https://github.com/geodynamics/citcoms

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7d64cb0 added benchmark files, Python scripts and workflow documentation to benchmarks folder 05 September 2014, 23:19 UTC
97d8b4a Added tic_method=6 and add_perturbations_at_all_layers_B for generating the temperature I.C. for the B benchmarks 27 August 2014, 16:14 UTC
cbbe1c4 Moved CDPEV initialization back to Viscosity_structures.c for CDEPV=off to work on Stampede 26 August 2014, 23:07 UTC
759d1e5 Added geoid output functionality to Output_vtk 02 May 2014, 23:33 UTC
5a059ba Added surf and botm output functionality to Output_vtk 02 May 2014, 23:24 UTC
290eea8 Added horizontal average to VTK output 02 May 2014, 23:10 UTC
9a8a520 Added the A2 and A4 benchmark config files; corrected A1,A3,A8 02 May 2014, 20:31 UTC
03f2b08 Added volume_average functionality to VTK output 23 April 2014, 18:56 UTC
0c00129 Fixed bugs in compute_volume_avg due to incompatible pointer types 01 April 2014, 23:27 UTC
aa1bd87 Added the A1, A3 and A8 benchmarks to the repository 31 March 2014, 23:13 UTC
e2625af Changed output_volume_avg to write to a single file with output in the following format: cycle time <T> <V_rms> 31 March 2014, 22:32 UTC
c8bfee6 Added the output_volume_avg method to output <T> and <V_rms> 31 March 2014, 21:32 UTC
48947d1 Added the volume_avg flag to the Output structure to control the output of <T> and <V_rms> 31 March 2014, 20:03 UTC
1a47b80 Added the compute_volume_avg method to compute <T> and <V_rms> 31 March 2014, 19:29 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
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
1cf026d 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 UTC
1efa65c Trial implementation of anisotropic viscosity. 06 September 2010, 05:20 UTC
4ecc25c 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 UTC
bd28b8f And a typo fix. 25 May 2010, 02:47 UTC
f71b317 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 UTC
ed7e8ae Improvements for internal BCs. 12 March 2010, 00:41 UTC
b732e74 This logic should make more sense for internal BCs, but still testing. 10 March 2010, 19:55 UTC
8a2427e 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 UTC
70a834f Fix a misleading comment 26 February 2010, 21:04 UTC
4ff7faa Fix an error when running autoreconf -i 02 February 2010, 23:41 UTC
f5834c5 Changed internal variable name for use_se_smoothing, as per Eh's suggestion. 01 February 2010, 19:43 UTC
2a3b029 Added old CitcomS element -> nodes -> element viscosity smoothing with new use_ne_visc_smooth parameter, default is off. 29 January 2010, 14:48 UTC
8bb44b5 Added pyre input for the new parameters added in r16138. 21 January 2010, 21:23 UTC
3ad8c8c Replaced fixed accuracy setting. Bug reported by Rob Moucha. 21 January 2010, 21:22 UTC
c4154bc Added opendx macro to visualize opt (e.g. composition) fields. This fixed Issue99. 21 January 2010, 20:11 UTC
0dc0383 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 UTC
110bd1c 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 UTC
33e0d0b Replaced TRUE and FALSE. Added function prototypes. 09 December 2009, 02:25 UTC
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