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Revision Author Date Message Commit Date
4bc0ea7 Compute phase change wrt reference density and gravity profiles. 23 August 2007, 20:18 UTC
d0098c3 Avoid reading unused input parameters 23 August 2007, 20:18 UTC
1268a26 assert solver.tsolver.monitor_max_T is off in coupled run and remove debugging output 23 August 2007, 20:17 UTC
ae9b86a Renamed E->control.filter_temperature to E->advection.filter_temperature 23 August 2007, 20:16 UTC
8233668 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. 23 August 2007, 20:16 UTC
447f924 Removed unused var. in struct advection 23 August 2007, 20:15 UTC
80a070b A new way to compute TMass 23 August 2007, 20:14 UTC
6d31d51 Minor refactoring: add comments, rename variables 23 August 2007, 20:14 UTC
a169ee5 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.) 22 August 2007, 01:00 UTC
7616c27 Removed the 2nd exit condition for bicg solver because the convergence criterion is hard to determine. 21 August 2007, 22:42 UTC
239522f Fixed the scaling constants in geoid calculation with reference state 21 August 2007, 22:41 UTC
eb5aedc Disable phase change in compressible flow 21 August 2007, 22:41 UTC
2473c52 Added Wei Leng to author list 21 August 2007, 20:28 UTC
1420d4e 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. 21 August 2007, 20:27 UTC
dee9a51 Refactored non-newtonian stokes solver and iter-CG compressible stokes solver 21 August 2007, 20:26 UTC
9aa0d94 Forgot this file. 20 August 2007, 19:44 UTC
9370fcf Added #ifdef block around vtk_io in output_finalize() 20 August 2007, 18:11 UTC
316e0b2 Made CDEPV and Q0.enriched work only with ncomp=1 for now. 20 August 2007, 00:11 UTC
e53e0c8 - 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. 19 August 2007, 23:54 UTC
5cbae2e Added excutable permission to testing shell script 17 August 2007, 21:41 UTC
cac7d92 Added comments to restart example 17 August 2007, 21:39 UTC
fec6071 Converting TWB's ascii-gz and vtkio output and CDEPV and tracer_enriched for multi-component chemical convection. 17 August 2007, 18:35 UTC
5345880 Multi-component chemical convection. By setting tracer_flavors > 2, one can enable multi-component chemical convection. See tests/checkpoint/tracer.cfg for example input. 17 August 2007, 18:33 UTC
8f2682a 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. 16 August 2007, 21:36 UTC
7c82fa3 When the element is close to the poles, use a more precise method to compute the strain rate. 16 August 2007, 20:10 UTC
2343a70 Forgot to add two files to the repository 16 August 2007, 19:38 UTC
61655f0 Merging compressible branch to trunk. The TALA solver is working. Two new input parameters: dissipation_number and gruneisen. 16 August 2007, 19:28 UTC
33d700d Updated Cookbook5 so that it uses only 2 processors. 16 August 2007, 01:42 UTC
c3fdb31 Merging compressible branch (up to r6584) to trunk. 16 August 2007, 00:27 UTC
fe53297 - 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? 14 August 2007, 03:33 UTC
d6e512c Minor refactoring, clean-up and moving functions between files 13 August 2007, 22:55 UTC
45a5e52 Moved obsolete functions phae_change_* from Phase_change.c to Obsolete.c and declared private functions to be static 13 August 2007, 21:43 UTC
408e100 Update the author list 10 August 2007, 23:56 UTC
d603970 additions per becker, tan2 10 August 2007, 23:56 UTC
d9f152e Fixed two type-mismatch errors. Issue127 is fixed by this change and r7802. 10 August 2007, 23:44 UTC
f036e33 Prevent the original force vector being modified by Uzawa solver. This is needed for the non-Newtonian iterations. 10 August 2007, 23:43 UTC
da4b2ca - 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 10 August 2007, 20:51 UTC
a77c186 - 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 09 August 2007, 01:27 UTC
8e448b0 - 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) 08 August 2007, 22:55 UTC
2f477b3 Forgot to actually add the new file that is needed for gzipped and "vtk" I/O. 08 August 2007, 16:41 UTC
46ad5e8 - 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 08 August 2007, 05:58 UTC
5d9b20c Ignore most files generated by build system 02 August 2007, 22:44 UTC
3d5f153 M Boundary.cc fixed a bug on topbc 27 July 2007, 23:33 UTC
fa788b9 Fixed a typo, which was introduced in svn r5399 26 July 2007, 00:20 UTC
81df091 Fixed a bug that *opt*.general files are mistakenly named. This bug is introduced by svn r7236 26 July 2007, 00:13 UTC
6542116 Fixed a bug in ordering of mesh nodes. The bug was introduced in svn r6510. 25 July 2007, 23:19 UTC
36a1b8a 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. 23 July 2007, 19:50 UTC
4f7c56a M coupled.cfg alligned nodes in the solvers for comparing velocity directly. 20 July 2007, 21:52 UTC
