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https://github.com/geodynamics/citcoms
10 January 2021, 21:22:13 UTC
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Revision Author Date Message Commit Date
e7c2ea3 Sue Kientz 07 December 2006, 22:09:17 UTC text fixes to recent additions 07 December 2006, 22:09:17 UTC
b7662aa Eh Tan 07 December 2006, 21:30:53 UTC * Put back the HDFView sections * Added a screenshot of HDFView * Added a warning on "-O3" compiler flag 07 December 2006, 21:30:53 UTC
7bf8a4b Sue Kientz 07 December 2006, 05:03:23 UTC text edits to appendices and bib 07 December 2006, 05:03:23 UTC
cf68821 Sue Kientz 07 December 2006, 00:12:17 UTC small changes to chapt 6; standardized cross refference style; sstandardized code spacing 07 December 2006, 00:12:17 UTC
8910ace Sue Kientz 06 December 2006, 23:31:57 UTC enumerating several sections of the instructions in chap 5 for clarity, and a few minor text fixes 06 December 2006, 23:31:57 UTC
cd4ffb9 Sue Kientz 06 December 2006, 20:59:49 UTC a few text fixes in chapter 3 06 December 2006, 20:59:49 UTC
bb3c41c Sue Kientz 06 December 2006, 20:33:12 UTC a few text fixes, preface to end of chapt 2 06 December 2006, 20:33:12 UTC
6f35a8c Sue Kientz 06 December 2006, 18:59:56 UTC gurnis corrections and some other fixes 06 December 2006, 18:59:56 UTC
8cee12e Luis Armendariz 06 December 2006, 08:52:50 UTC Temporarily removing Mayavi2 files from Makefile.am 06 December 2006, 08:52:50 UTC
3c51bb9 Luis Armendariz 06 December 2006, 08:23:54 UTC Archive files created during Martin Weier's internship 06 December 2006, 08:23:54 UTC
bb9bfc7 Luis Armendariz 06 December 2006, 08:16:37 UTC Reorganized structure of the Mayavi2 plugin modules 06 December 2006, 08:16:37 UTC
0dce83c Luis Armendariz 06 December 2006, 08:13:00 UTC Simplified the file that will be be copied to user's ~/.mayavi2 directory. 06 December 2006, 08:13:00 UTC
845881d Luis Armendariz 06 December 2006, 06:55:03 UTC Group all CitcomS options under a single menu group. 06 December 2006, 06:55:03 UTC
d7337ee Luis Armendariz 06 December 2006, 05:58:52 UTC Quick fixes to manual. 06 December 2006, 05:58:52 UTC
1797b61 Leif Strand 06 December 2006, 01:08:58 UTC 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. 06 December 2006, 01:08:58 UTC
57aeaf3 Sue Kientz 06 December 2006, 00:49:49 UTC small changes in one image caption and in citation 06 December 2006, 00:49:49 UTC
f0944ca Leif Strand 06 December 2006, 00:42:34 UTC 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. 06 December 2006, 00:42:34 UTC
ab08284 Luis Armendariz 06 December 2006, 00:18:47 UTC Added actions for ReduceFilter and ShowCapsFilter 06 December 2006, 00:18:47 UTC
59f42cb Leif Strand 05 December 2006, 23:13:27 UTC Require final release version of Pythia. Include egg-related files in release tarball ("make dist"). 05 December 2006, 23:13:27 UTC
f17e43c Sue Kientz 05 December 2006, 20:46:57 UTC edited text and images placement in 5.8 05 December 2006, 20:46:57 UTC
770fe7c Sue Kientz 05 December 2006, 20:34:19 UTC slghtly widened l. col in appendix a tables as using typewriter widened lines; fixed other formatting issues in appendices 05 December 2006, 20:34:19 UTC
9e69630 Sue Kientz 05 December 2006, 20:11:44 UTC changing font style to typewriter small in appendix a tablesi and a few typos 05 December 2006, 20:11:44 UTC
