https://github.com/geodynamics/citcoms

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Revision Author Date Message Commit Date
3d926d3 Removing read_comp(), which is not used anymore 19 March 2007, 23:29:00 UTC
4c3acc7 Advect the tracers right after temperature advection, before solving velocity 19 March 2007, 23:25:14 UTC
0bf6d88 Replaced for-loop by an if, which matchs the intention better 19 March 2007, 23:08:40 UTC
71b53f2 Init'd advection.timestep and advection.timesteps earlier. The time output uses these parameters. 19 March 2007, 22:53:40 UTC
f4292ca Reimplemented my version of low_viscosity_channel_factor() and low_viscosity_wedge_factor() 19 March 2007, 22:51:35 UTC
b9a5f9d Clean up the function prototype declaration 19 March 2007, 22:50:09 UTC
6ad7c85 Moving tracer initialization code to a function 19 March 2007, 22:48:13 UTC
0fcf84e Compute the volume of the mesh, use it to estimate the # of tracers in the proc. make_tracer_array() now works for both versions 19 March 2007, 22:45:38 UTC
a95684d Apply chemical buoyancy only when using tracer 17 March 2007, 00:38:06 UTC
417b7d9 Merged the regional and global tracer codes. Basically, Vlad's code is mostly gone and is replaced by Allen's and mine code. A few functions, eg. analytical_test(), low_viscosity_*_factor(), are disabled, need to work on them later. 17 March 2007, 00:21:01 UTC
a9782f6 Removed broken usage() method. (Pythia v0.8.1.3 will have a reasonable default for this method.) 15 March 2007, 02:51:13 UTC
94c4295 Refactored the regional parts of the code so that the age grids are read in from the same code as are the velocity and material files. Moved the guts of Regional_lith_age_read_files.c to Regional_read_input_from_files.c. This nearly makes the structure of Full and Regional the same -- refactoring that Leif initiated last year 13 March 2007, 00:56:07 UTC
14d3b40 Commented out code about compositional_rheology, which is not implemented 12 March 2007, 23:27:29 UTC
132480a Removed static variables, added some code documentation 12 March 2007, 23:11:49 UTC
51cd3fe A new input parameter "ic_method_for_flavors", to specify which way to initialize the flavors when the tracers are init'd randomly Currrently, only ic_method_for_flavors=0 is allowed, which produces a layered structure, any tracer above z_interface is of flavor 0, below z_interface is of flavor 1. 12 March 2007, 22:14:36 UTC
1f8c67a Initial bulk composition 12 March 2007, 22:07:19 UTC
bfb796a Output the total composition information to the log file, get rid of extra file handles in trace struct 12 March 2007, 22:06:37 UTC
beb0afe Compute the Cartesian velocity on the fly, not storing it in a seperated array 12 March 2007, 22:05:31 UTC
8b8c041 Modified Regional_read_input_from_files.c so that it now opens and reads in material files. Material files are organized by elements. Previsouly only worked for Full 12 March 2007, 20:08:12 UTC
24ec419 A new way to compute composition. Each tracer has a "flavor" (can only be either 0 or 1 currently). In the ratio method, the composition of an element is determined by: (# of tracers of flavor i)/(# of total tracers) 11 March 2007, 05:27:50 UTC
11698e0 * Unifying output for extra tracer quantities * Renamed rtrac to basicq, etrac to extraq, to match the basic/extra quantities for advection * Renamed itrac to ielement, itracsize to ielementsize, ielementsize to max_ntracers * A new member for the # of tracers * Removed some unused members in trace struct * Untabify and indent the code 11 March 2007, 05:20:43 UTC
a8d1a1b Add Vlad to the author list 09 March 2007, 00:26:17 UTC
45be8f2 A big patch for tracers and composition: * Seperating composition codes from tracer codes, several struct members in E->trace are moved to E->composition * Add chemical buoyancy term * Renamed thermal_buoyancy() to get_buoyancy() to reflect the fact that this function computes buoyancy according to temperature/composition/phase * Fix and optimize the fix_*() functions * Remove some static variables, or converte them to const * Change the type of E->SinCos from float to double, and replace E->trace.DSinCos * Provide default values for "required" input parameters * Renamed tracer_restart to tracer_ic_method, also remapped the options * Removed option for Cartesian tracer input and trace.iwrite_tracers_every * Replaced trace.itracer_type by composition.ichemical_buoyancy * Optionally output tracers and composition fields 09 March 2007, 00:25:03 UTC
