| a77c186 | Thorsten Becker | 09 August 2007, 01:27:32 UTC | - 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, 01:27:32 UTC |
| 8e448b0 | Thorsten Becker | 08 August 2007, 22:55:39 UTC | - 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, 22:55:39 UTC |
| 2f477b3 | Thorsten Becker | 08 August 2007, 16:41:20 UTC | Forgot to actually add the new file that is needed for gzipped and "vtk" I/O. | 08 August 2007, 16:41:20 UTC |
| 46ad5e8 | Thorsten Becker | 08 August 2007, 05:58:48 UTC | - 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, 05:58:48 UTC |
| 5d9b20c | Luis Armendariz | 02 August 2007, 22:44:47 UTC | Ignore most files generated by build system | 02 August 2007, 22:44:47 UTC |
| 3d5f153 | Lijie Han | 27 July 2007, 23:33:47 UTC | M Boundary.cc fixed a bug on topbc | 27 July 2007, 23:33:47 UTC |
| fa788b9 | Eh Tan | 26 July 2007, 00:20:05 UTC | Fixed a typo, which was introduced in svn r5399 | 26 July 2007, 00:20:05 UTC |
| 81df091 | Eh Tan | 26 July 2007, 00:13:39 UTC | Fixed a bug that *opt*.general files are mistakenly named. This bug is introduced by svn r7236 | 26 July 2007, 00:13:39 UTC |
| 6542116 | Eh Tan | 25 July 2007, 23:19:21 UTC | Fixed a bug in ordering of mesh nodes. The bug was introduced in svn r6510. | 25 July 2007, 23:19:21 UTC |
| 36a1b8a | Lijie Han | 23 July 2007, 19:50:29 UTC | 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, 19:50:29 UTC |
| 4f7c56a | Lijie Han | 20 July 2007, 21:52:18 UTC | M coupled.cfg alligned nodes in the solvers for comparing velocity directly. | 20 July 2007, 21:52:18 UTC |
| 9a699d2 | Eh Tan | 19 July 2007, 18:51:47 UTC | Fixed a bug in setting stable timestep | 19 July 2007, 18:51:47 UTC |
| abb2c52 | Eh Tan | 19 July 2007, 18:51:12 UTC | 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, 18:51:12 UTC |
| e108cfa | Lijie Han | 19 July 2007, 18:37:13 UTC | 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, 18:37:13 UTC |
| 4e60f5e | Lijie Han | 18 July 2007, 23:06:35 UTC | 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, 23:06:35 UTC |
| b639d7b | Eh Tan | 18 July 2007, 21:01:09 UTC | 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, 21:01:09 UTC |
| 0f29122 | Eh Tan | 17 July 2007, 22:49:10 UTC | An input file for multicoupled run | 17 July 2007, 22:49:10 UTC |
| 6ff6d36 | Eh Tan | 17 July 2007, 22:48:51 UTC | Fixed a few typos and attached MultiC_Coupler as the default factory for the ccoupler facility | 17 July 2007, 22:48:51 UTC |
| c72dd9f | Eh Tan | 17 July 2007, 22:48:26 UTC | Simplified the MultiC_*Solver classes | 17 July 2007, 22:48:26 UTC |
| 3b731ec | Lijie Han | 16 July 2007, 23:45:52 UTC | 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, 23:45:52 UTC |
| 85be698 | Lijie Han | 16 July 2007, 21:21:10 UTC | 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, 21:21:10 UTC |
| 690124c | Lijie Han | 13 July 2007, 23:24:27 UTC | M Coupler/ContainingCoupler.py trivial modification on comments | 13 July 2007, 23:24:27 UTC |
| 6569f99 | Lijie Han | 13 July 2007, 23:23:43 UTC | M Coupler/MultiC_Coupler.py add __init__, initialize, createMesh some of createMesh are commented out because I do not understand it. | 13 July 2007, 23:23:43 UTC |
| 313ee04 | Lijie Han | 13 July 2007, 21:09:27 UTC | A Coupler/MultiC_Coupler.py It's a child of Containing Coupler It has nothing now. | 13 July 2007, 21:09:27 UTC |
| 8c2b9ce | Eh Tan | 11 July 2007, 20:17:32 UTC | Added some comments | 11 July 2007, 20:17:32 UTC |
