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26 October 2024, 18:30:49 UTC
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RevisionAuthorDateMessageCommit Date
bcf06ab Eh Tan09 August 2007, 22:57:28 UTCFinished the compressible Stokes solver for TALA. Two non-dimensional parameters are added: "dissipation_number" and "gruneisen" under the Solver component. One can use the original incompressible solver by setting "gruneisen=0". The code will treat this as "gruneisen=infinity". Setting non-zero value to "gruneisen" will switch to compressible solver. One can use the TALA solver for incompressible case by setting "gruneisen" to a non-zero value while setting "dissipation_number=0". This is useful when debugging the compressible solver. Two implementations are available: one by Wei Leng (U. Colorado) and one by Eh Tan (CIG). Leng's version uses the original conjugate gradient method for the Uzawa iteration and moves the contribution of compressibility to the RHS, similar to the method of Ita and King, JGR, 1994. Tan's version uses the bi-conjugate gradient stablized method for the Uzawa iteration, similar to the method of Tan and Gurnis, JGR, 2007. Both versions agree very well. In the benchmark case, 33x33x33 nodes per cap, Di/gamma=1.0, Ra=1.0, delta function of load at the mid mantle, the peak velocity differs by only 0.007%. Leng's version is enabled by default. Edit function solve_Ahat_p_fhat() in lib/Stokes_flow_Incomp.c to switch to Tan's version.09 August 2007, 22:57:28 UTC
91bcb85 Eh Tan03 August 2007, 19:01:02 UTCRearranged the code calculating element stiffness matrix03 August 2007, 19:01:02 UTC
718df88 Eh Tan03 August 2007, 19:00:41 UTCNaming the functions for Uzawa iteration by the algorithm (CG or BiCG), instead of by the approximation (BA or TALA)03 August 2007, 19:00:41 UTC
b3ea5b1 Eh Tan03 August 2007, 18:59:06 UTCFixed a bug. fabs() returns a float, but abs() returns an int.03 August 2007, 18:59:06 UTC
03bd866 Eh Tan26 July 2007, 22:58:03 UTCPorting r7748. Fixed a bug that *opt*.general files are mistakenly named. This bug is introduced by svn r723626 July 2007, 22:58:03 UTC
6098ee4 Eh Tan26 July 2007, 22:57:44 UTCUpdate for new format of comp_nd files26 July 2007, 22:57:44 UTC
86d9691 Eh Tan26 July 2007, 22:03:09 UTCFixed a bug in ordering of mesh nodes. The bug was introduced in svn r6510.26 July 2007, 22:03:09 UTC
dcb51dc Eh Tan26 July 2007, 22:02:43 UTCFixed a bug in stable timestep26 July 2007, 22:02:43 UTC
154b603 Eh Tan14 June 2007, 21:40:29 UTCPorting r7245 from trunk -- Zeroing geoid arrays before every geoid calculation. This fixes issue11414 June 2007, 21:40:29 UTC
de64ba2 Eh Tan14 June 2007, 20:38:42 UTCPorting r7236 from trunk14 June 2007, 20:38:42 UTC
997dc47 Eh Tan14 June 2007, 01:38:16 UTCPorting r7221 from trunk -- Fixing issue111: Expanding %RANK in autocombine.py14 June 2007, 01:38:16 UTC
ccd1ab4 Eh Tan12 June 2007, 00:05:50 UTCFixing issue11212 June 2007, 00:05:50 UTC
0c34be6 Eh Tan07 June 2007, 14:02:13 UTCFixed issue11007 June 2007, 14:02:13 UTC
ec719d4 Eh Tan08 May 2007, 21:28:45 UTCChanging the header format of comp_nd/comp_el ASCII outputs. The combining scripts are updated as well. The header has two lines, in the format of: ijunk n_rows time n_columns initial_bulk_composition[i] current_bulk_composition[i] (i = 0 to n_columns)08 May 2007, 21:28:45 UTC
