()
2004-06-29 02:56 tan2
* drivers/Full/Make.mm, drivers/Regional/Make.mm: changed export
rule so that mm will create symbolic links of binary executables
in $EXPORT_ROOT/bin
2004-06-29 02:54 tan2
* module/Regional/mesher.cc: calling lith_age_init() in
mehser_init()
2004-06-29 02:53 tan2
* lib/Common/Instructions.c, lib/Common/lith_age.h,
lib/Regional/Lith_age.c: 1. moved initialization of lith_age to
lith_age_init() 2. calling lith_age_init() in read_instructions()
2004-06-29 02:49 tan2
* lib/Regional/Boundary_conditions.c: called
temperatures_conform_bcs() after setting tbc
2004-06-29 01:36 tan2
* lib/Common/Pan_problem_misc_functions.c: bug fix
2004-06-29 01:10 tan2
* examples/example1.sh: typos fixed
2004-06-27 08:04 tan2
* module/Regional/initial_conditions.cc: enable lith_age support
2004-06-27 08:03 tan2
* lib/Regional/Lith_age.c: fixed a 'access unallocated memory' bug
2004-06-27 07:59 tan2
* lib/Common/Initial_temperature.c,
lib/Common/initial_temperature.h: added declaration of
restart_tic() and restart_tic() in header
2004-06-26 03:06 tan2
* visual/visFull.cfg, visual/visFull.net: 1. show (reduced) surface
grid 2. make rotating the Plane easier
2004-06-26 01:50 tan2
* visual/visFull.cfg, visual/visFull.net: new OpenDX network for
CitcomS Full
2004-06-26 01:49 tan2
* visual/visRegional.cfg, visual/visRegional.net: 1. import
viscosity 2. changed names of transmitters/receivers
2004-06-26 01:48 tan2
* visual/OpenDXMacro/CitcomSFullImport.net,
visual/OpenDXMacro/CitcomSImport.net,
visual/OpenDXMacro/CitcomSViscosity.net: added viscosity import
2004-06-26 01:28 tan2
* visual/samples/fulltest.cap0.0,
visual/samples/fulltest.cap0.0.general,
visual/samples/fulltest.cap1.0,
visual/samples/fulltest.cap1.0.general,
visual/samples/fulltest.cap10.0,
visual/samples/fulltest.cap10.0.general,
visual/samples/fulltest.cap11.0,
visual/samples/fulltest.cap11.0.general,
visual/samples/fulltest.cap2.0,
visual/samples/fulltest.cap2.0.general,
visual/samples/fulltest.cap3.0,
visual/samples/fulltest.cap3.0.general,
visual/samples/fulltest.cap4.0,
visual/samples/fulltest.cap4.0.general,
visual/samples/fulltest.cap5.0,
visual/samples/fulltest.cap5.0.general,
visual/samples/fulltest.cap6.0,
visual/samples/fulltest.cap6.0.general,
visual/samples/fulltest.cap7.0,
visual/samples/fulltest.cap7.0.general,
visual/samples/fulltest.cap8.0,
visual/samples/fulltest.cap8.0.general,
visual/samples/fulltest.cap9.0,
visual/samples/fulltest.cap9.0.general: added sample data file of
CitcomS Full
2004-06-25 02:38 tan2
* examples/example1.sh: first example for Cookbook
2005-08-23 03:32 unknown_user
* examples/Full/Make.mm, examples/Full/local.def, examples/Make.mm,
examples/Regional/Make.mm, examples/Regional/local.def,
examples/local.def: [vcp] delete of edited revision with dead
state
2004-06-25 02:31 tan2
* Make.mm, examples/Full/Make.mm, examples/Full/local.def,
examples/Make.mm, examples/Regional/Make.mm,
examples/Regional/local.def, examples/local.def: removed
makefiles in examples/
2004-06-25 02:26 tan2
* pyre/Solver/Solver.py: new default value for Rayleight number
2004-06-25 02:25 tan2
* pyre/Components/Sphere/RegionalSphere.py: new default values for
domain size
2004-06-25 02:24 tan2
* pyre/Components/IC.py: new default values, number of initial
temperature perturbation is default to 1, perturbl and perturbm
to 1, perturblayer to 5.
2004-06-12 03:14 tan2
* module/Exchanger/Make.mm, module/Full/Make.mm,
module/Regional/Make.mm: modified library and include pathes
2004-06-11 06:07 tan2
* visual/visRegional.cfg, visual/visRegional.net: 1. added integer
interactor to control the cutting dimension of Slab 2. made the
names of interactor more descriptive 3. set the min of slab
cutting position to 0 4. set the min and max of slab Autocolor to
0 and 1, respectively
2004-06-09 00:40 tan2
* module/Full/.cvsignore: tell cvs to ignore linked source codes in
this directory
2004-06-09 00:32 tan2
* lib/Common/Output.c: disable pressure and stress output
2004-06-08 08:35 tan2
* visual/batchsurf.py, visual/combinesurf.py,
visual/dxgeneralsurf.sh, visual/getsurf.sh: scripts to get back
and combine the surf file (containing x, y, topography, heatflux,
vx, vy)
2004-06-08 08:32 tan2
* visual/getcoord.sh: script to get the coord file
2004-06-08 05:29 tan2
* visual/batchcombine.py: changed the way to generate machine list
2004-06-08 04:51 tan2
* visual/batchpaste.sh: Removed hard-wired path. Users have to set
CitcomS/visual in their path.
2004-06-08 02:54 tan2
* visual/batchcombine.py: removed debugging output
2004-06-08 02:45 tan2
* visual/batchcombine.py: When the length of machinefile mismatch
the number of processors, the script will give a warging and try
to match number of processors by applying machinefile multiple
times.
2004-06-03 04:49 tan2
* citcoms_profile: environment variables for Pyre-ized CitcomS
package. Users need to modify $GEOFRAMEWORK to the installation
path
2004-06-03 03:30 tan2
* module/Exchanger/misc.cc: remove unused header file
2004-06-03 03:28 tan2
* module/Exchanger/exchangers.cc: fixed a bug in passing int when
*int is expected
2004-06-03 03:27 tan2
* module/Exchanger/Boundary.cc: enable journal output
2004-06-03 03:23 tan2
* module/Exchanger/CitcomInterpolator.cc: throw an exception if
selfTest() is failed
2004-06-02 06:59 tan2
* Make.mm, local.def: remove incorrect copyright listing
2004-05-29 08:19 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: 1. added new
boolean property 'two_way_communication' in Exchanger.py. If it
is false, communication is only one way (coarse to fine). 2.
added new boolean properties 'excludeTop' and 'excludeBottom' in
FineGridExchanger.py. These two are new construtor arguments of
Boundary class.
2004-05-29 04:26 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/exchangers.cc: 1. Boundary can be constucted
without top or bottom surfaces. This is done through two c'tor
argument 'bool excludeTop, excludeBottom'. 2. disable journal
2004-05-27 06:56 tan2
* module/Regional/bindings.cc, module/Regional/misc.cc,
module/Regional/misc.h: split 'BC_update_bc()' into
'Visc_update_material()' and 'BC_update_plate_velocity()'
2004-05-27 06:55 tan2
* pyre/Components/BC.py, pyre/Components/Visc.py,
pyre/Solver/Solver.py: split 'BC.updateBC()' into
'Visc.updateMaterial()' and 'BC.updatePlateVelocity()'
2004-05-27 06:53 tan2
* pyre/Components/Advection_diffusion/Advection_diffusion.py: made
"fixed_timestep" and "finetunedt" an inventory property (they
were ordinary class member).
2004-05-26 05:41 tan2
* visual/visRegional.net: using relative path to the data files
2004-05-26 05:34 tan2
* visual/visRegional.cfg, visual/visRegional.net: basic OpenDX
network script to visualize result from regional version of
CitcomS
2004-05-26 05:24 tan2
* visual/samples, visual/samples/regtest.cap0.0,
visual/samples/regtest.cap0.0.general: added new sample files for
visualization
2004-05-25 07:29 tan2
* module/Exchanger/CitcomSource.cc, module/Exchanger/SVTInlet.cc,
module/Exchanger/SVTOutlet.cc: journal is known to leak memory.
Commented out journal output before the leak is fixed.
2004-05-25 03:32 tan2
* module/Regional/bindings.cc, module/Regional/misc.cc,
module/Regional/misc.h, pyre/Components/BC.py,
pyre/Solver/Solver.py: added support to read vel_bc files at
every timestep
2004-05-25 03:30 tan2
* module/Regional/stokes_solver.cc: added function name in the
argument to PyArg_ParseTuple()
2004-05-25 03:27 tan2
* tests/.cvsignore: tell cvs to ignore files generated by citcoms
output
2004-05-25 02:59 tan2
* module/Exchanger/SVTInlet.cc: Two types of temperature b.c:
upwind/normal. In upwind bc, bc can be either fixed
temperature/heatflux depending on the direction of flow. In
normal bc, bc is always fixed temperature. After more testing, I
found normal bc works better than upwind bc.
2004-05-24 02:13 tan2
* lib/Common/Pan_problem_misc_functions.c: 'side_sbc' is applicable
in regional version only. add a sanity check here. also remove
some (incorrect) conditional #include
2004-05-24 02:10 tan2
* lib/Common/Topo_gravity.c, lib/Full/Boundary_conditions.c,
lib/Regional/Boundary_conditions.c: fully implemented
stress_conform_bcs() and moved it from Boundary_conditions.c to
Topo_gravity.c
2004-05-24 01:45 tan2
* examples/Regional/input.sample: add missing parameter
'perturblayer'
2004-05-19 04:21 ces74
* module/Exchanger/Make.mm, module/Exchanger/bindings.cc,
module/Exchanger/inlets_outlets.cc: * bindings for VOutlet, which
sends only the velocity to a sink.
2004-05-19 04:18 ces74
* module/Exchanger/VOutlet.cc, module/Exchanger/VOutlet.h,
module/Exchanger/inlets_outlets.h: * Binding for VOutlet created:
this send only the velocity to a sink.
2004-05-19 04:15 ces74
* pyre/Components/Exchanger/Outlet.py: * a class added for
exchanging only the velocity.
2004-05-19 03:40 tan2
* visual/OpenDXMacro/ScaledGlyphs.net: macro that takes two data
and plot them as two glyphs that has the same size (eg. length of
arrow) scale. The shape (eg. the thickness of arrow) cannot be
scaled automaticly though.
2004-05-19 03:38 tan2
* visual/OpenDXMacro/ShowSphere.net: input1: origin of sphere;
default=[0 0 0] input2: radius of sphere; default=0.5 output:
sphere object
2004-05-13 02:10 patrick
* doc/Exchanger.doxyconf: * Updated the package name in the Doxygen
docs
2004-05-13 02:05 tan2
* visual/OpenDXMacro/CitcomSFullImport.net: Added two more inputs.
One is an integer indicating the starting cap number. The other
is an integer indicating the ending cap number. The default is
0-11, ie. all caps. If you wanna plot some specific caps only,
change these two values.
2004-05-13 02:01 tan2
* visual/dxgeneral.sh: Changed the order of 'grid'. Now it is YXZ.
Don't know why, but the old XYZ ordering doesn't work.
2004-05-12 02:32 tan2
* visual/OpenDXMacro, visual/OpenDXMacro/CitcomSFullImport.net,
visual/OpenDXMacro/CitcomSImport.net,
visual/OpenDXMacro/CitcomSTemperature.net,
visual/OpenDXMacro/CitcomSVelocity.net,
visual/OpenDXMacro/RTFtoXYZ.net,
visual/OpenDXMacro/VelocityRTFtoXYZ.net: * OpenDX macros for
importing CitcomS data file * how to use: 1. create the 'cap'
files and '.general' files using scripts in CitcomS/visual/
directory. 2. use CitcomSImport to import single cap-file. use
CitcomSFullImport to import 12 cap-files.
2005-08-23 03:30 unknown_user
* module/Exchanger/TractionInlet.cc,
module/Exchanger/TractionInlet.h,
module/Exchanger/TractionOutlet.cc,
module/Exchanger/TractionOutlet.h: [vcp] delete of edited
revision with dead state
2004-05-12 01:36 tan2
* module/Exchanger/TractionInlet.cc,
module/Exchanger/TractionInlet.h,
module/Exchanger/TractionOutlet.cc,
module/Exchanger/TractionOutlet.h: obsolete classes
2004-05-12 01:35 tan2
* module/Exchanger/AreaWeightedNormal.cc,
module/Exchanger/AreaWeightedNormal.h,
module/Exchanger/BoundaryVTInlet.cc,
module/Exchanger/BoundaryVTInlet.h: modified these classes using
new base exchanger. these classes are not used currently and I
didn't write any binding for them.
2004-05-11 14:59 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
pyre/Components/Exchanger/Inlet.py,
pyre/Components/Exchanger/Outlet.py: * using new c++ class
hierarchy
2005-08-23 03:30 unknown_user
* module/Exchanger/AbstractSource.cc,
module/Exchanger/AbstractSource.h, module/Exchanger/Array2D.cc,
module/Exchanger/Array2D.h, module/Exchanger/BoundedBox.cc,
module/Exchanger/BoundedBox.h, module/Exchanger/BoundedMesh.cc,
module/Exchanger/BoundedMesh.h,
module/Exchanger/CartesianCoord.cc,
module/Exchanger/CartesianCoord.h, module/Exchanger/DIM.h,
module/Exchanger/FEMInterpolator.cc,
module/Exchanger/FEMInterpolator.h, module/Exchanger/Inlet.cc,
module/Exchanger/Inlet.h, module/Exchanger/Outlet.cc,
module/Exchanger/Outlet.h, module/Exchanger/Sink.cc,
module/Exchanger/Sink.h,
module/Exchanger/TractionInterpolator.cc,
module/Exchanger/TractionInterpolator.h,
module/Exchanger/TractionSource.cc,
module/Exchanger/TractionSource.h,
module/Exchanger/VTInterpolator.cc,
module/Exchanger/VTInterpolator.h, module/Exchanger/VTSource.cc,
module/Exchanger/VTSource.h, module/Exchanger/utilTemplate.cc,
module/Exchanger/utilTemplate.h, module/Exchanger/utility.cc,
module/Exchanger/utility.h: [vcp] delete of edited revision with
dead state
2004-05-11 14:55 tan2
* module/Exchanger/AbstractSource.cc,
module/Exchanger/AbstractSource.h, module/Exchanger/Array2D.cc,
module/Exchanger/Array2D.h, module/Exchanger/Boundary.cc,
module/Exchanger/Boundary.h, module/Exchanger/BoundedBox.cc,
module/Exchanger/BoundedBox.h, module/Exchanger/BoundedMesh.cc,
module/Exchanger/BoundedMesh.h,
module/Exchanger/CartesianCoord.cc,
module/Exchanger/CartesianCoord.h,
module/Exchanger/CitcomInterpolator.cc,
module/Exchanger/CitcomInterpolator.h,
module/Exchanger/CitcomSource.cc,
module/Exchanger/CitcomSource.h, module/Exchanger/Convertor.cc,
module/Exchanger/Convertor.h, module/Exchanger/DIM.h,
module/Exchanger/FEMInterpolator.cc,
module/Exchanger/FEMInterpolator.h, module/Exchanger/Inlet.cc,
module/Exchanger/Inlet.h, module/Exchanger/Interior.cc,
module/Exchanger/Interior.h, module/Exchanger/Make.mm,
module/Exchanger/Outlet.cc, module/Exchanger/Outlet.h,
module/Exchanger/SIUnit.cc, module/Exchanger/SIUnit.h,
module/Exchanger/SVTInlet.cc, module/Exchanger/SVTInlet.h,
module/Exchanger/SVTOutlet.cc, module/Exchanger/SVTOutlet.h,
module/Exchanger/Sink.cc, module/Exchanger/Sink.h,
module/Exchanger/TInlet.cc, module/Exchanger/TInlet.h,
module/Exchanger/TOutlet.cc, module/Exchanger/TOutlet.h,
module/Exchanger/TractionInterpolator.cc,
module/Exchanger/TractionInterpolator.h,
module/Exchanger/TractionSource.cc,
module/Exchanger/TractionSource.h, module/Exchanger/VTInlet.cc,
module/Exchanger/VTInlet.h, module/Exchanger/VTInterpolator.cc,
module/Exchanger/VTInterpolator.h, module/Exchanger/VTOutlet.cc,
module/Exchanger/VTOutlet.h, module/Exchanger/VTSource.cc,
module/Exchanger/VTSource.h, module/Exchanger/bindings.cc,
module/Exchanger/bindings.h, module/Exchanger/exceptions.h,
module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h,
module/Exchanger/global_bbox.cc, module/Exchanger/global_bbox.h,
module/Exchanger/initTemperature.cc,
module/Exchanger/initTemperature.h,
module/Exchanger/inlets_outlets.cc,
module/Exchanger/inlets_outlets.h, module/Exchanger/misc.cc,
module/Exchanger/misc.h, module/Exchanger/utilTemplate.cc,
module/Exchanger/utilTemplate.h, module/Exchanger/utility.cc,
module/Exchanger/utility.h: * New class hierarchy. All base
classes are moved to packages/Exchanger, so does
non-CitcomS-specific utility classes. * Removed 'mode' argument
in VTInlet and VTOutlet c'tors. Every Inlet and Outlet class is
reponsible for only one job. * Merged all Interpolator into
CitcomInterpolator * Merged all Source into CitcomSource
2004-05-08 01:44 tan2
* module/Exchanger/SVTInlet.cc: impose temperature b.c. when flow
is toward into my domain. Otherwise, impose no-heatflux b.c.
2004-05-08 01:41 tan2
* module/Exchanger/misc.cc: changed default initial temperature
field -- a hot spherical blob below the fine mesh
2004-05-01 01:41 tan2
* module/Exchanger/Sink.cc: added another self test. This test will
make sure that every mesh node is interpolated.
2004-04-30 05:19 tan2
* lib/Common/Instructions.c: remove debug print out
2004-04-30 04:41 tan2
* module/Exchanger/SVTInlet.cc: implemented imposeSV(), passed
benchmark.
2004-04-30 04:36 tan2
* module/Exchanger/VTInterpolator.cc: fixed a bug in accessing
E->gstress array
2004-04-30 04:35 tan2
* lib/Common/Topo_gravity.c, lib/Full/Boundary_conditions.c,
lib/Regional/Boundary_conditions.c: After stress is calculated,
replace stress of boundary nodes with boundary conditions (if
stress BC is specified). This is partially done in Regional
version (if E->control.side_sbcs is on, should use different bc
arrays). Not implemented in Full version.
