d2d1b09 | Rajesh Kommu | 25 June 2014, 22:04:27 UTC | Removed Cookbook 9 from the CitcomS manual | 25 June 2014, 22:04:27 UTC |
6ceb31d | Rajesh Kommu | 25 June 2014, 21:58:24 UTC | Removed Cookbook 10 from the CitcomS manual | 25 June 2014, 21:58:24 UTC |
eb40d8e | Rajesh Kommu | 13 June 2014, 23:26:26 UTC | 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, 23:26:26 UTC |
723802a | Rajesh Kommu | 05 June 2014, 20:23:48 UTC | Removed references to Python and Pyre from chapter 2 of the manual | 05 June 2014, 20:23:48 UTC |
4f1ae8b | Rajesh Kommu | 09 April 2014, 16:28:32 UTC | Removed section 2 from Appendix A of the manual, which describes the Pyre based parameters and settings. | 09 April 2014, 16:28:32 UTC |
c23d985 | Rajesh Kommu | 08 April 2014, 22:13:24 UTC | Got rid of come nested comment warnings from clang | 08 April 2014, 22:13:24 UTC |
0777e0d | Rajesh Kommu | 08 April 2014, 21:47:16 UTC | 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, 21:47:16 UTC |
6b8f809 | Rajesh Kommu | 25 March 2014, 23:11:38 UTC | cleaned up the repository to match the .gitignore file. Started adding functionality for writing all parameters to a pidXXXXXX file | 25 March 2014, 23:11:38 UTC |
5992bf0 | Rajesh Kommu | 05 March 2014, 00:26:55 UTC | 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, 00:26:55 UTC |
83b32f9 | Rajesh Kommu | 05 February 2014, 23:18:38 UTC | 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, 23:18:38 UTC |
8fde56f | Eh Tan | 18 October 2013, 03:58:15 UTC | update ignore list | 18 October 2013, 03:58:15 UTC |
fd2b0d6 | CIG Backend | 11 October 2013, 16:35:38 UTC | Update gitignore | 11 October 2013, 16:35:38 UTC |
754dc95 | CIG Backend | 11 October 2013, 16:24:31 UTC | Readd archimedes | 11 October 2013, 16:24:31 UTC |
7c6b5ad | CIG Backend | 11 October 2013, 05:10:13 UTC | m4 submodule | 11 October 2013, 05:10:13 UTC |
8c294e9 | CIG Backend | 10 October 2013, 22:03:31 UTC | Readd anisotropic code | 10 October 2013, 22:03:31 UTC |
f886a03 | Thorsten Becker | 20 September 2013, 14:58:59 UTC | | 20 September 2013, 14:58:59 UTC |
3cd9e30 | Eric Heien | 24 May 2013, 17:42:50 UTC | Added reference viscosity fix from Shijie Zhong | 24 May 2013, 17:42:50 UTC |
ed21917 | Thorsten Becker | 25 March 2013, 21:56:47 UTC | Updating to newest version for testing purposes. | 25 March 2013, 21:56:47 UTC |
c5526ec | Thorsten Becker | 01 September 2012, 23:51:37 UTC | 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, 23:51:37 UTC |
2b8ed1f | Thorsten Becker | 22 August 2012, 21:21:52 UTC | 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, 21:21:52 UTC |
11854a5 | Thorsten Becker | 21 August 2012, 16:30:28 UTC | Implemented Output_vtk.c fixes from Rene. | 21 August 2012, 16:30:28 UTC |
74c56ef | Thorsten Becker | 28 June 2012, 09:30:30 UTC | Minor changes to instructions | 28 June 2012, 09:30:30 UTC |
d5fbdb0 | Eric Heien | 02 February 2012, 18:23:14 UTC | Changing to version 3.2.0 since there are many significant changes | 02 February 2012, 18:23:14 UTC |
8d8016f | Eric Heien | 02 February 2012, 00:41:19 UTC | Added missing file to distribution | 02 February 2012, 00:41:19 UTC |
b0d8a75 | Eric Heien | 02 February 2012, 00:29:10 UTC | Updated NEWS for past 2.5 years | 02 February 2012, 00:29:10 UTC |
162e668 | Eric Heien | 01 February 2012, 21:11:35 UTC | 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, 21:11:35 UTC |
