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bcf06ab Finished 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 UTC
91bcb85 Rearranged the code calculating element stiffness matrix 03 August 2007, 19:01 UTC
718df88 Naming the functions for Uzawa iteration by the algorithm (CG or BiCG), instead of by the approximation (BA or TALA) 03 August 2007, 19:00 UTC
b3ea5b1 Fixed a bug. fabs() returns a float, but abs() returns an int. 03 August 2007, 18:59 UTC
03bd866 Porting r7748. Fixed a bug that *opt*.general files are mistakenly named. This bug is introduced by svn r7236 26 July 2007, 22:58 UTC
6098ee4 Update for new format of comp_nd files 26 July 2007, 22:57 UTC
86d9691 Fixed a bug in ordering of mesh nodes. The bug was introduced in svn r6510. 26 July 2007, 22:03 UTC
dcb51dc Fixed a bug in stable timestep 26 July 2007, 22:02 UTC
154b603 Porting r7245 from trunk -- Zeroing geoid arrays before every geoid calculation. This fixes issue114 14 June 2007, 21:40 UTC
de64ba2 Porting r7236 from trunk 14 June 2007, 20:38 UTC
997dc47 Porting r7221 from trunk -- Fixing issue111: Expanding %RANK in autocombine.py 14 June 2007, 01:38 UTC
ccd1ab4 Fixing issue112 12 June 2007, 00:05 UTC
0c34be6 Fixed issue110 07 June 2007, 14:02 UTC
ec719d4 Changing 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 UTC
6f312c5 Multi-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 UTC
6177b48 Forgot to remove 'composition.ireset_initial_composition' from the header file 07 May 2007, 21:23 UTC
fc5decb Incorporating the effect of density/expansivity/gravity profiles when computing geoid 03 May 2007, 00:02 UTC
89f7438 Forgot to update the makefile 02 May 2007, 20:06 UTC
067f35e Updated Cookbook5 so that it uses only 2 processors 02 May 2007, 00:00 UTC
61465a8 Using tic_method=-1 to read initial termpature from files 30 April 2007, 23:22 UTC
d07bf8c Expand datadir_old when post_processing=on or tic_method=-1 30 April 2007, 23:22 UTC
70fd7f4 Added a functional test for checkpoint 27 April 2007, 19:31 UTC
0af6033 Init'd E->mat in initial_conditions() and read_checkpoint() 27 April 2007, 19:24 UTC
ec80762 Updating CoupledSolver for the checkpoint and tracers. The checkpoint stuff is not finished. 26 April 2007, 00:46 UTC
1b26944 Removed the restart hack from Solver.py, which was required by solver coupling. The hack is still useful in CoupledSolver.py 26 April 2007, 00:45 UTC
a7111d6 Clean up restart in lith_age 26 April 2007, 00:45 UTC
dea4ac2 Setting solver.ic.tic_method=-1 will read the temperature field from old velo files. 26 April 2007, 00:44 UTC
55a6bec Append timestep to the checkpoint filename. Write/read timing information correctly. 25 April 2007, 20:17 UTC
6962d60 Clean 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 UTC
12e75b9 Fixed a bug in tracer setup 25 April 2007, 19:03 UTC
f8acab5 Implemented 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 UTC
7867dae Compute adiabatic cooling correctly. Assuming gravity is constant. Slightly modified viscous heating computation to improve the efficiency. 16 April 2007, 22:38 UTC
1c88d2f Compute Tmass matrix with density (missing heat capacity) 16 April 2007, 22:37 UTC
17ff14a Fixed a typo 16 April 2007, 22:36 UTC
fccccc5 Removed some unused variables in global_defs.h 16 April 2007, 22:35 UTC
93687ef Added indentation and comments to mass_matrix() 16 April 2007, 22:34 UTC
a34172d Merging r6541-r6542 from trunk 10 April 2007, 23:43 UTC
de3d198 Merging r6041 to r6510 from trunk 06 April 2007, 23:07 UTC
0fb9bb0 Merging r6365 from trunk 06 April 2007, 23:00 UTC
0753462 Merging r6364 from trunk 06 April 2007, 22:57 UTC
7bc7173 Porting r5956 to r5980 from trunk 08 February 2007, 00:19 UTC
494622d Porting r5952 from trunk 02 February 2007, 20:32 UTC
9d9a7dd Fixed two bugs in heating 31 January 2007, 20:58 UTC
134d38a Porting r5942 from trunk 31 January 2007, 20:50 UTC
3581735 Porting r5930-5935 from trunk 30 January 2007, 21:32 UTC
2008acc Porting r5921-5928 from trunk 30 January 2007, 19:10 UTC
0504ed7 First 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 UTC
60884b1 Renamed the input parameter for dissipation number to be consistent with CitcomCU 25 January 2007, 23:41 UTC
b5cdfc8 Porting r5896 from trunk 25 January 2007, 23:41 UTC
5a6a5be Porting r5886-5887 from trunk 25 January 2007, 01:45 UTC
fa6fd60 Removed unused functions and struct members 24 January 2007, 02:17 UTC
a8c708a Fixed 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 UTC
