| 0693207 | Leif Strand | 15 November 2006, 02:06:20 UTC | Corrections to the section, "Changing Parameters". | 15 November 2006, 02:06:20 UTC |
| 901d882 | Leif Strand | 15 November 2006, 01:14:49 UTC | Updated the installation chapter. | 15 November 2006, 01:14:49 UTC |
| 80a98d3 | Leif Strand | 14 November 2006, 03:25:28 UTC | 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. | 14 November 2006, 03:25:28 UTC |
| 4bd3a75 | Leif Strand | 11 November 2006, 03:34:08 UTC | 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... | 11 November 2006, 03:34:08 UTC |
| 79e53b1 | Sue Kientz | 10 November 2006, 19:20:56 UTC | created formulas for sec a.1.11 | 10 November 2006, 19:20:56 UTC |
| 8cac7ae | Sue Kientz | 10 November 2006, 18:54:31 UTC | cookbook 6 graphic edited, various small tweaks | 10 November 2006, 18:54:31 UTC |
| fdd2455 | Sue Kientz | 10 November 2006, 01:59:45 UTC | finished various typos and fixes after checking with Luis on questions | 10 November 2006, 01:59:45 UTC |
| 897706c | Sue Kientz | 09 November 2006, 19:37:41 UTC | various typos and fixes | 09 November 2006, 19:37:41 UTC |
| 967ea83 | Eh Tan | 07 November 2006, 19:33:31 UTC | * Fixed a few typos * Added "TODO" in front of all unfinished text. | 07 November 2006, 19:33:31 UTC |
| f89ab8a | Leif Strand | 07 November 2006, 02:30:04 UTC | Moved CitcomS HDF5 macros to cs/autoconf. | 07 November 2006, 02:30:04 UTC |
| 02fbe2f | Leif Strand | 07 November 2006, 01:33:06 UTC | 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. | 07 November 2006, 01:33:06 UTC |
| c20d5e5 | Sue Kientz | 07 November 2006, 00:49:42 UTC | pdf generated | 07 November 2006, 00:49:42 UTC |
| bd49eb5 | Sue Kientz | 07 November 2006, 00:49:04 UTC | gurnis edits, new pdf | 07 November 2006, 00:49:04 UTC |
| b93974f | Sue Kientz | 06 November 2006, 18:53:08 UTC | added authors to cover | 06 November 2006, 18:53:08 UTC |
| 2dbb7e7 | Sue Kientz | 06 November 2006, 18:33:16 UTC | added new section 1.7 per gurnis and supporting graphic | 06 November 2006, 18:33:16 UTC |
| 8bab2a8 | Luis Armendariz | 01 November 2006, 20:47:53 UTC | Re-typed most of the changes from my copy of the citcoms.lyx file | 01 November 2006, 20:47:53 UTC |
| b472059 | Eh Tan | 27 October 2006, 21:26:23 UTC | Removed legacy file .cvsignore | 27 October 2006, 21:26:23 UTC |
| 6cdac9f | Eh Tan | 27 October 2006, 21:25:51 UTC | Removed legary file .cvsignore | 27 October 2006, 21:25:51 UTC |
| ff62a3e | Eh Tan | 20 October 2006, 19:36:03 UTC | 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. | 20 October 2006, 19:36:03 UTC |
| 47c4c2b | Eh Tan | 20 October 2006, 19:00:27 UTC | * Removed extra output_time(), which was used for profiling * Converted tab to 4 spaces | 20 October 2006, 19:00:27 UTC |
| caf7f85 | Leif Strand | 20 October 2006, 08:19:58 UTC | Fail if MPI lib/header is not found. | 20 October 2006, 08:19:58 UTC |
| 19f0a1b | Leif Strand | 17 October 2006, 11:00:23 UTC | Fixed legacy build. | 17 October 2006, 11:00:23 UTC |
| 2e201da | Leif Strand | 17 October 2006, 09:18:15 UTC | Transitioning to Merlin. (Warning: still under construction.) | 17 October 2006, 09:18:15 UTC |
| addc0ee | Eh Tan | 14 October 2006, 00:29:17 UTC | Undid the accidental checkin at r4998 | 14 October 2006, 00:29:17 UTC |
| d6ccdc2 | Eh Tan | 14 October 2006, 00:27:09 UTC | Renamed reference of "average" to "horiz_avg" | 14 October 2006, 00:27:09 UTC |
| a16042e | Eh Tan | 14 October 2006, 00:06:56 UTC | Added description on new features and bug fixes for v2.1.0 | 14 October 2006, 00:06:56 UTC |
| 73c5c0d | Luis Armendariz | 13 October 2006, 23:59:48 UTC | Settled on /horiz_avg/ instead of /have/ | 13 October 2006, 23:59:48 UTC |
