https://github.com/geodynamics/citcoms

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Revision Author Date Message Commit Date
8cee12e Temporarily removing Mayavi2 files from Makefile.am 06 December 2006, 08:52:50 UTC
3c51bb9 Archive files created during Martin Weier's internship 06 December 2006, 08:23:54 UTC
bb9bfc7 Reorganized structure of the Mayavi2 plugin modules 06 December 2006, 08:16:37 UTC
0dce83c Simplified the file that will be be copied to user's ~/.mayavi2 directory. 06 December 2006, 08:13:00 UTC
845881d Group all CitcomS options under a single menu group. 06 December 2006, 06:55:03 UTC
d7337ee Quick fixes to manual. 06 December 2006, 05:58:52 UTC
1797b61 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 small changes in one image caption and in citation 06 December 2006, 00:49:49 UTC
f0944ca 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 Added actions for ReduceFilter and ShowCapsFilter 06 December 2006, 00:18:47 UTC
59f42cb Require final release version of Pythia. Include egg-related files in release tarball ("make dist"). 05 December 2006, 23:13:27 UTC
f17e43c edited text and images placement in 5.8 05 December 2006, 20:46:57 UTC
770fe7c 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 changing font style to typewriter small in appendix a tablesi and a few typos 05 December 2006, 20:11:44 UTC
8b31f43 small fixes to chap 4, text and table placement 05 December 2006, 19:19:02 UTC
e8ab235 making use of typewriter font and quotes consistent in appendix a 05 December 2006, 18:04:11 UTC
8ea8984 Updated Chapter 4 05 December 2006, 07:09:01 UTC
ea21745 Example h5 files including all optional output 05 December 2006, 06:17:15 UTC
66962d1 Forgot to update the makefile 05 December 2006, 06:14:50 UTC
35521dd 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 * Renamed estimate.py to estimate_size.py * Added license text * Update for new HDF5 layout 05 December 2006, 04:19:42 UTC
318477c 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 Mentioned change of naming scheme for capfiles in NEWS 05 December 2006, 00:40:12 UTC
ad9f299 fixed quotes; added degree symbols as requested 05 December 2006, 00:31:25 UTC
0c3e62b Finished the GMT script section 05 December 2006, 00:14:58 UTC
c4f1afa Renamed "center" to "starting point" 04 December 2006, 23:47:57 UTC
90487f5 minor sentence/word form changes in 5.1 and 5.2 04 December 2006, 22:42:59 UTC
b3365ac reformatted column names in c.4.9 04 December 2006, 22:33:47 UTC
f4f3bca 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 fixed more quotes, fixed table breaks, lines in table missing, other minor format problems 04 December 2006, 20:33:20 UTC
1daa462 Added OpenHDF5 and OpenVTK actions for mayavi2 04 December 2006, 19:48:19 UTC
a7c9af3 Fixes to manual 04 December 2006, 17:24:39 UTC
d0d65c0 Fixed typos 04 December 2006, 17:24:24 UTC
192f787 Added vim modeline 04 December 2006, 16:54:12 UTC
02556dd Mayavi2 UI customizations 04 December 2006, 14:21:20 UTC
7fcb642 Added python module namespace for the citcoms mayavi2 plugins 04 December 2006, 14:11:12 UTC
586ea34 Removed executable permissions 04 December 2006, 13:43:01 UTC
33b38bf Update for new HDF5 layout 02 December 2006, 07:41:50 UTC
a822c42 * Removed obsolete parameters * Added new parameters * Only one "parameter=value" per line 02 December 2006, 07:14:16 UTC
59540cb Updated for new HDF5 layout 02 December 2006, 06:04:50 UTC
409e719 Minor tweaks 02 December 2006, 06:04:05 UTC
737d6d7 Moved utility functions to h5util.c 02 December 2006, 04:43:50 UTC
c9f5f73 Fixed a bug of counting argc 02 December 2006, 04:15:26 UTC
95de6c6 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 Updated h5tocap.py for new layout of HDF5 files 02 December 2006, 00:38:50 UTC
d5da530 Added a program to convert h5 file to velo files for restart 02 December 2006, 00:03:01 UTC
6d40d87 removed todo at 4.5.1, no issue there 01 December 2006, 23:34:49 UTC
6f8787c 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 Added samples of HDF5 output 01 December 2006, 21:56:58 UTC