068a4d5 Minor Makefile fix I made while working on Nemesis (i.e. with embedding disabled). 08 March 2007, 00:35:52 UTC
b233c5a * Simplified checking in the radial direction * Removed obsolete variables in trace struct 02 March 2007, 00:09:47 UTC
8467ab6 Finally, exchanging tracers between processors works, at least in 12-proc cases 01 March 2007, 21:23:25 UTC
8a9b494 * Communicate cap boundary information with neighboring processors. This information will be used in icheck_cap() later * Update icheck_cap() for our paralleism * Disable composition-related output 01 March 2007, 21:21:45 UTC
513bb8e Fixed two errors reported by icc 01 March 2007, 21:17:17 UTC
c29ef92 * Create pyre inventory for tracer input * Changed the default values of some tracer parameters to be consistent with pyre inventory 01 March 2007, 21:16:47 UTC
30792de Migrating the tracer code (not finished) 01 March 2007, 21:15:21 UTC
7f019a8 Copied from Allen McNamara's tracer code. The code will fail to compile 01 March 2007, 21:02:00 UTC
5e312c7 Resurrected Exchanger source. 16 February 2007, 17:44:30 UTC
734c621 Spherical version of the temperature solver 08 February 2007, 00:15:03 UTC
4f896c0 Removed the use of a new feature in python 2.4 ("substring" in "string") 08 February 2007, 00:14:46 UTC
9248203 Added input parameters that controlling the predictor-corrector scheme 06 February 2007, 02:23:07 UTC
06c809e Fixed a bug when reading coor_file in full CitcomS 06 February 2007, 02:22:47 UTC
d6b6188 Changed smoothing method for viscosity to be consistent with CitcomCU 06 February 2007, 02:22:32 UTC
e5e8487 A new option for initial temperature, which is used in Shijie's benchmark When tic_method==3, the initial temperature is a linear profile plus mag * modified_plgndr_a(ll, mm, theta) * (cos(mm*phi) + sin(mm*phi)) * sin(M_PI * (r - E->sphere.ri) / (E->sphere.ro - E->sphere.ri)) 02 February 2007, 23:30:07 UTC
7350e59 Disable pid output for processors of rank>0 02 February 2007, 20:10:45 UTC
fdbac82 Removed spaces around the equal sign when writing pid file, which confused parser.py 31 January 2007, 20:46:02 UTC
c009c18 Moved Python egg stuff into our Autoconf macro library. 30 January 2007, 21:16:23 UTC
ec54f98 added spaces after = in sec b.2; redid table in c.4.9 prev updated by eh; regen pdf 30 January 2007, 19:29:30 UTC
1f34cc0 Compute the 2nd invariant of strain rate tensor in spherical coordinate 30 January 2007, 19:04:35 UTC
c27c716 The functionality of this routine is now expanded so that for evey time step the element materials are read in. The code for determining the material file names and opening the file name and then reading in the element files is placed in the same code that the age grids and velocity files are processed. Obviously, reading in materials currently only works for Full; fill be working on Regional next. 29 January 2007, 20:51:24 UTC
a60c042 Changed the seequence placement in the time step when the age grids are assimilated into the temperature field. Previously, going back to the original code contributed by CC, the assimilation occurred avery time the temperature BCs were set (meaning multiple times in a PC loop). Now assimilation happens only once at the end of the time step. This is placed at the end of the routine PG_time_step_solve. Once we have worked with this some more, we will want to expose this code at a higher level so that assimulation will work properly from either plain C code or the Pyre version. Currently only tested with Full. 29 January 2007, 20:46:28 UTC
d9e66bf A minor change so that restart now works properly when lith_age=1. Now restart from old temperature fields appear to work without any obvious corruption of the Temp field. Only tested with Full. 29 January 2007, 20:37:00 UTC
55cca22 Small change for rheol=5 to use harmonic mean when element materials are read in. Also, this involved a minor conflict resolution with Eh s recent change to this file 29 January 2007, 20:32:27 UTC
fe3fb9f Write controller inventory to pid file. This is a heck! 26 January 2007, 21:32:04 UTC
38bdaf9 Compute the velocity in Cartesian coord on the fly. The previous code computed and stored the Cartesian velocity in E->temp in v_from_vector() and accessed E->temp in velo_from_element. This is bug prone. E->temp is a temporary array and should be used for storage. Also, in previous code, if E->sphere.cap[m].V is modified, one has to recompute E->temp. Otherwise, the Cartesian velocity will be incorrect. 25 January 2007, 23:30:49 UTC
8734680 Get rid of static variables 25 January 2007, 01:38:10 UTC