eb74d9f | Thorsten Becker | 24 January 2012, 21:54:19 UTC | Fixed minor ggrd assignment bug. | 24 January 2012, 21:54:19 UTC |
199d1d8 | Thorsten Becker | 24 January 2012, 18:44:23 UTC | Debugging GGrd | 24 January 2012, 18:44:23 UTC |
74ce5d8 | Thorsten Becker | 24 January 2012, 18:03:52 UTC | Updating to latest version for sync. | 24 January 2012, 18:03:52 UTC |
552bc26 | Eh Tan | 19 January 2012, 19:24:59 UTC | Stop configure if pyre is enabled and python 2.7 is used. See Issue622. | 19 January 2012, 19:24:59 UTC |
f4cf4db | Eh Tan | 17 January 2012, 04:57:06 UTC | updated installation instruction | 17 January 2012, 04:57:06 UTC |
3a23d00 | Eh Tan | 17 January 2012, 02:41:15 UTC | When python 2.7 is used, ask users to download pythia manually. See issue622 and issue606. | 17 January 2012, 02:41:15 UTC |
15a09f1 | Thorsten Becker | 14 January 2012, 08:00:41 UTC | Made sure that compositional viscosity without compositional buoyancy can be assigned without setting ibuoy=1 and the buoyancy number to zero. | 14 January 2012, 08:00:41 UTC |
c9704b3 | Thorsten Becker | 20 December 2011, 18:04:26 UTC | Merged with recent check in, minor changes. | 20 December 2011, 18:04:26 UTC |
51e1984 | Eh Tan | 14 November 2011, 05:06:30 UTC | 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, 05:06:30 UTC |
d8f08c4 | Eh Tan | 14 October 2011, 18:27:24 UTC | fixed a bug that h5close_field() didn't have a return statement, reported by Nicolas Flament in issue611. | 14 October 2011, 18:27:24 UTC |
0f1fbbf | Eh Tan | 18 September 2011, 03:54:13 UTC | 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, 03:54:13 UTC |
cebdfcb | Thorsten Becker | 31 July 2011, 20:38:35 UTC | Updating to newest version, don't think that there should be any significant changes on my side. | 31 July 2011, 20:38:35 UTC |
1e7ff88 | Eh Tan | 12 July 2011, 16:27:58 UTC | 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, 16:27:58 UTC |
56f6015 | Thorsten Becker | 21 March 2011, 00:13:58 UTC | Fixed typo for anisotropic stress computation. | 21 March 2011, 00:13:58 UTC |
a0153f3 | Thorsten Becker | 22 February 2011, 04:13:21 UTC | 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, 04:13:21 UTC |
966fcd8 | Thorsten Becker | 18 February 2011, 19:45:49 UTC | Modified storage of anisotropic viscosity files. Those are now | 18 February 2011, 19:45:49 UTC |
7ea7b1d | Thorsten Becker | 14 February 2011, 05:45:26 UTC | Improved vtk output, still for Dan to test. | 14 February 2011, 05:45:26 UTC |
446b149 | Thorsten Becker | 12 February 2011, 05:30:30 UTC | Aedded the actual files because I didn't know how to link from CitcomCU. Those are didentical | 12 February 2011, 05:30:30 UTC |
7a6fa87 | Thorsten Becker | 12 February 2011, 05:20:32 UTC | | 12 February 2011, 05:20:32 UTC |
1cfc861 | Thorsten Becker | 08 February 2011, 04:06:28 UTC | 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, 04:06:28 UTC |
9086505 | Thorsten Becker | 07 February 2011, 19:00:57 UTC | Added one missing line for anisotropic viscosity init. | 07 February 2011, 19:00:57 UTC |
8507b40 | Thorsten Becker | 07 February 2011, 00:32:59 UTC | Reversed, temporarily, the use of nearneighbor because it makes it easier to compare model computations with previous versions. | 07 February 2011, 00:32:59 UTC |
12ac22c | Thorsten Becker | 06 February 2011, 23:57:18 UTC | Fixed typo that was introduced in 17555 and made temperature field assignment apparently screwed up. | 06 February 2011, 23:57:18 UTC |
