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26 October 2024, 18:30:49 UTC
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21104b6 Eh Tan15 June 2007, 21:01:27 UTCTag for v2.2.2 release15 June 2007, 21:01:27 UTC
93827a4 Eh Tan14 June 2007, 22:59:37 UTCUpdate ChangeLog upto r724914 June 2007, 22:59:37 UTC
8897df0 Eh Tan14 June 2007, 22:58:05 UTCUpdate NEWS and configure.ac for v2.2.2 release14 June 2007, 22:58:05 UTC
8682d89 Eh Tan14 June 2007, 21:39:17 UTCPorting r7245 from trunk -- Zeroing geoid arrays before every geoid calculation. This fixes issue11414 June 2007, 21:39:17 UTC
f0085aa Eh Tan14 June 2007, 17:57:03 UTCPorting r7236 from trunk14 June 2007, 17:57:03 UTC
b25d904 Eh Tan14 June 2007, 01:37:29 UTCPorting r7221 from trunk -- Fixing issue111: Expanding %RANK in autocombine.py14 June 2007, 01:37:29 UTC
7c75162 Eh Tan13 June 2007, 00:02:51 UTCMerging r7137 from trunk13 June 2007, 00:02:51 UTC
3531770 Eh Tan13 June 2007, 00:02:02 UTCMerging r6509-6850 from trunk13 June 2007, 00:02:02 UTC
8e9a7f0 Eh Tan12 June 2007, 23:49:07 UTCA branch for bug-fix12 June 2007, 23:49:07 UTC
3654872 Eh Tan27 March 2007, 04:40:15 UTCTag for v2.2.127 March 2007, 04:40:15 UTC
78e36d1 Eh Tan27 March 2007, 04:39:34 UTCRegenerated ChangeLog upto r641727 March 2007, 04:39:34 UTC
190e4e8 Eh Tan27 March 2007, 04:37:54 UTCUpdated NEWS for the upcoming 2.2.127 March 2007, 04:37:54 UTC
1ab1ba9 Eh Tan27 March 2007, 04:20:05 UTCForgot to add cookbook7.cfg to the file list27 March 2007, 04:20:05 UTC
d1623a6 Eh Tan26 March 2007, 18:48:36 UTCRegenerated ChangeLog upto r640926 March 2007, 18:48:36 UTC
074e8d9 Eh Tan26 March 2007, 18:45:16 UTCForgot to add a header file to the file list26 March 2007, 18:45:16 UTC
585244b Eh Tan26 March 2007, 18:25:42 UTCRegenerated ChangeLog upto r640326 March 2007, 18:25:42 UTC
e8056e6 Eh Tan26 March 2007, 18:20:19 UTCSet the length unit to cm to fit within the page26 March 2007, 18:20:19 UTC
c7236d2 Eh Tan26 March 2007, 18:11:02 UTCChanged the size of gmt plots to fit within the page26 March 2007, 18:11:02 UTC
8ccaa32 Sue Kientz26 March 2007, 18:05:31 UTCrestored edits to stable copy; regen pdf, images showing26 March 2007, 18:05:31 UTC
3b056f3 Eh Tan26 March 2007, 06:01:18 UTCEnlarged the figure of cookbook7. Rephrased the description of the low-viscosity-zone parameters, per Sue's suggestion.26 March 2007, 06:01:18 UTC
d79404c Sue Kientz26 March 2007, 00:23:55 UTCchasing down image problem26 March 2007, 00:23:55 UTC
6f388ea Sue Kientz25 March 2007, 23:07:31 UTCchanged verbage in History 1.2, paragraphs on version 2.1, to past tense, since notes on 2.2 should be only ones in present tense \c25 March 2007, 23:07:31 UTC
723f757 Sue Kientz25 March 2007, 22:55:42 UTCedits of new copy; attempt to fix an image that is not displaying, still unresolved25 March 2007, 22:55:42 UTC
8688ee2 Eh Tan24 March 2007, 23:05:03 UTCFinished Cookbook724 March 2007, 23:05:03 UTC
0a6d3bd Eh Tan24 March 2007, 23:03:00 UTCChanged the version number to 2.224 March 2007, 23:03:00 UTC
1af6a2d Eh Tan24 March 2007, 00:02:43 UTCAdded new cookbook724 March 2007, 00:02:43 UTC
3cd5331 Eh Tan23 March 2007, 22:21:32 UTCUpdated the NEWS for v2.2.023 March 2007, 22:21:32 UTC
5fc07c2 Eh Tan23 March 2007, 22:21:06 UTCAdded new parameter 'adv_gamme' to the manual and input samples. Documented a new tic_method=323 March 2007, 22:21:06 UTC