a8b86a8 Porting r5744-5837 from trunk 19 January 2007, 20:14 UTC
678a6a7 BiCGStab 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 UTC
7d3eb44 Refactoring Stokes solver 19 January 2007, 00:10 UTC
b519e61 Cleaned up, beautified and added some comments 12 January 2007, 00:06 UTC
d9a2d84 1. Stored the Gruneisen parameter in its inverse 2. Calculated reference state 3. Removed contribution of ref. temperature from buoyancy 11 January 2007, 21:01 UTC
e66e0c6 Taking variable density field into the calculation of thermal buoyancy 10 January 2007, 22:01 UTC
ccd7d8c Minor refactoring 10 January 2007, 21:59 UTC
419bb1f 1. Added two non-dimensional number: dissipation # and gruneisen parameter 2. Modified stiffness matrix for TALA 3. Modified stress calculation for TALA 09 January 2007, 22:20 UTC
3f8a9fe Porting r5743 from trunk to branch 09 January 2007, 22:01 UTC
509fb47 Branch for compressible (Truncated Anelastic Liquid Approximation) convection 09 January 2007, 20:04 UTC
1be8307 Another document fix for issue75, related to "how to specify time-invariant velocity boundary conditions?" 08 January 2007, 23:09 UTC
0bfa938 1. 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 UTC
8fb120b Truncate 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 UTC
bf5e730 Fix 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 UTC
7d3ef92 Fix for issue72: "'make install' broken for non-pyred CitcomS". 05 January 2007, 00:06 UTC
9b67fc5 added note about updating to 2.10.3 20 December 2006, 22:13 UTC
0b9c4d2 Regenerated ChangeLog upto r5565 09 December 2006, 00:26 UTC
545c4df gurnis final changes; image resize; ready for release 09 December 2006, 00:22 UTC
47bdc2d small text changes; image resize 08 December 2006, 23:50 UTC
7da60aa Added "created by OpenDX" on several figure captions 08 December 2006, 23:45 UTC
03df21a Updated MayaVi2 section 08 December 2006, 23:36 UTC
8f5c823 Renamed the MayaVi launching script and move it to visual/ 08 December 2006, 23:30 UTC
dd70690 Added executable bit to file permission 08 December 2006, 23:26 UTC
742ed51 Add plugins for MayaVi2 to installation 08 December 2006, 22:44 UTC
92235c0 Added README files 08 December 2006, 22:27 UTC
c60971f fixed image size, text size and other small text changes 08 December 2006, 22:00 UTC
8c92de8 Removing reduce filter from comments, as it is currently obsolete. 08 December 2006, 21:16 UTC
4511a3d Added MayaVi screenshot to manual, along with a couple of other fixes. 08 December 2006, 21:15 UTC
13061f6 Last set of patches to citcoms_plugins * Display filename in mayavi pipeline * Changed glob pattern so that only HDF5 timestep files can be selected 08 December 2006, 20:03 UTC
af17846 Forgot to rename data filters. 08 December 2006, 19:47 UTC
de6f70d Added MayaVi2 screenshot for the manual. 08 December 2006, 17:53 UTC
75bb12b Various patches. 08 December 2006, 17:44 UTC
b3423fa Forking original plugins 08 December 2006, 17:40 UTC
9c83a26 Archiving original plugins. 08 December 2006, 17:32 UTC
42b3b3e Modify plugins directory 08 December 2006, 17:31 UTC
3c488f3 Explain contents of each directory. 08 December 2006, 17:29 UTC
849cea5 Made 'install_deps' actually do what 'configure' says it's doing (*missing* deps, not *all*). 08 December 2006, 02:29 UTC
8465d3f reinstated a few lost changes; changed caption position on fig 5.3 on request; enlarged fig 5.4; regen pdf 07 December 2006, 23:26 UTC
79a8733 chapter 5 * Added MayaVi2 in the introduction * Added links to MayaVi2 installation 07 December 2006, 22:34 UTC
6e256a7 fixed image size; regen pdf 07 December 2006, 22:19 UTC
e7c2ea3 text fixes to recent additions 07 December 2006, 22:09 UTC
b7662aa * Put back the HDFView sections * Added a screenshot of HDFView * Added a warning on "-O3" compiler flag 07 December 2006, 21:30 UTC
7bf8a4b text edits to appendices and bib 07 December 2006, 05:03 UTC
cf68821 small changes to chapt 6; standardized cross refference style; sstandardized code spacing 07 December 2006, 00:12 UTC
8910ace enumerating several sections of the instructions in chap 5 for clarity, and a few minor text fixes 06 December 2006, 23:31 UTC
cd4ffb9 a few text fixes in chapter 3 06 December 2006, 20:59 UTC
bb3c41c a few text fixes, preface to end of chapt 2 06 December 2006, 20:33 UTC
6f35a8c gurnis corrections and some other fixes 06 December 2006, 18:59 UTC
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