4fb41eb | Thorsten Becker | 05 February 2011, 23:45:04 UTC | Backward compatibility of neglect of both divergence and pressure for convergence checks. | 05 February 2011, 23:45:04 UTC |
c21beb1 | Thorsten Becker | 04 February 2011, 05:03:01 UTC | Temporarily moved velocity gradient computation to ensure compilation. | 04 February 2011, 05:03:01 UTC |
9c045e8 | Thorsten Becker | 03 February 2011, 21:06:35 UTC | 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, 21:06:35 UTC |
8dcea68 | Thorsten Becker | 03 February 2011, 17:11:42 UTC | Forgot some functions, not sure why the linker didn't complain previously. | 03 February 2011, 17:11:42 UTC |
93f3131 | Thorsten Becker | 02 February 2011, 01:09:51 UTC | Futher synchronization with CitcomCU anisotropic viscosity. | 02 February 2011, 01:09:51 UTC |
4d1c25b | Thorsten Becker | 02 February 2011, 00:30:25 UTC | Trial synchronization between CitcomCU and CitcomS anisotropic viscosity. | 02 February 2011, 00:30:25 UTC |
2f2115e | Thorsten Becker | 26 January 2011, 00:14:53 UTC | Added parentheses for logic statements as per compiler suggestion | 26 January 2011, 00:14:53 UTC |
2598655 | Thorsten Becker | 19 January 2011, 21:00:20 UTC | Checking in Shijie Zhong's revised Advection_diffusion routine. | 19 January 2011, 21:00:20 UTC |
452a6d7 | Thorsten Becker | 29 December 2010, 20:47:43 UTC | Added support for non-interpolated grd input. | 29 December 2010, 20:47:43 UTC |
b6fe6e9 | Thorsten Becker | 22 December 2010, 21:53:36 UTC | Minor fixes for compile, still hunting for convergence problem. | 22 December 2010, 21:53:36 UTC |
dc5cd22 | Thorsten Becker | 08 December 2010, 21:06:36 UTC | 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, 21:06:36 UTC |
4ea70e2 | Thorsten Becker | 08 December 2010, 20:14:32 UTC | Reverted the rowl adjustment since it didn't fix the problem reported by Dan. | 08 December 2010, 20:14:32 UTC |
df821c0 | Thorsten Becker | 08 December 2010, 18:43:58 UTC | Added definition of TRUE (1) and FALSE (0) in case undefined (was defined for GMT/ggrd compile before). | 08 December 2010, 18:43:58 UTC |
cf7495e | Thorsten Becker | 08 December 2010, 00:54:48 UTC | 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, 00:54:48 UTC |
9bc8fb6 | Thorsten Becker | 12 October 2010, 06:36:01 UTC | More accurate computation of element coordinates in anisotropic part. | 12 October 2010, 06:36:01 UTC |
010b460 | Thorsten Becker | 24 September 2010, 03:35:36 UTC | Augmented G matrix with anisotropic computation, may or may not be a good idea. | 24 September 2010, 03:35:36 UTC |
cbf9149 | Thorsten Becker | 15 September 2010, 10:40:50 UTC | Missed one routine. | 15 September 2010, 10:40:50 UTC |
1e59dd6 | Thorsten Becker | 15 September 2010, 10:36:58 UTC | Suggested use of general prototypes Retired N>3 matrix determinant functions (because they caused compile problems) | 15 September 2010, 10:36:58 UTC |
0c84e99 | Thorsten Becker | 14 September 2010, 01:08:34 UTC | Read in sdepv_misfit regardless of rheology. | 14 September 2010, 01:08:34 UTC |
bf59b6b | Thorsten Becker | 13 September 2010, 14:07:10 UTC | Added option to start with isotropic viscosity during first anisotropic iteration. | 13 September 2010, 14:07:10 UTC |
a112ea8 | Thorsten Becker | 13 September 2010, 12:01:43 UTC | Forgot part of the rotation matrix, minor fixes else, still experimental. | 13 September 2010, 12:01:43 UTC |