2004-04-30 03:40 patrick
* doc, doc/.cvsignore, doc/Exchanger.doxyconf: Commiting Doxygen
config file to build the documents for the exchanger
2004-04-29 07:23 tan2
* pyre/Components/BC.py: side_sbcs default to False
2004-04-29 07:23 tan2
* lib/Common/Instructions.c: E->control.side_sbcs default to 0
2004-04-29 07:21 tan2
* lib/Common/Output.c: added new function output_stress()
2004-04-29 07:13 tan2
* lib/Regional/Version_dependent.c: added some comment for initial
temperature in spherical harmonic for future reference
2005-08-23 03:29 unknown_user
* tests/citcomsfull.py, tests/citcomsregional.py,
tests/coupledcitcoms.py: [vcp] delete of edited revision with
dead state
2004-04-24 05:15 tan2
* tests/citcomsfull.py, tests/citcomsfull.sh,
tests/citcomsregional.py, tests/citcomsregional.sh,
tests/coupledcitcoms.py, tests/coupledcitcoms.sh: update the
scripts that executes pyreized versions
2004-04-24 04:15 tan2
* drivers/Regional/Make.mm: export binary executable
2004-04-23 03:52 tan2
* drivers/Full/Make.mm: export binary
2004-04-17 02:12 tan2
* lib/Common/Pan_problem_misc_functions.c: bug fix
2004-04-16 08:17 tan2
* module/Regional/setProperties.cc, pyre/Components/BC.py: add
'side_sbcs' to property list
2004-04-16 07:08 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: use SVTInlet and
SVTOutlet as BC
2004-04-16 07:05 tan2
* pyre/Components/Exchanger/Inlet.py,
pyre/Components/Exchanger/Outlet.py: add SVTOutlet and SVTInlet
classes and their bindings. These classes are for CitcomS-CitcomS
coupling, b.c. with temperature, normal velocity and shear
traction
2004-04-16 07:03 tan2
* module/Exchanger/Make.mm, module/Exchanger/SVTInlet.cc,
module/Exchanger/SVTInlet.h, module/Exchanger/SVTOutlet.cc,
module/Exchanger/SVTOutlet.h, module/Exchanger/bindings.cc,
module/Exchanger/inlets_outlets.cc,
module/Exchanger/inlets_outlets.h: add SVTOutlet and SVTInlet
classes and their bindings. These classes are for CitcomS-CitcomS
coupling, b.c. with temperature, normal velocity and shear
traction
2004-04-16 07:01 tan2
* module/Exchanger/VTSource.cc: add some journal debug output
2004-04-16 01:39 tan2
* lib/Common/Topo_gravity.c,
module/Exchanger/TractionInterpolator.cc: rearranged the order of
stress vector so that it conforms with Hugh's convention
| 1 4 5 | stress =| 4 2 6 | | 5 6 3 |
2004-04-16 01:35 tan2
* lib/Common/Make.mm, lib/Common/Process_velocity.c: remove the
empty file, Process_velocity.c, from the repository
2004-04-16 01:33 tan2
* lib/Common/Obsolete.c, lib/Common/Process_velocity.c,
lib/Common/Topo_gravity.c: 1. move get_surf_stress() from
Process_velocity.c to Topo_gravity.c 2. move get_ele_visc() from
Process_velocity.c to Obsolete.c
2004-04-15 03:12 tan2
* module/Exchanger/VTSource.cc, module/Exchanger/VTSource.h:
implement interpolateStress()
2004-04-15 03:06 tan2
* module/Exchanger/VTInterpolator.cc,
module/Exchanger/VTInterpolator.h: implement interpolateStress()
2004-04-15 02:41 tan2
* module/Exchanger/AbstractSource.h, module/Exchanger/DIM.h,
module/Exchanger/FEMInterpolator.h,
module/Exchanger/TractionInterpolator.h,
module/Exchanger/TractionSource.h,
module/Exchanger/VTInterpolator.h, module/Exchanger/VTSource.h:
1. add a new constant, 'STRESS_DIM', for the dimension of stress
(=6 in 3D) 2. in Interpolator and Source, stress has correct
dimension now 3. add virtual function 'interpolateDisplacement'
in Source
2004-04-15 01:29 tan2
* lib/Common/Element_calculations.c, lib/Common/Instructions.c,
lib/Common/Pan_problem_misc_functions.c,
lib/Common/global_defs.h, lib/Full/Boundary_conditions.c,
lib/Regional/Boundary_conditions.c: convert b.c. data structure
to support traction b.c. on all sides of a element
2004-04-13 06:30 tan2
* lib/Common/Element_calculations.c: bug fix
2004-04-13 06:23 tan2
* lib/Common/Element_calculations.c: modify get_elt_tr() so that it
computes traction per side, not per element. Also, some minor
speed improvement.
2004-04-10 08:05 tan2
* module/Exchanger/TractionInterpolator.cc: changes in interfaces
of construct_side_c3x3matrix_el() and
get_global_side_1d_shape_fn()
2004-04-10 08:03 tan2
* lib/Common/Size_does_matter.c: change the interface of
get_global_side_1d_shape_fn(): NS and far is replaced by side
2004-04-10 07:49 tan2
* lib/Common/Element_calculations.c, lib/Common/Size_does_matter.c:
1. change interface of construct_side_c3x3matrix_el(): NS, far is
replaced by side 2. in get_elt_tr(), traction is only imposed on
top/bottom sides (will relax this constraint later)
2004-04-10 07:00 tan2
* lib/Common/Element_calculations.c: bug fix
2004-04-10 06:56 tan2
* lib/Common/Element_calculations.c, lib/Common/Obsolete.c: move
get_elt_h() from Element_calculations.c to Obsolete.c
2004-04-10 06:31 tan2
* lib/Common/Element_calculations.c: 1. finished get_elt_tr(),
which computes RHS vector contributed to traction b.c. 2. remove
declaration of unused variables
2004-04-10 06:20 tan2
* lib/Common/Size_does_matter.c: 1. finished construct_bdry_det()
2. modify other functions related to sides 3. remove declaration
unused variables
2004-04-10 06:19 tan2
* lib/Common/element_definitions.h: add/change side definition
2004-04-10 02:05 tan2
* lib/Common/Element_calculations.c: fixed a bug in calculating RHS
force vector due to boundary velocity
2004-04-10 01:39 tan2
* lib/Common/Element_calculations.c: undo previous (uninit'd
memory) bug fix -- it is not a bug
2004-04-09 07:13 tan2
* lib/Common/Element_calculations.c: fixed a bug in initializing
array
2004-04-06 02:36 tan2
* module/Exchanger/FEMInterpolator.cc: minor modification to
previous check-in
2004-04-05 06:03 tan2
* module/Exchanger/FEMInterpolator.cc: sometimes after coordinate
conversion, surface nodes of different solvers won't line up,
need this special treatment -- if x is a little bit above my top
surface, move it back to the surface
2004-03-29 07:31 tan2
* module/Regional/mesher.cc: in sphere_launch(), call
construct_bdry_det() to compute (6-side) surface determinants of
boundary elements
2004-03-29 07:22 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: usage of VTOutlet
and VTInlet is replaced by TractionInlet and TractionOutlet.
Goal: impose normal velocity and shear traction as bounary
conditions
2004-03-29 07:20 tan2
* pyre/Components/Exchanger/Inlet.py: bug fix
2004-03-29 07:19 tan2
* module/Exchanger/TractionInterpolator.cc,
module/Exchanger/TractionInterpolator.h,
module/Exchanger/TractionOutlet.cc,
module/Exchanger/TractionOutlet.h,
module/Exchanger/TractionSource.cc,
module/Exchanger/TractionSource.h,
module/Exchanger/exchangers.cc: 1. TractionOutlet c'tor has a new
argument to specify 'mode'. Avaiable modes are: 'F': send
traction only 'V": send velocity only (this is somewhat
duplicated with VTOutlet) 'FV": send both traction and velocity
2. TractionSource and TractionInterpolateor have to know how to
interpolate velocity (because of 1) 3. remove domian_cutout() 4.
restructure TractionInterpolateor class to reuse CitcomS library
2004-03-29 07:05 tan2
* module/Exchanger/bindings.cc: add bindings to TractionOutlet and
TractionInlet
2004-03-29 07:05 tan2
* module/Exchanger/Make.mm, module/Exchanger/TractionInlet.cc,
module/Exchanger/TractionInlet.h,
module/Exchanger/inlets_outlets.cc,
module/Exchanger/inlets_outlets.h: add new class TractionInlet
and its bindings
2004-03-29 07:01 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h:
send/recv/broadcast normal array as well
2004-03-27 08:10 steve
* module/Exchanger/Make.mm: changed from $TOOLS_DIR/lib to
$TOOL_LIBDIR
2004-03-27 08:04 tan2
* lib/Common/Element_calculations.c: 1. extract repeated codes to a
new function add_force() 2. remove unused variables 3. add new
function to compute RHS of momemtum eqn due to traction b.c. (not
finished yet)
2004-03-27 07:42 tan2
* lib/Common/Size_does_matter.c: 1. move get_global_1d_shape_fn_1()
form Size_does_matter.c to Obsolete.c 2. add new function
construct_bdry_det() to compute (6-side) surface determinant of
boundary element 3. isolate some repeated codes to new function
get_x_cart()
2004-03-27 07:41 tan2
* lib/Common/Obsolete.c: move get_global_1d_shape_fn_1() form
Size_does_matter.c to Obsolete.c
2004-03-27 07:39 tan2
* lib/Common/element_definitions.h: add a section defines the
ordering of the 6 surfaces of a element and the ordering of 4
nodes within each surface
2004-03-27 07:39 tan2
* lib/Common/global_defs.h: add definition of new structure Bdry
and declaration of E->boundary. This structure is used to mark
boundary element and store its (6-side) surface determinants
2004-03-27 07:36 tan2
* lib/Full/Version_dependent.c, lib/Regional/Version_dependent.c:
1. add new function construct_boundary() to find boundary
elements 2. fix bug in using fscanf() 3. remove unused variables
2004-03-27 01:53 tan2
* lib/Common/Instructions.c: 'read uninitialized value' bug fixed
2004-03-26 06:45 tan2
* lib/Common/Tracer_advection.c: minor bug fixed
2004-03-26 06:42 tan2
* lib/Regional/Sphere_related.c: minor bug fixed
2004-03-25 04:14 tan2
* lib/Common/Instructions.c: *** empty log message ***
2004-03-25 04:13 tan2
* lib/Common/Convection.c, lib/Common/Instructions.c: input of
Rayleigh number is moved
2004-03-17 07:17 tan2
* lib/Common/Topo_gravity.c, lib/Common/global_defs.h,
lib/Full/Parallel_related.c, lib/Regional/Parallel_related.c: 1.
add function pointers void (* exchange_node_d) and void (*
exchange_node_f) in struct All_variables 2. replace calls to
exchange_node_d() by void (* exchange_node_d) in Topo_gravity.c.
Because exchange_node_d() is version dependent and can't be
called from Exchanger.
2004-03-17 05:07 tan2
* module/Regional/mesher.cc: construct surface arrays and compute
surface determinant
2004-03-17 05:03 tan2
* lib/Common/Construct_arrays.c, lib/Common/Instructions.c,
lib/Common/Size_does_matter.c: 1. construct surface node and
element array for bookkeeping 2. compute surface determinant
2004-03-14 07:11 tan2
* lib/Common/Size_does_matter.c: remove debugging print out
2004-03-13 07:13 tan2
* lib/Common/Topo_gravity.c: another bug fix
2004-03-13 07:05 tan2
* lib/Common/Topo_gravity.c: restructure function get_STD_topo()
2004-03-13 07:05 tan2
* lib/Common/Output.c: bug fix
2004-03-13 07:01 tan2
* lib/Common/Output.c: isolate calculation and output of horizontal
average into one function
2004-03-12 07:25 tan2
* pyre/Components/Exchanger/Inlet.py,
pyre/Components/Exchanger/Outlet.py: 1. add TractionInlet class
2. simplified bindings for inlets and outlets
2004-03-12 07:23 tan2
* module/Exchanger/bindings.cc, module/Exchanger/inlets_outlets.cc,
module/Exchanger/inlets_outlets.h: simplified bindings to inlets
and outlets
2004-03-12 06:50 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: add
attribute 'normal_' to indicate the direction of outward normal
on each node.
2004-03-12 06:46 tan2
* module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: remove obsolete bindings
2004-03-12 06:42 tan2
* module/Exchanger/Sink.cc, module/Exchanger/VTInlet.cc: bug fixed
2004-03-12 06:36 tan2
* module/Exchanger/Sink.h, module/Exchanger/VTInlet.cc: change
method name: 'recvArray2D' --> 'recv'
2005-08-23 03:27 unknown_user
* module/Exchanger/BoundaryCondition.cc,
module/Exchanger/BoundaryCondition.h,
module/Exchanger/InteriorImposing.cc,
module/Exchanger/InteriorImposing.h, module/Exchanger/Source.cc,
module/Exchanger/Source.h, module/Exchanger/TractionBC.cc,
module/Exchanger/TractionBC.h: [vcp] delete of edited revision
with dead state
2004-03-12 06:22 tan2
* module/Exchanger/BoundaryCondition.cc,
module/Exchanger/BoundaryCondition.h,
module/Exchanger/InteriorImposing.cc,
module/Exchanger/InteriorImposing.h, module/Exchanger/Make.mm,
module/Exchanger/Source.cc, module/Exchanger/Source.h,
module/Exchanger/TractionBC.cc, module/Exchanger/TractionBC.h:
remove obsolete files
2004-03-11 09:07 tan2
* pyre/Components/Exchanger/Inlet.py: method 'storeTimestep' is
moved up to the parent class
2004-03-11 09:06 tan2
* module/Exchanger/Inlet.cc, module/Exchanger/Inlet.h,
module/Exchanger/VTInlet.cc, module/Exchanger/VTInlet.h,
module/Exchanger/bindings.cc, module/Exchanger/inlets_outlets.cc,
module/Exchanger/inlets_outlets.h: 1. move attributes 'fge_t' and
'cge_t', methods 'storeTimestep' and 'getFactor' from VTInlet to
Inlet. 2. change the binding accordingly
2004-02-27 07:04 tan2
* module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/initTemperature.cc,
module/Exchanger/initTemperature.h: delete
initTemperatureSource(), initTemperatureSink() and their
bindings.
2004-02-27 06:29 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: use Inlet and
Outlet
2004-02-27 06:29 tan2
* pyre/Components/Exchanger/Inlet.py,
pyre/Components/Exchanger/Make.mm,
pyre/Components/Exchanger/Outlet.py: add various classes for
exchanger
2004-02-27 03:27 tan2
* module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h:
1. remove "before_send_bbox" and "converted_bbox" journal log 2.
add 'send' and 'recv' methods
2005-08-23 03:27 unknown_user
* module/Exchanger/InformationSourceSink.h: [vcp] delete of edited
revision with dead state
2004-02-26 07:29 tan2
* module/Exchanger/InformationSourceSink.h: obsolete (actually
never used), replaced by Inlet and Outlet classes.
2004-02-26 07:25 tan2
* pyre/Components/Exchanger/FineGridExchanger.py: activate
journal.info("incompressibility")
2004-02-26 07:24 tan2
* module/Exchanger/AreaWeightedNormal.cc: outputing outflow
information is moved to journal.info category
2004-02-26 07:07 tan2
* module/Exchanger/Make.mm: add AbstractSource.cc
2004-02-26 07:07 tan2
* module/Exchanger/AbstractSource.cc,
module/Exchanger/AbstractSource.h,
module/Exchanger/TractionSource.cc,
module/Exchanger/TractionSource.h, module/Exchanger/VTSource.cc,
module/Exchanger/VTSource.h: 1. add AbstractSource.cc 2. move
initialization of TractionSource and VTSource to AbstractSource
2004-02-25 08:54 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: new Exchanger,
using inlets and outlets.
2004-02-25 04:40 tan2
* module/Exchanger/Make.mm: add new source files
2004-02-25 04:39 tan2
* module/Exchanger/bindings.cc: add bindings to various inlet and
outlet classes in method table
2004-02-25 04:37 tan2
* module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h:
move 'createVTSource' function to inlets_outlets.cc
2004-02-25 04:35 tan2
* module/Exchanger/inlets_outlets.cc,
module/Exchanger/inlets_outlets.h: bindings for various inlets
and outlets classes
2004-02-25 04:34 tan2
* module/Exchanger/BoundaryVTInlet.cc,
module/Exchanger/BoundaryVTInlet.h: class which consumes nodal
velocities and temperature and enforce imcompressibility
constraint, replacing BoundaryConditionSink class.
2004-02-25 04:26 tan2
* module/Exchanger/VTInlet.cc, module/Exchanger/VTInlet.h: class
which consuming nodal velocities and temperature, replacing (part
of) BoundaryConditionSink class.
2004-02-25 04:24 tan2
* module/Exchanger/VTOutlet.cc, module/Exchanger/VTOutlet.h: class
which provides nodal velocities and temperature, replacing (part
of) BoundaryConditionSource class.
2004-02-25 04:20 tan2
* module/Exchanger/VTSource.cc, module/Exchanger/VTSource.h: class
which sends velocity and temperature across the network,
replacing Source class.
2004-02-25 04:14 tan2
* module/Exchanger/TractionOutlet.cc,
module/Exchanger/TractionOutlet.h: class which provides nodal
traction, replacing TractionBC class.
2004-02-25 04:09 tan2
* module/Exchanger/FEMInterpolator.cc: small modification on
convergence criterion
2004-02-25 04:03 tan2
* module/Exchanger/Inlet.cc, module/Exchanger/Inlet.h,
module/Exchanger/Outlet.cc, module/Exchanger/Outlet.h: base
classes for send/receive/impose exchanged information
2004-02-12 07:34 ces74
* lib/Common/Output.c: Pressure output added
2004-02-07 07:28 tan2
* lib/Common/Output.c: increase number of digits for coordinate and
viscosity output
2004-02-06 04:17 tan2
* lib/Common/Initial_temperature.c,
lib/Common/convection_variables.h,
module/Regional/setProperties.cc: increase max. allowed # of
perturbations to 255
2004-02-06 03:56 tan2
* module/Regional/setProperties.cc: change echo format of
get*Property
2004-02-06 03:46 tan2
* module/Exchanger/misc.cc: allocate and init temperature boundary
condition flags
2004-02-06 03:45 tan2
* module/Exchanger/FEMInterpolator.cc, module/Exchanger/Sink.cc:
changes in journal log
2004-02-06 03:06 tan2
* pyre/Components/IC.py, pyre/Components/Visc.py: use
pyre.properties.list instead of pyre.properties.sequence for
several component properties because: 1. sequence only accepts
integer from command line input 2. list doesn't require '[]'
around command line input
2004-02-05 08:46 tan2
* visual/pasteCitcomData.sh: use space char. as field delimiter
instead of tab char.
2004-01-23 04:06 puru
* module/Exchanger/InteriorImposing.cc,
module/Exchanger/InteriorImposing.h: Temporarily setVBCFlag is
called inside recvV, which is computationally inefficient for
testing purpose.
2004-01-22 11:38 puru
* module/Exchanger/BoundedBox.cc: Corrected to include the case
when one bounded box completely subsumes the other boundedbox
2004-01-22 04:46 tan2
* module/Exchanger/AreaWeightedNormal.h: #include mpi.h in the
header
2004-01-22 02:09 tan2
* module/Exchanger/Source.h: #include BoundedBox.h in the header
2004-01-22 01:40 tan2
* module/Exchanger/AreaWeightedNormal.cc,
module/Exchanger/AreaWeightedNormal.h: remove Sink from the
arguement list of computeWeightedNormal()
2004-01-21 08:13 puru
* module/Exchanger/InteriorImposing.cc: A typo has been corrected
2004-01-21 08:13 puru
* module/Exchanger/exchangers.cc: Corrected a typo
2004-01-21 06:57 tan2
* module/Exchanger/misc.cc: 1. seperate codes that is in original
initTemperatureTest() to new functions: hot_blob(),
add_hot_blob() and debug_output() 2. add new function
five_hot_blob(), which put a hot blob in the center of bbox, and
4 hot blobs outside and around bbox.
2004-01-19 05:07 tan2
* module/Exchanger/FEMInterpolator.cc: add comments
2004-01-18 06:22 ces74
* module/Exchanger/TractionInterpolator.cc: a bug fixed in traction
calculation.
2004-01-17 10:10 puru
* module/Exchanger/InteriorImposing.cc,
module/Exchanger/InteriorImposing.h,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: Facility to impose velocity from
Snac to Citcom has been added.