| 2d20c72 | Sue Kientz | 13 October 2006, 23:46:36 UTC | updated url handling | 13 October 2006, 23:46:36 UTC |
| bfdbda6 | Eh Tan | 13 October 2006, 23:18:11 UTC | * 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 | 13 October 2006, 23:18:11 UTC |
| d87840e | Eh Tan | 13 October 2006, 07:39:03 UTC | * 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) | 13 October 2006, 07:39:03 UTC |
| ea97058 | Eh Tan | 13 October 2006, 06:43:36 UTC | Gave default values to several parameters | 13 October 2006, 06:43:36 UTC |
| b3ab31f | Eh Tan | 13 October 2006, 04:15:53 UTC | Removed obsolete input parameter "maxadvtime" from the input samples | 13 October 2006, 04:15:53 UTC |
| 0e734d9 | Eh Tan | 13 October 2006, 04:10:32 UTC | 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. | 13 October 2006, 04:10:32 UTC |
| 701b1ec | Eh Tan | 12 October 2006, 21:43:09 UTC | 'half_space_age' was not used when 'tic_method'=1. So, fixed the comment and removed the conditional input | 12 October 2006, 21:43:09 UTC |
| fa4793e | Leif Strand | 12 October 2006, 14:48:43 UTC | 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 :-) | 12 October 2006, 14:48:43 UTC |
| 37db3e3 | Sue Kientz | 11 October 2006, 20:01:04 UTC | took care of some todo items | 11 October 2006, 20:01:04 UTC |
| 4791fdb | Eh Tan | 10 October 2006, 23:48:38 UTC | * Added subsection on installing OpenDXutils package * Aligned figures to the center * Changed the layout of the Appendices | 10 October 2006, 23:48:38 UTC |
| 21245be | Sue Kientz | 10 October 2006, 20:37:07 UTC | added hdf5 install and addt tools chapters | 10 October 2006, 20:37:07 UTC |
| 5717745 | Luis Armendariz | 10 October 2006, 18:42:58 UTC | Inserted a few TODO items | 10 October 2006, 18:42:58 UTC |
| 55ddf81 | Luis Armendariz | 10 October 2006, 13:00:23 UTC | 1. Reorganized routines in a more logical order. 2. Consolidated routines from PyTables.[ch] into Output_h5.c | 10 October 2006, 13:00:23 UTC |
| 509de08 | Luis Armendariz | 10 October 2006, 11:54:13 UTC | Renamed local function to conform with h5 prefix. | 10 October 2006, 11:54:13 UTC |
| 7f010dc | Luis Armendariz | 10 October 2006, 07:29:28 UTC | 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 | 10 October 2006, 07:29:28 UTC |
| 24fcb93 | Luis Armendariz | 10 October 2006, 00:52:53 UTC | Forgot to delete reference to obsolete data_group. | 10 October 2006, 00:52:53 UTC |
| 3ee3b7e | Eh Tan | 10 October 2006, 00:52:45 UTC | Set MIME type to pdf | 10 October 2006, 00:52:45 UTC |
| 2fc3b57 | Eh Tan | 10 October 2006, 00:51:15 UTC | Set MIME type to image | 10 October 2006, 00:51:15 UTC |
| b992618 | Eh Tan | 10 October 2006, 00:48:41 UTC | Set MIME type to image | 10 October 2006, 00:48:41 UTC |
| 5f2b697 | Luis Armendariz | 10 October 2006, 00:45:25 UTC | Shortened /average/ group into /have/ | 10 October 2006, 00:45:25 UTC |
| a7bc5d4 | Eh Tan | 10 October 2006, 00:42:50 UTC | Figure for HDF5 visualization | 10 October 2006, 00:42:50 UTC |
| 282370e | Eh Tan | 10 October 2006, 00:41:19 UTC | Added section on visualizing HDF5 output | 10 October 2006, 00:41:19 UTC |
| 3729221 | Luis Armendariz | 10 October 2006, 00:38:19 UTC | Fix mispelling in input parameters (allignment options). | 10 October 2006, 00:38:19 UTC |
| bdd582d | Eh Tan | 09 October 2006, 23:25:06 UTC | * 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 | 09 October 2006, 23:25:06 UTC |
| 64710e9 | Sue Kientz | 09 October 2006, 23:14:47 UTC | change equation numbering | 09 October 2006, 23:14:47 UTC |
| 5248caf | Eh Tan | 09 October 2006, 20:41:31 UTC | Changed the order of input parameters | 09 October 2006, 20:41:31 UTC |