| d9f6e03 | Eh Tan | 10 July 2007, 20:08:44 UTC | Renamed variables for clarification | 10 July 2007, 20:08:44 UTC |
| c1c6dd3 | Eh Tan | 09 July 2007, 22:03:45 UTC | 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, 22:03:45 UTC |
| 64a5133 | Eh Tan | 06 July 2007, 20:48:44 UTC | Added svn:keywords Id | 06 July 2007, 20:48:44 UTC |
| bcff7e0 | Eh Tan | 06 July 2007, 20:46:10 UTC | Debugged MultiLayout.initialize() and MultiCoupledApp.findLayout(). Fixed some typos. | 06 July 2007, 20:46:10 UTC |
| 2931729 | Eh Tan | 06 July 2007, 18:00:49 UTC | Using log() instead of line() to flush the journal buffer, otherwise no output at all. | 06 July 2007, 18:00:49 UTC |
| ccf633e | Lijie Han | 06 July 2007, 17:50:59 UTC | fix myPlus and remotePlus and report in MultiCoupledApp edit some comments in MultiLayout | 06 July 2007, 17:50:59 UTC |
| 4bc84ca | Lijie Han | 05 July 2007, 23:45:19 UTC | add MultiLayout not sure about number of processor, currently assign 1-10 for ccom 11 for ecom1, and 12 for ecom2 | 05 July 2007, 23:45:19 UTC |
| 9126f66 | Lijie Han | 05 July 2007, 22:36:06 UTC | | 05 July 2007, 22:36:06 UTC |
| f54025a | Lijie Han | 05 July 2007, 20:49:14 UTC | | 05 July 2007, 20:49:14 UTC |
| a4173da | Lijie Han | 04 July 2007, 00:02:42 UTC | a draft for multicoupled application | 04 July 2007, 00:02:42 UTC |
| 3b48492 | Eh Tan | 02 July 2007, 22:21:36 UTC | Removing outdated and redundant documentation | 02 July 2007, 22:21:36 UTC |
| 0eb8131 | Eh Tan | 02 July 2007, 22:21:21 UTC | Using log() instead of line() to flush the journal buffer, otherwise no output at all. | 02 July 2007, 22:21:21 UTC |
| a1c3da7 | Eh Tan | 28 June 2007, 19:35:29 UTC | Renamed ccomm -> containing_group and ecomm -> embedded_group. Added more checks to the groups | 28 June 2007, 19:35:29 UTC |
| 0ef55d1 | Eh Tan | 27 June 2007, 01:04:41 UTC | Added/updated a bunch of comments, renamed variables | 27 June 2007, 01:04:41 UTC |
| 36f8d4f | Eh Tan | 26 June 2007, 00:37:32 UTC | Added mime-type property to the PDF files | 26 June 2007, 00:37:32 UTC |
| 9dddcd2 | Eh Tan | 23 June 2007, 00:33:20 UTC | Giving Exchanger/Coupler/CoupledApp as new life. The testing script tests/coupled.cfg finished successfully. | 23 June 2007, 00:33:20 UTC |
| 54685e2 | Eh Tan | 23 June 2007, 00:30:33 UTC | Useful debuggin output, but disabled | 23 June 2007, 00:30:33 UTC |
| 34b601d | Eh Tan | 23 June 2007, 00:29:36 UTC | Print CXX and CXXFLAGS after finishing configure | 23 June 2007, 00:29:36 UTC |
| 55c8dd2 | Eh Tan | 23 June 2007, 00:28:23 UTC | Removed the back-and-forth interpolation of viscosity, which smoothes the viscosity field unnecessarily | 23 June 2007, 00:28:23 UTC |
| ed4ce7b | Eh Tan | 22 June 2007, 23:43:21 UTC | Forgot to commit module/setProperties.c in r7289. This should fix issue115 in the pyre version also. | 22 June 2007, 23:43:21 UTC |
| 1069325 | Leif Strand | 22 June 2007, 04:36:08 UTC | Added BuildBot config. | 22 June 2007, 04:36:08 UTC |
| fcdc999 | Lijie Han | 21 June 2007, 22:35:33 UTC | Resolved the conflict | 21 June 2007, 22:35:33 UTC |
| 6e82004 | Eh Tan | 21 June 2007, 22:25:40 UTC | Preparing a conflict test, again | 21 June 2007, 22:25:40 UTC |
| 3d9403f | Eh Tan | 21 June 2007, 22:22:08 UTC | Preparing a conflict test, again | 21 June 2007, 22:22:08 UTC |
| 0a261b2 | Eh Tan | 21 June 2007, 22:19:44 UTC | Preparing a conflict test | 21 June 2007, 22:19:44 UTC |
