https://github.com/geodynamics/citcoms

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Revision Author Date Message Commit Date
81148ac Merge branch 'master' into python-removal 09 October 2014, 23:22 UTC
7389970 Update version, changelog 09 October 2014, 21:59 UTC
cb811fc Add files to .gitignore 09 October 2014, 21:41 UTC
bb91e3a Added a more detailed usage string 05 September 2014, 18:05 UTC
faabbdc removed std=c++11 from Py2C/Makefile.am 05 September 2014, 17:17 UTC
d362fe7 Removed all C++11 features from the Py2C code 05 September 2014, 17:09 UTC
3a7ef1b minor corrections to get Py2C to build automatically 27 August 2014, 22:00 UTC
75fda8c Changes to include Py2C in the build process 27 August 2014, 21:31 UTC
1fe296f removed python versions of Cookbook parameter files 27 August 2014, 19:52 UTC
c9d9c4b Fixed Makefile.am files for Python and Pyre removal 21 August 2014, 17:32 UTC
369667f Removed Pyre and Exchanger related checks from all Makefile.am files 20 August 2014, 23:06 UTC
f0d7acd removed Python,Pyre and Exchanger related code from configure.ac 20 August 2014, 22:55 UTC
1d93862 removed the CitcomS directory which has only Python scripts 20 August 2014, 22:39 UTC
74d65f3 some more Python removal related cleanup; removed archimedes, module, setup.py and Cookbooks 9 and 10 20 August 2014, 22:34 UTC
85faa25 Updated Cookbook 1 in the CitcomS manual to the pure C version 26 June 2014, 04:12 UTC
a2cf0e8 Updated Cookbook 2 in the CitcomS manual to the pure C version. Cleaned up cookbook2 file in the examples/Cookbook2 directory 26 June 2014, 03:58 UTC
79bf0c0 Updated Cookbook 3 in the CitcomS manual to the pure C version 25 June 2014, 23:18 UTC
5a0eadf Updated Cookbook 4 in the CitcomS manual to the pure C version. Removed parameters with default values from cookbook4 in the examples/Cookbook4 directory 25 June 2014, 23:11 UTC
e13ba7e Updated Cookbook 5 in the CitcomS manual to the pure C version 25 June 2014, 23:03 UTC
255fd82 Updated Cookbook 6 in the CitcomS manual to the pure C version 25 June 2014, 22:53 UTC
573c33f Updated Cookbook 7 in the CitcomS manual to the pure C version 25 June 2014, 22:48 UTC
a2705af Updated Cookbook 8 to the pure C version 25 June 2014, 22:36 UTC
d2d1b09 Removed Cookbook 9 from the CitcomS manual 25 June 2014, 22:04 UTC
6ceb31d Removed Cookbook 10 from the CitcomS manual 25 June 2014, 21:58 UTC
eb40d8e Removed Pyre and Python references from Chapter 3 of the manual. Updated the example config files in Chapter 3 to the C version. 13 June 2014, 23:26 UTC
723802a Removed references to Python and Pyre from chapter 2 of the manual 05 June 2014, 20:23 UTC
4f1ae8b Removed section 2 from Appendix A of the manual, which describes the Pyre based parameters and settings. 09 April 2014, 16:28 UTC
c23d985 Got rid of come nested comment warnings from clang 08 April 2014, 22:13 UTC
0777e0d Completed the implementation of the print_all_config_parameters function. All parameters used in the simulation are output to a file whose name begins with letters pid and is followed by the process id of MPI process 0 08 April 2014, 21:47 UTC
6b8f809 cleaned up the repository to match the .gitignore file. Started adding functionality for writing all parameters to a pidXXXXXX file 25 March 2014, 23:11 UTC
5992bf0 Added the LaTex source for the manual. Added missing parameters to the Py2C conversion tool Cookbook 4 has been fixed to get rid of the "solver not converging" warnings. 05 March 2014, 00:26 UTC
fb1839e Merge pull request #1 from karredondo/master Add ability to combine "heating" output 14 February 2014, 22:32 UTC
7ca37a6 Add ability to combine "heating" output Katrina Arredondo Heating output is in terms of elements instead of nodes. The data is placed in a third combine file "ele" aside from "cap" and "opt." 14 February 2014, 22:30 UTC
c770f8e Further cleanup of the cover page of the manual 13 February 2014, 19:46 UTC
3ebabdc Improved manual cover layout, removed old cover file 13 February 2014, 18:02 UTC
90cb771 Checked in the LaTeX source file for the CitcomS manual, along with the images needed to generate the PDF version of the manual. 11 February 2014, 00:19 UTC
83b32f9 Initial checkin of the Python to C config file conversion tool. Cookbooks 1-8, and Cookbook10 have been converted and the C versions of the config files are located in the corresponding examples/Cookbook directory 05 February 2014, 23:18 UTC
8fde56f update ignore list 18 October 2013, 03:58 UTC
fd2b0d6 Update gitignore 11 October 2013, 16:35 UTC