ab35881 | Thorsten Becker | 13 September 2010, 07:13:07 UTC | Made sure current version compiled nicely without additional flags. Anisotropic viscosity is set up more flexibly. | 13 September 2010, 07:13:07 UTC |
b5d6c30 | Thorsten Becker | 07 September 2010, 07:05:09 UTC | Made sure that viscosity prefactors get assigned for material dependent viscosity only (TDEPV = off) | 07 September 2010, 07:05:09 UTC |
a345eef | Thorsten Becker | 07 September 2010, 02:22:48 UTC | 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, 02:22:48 UTC |
1cf026d | Thorsten Becker | 07 September 2010, 01:40:02 UTC | Checking in current version because of need for debugging. Revision 17172, compared to (presumably) 17153 give strange multigrid convergence behavior. Checking why that is now. | 07 September 2010, 01:40:02 UTC |
1efa65c | Thorsten Becker | 06 September 2010, 05:20:44 UTC | Trial implementation of anisotropic viscosity. | 06 September 2010, 05:20:44 UTC |
4ecc25c | Eh Tan | 30 August 2010, 20:41:40 UTC | Added support of multigrid solver in Exchanger. Lifted the solver assertion in Coupler. Cookbook9 can be converted to multigrid solver once appropriate parameters (*solver.mesher.levels=2 and *solver.vsolver.Solver=multigrid) are added. However, the embedded solver will converge incorrectly. Setting esolver.vsolver.accuracy=6e-3 seems to fix the problem. | 30 August 2010, 20:41:40 UTC |
bd28b8f | Thorsten Becker | 25 May 2010, 02:47:46 UTC | And a typo fix. | 25 May 2010, 02:47:46 UTC |
f71b317 | Thorsten Becker | 24 May 2010, 18:00:39 UTC | toplayerbc > 0 will now assign BCs for all noes with r >= toplayerbc_r, which defaults to 0.984303876942 i.e. 100 km depth. (Still experimental.) | 24 May 2010, 18:00:39 UTC |
ed7e8ae | Thorsten Becker | 12 March 2010, 00:41:46 UTC | Improvements for internal BCs. | 12 March 2010, 00:41:46 UTC |
b732e74 | Thorsten Becker | 10 March 2010, 19:55:02 UTC | This logic should make more sense for internal BCs, but still testing. | 10 March 2010, 19:55:02 UTC |
8a2427e | Thorsten Becker | 10 March 2010, 19:38:15 UTC | Experimental implementation of a single node layer for internal boundary condition assignment, assigned if toplayerbc < 0, to nodes at layer noz+toplayerbc, but only for the top level multigrid, for now. | 10 March 2010, 19:38:15 UTC |
70a834f | Walter Landry | 26 February 2010, 21:04:48 UTC | Fix a misleading comment | 26 February 2010, 21:04:48 UTC |
4ff7faa | Walter Landry | 02 February 2010, 23:41:21 UTC | Fix an error when running autoreconf -i | 02 February 2010, 23:41:21 UTC |
f5834c5 | Thorsten Becker | 01 February 2010, 19:43:36 UTC | Changed internal variable name for use_se_smoothing, as per Eh's suggestion. | 01 February 2010, 19:43:36 UTC |
2a3b029 | Thorsten Becker | 29 January 2010, 14:48:36 UTC | Added old CitcomS element -> nodes -> element viscosity smoothing with new use_ne_visc_smooth parameter, default is off. | 29 January 2010, 14:48:36 UTC |
8bb44b5 | Eh Tan | 21 January 2010, 21:23:26 UTC | Added pyre input for the new parameters added in r16138. | 21 January 2010, 21:23:26 UTC |
3ad8c8c | Eh Tan | 21 January 2010, 21:22:46 UTC | Replaced fixed accuracy setting. Bug reported by Rob Moucha. | 21 January 2010, 21:22:46 UTC |
c4154bc | Eh Tan | 21 January 2010, 20:11:11 UTC | Added opendx macro to visualize opt (e.g. composition) fields. This fixed Issue99. | 21 January 2010, 20:11:11 UTC |