| 45b6126 | Eh Tan | 09 October 2006, 19:58:46 UTC | Updated for the new layout of hdf5 output | 09 October 2006, 19:58:46 UTC |
| f99228b | Michael Gurnis | 09 October 2006, 00:14:42 UTC | 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. | 09 October 2006, 00:14:42 UTC |
| 5a1d516 | Leif Strand | 08 October 2006, 12:04:43 UTC | Pointed CitcomS egg-downloading at the new "Eggs" section on the web site, to insulate CitcomS from the imminent chaos in pythia-dev. | 08 October 2006, 12:04:43 UTC |
| db95387 | Eh Tan | 07 October 2006, 01:15:53 UTC | Updated for the new layout in the h5 file | 07 October 2006, 01:15:53 UTC |
| 9b4a1e9 | Luis Armendariz | 07 October 2006, 00:01:54 UTC | Eliminated data group in HDF5 file. Main datasets are now on the root-level. | 07 October 2006, 00:01:54 UTC |
| 731ed51 | Eh Tan | 06 October 2006, 21:10:34 UTC | The type of elt_g should be "higher_precision" instead of "double". | 06 October 2006, 21:10:34 UTC |
| e54baed | Eh Tan | 06 October 2006, 20:18:08 UTC | Changed the signature of the signal handler from (void)(interuption(void)) to (void)(interuption(int)) to conform with the C standard | 06 October 2006, 20:18:08 UTC |
| 15b4a0f | Eh Tan | 06 October 2006, 20:02:56 UTC | Missing braces around initializers for array structs node_point[] and offset[] | 06 October 2006, 20:02:56 UTC |
| 1ae2dff | Eh Tan | 06 October 2006, 17:17:18 UTC | Some minor edits | 06 October 2006, 17:17:18 UTC |
| 7394a1a | Eh Tan | 05 October 2006, 20:07:32 UTC | Using 2-digit number for the cap filename, eg. prefix.cap00.step | 05 October 2006, 20:07:32 UTC |
| 4adbd5f | Eh Tan | 05 October 2006, 00:38:05 UTC | Updated macros to use new samples files and fixed a few stylus issues | 05 October 2006, 00:38:05 UTC |
| a43e1c9 | Eh Tan | 05 October 2006, 00:15:53 UTC | Rearranged file list | 05 October 2006, 00:15:53 UTC |
| c57c41c | Eh Tan | 05 October 2006, 00:15:03 UTC | Updated file list | 05 October 2006, 00:15:03 UTC |
| eb56b58 | Eh Tan | 05 October 2006, 00:04:43 UTC | Replaced sample files at 0th time step with sample files at 100th time step, which have more interesting features in the visualization, | 05 October 2006, 00:04:43 UTC |
| dec5cc0 | Eh Tan | 04 October 2006, 18:34:45 UTC | * Removed some unnecessary parameters * Changed the layout slightly * Updated the cookbook scripts to be consistent with the manual | 04 October 2006, 18:34:45 UTC |
| 4803b77 | Eh Tan | 04 October 2006, 18:32:04 UTC | Updated the Cookbook chapter | 04 October 2006, 18:32:04 UTC |
| e7d317f | Eh Tan | 04 October 2006, 18:24:10 UTC | Removed unused figures | 04 October 2006, 18:24:10 UTC |
| 32797c1 | Eh Tan | 04 October 2006, 01:56:32 UTC | Renamed file to be consistent with the manual | 04 October 2006, 01:56:32 UTC |
| 9512254 | Eh Tan | 04 October 2006, 01:54:28 UTC | Renamed directory to be consistent with the manual | 04 October 2006, 01:54:28 UTC |
| ab8b6c4 | Eh Tan | 02 October 2006, 22:46:19 UTC | Using default Rayleigh number, which is stated in the manual. Also updated the comment to be consistent with the manual. | 02 October 2006, 22:46:19 UTC |
| 3753e94 | Eh Tan | 02 October 2006, 22:43:45 UTC | Slightly updated postprocessing chapter. Revised Cookbook 1. | 02 October 2006, 22:43:45 UTC |
| 5e5597c | Eh Tan | 30 September 2006, 00:56:33 UTC | Updated Chapter 3 "Running CitComS.py" for the .cfg input format, also explained how to launch a parallel job. Some TODO items left. | 30 September 2006, 00:56:33 UTC |
| 4e33dfd | Michael Gurnis | 29 September 2006, 23:14:31 UTC | Fixed age bug in Regional. In Regional_lith_age_read_files.c, find_age_in_MY() was not being converted to a float | 29 September 2006, 23:14:31 UTC |