2004-01-16 10:05 tan2
* module/Exchanger/FEMInterpolator.cc: revert to previous version
2004-01-16 09:50 tan2
* module/Exchanger/FEMInterpolator.cc: changes to make floating
point comparison friendly
2004-01-15 11:00 ces74
* module/Exchanger/TractionInterpolator.h: header file for
TractionInterpolator.cc
2004-01-15 10:59 ces74
* module/Exchanger/TractionBC.cc: converted fbc can be printed out
for debugging.
2004-01-15 09:04 ces74
* module/Exchanger/TractionInterpolator.cc: 1. in
initComputeTraction, bbox is now boundedMesh.tightBBox().
2. domain_cutout() causes a problem in Citcom. Until fixed, it's
not called.
2004-01-15 08:48 tan2
* visual/batchcombine.py: script to retrieve/combine Citcom data in
OpenDX-friendly format
2004-01-15 08:47 tan2
* visual/batchpaste.sh: run 'rsh ...' in the foreground
2004-01-15 08:17 tan2
* visual/dxgeneral.sh: can have multiple input files now
2004-01-15 07:22 tan2
* visual, visual/batchpaste.sh, visual/combine.py,
visual/dxgeneral.sh, visual/getlog.sh, visual/pasteCitcomData.sh:
add scripts to combine/retrieve Citcom data
2004-01-15 03:07 tan2
* module/Exchanger/BoundedMesh.cc: small improvement
2004-01-15 02:52 tan2
* module/Exchanger/Boundary.cc: call tightBBox() to init bbox_
2004-01-15 02:49 tan2
* module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h:
add new method tightBBox() which returns a tight bounding box for
current X_
2005-08-23 03:26 unknown_user
* module/Exchanger/TractionBC.cc~, module/Exchanger/TractionBC.h~:
[vcp] delete of edited revision with dead state
2004-01-15 00:52 puru
* module/Exchanger/TractionBC.cc~, module/Exchanger/TractionBC.h~:
TractionBC.cc~ and Traction.h~ have been removed from repository
2004-01-14 10:40 ces74
* module/Exchanger/TractionBC.cc,
module/Exchanger/TractionInterpolator.cc,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.h: bug
fixed. The changes in the name of classes are corrected.
2004-01-14 10:11 ces74
* module/Exchanger/Make.mm, module/Exchanger/TractionBC.cc,
module/Exchanger/TractionBC.cc~, module/Exchanger/TractionBC.h,
module/Exchanger/TractionBC.h~,
module/Exchanger/TractionSource.cc,
module/Exchanger/TractionSource.h, module/Exchanger/bindings.cc,
module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1)
New files TractionBC.cc TractionBC.h have been added. 2)
sendTraction is now a method of TractionSource.
2004-01-14 08:34 tan2
* module/Exchanger/initTemperature.cc: add function
basal_tbl_central_hot_blob()
2004-01-14 08:34 tan2
* module/Exchanger/Source.cc, module/Exchanger/Source.h: definition
of destructor is moved from Source.h to Source.cc
2004-01-14 02:53 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
pyre/Solver/Solver.py: change Solver attributes so that
Exchangers don't access Solver.inventory.IC.inventory directly
2004-01-13 11:55 tan2
* module/Exchanger/FEMInterpolator.cc,
module/Exchanger/FEMInterpolator.h, module/Exchanger/misc.cc: new
FEMInterpolator using every element nodes to do interpolation
(was using 4 element nodes)
2004-01-13 11:01 ces74
* pyre/Solver/Solver.py: initialization was improper.
2004-01-13 09:32 tan2
* drivers/Full/Make.mm, drivers/Regional/Make.mm: when linking
binary file, will check dependency on object file
2004-01-13 09:21 ces74
* module/Exchanger/BoundaryCondition.cc,
module/Exchanger/BoundedMesh.cc, module/Exchanger/Interior.cc,
module/Exchanger/InteriorImposing.cc, module/Exchanger/Make.mm,
module/Exchanger/SIUnit.cc, module/Exchanger/Sink.cc,
module/Exchanger/Source.cc, module/Exchanger/exchangers.cc: bugs
fixed. For synchronization between users.
2004-01-10 06:42 ces74
* module/Exchanger/FEMInterpolator.cc: Added a comment line
2004-01-09 14:10 ces74
* module/Exchanger/CartesianCoord.cc: fixed bugs in degenerate
cases.
2004-01-09 09:25 tan2
* module/Exchanger/Convertor.cc: when unconverting, un-transformate
first, then non-dimensionalize next.
2004-01-09 08:38 ces74
* module/Exchanger/CartesianCoord.cc: fixed bug in degenerate case
2004-01-09 07:43 tan2
* pyre/Solver/Solver.py: coupler get init'ed after setProperties()
is called
2005-08-23 03:25 unknown_user
* module/Exchanger/Dimensional.cc, module/Exchanger/Dimensional.h:
[vcp] delete of edited revision with dead state
2004-01-09 07:31 tan2
* module/Exchanger/Dimensional.cc, module/Exchanger/Dimensional.h:
renamed to SIUnit
2004-01-09 05:19 tan2
* module/Exchanger/CartesianCoord.cc: 'Array2D: second index out of
range' bug fixed
2005-08-23 03:25 unknown_user
* module/Exchanger/Interpolator.cc,
module/Exchanger/Interpolator.h: [vcp] delete of edited revision
with dead state
2004-01-09 04:42 tan2
* module/Exchanger/FEMInterpolator.cc,
module/Exchanger/FEMInterpolator.h,
module/Exchanger/Interpolator.cc,
module/Exchanger/Interpolator.h, module/Exchanger/Make.mm,
module/Exchanger/Source.cc, module/Exchanger/Source.h,
module/Exchanger/TractionInterpolator.cc,
module/Exchanger/TractionInterpolator.h,
module/Exchanger/TractionSource.cc,
module/Exchanger/VTInterpolator.cc,
module/Exchanger/VTInterpolator.h: 1. Interpolator is renamed to
VTInterpolator 2. Calculation of shape function is moved to
FEMInterpolator 3. VTInterpolator and TractionInterpolatore
inherit from FEMInterpolator 4. change Source and TractionSource
accordingly
2004-01-09 02:40 tan2
* module/Exchanger/dimensionalization.h: obsolete
2004-01-09 02:38 tan2
* module/Exchanger/SIUnit.cc, module/Exchanger/SIUnit.h:
dimensionalize temperature is done
2004-01-09 02:37 tan2
* module/Regional/setProperties.cc: bug fix
2004-01-09 02:26 tan2
* lib/Common/Instructions.c, module/Regional/setProperties.cc,
pyre/Components/Const.py: 1. Const class has new property
'surftemp' 2. Instruction.c and setProperties.cc readin
E->data.surf_temp and calculate temperature scale from Rayleigh
number and other dimensional constants
2004-01-09 02:04 tan2
* module/Exchanger/Convertor.cc, module/Exchanger/Convertor.h: use
plain pointer instead of auto_ptr
2004-01-09 00:28 puru
* module/Exchanger/CartesianCoord.cc: Bounded box has been
transformed while accounting for degenerate cases
2004-01-08 10:29 tan2
* module/Exchanger/AbstractSource.h,
module/Exchanger/BoundaryCondition.cc,
module/Exchanger/Convertor.cc, module/Exchanger/Interpolator.cc,
module/Exchanger/Sink.cc, module/Exchanger/Sink.h,
module/Exchanger/Source.cc, module/Exchanger/Source.h,
module/Exchanger/TractionInterpolator.cc,
module/Exchanger/TractionSource.cc,
module/Exchanger/TractionSource.h: convert (dimensionalization +
coordinate transformation) of exchanged velocity/temperature is
done
2004-01-08 09:50 tan2
* module/Exchanger/exchangers.cc: bug fixed
2004-01-08 09:50 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: typo fixed
2004-01-08 07:54 tan2
* module/Exchanger/InteriorImposing.cc,
module/Exchanger/InteriorImposing.h,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: 1. remove unnecessary functions in
InteriorImposingSink and their bindings 2. convert/unconvert
temperature to standard/internal representation
2004-01-08 06:01 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: changes in
dimensionalization and coordinate transformation scheme
2004-01-08 05:54 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h,
module/Exchanger/CartesianCoord.cc,
module/Exchanger/CartesianCoord.h, module/Exchanger/Convertor.cc,
module/Exchanger/Convertor.h, module/Exchanger/Interior.cc,
module/Exchanger/Interior.h, module/Exchanger/Interpolator.cc,
module/Exchanger/Make.mm, module/Exchanger/SIUnit.cc,
module/Exchanger/SIUnit.h, module/Exchanger/bindings.cc,
module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1.
Convertor class will convert
coordinate/velocity/traction/time/... from CitcomS' internal
representation to some standard representation (currently in SI
unit and Cartesian coordinate) 2. change other parts of code
accordingly
2004-01-07 16:12 tan2
* module/Exchanger/exchangers.cc: remove calls to Transformation
class
2005-08-23 03:24 unknown_user
* module/Exchanger/Transformational.h: [vcp] delete of edited
revision with dead state
2004-01-07 15:41 tan2
* module/Exchanger/Transformational.cc,
module/Exchanger/Transformational.h: renamed to CartesianCoord
2004-01-07 09:07 tan2
* module/Exchanger/Interpolator.cc,
module/Exchanger/Interpolator.h: remove obsolete function
findMaxGridSpacing()
2004-01-07 06:40 puru
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h,
module/Exchanger/Interior.cc, module/Exchanger/Interior.h,
module/Exchanger/exchangers.cc: Transformation from Spherical
coordinate system to Euclidean coordinate is done at citcom end
2004-01-07 06:38 puru
* module/Exchanger/CartesianCoord.cc,
module/Exchanger/CartesianCoord.h,
module/Exchanger/Transformational.cc,
module/Exchanger/Transformational.h: Added a new cleass
Transformational for transforming from one coordinate system to
another coordinate system
2003-12-31 05:46 tan2
* module/Exchanger/BoundaryCondition.cc: temporary fix
2003-12-31 05:46 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/BoundedBox.cc, module/Exchanger/BoundedMesh.cc,
module/Exchanger/BoundedMesh.h, module/Exchanger/Interior.cc,
module/Exchanger/Interior.h, module/Exchanger/bindings.cc,
module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h:
optional dimensionalization
2003-12-31 05:44 tan2
* module/Exchanger/Dimensional.cc, module/Exchanger/Dimensional.h,
module/Exchanger/Make.mm, module/Exchanger/SIUnit.cc,
module/Exchanger/SIUnit.h: add Dimensional class
2003-12-31 05:42 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: 1. add new
property 'dimensional': if it is true, quantities exchanged are
dimensional 2. (optional) dimensional BoundedBox, Boundary,
Interior and timestep
2003-12-30 08:31 ces74
* module/Exchanger/BoundedBox.cc: dimensional_len was being used
without a value assigned. --> temporarily, not used in
regionalGlobalBoundedBox().
2003-12-25 06:46 ces74
* pyre/Solver/Solver.py: a bug fixed: initTemperature is an
attribute of exchanger, not coupler.
2003-12-23 15:02 puru
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: Initial condition
initialization has been done at a higher level
2003-12-23 08:42 puru
* module/Exchanger/Boundary.cc,
module/Exchanger/InteriorImposing.cc,
module/Exchanger/dimensionalization.h: fixed dimensionalization
2003-12-23 01:47 puru
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: all_variables has
been moved from Exchanger to Finegrid and Coarsegrid Exchangers
(for CitcomS-Snac Coupling)
2003-12-20 02:21 tan2
* module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: add bindings to functions
initTemperatureSink(), initTemperatureSource() and modifyT() for
exchange initial temperature field between CitcomS-CitcomS
2003-12-19 16:05 tan2
* module/Exchanger/initTemperature.h: add functions
initTemperatureSink(), initTemperatureSource() and modifyT() for
exchange initial temperature field between CitcomS-CitcomS
2003-12-19 06:30 puru
* pyre/Components/Exchanger/__init__.py: Changed __init__.py to
export Exchange class
2003-12-17 12:27 puru
* module/Exchanger/Boundary.cc,
module/Exchanger/BoundaryCondition.cc,
module/Exchanger/BoundedBox.cc, module/Exchanger/Interior.cc,
module/Exchanger/InteriorImposing.cc,
module/Exchanger/Interpolator.cc,
module/Exchanger/TractionInterpolator.cc,
module/Exchanger/dimensionalization.h: 1) Added dimensionalize.h
which contains variables for dimensionalizing CitcomS variables
2) All variables sent out by Citcom exchanger are dimensionalized
3) All variables received in by Citcom exchanger are
non-dimensionalized
2003-12-17 09:35 puru
* module/Exchanger/Interpolator.cc: fixed bug
2003-12-17 03:09 tan2
* module/Exchanger/Make.mm: add compilation for
TractionInterpolator.cc and TractionSource.cc
2003-12-17 03:08 tan2
* module/Exchanger/Source.cc, module/Exchanger/Source.h: remove
functions about traction interpolation (moved to TractionSource)
2003-12-17 02:50 tan2
* module/Exchanger/TractionSource.cc,
module/Exchanger/TractionSource.h: source for CitcomS-Snac
coupling
2003-12-16 11:01 puru
* module/Exchanger/Boundary.cc, module/Exchanger/BoundedBox.cc,
module/Exchanger/Interior.cc, module/Exchanger/Interpolator.cc:
Dimensionalized exchanger part for the ease of interaction with
Snac
2003-12-16 10:14 tan2
* module/Exchanger/FEMInterpolator.h,
module/Exchanger/TractionInterpolator.cc,
module/Exchanger/TractionInterpolator.h: 1. remove const-ness in
Interpolate*() functions 2. remove passing E in
TractionInterpolator 3. remove static qualifier of some local
var. in TractionInterpolator
2003-12-04 08:28 puru
* module/Exchanger/InteriorImposing.cc,
module/Exchanger/TractionInterpolator.cc: Conevrsion from
dimensional to non-dimensional and vice-versa 1) Forces have been
dimensionalized in TractioInterpolator before sent to Snac 2)
Velocities have been non-dimensionalized in InteriorImposing
after receiving from Snac
2003-11-30 09:22 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: add
restartTemperature() for read/send/receive/modify restarted
temperature
2003-11-30 09:21 tan2
* module/Exchanger/initTemperature.cc: add comments and call
temperatures_conform_bcs()
2003-11-30 08:12 tan2
* lib/Common/Process_buoyancy.c: fix a bug of flushing (maybe)
non-existing file handle
2003-11-29 06:34 ces74
* module/Exchanger/TractionInterpolator.cc,
module/Exchanger/TractionInterpolator.h: a new class added, but
not being used yet.
2003-11-29 06:32 ces74
* module/Exchanger/Interpolator.cc: interpolateF removed.
2003-11-29 06:32 ces74
* module/Exchanger/Interpolator.h: interpolateF removed
2003-11-29 06:25 ces74
* module/Exchanger/exchangers.h: new definitions added for
domain_cutout and sendTraction
2003-11-29 06:23 ces74
* module/Exchanger/exchangers.cc: new bindings added:
PyObject * pyExchanger_sendTraction(PyObject *, PyObject *args)
PyObject * pyExchanger_domain_cutout(PyObject *, PyObject *args)
2003-11-29 06:21 ces74
* module/Exchanger/bindings.cc: two entries added: sendTraction and
domain_cutout
2003-11-29 06:20 ces74
* module/Exchanger/BoundaryCondition.h: new functions added: void
sendTraction() void domain_cutout()
2003-11-29 06:20 tan2
* module/Regional/bindings.cc,
module/Regional/initial_conditions.cc,
module/Regional/initial_conditions.h: add bindings to
'restartTemperature()' and 'constructTemperature()', which are
used for temperature initial condition
2003-11-29 06:19 ces74
* module/Exchanger/Source.h: new functions defined:
void interpolateF(Array2D<double,DIM>& F, All_variables* E)
const; void domain_cutout(const All_variables* E) const;
2003-11-29 06:18 ces74
* module/Exchanger/Source.cc: new functions added:
void Source::interpolateF() void Source::domain_cutout()
2003-11-29 06:18 tan2
* module/Regional/setProperties.cc: *** empty log message ***
2003-11-29 06:17 tan2
* pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/IC.py, pyre/Solver/Solver.py: move properties
'inputdiffusivity' from Solver to Advecton_diffusion; 'restart',
'post_p', 'solution_cycles_init', and 'zero_elapsed_time' from
Solver to IC
2003-11-29 06:16 ces74
* module/Exchanger/BoundaryCondition.cc: The body of the following
functions are commented out:
void BoundaryConditionSource::sendTraction() void
BoundaryConditionSource::domain_cutout()
2003-11-29 06:14 tan2
* pyre/CoupledApp.py, pyre/SimpleApp.py: add factory functions
2003-11-29 05:42 ces74
* lib/Common/Size_does_matter.c: two new functions added: 1. void
construct_side_c3x3matrix_el() 2. void
get_global_side_1d_shape_fn()
2003-11-27 07:27 tan2
* drivers/Full/Make.mm, drivers/Regional/Make.mm: modify Make.mm so
that it always make a new binary file
2003-11-27 07:25 tan2
* lib/Regional/Parallel_related.c: fix a bug of memory leak
2003-11-27 06:31 tan2
* lib/Regional/Geometry_cartesian.c: fix a bug when reading input
parameters
2003-11-27 05:26 tan2
* lib/Common/Initial_temperature.c, lib/Full/Version_dependent.c,
lib/Regional/Version_dependent.c: 1. combine and move
'restart_tic_from_file()' from Version_dependent.c to
Initial_temperature.c 2. fix bug in calculating dimensional
information: E->data.layer_km is in kilometers, not in meters.
2003-11-27 05:24 tan2
* lib/Full/Make.mm, lib/Regional/Make.mm: remove options related to
library linking
2003-11-26 02:41 puru
* module/Exchanger/InteriorImposing.cc: fixed a bug
2003-11-26 01:58 puru
* module/Exchanger/InteriorImposing.cc,
module/Exchanger/InteriorImposing.h,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: Added facility (recvV) for CitcomS
to receive velocity boundary condition in Snac-Citcom coupling
2003-11-25 10:59 tan2
* module/Exchanger/AbstractSource.h,
module/Exchanger/FEMInterpolator.h,
module/Exchanger/InformationSourceSink.h: base classes for
exchanger
2003-11-25 05:38 ces74
* lib/Common/Instructions.c: The line for assigning memory to
E->traction[] has been removed.
2003-11-25 05:37 ces74
* lib/Common/global_defs.h: traction[] array removed.
2003-11-25 05:37 ces74
* lib/Common/Topo_gravity.c: populate E->gstress in get_STD_topo.
2003-11-25 05:26 ces74
* lib/Common/Instructions.c: memory allocation to "E->gstress" and
"E->traction[j]".
2003-11-25 05:25 ces74
* lib/Common/global_defs.h: new data members, "gstress" and
"traction", added to the "All_variables" structure.
2003-11-25 05:22 ces74
* module/Exchanger/Interpolator.cc: a typo fixed
2003-11-25 05:03 ces74
* module/Exchanger/Interpolator.h: The prototype of "interpolateF"
added to the class "Interpolator" as a public member function.
2003-11-25 05:03 ces74
* module/Exchanger/Source.h: The prototype of "interpolateF" added
to the class "Source" as a public member function.
2003-11-24 03:08 ces74
* module/Exchanger/exchangers.h: the definition of
"pyExchanger_sendTraction" added.
2003-11-24 03:06 ces74
* module/Exchanger/exchangers.cc: Python binding for sendTraction
implemented.