99f6b02 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 The "make install" command now works again. 01 December 2006, 04:40:37 UTC
4602470 fixed sentence in A.1.2 last row 30 November 2006, 23:38:30 UTC
e83fdc3 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 Moved path name of restart file to "datadir_old" 30 November 2006, 22:55:21 UTC
7b4029c Fixed issue63, Change "monitoringfrequency" comment in citcoms cookbooks 30 November 2006, 22:53:31 UTC
bfd0022 Done with Chapter 4 references. 30 November 2006, 22:21:14 UTC
91e3d58 The concept of caps is explained in section 1.7 30 November 2006, 21:16:44 UTC
31ea96a Removing obsolete program h5steps.c 30 November 2006, 21:10:38 UTC
1b23e41 Updated Appendices 30 November 2006, 20:57:36 UTC
bbe34e1 Updated section 3.6.1 30 November 2006, 20:26:51 UTC
63b4155 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 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 various edits to 3.6.1 and 3.7 28 November 2006, 19:26:20 UTC
e195f6d 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 Clarified the comment 28 November 2006, 05:00:42 UTC
408a073 Updated for new features 28 November 2006, 04:42:18 UTC
172b656 Added a reference to NEWS 28 November 2006, 04:41:56 UTC
573d06e Chapter 3 updated 28 November 2006, 03:34:23 UTC
80c8616 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 Updated the dimensional const 28 November 2006, 02:57:07 UTC
2d35142 Updated to be consistent with the manual 28 November 2006, 02:55:44 UTC
61249ec Changed the default value of "datadir" to "." 27 November 2006, 23:09:42 UTC
944d4da Changed postprocessing scripts for the new "datadir" parameter 27 November 2006, 22:37:27 UTC
510c2e5 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 Added extern program to determine "datadir" 27 November 2006, 20:05:42 UTC
2cd498c 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 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 Ignoring overlapping nodes when counting # of global nodes 22 November 2006, 21:25:47 UTC
5c19bff typo; made references into an itemized list 22 November 2006, 20:25:40 UTC
32fc3c9 Removed unused codes and files 22 November 2006, 20:05:23 UTC
2d8467a Refactored geoid calculation 22 November 2006, 19:41:43 UTC
8463943 Expanded section on optimizing parallel I/O. 21 November 2006, 23:03:38 UTC
91c9c75 Added scripts for 2D temperature plots, using GMT commands 21 November 2006, 20:18:02 UTC
201713b Forgot to declare function prototype 20 November 2006, 19:24:40 UTC
401efaa 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 The function loadObject() has been moved from Pythia to Merlin. 18 November 2006, 01:29:12 UTC
7d6ea27 Updated the vbc files and input file 18 November 2006, 00:48:49 UTC
a4596a5 Updated the vbc files and input file. 18 November 2006, 00:41:52 UTC
63a29c8 HDF5 output for geoid is working 18 November 2006, 00:20:26 UTC
4b8c00e Cleaned up 'svn status' by updating svn:ignore property 17 November 2006, 22:37:12 UTC
1d9227a 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 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
30bb98f Fixed a minor bug in Output.py. 17 November 2006, 05:34:42 UTC
7da74a3 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...) 17 November 2006, 02:24:51 UTC
86701e5 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. 16 November 2006, 21:58:42 UTC
6d6764b 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!!! 16 November 2006, 21:36:50 UTC
d5b200b Corrections with respect to r5302: the binaries/scripts are now once again built under the 'bin' subdirectory. Also reviewed all references to PREFIX. 16 November 2006, 21:25:54 UTC
a1e12dc 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. 16 November 2006, 14:40:41 UTC
2642094 Forgot to commit module/ directory 16 November 2006, 03:04:21 UTC
6602642 Declared function prototype at the top 16 November 2006, 03:01:59 UTC
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