6f312c5 Eh Tan07 May 2007, 21:30:13 UTCMulti-component chemical convection. By setting tracer_flavors > 2, one can enable multi-component chemical convection. See tests/checkpoint/tracer.cfg for example input.07 May 2007, 21:30:13 UTC
6177b48 Eh Tan07 May 2007, 21:23:11 UTCForgot to remove 'composition.ireset_initial_composition' from the header file07 May 2007, 21:23:11 UTC
fc5decb Eh Tan03 May 2007, 00:02:06 UTCIncorporating the effect of density/expansivity/gravity profiles when computing geoid03 May 2007, 00:02:06 UTC
89f7438 Eh Tan02 May 2007, 20:06:42 UTCForgot to update the makefile02 May 2007, 20:06:42 UTC
067f35e Eh Tan02 May 2007, 00:00:31 UTCUpdated Cookbook5 so that it uses only 2 processors02 May 2007, 00:00:31 UTC
61465a8 Eh Tan30 April 2007, 23:22:34 UTCUsing tic_method=-1 to read initial termpature from files30 April 2007, 23:22:34 UTC
d07bf8c Eh Tan30 April 2007, 23:22:15 UTCExpand datadir_old when post_processing=on or tic_method=-130 April 2007, 23:22:15 UTC
70fd7f4 Eh Tan27 April 2007, 19:31:10 UTCAdded a functional test for checkpoint27 April 2007, 19:31:10 UTC
0af6033 Eh Tan27 April 2007, 19:24:44 UTCInit'd E->mat in initial_conditions() and read_checkpoint()27 April 2007, 19:24:44 UTC
ec80762 Eh Tan26 April 2007, 00:46:11 UTCUpdating CoupledSolver for the checkpoint and tracers. The checkpoint stuff is not finished.26 April 2007, 00:46:11 UTC
1b26944 Eh Tan26 April 2007, 00:45:51 UTCRemoved the restart hack from Solver.py, which was required by solver coupling. The hack is still useful in CoupledSolver.py26 April 2007, 00:45:51 UTC
a7111d6 Eh Tan26 April 2007, 00:45:09 UTCClean up restart in lith_age26 April 2007, 00:45:09 UTC
dea4ac2 Eh Tan26 April 2007, 00:44:38 UTCSetting solver.ic.tic_method=-1 will read the temperature field from old velo files.26 April 2007, 00:44:38 UTC
55a6bec Eh Tan25 April 2007, 20:17:19 UTCAppend timestep to the checkpoint filename. Write/read timing information correctly.25 April 2007, 20:17:19 UTC
6962d60 Eh Tan25 April 2007, 19:30:44 UTCClean up the old way of tracers/composition restart. Setting solver.ic.restart=on won't read the *.tracer.* and *.comp_el.* files anymore. Setting solver.tracer.ic_method=2 will read the old *.tracer.* files as before, but the composition field will be calculated according to the tracers, not read from the *.comp_el.* files. The parameter solver.tracer.reset_initial_composition becomes obsolete.25 April 2007, 19:30:44 UTC
12e75b9 Eh Tan25 April 2007, 19:03:00 UTCFixed a bug in tracer setup25 April 2007, 19:03:00 UTC
f8acab5 Eh Tan24 April 2007, 22:16:50 UTCImplemented writing and reading (binary) checkpoints. The checkpoint file is called [datafile].chkpt.[rank] and is outputed with an interval of controller.checkpointFrequency. Before writing the checkpoint file, the previous checkpoint file (if exists) is renamed to [datafile].chkpt.[rank].bak. To read back the checkpoint file, set solver.ic.restart=on. The old checkpoint file, [datafile_old].chkpt.[rank] will be read in. The timestep information is stored in the checkpoint file. There is no need to specify solution_cycles_init, as the old way of restarting. The old way of restarting (read in temperature from the velo files) will still be available through solver.ic.tic_method=-1. (To do.) Several things to do: clean up the old way of restarting tracers/composition, documentation, does mat_control need checkpoints?24 April 2007, 22:16:50 UTC