2003-11-24 03:04 ces74
* module/Exchanger/bindings.cc: "sendTraction" added to Exchanger's
method table
2003-11-24 02:25 ces74
* module/Exchanger/BoundaryCondition.cc: a typo fixed
2003-11-24 02:25 ces74
* module/Exchanger/BoundaryCondition.cc:
BoundaryConditionSource::sendTraction() has been implemented.
This is for sending CitcomS' traction to other app as force BC.
2003-11-24 02:21 ces74
* module/Exchanger/BoundaryCondition.h: 1. A datamember, "fbc",
added to the class, "BoundaryConditionSource". 2. A public
memberfunction, "sendTraction()" added to
"BoundaryConditionSource".
These are for sending CitcomS' traction to other app. as force
BC.
2003-11-24 02:11 ces74
* module/Exchanger/Source.cc: a typo fixed
2003-11-24 02:10 ces74
* module/Exchanger/Source.cc: Source::interpolateF added. This is
for sending CitcomS' traction to other app's as force BC.
2003-11-24 02:05 ces74
* module/Exchanger/Interpolator.cc: a typo fixed
2003-11-24 02:02 ces74
* module/Exchanger/Interpolator.cc: interpolateF added. This is for
sending CitcomS' traction to other app's force BC.
2003-11-23 16:33 steve
* module/Regional/Make.mm: changed from $(TOOLS_DIR)/lib to
$(TOOLS_LIBDIR) as the former is not always true (if you let pyre
choose the export dir it will be in .../lib/Linux...)
2003-11-23 16:31 steve
* module/Full/Make.mm: changed from $(TOOLS_DIR)/lib to
$(TOOLS_LIBDIR) as the former is not always true (if you let pyre
choose the export dir it will be in .../lib/Linux...)
2003-11-22 07:15 tan2
* module/Exchanger/AreaWeightedNormal.cc,
module/Exchanger/Boundary.cc,
module/Exchanger/BoundaryCondition.cc,
module/Exchanger/BoundedMesh.h, module/Exchanger/Interior.cc,
module/Exchanger/InteriorImposing.cc: 1. attribute name changed:
BoundedMesh.meshID ==> BounedMesh.nodeID 2. in
BoundaryConditionSink::imposeTBC, call 'temperatures_conform_bcs'
2003-11-20 03:06 tan2
* lib/Full/Read_input_from_files.c: restart file has cap number
0~11 (was 1~12)
2003-11-12 03:45 ces74
* module/Exchanger/BoundaryCondition.cc: setTBCFlag and imposeTBC
completed.
2003-11-12 03:29 tan2
* module/Exchanger/AreaWeightedNormal.cc,
module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h,
module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/Interior.cc, module/Exchanger/Interior.h,
module/Exchanger/InteriorImposing.cc,
module/Exchanger/InteriorImposing.h,
module/Exchanger/Interpolator.cc, module/Exchanger/Sink.cc,
module/Exchanger/Sink.h, module/Exchanger/Source.h,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h, module/Exchanger/misc.cc,
pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: 2-way
communication
2003-11-11 05:59 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: change in
BoundaryConditionSink c'tor
2003-11-11 05:55 tan2
* module/Exchanger/AreaWeightedNormal.cc,
module/Exchanger/AreaWeightedNormal.h,
module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h,
module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/BoundaryCondition.cc,
module/Exchanger/BoundaryCondition.h,
module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h,
module/Exchanger/Interior.h, module/Exchanger/Make.mm,
module/Exchanger/Sink.h, module/Exchanger/Source.h,
module/Exchanger/exchangers.cc, module/Exchanger/utilTemplate.cc,
module/Exchanger/utilTemplate.h, module/Exchanger/utility.cc,
module/Exchanger/utility.h: 1. multi-processor AreaWeightedNormal
2. small improvements
2003-11-08 05:43 puru
* module/Exchanger/InteriorImposing.cc,
module/Exchanger/InteriorImposing.h,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: added bindings for two way
communication
2003-11-08 04:41 puru
* module/Exchanger/Interior.cc: Made it easier to read and
initialized bbox_
2003-11-08 04:39 puru
* module/Exchanger/InteriorImposing.cc,
module/Exchanger/InteriorImposing.h: Added InteriorImposing for
two-way communication
2003-11-07 13:47 puru
* module/Exchanger/Interior.cc: fixed the bug
2003-11-07 13:14 puru
* module/Exchanger/Interior.cc: Set interior nodes for two way
communication
2003-11-07 09:20 tan2
* module/Exchanger/BoundaryCondition.cc,
module/Exchanger/BoundaryCondition.h: remove unnecessary base
class BoundaryCondition
2005-08-23 03:21 unknown_user
* module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h,
module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h,
module/Exchanger/auto_array_ptr.h: [vcp] delete of edited
revision with dead state
2003-11-07 09:08 tan2
* module/Exchanger/AreaWeightedNormal.cc,
module/Exchanger/AreaWeightedNormal.h,
module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h,
module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/BoundaryCondition.cc,
module/Exchanger/BoundaryCondition.h,
module/Exchanger/BoundedBox.cc, module/Exchanger/BoundedBox.h,
module/Exchanger/BoundedMesh.cc, module/Exchanger/BoundedMesh.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h, module/Exchanger/DIM.h,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/Exchangermodule.cc,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h,
module/Exchanger/Interior.cc, module/Exchanger/Interior.h,
module/Exchanger/Interpolator.cc,
module/Exchanger/Interpolator.h, module/Exchanger/Make.mm,
module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h,
module/Exchanger/Sink.cc, module/Exchanger/Sink.h,
module/Exchanger/Source.cc, module/Exchanger/Source.h,
module/Exchanger/auto_array_ptr.h, module/Exchanger/bindings.cc,
module/Exchanger/bindings.h, module/Exchanger/exceptions.cc,
module/Exchanger/exceptions.h, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h,
module/Exchanger/initTemperature.cc,
module/Exchanger/initTemperature.h, module/Exchanger/misc.cc,
module/Exchanger/misc.h, module/Exchanger/utilTemplate.cc,
module/Exchanger/utilTemplate.h,
pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
pyre/CoupledApp.py, pyre/Coupler.py, pyre/Layout.py,
pyre/Solver/Solver.py: point-to-point communication
2003-10-31 07:36 tan2
* module/Exchanger/ExchangerClass.cc, module/Exchanger/Mapping.cc:
replace c functions/macros (fabs, min, max) with c++ functions
2003-10-31 07:28 tan2
* lib/Common/global_defs.h: add "#if defined(__cplusplus)" clause
to skip macro (max, min, SWAP) definition when included in C++
2003-10-31 06:45 tan2
* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: fixed a
bug that send/receive used different tag.
2003-10-31 06:25 tan2
* tests/Make.mm, tests/array2d.cc: add tests for Array2D class
2003-10-31 06:21 tan2
* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: 1. add
non-blocking version of send/receive 2. move inlined function
definition from .h to .cc file
2003-10-30 02:40 tan2
* module/Full/Make.mm, module/Regional/Make.mm,
module/Regional/bindings.cc,
module/Regional/initial_conditions.cc,
module/Regional/initial_conditions.h, module/Regional/mesher.cc,
module/Regional/stokes_solver.cc,
module/Regional/stokes_solver.h, pyre/Components/IC.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Solver/Solver.py: 1. let IC initialize temperature,
pressure, velocity, and viscosity fields 2. let Incompressible
call general_stokes_solver_setup() 3. coupler.initTemperature
replaces ic.initTemperature
2003-10-30 01:18 tan2
* module/Exchanger/Array2D.h: index range check when debugging
2003-10-29 09:13 tan2
* pyre/CoupledApp.py, pyre/Coupler.py, pyre/Solver/Solver.py: bug
fix and small improvement
2003-10-29 07:52 tan2
* module/Regional/bindings.cc, module/Regional/setProperties.cc,
module/Regional/setProperties.h: add Solver_set_properties() and
its binding
2005-08-23 03:20 unknown_user
* pyre/Components/Stokes_solver/Stokes_solver.py: [vcp] delete of
edited revision with dead state
2003-10-29 07:51 tan2
* pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/Advection_diffusion/__init__.py,
pyre/Components/BC.py, pyre/Components/Const.py,
pyre/Components/Exchanger/__init__.py, pyre/Components/IC.py,
pyre/Components/Param.py, pyre/Components/Phase.py,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Sphere/Sphere.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Stokes_solver/Stokes_solver.py,
pyre/Components/Stokes_solver/__init__.py,
pyre/Components/Visc.py, pyre/CoupledApp.py, pyre/SimpleApp.py,
pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py,
pyre/Solver/Solver.py: 1. move properties around 2. provide
default argurments to all constructors or factories
2003-10-29 03:57 tan2
* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: 1. add
sendSize(), receiveSize(), broadcastSize() and empty() methods 2.
send(), receive(), and broadcast() will send/recieve size
information and adjust its memory accordingly
2003-10-29 01:24 tan2
* pyre/Controller.py: *** empty log message ***
2003-10-28 10:34 puru
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h,
module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: Two way
communication between Coarse and Fine Grid has been incorporated
2003-10-28 09:56 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Solver/Solver.py: fixed bugs in time marching and output
2003-10-28 09:55 tan2
* pyre/Components/Sphere/__init__.py: add default component name
2003-10-28 09:52 tan2
* module/Make.mm: change the order of complilation: Exchanger/ is
done last
2003-10-28 09:51 tan2
* module/Exchanger/ExchangerClass.cc: change to Array2D.swap()
2003-10-28 09:51 tan2
* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: 1.
implementation changed: using vector as internal representation
2. swap() becomes a member function
2003-10-25 07:45 ces74
* lib/Full/Version_dependent.c: a bug fixed in
global_derived_values(): nox = E->mesh.mgunitx * (int)
pow(2.0,(double)i), etc. ===> nox = E->mesh.mgunitx * (int)
pow(2.0,(double)i)*E->parallel.nprocx, etc.
2003-10-24 12:23 tan2
* tests/coupledcitcoms.py, tests/exchange.py, tests/test1.sh,
tests/test2.sh: update tests according to changes in module/ and
pyre/
2003-10-24 12:04 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
pyre/Components/Exchanger/__init__.py: 1. remove unsed attributes
'localLeader' 2. in __init__.py, factory methods now doesn't need
any argument
2005-08-23 03:19 unknown_user
* pyre/Controller/Make.mm, pyre/Controller/__init__.py,
pyre/Coupler/Coupler.py, pyre/Coupler/Make.mm,
pyre/Coupler/__init__.py, pyre/Layout/Layout.py,
pyre/Layout/Make.mm, pyre/Layout/__init__.py: [vcp] delete of
edited revision with dead state
2003-10-24 11:55 tan2
* pyre/Controller.py, pyre/Controller/Controller.py,
pyre/Controller/Make.mm, pyre/Controller/__init__.py,
pyre/CoupledApp.py, pyre/Coupler.py, pyre/Coupler/Coupler.py,
pyre/Coupler/Make.mm, pyre/Coupler/__init__.py, pyre/Layout.py,
pyre/Layout/Layout.py, pyre/Layout/Make.mm,
pyre/Layout/__init__.py, pyre/Make.mm, pyre/Solver/Solver.py: 1.
move Controller.py, Coupler.py, and Layout.py to pyre/ directory
2. change Make.mm accordingly 3. remove unused attributes
'self.localLeader' in Layout, CoupledApp, and Solver
2003-10-24 11:51 tan2
* module/Exchanger/AreaWeightedNormal.cc,
module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h,
module/Exchanger/Boundary.cc,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h,
module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h,
module/Exchanger/exchangers.cc: 1. add shrink() in Array2D 2. add
shrinksize() in Boundary and Mapping 3. write (most) output via
journal 4. remove unused attribute 'localLeader' in Exchanger
2003-10-24 02:06 puru
* module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: fixed
bugs
2003-10-24 01:26 puru
* module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: added
FindInteriorNodes
2003-10-23 03:33 ces74
* module/Exchanger/AreaWeightedNormal.cc: a bug fixed: in
AreaWeightedNormal::imposeConstraint()
if(outflow > toleranceOutflow_) ==> if (fabs(outflow) >
toleranceOutflow_)
2003-10-22 08:15 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: add
resize() method
2003-10-22 08:13 tan2
* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: 1.
resize() will copy the old data to new memory location 2. make
reset() private (because its syntax in error-prone)
2003-10-22 00:32 tan2
* tests/test2.sh: with correction on outflow
2003-10-22 00:31 tan2
* tests/test2.sh: coupled citcoms test (4-proc coarse-grid solver,
1-proc fine-grid solver, no correction on outflow)
2003-10-22 00:26 tan2
* tests/test1.sh: functional test of exchanger
2003-10-21 00:13 tan2
* module/Exchanger/AreaWeightedNormal.cc,
module/Exchanger/AreaWeightedNormal.h,
module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm:
more small improvements
2003-10-21 00:12 tan2
* module/Exchanger/Array2D.cc: bug in memory allocation fixed
2003-10-20 02:54 tan2
* module/Exchanger/Array2D.h, module/Exchanger/Mapping.h: fixed a
bug in declaration
2003-10-19 08:01 tan2
* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h,
module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h,
module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: many many small improvements
2003-10-18 03:18 ces74
* lib/Common/General_matrix_functions.c: A bug fixed in
solve_del2_u(): now multigrid method can be used.
2003-10-17 03:06 tan2
* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h: 1.
generalize template Array2D<class T, int N>, T can be double,
float, int, or char. 2. using Array2D in class Mapping 3. throw
exception when selftest failed
2003-10-16 01:51 tan2
* module/Exchanger/FineGridExchanger.cc: bug in reduceOutflow()
fixed
2003-10-11 07:40 tan2
* pyre/Components/Exchanger/FineGridExchanger.py: add call to
module.imposeConstraint()
2003-10-11 07:38 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm,
module/Exchanger/Mapping.cc, module/Exchanger/Mapping.h,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: 1. add class 'Mapping' and its
derived classes 'CoarseGridMapping' and 'FineGridMapping' 2. move
'bid2gid', 'bid2proc', 'bid2elem', and 'shape' from Boundary to
Mapping 3. change Exchanger classes accordingly
2003-10-11 07:35 tan2
* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h: add
prefix to the output
2003-10-11 01:14 tan2
* module/Exchanger/Array2D.cc, module/Exchanger/Array2D.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h: 1. replace 'strcut Data' by
'Array2D<int N>', replace 'incoming' and 'outgoing' by
'incomingV', 'outgoingV', 'incomingT' and 'outgoingT' 2.
decompose 'imposeConstraint()' into 'computeWeightedNormal()',
'computeOutflow()', and 'reduceOutflow()'
2003-10-06 11:31 tan2
* lib/Common/global_defs.h: header guard #define directive is added
2003-10-06 11:30 tan2
* lib/Common/Viscosity_structures.c: bug preventing viscosity
initialization is fixed
2003-10-06 08:09 puru
* module/Exchanger/Boundary.cc: Bug associated with round off error
of degenerate case in fine grid node to Coarse grid element map
has been fixed.
2003-10-06 07:53 puru
* module/Exchanger/ExchangerClass.cc: bug associated switching of
indices of theta and of theta fi has been fixed
2003-10-06 01:55 tan2
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h: 1. smoother temperature field
in initTemperature() 2. remove obsolete functions
2003-10-05 06:37 puru
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h: added method imposeConstraint
to correct velocities which are consistent with incompressibility
of the fluid.
2003-10-04 21:24 puru
* module/Exchanger/ExchangerClass.cc: Boundary conditions for fine
mesh have been modified to satisfy incompressiblility constraint
in receiveVelocities
2003-10-04 04:50 puru
* module/Exchanger/ExchangerClass.cc: net outflow corresponding to
velocity boundary conditions has been added.
2003-10-04 02:20 tan2
* module/Exchanger/Boundary.cc: bug fix
2003-10-04 01:36 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: 1.
decompose init() to two functions initBound() and
findBoundaryNodes() 2. remove init(), all of its functionality is
done in mapFindGrid() 3. in mapCoarseGrid(), extend the domain
when searching for node mapping 4. use auto_array_ptr for all
member arrays to improve exception safety
2003-10-04 01:25 tan2
* module/Exchanger/auto_array_ptr.h: first import, modified from
Jack W. Reeves' code on March 1996 issue of the C++ Report.
2003-10-04 01:18 tan2
* pyre/Solver/Solver.py: call coupler.launch() right after
mesher.run() to set BC flag and reconstruct ID array
2003-10-04 01:17 tan2
* pyre/Components/Exchanger/FineGridExchanger.py: 1. add call to
self.module.setBCFlag() 2. call mapBoundary() before
sendBoundary() to reflect change in module/Exchanger/Boundary.cc
2003-10-04 01:12 tan2
* module/Exchanger/FineGridExchanger.cc: 1. calculate boundary.size
in a simplified way 2. remove call to boundary.init() (the job of
init() is done in mapFindGrid() now)
2003-10-04 01:10 tan2
* module/Exchanger/misc.cc: init E->mesh.nno in commonE()
2003-10-02 08:14 tan2
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h, module/Exchanger/Make.mm,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: 1. add Exchanger::setBCFlag() to
set BC Flag and reconstruct E->ID 2. add binding to
Exchanger::setBCFlag()
2003-10-02 05:21 tan2
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h:
add Exchanger::initTemperature() and its binding
2003-10-02 05:16 tan2
* pyre/Solver/Solver.py: 1. pass Solver.inventory.datafile to
Param.inventory.datafile to get around a bug in pyre 2. add
solveVelocities() and solverTemperature() 3. comment out
applyBoundaryConditions(). BC is applied by FGE.preVSolverRun()
or CGE.postVSolverRun() 4. fix a logical bug, exchanging
velocities is done at the correct timestep
2003-10-02 05:07 tan2
* pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py: add
property 'datafile' to get around a bug in pyre
2003-10-02 05:06 tan2
* pyre/Coupler.py, pyre/Coupler/Coupler.py: 1. remove
solveVelocities() 2. add preVSolverRun() and postVSolverRun()
2003-10-02 05:04 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: 1. remove
solverVelocities() 2. add preVSolverRun() and postVSolverRun() 3.
add attribute 'toApplyBC' in FGE, which flags applying BC or not
4. print time marching information
2003-09-30 09:02 puru
* module/Exchanger/ExchangerClass.cc: fixed degeneracy associated
with cge=0
2003-09-30 08:50 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: add
solveVelocities() and storeTimestep()
2003-09-30 08:49 tan2
* pyre/Controller.py, pyre/Controller/Controller.py: disable call
to applyBoundaryConditions()
2003-09-30 08:48 tan2
* pyre/Coupler.py, pyre/Coupler/Coupler.py: add solveVelocities()
2003-09-30 08:47 tan2
* pyre/Solver/Solver.py: when coupled, call solveVelocities()
instead of vsolver.run()
2003-09-30 08:45 puru
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h: Interpolated Boundary
conditions for fine mesh from coarse mesh has been added
2003-09-30 08:33 tan2
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1.
