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26 October 2024, 18:30:49 UTC
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f886a03 Thorsten Becker20 September 2013, 14:58:59 UTC20 September 2013, 14:58:59 UTC
3cd9e30 Eric Heien24 May 2013, 17:42:50 UTCAdded reference viscosity fix from Shijie Zhong24 May 2013, 17:42:50 UTC
ed21917 Thorsten Becker25 March 2013, 21:56:47 UTCUpdating to newest version for testing purposes.25 March 2013, 21:56:47 UTC
c5526ec Thorsten Becker01 September 2012, 23:51:37 UTCFixed 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 Becker22 August 2012, 21:21:52 UTCImplemented 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 Becker21 August 2012, 16:30:28 UTCImplemented Output_vtk.c fixes from Rene.21 August 2012, 16:30:28 UTC
74c56ef Thorsten Becker28 June 2012, 09:30:30 UTCMinor changes to instructions28 June 2012, 09:30:30 UTC
d5fbdb0 Eric Heien02 February 2012, 18:23:14 UTCChanging to version 3.2.0 since there are many significant changes02 February 2012, 18:23:14 UTC
8d8016f Eric Heien02 February 2012, 00:41:19 UTCAdded missing file to distribution02 February 2012, 00:41:19 UTC
b0d8a75 Eric Heien02 February 2012, 00:29:10 UTCUpdated NEWS for past 2.5 years02 February 2012, 00:29:10 UTC
162e668 Eric Heien01 February 2012, 21:11:35 UTCUpdated ChangeLog, configure.ac for 3.1.2 release Set default configuration to not setup Pyre Added note in examples directory regarding Pyre and Cookbooks01 February 2012, 21:11:35 UTC
eb74d9f Thorsten Becker24 January 2012, 21:54:19 UTCFixed minor ggrd assignment bug.24 January 2012, 21:54:19 UTC
199d1d8 Thorsten Becker24 January 2012, 18:44:23 UTCDebugging GGrd24 January 2012, 18:44:23 UTC
74ce5d8 Thorsten Becker24 January 2012, 18:03:52 UTCUpdating to latest version for sync.24 January 2012, 18:03:52 UTC
552bc26 Eh Tan19 January 2012, 19:24:59 UTCStop configure if pyre is enabled and python 2.7 is used. See Issue622.19 January 2012, 19:24:59 UTC
f4cf4db Eh Tan17 January 2012, 04:57:06 UTCupdated installation instruction17 January 2012, 04:57:06 UTC
3a23d00 Eh Tan17 January 2012, 02:41:15 UTCWhen python 2.7 is used, ask users to download pythia manually. See issue622 and issue606.17 January 2012, 02:41:15 UTC
15a09f1 Thorsten Becker14 January 2012, 08:00:41 UTCMade 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 Becker20 December 2011, 18:04:26 UTCMerged with recent check in, minor changes.20 December 2011, 18:04:26 UTC
51e1984 Eh Tan14 November 2011, 05:06:30 UTCFixed 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 Tan14 October 2011, 18:27:24 UTCfixed 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 Tan18 September 2011, 03:54:13 UTCfixed 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 Becker31 July 2011, 20:38:35 UTCUpdating 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 Tan12 July 2011, 16:27:58 UTCenhancing 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 Becker21 March 2011, 00:13:58 UTCFixed typo for anisotropic stress computation.21 March 2011, 00:13:58 UTC
a0153f3 Thorsten Becker22 February 2011, 04:13:21 UTCAdded 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 Becker18 February 2011, 19:45:49 UTCModified storage of anisotropic viscosity files. Those are now18 February 2011, 19:45:49 UTC
7ea7b1d Thorsten Becker14 February 2011, 05:45:26 UTCImproved vtk output, still for Dan to test.14 February 2011, 05:45:26 UTC
446b149 Thorsten Becker12 February 2011, 05:30:30 UTCAedded the actual files because I didn't know how to link from CitcomCU. Those are didentical12 February 2011, 05:30:30 UTC
7a6fa87 Thorsten Becker12 February 2011, 05:20:32 UTC12 February 2011, 05:20:32 UTC
1cfc861 Thorsten Becker08 February 2011, 04:06:28 UTCRemoved 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 Becker07 February 2011, 19:00:57 UTCAdded one missing line for anisotropic viscosity init.07 February 2011, 19:00:57 UTC
8507b40 Thorsten Becker07 February 2011, 00:32:59 UTCReversed, 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 Becker06 February 2011, 23:57:18 UTCFixed typo that was introduced in 17555 and made temperature field assignment apparently screwed up.06 February 2011, 23:57:18 UTC
4fb41eb Thorsten Becker05 February 2011, 23:45:04 UTCBackward compatibility of neglect of both divergence and pressure for convergence checks.05 February 2011, 23:45:04 UTC
c21beb1 Thorsten Becker04 February 2011, 05:03:01 UTCTemporarily moved velocity gradient computation to ensure compilation.04 February 2011, 05:03:01 UTC