9a699d2 Fixed a bug in setting stable timestep 19 July 2007, 18:51 UTC
abb2c52 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. 19 July 2007, 18:51 UTC
e108cfa 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. 19 July 2007, 18:37 UTC
4e60f5e 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. 18 July 2007, 23:06 UTC
b639d7b 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. 18 July 2007, 21:01 UTC
0f29122 An input file for multicoupled run 17 July 2007, 22:49 UTC
6ff6d36 Fixed a few typos and attached MultiC_Coupler as the default factory for the ccoupler facility 17 July 2007, 22:48 UTC
c72dd9f Simplified the MultiC_*Solver classes 17 July 2007, 22:48 UTC
3b731ec 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. 16 July 2007, 23:45 UTC
85be698 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. 16 July 2007, 21:21 UTC
690124c M Coupler/ContainingCoupler.py trivial modification on comments 13 July 2007, 23:24 UTC
6569f99 M Coupler/MultiC_Coupler.py add __init__, initialize, createMesh some of createMesh are commented out because I do not understand it. 13 July 2007, 23:23 UTC
313ee04 A Coupler/MultiC_Coupler.py It's a child of Containing Coupler It has nothing now. 13 July 2007, 21:09 UTC
8c2b9ce Added some comments 11 July 2007, 20:17 UTC
d9f6e03 Renamed variables for clarification 10 July 2007, 20:08 UTC
c1c6dd3 Small changes in *Coupler class. * consolidated __init__() and initialize() * renamed numSrc -> remoteSize, boundary -> remoteBdryList, interior -> remoteIntrList * defaulted the dimensional and transformational properties to False 09 July 2007, 22:03 UTC
64a5133 Added svn:keywords Id 06 July 2007, 20:48 UTC
bcff7e0 Debugged MultiLayout.initialize() and MultiCoupledApp.findLayout(). Fixed some typos. 06 July 2007, 20:46 UTC
2931729 Using log() instead of line() to flush the journal buffer, otherwise no output at all. 06 July 2007, 18:00 UTC
ccf633e fix myPlus and remotePlus and report in MultiCoupledApp edit some comments in MultiLayout 06 July 2007, 17:50 UTC
4bc84ca add MultiLayout not sure about number of processor, currently assign 1-10 for ccom 11 for ecom1, and 12 for ecom2 05 July 2007, 23:45 UTC
9126f66 05 July 2007, 22:36 UTC
f54025a 05 July 2007, 20:49 UTC
a4173da a draft for multicoupled application 04 July 2007, 00:02 UTC
3b48492 Removing outdated and redundant documentation 02 July 2007, 22:21 UTC
0eb8131 Using log() instead of line() to flush the journal buffer, otherwise no output at all. 02 July 2007, 22:21 UTC
a1c3da7 Renamed ccomm -> containing_group and ecomm -> embedded_group. Added more checks to the groups 28 June 2007, 19:35 UTC
0ef55d1 Added/updated a bunch of comments, renamed variables 27 June 2007, 01:04 UTC
36f8d4f Added mime-type property to the PDF files 26 June 2007, 00:37 UTC
9dddcd2 Giving Exchanger/Coupler/CoupledApp as new life. The testing script tests/coupled.cfg finished successfully. 23 June 2007, 00:33 UTC
54685e2 Useful debuggin output, but disabled 23 June 2007, 00:30 UTC
34b601d Print CXX and CXXFLAGS after finishing configure 23 June 2007, 00:29 UTC
55c8dd2 Removed the back-and-forth interpolation of viscosity, which smoothes the viscosity field unnecessarily 23 June 2007, 00:28 UTC
ed4ce7b Forgot to commit module/setProperties.c in r7289. This should fix issue115 in the pyre version also. 22 June 2007, 23:43 UTC
1069325 Added BuildBot config. 22 June 2007, 04:36 UTC
fcdc999 Resolved the conflict 21 June 2007, 22:35 UTC
6e82004 Preparing a conflict test, again 21 June 2007, 22:25 UTC
3d9403f Preparing a conflict test, again 21 June 2007, 22:22 UTC
0a261b2 Preparing a conflict test 21 June 2007, 22:19 UTC
a2f4ad6 Renamed 'XXX1' -> 'cXXX' and 'XXX2' -> 'eXXX' 18 June 2007, 23:21 UTC
e546ce6 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. 18 June 2007, 23:06 UTC
fe97c4c Fix for problem with GCC 3.4.5 (observed on CITerra): mv: cannot stat `.deps/dummy.Tpo': No such file or directory 15 June 2007, 18:01 UTC
d839465 Zeroing geoid arrays before every geoid calculation. This fixes issue114 14 June 2007, 21:38 UTC
7384d4c A better fix for issue110 14 June 2007, 17:55 UTC
25bb6b1 Fixing issue111: Expanding %RANK in autocombine.py 14 June 2007, 01:36 UTC
9c3dfa7 A trivial change 13 June 2007, 17:55 UTC
65ee539 Fixing issue112 12 June 2007, 00:05 UTC
50c2d55 Fixed LINK problem w/Automake. 11 May 2007, 20:19 UTC
9caddf1 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. 11 May 2007, 02:02 UTC
6019291 Forgot to update the makefile in r6541 11 April 2007, 00:40 UTC
60030f4 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. 10 April 2007, 21:59 UTC
247bcc7 Removed obsolete pyre components in tests/ 10 April 2007, 21:58 UTC
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