add attributes 'fge_t' and 'cge_t' in Exchanger class 2. init
'fge_t' and 'cge_t' in constructor 3. add functions
storeTimestep() in Exchanger class 4. add binding to
storeTimestep()
2003-09-30 07:48 puru
* module/Exchanger/Boundary.cc: Modified to account for multiple
processes
2003-09-30 07:39 tan2
* module/Full/Make.mm, module/Regional/Make.mm: bug fixed
2003-09-30 05:31 puru
* module/Exchanger/Boundary.cc, module/Exchanger/misc.cc: Modified
to account for 2*PI crossover in spherical coordinates system
2003-09-30 03:25 tan2
* module/Full/Make.mm, module/Regional/Make.mm: update library and
include path
2003-09-30 03:23 tan2
* pyre/Layout.py, pyre/Layout/Layout.py: cosmetics
2003-09-30 03:22 tan2
* pyre/Coupler.py, pyre/Coupler/Coupler.py: bug fix
2003-09-30 03:22 tan2
* module/Regional/setProperties.cc: bug in output fixed
2003-09-30 03:21 tan2
* drivers/Citcom.c, lib/Common/Instructions.c,
module/Regional/mesher.cc, pyre/Controller.py,
pyre/Controller/Controller.py, pyre/Solver/Solver.py: 1. open
'fptime' is moved to drivers/Citcom.c 2. rename
open_log_and_time() to open_log() 3. add time ouput in pyre
version
2003-09-30 01:34 puru
* module/Exchanger/Boundary.cc: Implemented more efficient search
of coarse element for fine mesh nodes
2003-09-30 01:06 tan2
* module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h: 1. add helper functions
printDataT() and printDataV() 2. replace old debugging output by
printDataV()
2003-09-30 01:03 tan2
* module/Exchanger/misc.cc: 1. allocate and initialize
E->sphere.cap[].V 2. change debugging output accordingly
2003-09-29 09:52 puru
* module/Exchanger/CoarseGridExchanger.cc: *** empty log message
***
2003-09-29 09:20 puru
* module/Exchanger/misc.cc: fixed a bug
2003-09-29 09:09 puru
* module/Exchanger/misc.cc: converted from cartesian to spherical
coordinates
2003-09-29 09:04 puru
* module/Exchanger/Boundary.cc: Converted from cartesian
coordinates to spherical coordinates
2003-09-29 04:44 tan2
* pyre/CoupledApp.py: change default coarse solver to full version
2003-09-29 04:44 tan2
* pyre/Controller.py, pyre/Controller/Controller.py: pass
'totalTime' and 'steps' to endTimestep()
2003-09-29 04:43 tan2
* pyre/Coupler.py, pyre/Coupler/Coupler.py: 1. remove call to
exchanger.mapBoundary() 2. comment out call to
exchanger.initTemperature()
2003-09-29 03:45 tan2
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1.
wait() and nowait() is replaced by exchangeSignal() 2. add helper
functions exchangeInt(), exchangeDouble() and exchangeFloat()
2003-09-29 03:41 tan2
* module/Exchanger/misc.cc: cosmetics
2003-09-29 03:40 tan2
* pyre/Controller.py, pyre/Controller/Controller.py,
pyre/Coupler.py, pyre/Coupler/Coupler.py, pyre/Solver/Solver.py:
1. add attribute 'self.done' in Controller indicating end of
simulation 2. change argument list and return list of
endTimestep() 3. Coupler can terminate the time marching by
returning False at endTimestep() 4. synchronization between
solvers is done in endTimestep
2003-09-29 03:36 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
tests/exchange.py: 1. synchronization between solvers is done in
endTimestep() (was in NewStep()) 2. pass the test on
synchronization 3. delete functions createDataArrays() and
deleteDataArrays()
2003-09-28 22:47 tan2
* module/Exchanger/ExchangerClass.cc: check proc. rank in
imposeBC()
2003-09-28 22:36 tan2
* module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/FineGridExchanger.cc: call createDataArrays()
inside mapBoundary()
2003-09-28 13:03 tan2
* module/Exchanger/misc.cc: allocate and init E->node and E->cap.VB
2003-09-28 13:01 tan2
* pyre/Components/Exchanger/FineGridExchanger.py: finish test
2003-09-28 07:35 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
tests/exchange.py: 1. rename 'leaderRank' to 'leader' 2. remove
unused functions
2003-09-28 07:34 tan2
* module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: remove unused bindings
2003-09-28 07:30 tan2
* pyre/Layout.py, pyre/Layout/Layout.py, pyre/Solver/Solver.py:
rename attribute 'leaderRank' to 'leader'
2003-09-28 07:11 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h,
module/Exchanger/exchangers.cc: 1. remove attribute 'lrank' in
Exchanger class 2. 'rank' is processor rank in local communicator
3. modify Exchanger::createDataArray() and
Exchanger::deleteDataArray() 4. gather() and distribute() become
pure virtual functions 5. finish CGE::gather() 6. rename
interpolate() to interpretate() 7. modify CGE::interpretate()
2003-09-28 04:04 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: 1.
bid2proc contains current proc. rank (was current capid) 2. add
sendBid2proc(), which send bid2proc array of each processor to
localLeader 3. add printBid2proc() and printBid2elem() for
debugging
2003-09-28 03:52 tan2
* module/Exchanger/exchangers.cc: change argument list of
create*Exchanger()
2003-09-28 03:30 tan2
* module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h: 1. add attribute
'leaderRank' 2. change argument list of constructors 3. rewrite
sendVelocities() and receiveVelocities()
2003-09-28 03:24 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
pyre/CoupledApp.py, pyre/Solver/Solver.py: 1. add attribute
'leaderRank' 2. pass 'leaderRank' to createExchanger()
2003-09-28 03:17 tan2
* pyre/Layout.py, pyre/Layout/Layout.py: add attribute 'leaderRank'
2003-09-28 03:16 tan2
* module/Exchanger/misc.cc: init E->parallel.nproc
2003-09-28 00:12 tan2
* module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h,
module/Exchanger/exchangers.cc: 1. add new attributes 'lrank' 2.
change arugment list of consturctors of all exchangers 3.
cosmetics
2003-09-27 07:30 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py: remove
getBid2crseelem()
2003-09-27 07:29 tan2
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h: add dummy definition of
gather() and distribute()
2003-09-27 07:28 tan2
* module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: 1. remove binding to
CoarseGridExchanger::getBid2crseelem()
2003-09-27 07:27 tan2
* module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h: 1. sendBoundary() and
receiveBoundary() delegate most of their jobs to
Boundary::send(), Boundary::receive() and Boundary::broadcast()
2. change return type of sendBoundary() from int to void 3.
change argument list of mapFineGrid() and mapCoarseGrid() 4.
remove CoarseGridExchanger::getBid2crseelem()
2003-09-27 07:09 tan2
* module/Exchanger/misc.cc: 1. init E->X according domain bound
information in commonE() 2. add initialization of
E->sphere.capid[] 3. change domain bound in FinereturnE()
2003-09-27 07:05 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: 1.
delete attribute 'connectivity' 2. change argument list of
mapFineGrid() and mapCoarseGrid() 3. add send(), receive() and
broadcast() 4. add printBound() 5. move Tetrahedronvolume() and
det3_sub() to private section 6. fix 'delete []' bug in
mapFineGrid() 7. remove redundant initialization of X in
mapFineGrid() 8. cosmetics
2003-09-27 05:04 puru
* module/Exchanger/Boundary.cc: bug fixed
2003-09-27 04:54 ces74
* pyre/Solver/Solver.py: a typo fixed.
2003-09-27 04:11 tan2
* module/Exchanger/misc.cc: reduce repeated codes and do some
cosmetics
2003-09-27 02:04 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
tests/exchange.py: replace self.fine_E and self.coarse_E by
self.all_variables
2003-09-27 02:03 tan2
* pyre/Layout.py, pyre/Layout/Layout.py: change back: 'coarse' is
full CitcomS
2003-09-27 01:24 puru
* module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc: bid2crseelem has been
replaced with more obvious bid2elem and bid2proc
2003-09-27 01:23 puru
* module/Exchanger/Boundary.cc: bid2crseelem with more obvious
bid2elem and bid2proc have been introduced
2003-09-27 00:33 tan2
* module/Exchanger/Boundary.cc: uncomment self test
2003-09-27 00:01 ces74
* module/Exchanger/ExchangerClass.cc: Exchanger::imposeBC fixed.
2003-09-26 08:05 ces74
* module/Exchanger/ExchangerClass.cc: ImposeBC now changes flags of
boundary nodes.
2003-09-26 05:47 ces74
* module/Exchanger/CoarseGridExchanger.cc: test output modified in
CoarseGridExchanger::interpolate
2003-09-26 05:45 ces74
* module/Exchanger/Boundary.cc: an error fixed in
Boundary::getBid2crseelem
2003-09-26 05:37 ces74
* module/Exchanger/Boundary.cc: Test part of
Boundary::getBid2crseelem() is temporarily commented out.
2003-09-26 05:25 ces74
* module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/FineGridExchanger.h: gather and distribute are
members of Exchanger Class.
2003-09-26 05:14 ces74
* module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h:
CoarseGridExchanger.interpolateTemperature added
2003-09-26 05:14 ces74
* module/Exchanger/bindings.cc:
CoarseGridExchanger.interpolateTemperature addedcc
2003-09-26 02:17 ces74
* module/Exchanger/CoarseGridExchanger.cc: errors fixed in
CoarseGridExchanger::interpolate.
2003-09-26 02:16 ces74
* module/Exchanger/FineGridExchanger.cc: boundary->bid2gid is
transferred from Fine to Coarse Grid.
2003-09-25 10:37 ces74
* module/Exchanger/Boundary.cc: theta_max, theta_min, fi_max,
fi_min, ro ,ri were being redeclared as local variables --> fixed
so that they are used only as members of boundary class.
2003-09-25 09:51 ces74
* module/Exchanger/CoarseGridExchanger.cc: typo fixed.
2003-09-25 03:14 puru
* module/Exchanger/Boundary.cc,
module/Exchanger/CoarseGridExchanger.cc: Interpolation with
arbitrary element shapes has been added
2003-09-25 02:42 puru
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc: interpolation test added
2003-09-24 11:53 puru
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h:
interpolation from corase to fine has been added
2003-09-23 01:14 ces74
* lib/Common/global_defs.h, lib/Regional/Boundary_conditions.c,
module/Exchanger/Boundary.cc,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h, module/Exchanger/misc.cc,
pyre/Components/Exchanger/FineGridExchanger.py,
tests/exchange.py: 1. in Boundary.cc, bid2gid is now generated in
a consistent way with assigning boundary.X arrays.
2. in ExchangerClass.cc, imposeBC method is added and tested.
2003-09-22 05:24 ces74
* lib/Common/element_definitions.h, module/Exchanger/Boundary.cc,
module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.cc, module/Exchanger/bindings.cc,
module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h,
module/Exchanger/misc.cc,
pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
tests/exchange.py: All the functions needed by Exchanger are
created and tested.
2003-09-20 08:32 ces74
* lib/Common/element_definitions.h, module/Exchanger/Boundary.cc,
module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h,
module/Exchanger/misc.cc,
pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
tests/exchange.py: intermediate updates
2003-09-19 13:32 ces74
* module/Exchanger/Boundary.cc,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h,
module/Exchanger/misc.cc,
pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
tests/exchange.py: send/receive temperature between leader
processors tested.
2003-09-19 05:37 ces74
* module/Exchanger/ExchangerClass.h: *** empty log message ***
2003-09-19 05:03 ces74
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/bindings.cc, module/Exchanger/misc.cc,
module/Exchanger/misc.h,
pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
tests/exchange.py: intermediate updates
2003-09-19 00:16 puru
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/ExchangerClass.h: Exchanger for Coarse grid has
been introduced
2003-09-18 23:12 puru
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/FineGridExchanger.cc: New variables added to
Boundary Class
2003-09-18 06:15 ces74
* module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
tests/exchange.py: two methods for exchanger added: 'gather' and
'distribute'
2003-09-12 23:25 tan2
* tests/citcomsfull.py, tests/citcomsregional.py,
tests/coupledcitcoms.py: test
2003-09-12 05:10 tan2
* module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h: 1. change argument lists of
createBoundary(), sendBoundary(), receiveBoundary() and
mapBoundary() 2. createBoundary(), sendBoundary(),
receiveBoundary() and mapBoundary() have passed test
2003-09-12 04:56 tan2
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h: 1. comment out send() and
receive() declaration 2. change argument list of mapBoundary() 3.
fix some bugs in sendVelocities() and receiveVelocities() 4.
comment out reset_target() 5. add some output in constructor
(commented out)
2003-09-12 04:50 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h: add
printX() and printBid2gid() methods
2003-09-12 04:43 tan2
* module/Exchanger/exchangers.cc: change the argument lists of
createBoundary(), sendBoundary(), receiveBoundary(), and
mapBoundary()
2003-09-12 04:41 tan2
* module/Exchanger/misc.cc: add All_variables data, which is
required by Boundary object
2003-09-12 04:33 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: findBoundary will
not return boundary object
2003-09-12 04:32 tan2
* tests/exchange.py: change output slightly
2003-09-11 11:07 puru
* module/Exchanger/Boundary.cc: duplication of nodes on edges and
vertices are removed
2003-09-11 06:40 puru
* module/Exchanger/Boundary.cc: Duplication of nodes on edges and
vertices has been fixed
2003-09-11 04:11 puru
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h: Boundary mapping completed
2003-09-11 01:51 ces74
* module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/ExchangerClass.cc: Added: functions to
send/receive velocities between leader and workers
2003-09-10 11:03 tan2
* module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h, module/Exchanger/bindings.cc,
module/Exchanger/exchangers.cc, module/Exchanger/exchangers.h: 1.
finish exchangeTimestep(), wait() and nowait() to Exchanger, test
passed 2. add skeleton of sendTemperature() and
receiveTemperature() to Exchanger 3. add bindings to the
functions above
2003-09-10 11:01 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: finish
stableTimestep() and NewStep()
2003-09-10 11:00 tan2
* tests/exchange.py: 1. add test for stableTimestep() and NewStep()
2003-09-10 04:08 tan2
* tests/exchange.py: reflecting changes in Exchanger.py
2003-09-10 04:04 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py, pyre/Coupler.py,
pyre/Coupler/Coupler.py, pyre/Solver/Solver.py: 1. remove
exchanger.initialize() 2. change argument lists of
initTemperature() and applyBoundaryConditions() 3. add more calls
to Coupler in Solver
2003-09-10 03:57 tan2
* module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h, module/Exchanger/misc.cc,
module/Exchanger/misc.h: 1. add boundary as a data member of
Exchanger 2. assign boundary at sendBoundary and receiveBoundary
3. change argument list of gather, distribute, send and receive
functions
2003-09-10 03:41 puru
* module/Exchanger/FineGridExchanger.cc: global_defs.h has been
included
2003-09-10 03:07 puru
* module/Exchanger/FineGridExchanger.cc: fixed bug
2003-09-10 03:03 puru
* module/Exchanger/FineGridExchanger.cc: size in
FineGridExchanger::createBoundary has been set
2003-09-10 01:25 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: 1. declare map() in Boundary class
2. changer argument list of several Exchanger functions
2003-09-09 09:35 tan2
* module/Exchanger/Boundary.cc, module/Exchanger/Boundary.h,
module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h: 1. move declartion and definition
of Boundary class to seperated files (was in ExchangerClass.h) 2.
add boundary creation and exchanging functions 3. add bindings to
boundary creation and exchanging functions
2003-09-09 09:28 tan2
* tests/exchange.py: add test to Exchanger.findBoundary()
2003-09-09 09:27 tan2
* pyre/Layout.py, pyre/Layout/Layout.py: createIntercomm() returns
mpi.world()
2005-08-23 03:11 unknown_user
* module/Exchanger/Exchanger.cc, module/Exchanger/Exchanger.h:
[vcp] delete of edited revision with dead state
2003-09-09 04:47 tan2
* module/Exchanger/CoarseGridExchanger.cc,
module/Exchanger/CoarseGridExchanger.h,
module/Exchanger/Exchanger.cc, module/Exchanger/Exchanger.h,
module/Exchanger/ExchangerClass.cc,
module/Exchanger/ExchangerClass.h,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm,
module/Exchanger/bindings.cc, module/Exchanger/exchangers.cc,
module/Exchanger/exchangers.h, module/Exchanger/misc.cc: 1.
change filename Exchanger.* -> ExchangerClass.* to avoid import
problem in python 2. add constructors to Exchanger and its child
class 3. add bindings to constructors
2003-09-09 04:38 tan2
* module/Make.mm: add Exchanger module`
2003-09-09 04:37 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py: createExchanger()
is done
2003-09-09 04:35 tan2
* tests/exchange.py: test for Exchanger component
2003-09-07 06:44 tan2
* module/Exchanger, module/Exchanger/Exchanger.cc,
module/Exchanger/Exchanger.h,
module/Exchanger/Exchangermodule.cc,
module/Exchanger/FineGridExchanger.cc,
module/Exchanger/FineGridExchanger.h, module/Exchanger/Make.mm,
module/Exchanger/bindings.cc, module/Exchanger/bindings.h,
module/Exchanger/exceptions.cc, module/Exchanger/exceptions.h,
module/Exchanger/misc.cc, module/Exchanger/misc.h: original
source
2003-09-06 02:49 tan2
* pyre/Components/Exchanger/CoarseGridExchanger.py,
pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/FineGridExchanger.py,
pyre/Components/Exchanger/Make.mm,
pyre/Components/Exchanger/__init__.py, pyre/CoupledApp.py,
pyre/Coupler.py, pyre/Coupler/Coupler.py,
pyre/Coupler/__init__.py, pyre/Layout.py, pyre/Layout/Layout.py,
pyre/Layout/__init__.py, pyre/Solver/FullSolver.py,
pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: add
skeletons of coupler and exchanger, change application, layout,
and solver accordingly.
2005-08-23 03:10 unknown_user
* pyre/FullApp.py, pyre/RegionalApp.py: [vcp] delete of edited
revision with dead state
2003-09-06 02:26 tan2
* pyre/FullApp.py, pyre/RegionalApp.py: obsolete
2005-08-23 03:10 unknown_user
* pyre/CoupledRegionalApp.py: [vcp] delete of edited revision with
dead state
2003-09-06 02:25 tan2
* pyre/CoupledRegionalApp.py: obsolete
2003-09-04 04:18 tan2
* pyre/CoupledApp.py, pyre/SimpleApp.py: 1. change layout() to
findLayout() 2. change calling sequence in initialize()
2003-09-04 04:16 tan2
* pyre/Layout.py, pyre/Layout/Layout.py: 1. change layout() to
initialize() 2. create intercommunicator (not finished)
2003-09-04 04:13 tan2
* pyre/Controller.py, pyre/Controller/Controller.py: add
Controller.initialize()
2003-09-04 04:08 tan2
* pyre/Solver/Solver.py: Solver is now "coupler-awared". It will
initialize/launch coupler and call coupler.stableTimestep() and
coupler.applyBoundaryConditions() if necessary.
2003-09-03 11:02 ces74
* examples/Full/velbc/README: Typos fixed.
2003-09-03 11:01 ces74
* examples/Regional/velbc/README,
examples/Regional/velbc/velbc_regional.tar.gz: 1. Velbc example
files are now tarred and compressed.
2. README file explains how to untar the provided velbc archive
and the naming scheme of the velbc files.
2003-09-03 10:57 ces74
* examples/Full/input.sample, examples/Full/velbc,
examples/Full/velbc/README,
examples/Full/velbc/velbc_full.tar.gz: 1. input.sample has been
modified to show how to read in velocity b.c. from files.
2. The gzipped tar file, velbc_full.tar.gz, contains velbc files
for each M.Y. and for each sphereical cap.
3. README explains how to untar the velbc files and their naming
scheme.
2003-09-03 07:23 ces74
* examples/Regional/input.sample, examples/Regional/velbc,
examples/Regional/velbc/velbc_regional40,
examples/Regional/velbc/velbc_regional41: 1. The example input
file is modified to show how to use velbc files.
2. velbc directory is added together with velbc examples.
2003-09-02 01:30 ces74
* lib/Common/Problem_related.c, lib/Full/Make.mm,
lib/Full/Read_input_from_files.c, lib/Regional/Make.mm,
lib/Regional/Read_input_from_files.c: 1. The function to read in
velocity boundary conditions for every My is removed from
Common/Problem_related.c.