7867dae Eh Tan16 April 2007, 22:38:30 UTCCompute adiabatic cooling correctly. Assuming gravity is constant. Slightly modified viscous heating computation to improve the efficiency.16 April 2007, 22:38:30 UTC
1c88d2f Eh Tan16 April 2007, 22:37:27 UTCCompute Tmass matrix with density (missing heat capacity)16 April 2007, 22:37:27 UTC
17ff14a Eh Tan16 April 2007, 22:36:30 UTCFixed a typo16 April 2007, 22:36:30 UTC
fccccc5 Eh Tan16 April 2007, 22:35:39 UTCRemoved some unused variables in global_defs.h16 April 2007, 22:35:39 UTC
93687ef Eh Tan16 April 2007, 22:34:53 UTCAdded indentation and comments to mass_matrix()16 April 2007, 22:34:53 UTC
a34172d Eh Tan10 April 2007, 23:43:47 UTCMerging r6541-r6542 from trunk10 April 2007, 23:43:47 UTC
de3d198 Eh Tan06 April 2007, 23:07:02 UTCMerging r6041 to r6510 from trunk06 April 2007, 23:07:02 UTC
0fb9bb0 Eh Tan06 April 2007, 23:00:39 UTCMerging r6365 from trunk06 April 2007, 23:00:39 UTC
0753462 Eh Tan06 April 2007, 22:57:44 UTCMerging r6364 from trunk06 April 2007, 22:57:44 UTC
7bc7173 Eh Tan08 February 2007, 00:19:05 UTCPorting r5956 to r5980 from trunk08 February 2007, 00:19:05 UTC
494622d Eh Tan02 February 2007, 20:32:09 UTCPorting r5952 from trunk02 February 2007, 20:32:09 UTC
9d9a7dd Eh Tan31 January 2007, 20:58:23 UTCFixed two bugs in heating31 January 2007, 20:58:23 UTC
134d38a Eh Tan31 January 2007, 20:50:30 UTCPorting r5942 from trunk31 January 2007, 20:50:30 UTC
3581735 Eh Tan30 January 2007, 21:32:04 UTCPorting r5930-5935 from trunk30 January 2007, 21:32:04 UTC
2008acc Eh Tan30 January 2007, 19:10:00 UTCPorting r5921-5928 from trunk30 January 2007, 19:10:00 UTC
0504ed7 Eh Tan30 January 2007, 02:07:30 UTCFirst cut on computing adibatic/viscous/latent heating. Most of the code is copied from CitcomCU r2546 and refactored later. It is not tested yet.30 January 2007, 02:07:30 UTC
60884b1 Eh Tan25 January 2007, 23:41:54 UTCRenamed the input parameter for dissipation number to be consistent with CitcomCU25 January 2007, 23:41:54 UTC
b5cdfc8 Eh Tan25 January 2007, 23:41:15 UTCPorting r5896 from trunk25 January 2007, 23:41:15 UTC
5a6a5be Eh Tan25 January 2007, 01:45:20 UTCPorting r5886-5887 from trunk25 January 2007, 01:45:20 UTC
fa6fd60 Eh Tan24 January 2007, 02:17:10 UTCRemoved unused functions and struct members24 January 2007, 02:17:10 UTC
a8c708a Eh Tan24 January 2007, 01:10:13 UTCFixed a bug when computing pressure correction. Using full spherical solver, Di=0, init T perturbation (l,m)=(3,2), and default values for other parameters, the differences in CG and BiCGstab solvers are 0.5% in velocity and stress, 0.2% in pressure.24 January 2007, 01:10:13 UTC
a8b86a8 Eh Tan19 January 2007, 20:14:41 UTCPorting r5744-5837 from trunk19 January 2007, 20:14:41 UTC
678a6a7 Eh Tan19 January 2007, 00:14:37 UTCBiCGStab algorithm for TALA Stokes solver Compared with the CG algorithm solver, the velocity differs by ~0.1% but the stress is way wrong.19 January 2007, 00:14:37 UTC
7d3eb44 Eh Tan19 January 2007, 00:10:53 UTCRefactoring Stokes solver19 January 2007, 00:10:53 UTC