8b31f43 Sue Kientz 05 December 2006, 19:19:02 UTC small fixes to chap 4, text and table placement 05 December 2006, 19:19:02 UTC
e8ab235 Sue Kientz 05 December 2006, 18:04:11 UTC making use of typewriter font and quotes consistent in appendix a 05 December 2006, 18:04:11 UTC
8ea8984 Eh Tan 05 December 2006, 07:09:01 UTC Updated Chapter 4 05 December 2006, 07:09:01 UTC
ea21745 Eh Tan 05 December 2006, 06:17:15 UTC Example h5 files including all optional output 05 December 2006, 06:17:15 UTC
66962d1 Eh Tan 05 December 2006, 06:14:50 UTC Forgot to update the makefile 05 December 2006, 06:14:50 UTC
35521dd Eh Tan 05 December 2006, 05:04:14 UTC 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. 05 December 2006, 05:04:14 UTC
e8a02da Eh Tan 05 December 2006, 04:19:42 UTC * Renamed estimate.py to estimate_size.py * Added license text * Update for new HDF5 layout 05 December 2006, 04:19:42 UTC
318477c Luis Armendariz 05 December 2006, 00:46:40 UTC Changed code in A.1.1 and A.1.2 to use small font with typewriter style. 05 December 2006, 00:46:40 UTC
ee84bec Eh Tan 05 December 2006, 00:40:12 UTC Mentioned change of naming scheme for capfiles in NEWS 05 December 2006, 00:40:12 UTC
ad9f299 Sue Kientz 05 December 2006, 00:31:25 UTC fixed quotes; added degree symbols as requested 05 December 2006, 00:31:25 UTC
0c3e62b Eh Tan 05 December 2006, 00:14:58 UTC Finished the GMT script section 05 December 2006, 00:14:58 UTC
c4f1afa Eh Tan 04 December 2006, 23:47:57 UTC Renamed "center" to "starting point" 04 December 2006, 23:47:57 UTC
90487f5 Sue Kientz 04 December 2006, 22:42:59 UTC minor sentence/word form changes in 5.1 and 5.2 04 December 2006, 22:42:59 UTC
b3365ac Sue Kientz 04 December 2006, 22:33:47 UTC reformatted column names in c.4.9 04 December 2006, 22:33:47 UTC
f4f3bca Eh Tan 04 December 2006, 22:19:15 UTC 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 04 December 2006, 22:19:15 UTC
2457cf3 Sue Kientz 04 December 2006, 20:33:20 UTC fixed more quotes, fixed table breaks, lines in table missing, other minor format problems 04 December 2006, 20:33:20 UTC
1daa462 Luis Armendariz 04 December 2006, 19:48:19 UTC Added OpenHDF5 and OpenVTK actions for mayavi2 04 December 2006, 19:48:19 UTC
a7c9af3 Luis Armendariz 04 December 2006, 17:24:39 UTC Fixes to manual 04 December 2006, 17:24:39 UTC
d0d65c0 Luis Armendariz 04 December 2006, 17:24:24 UTC Fixed typos 04 December 2006, 17:24:24 UTC
192f787 Luis Armendariz 04 December 2006, 16:54:12 UTC Added vim modeline 04 December 2006, 16:54:12 UTC
02556dd Luis Armendariz 04 December 2006, 14:21:20 UTC Mayavi2 UI customizations 04 December 2006, 14:21:20 UTC
7fcb642 Luis Armendariz 04 December 2006, 14:11:12 UTC Added python module namespace for the citcoms mayavi2 plugins 04 December 2006, 14:11:12 UTC
586ea34 Luis Armendariz 04 December 2006, 13:43:01 UTC Removed executable permissions 04 December 2006, 13:43:01 UTC
33b38bf Eh Tan 02 December 2006, 07:41:50 UTC Update for new HDF5 layout 02 December 2006, 07:41:50 UTC
a822c42 Eh Tan 02 December 2006, 07:14:16 UTC * Removed obsolete parameters * Added new parameters * Only one "parameter=value" per line 02 December 2006, 07:14:16 UTC
59540cb Eh Tan 02 December 2006, 06:04:50 UTC Updated for new HDF5 layout 02 December 2006, 06:04:50 UTC