| 0acc5c3 | Sue Kientz | 29 September 2006, 21:50:21 UTC | updated version on pdf cover and added pdf layered file | 29 September 2006, 21:50:21 UTC |
| 78036ea | Luis Armendariz | 28 September 2006, 14:56:04 UTC | 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). | 28 September 2006, 14:56:04 UTC |
| 3009045 | Luis Armendariz | 28 September 2006, 14:30:32 UTC | Fixed typo in names | 28 September 2006, 14:30:32 UTC |
| 45534b2 | Eh Tan | 27 September 2006, 23:33:15 UTC | * Removed debugging output * Added svn:keywords and svn:mime-type attributes | 27 September 2006, 23:33:15 UTC |
| a422171 | Leif Strand | 27 September 2006, 20:37:35 UTC | Relaxed setuptools version requirement to 0.6b1. | 27 September 2006, 20:37:35 UTC |
| c4c57a3 | Eh Tan | 27 September 2006, 00:24:45 UTC | * 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 | 27 September 2006, 00:24:45 UTC |
| 738492c | Luis Armendariz | 26 September 2006, 12:20:08 UTC | Fixed broken 'make dist' | 26 September 2006, 12:20:08 UTC |
| 12d4521 | Leif Strand | 26 September 2006, 01:09:16 UTC | 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. | 26 September 2006, 01:09:16 UTC |
| 5d463b3 | Eh Tan | 25 September 2006, 19:13:26 UTC | Disabled material output, since material control is not working (yet) | 25 September 2006, 19:13:26 UTC |
| 373b819 | Eh Tan | 24 September 2006, 07:28:19 UTC | 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. | 24 September 2006, 07:28:19 UTC |
| 5c1c7aa | Eh Tan | 22 September 2006, 23:26:49 UTC | Write surf and botm output by default (but can be disabled by setting output_optional=''), which is compatible with v2.0.x. | 22 September 2006, 23:26:49 UTC |
| 07ed10c | Eh Tan | 22 September 2006, 22:58:02 UTC | Removed debugging output | 22 September 2006, 22:58:02 UTC |
| 1fc1f3d | Eh Tan | 22 September 2006, 22:29:02 UTC | * Fixed issue55 "surf files got deleted by batchsurf.py" * Refactored the codes on machinefile -> nodelist | 22 September 2006, 22:29:02 UTC |
| 88b387e | Eh Tan | 22 September 2006, 22:14:37 UTC | These scripts accept 'localhost' as a valid machine name now | 22 September 2006, 22:14:37 UTC |
| fa022de | Luis Armendariz | 22 September 2006, 22:01:30 UTC | Bug fix: maxdims[0] is set to H5S_UNLIMITED in extendible datasets, so it should never be incremented. | 22 September 2006, 22:01:30 UTC |
| bec9f15 | Eh Tan | 22 September 2006, 20:37:27 UTC | Added 'Id' keyword to the files | 22 September 2006, 20:37:27 UTC |
| b0699e3 | Eh Tan | 22 September 2006, 19:19:11 UTC | Fixed two bugs in post-processing scripts | 22 September 2006, 19:19:11 UTC |
| 280c471 | Eh Tan | 21 September 2006, 23:03:16 UTC | Updated post-processing script for new output_format options. See issue53. | 21 September 2006, 23:03:16 UTC |
| 6819d58 | Luis Armendariz | 21 September 2006, 21:25:44 UTC | Allow for optional fields when extending datasets. | 21 September 2006, 21:25:44 UTC |
| f57748f | Eh Tan | 21 September 2006, 21:17:46 UTC | Refactored out the code computing horizontal average of temperature and rms velocity into a function. This fixes the bug in issue46. | 21 September 2006, 21:17:46 UTC |
| 3638975 | Eh Tan | 21 September 2006, 20:08:43 UTC | Forgot to change the default value in C | 21 September 2006, 20:08:43 UTC |
| ef5a5b2 | Eh Tan | 21 September 2006, 19:57:58 UTC | 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". | 21 September 2006, 19:57:58 UTC |
| 0257ab0 | Eh Tan | 21 September 2006, 17:51:16 UTC | Parser will skip lines starting with '[', so that it can parse .cfg file correctly | 21 September 2006, 17:51:16 UTC |
| 3d0ae13 | Eh Tan | 21 September 2006, 17:49:19 UTC | Removed quotes from output string | 21 September 2006, 17:49:19 UTC |