754dc95 Readd archimedes 11 October 2013, 16:24 UTC
7c6b5ad m4 submodule 11 October 2013, 05:10 UTC
8c294e9 Readd anisotropic code 10 October 2013, 22:03 UTC
f886a03 20 September 2013, 14:58 UTC
3cd9e30 Added reference viscosity fix from Shijie Zhong 24 May 2013, 17:42 UTC
ed21917 Updating to newest version for testing purposes. 25 March 2013, 21:56 UTC
c5526ec Fixed ggrd velocity boundary condition weirdness, I hope. This may go back to 16065 vs. 16067, and bug may have stuck through 20621. 01 September 2012, 23:51 UTC
2b8ed1f Implemented improved tracer fix by Rene. "a new method of finding the element of a tracer that is too close to an element boundary. Up to now such a tracer was shifted by a constant epsilon theta and phi. If the element boundary is parallel to this theta/phi direction it is not guaranteed to work well (thus the number_of_tries check), and additionally I got the problem that sometimes all elements refuse this tracer. Eh checked in a workaround for this (r15742), deleting orphan tracers in Tracer_setup.c. Because I did not know this, I created my own bugfix moving the tracers an epsilon amount orthogonal to all boundaries that are too close. In order to save computing time I use the already computed vectors for the element boundaries (this assumes that the element boundaries are nearly orthogonal to each other, but unless somebody tries to change CitcomS elements that should work fine). The shift happens now in cartesian coordinates since the boundary-vectors are cartesian and the radius-coordinate of the tracer is normalized prior to this check anyway, so I just need to re-normalize it after the shift. For now I did not touch all the now (hopefully) useless security checks but as far as I can see they do no harm either, so we can remove them later." 22 August 2012, 21:21 UTC
11854a5 Implemented Output_vtk.c fixes from Rene. 21 August 2012, 16:30 UTC
74c56ef Minor changes to instructions 28 June 2012, 09:30 UTC
d5fbdb0 Changing to version 3.2.0 since there are many significant changes 02 February 2012, 18:23 UTC
8d8016f Added missing file to distribution 02 February 2012, 00:41 UTC
b0d8a75 Updated NEWS for past 2.5 years 02 February 2012, 00:29 UTC
162e668 Updated ChangeLog, configure.ac for 3.1.2 release Set default configuration to not setup Pyre Added note in examples directory regarding Pyre and Cookbooks 01 February 2012, 21:11 UTC
eb74d9f Fixed minor ggrd assignment bug. 24 January 2012, 21:54 UTC
199d1d8 Debugging GGrd 24 January 2012, 18:44 UTC
74ce5d8 Updating to latest version for sync. 24 January 2012, 18:03 UTC
552bc26 Stop configure if pyre is enabled and python 2.7 is used. See Issue622. 19 January 2012, 19:24 UTC
f4cf4db updated installation instruction 17 January 2012, 04:57 UTC
3a23d00 When python 2.7 is used, ask users to download pythia manually. See issue622 and issue606. 17 January 2012, 02:41 UTC
15a09f1 Made sure that compositional viscosity without compositional buoyancy can be assigned without setting ibuoy=1 and the buoyancy number to zero. 14 January 2012, 08:00 UTC
c9704b3 Merged with recent check in, minor changes. 20 December 2011, 18:04 UTC
51e1984 Fixed a bug in reflective TBC where y-index should be used, not z-index. The bug is harmless though. I checked the code history. This bug exists since CitcomS 1.0, but not in CitcomCU nor CitcomT. 14 November 2011, 05:06 UTC
d8f08c4 fixed a bug that h5close_field() didn't have a return statement, reported by Nicolas Flament in issue611. 14 October 2011, 18:27 UTC
0f1fbbf fixed a bug that when the perturblayer is on the internal boundary, the temperature perturbation wasn't added to the lower processor. 18 September 2011, 03:54 UTC
cebdfcb Updating to newest version, don't think that there should be any significant changes on my side. 31 July 2011, 20:38 UTC
1e7ff88 enhancing VTK output, mostly contributed by Rene Gassmoeller at GFZ. - A new input parameter 'vtk_format', which can be either 'ascii' (default) or 'binary'. When 'binary', gzip and base64 encoding are used. - The node ordering is changed to CitcomS native ordering. The consequence is the axis are rotated as z in CitcomS is mapped to X in vtk, and x to Y, y to Z. - More data can be outputted in vtk format - Using .pvts file for regional model; .vtm and .visit file for global model (.vtm format provided by Tobias Hoeink at Rice, .visit format provided by Kat at visitusers.org/forum) 12 July 2011, 16:27 UTC
56f6015 Fixed typo for anisotropic stress computation. 21 March 2011, 00:13 UTC