409e719 Eh Tan 02 December 2006, 06:04:05 UTC Minor tweaks 02 December 2006, 06:04:05 UTC
737d6d7 Eh Tan 02 December 2006, 04:43:50 UTC Moved utility functions to h5util.c 02 December 2006, 04:43:50 UTC
c9f5f73 Eh Tan 02 December 2006, 04:15:26 UTC Fixed a bug of counting argc 02 December 2006, 04:15:26 UTC
95de6c6 Eh Tan 02 December 2006, 00:57:22 UTC Added more rheology options, which is required for benchmarks rheol=1: visc = visc0 * exp(viscE * (viscT - T)) rheol=2: visc = visc0 * exp(-T / viscT) 02 December 2006, 00:57:22 UTC
9dc129b Eh Tan 02 December 2006, 00:38:50 UTC Updated h5tocap.py for new layout of HDF5 files 02 December 2006, 00:38:50 UTC
d5da530 Eh Tan 02 December 2006, 00:03:01 UTC Added a program to convert h5 file to velo files for restart 02 December 2006, 00:03:01 UTC
6d40d87 Sue Kientz 01 December 2006, 23:34:49 UTC removed todo at 4.5.1, no issue there 01 December 2006, 23:34:49 UTC
6f8787c Leif Strand 01 December 2006, 22:00:25 UTC 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. 01 December 2006, 22:00:25 UTC
a348cee Eh Tan 01 December 2006, 21:56:58 UTC Added samples of HDF5 output 01 December 2006, 21:56:58 UTC
99f6b02 Leif Strand 01 December 2006, 21:33:03 UTC builddir != srcdir works again. The use of setup.py/distutils/setuptools forces the creation of files in srcdir. This bugs me. 01 December 2006, 21:33:03 UTC
72eaebe Leif Strand 01 December 2006, 04:40:37 UTC The "make install" command now works again. 01 December 2006, 04:40:37 UTC
4602470 Sue Kientz 30 November 2006, 23:38:30 UTC fixed sentence in A.1.2 last row 30 November 2006, 23:38:30 UTC
e83fdc3 Eh Tan 30 November 2006, 23:08:42 UTC 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. 30 November 2006, 23:08:42 UTC
68ecca0 Eh Tan 30 November 2006, 22:55:21 UTC Moved path name of restart file to "datadir_old" 30 November 2006, 22:55:21 UTC
7b4029c Eh Tan 30 November 2006, 22:53:31 UTC Fixed issue63, Change "monitoringfrequency" comment in citcoms cookbooks 30 November 2006, 22:53:31 UTC
bfd0022 Luis Armendariz 30 November 2006, 22:21:14 UTC Done with Chapter 4 references. 30 November 2006, 22:21:14 UTC
91e3d58 Eh Tan 30 November 2006, 21:16:44 UTC The concept of caps is explained in section 1.7 30 November 2006, 21:16:44 UTC
31ea96a Luis Armendariz 30 November 2006, 21:10:38 UTC Removing obsolete program h5steps.c 30 November 2006, 21:10:38 UTC
1b23e41 Eh Tan 30 November 2006, 20:57:36 UTC Updated Appendices 30 November 2006, 20:57:36 UTC
bbe34e1 Eh Tan 30 November 2006, 20:26:51 UTC Updated section 3.6.1 30 November 2006, 20:26:51 UTC
63b4155 Leif Strand 28 November 2006, 23:28:36 UTC 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.) 28 November 2006, 23:28:36 UTC
08658cd Leif Strand 28 November 2006, 21:08:18 UTC 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. 28 November 2006, 21:08:18 UTC
b1196e7 Sue Kientz 28 November 2006, 19:26:20 UTC various edits to 3.6.1 and 3.7 28 November 2006, 19:26:20 UTC
e195f6d Leif Strand 28 November 2006, 07:33:41 UTC 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.) 28 November 2006, 07:33:41 UTC
6da3152 Eh Tan 28 November 2006, 05:00:42 UTC Clarified the comment 28 November 2006, 05:00:42 UTC
408a073 Eh Tan 28 November 2006, 04:42:18 UTC Updated for new features 28 November 2006, 04:42:18 UTC