1e70a61 Eh Tan23 March 2007, 21:06:06 UTCAdded description to the tracer and composition input/output files23 March 2007, 21:06:06 UTC
c0753b2 Eh Tan23 March 2007, 20:40:27 UTCAdded the tracer parameters to the manual and sample input files23 March 2007, 20:40:27 UTC
c50ae40 Eh Tan23 March 2007, 20:39:12 UTCDisable the parameter "analytical_tracer_test", and make "chemical_buoyancy" a boolean23 March 2007, 20:39:12 UTC
2678c56 Eh Tan23 March 2007, 19:37:24 UTCAdded the low-visc-zone parameters to the manual and the sample input files23 March 2007, 19:37:24 UTC
b4b5b1c Eh Tan23 March 2007, 05:31:39 UTCAdded the image for cookbook7 (thermo-chemical convection23 March 2007, 05:31:39 UTC
130bee2 Eh Tan23 March 2007, 05:30:43 UTCWhen I renamed the old Cookbook7/ directory to Cookbook6/, I forgot to rename cookbook7.eps to cookbook6.eps. Now it is done.23 March 2007, 05:30:43 UTC
a2482bb Eh Tan23 March 2007, 05:25:10 UTCThese two EPS files are the leftover of an old cookbook23 March 2007, 05:25:10 UTC
801b1bb Eh Tan23 March 2007, 05:22:29 UTCGather theta and phi only in get_neighboring_caps()23 March 2007, 05:22:29 UTC
6bef184 Eh Tan23 March 2007, 05:21:38 UTCChanged the header format of comp_* output to be consistent with other data files23 March 2007, 05:21:38 UTC
da31e1c Sue Kientz22 March 2007, 22:11:02 UTCadded bib entry per eh, changed cover to citcoms (rem .py), changed to 2.2.0, todo notation removed; regen pdf22 March 2007, 22:11:02 UTC
3339bf3 Eh Tan22 March 2007, 19:58:11 UTCMake the output of 1st iteration consistent with later iterations22 March 2007, 19:58:11 UTC
8f757ca Eh Tan22 March 2007, 19:57:57 UTCCalling find_tracers() and count_tracers_of_flavors() in initialize_tracers(), so that the former two functions can become static/private22 March 2007, 19:57:57 UTC
1d3cb93 Eh Tan22 March 2007, 19:55:18 UTCRenamed initialize_tracer_arrays() to allocate_tracer_arrays()22 March 2007, 19:55:18 UTC
34b83e1 Eh Tan21 March 2007, 22:46:51 UTCUpdated the version number to 2.2.021 March 2007, 22:46:51 UTC
f1b0e00 Eh Tan21 March 2007, 22:46:34 UTCUpdated the dependency information21 March 2007, 22:46:34 UTC
c03947b Eh Tan21 March 2007, 22:46:08 UTCAdded chemical Rayleigh number to the equations21 March 2007, 22:46:08 UTC
ed136d5 Eh Tan21 March 2007, 22:45:51 UTCAdded history of v2.2 release21 March 2007, 22:45:51 UTC
9bf807f Eh Tan21 March 2007, 22:45:30 UTCAdded citation to McNamara & Zhong 200421 March 2007, 22:45:30 UTC
42b79b0 Eh Tan21 March 2007, 19:30:45 UTCAdded a safeguard against nprocx or nprocy greater than 121 March 2007, 19:30:45 UTC
064cf26 Eh Tan20 March 2007, 06:34:22 UTCfull_lost_souls() now works for nprocz>1 as well20 March 2007, 06:34:22 UTC
585d503 Eh Tan20 March 2007, 06:27:56 UTCRemoved the 'tracer_interpolation_scheme' and 'tracer_advection_scheme' parameters20 March 2007, 06:27:56 UTC
0860212 Eh Tan20 March 2007, 06:26:19 UTCReporting error if low viscosity channel/wedge is turned on, but tracer is turned off20 March 2007, 06:26:19 UTC
5812fbe Eh Tan19 March 2007, 23:49:51 UTClost_souls() cannot be shared by both versions. The parallel communications of both versions are too different. So, the original lost_souls() is renamed to full_lost_souls(). A new regional_lost_souls() is implemented. This code has been tested in 3x3x3 processors, running over 100 timesteps. The number of total tracers is conserved.19 March 2007, 23:49:51 UTC