| a2f4ad6 | Eh Tan | 18 June 2007, 23:21:10 UTC | Renamed 'XXX1' -> 'cXXX' and 'XXX2' -> 'eXXX' | 18 June 2007, 23:21:10 UTC |
| e546ce6 | Eh Tan | 18 June 2007, 23:06:40 UTC | 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, 23:06:40 UTC |
| fe97c4c | Leif Strand | 15 June 2007, 18:01:27 UTC | 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, 18:01:27 UTC |
| d839465 | Eh Tan | 14 June 2007, 21:38:19 UTC | Zeroing geoid arrays before every geoid calculation. This fixes issue114 | 14 June 2007, 21:38:19 UTC |
| 7384d4c | Eh Tan | 14 June 2007, 17:55:31 UTC | A better fix for issue110 | 14 June 2007, 17:55:31 UTC |
| 25bb6b1 | Eh Tan | 14 June 2007, 01:36:27 UTC | Fixing issue111: Expanding %RANK in autocombine.py | 14 June 2007, 01:36:27 UTC |
| 9c3dfa7 | Lijie Han | 13 June 2007, 17:55:22 UTC | A trivial change | 13 June 2007, 17:55:22 UTC |
| 65ee539 | Eh Tan | 12 June 2007, 00:05:11 UTC | Fixing issue112 | 12 June 2007, 00:05:11 UTC |
| 50c2d55 | Leif Strand | 11 May 2007, 20:19:28 UTC | Fixed LINK problem w/Automake. | 11 May 2007, 20:19:28 UTC |
| 9caddf1 | Leif Strand | 11 May 2007, 02:02:00 UTC | 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, 02:02:00 UTC |
| 6019291 | Eh Tan | 11 April 2007, 00:40:49 UTC | Forgot to update the makefile in r6541 | 11 April 2007, 00:40:49 UTC |
| 60030f4 | Eh Tan | 10 April 2007, 21:59:45 UTC | 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, 21:59:45 UTC |
| 247bcc7 | Eh Tan | 10 April 2007, 21:58:51 UTC | Removed obsolete pyre components in tests/ | 10 April 2007, 21:58:51 UTC |
| 6d942e7 | Eh Tan | 05 April 2007, 22:21:46 UTC | 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. | 05 April 2007, 22:21:46 UTC |
| f31b73c | Sue Kientz | 27 March 2007, 20:54:47 UTC | standardized typefaces on cover | 27 March 2007, 20:54:47 UTC |
| d7a7f7a | Sue Kientz | 27 March 2007, 06:51:53 UTC | changed version to 2.2.1 per tan2 | 27 March 2007, 06:51:53 UTC |
| 78e36d1 | Eh Tan | 27 March 2007, 04:39:34 UTC | Regenerated ChangeLog upto r6417 | 27 March 2007, 04:39:34 UTC |
| 190e4e8 | Eh Tan | 27 March 2007, 04:37:54 UTC | Updated NEWS for the upcoming 2.2.1 | 27 March 2007, 04:37:54 UTC |
| 1ab1ba9 | Eh Tan | 27 March 2007, 04:20:05 UTC | Forgot to add cookbook7.cfg to the file list | 27 March 2007, 04:20:05 UTC |
| d1623a6 | Eh Tan | 26 March 2007, 18:48:36 UTC | Regenerated ChangeLog upto r6409 | 26 March 2007, 18:48:36 UTC |
| 074e8d9 | Eh Tan | 26 March 2007, 18:45:16 UTC | Forgot to add a header file to the file list | 26 March 2007, 18:45:16 UTC |
| 585244b | Eh Tan | 26 March 2007, 18:25:42 UTC | Regenerated ChangeLog upto r6403 | 26 March 2007, 18:25:42 UTC |
| e8056e6 | Eh Tan | 26 March 2007, 18:20:19 UTC | Set the length unit to cm to fit within the page | 26 March 2007, 18:20:19 UTC |
| c7236d2 | Eh Tan | 26 March 2007, 18:11:02 UTC | Changed the size of gmt plots to fit within the page | 26 March 2007, 18:11:02 UTC |
| 8ccaa32 | Sue Kientz | 26 March 2007, 18:05:31 UTC | restored edits to stable copy; regen pdf, images showing | 26 March 2007, 18:05:31 UTC |
| 3b056f3 | Eh Tan | 26 March 2007, 06:01:18 UTC | Enlarged the figure of cookbook7. Rephrased the description of the low-viscosity-zone parameters, per Sue's suggestion. | 26 March 2007, 06:01:18 UTC |
| d79404c | Sue Kientz | 26 March 2007, 00:23:55 UTC | chasing down image problem | 26 March 2007, 00:23:55 UTC |