9c045e8 Thorsten Becker03 February 2011, 21:06:35 UTCUptdated 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 103 February 2011, 21:06:35 UTC
8dcea68 Thorsten Becker03 February 2011, 17:11:42 UTCForgot some functions, not sure why the linker didn't complain previously.03 February 2011, 17:11:42 UTC
93f3131 Thorsten Becker02 February 2011, 01:09:51 UTCFuther synchronization with CitcomCU anisotropic viscosity.02 February 2011, 01:09:51 UTC
4d1c25b Thorsten Becker02 February 2011, 00:30:25 UTCTrial synchronization between CitcomCU and CitcomS anisotropic viscosity.02 February 2011, 00:30:25 UTC
2f2115e Thorsten Becker26 January 2011, 00:14:53 UTCAdded parentheses for logic statements as per compiler suggestion26 January 2011, 00:14:53 UTC
2598655 Thorsten Becker19 January 2011, 21:00:20 UTCChecking in Shijie Zhong's revised Advection_diffusion routine.19 January 2011, 21:00:20 UTC
452a6d7 Thorsten Becker29 December 2010, 20:47:43 UTCAdded support for non-interpolated grd input.29 December 2010, 20:47:43 UTC
b6fe6e9 Thorsten Becker22 December 2010, 21:53:36 UTCMinor fixes for compile, still hunting for convergence problem.22 December 2010, 21:53:36 UTC
dc5cd22 Thorsten Becker08 December 2010, 21:06:36 UTCReverted 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 Becker08 December 2010, 20:14:32 UTCReverted the rowl adjustment since it didn't fix the problem reported by Dan.08 December 2010, 20:14:32 UTC
df821c0 Thorsten Becker08 December 2010, 18:43:58 UTCAdded 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 Becker08 December 2010, 00:54:48 UTCAddded 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 Becker12 October 2010, 06:36:01 UTCMore accurate computation of element coordinates in anisotropic part.12 October 2010, 06:36:01 UTC
010b460 Thorsten Becker24 September 2010, 03:35:36 UTCAugmented G matrix with anisotropic computation, may or may not be a good idea.24 September 2010, 03:35:36 UTC
cbf9149 Thorsten Becker15 September 2010, 10:40:50 UTCMissed one routine.15 September 2010, 10:40:50 UTC
1e59dd6 Thorsten Becker15 September 2010, 10:36:58 UTCSuggested use of general prototypes Retired N>3 matrix determinant functions (because they caused compile problems)15 September 2010, 10:36:58 UTC
0c84e99 Thorsten Becker14 September 2010, 01:08:34 UTCRead in sdepv_misfit regardless of rheology.14 September 2010, 01:08:34 UTC
bf59b6b Thorsten Becker13 September 2010, 14:07:10 UTCAdded option to start with isotropic viscosity during first anisotropic iteration.13 September 2010, 14:07:10 UTC
a112ea8 Thorsten Becker13 September 2010, 12:01:43 UTCForgot part of the rotation matrix, minor fixes else, still experimental.13 September 2010, 12:01:43 UTC
ab35881 Thorsten Becker13 September 2010, 07:13:07 UTCMade sure current version compiled nicely without additional flags. Anisotropic viscosity is set up more flexibly.13 September 2010, 07:13:07 UTC
b5d6c30 Thorsten Becker07 September 2010, 07:05:09 UTCMade sure that viscosity prefactors get assigned for material dependent viscosity only (TDEPV = off)07 September 2010, 07:05:09 UTC
a345eef Thorsten Becker07 September 2010, 02:22:48 UTCAdded 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 Becker07 September 2010, 01:40:02 UTCChecking 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 Becker06 September 2010, 05:20:44 UTCTrial implementation of anisotropic viscosity.06 September 2010, 05:20:44 UTC
4ecc25c Eh Tan30 August 2010, 20:41:40 UTCAdded 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 Becker25 May 2010, 02:47:46 UTCAnd a typo fix.25 May 2010, 02:47:46 UTC
f71b317 Thorsten Becker24 May 2010, 18:00:39 UTCtoplayerbc > 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 Becker12 March 2010, 00:41:46 UTCImprovements for internal BCs.12 March 2010, 00:41:46 UTC
b732e74 Thorsten Becker10 March 2010, 19:55:02 UTCThis logic should make more sense for internal BCs, but still testing.10 March 2010, 19:55:02 UTC
8a2427e Thorsten Becker10 March 2010, 19:38:15 UTCExperimental 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 Landry26 February 2010, 21:04:48 UTCFix a misleading comment26 February 2010, 21:04:48 UTC
4ff7faa Walter Landry02 February 2010, 23:41:21 UTCFix an error when running autoreconf -i02 February 2010, 23:41:21 UTC
f5834c5 Thorsten Becker01 February 2010, 19:43:36 UTCChanged internal variable name for use_se_smoothing, as per Eh's suggestion.01 February 2010, 19:43:36 UTC