7c2622b Eh Tan19 March 2007, 23:44:12 UTCInit'd E->composition.icompositional_rheology to 019 March 2007, 23:44:12 UTC
086ba84 Eh Tan19 March 2007, 23:42:50 UTC* Init'd E->composition.icompositional_rheology to 0 * Write composition instruction only if it is turned on * Clean up the code a bit19 March 2007, 23:42:50 UTC
3d926d3 Eh Tan19 March 2007, 23:29:00 UTCRemoving read_comp(), which is not used anymore19 March 2007, 23:29:00 UTC
4c3acc7 Eh Tan19 March 2007, 23:25:14 UTCAdvect the tracers right after temperature advection, before solving velocity19 March 2007, 23:25:14 UTC
0bf6d88 Eh Tan19 March 2007, 23:08:40 UTCReplaced for-loop by an if, which matchs the intention better19 March 2007, 23:08:40 UTC
71b53f2 Eh Tan19 March 2007, 22:53:40 UTCInit'd advection.timestep and advection.timesteps earlier. The time output uses these parameters.19 March 2007, 22:53:40 UTC
f4292ca Eh Tan19 March 2007, 22:51:35 UTCReimplemented my version of low_viscosity_channel_factor() and low_viscosity_wedge_factor()19 March 2007, 22:51:35 UTC
b9a5f9d Eh Tan19 March 2007, 22:50:09 UTCClean up the function prototype declaration19 March 2007, 22:50:09 UTC
6ad7c85 Eh Tan19 March 2007, 22:48:13 UTCMoving tracer initialization code to a function19 March 2007, 22:48:13 UTC
0fcf84e Eh Tan19 March 2007, 22:45:38 UTCCompute the volume of the mesh, use it to estimate the # of tracers in the proc. make_tracer_array() now works for both versions19 March 2007, 22:45:38 UTC
a95684d Eh Tan17 March 2007, 00:38:06 UTCApply chemical buoyancy only when using tracer17 March 2007, 00:38:06 UTC
417b7d9 Eh Tan17 March 2007, 00:21:01 UTCMerged 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 Leif Strand15 March 2007, 02:51:13 UTCRemoved broken usage() method. (Pythia v0.8.1.3 will have a reasonable default for this method.)15 March 2007, 02:51:13 UTC
94c4295 Michael Gurnis13 March 2007, 00:56:07 UTCRefactored 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 year13 March 2007, 00:56:07 UTC
14d3b40 Eh Tan12 March 2007, 23:27:29 UTCCommented out code about compositional_rheology, which is not implemented12 March 2007, 23:27:29 UTC
132480a Eh Tan12 March 2007, 23:11:49 UTCRemoved static variables, added some code documentation12 March 2007, 23:11:49 UTC
51cd3fe Eh Tan12 March 2007, 22:14:36 UTCA 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 Eh Tan12 March 2007, 22:07:19 UTCInitial bulk composition12 March 2007, 22:07:19 UTC
bfb796a Eh Tan12 March 2007, 22:06:37 UTCOutput the total composition information to the log file, get rid of extra file handles in trace struct12 March 2007, 22:06:37 UTC
beb0afe Eh Tan12 March 2007, 22:05:31 UTCCompute the Cartesian velocity on the fly, not storing it in a seperated array12 March 2007, 22:05:31 UTC
8b8c041 Michael Gurnis12 March 2007, 20:08:12 UTCModified 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 Full12 March 2007, 20:08:12 UTC
24ec419 Eh Tan11 March 2007, 05:27:50 UTCA 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 Eh Tan11 March 2007, 05:20:43 UTC* 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 code11 March 2007, 05:20:43 UTC
a8d1a1b Eh Tan09 March 2007, 00:26:17 UTCAdd Vlad to the author list09 March 2007, 00:26:17 UTC