| 6f388ea | Sue Kientz | 25 March 2007, 23:07:31 UTC | 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 | 25 March 2007, 23:07:31 UTC |
| 723f757 | Sue Kientz | 25 March 2007, 22:55:42 UTC | edits of new copy; attempt to fix an image that is not displaying, still unresolved | 25 March 2007, 22:55:42 UTC |
| 8688ee2 | Eh Tan | 24 March 2007, 23:05:03 UTC | Finished Cookbook7 | 24 March 2007, 23:05:03 UTC |
| 0a6d3bd | Eh Tan | 24 March 2007, 23:03:00 UTC | Changed the version number to 2.2 | 24 March 2007, 23:03:00 UTC |
| 1af6a2d | Eh Tan | 24 March 2007, 00:02:43 UTC | Added new cookbook7 | 24 March 2007, 00:02:43 UTC |
| 3cd5331 | Eh Tan | 23 March 2007, 22:21:32 UTC | Updated the NEWS for v2.2.0 | 23 March 2007, 22:21:32 UTC |
| 5fc07c2 | Eh Tan | 23 March 2007, 22:21:06 UTC | Added new parameter 'adv_gamme' to the manual and input samples. Documented a new tic_method=3 | 23 March 2007, 22:21:06 UTC |
| 1e70a61 | Eh Tan | 23 March 2007, 21:06:06 UTC | Added description to the tracer and composition input/output files | 23 March 2007, 21:06:06 UTC |
| c0753b2 | Eh Tan | 23 March 2007, 20:40:27 UTC | Added the tracer parameters to the manual and sample input files | 23 March 2007, 20:40:27 UTC |
| c50ae40 | Eh Tan | 23 March 2007, 20:39:12 UTC | Disable the parameter "analytical_tracer_test", and make "chemical_buoyancy" a boolean | 23 March 2007, 20:39:12 UTC |
| 2678c56 | Eh Tan | 23 March 2007, 19:37:24 UTC | Added the low-visc-zone parameters to the manual and the sample input files | 23 March 2007, 19:37:24 UTC |
| b4b5b1c | Eh Tan | 23 March 2007, 05:31:39 UTC | Added the image for cookbook7 (thermo-chemical convection | 23 March 2007, 05:31:39 UTC |
| 130bee2 | Eh Tan | 23 March 2007, 05:30:43 UTC | When I renamed the old Cookbook7/ directory to Cookbook6/, I forgot to rename cookbook7.eps to cookbook6.eps. Now it is done. | 23 March 2007, 05:30:43 UTC |
| a2482bb | Eh Tan | 23 March 2007, 05:25:10 UTC | These two EPS files are the leftover of an old cookbook | 23 March 2007, 05:25:10 UTC |
| 801b1bb | Eh Tan | 23 March 2007, 05:22:29 UTC | Gather theta and phi only in get_neighboring_caps() | 23 March 2007, 05:22:29 UTC |
| 6bef184 | Eh Tan | 23 March 2007, 05:21:38 UTC | Changed the header format of comp_* output to be consistent with other data files | 23 March 2007, 05:21:38 UTC |
| da31e1c | Sue Kientz | 22 March 2007, 22:11:02 UTC | added bib entry per eh, changed cover to citcoms (rem .py), changed to 2.2.0, todo notation removed; regen pdf | 22 March 2007, 22:11:02 UTC |
| 3339bf3 | Eh Tan | 22 March 2007, 19:58:11 UTC | Make the output of 1st iteration consistent with later iterations | 22 March 2007, 19:58:11 UTC |
| 8f757ca | Eh Tan | 22 March 2007, 19:57:57 UTC | Calling find_tracers() and count_tracers_of_flavors() in initialize_tracers(), so that the former two functions can become static/private | 22 March 2007, 19:57:57 UTC |
| 1d3cb93 | Eh Tan | 22 March 2007, 19:55:18 UTC | Renamed initialize_tracer_arrays() to allocate_tracer_arrays() | 22 March 2007, 19:55:18 UTC |
| 34b83e1 | Eh Tan | 21 March 2007, 22:46:51 UTC | Updated the version number to 2.2.0 | 21 March 2007, 22:46:51 UTC |
| f1b0e00 | Eh Tan | 21 March 2007, 22:46:34 UTC | Updated the dependency information | 21 March 2007, 22:46:34 UTC |
| c03947b | Eh Tan | 21 March 2007, 22:46:08 UTC | Added chemical Rayleigh number to the equations | 21 March 2007, 22:46:08 UTC |