2a3b029 Thorsten Becker29 January 2010, 14:48:36 UTCAdded 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 Tan21 January 2010, 21:23:26 UTCAdded pyre input for the new parameters added in r16138.21 January 2010, 21:23:26 UTC
3ad8c8c Eh Tan21 January 2010, 21:22:46 UTCReplaced fixed accuracy setting. Bug reported by Rob Moucha.21 January 2010, 21:22:46 UTC
c4154bc Eh Tan21 January 2010, 20:11:11 UTCAdded opendx macro to visualize opt (e.g. composition) fields. This fixed Issue99.21 January 2010, 20:11:11 UTC
0dc0383 Dan Bower17 January 2010, 01:19:24 UTCPreliminary 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 Becker16 January 2010, 02:47:04 UTCImplementation 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 Tan09 December 2009, 02:25:05 UTCReplaced TRUE and FALSE. Added function prototypes.09 December 2009, 02:25:05 UTC
ef97d2c Eh Tan08 December 2009, 21:44:25 UTCAdded 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 Tan08 December 2009, 21:43:38 UTCremoved unused variables in Drive_solvers.c08 December 2009, 21:43:38 UTC
e829bf5 Eh Tan08 December 2009, 21:43:15 UTCMerged 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.c08 December 2009, 21:43:15 UTC
0c6082f Thorsten Becker08 December 2009, 17:19:49 UTCTruly 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 Becker04 December 2009, 23:16:49 UTCModified handling of internal BCs, as per Eh's suggestion, now handled in a separate function.04 December 2009, 23:16:49 UTC
21c984f Eh Tan04 December 2009, 21:57:59 UTCRemoved metioning the version number in README. Added the url of the manual.04 December 2009, 21:57:59 UTC
e20fdfc Thorsten Becker04 December 2009, 17:44:24 UTCSuggested 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 Becker04 December 2009, 02:33:07 UTCTemporary fix for regular operations, for Eh's review. Ggrd assignment still needs tending to.04 December 2009, 02:33:07 UTC
1f61de1 Thorsten Becker03 December 2009, 23:51:48 UTCExperimental 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
adf8b19 Thorsten Becker21 November 2009, 00:15:57 UTCExit criterion for incompressibility iteration allowed for velocity and pressure convergence at finite compressibility > accuracy. Changed criterion to loop while (convergence < 2) OR (compressibility < imp) Please review Also modified the sloppy iteration branch, where pressure isn't checked.21 November 2009, 00:15:57 UTC
5f38ecb Eh Tan20 November 2009, 21:58:43 UTCClean up #include20 November 2009, 21:58:43 UTC
aca8438 Eh Tan20 November 2009, 21:58:26 UTCFixed two minor errors20 November 2009, 21:58:26 UTC
0ba4cb4 Eh Tan19 November 2009, 23:11:05 UTCCreated a new array E->sphere.gr for the radii of all layers. This makes gather_r() obsolete.19 November 2009, 23:11:05 UTC
7ae00fb Eh Tan19 November 2009, 23:09:04 UTCrefactor viscosity definition19 November 2009, 23:09:04 UTC
8e9f046 Eh Tan19 November 2009, 23:08:27 UTC'localhost' can abbr. as '-'19 November 2009, 23:08:27 UTC
09cea7d Thorsten Becker14 October 2009, 18:26:26 UTCChanged defaults for z_410, z_lmantle, z_lith to more Earth like parameters. Does this break any tests?14 October 2009, 18:26:26 UTC
3ee0608 Thorsten Becker13 October 2009, 16:37:49 UTCFixed typo.13 October 2009, 16:37:49 UTC
0271108 Eh Tan08 October 2009, 18:01:00 UTCz_layer needs 4 elements08 October 2009, 18:01:00 UTC
4e0b2f4 Dan Bower07 October 2009, 04:39:33 UTCadded only_check_vel_convergence to pyre version.07 October 2009, 04:39:33 UTC
4b0faab Thorsten Becker06 October 2009, 18:48:28 UTCModified handling of ggrd_mat_control, > 0 will select all layers above, < 0 will select individual layer == - ggrd_mat_control06 October 2009, 18:48:28 UTC
ee214e5 Eh Tan05 October 2009, 19:06:34 UTCAdd pyre binding of z_layer, r_grid_layers, rr, and nr. replace MAX_MAT with CITCOM_MAX_VISC_LAYER.05 October 2009, 19:06:34 UTC
2622434 Eh Tan05 October 2009, 19:05:33 UTCRefactoring z_layer input validation.05 October 2009, 19:05:33 UTC
599ab80 Eh Tan05 October 2009, 19:05:04 UTCDealing with tracers that belong to the current processor but cannot find its element. When itracer_warning is off, the code will ignore the lost tracers. When itracer_warning is on (default), the code will abort.05 October 2009, 19:05:04 UTC
a3b2b41 Thorsten Becker02 October 2009, 23:16:39 UTCExperimental traction surface BC from grds.02 October 2009, 23:16:39 UTC
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