45be8f2 Eh Tan09 March 2007, 00:25:03 UTCA 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 fields09 March 2007, 00:25:03 UTC
068a4d5 Leif Strand08 March 2007, 00:35:52 UTCMinor Makefile fix I made while working on Nemesis (i.e. with embedding disabled).08 March 2007, 00:35:52 UTC
b233c5a Eh Tan02 March 2007, 00:09:47 UTC* Simplified checking in the radial direction * Removed obsolete variables in trace struct02 March 2007, 00:09:47 UTC
8467ab6 Eh Tan01 March 2007, 21:23:25 UTCFinally, exchanging tracers between processors works, at least in 12-proc cases01 March 2007, 21:23:25 UTC
8a9b494 Eh Tan01 March 2007, 21:21:45 UTC* 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 output01 March 2007, 21:21:45 UTC
513bb8e Eh Tan01 March 2007, 21:17:17 UTCFixed two errors reported by icc01 March 2007, 21:17:17 UTC
c29ef92 Eh Tan01 March 2007, 21:16:47 UTC* Create pyre inventory for tracer input * Changed the default values of some tracer parameters to be consistent with pyre inventory01 March 2007, 21:16:47 UTC
30792de Eh Tan01 March 2007, 21:15:21 UTCMigrating the tracer code (not finished)01 March 2007, 21:15:21 UTC
7f019a8 Eh Tan01 March 2007, 21:02:00 UTCCopied from Allen McNamara's tracer code. The code will fail to compile01 March 2007, 21:02:00 UTC
5e312c7 Leif Strand16 February 2007, 17:44:30 UTCResurrected Exchanger source.16 February 2007, 17:44:30 UTC
734c621 Eh Tan08 February 2007, 00:15:03 UTCSpherical version of the temperature solver08 February 2007, 00:15:03 UTC
4f896c0 Eh Tan08 February 2007, 00:14:46 UTCRemoved the use of a new feature in python 2.4 ("substring" in "string")08 February 2007, 00:14:46 UTC
9248203 Eh Tan06 February 2007, 02:23:07 UTCAdded input parameters that controlling the predictor-corrector scheme06 February 2007, 02:23:07 UTC
06c809e Eh Tan06 February 2007, 02:22:47 UTCFixed a bug when reading coor_file in full CitcomS06 February 2007, 02:22:47 UTC
d6b6188 Eh Tan06 February 2007, 02:22:32 UTCChanged smoothing method for viscosity to be consistent with CitcomCU06 February 2007, 02:22:32 UTC
e5e8487 Eh Tan02 February 2007, 23:30:07 UTCA 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 Eh Tan02 February 2007, 20:10:45 UTCDisable pid output for processors of rank>002 February 2007, 20:10:45 UTC
fdbac82 Eh Tan31 January 2007, 20:46:02 UTCRemoved spaces around the equal sign when writing pid file, which confused parser.py31 January 2007, 20:46:02 UTC
c009c18 Leif Strand30 January 2007, 21:16:23 UTCMoved Python egg stuff into our Autoconf macro library.30 January 2007, 21:16:23 UTC
ec54f98 Sue Kientz30 January 2007, 19:29:30 UTCadded spaces after = in sec b.2; redid table in c.4.9 prev updated by eh; regen pdf30 January 2007, 19:29:30 UTC
1f34cc0 Eh Tan30 January 2007, 19:04:35 UTCCompute the 2nd invariant of strain rate tensor in spherical coordinate30 January 2007, 19:04:35 UTC
c27c716 Michael Gurnis29 January 2007, 20:51:24 UTCThe 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 Michael Gurnis29 January 2007, 20:46:28 UTCChanged 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 Michael Gurnis29 January 2007, 20:37:00 UTCA 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 Michael Gurnis29 January 2007, 20:32:27 UTCSmall 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 file29 January 2007, 20:32:27 UTC
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