3cf8bd1 Refactoring various functions to simplify their pyre counterpart 25 January 2007, 00:57:21 UTC
f727da9 Fixed a bug in locating elements right above tracers 17 January 2007, 20:02:37 UTC
495961c Replaced 'exit(0)' with correct MPI exit, related to issue69 17 January 2007, 01:54:39 UTC
ccfc46d Fixed issue77 - velocity b.c not scaled correctly when age becomes negative 16 January 2007, 20:37:14 UTC
2ca42ed Read input parameter 'half_space_age' when tic_method=1 16 January 2007, 19:49:51 UTC
efe5b97 Fixed incorrect prototype 16 January 2007, 18:50:16 UTC
cada3c8 When "tic_method=1", the temperature is isothermal (== bottom b.c.) with a uniformly cold plate (thickness specified by 'half_space_age') 16 January 2007, 18:43:28 UTC
02def5d Tracer-defined rheology -- low viscosity channel/wedge 16 January 2007, 17:41:55 UTC
3aef1cf Added regional (passive) tracers 15 January 2007, 21:42:04 UTC
e7950e5 Fix for time-invariant velocity boundary conditions, issue75 09 January 2007, 21:11:58 UTC
1be8307 Another document fix for issue75, related to "how to specify time-invariant velocity boundary conditions?" 08 January 2007, 23:09:47 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, 22:19:35 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, 22:19:14 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, 22:33:03 UTC
7d3ef92 Fix for issue72: "'make install' broken for non-pyred CitcomS". 05 January 2007, 00:06:11 UTC
9b67fc5 added note about updating to 2.10.3 20 December 2006, 22:13:44 UTC
0b9c4d2 Regenerated ChangeLog upto r5565 09 December 2006, 00:26:38 UTC
545c4df gurnis final changes; image resize; ready for release 09 December 2006, 00:22:28 UTC
47bdc2d small text changes; image resize 08 December 2006, 23:50:10 UTC
7da60aa Added "created by OpenDX" on several figure captions 08 December 2006, 23:45:26 UTC
03df21a Updated MayaVi2 section 08 December 2006, 23:36:57 UTC
8f5c823 Renamed the MayaVi launching script and move it to visual/ 08 December 2006, 23:30:39 UTC
dd70690 Added executable bit to file permission 08 December 2006, 23:26:02 UTC
742ed51 Add plugins for MayaVi2 to installation 08 December 2006, 22:44:00 UTC
92235c0 Added README files 08 December 2006, 22:27:26 UTC
c60971f fixed image size, text size and other small text changes 08 December 2006, 22:00:21 UTC
8c92de8 Removing reduce filter from comments, as it is currently obsolete. 08 December 2006, 21:16:47 UTC
4511a3d Added MayaVi screenshot to manual, along with a couple of other fixes. 08 December 2006, 21:15:17 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, 20:03:11 UTC
af17846 Forgot to rename data filters. 08 December 2006, 19:47:43 UTC
de6f70d Added MayaVi2 screenshot for the manual. 08 December 2006, 17:53:20 UTC
75bb12b Various patches. 08 December 2006, 17:44:47 UTC
b3423fa Forking original plugins 08 December 2006, 17:40:08 UTC
9c83a26 Archiving original plugins. 08 December 2006, 17:32:25 UTC
42b3b3e Modify plugins directory 08 December 2006, 17:31:25 UTC
3c488f3 Explain contents of each directory. 08 December 2006, 17:29:46 UTC
849cea5 Made 'install_deps' actually do what 'configure' says it's doing (*missing* deps, not *all*). 08 December 2006, 02:29:09 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, 23:26:14 UTC
79a8733 chapter 5 * Added MayaVi2 in the introduction * Added links to MayaVi2 installation 07 December 2006, 22:34:26 UTC
6e256a7 fixed image size; regen pdf 07 December 2006, 22:19:37 UTC
e7c2ea3 text fixes to recent additions 07 December 2006, 22:09:17 UTC
b7662aa * Put back the HDFView sections * Added a screenshot of HDFView * Added a warning on "-O3" compiler flag 07 December 2006, 21:30:53 UTC
7bf8a4b text edits to appendices and bib 07 December 2006, 05:03:23 UTC
cf68821 small changes to chapt 6; standardized cross refference style; sstandardized code spacing 07 December 2006, 00:12:17 UTC
8910ace enumerating several sections of the instructions in chap 5 for clarity, and a few minor text fixes 06 December 2006, 23:31:57 UTC
cd4ffb9 a few text fixes in chapter 3 06 December 2006, 20:59:49 UTC
bb3c41c a few text fixes, preface to end of chapt 2 06 December 2006, 20:33:12 UTC
6f35a8c gurnis corrections and some other fixes 06 December 2006, 18:59:56 UTC
8cee12e Temporarily removing Mayavi2 files from Makefile.am 06 December 2006, 08:52:50 UTC
3c51bb9 Archive files created during Martin Weier's internship 06 December 2006, 08:23:54 UTC
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