0dc0383 | Dan Bower | 17 January 2010, 01:19:24 UTC | Preliminary support for the absolute tracer method. Only tested with one flavor, reading in from a file, and the initial volume of the tracers is HARD-CODED! In addition, the code automaticaly truncates the composition to one, although this should be a switch for the user to specify. | 17 January 2010, 01:19:24 UTC |
110bd1c | Thorsten Becker | 16 January 2010, 02:47:04 UTC | Implementation of two, perhaps entirely unnecessary features, in search of why certain prescribed velocity models do not converge like they should. - allow for each inner loop solution to have a higher accuracy than the outer, Uzawa loop. This is set by new parameter "inner_accuracy_scale", which pre-multiplies the inner accuracy (imp) setting (defaults to unity) - remove any rigid body rotation at each Uzawa iteration step. Parmaeter "inner_remove_rigid_rotation", by default off. For this, I also added an experimental routine assign_v_to_vector() in order to reasign the V velocities to the U solution vector after removing the net rotations from V (how is supposed to work for the regular operational mode?) | 16 January 2010, 02:47:04 UTC |
33e0d0b | Eh Tan | 09 December 2009, 02:25:05 UTC | Replaced TRUE and FALSE. Added function prototypes. | 09 December 2009, 02:25:05 UTC |
ef97d2c | Eh Tan | 08 December 2009, 21:44:25 UTC | Added two boolean parameters for controlling convergence criterion: check_continuity_convergence (default=on): include div/v in the criterion. check_pressure_convergence (default=on): include dp/p in the criterion. Retired the parameter: only_check_vel_convergence. | 08 December 2009, 21:44:25 UTC |
7efded4 | Eh Tan | 08 December 2009, 21:43:38 UTC | removed unused variables in Drive_solvers.c | 08 December 2009, 21:43:38 UTC |
e829bf5 | Eh Tan | 08 December 2009, 21:43:15 UTC | Merged solve_constrained_flow_iterative_pseudo_surf() with void solve_constrained_flow_iterative(); assemble_forces_pseudo_surf() wi Removed used python bindings in module/stokes_solver.c | 08 December 2009, 21:43:15 UTC |
0c6082f | Thorsten Becker | 08 December 2009, 17:19:49 UTC | Truly apply internal boundary conditions on horizontal surfaces for E->mesh.toplayerbc > 0 (default, of course, 0) | 08 December 2009, 17:19:49 UTC |
025e452 | Thorsten Becker | 04 December 2009, 23:16:49 UTC | Modified handling of internal BCs, as per Eh's suggestion, now handled in a separate function. | 04 December 2009, 23:16:49 UTC |
21c984f | Eh Tan | 04 December 2009, 21:57:59 UTC | Removed metioning the version number in README. Added the url of the manual. | 04 December 2009, 21:57:59 UTC |
e20fdfc | Thorsten Becker | 04 December 2009, 17:44:24 UTC | Suggested unified treatment of horizontal_bc (moved to BC_util) for review by Eh Improved handling of grd-read velocity and traction boundary conditions. | 04 December 2009, 17:44:24 UTC |
45144ae | Thorsten Becker | 04 December 2009, 02:33:07 UTC | Temporary fix for regular operations, for Eh's review. Ggrd assignment still needs tending to. | 04 December 2009, 02:33:07 UTC |
1f61de1 | Thorsten Becker | 03 December 2009, 23:51:48 UTC | Experimental implementation of internal stress or velocity boundary conditions. As of right now, toplayerbc > 0 (default = 0) will assign the surface boundary condition to all nodes within the first toplayerbc layers. If BCs are assigned from file, this will only work for the grd method, not the regular file I/O. | 03 December 2009, 23:51:48 UTC |