2. A new file, Read_input_from_files.c is added to lib/Full/ and
lib/Regional/. This file contains a sinlge function
'read_input_files_for_timesteps'.
3. Full/Make.mm and Regional/Make.mm have been changed
accordingly.
2003-09-01 09:02 ces74
* drivers/Full/Make.mm, drivers/Regional/Make.mm: A bug fixed in
the Makefiles:
The rule for linking binaries, CitcomSFull and CitcomSRegional,
had libCitcomSCommon.a and libCitcomSFull(or Regional).a as
dependencies.
--> now these are treated as libraries to which Citcom.o is
linked.
2005-08-23 03:10 unknown_user
* pyre/Components/Coupler.py, pyre/Components/Exchanger.py: [vcp]
delete of edited revision with dead state
2003-08-30 07:45 tan2
* pyre/Components/Coupler.py, pyre/Components/Exchanger.py,
pyre/Components/Make.mm, pyre/Make.mm: change directory structure
2003-08-30 07:44 tan2
* pyre/Components/Exchanger/Exchanger.py,
pyre/Components/Exchanger/Make.mm,
pyre/Components/Exchanger/__init__.py: original source
2003-08-30 07:39 tan2
* pyre/Components/Exchanger,
pyre/Components/Exchanger/Exchanger.py, pyre/CoupledApp.py:
original source
2003-08-30 07:37 tan2
* pyre/Coupler, pyre/Coupler/Make.mm, pyre/Coupler/__init__.py:
original source
2003-08-30 07:35 tan2
* pyre/Layout, pyre/Layout.py, pyre/Layout/Layout.py,
pyre/Layout/Make.mm, pyre/Layout/__init__.py: original source
2003-08-30 07:29 ces74
* pyre/Components/Advection_diffusion/Advection_diffusion.py:
'maxadvtime' is removed from Advection_diffusion.inventory.
2003-08-30 07:27 ces74
* pyre/Components/Param.py: The following five parameters are
removed from the Param.inventory.
minstep, maxstep, maxtotstep, storage_spacing,
cpu_limits_in_seconds
2003-08-30 07:24 ces74
* drivers/Citcom.c: 1. A step is added to decide whether to proceed
time-marching.
2. max_dimensionless_time is not a criterion for time-marching
any more.
2003-08-30 07:19 ces74
* lib/Common/Advection_diffusion.c: The following parameters are no
more used in PG_timestep_solve:
minstep, maxstep, and maxtotstep
2003-08-30 03:41 tan2
* pyre/SimpleApp.py, pyre/Solver/FullSolver.py,
pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: use new
interface of Facilities
2003-08-30 03:40 tan2
* pyre/Facilities/Mesher.py, pyre/Facilities/Solver.py,
pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py: change
argument list of __init__() to be compatible with pyre facility
2003-08-30 02:46 tan2
* pyre/Facilities/Make.mm, pyre/Facilities/Solver.py,
pyre/SimpleApp.py: add Solver facility and use it in SimpleApp.py
2003-08-30 01:33 tan2
* pyre/Controller.py, pyre/Controller/Controller.py: 1. change
march() so that final step is saved 2. remove
run_init_simulation() 3. change the argument list of save()
2003-08-30 01:31 tan2
* pyre/Solver/Solver.py: merge run_init_simulation() with launch()
2003-08-30 01:06 tan2
* pyre/SimpleApp.py, pyre/Solver/Solver.py: communicator is
assigned in Application
2003-08-29 07:43 tan2
* pyre/Make.mm: add SimpleApp.py
2003-08-29 07:08 tan2
* pyre/SimpleApp.py, tests/citcomsregional.py: 1. add SimpleApp,
which using Controller and Solver componets 2. change
citcomsregional.py accordingly
2003-08-29 06:58 tan2
* pyre/Controller.py, pyre/Controller/Controller.py,
pyre/Solver/Solver.py: fix typos
2003-08-29 06:18 ces74
* pyre/Solver/Solver.py: bug fixed in the 'advance' method: tsolver
and vsolver are now defined before being used.
2003-08-29 06:12 ces74
* pyre/Controller/__init__.py: bug fixed: Controller is now
imported before being used.
2003-08-29 06:10 ces74
* pyre/Make.mm: Controller is added to 'BLD_DIRS'
2003-08-29 06:04 ces74
* pyre/Controller.py, pyre/Controller/Controller.py,
pyre/Controller/Make.mm, pyre/Controller/__init__.py,
pyre/Solver/Solver.py: 1. Controller.py modified:
self.solver.start_simulation --> self.solver.launch 2. Solver. py
modified: self.start_simulation --> self.launch 3. Make.mm and
__init__.py added to CitcomS/pyre/Controller/
2003-08-29 05:53 ces74
* pyre/Controller, pyre/Controller.py,
pyre/Controller/Controller.py: Controller.py newly added. It's a
derivation from pyre/components/SimulationController.py.
2003-08-29 05:49 ces74
* pyre/Solver/Solver.py: method endSimulation modified:
endSimulation(self) --> endSimulation(self,step)
2003-08-29 05:37 ces74
* pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Solver/Solver.py: 1. Solver.py modified to be consistent
with 'Controller'.
2. Advection_diffusion.py A new method, 'launch', runs
PG_timestep_init(). The '_solve' method now executes only
PG_timestep_solve()
2005-08-23 03:09 unknown_user
* pyre/Citcom.py, pyre/CitcomSFull.py, pyre/CitcomSRegional.py:
[vcp] delete of edited revision with dead state
2003-08-28 05:24 tan2
* pyre/Citcom.py, pyre/CitcomSFull.py, pyre/CitcomSRegional.py,
pyre/FullApp.py, pyre/Make.mm, pyre/RegionalApp.py,
pyre/Solver/FullSolver.py, pyre/Solver/Make.mm,
pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py,
pyre/Solver/__init__.py: 1. move and rename files: Citcom.py ->
Solver/Solver.py CitcomSFull.py -> Solver/FullSolver.py
CitcomSRegional.py -> Solver/RegionalSolver.py 2. add Solver
module 3. change Make.mm, FullApp.py and RegionalApp.py
accordingly
2005-08-23 03:08 unknown_user
* pyre/Components/Parallel.py: [vcp] delete of edited revision with
dead state
2003-08-28 03:52 tan2
* pyre/Citcom.py, pyre/CitcomSFull.py, pyre/CitcomSRegional.py,
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/Advection_diffusion/__init__.py,
pyre/Components/BC.py, pyre/Components/CitcomComponent.py,
pyre/Components/Const.py, pyre/Components/IC.py,
pyre/Components/Parallel.py, pyre/Components/Param.py,
pyre/Components/Phase.py, pyre/Components/Sphere/FullSphere.py,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Sphere/Sphere.py,
pyre/Components/Sphere/__init__.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Stokes_solver/__init__.py,
pyre/Components/Visc.py, pyre/CoupledRegionalApp.py,
pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py,
pyre/Solver/Solver.py: simplified components layout
2003-08-27 03:58 tan2
* pyre/Components/Advection_diffusion/Advection_diffusion.py: add
stable_timestep() method
2003-08-27 03:56 tan2
* lib/Common/Advection_diffusion.c,
lib/Common/advection_diffusion.h, module/Regional/advdiffu.cc,
module/Regional/advdiffu.h, module/Regional/bindings.cc: add
stable_timestep() to lib/ and its binding to module/
2003-08-26 02:34 tan2
* pyre/CitcomSFull.py, pyre/FullApp.py, pyre/Solver/FullSolver.py:
add components CitcomSRegional and CitcomSFull
2005-08-23 03:08 unknown_user
* pyre/CitcomApp.py: [vcp] delete of edited revision with dead
state
2003-08-26 02:16 tan2
* pyre/Citcom.py, pyre/CitcomApp.py, pyre/CitcomSRegional.py,
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/Sphere/Sphere.py,
pyre/Components/Stokes_solver/Incompressible.py, pyre/Make.mm,
pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py,
pyre/Solver/Solver.py: add components CitcomSRegional and
CitcomSFull
2003-08-23 05:35 tan2
* pyre/Citcom.py, pyre/CitcomApp.py, pyre/CitcomSFull.py,
pyre/CitcomSRegional.py, pyre/FullApp.py, pyre/RegionalApp.py,
pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py,
pyre/Solver/Solver.py: fix bug introduced by previous check-in
2003-08-23 05:35 tan2
* module/Regional/bindings.cc, module/Regional/setProperties.cc,
module/Regional/setProperties.h: fix typo
2005-08-23 03:07 unknown_user
* pyre/Components/Stokes_solver/Imcompressible.py: [vcp] delete of
edited revision with dead state
2003-08-23 05:24 tan2
* pyre/Components/Stokes_solver/Imcompressible.py: rename file
2003-08-23 05:21 tan2
* drivers/Citcom.c: output is performed every 'storage_spacing'
time step
2003-08-23 05:19 tan2
* tests/citcomsfull.py, tests/citcomsregional.py,
tests/coupledcitcoms.py: *** empty log message ***
2005-08-23 03:07 unknown_user
* pyre/RadiusDepth.py: [vcp] delete of edited revision with dead
state
2003-08-23 05:18 tan2
* pyre/Citcom.py, pyre/CitcomApp.py, pyre/CitcomSFull.py,
pyre/CitcomSRegional.py, pyre/Components/Coupler.py,
pyre/Components/Exchanger.py, pyre/Components/Make.mm,
pyre/CoupledRegionalApp.py, pyre/FullApp.py, pyre/Make.mm,
pyre/RadiusDepth.py, pyre/RegionalApp.py,
pyre/Solver/FullSolver.py, pyre/Solver/RegionalSolver.py,
pyre/Solver/Solver.py: a small step toward coupled application
2003-08-23 05:16 tan2
* pyre/Facilities/VSolver.py: *** empty log message ***
2003-08-23 05:14 tan2
* pyre/Components/Stokes_solver/Imcompressible.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Stokes_solver/Make.mm,
pyre/Components/Stokes_solver/__init__.py: fix typo
2003-08-21 02:18 tan2
* lib/Common/Instructions.c, lib/Common/convection_variables.h,
lib/Common/global_defs.h: remove several obsolelte variables
2003-08-21 01:54 tan2
* lib/Regional/Boundary_conditions.c: add open_top velocity
boundary condition
2003-08-20 09:45 tan2
* tests/citcomsfull.py, tests/citcomsregional.py: determine
staging.nodes from input parameters automatically
2003-08-20 04:24 tan2
* pyre/Citcom.py, pyre/CitcomApp.py,
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/CitcomComponent.py,
pyre/Components/Sphere/FullSphere.py,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Stokes_solver/Imcompressible.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Solver/Solver.py: create a python variable
CitcomApp.all_variables, which holds the C pointer "struct
All_varialbes *E". CitcomApp.all_variables is passed as an
argument to most CitcomModule functions.
2003-08-20 04:21 tan2
* module/Regional/advdiffu.cc, module/Regional/mesher.cc,
module/Regional/misc.cc, module/Regional/outputs.cc,
module/Regional/setProperties.cc,
module/Regional/stokes_solver.cc: remove global declaration of
"struct All_variables *E", E is passed as an argument to all
functions.
2003-08-20 04:20 tan2
* drivers/Citcom.c, lib/Common/Citcom_init.c,
lib/Common/Instructions.c, lib/Common/citcom_init.h: 1. remove
declaration of "extern struct All_variables *E" in citcom_init.h
2. E is allocated in Citcom_init() and returned to main() 3.
change other files accordingly.
2003-08-16 01:59 tan2
* lib/Common/Drive_solvers.c, lib/Common/drive_solvers.h: *** empty
log message ***
2003-08-16 01:56 tan2
* module/Regional/bindings.cc, module/Regional/stokes_solver.cc,
module/Regional/stokes_solver.h: remove obsolete bindings to
general_stokes_solver_*()
2003-08-16 01:56 tan2
* module/Regional/setProperties.cc,
module/Regional/setProperties.h: change function name:
pyCitcom_Stokes_solver_set_properties() ->
pyCitcom_Imcompressible_set_properties()
2003-08-16 01:47 tan2
* pyre/Components/Stokes_solver/Imcompressible.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Stokes_solver/__init__.py: merge
ImcompressibleNewtonian() and ImcompressibleNonNewtonian() to
Imcompressible(), Stokes_solver() becomes obsolete.
2003-08-15 07:28 tan2
* lib/Common/Convection.c, lib/Common/Element_calculations.c,
lib/Common/General_matrix_functions.c, lib/Common/global_defs.h,
lib/Full/Lith_age.c, lib/Regional/Boundary_conditions.c,
lib/Regional/Lith_age.c: eliminate static variables
2003-08-15 05:50 tan2
* module/Regional/bindings.cc, module/Regional/mesher.cc,
module/Regional/stokes_solver.cc,
module/Regional/stokes_solver.h,
pyre/Components/Stokes_solver/Stokes_solver.py: reflect the
change in general_stokes_solver()
2003-08-15 05:43 tan2
* lib/Common/Construct_arrays.c, lib/Common/Drive_solvers.c,
lib/Common/Instructions.c: 1. change the flowline of
general_stokes_solver() 2. eliminate static variables in
construct_stiffness_B_matrix() 3. add call to
general_stokes_solver_setup() in read_instructions()
2003-08-15 01:36 tan2
* lib/Full/Parallel_related.c: elimanate static variables.
2003-08-15 01:35 tan2
* module/Full/Make.mm, module/Regional/Make.mm: add
$(TOOLS_DIR)/lib to library path
2003-08-13 08:22 tan2
* module/Full/Make.mm, module/Regional/Make.mm: change the library
link paths
2003-08-13 03:43 ces74
* drivers/Full/Make.mm, drivers/Regional/Make.mm: Modified in order
to use separate static libraries:
libCitcomSCommon.a, libCitcomSFull.a, and libCitcomSRegional.a
2003-08-13 03:40 ces74
* lib/Common/Initial_temperature.c: Typo fixed:
"Missing input parameter: 'perturbml' -> "Missing input
parameter: 'perturbl'
2003-08-12 23:54 ces74
* lib/Full/Make.mm, lib/Regional/Make.mm: a bug fixed: lib/Common
is now included in paths for header files.
2003-08-12 23:34 ces74
* lib/Common/Make.mm, lib/Full/Make.mm, lib/Make.mm,
lib/Regional/Make.mm, module/Full/Make.mm,
module/Regional/Make.mm: Makefiles in module/ and lib/ modified
to create three separate static libraries: libCitcomSCommon.a,
libCitcomSFull.a, and libCitcomSRegional.a
These libraries are used when linking *.so objects.
2003-08-10 03:25 tan2
* lib/Common/Instructions.c, lib/Full/Version_dependent.c,
lib/Regional/Version_dependent.c: unifying
read_initial_settings()
2003-08-09 05:51 tan2
* lib/Common/Make.mm, lib/Full/Make.mm, lib/Full/Output.c,
lib/Regional/Make.mm, lib/Regional/Obsolete.c,
lib/Regional/Output.c: unifying
2003-08-09 05:34 tan2
* lib/Common/Make.mm, lib/Full/Make.mm,
lib/Full/Process_buoyancy.c, lib/Regional/Make.mm,
lib/Regional/Process_buoyancy.c: unifying
2005-08-23 03:05 unknown_user
* pyre/Components/Advection_diffusion/Temperature_diffadv.py: [vcp]
delete of edited revision with dead state
2003-08-09 05:13 tan2
* examples/Full/input.sample, examples/Full/machine.sample,
pyre/Components/Advection_diffusion/Temperature_diffadv.py:
obsolete
2003-08-09 05:03 tan2
* lib/Common/Output.c, lib/Common/Problem_related.c,
lib/Common/Tracer_advection.c, lib/Common/global_defs.h,
lib/Full/Output.c, lib/Full/Parallel_related.c,
lib/Regional/Boundary_conditions.c, lib/Regional/Obsolete.c,
lib/Regional/Output.c, lib/Regional/Parallel_related.c,
lib/Regional/Process_buoyancy.c, lib/Regional/Sphere_related.c,
lib/Regional/Version_dependent.c, module/Regional/bindings.cc,
module/Regional/setProperties.cc,
module/Regional/setProperties.h: 1. eliminate several global
variables- parallel: mst, nproc[xyz]l, me_locl sphere:
local_capid, pid_surf, cap.connection 2. change the way
Regional/Parallel_related.c used to assign me_loc and
PROCESSOR.pass
2003-08-08 05:05 tan2
* module/Make.mm: default action will link files from Regional/ to
Full/
2003-08-08 04:34 tan2
* module/Regional/setProperties.cc: only processor 0 can write to
stderr now Note: device /dev/null and /dev/stderr are used, may
not portable to non-unix platform
2003-08-08 02:49 tan2
* drivers/Citcom.c, lib/Common/Instructions.c,
lib/Common/Sphere_harmonics.c, lib/Common/parallel_related.h,
lib/Full/Obsolete.c, lib/Full/Parallel_related.c,
lib/Regional/Obsolete.c, lib/Regional/Parallel_related.c,
module/Regional/mesher.cc: *** empty log message ***
2003-08-08 01:41 tan2
* drivers/Full/Make.mm, drivers/Full/local.def, drivers/Make.mm,
drivers/Regional/Make.mm, drivers/Regional/local.def,
drivers/local.def, lib/Common/Output.c, lib/Common/global_defs.h,
lib/Full/Output.c, lib/Full/global_defs.h, lib/Full/lith_age.h,
lib/Full/output.h, lib/Full/parallel_related.h, lib/Make.mm,
lib/Regional/global_defs.h, lib/Regional/lith_age.h,
lib/Regional/output.h, lib/Regional/parallel_related.h,
lib/local.def: move header files global_defs.h, lith_age.h,
output.h, and parallel_related.h to Common/
2003-08-07 04:09 tan2
* lib/Common/Make.mm, lib/Full/Make.mm, lib/Full/Problem_related.c,
lib/Regional/Make.mm, lib/Regional/Problem_related.c: unify
Problem_related.c
2003-08-07 04:00 tan2
* lib/Common/Initial_temperature.c, lib/Common/Make.mm,
lib/Common/convection_variables.h,
lib/Full/Initial_temperature.c, lib/Full/Make.mm,
lib/Full/Version_dependent.c, lib/Full/initial_temperature.h,
lib/Regional/Initial_temperature.c, lib/Regional/Make.mm,
lib/Regional/Version_dependent.c,
lib/Regional/initial_temperature.h,
module/Regional/setProperties.cc: unify Initial_temperature.c and
initial_temperature.h
2003-08-07 01:56 tan2
* lib/Common/Output.c, lib/Full/Obsolete.c, lib/Full/Output.c: move
obsolete functions from Output.c to Obsolete.c
2003-08-07 01:47 tan2
* lib/Common/Global_operations.c, lib/Common/Make.mm,
lib/Full/Global_operations.c, lib/Full/Make.mm,
lib/Full/Obsolete.c, lib/Regional/Global_operations.c,
lib/Regional/Make.mm, lib/Regional/Obsolete.c: unify two versions
of Global_operations.c, and put it to Common/
2003-08-03 07:43 tan2
* module/Regional/setProperties.cc: bug fixed, tests/citcomsfull.py
now gives correct result
2003-08-02 05:57 tan2
* tests/citcomsfull.py, tests/hrothgar.py: to run a Full version of
CitcomS, use the following command: ./citcomsfull.py
--staging=hrothgar --param.datafile=/SOME_PATH/test
2005-08-23 03:02 unknown_user
* module/local.def: [vcp] delete of edited revision with dead state
2003-08-02 05:53 tan2
* module/Make.mm, module/Regional/Regionalmodule.cc,
module/Regional/advdiffu.cc, module/Regional/advdiffu.h,
module/Regional/bindings.cc, module/Regional/bindings.h,
module/Regional/exceptions.cc, module/Regional/exceptions.h,
module/Regional/local.def, module/Regional/mesher.cc,
module/Regional/mesher.h, module/Regional/misc.cc,
module/Regional/misc.h, module/Regional/outputs.cc,
module/Regional/outputs.h, module/Regional/setProperties.cc,
module/Regional/setProperties.h,
module/Regional/stokes_solver.cc,
module/Regional/stokes_solver.h, module/local.def: make some
changes in function names so that both Full and Regioanl versions
can use the same source code.