b519e61 Eh Tan12 January 2007, 00:06:11 UTCCleaned up, beautified and added some comments12 January 2007, 00:06:11 UTC
d9a2d84 Eh Tan11 January 2007, 21:01:06 UTC1. Stored the Gruneisen parameter in its inverse 2. Calculated reference state 3. Removed contribution of ref. temperature from buoyancy11 January 2007, 21:01:06 UTC
e66e0c6 Eh Tan10 January 2007, 22:01:50 UTCTaking variable density field into the calculation of thermal buoyancy10 January 2007, 22:01:50 UTC
ccd7d8c Eh Tan10 January 2007, 21:59:32 UTCMinor refactoring10 January 2007, 21:59:32 UTC
419bb1f Eh Tan09 January 2007, 22:20:08 UTC1. Added two non-dimensional number: dissipation # and gruneisen parameter 2. Modified stiffness matrix for TALA 3. Modified stress calculation for TALA09 January 2007, 22:20:08 UTC
3f8a9fe Eh Tan09 January 2007, 22:01:20 UTCPorting r5743 from trunk to branch09 January 2007, 22:01:20 UTC
509fb47 Eh Tan09 January 2007, 20:04:02 UTCBranch for compressible (Truncated Anelastic Liquid Approximation) convection09 January 2007, 20:04:02 UTC
1be8307 Eh Tan08 January 2007, 23:09:47 UTCAnother document fix for issue75, related to "how to specify time-invariant velocity boundary conditions?"08 January 2007, 23:09:47 UTC
0bfa938 Eh Tan08 January 2007, 22:19:35 UTC1. Fixed a reference error, "Section 1.6" should be "Equation 1.6" 2. Velocity BC input and geoid output are dimensional. The units were undocumented in previous release. This fix the issue75. 3. More information about geoid output: the meaning of each column and how to compute the geoid field.08 January 2007, 22:19:35 UTC
8fb120b Eh Tan08 January 2007, 22:19:14 UTCTruncate the temperature grd file at specified min/max Sometimes the temperature field has overshoot/undershoot, which would be leave a blank area in the contour plot. This is a simple workaround.08 January 2007, 22:19:14 UTC
bf5e730 Eh Tan05 January 2007, 22:33:03 UTCFix for issue73 "problems with autocombine.py in single workstation mode" $HOSTNAME is not defined in the non-interactive shell in Ubuntu 6.10. Need to put a quote around it.05 January 2007, 22:33:03 UTC
7d3ef92 Leif Strand05 January 2007, 00:06:11 UTCFix for issue72: "'make install' broken for non-pyred CitcomS".05 January 2007, 00:06:11 UTC
9b67fc5 Sue Kientz20 December 2006, 22:13:44 UTCadded note about updating to 2.10.320 December 2006, 22:13:44 UTC
0b9c4d2 Eh Tan09 December 2006, 00:26:38 UTCRegenerated ChangeLog upto r556509 December 2006, 00:26:38 UTC
545c4df Sue Kientz09 December 2006, 00:22:28 UTCgurnis final changes; image resize; ready for release09 December 2006, 00:22:28 UTC
47bdc2d Sue Kientz08 December 2006, 23:50:10 UTCsmall text changes; image resize08 December 2006, 23:50:10 UTC
7da60aa Eh Tan08 December 2006, 23:45:26 UTCAdded "created by OpenDX" on several figure captions08 December 2006, 23:45:26 UTC
03df21a Eh Tan08 December 2006, 23:36:57 UTCUpdated MayaVi2 section08 December 2006, 23:36:57 UTC
8f5c823 Eh Tan08 December 2006, 23:30:39 UTCRenamed the MayaVi launching script and move it to visual/08 December 2006, 23:30:39 UTC
dd70690 Eh Tan08 December 2006, 23:26:02 UTCAdded executable bit to file permission08 December 2006, 23:26:02 UTC
742ed51 Luis Armendariz08 December 2006, 22:44:00 UTCAdd plugins for MayaVi2 to installation08 December 2006, 22:44:00 UTC
