8f757ca | Eh Tan | 22 March 2007, 19:57:57 UTC | Calling find_tracers() and count_tracers_of_flavors() in initialize_tracers(), so that the former two functions can become static/private | 22 March 2007, 19:57:57 UTC |
1d3cb93 | Eh Tan | 22 March 2007, 19:55:18 UTC | Renamed initialize_tracer_arrays() to allocate_tracer_arrays() | 22 March 2007, 19:55:18 UTC |
34b83e1 | Eh Tan | 21 March 2007, 22:46:51 UTC | Updated the version number to 2.2.0 | 21 March 2007, 22:46:51 UTC |
f1b0e00 | Eh Tan | 21 March 2007, 22:46:34 UTC | Updated the dependency information | 21 March 2007, 22:46:34 UTC |
c03947b | Eh Tan | 21 March 2007, 22:46:08 UTC | Added chemical Rayleigh number to the equations | 21 March 2007, 22:46:08 UTC |
ed136d5 | Eh Tan | 21 March 2007, 22:45:51 UTC | Added history of v2.2 release | 21 March 2007, 22:45:51 UTC |
9bf807f | Eh Tan | 21 March 2007, 22:45:30 UTC | Added citation to McNamara & Zhong 2004 | 21 March 2007, 22:45:30 UTC |
42b79b0 | Eh Tan | 21 March 2007, 19:30:45 UTC | Added a safeguard against nprocx or nprocy greater than 1 | 21 March 2007, 19:30:45 UTC |
064cf26 | Eh Tan | 20 March 2007, 06:34:22 UTC | full_lost_souls() now works for nprocz>1 as well | 20 March 2007, 06:34:22 UTC |
585d503 | Eh Tan | 20 March 2007, 06:27:56 UTC | Removed the 'tracer_interpolation_scheme' and 'tracer_advection_scheme' parameters | 20 March 2007, 06:27:56 UTC |
0860212 | Eh Tan | 20 March 2007, 06:26:19 UTC | Reporting error if low viscosity channel/wedge is turned on, but tracer is turned off | 20 March 2007, 06:26:19 UTC |
5812fbe | Eh Tan | 19 March 2007, 23:49:51 UTC | lost_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 Tan | 19 March 2007, 23:44:12 UTC | Init'd E->composition.icompositional_rheology to 0 | 19 March 2007, 23:44:12 UTC |
086ba84 | Eh Tan | 19 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 bit | 19 March 2007, 23:42:50 UTC |
3d926d3 | Eh Tan | 19 March 2007, 23:29:00 UTC | Removing read_comp(), which is not used anymore | 19 March 2007, 23:29:00 UTC |
4c3acc7 | Eh Tan | 19 March 2007, 23:25:14 UTC | Advect the tracers right after temperature advection, before solving velocity | 19 March 2007, 23:25:14 UTC |
0bf6d88 | Eh Tan | 19 March 2007, 23:08:40 UTC | Replaced for-loop by an if, which matchs the intention better | 19 March 2007, 23:08:40 UTC |
71b53f2 | Eh Tan | 19 March 2007, 22:53:40 UTC | Init'd advection.timestep and advection.timesteps earlier. The time output uses these parameters. | 19 March 2007, 22:53:40 UTC |
f4292ca | Eh Tan | 19 March 2007, 22:51:35 UTC | Reimplemented my version of low_viscosity_channel_factor() and low_viscosity_wedge_factor() | 19 March 2007, 22:51:35 UTC |
b9a5f9d | Eh Tan | 19 March 2007, 22:50:09 UTC | Clean up the function prototype declaration | 19 March 2007, 22:50:09 UTC |
6ad7c85 | Eh Tan | 19 March 2007, 22:48:13 UTC | Moving tracer initialization code to a function | 19 March 2007, 22:48:13 UTC |
0fcf84e | Eh Tan | 19 March 2007, 22:45:38 UTC | 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 | Eh Tan | 17 March 2007, 00:38:06 UTC | Apply chemical buoyancy only when using tracer | 17 March 2007, 00:38:06 UTC |
417b7d9 | Eh Tan | 17 March 2007, 00:21:01 UTC | 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 | Leif Strand | 15 March 2007, 02:51:13 UTC | 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 | Michael Gurnis | 13 March 2007, 00:56:07 UTC | 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 | Eh Tan | 12 March 2007, 23:27:29 UTC | Commented out code about compositional_rheology, which is not implemented | 12 March 2007, 23:27:29 UTC |
132480a | Eh Tan | 12 March 2007, 23:11:49 UTC | Removed static variables, added some code documentation | 12 March 2007, 23:11:49 UTC |
51cd3fe | Eh Tan | 12 March 2007, 22:14:36 UTC | 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 | Eh Tan | 12 March 2007, 22:07:19 UTC | Initial bulk composition | 12 March 2007, 22:07:19 UTC |
bfb796a | Eh Tan | 12 March 2007, 22:06:37 UTC | 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 | Eh Tan | 12 March 2007, 22:05:31 UTC | Compute the Cartesian velocity on the fly, not storing it in a seperated array | 12 March 2007, 22:05:31 UTC |