2005-08-23 03:02 unknown_user
* module/Full/bindings.cc, module/Full/bindings.h,
module/Full/exceptions.cc, module/Full/exceptions.h,
module/Full/misc.cc, module/Full/misc.h: [vcp] delete of edited
revision with dead state
2003-08-02 05:52 tan2
* module/Full/Fullmodule.cc, module/Full/Make.mm,
module/Full/bindings.cc, module/Full/bindings.h,
module/Full/exceptions.cc, module/Full/exceptions.h,
module/Full/local.def, module/Full/misc.cc, module/Full/misc.h:
module/Full and module/Regional now use the same files, except
$(TYPE)module.cc and Make.mm.
***** Important ***** When you check out this directory
(module/Full) in the first time, do 'mm link' in this directory.
This will hard-link every source files in module/Regional to this
directory.
2003-08-02 05:25 tan2
* lib/Full/global_defs.h: add some variable declaration which are
only used by regional version
2003-08-02 05:24 tan2
* pyre/Citcom.py, pyre/CitcomApp.py, pyre/CitcomSFull.py,
pyre/CitcomSRegional.py, pyre/FullApp.py, pyre/Make.mm,
pyre/RegionalApp.py, pyre/Solver/FullSolver.py,
pyre/Solver/RegionalSolver.py, pyre/Solver/Solver.py: 1. add base
class CitcomApp 2. derive FullApp and RegionalApp form CitcomApp
2003-08-02 02:05 tan2
* pyre/Components/Sphere/FullSphere.py,
pyre/Components/Sphere/Make.mm,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Sphere/Sphere.py,
pyre/Components/Sphere/__init__.py, pyre/Facilities/Mesher.py: 1.
add a base class Sphere for component Sphere 2. add a new
component FullSphere for Full version 3. change Make.mm,
__init__.py, and the binder of facility Mesher accordingly
2003-08-01 02:41 tan2
* lib/Common/General_matrix_functions.c,
lib/Common/Initial_temperature.c, lib/Common/Instructions.c,
lib/Full/Initial_temperature.c, lib/Full/Parallel_related.c,
lib/Regional/Initial_temperature.c: bug fix
2003-08-01 02:40 tan2
* lib/Common/Process_buoyancy.c, lib/Full/Obsolete.c,
lib/Full/Process_buoyancy.c: remove obsolete function
2003-07-30 03:54 tan2
* drivers/Make.mm, lib/Make.mm: *** empty log message ***
2003-07-30 03:54 tan2
* lib/Common/Output.c, lib/Common/Process_buoyancy.c,
lib/Full/Boundary_conditions.c, lib/Full/Global_operations.c,
lib/Full/Initial_temperature.c, lib/Full/Lith_age.c,
lib/Full/Make.mm, lib/Full/Output.c, lib/Full/Parallel_related.c,
lib/Full/Problem_related.c, lib/Full/Process_buoyancy.c,
lib/Full/Version_dependent.c, lib/Full/global_defs.h,
lib/Full/initial_temperature.h, lib/Full/lith_age.h,
lib/Full/output.h, lib/Full/parallel_related.h: copy changes in
Regional version to Full version
2003-07-29 06:03 tan2
* pyre/CitcomSRegional.py,
pyre/Components/Advection_diffusion/Make.mm,
pyre/Components/Make.mm, pyre/Components/Sphere/Make.mm,
pyre/Components/Stokes_solver/Make.mm, pyre/Facilities/Mesher.py,
pyre/Facilities/TSolver.py, pyre/Facilities/VSolver.py,
pyre/Make.mm, pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py:
change directory structures
2003-07-29 04:57 tan2
* lib/Common/Convection.c, lib/Common/Solver_multigrid.c,
module/Regional/bindings.cc, module/Regional/outputs.cc,
module/Regional/outputs.h, module/Regional/setProperties.cc,
pyre/CitcomSRegional.py,
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Stokes_solver/Stokes_solver.py,
pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: 1.
RegionalApp._setProperties() is called before Component.init() 2.
some cosmetics
2003-07-27 04:47 tan2
* drivers/Citcom.c, lib/Common/Instructions.c,
lib/Common/Problem_related.c, lib/Common/Process_velocity.c,
lib/Common/output.h, lib/Regional/Obsolete.c,
lib/Regional/Output.c, lib/Regional/Problem_related.c,
lib/Regional/Process_buoyancy.c,
lib/Regional/Version_dependent.c, lib/Regional/output.h,
module/Regional/bindings.cc, module/Regional/mesher.cc,
module/Regional/misc.cc, module/Regional/misc.h,
module/Regional/outputs.cc, module/Regional/outputs.h,
pyre/CitcomSRegional.py, pyre/RegionalApp.py,
pyre/Solver/RegionalSolver.py: complete output part
2003-07-26 03:43 tan2
* drivers/Citcom.c, lib/Common/Advection_diffusion.c,
lib/Common/Initial_temperature.c,
lib/Regional/Initial_temperature.c, module/Regional/advdiffu.cc,
module/Regional/bindings.cc, module/Regional/mesher.cc,
module/Regional/misc.cc, module/Regional/misc.h,
module/Regional/setProperties.cc, pyre/CitcomSRegional.py,
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/Advection_diffusion/__init__.py,
pyre/Components/BC.py, pyre/Components/Const.py,
pyre/Components/Param.py, pyre/Components/Phase.py,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Stokes_solver/Stokes_solver.py,
pyre/Components/Visc.py, pyre/RegionalApp.py,
pyre/Solver/RegionalSolver.py: complete VSolver and TSolver
2003-07-26 02:17 tan2
* lib/Common/Parsing.c: bug fix
2003-07-26 02:13 tan2
* lib/Common/Parsing.c: cosmetic output
2003-07-25 03:10 tan2
* lib/Common/Global_operations.c, lib/Regional/Global_operations.c,
lib/Regional/Parallel_related.c, module/Regional/bindings.cc,
module/Regional/mesher.cc, module/Regional/mesher.h,
module/Regional/setProperties.cc, pyre/CitcomSRegional.py,
pyre/Components/Sphere/RegionalSphere.py, pyre/RegionalApp.py,
pyre/Solver/RegionalSolver.py: finish RegionalSphere.run(), it
gives identical results as stand-alone CitcomSRegional
2003-07-25 00:46 tan2
* pyre/CitcomSRegional.py,
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/Advection_diffusion/__init__.py,
pyre/Components/BC.py, pyre/Components/CitcomComponent.py,
pyre/Components/Const.py, pyre/Components/IC.py,
pyre/Components/Make.mm, pyre/Components/Parallel.py,
pyre/Components/Param.py, pyre/Components/Phase.py,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Sphere/__init__.py,
pyre/Components/Stokes_solver/Imcompressible.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Stokes_solver/Stokes_solver.py,
pyre/Components/Stokes_solver/__init__.py,
pyre/Components/Visc.py, pyre/RegionalApp.py,
pyre/Solver/RegionalSolver.py, tests/citcomsregional.py,
tests/signon.py: 1. remove passing filename to
RegionalApp.__init__() 2. add new base component
CitcomComponent(), derive every component from CitcomComponent,
the interface to __init__ and setProperties are changed
2003-07-24 07:04 tan2
* module/Regional/advdiffu.cc, module/Regional/advdiffu.h,
module/Regional/bindings.cc, module/Regional/misc.cc,
module/Regional/misc.h,
pyre/Components/Advection_diffusion/Advection_diffusion.py: add
binding of set_convection_defaults()
2003-07-24 06:00 tan2
* lib/Common/Initial_temperature.c,
lib/Common/initial_temperature.h,
lib/Regional/Initial_temperature.c,
lib/Regional/Version_dependent.c,
lib/Regional/initial_temperature.h: seperate input and init
phases of temperature IC
2003-07-24 05:59 tan2
* lib/Common/global_defs.h, lib/Regional/global_defs.h,
module/Regional/setProperties.cc: remove global variables
VERBOSE, DESCRIBE, and BEGINNER
2003-07-24 05:00 tan2
* module/Regional/bindings.cc, module/Regional/setProperties.cc,
module/Regional/setProperties.h, pyre/CitcomSRegional.py,
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/Const.py, pyre/Components/Parallel.py,
pyre/Components/Param.py,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Stokes_solver/Stokes_solver.py,
pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: finished
setting properties
2003-07-24 02:00 tan2
* pyre/Components/IC.py: typo fixed
2003-07-23 12:29 ces74
* pyre/Components/BC.py, pyre/Components/Const.py,
pyre/Components/IC.py, pyre/Components/Parallel.py,
pyre/Components/Param.py, pyre/Components/Phase.py,
pyre/Components/Visc.py: '*_set_prop' methods of the 'Regioanl'
module are now called
'*_set_properties'.
2003-07-23 12:27 ces74
* lib/Common/global_defs.h, lib/Regional/global_defs.h: New members
of the "CONTROL" and the "All_variables" structure added.
2003-07-23 12:26 ces74
* lib/Common/Initial_temperature.c,
lib/Regional/Initial_temperature.c: Originally local variables,
number_of_perturbations, perturb_ll, perturb_mm, load_depth, and
perturb_mag,
are now members of the global "All_variables" structure.
2003-07-23 12:22 ces74
* lib/Common/Parsing.c: Originally local variables, VERBOSE,
DESCRIBE, and BEGINNER,
are now global: members of the 'All_variables' structure.
2003-07-23 12:19 ces74
* module/Regional/bindings.cc, module/Regional/outputs.cc,
module/Regional/stokes_solver.cc: function name changed from
*_set_prop to *_set_properties.
2003-07-23 12:18 ces74
* module/Regional/setProperties.cc,
module/Regional/setProperties.h: Properties for the following
components added: IC, Const, Param, Phase, and Parallel.
2003-07-23 04:58 tan2
* module/Regional/bindings.cc, module/Regional/mesher.cc,
module/Regional/misc.cc, module/Regional/misc.h,
pyre/CitcomSRegional.py, pyre/RegionalApp.py,
pyre/Solver/RegionalSolver.py: 1. change Citcom_Init() to
citcom_init() (finished) 2. add binding to open info_file
2003-07-23 02:52 tan2
* lib/Common/Advection_diffusion.c, lib/Common/advection.h: ***
empty log message ***
2003-07-22 04:58 ces74
* lib/Common/Drive_solvers.c: Functions uncommented: void
general_stokes_solver_init(struct All_variables *E) void
general_stokes_solver_fini(struct All_variables *E) void
general_stokes_solver_update_velo(struct All_variables *E) void
general_stokes_solver_Unorm(struct All_variables *E, double
*Udot_mag, double *dUdot_mag) void
general_stokes_solver_log(struct All_variables *E, float
Udot_mag, float dUdot_mag, int count)
2003-07-22 04:44 tan2
* lib/Common/output.h, lib/Regional/Boundary_conditions.c,
lib/Regional/Obsolete.c, lib/Regional/Output.c,
lib/Regional/Parallel_related.c, lib/Regional/output.h: partially
eliminate use of static variables
2003-07-19 07:34 tan2
* lib/Common/Global_operations.c, lib/Common/global_defs.h,
lib/Regional/Global_operations.c,
lib/Regional/Parallel_related.c, lib/Regional/global_defs.h: add
communicators E->parallel.horizontal_comm and
E->parallel.vertical_comm and initialize them at
set_horizontal_communicator() and set_vertical_communicator()
2003-07-19 05:15 tan2
* drivers/Citcom.c: change Citcom_Init() to citcom_init()
2003-07-18 07:10 tan2
* lib/Common/Citcom_init.c, lib/Common/Drive_solvers.c,
lib/Common/Element_calculations.c,
lib/Common/General_matrix_functions.c, lib/Common/Instructions.c,
lib/Common/Interuption.c, lib/Common/Process_velocity.c,
lib/Common/Solver_multigrid.c, lib/Common/Stokes_flow_Incomp.c,
lib/Common/Tracer_advection.c, lib/Common/Viscosity_structures.c,
lib/Common/citcom_init.h, lib/Common/interuption.h: 1. change
Citcom_Init() to citcom_init() 2. add interuption.h, header file
of Interuption.c 3. partially eliminate use of static variables
2003-07-18 06:31 tan2
* lib/Common/Global_operations.c, lib/Regional/Global_operations.c:
vnorm_nonnewt() returned NaN if there was only one material type.
bug? fixed.
2003-07-18 04:19 tan2
* lib/Regional/Sphere_related.c: memory-leak fixed
2003-07-17 04:52 tan2
* lib/Common/global_defs.h, lib/Regional/global_defs.h: add
argument declaration for function pointers (necessarily when
linking with C++)
2003-07-17 04:49 tan2
* module/Regional/Make.mm, module/Regional/bindings.cc,
module/Regional/mesher.cc, module/Regional/mesher.h: add bindings
of component RegionalSphere()
2005-08-23 02:55 unknown_user
* pyre/Components/Mesh.py: [vcp] delete of edited revision with
dead state
2003-07-16 04:53 tan2
* pyre/Components/Make.mm, pyre/Components/Mesh.py: component
Mesh() is replaced by component RegionalSphere()
2003-07-16 04:50 tan2
* pyre/CitcomSRegional.py, pyre/Components/Sphere,
pyre/Components/Sphere/Make.mm,
pyre/Components/Sphere/RegionalSphere.py,
pyre/Components/Sphere/__init__.py, pyre/Facilities/Make.mm,
pyre/Facilities/Mesher.py, pyre/RegionalApp.py,
pyre/Solver/RegionalSolver.py: add new facility Mesher() and its
default component RegionalSphere()
2003-07-16 04:47 tan2
* pyre/Components/Stokes_solver/Stokes_solver.py: typo fixed
2003-07-16 01:17 ces74
* module/Regional/bindings.cc: A missing part of the method talbe
added: set_cg_defaults, set_mg_defaults, set_mg_el_defaults.
2005-08-23 02:55 unknown_user
* pyre/Components/Adv_solver.py: [vcp] delete of edited revision
with dead state
2003-07-16 01:06 ces74
* pyre/Components/Adv_solver.py: Binding for advection-diffusion
solver is now in pyre/Regional/Facilities/TSolver.py
2003-07-16 01:04 ces74
* pyre/Facilities/TSolver.py: Binding of TSolver with a component
(Temperature_diffadv.py) is implemented.
2003-07-16 01:03 ces74
* pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/Advection_diffusion/Temperature_diffadv.py,
pyre/Components/Advection_diffusion/__init__.py:
Temperature_diffadv now can call CitcomS subroutines to
initialize and solve for the advection/diffusion of temperature
field.
2003-07-16 01:01 ces74
* pyre/CitcomSRegional.py, pyre/RegionalApp.py,
pyre/Solver/RegionalSolver.py: modified to initialize the
Advection_diffusion facility
2003-07-15 07:40 tan2
* module/Regional/Make.mm, module/Regional/bindings.cc,
module/Regional/misc.cc, module/Regional/misc.h,
module/Regional/stokes_solver.cc,
module/Regional/stokes_solver.h, pyre/CitcomSRegional.py,
pyre/Components/Stokes_solver/Stokes_solver.py,
pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: 1. move
bindings related to Stokes_solver() to stokes_solver.cc 2. call
set_cg_defaults()/set_mg_defaults() in Stokes_solver.init()
2003-07-15 04:08 tan2
* lib/Common/Instructions.c, lib/Common/Interuption.c,
lib/Common/Make.mm: move everything related to System Signal to
interuption.c
2003-07-15 02:44 tan2
* module/Regional/setProperties.cc: change helper functions to
templates
2003-07-14 05:58 tan2
* module/Regional/bindings.cc, module/Regional/setProperties.cc,
module/Regional/setProperties.h, pyre/CitcomSRegional.py,
pyre/Components/Visc.py, pyre/RegionalApp.py,
pyre/Solver/RegionalSolver.py, tests/signon.py: 1. more helper
functions in setProperties.cc 2. Regional.BC_set_prop() and its
binding 3. RegionalApp._setProperties() 4. some test in singon.py
2005-08-23 02:54 unknown_user
* pyre/Components/Stokes_solver.py: [vcp] delete of edited revision
with dead state
2003-07-10 02:42 tan2
* pyre/CitcomSRegional.py, pyre/Components/Adv_solver.py,
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/BC.py, pyre/Components/Const.py,
pyre/Components/IC.py, pyre/Components/Mesh.py,
pyre/Components/Parallel.py, pyre/Components/Param.py,
pyre/Components/Phase.py, pyre/Components/Stokes_solver.py,
pyre/Components/Stokes_solver/Imcompressible.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Stokes_solver/Stokes_solver.py,
pyre/Components/Visc.py, pyre/Facilities/VSolver.py,
pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: migrate
toward pythia-0.4
2003-07-04 06:56 ces74
* pyre/CitcomSRegional.py, pyre/RegionalApp.py,
pyre/Solver/RegionalSolver.py: Typos corrected
2003-07-04 06:52 ces74
* pyre/CitcomSRegional.py, pyre/RegionalApp.py,
pyre/Solver/RegionalSolver.py: Modified to use the TSolver
facility.
2003-07-04 06:43 ces74
* pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/Advection_diffusion/Make.mm,
pyre/Components/Advection_diffusion/Temperature_diffadv.py,
pyre/Components/Advection_diffusion/__init__.py: A component of
"TSoler" facility added.
Advection_diffusion.py is a general class of advection_diffusion
solvers.
Temperature_diffadv.py is a solver for temperature field.
__init__.py exports temperature_diffadv under Advection_diffusion
module.
2003-07-04 06:40 ces74
* pyre/Facilities/Make.mm, pyre/Facilities/TSolver.py: TSolver
facility added. Make.mm modified accordingly.
2003-06-27 07:15 tan2
* module/Regional/Make.mm, module/Regional/bindings.cc,
module/Regional/setProperties.cc,
module/Regional/setProperties.h, pyre/CitcomSRegional.py,
pyre/Components/BC.py, pyre/Components/Make.mm,
pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: passing
properties of BC() to C variables
2003-06-27 06:14 tan2
* pyre/Components/Stokes_solver/Imcompressible.py,
pyre/Components/Stokes_solver/Incompressible.py:
ImcompressibleNonNewtonian() is inherited from
ImcompressibleNewtonian() now
2003-06-27 06:14 tan2
* pyre/Components/Stokes_solver/Stokes_solver.py: remove properties
related to viscosity
2003-06-24 04:01 tan2
* pyre/Facilities/VSolver.py: bug fix
2003-06-24 03:54 tan2
* pyre/Components/Stokes_solver/Imcompressible.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Stokes_solver/Make.mm,
pyre/Components/Stokes_solver/Stokes_solver.py,
pyre/Components/Stokes_solver/__init__.py: 1. Stokes_solver() is
a Component of new facility VSolver() 2. add properties to
Stokes_solver(), including properties belong to (future)
Viscosity component 3. change ImcompressibleNewtonian() and
ImcompressibleNonNewtonian() accordingly
2003-06-24 03:43 tan2
* pyre/Facilities, pyre/Facilities/Make.mm,
pyre/Facilities/VSolver.py, pyre/Facilities/__init__.py: add new
facilities
2003-06-14 00:12 tan2
* pyre/CitcomSRegional.py, pyre/RegionalApp.py,
pyre/Solver/RegionalSolver.py: add facilities
2003-06-14 00:11 tan2
* tests/citcomsregional.py: tests for facilities
2003-06-13 01:25 tan2
* pyre/Components/__init__.py, pyre/__init__.py: 1. remove
'license_text' 2. add Common/Component/__init__.py
2003-06-12 06:02 tan2
* pyre/Components/Adv_solver.py, pyre/Components/BC.py,
pyre/Components/Const.py, pyre/Components/IC.py,
pyre/Components/Make.mm, pyre/Components/Mesh.py,
pyre/Components/Parallel.py, pyre/Components/Param.py,
pyre/Components/Phase.py, pyre/Components/Stokes_solver.py,
pyre/Components/Visc.py: 1. move all components to new directory
Component/ 2. all components have a new and shorter name 3.