92235c0 Luis Armendariz08 December 2006, 22:27:26 UTCAdded README files08 December 2006, 22:27:26 UTC
c60971f Sue Kientz08 December 2006, 22:00:21 UTCfixed image size, text size and other small text changes08 December 2006, 22:00:21 UTC
8c92de8 Luis Armendariz08 December 2006, 21:16:47 UTCRemoving reduce filter from comments, as it is currently obsolete.08 December 2006, 21:16:47 UTC
4511a3d Luis Armendariz08 December 2006, 21:15:17 UTCAdded MayaVi screenshot to manual, along with a couple of other fixes.08 December 2006, 21:15:17 UTC
13061f6 Luis Armendariz08 December 2006, 20:03:11 UTCLast set of patches to citcoms_plugins * Display filename in mayavi pipeline * Changed glob pattern so that only HDF5 timestep files can be selected08 December 2006, 20:03:11 UTC
af17846 Luis Armendariz08 December 2006, 19:47:43 UTCForgot to rename data filters.08 December 2006, 19:47:43 UTC
de6f70d Luis Armendariz08 December 2006, 17:53:20 UTCAdded MayaVi2 screenshot for the manual.08 December 2006, 17:53:20 UTC
75bb12b Luis Armendariz08 December 2006, 17:44:47 UTCVarious patches.08 December 2006, 17:44:47 UTC
b3423fa Luis Armendariz08 December 2006, 17:40:08 UTCForking original plugins08 December 2006, 17:40:08 UTC
9c83a26 Luis Armendariz08 December 2006, 17:32:25 UTCArchiving original plugins.08 December 2006, 17:32:25 UTC
42b3b3e Luis Armendariz08 December 2006, 17:31:25 UTCModify plugins directory08 December 2006, 17:31:25 UTC
3c488f3 Luis Armendariz08 December 2006, 17:29:46 UTCExplain contents of each directory.08 December 2006, 17:29:46 UTC
849cea5 Leif Strand08 December 2006, 02:29:09 UTCMade 'install_deps' actually do what 'configure' says it's doing (*missing* deps, not *all*).08 December 2006, 02:29:09 UTC
8465d3f Sue Kientz07 December 2006, 23:26:14 UTCreinstated a few lost changes; changed caption position on fig 5.3 on request; enlarged fig 5.4; regen pdf07 December 2006, 23:26:14 UTC
79a8733 Eh Tan07 December 2006, 22:34:26 UTCchapter 5 * Added MayaVi2 in the introduction * Added links to MayaVi2 installation07 December 2006, 22:34:26 UTC
6e256a7 Sue Kientz07 December 2006, 22:19:37 UTCfixed image size; regen pdf07 December 2006, 22:19:37 UTC
e7c2ea3 Sue Kientz07 December 2006, 22:09:17 UTCtext fixes to recent additions07 December 2006, 22:09:17 UTC
b7662aa Eh Tan07 December 2006, 21:30:53 UTC* Put back the HDFView sections * Added a screenshot of HDFView * Added a warning on "-O3" compiler flag07 December 2006, 21:30:53 UTC
7bf8a4b Sue Kientz07 December 2006, 05:03:23 UTCtext edits to appendices and bib07 December 2006, 05:03:23 UTC
cf68821 Sue Kientz07 December 2006, 00:12:17 UTCsmall changes to chapt 6; standardized cross refference style; sstandardized code spacing07 December 2006, 00:12:17 UTC
8910ace Sue Kientz06 December 2006, 23:31:57 UTCenumerating several sections of the instructions in chap 5 for clarity, and a few minor text fixes06 December 2006, 23:31:57 UTC
cd4ffb9 Sue Kientz06 December 2006, 20:59:49 UTCa few text fixes in chapter 306 December 2006, 20:59:49 UTC
bb3c41c Sue Kientz06 December 2006, 20:33:12 UTCa few text fixes, preface to end of chapt 206 December 2006, 20:33:12 UTC
6f35a8c Sue Kientz06 December 2006, 18:59:56 UTCgurnis corrections and some other fixes06 December 2006, 18:59:56 UTC
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