172b656 Eh Tan 28 November 2006, 04:41:56 UTC Added a reference to NEWS 28 November 2006, 04:41:56 UTC
573d06e Eh Tan 28 November 2006, 03:34:23 UTC Chapter 3 updated 28 November 2006, 03:34:23 UTC
80c8616 Leif Strand 28 November 2006, 03:01:37 UTC 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(). 28 November 2006, 03:01:37 UTC
f503267 Eh Tan 28 November 2006, 02:57:07 UTC Updated the dimensional const 28 November 2006, 02:57:07 UTC
2d35142 Eh Tan 28 November 2006, 02:55:44 UTC Updated to be consistent with the manual 28 November 2006, 02:55:44 UTC
61249ec Eh Tan 27 November 2006, 23:09:42 UTC Changed the default value of "datadir" to "." 27 November 2006, 23:09:42 UTC
944d4da Eh Tan 27 November 2006, 22:37:27 UTC Changed postprocessing scripts for the new "datadir" parameter 27 November 2006, 22:37:27 UTC
510c2e5 Eh Tan 27 November 2006, 21:27:15 UTC 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. 27 November 2006, 21:27:15 UTC
baf9708 Eh Tan 27 November 2006, 20:05:42 UTC Added extern program to determine "datadir" 27 November 2006, 20:05:42 UTC
2cd498c Eh Tan 27 November 2006, 20:05:11 UTC 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. 27 November 2006, 20:05:11 UTC
eaffb18 Eh Tan 22 November 2006, 21:26:09 UTC 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 22 November 2006, 21:26:09 UTC
26f0c05 Eh Tan 22 November 2006, 21:25:47 UTC Ignoring overlapping nodes when counting # of global nodes 22 November 2006, 21:25:47 UTC
5c19bff Sue Kientz 22 November 2006, 20:25:40 UTC typo; made references into an itemized list 22 November 2006, 20:25:40 UTC
32fc3c9 Eh Tan 22 November 2006, 20:05:23 UTC Removed unused codes and files 22 November 2006, 20:05:23 UTC
2d8467a Eh Tan 22 November 2006, 19:41:43 UTC Refactored geoid calculation 22 November 2006, 19:41:43 UTC
8463943 Luis Armendariz 21 November 2006, 23:03:38 UTC Expanded section on optimizing parallel I/O. 21 November 2006, 23:03:38 UTC
91c9c75 Eh Tan 21 November 2006, 20:18:02 UTC Added scripts for 2D temperature plots, using GMT commands 21 November 2006, 20:18:02 UTC
201713b Eh Tan 20 November 2006, 19:24:40 UTC Forgot to declare function prototype 20 November 2006, 19:24:40 UTC
401efaa Eh Tan 18 November 2006, 05:17:07 UTC Disabled a debugging output, which is not protected by a "if(E->control.verbose)" and caused Segmentation Fault. 18 November 2006, 05:17:07 UTC
1433785 Leif Strand 18 November 2006, 01:29:12 UTC The function loadObject() has been moved from Pythia to Merlin. 18 November 2006, 01:29:12 UTC
7d6ea27 Eh Tan 18 November 2006, 00:48:49 UTC Updated the vbc files and input file 18 November 2006, 00:48:49 UTC
a4596a5 Eh Tan 18 November 2006, 00:41:52 UTC Updated the vbc files and input file. 18 November 2006, 00:41:52 UTC
63a29c8 Eh Tan 18 November 2006, 00:20:26 UTC HDF5 output for geoid is working 18 November 2006, 00:20:26 UTC
4b8c00e Luis Armendariz 17 November 2006, 22:37:12 UTC Cleaned up 'svn status' by updating svn:ignore property 17 November 2006, 22:37:12 UTC
1d9227a Eh Tan 17 November 2006, 20:25:45 UTC 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 17 November 2006, 20:25:45 UTC
c947d7a Eh Tan 17 November 2006, 06:26:37 UTC 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 17 November 2006, 06:26:37 UTC
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