a0153f3 Added a flag force_iteration which if on (off by default), will enforce an iterative solution to the velocity fields even if linear rheologies were chosen. This is useful for debugging/robustness tests. 22 February 2011, 04:13 UTC
966fcd8 Modified storage of anisotropic viscosity files. Those are now 18 February 2011, 19:45 UTC
7ea7b1d Improved vtk output, still for Dan to test. 14 February 2011, 05:45 UTC
446b149 Aedded the actual files because I didn't know how to link from CitcomCU. Those are didentical 12 February 2011, 05:30 UTC
7a6fa87 12 February 2011, 05:20 UTC
1cfc861 Removed the srand() call that seemed like a good idea (rev. 17175) but screwed up tracer-based runs with large number of processors (12x3x3x2). Weird, but oh well. Someone advise why this didn't work? 08 February 2011, 04:06 UTC
9086505 Added one missing line for anisotropic viscosity init. 07 February 2011, 19:00 UTC
8507b40 Reversed, temporarily, the use of nearneighbor because it makes it easier to compare model computations with previous versions. 07 February 2011, 00:32 UTC
12ac22c Fixed typo that was introduced in 17555 and made temperature field assignment apparently screwed up. 06 February 2011, 23:57 UTC
4fb41eb Backward compatibility of neglect of both divergence and pressure for convergence checks. 05 February 2011, 23:45 UTC
c21beb1 Temporarily moved velocity gradient computation to ensure compilation. 04 February 2011, 05:03 UTC
9c045e8 Uptdated prototypes file. Fixed a few compiler complaints. Made sure that atemp is always set in Viscosity_structures, making mat_control > 0 feasible, not just 0 or 1 03 February 2011, 21:06 UTC
8dcea68 Forgot some functions, not sure why the linker didn't complain previously. 03 February 2011, 17:11 UTC
93f3131 Futher synchronization with CitcomCU anisotropic viscosity. 02 February 2011, 01:09 UTC
4d1c25b Trial synchronization between CitcomCU and CitcomS anisotropic viscosity. 02 February 2011, 00:30 UTC
2f2115e Added parentheses for logic statements as per compiler suggestion 26 January 2011, 00:14 UTC
2598655 Checking in Shijie Zhong's revised Advection_diffusion routine. 19 January 2011, 21:00 UTC
452a6d7 Added support for non-interpolated grd input. 29 December 2010, 20:47 UTC
b6fe6e9 Minor fixes for compile, still hunting for convergence problem. 22 December 2010, 21:53 UTC
dc5cd22 Reverted to separate horizontal_bc routines for regional and full. the former has a check for ROW==E->lmesh.NOZ[level] && E->parallel.me_loc[3]==E->parallel.nprocz-1 while the full version has ROW==E->mesh.NOZ[level]) && (E->parallel.me_loc[3]==E->parallel.nprocz-1) ) 08 December 2010, 21:06 UTC
4ea70e2 Reverted the rowl adjustment since it didn't fix the problem reported by Dan. 08 December 2010, 20:14 UTC
df821c0 Added definition of TRUE (1) and FALSE (0) in case undefined (was defined for GMT/ggrd compile before). 08 December 2010, 18:43 UTC
cf7495e Addded a test for top or bottom nodal row back into horizontal_bc (earlier moved from Regional_boundary_conditions and Full_boundary_conditions to BC_util.c) to see if this helps fix a bug reported by Dan that I could not reproduce in the non-pyre version. 08 December 2010, 00:54 UTC
9bc8fb6 More accurate computation of element coordinates in anisotropic part. 12 October 2010, 06:36 UTC
010b460 Augmented G matrix with anisotropic computation, may or may not be a good idea. 24 September 2010, 03:35 UTC
cbf9149 Missed one routine. 15 September 2010, 10:40 UTC
1e59dd6 Suggested use of general prototypes Retired N>3 matrix determinant functions (because they caused compile problems) 15 September 2010, 10:36 UTC
0c84e99 Read in sdepv_misfit regardless of rheology. 14 September 2010, 01:08 UTC
bf59b6b Added option to start with isotropic viscosity during first anisotropic iteration. 13 September 2010, 14:07 UTC
a112ea8 Forgot part of the rotation matrix, minor fixes else, still experimental. 13 September 2010, 12:01 UTC
ab35881 Made sure current version compiled nicely without additional flags. Anisotropic viscosity is set up more flexibly. 13 September 2010, 07:13 UTC
b5d6c30 Made sure that viscosity prefactors get assigned for material dependent viscosity only (TDEPV = off) 07 September 2010, 07:05 UTC
a345eef Added random number generator initialization to ensure exact reproducibility of all runs, including those with tracers. Earlier reported solver issues might be related to our cluster, at least all revisions seems to give the same answer now. 07 September 2010, 02:22 UTC
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