'SimulationSolver' is splited into two components: 'Adv_solver'
and 'Stokes_solver' 4. change Make.mm accordingly
2003-06-08 15:11 tan2
* module/Regional/Make.mm: fixed bug in linking with
'libmpimodule.a' (I don't like this solution though)
2003-06-07 02:04 tan2
* module/Regional/Make.mm, module/Regional/misc.cc: passing mpi
communicator to Citcom_Init()
2003-05-24 00:58 tan2
* tests/asap.py, tests/hrothgar.py: add two staging classes (copied
from specfem_globe/tests/)
2003-05-24 00:49 tan2
* module/Regional/misc.cc, module/Regional/outputs.cc: append
function name to the argument of PyArg_ParseTuple()
2003-05-24 00:07 tan2
* module/Make.mm: fix a typo
2003-05-23 12:12 ces74
* module/Regional/advdiffu.cc, module/Regional/advdiffu.h,
module/Regional/bindings.cc, module/Regional/misc.cc,
module/Regional/misc.h: test methods are removed. class
PG_timestep now has only two methods: init and solve
2003-05-23 12:11 ces74
* lib/Common/Drive_solvers.c,
lib/Common/General_matrix_functions.c,
lib/Common/Stokes_flow_Incomp.c, lib/Common/drive_solvers.h: test
functions removed.
2003-05-23 11:47 ces74
* lib/Common/Advection_diffusion.c, lib/Common/Drive_solvers.c,
lib/Common/General_matrix_functions.c,
lib/Common/Stokes_flow_Incomp.c,
lib/Common/advection_diffusion.h, lib/Common/drive_solvers.h:
Fixed a bug related to deciding the validity of velocity solution
in General_matrix_functions.c
Functions reorganized for PG_timestep class.
2003-05-23 11:22 ces74
* pyre/Components/Advection_diffusion/Advection_diffusion.py: class
PG_timestep now has only two methods: .init and .solve
2003-05-23 09:41 tan2
* module/Regional/outputs.cc, pyre/CitcomSRegional.py,
pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: add class
OutputVisc and its bindings
2003-05-23 07:46 ces74
* lib/Common/Advection_diffusion.c, lib/Common/Make.mm,
lib/Common/advection_diffusion.h: bug in Make.mm fixed.
advection_diffusion.h is now included in Advection_diffusion.c
2003-05-23 06:18 tan2
* lib/Common/output.h, lib/Regional/Output.c,
lib/Regional/output.h: *** empty log message ***
2003-05-23 06:10 tan2
* module/Regional/bindings.cc: *** empty log message ***
2003-05-23 06:08 tan2
* module/Regional/outputs.cc, module/Regional/outputs.h: add
bindings to class OutputVisc
2003-05-23 05:41 ces74
* module/Regional/outputs.cc: bug fixed: include outputs.h, not
output_binding.h
2003-05-23 05:39 ces74
* module/Regional/advdiffu.cc: bug fixed: PG_timestep_Init to
..._init PG_timestep_Fini to ..._fini
2003-05-23 05:37 ces74
* lib/Common/advection_diffusion.h, lib/Regional/Output.c: Bugs
fixed.
2003-05-23 05:27 ces74
* pyre/Components/Advection_diffusion/Advection_diffusion.py:
Changed class name from Advection_diffusion to PG_timestep
2003-05-23 01:32 ces74
* module/Regional/Make.mm, module/Regional/advdiffu.cc,
module/Regional/advdiffu.h, module/Regional/bindings.cc,
module/Regional/misc.cc, module/Regional/misc.h: Inconsistency
caused by adding advdiffu modules has been fixed.
2003-05-23 01:21 tan2
* lib/Regional/Output.c, module/Regional/Make.mm,
module/Regional/bindings.cc: 1. change filename from
'output_bindings.*' to 'outputs.*' 2. delete
OutputCoord.writeheader() method 3. fix a typo in Output.py
2003-05-23 01:20 ces74
* pyre/CitcomSRegional.py, pyre/Components/Advection_diffusion,
pyre/Components/Advection_diffusion/Advection_diffusion.py,
pyre/Components/Advection_diffusion/Make.mm,
pyre/Components/Advection_diffusion/__init__.py,
pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: A new package
Advection_diffusion created. This package includes a new class,
PG_timestep.
2003-05-23 01:17 ces74
* lib/Common/Advection_diffusion.c, lib/Common/Make.mm,
lib/Common/advection_diffusion.h: Functions added and modified
for PG_timestep class
2003-05-22 04:28 tan2
* lib/Common/output.h, lib/Regional/Output.c,
lib/Regional/output.h, module/Regional/Make.mm,
module/Regional/bindings.cc, module/Regional/misc.cc,
module/Regional/misc.h, module/Regional/outputs.cc,
module/Regional/outputs.h, pyre/CitcomSRegional.py,
pyre/RegionalApp.py, pyre/Solver/RegionalSolver.py: 1. add class
CitcomOutput 2. add classes OutputCoord and OutputVelo, which
write out coordinate and velocity output 3. add some functions in
lib/Regional/Output.c for bindings 4. add python bindings to all
above
2003-05-21 01:56 tan2
* pyre/Components/Stokes_solver/Imcompressible.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Stokes_solver/Stokes_solver.py: 1. change
implementation of Stokes_solver 2. change ImcompressibleNewtonian
and ImcompressibleNonNewtonian accordingly
2003-05-21 01:55 tan2
* lib/Common/Drive_solvers.c: initialize
'monitor.elapsed_time_vsoln'
2003-05-17 04:11 tan2
* lib/Common/Drive_solvers.c, lib/Common/drive_solvers.h,
module/Regional/bindings.cc, module/Regional/misc.cc,
module/Regional/misc.h, pyre/CitcomSRegional.py,
pyre/Components/Stokes_solver/Imcompressible.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Stokes_solver/Make.mm,
pyre/Components/Stokes_solver/Stokes_solver.py,
pyre/Components/Stokes_solver/__init__.py, pyre/RegionalApp.py,
pyre/Solver/RegionalSolver.py, tests/citcomsregional.py,
tests/signon.py: 1. add python class Stokes_solver 2. add python
classes ImcompressibleNewtonian and ImcompressibleNonNewtonian,
derived from Stokes_solver 3. add python binding to methods of
ImcompressibleNewtonian 4. modify tests accordingly
2003-05-15 07:07 tan2
* pyre/Components, pyre/Components/Stokes_solver,
pyre/Components/Stokes_solver/Imcompressible.py,
pyre/Components/Stokes_solver/Incompressible.py,
pyre/Components/Stokes_solver/Make.mm,
pyre/Components/Stokes_solver/Stokes_solver.py,
pyre/Components/Stokes_solver/__init__.py: Initial revision
2003-05-15 01:31 tan2
* lib/Common/Instructions.c, lib/Common/Viscosity_structures.c,
lib/Regional/Version_dependent.c, module/Regional/misc.cc,
tests/signon.py: seperate viscosity input and computation into
different functions
2003-05-14 02:51 tan2
* drivers/Citcom.c, lib/Common/Citcom_init.c,
lib/Common/Global_operations.c, lib/Common/citcom_init.h,
lib/Common/global_defs.h, lib/Common/parallel_related.h,
lib/Regional/Global_operations.c,
lib/Regional/Parallel_related.c, lib/Regional/global_defs.h,
lib/Regional/parallel_related.h, module/Regional/misc.cc,
tests/signon.py: 1. creat a new global variable E->parallel.world
2. replace all MPI_COMM_WORLD by E->parallel.world
2003-04-30 03:14 tan2
* lib/Common/phase_change.h: add function prototypes
2003-04-30 03:13 tan2
* lib/Regional/Version_dependent.c: fix bugs when input
'control.coor_file', 'control.reset_startage', and
'control.zero_elapsed_time'
2003-04-29 01:55 tan2
* lib/Common/Instructions.c,
lib/Common/Pan_problem_misc_functions.c,
lib/Common/Phase_change.c, lib/Regional/Version_dependent.c: 1.
move everything about phase change to 'Phase_change.c' 2.
restructure phase change functions
2003-04-26 07:59 tan2
* lib/Common/Problem_related.c, lib/Common/global_defs.h,
lib/Regional/Boundary_conditions.c,
lib/Regional/Problem_related.c, lib/Regional/Version_dependent.c,
lib/Regional/global_defs.h: 1. change 'control.mantle_temp' to
'control.lith_age_mantle_temp' 2. move functions deal with
'lith_age' to a 'Lith_age.c' (complete)
2003-04-26 07:36 tan2
* lib/Common/Element_calculations.c, lib/Common/Sphere_harmonics.c:
bug fix in original code
2003-04-26 05:58 tan2
* drivers/Make.mm, lib/Make.mm, module/Make.mm, pyre/Make.mm:
diable build on 'Full' version
2003-04-26 05:29 tan2
* lib/Common/Initial_temperature.c, lib/Common/global_defs.h,
lib/Common/initial_temperature.h, lib/Common/lith_age.h,
lib/Common/parsing.h, lib/Regional/Initial_temperature.c,
lib/Regional/Lith_age.c, lib/Regional/Make.mm,
lib/Regional/global_defs.h, lib/Regional/initial_temperature.h,
lib/Regional/lith_age.h: 1. add parsing.h 2. modularize
convection_initial_temperature() 3. move functions deal with
'lith_age' to a 'Lith_age.c' (not finished)
2003-04-26 05:12 tan2
* drivers/Citcom.c, lib/Common/Citcom_init.c: 1. more
initialization done in Citcom_Init() 2. fix bug from previous
commit in main()
2003-04-25 02:07 tan2
* lib/Common/Element_calculations.c,
lib/Common/General_matrix_functions.c: bug fix
2003-04-11 08:31 tan2
* lib/Common/Citcom_init.c, module/Regional/misc.cc: clean up debug
message
2003-04-11 08:27 ces74
* pyre/CitcomSRegional.py, pyre/RegionalApp.py,
pyre/Solver/RegionalSolver.py: class name changed to RegionalApp
2003-04-11 06:40 tan2
* tests/citcomsregional.py, tests/signon.py: change module name
from CitcomSRegional to Regional
2003-04-11 06:34 tan2
* pyre/CitcomSRegional.py, pyre/RegionalApp.py,
pyre/Solver/RegionalSolver.py: 1. add preInit() and postInit() 2.
change EarthModelGrid to SimulationGrid
2003-04-11 06:25 tan2
* module/Full/Fullmodule.cc, module/Full/Make.mm,
module/Full/bindings.cc, module/Full/bindings.h,
module/Full/exceptions.cc, module/Full/exceptions.h,
module/Full/misc.cc, module/Full/misc.h: change module name from
CitcomSFull to Full
2003-04-11 06:18 tan2
* module/Regional/Make.mm, module/Regional/Regionalmodule.cc,
module/Regional/bindings.cc, module/Regional/bindings.h,
module/Regional/exceptions.cc, module/Regional/exceptions.h,
module/Regional/misc.cc, module/Regional/misc.h: change module
name from CitcomSRegional to Regional
2003-04-11 03:15 tan2
* tests/signon.py: test for new Citcom_Init(), which takes 2
arguments now.
2003-04-11 02:07 tan2
* drivers/Citcom.c, lib/Common/Citcom_init.c,
lib/Common/citcom_init.h, module/Regional/misc.cc: 1. Pass rank
and size to Citcom_Init(). 2. Disable
parallel_process_initilization(). Its functionality is performed
by Citcom_Init().
2003-04-10 01:59 ces74
* pyre/CitcomSRegional.py, pyre/RegionalApp.py, pyre/Solver,
pyre/Solver/RegionalSolver.py: Modified to reflect changes in
moduels in pyre/Common
2003-04-06 07:51 tan2
* drivers/Citcom.c, lib/Common/Citcom_init.c,
lib/Common/Instructions.c, lib/Common/Parsing.c,
module/Regional/bindings.cc, module/Regional/misc.cc,
module/Regional/misc.h, tests/signon.py: 1. pass input filename,
rather than argc and argv, to read_instructions() 2. pass input
filename, rather than argc and argv, to setup_parser() 3. more
initialization done in Citcom_Init() 4. add python binding to
read_instructions()
2003-04-06 04:57 tan2
* drivers/Citcom.c, lib/Common/Citcom_init.c,
lib/Common/citcom_init.h, module/Regional/misc.cc: binding of
Citcom_Init(), finished
2003-04-06 04:25 tan2
* drivers/Full/Make.mm, drivers/Make.mm, drivers/Regional/Make.mm,
examples/Full/Make.mm, examples/Make.mm,
examples/Regional/Make.mm, lib/Common/Make.mm, lib/Full/Make.mm,
lib/Make.mm, lib/Regional/Make.mm, module/Full/Make.mm,
module/Make.mm, module/Regional/Make.mm, pyre/Make.mm,
tests/Make.mm: PROJ_TMPDIR is specified by PACKAGE too
2003-04-04 08:42 tan2
* module/Regional/Make.mm, module/Regional/bindings.cc,
module/Regional/misc.cc, module/Regional/misc.h, tests/signon.py:
trial on binding of Citcom_Init(), not finished.
2003-04-04 08:41 tan2
* lib/Full/Make.mm, lib/Regional/Make.mm: export header files
2003-04-04 08:40 tan2
* drivers/Citcom.c: 1. declare "struct All_variables *E" as global
in read_instruction() 2. allocate *E in Citcom_Init()
2003-04-04 08:39 tan2
* lib/Common/Citcom.c: redundant file
2003-04-04 08:37 tan2
* lib/Common/Citcom_init.c, lib/Common/Instructions.c,
lib/Common/Make.mm, lib/Common/citcom_init.h: 1. declare "struct
All_variables *E" as global in read_instruction() 2. allocate *E
in Citcom_Init()
2003-04-04 03:40 tan2
* lib/Make.mm, module/Make.mm, pyre/RadiusDepth.py: cosmetics
2003-04-04 03:38 tan2
* drivers/Full/Make.mm, drivers/Make.mm, drivers/Regional/Make.mm:
fix bugs caused by symlink to Citcom.c
2003-03-26 08:49 ces74
* tests/citcomsregional.py: for testing EarthModel properties
2003-03-25 05:48 tan2
* pyre/RadiusDepth.py: 1. change attribute 'R0' to 'outer_radius'
2. outer_radius, inRadius, and inDepth are read-only now 3. add
self-test section
2003-03-25 03:48 tan2
* pyre/RadiusDepth.py: Add RadiusDepth.py, which defines two
classed converting depth to radius, and vise versa.
2003-03-25 01:38 tan2
* drivers/Make.mm, module/Make.mm, pyre/Make.mm: add
BLD_ACTION="all"
2003-03-24 09:46 tan2
* Make.mm, drivers, drivers/Citcom.c, drivers/Full,
drivers/Full/Make.mm, drivers/Full/local.def, drivers/Make.mm,
drivers/Regional, drivers/Regional/Make.mm,
drivers/Regional/local.def, drivers/local.def, examples,
examples/.reset-temporary, examples/Full, examples/Full/Make.mm,
examples/Full/input.sample, examples/Full/local.def,
examples/Full/machine.sample, examples/Make.mm,
examples/Regional, examples/Regional/Make.mm,
examples/Regional/input.sample, examples/Regional/local.def,
examples/Regional/machines.sample, examples/local.def, lib,
lib/Common, lib/Common/Advection_diffusion.c,
lib/Common/Citcom.c, lib/Common/Construct_arrays.c,
lib/Common/Convection.c, lib/Common/Drive_solvers.c,
lib/Common/Element_calculations.c,
lib/Common/General_matrix_functions.c,
lib/Common/Global_operations.c, lib/Common/Initial_temperature.c,
lib/Common/Instructions.c, lib/Common/Make.mm,
lib/Common/Nodal_mesh.c, lib/Common/Output.c,
lib/Common/Pan_problem_misc_functions.c, lib/Common/Parsing.c,
lib/Common/Phase_change.c, lib/Common/Problem_related.c,
lib/Common/Process_buoyancy.c, lib/Common/Process_velocity.c,
lib/Common/Shape_functions.c, lib/Common/Size_does_matter.c,
lib/Common/Solver_conj_grad.c, lib/Common/Solver_multigrid.c,
lib/Common/Sphere_harmonics.c, lib/Common/Stokes_flow_Incomp.c,
lib/Common/Topo_gravity.c, lib/Common/Tracer_advection.c,
lib/Common/Viscosity_structures.c, lib/Common/advection.h,
lib/Common/convection_variables.h,
lib/Common/element_definitions.h, lib/Common/global_defs.h,
lib/Common/local.def, lib/Common/sphere_communication.h,
lib/Common/temperature_descriptions.h, lib/Common/tracer_defs.h,
lib/Common/viscosity_descriptions.h, lib/Full,
lib/Full/Boundary_conditions.c, lib/Full/Geometry_cartesian.c,
lib/Full/Global_operations.c, lib/Full/Initial_temperature.c,
lib/Full/Make.mm, lib/Full/Output.c, lib/Full/Parallel_related.c,
lib/Full/Problem_related.c, lib/Full/Process_buoyancy.c,
lib/Full/Sphere_related.c, lib/Full/Version_dependent.c,
lib/Full/global_defs.h, lib/Full/local.def, lib/Make.mm,
lib/Regional, lib/Regional/Boundary_conditions.c,
lib/Regional/Geometry_cartesian.c,
lib/Regional/Global_operations.c,
lib/Regional/Initial_temperature.c, lib/Regional/Make.mm,
lib/Regional/Output.c, lib/Regional/Parallel_related.c,
lib/Regional/Problem_related.c, lib/Regional/Process_buoyancy.c,
lib/Regional/Sphere_related.c, lib/Regional/Version_dependent.c,
lib/Regional/global_defs.h, lib/Regional/local.def,
lib/local.def, local.def, module, module/Full,
module/Full/Fullmodule.cc, module/Full/Make.mm,
module/Full/bindings.cc, module/Full/bindings.h,
module/Full/exceptions.cc, module/Full/exceptions.h,
module/Full/local.def, module/Full/misc.cc, module/Full/misc.h,
module/Make.mm, module/Regional, module/Regional/Make.mm,
module/Regional/Regionalmodule.cc, module/Regional/bindings.cc,
module/Regional/bindings.h, module/Regional/exceptions.cc,
module/Regional/exceptions.h, module/Regional/local.def,
module/Regional/misc.cc, module/Regional/misc.h,
module/local.def, pyre, pyre/Make.mm, pyre/__init__.py,
pyre/local.def, tests, tests/Make.mm, tests/local.def,
tests/signon.py: Initial revision
2005-08-23 02:43 boo
* .: [vcp] select <> as trunk
2005-08-23 02:42 VCP
* mc/3D/CitcomS/branches, .: VCP: initializing layout