8b8c041 | Michael Gurnis | 12 March 2007, 20:08:12 UTC | 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 | Eh Tan | 11 March 2007, 05:27:50 UTC | 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 | Eh Tan | 11 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 code | 11 March 2007, 05:20:43 UTC |
a8d1a1b | Eh Tan | 09 March 2007, 00:26:17 UTC | Add Vlad to the author list | 09 March 2007, 00:26:17 UTC |
45be8f2 | Eh Tan | 09 March 2007, 00:25:03 UTC | 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 | Leif Strand | 08 March 2007, 00:35:52 UTC | Minor Makefile fix I made while working on Nemesis (i.e. with embedding disabled). | 08 March 2007, 00:35:52 UTC |
b233c5a | Eh Tan | 02 March 2007, 00:09:47 UTC | * Simplified checking in the radial direction * Removed obsolete variables in trace struct | 02 March 2007, 00:09:47 UTC |
8467ab6 | Eh Tan | 01 March 2007, 21:23:25 UTC | Finally, exchanging tracers between processors works, at least in 12-proc cases | 01 March 2007, 21:23:25 UTC |
8a9b494 | Eh Tan | 01 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 output | 01 March 2007, 21:21:45 UTC |
513bb8e | Eh Tan | 01 March 2007, 21:17:17 UTC | Fixed two errors reported by icc | 01 March 2007, 21:17:17 UTC |
c29ef92 | Eh Tan | 01 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 inventory | 01 March 2007, 21:16:47 UTC |
30792de | Eh Tan | 01 March 2007, 21:15:21 UTC | Migrating the tracer code (not finished) | 01 March 2007, 21:15:21 UTC |
7f019a8 | Eh Tan | 01 March 2007, 21:02:00 UTC | Copied from Allen McNamara's tracer code. The code will fail to compile | 01 March 2007, 21:02:00 UTC |
5e312c7 | Leif Strand | 16 February 2007, 17:44:30 UTC | Resurrected Exchanger source. | 16 February 2007, 17:44:30 UTC |
734c621 | Eh Tan | 08 February 2007, 00:15:03 UTC | Spherical version of the temperature solver | 08 February 2007, 00:15:03 UTC |
4f896c0 | Eh Tan | 08 February 2007, 00:14:46 UTC | Removed the use of a new feature in python 2.4 ("substring" in "string") | 08 February 2007, 00:14:46 UTC |
9248203 | Eh Tan | 06 February 2007, 02:23:07 UTC | Added input parameters that controlling the predictor-corrector scheme | 06 February 2007, 02:23:07 UTC |
06c809e | Eh Tan | 06 February 2007, 02:22:47 UTC | Fixed a bug when reading coor_file in full CitcomS | 06 February 2007, 02:22:47 UTC |
d6b6188 | Eh Tan | 06 February 2007, 02:22:32 UTC | Changed smoothing method for viscosity to be consistent with CitcomCU | 06 February 2007, 02:22:32 UTC |
e5e8487 | Eh Tan | 02 February 2007, 23:30:07 UTC | 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 | Eh Tan | 02 February 2007, 20:10:45 UTC | Disable pid output for processors of rank>0 | 02 February 2007, 20:10:45 UTC |
fdbac82 | Eh Tan | 31 January 2007, 20:46:02 UTC | Removed spaces around the equal sign when writing pid file, which confused parser.py | 31 January 2007, 20:46:02 UTC |
c009c18 | Leif Strand | 30 January 2007, 21:16:23 UTC | Moved Python egg stuff into our Autoconf macro library. | 30 January 2007, 21:16:23 UTC |
ec54f98 | Sue Kientz | 30 January 2007, 19:29:30 UTC | 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 | Eh Tan | 30 January 2007, 19:04:35 UTC | Compute the 2nd invariant of strain rate tensor in spherical coordinate | 30 January 2007, 19:04:35 UTC |
c27c716 | Michael Gurnis | 29 January 2007, 20:51:24 UTC | 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 | Michael Gurnis | 29 January 2007, 20:46:28 UTC | 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 | Michael Gurnis | 29 January 2007, 20:37:00 UTC | 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 | Michael Gurnis | 29 January 2007, 20:32:27 UTC | 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 | Eh Tan | 26 January 2007, 21:32:04 UTC | Write controller inventory to pid file. This is a heck! | 26 January 2007, 21:32:04 UTC |
38bdaf9 | Eh Tan | 25 January 2007, 23:30:49 UTC | 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 | Eh Tan | 25 January 2007, 01:38:10 UTC | Get rid of static variables | 25 January 2007, 01:38:10 UTC |
3cf8bd1 | Eh Tan | 25 January 2007, 00:57:21 UTC | Refactoring various functions to simplify their pyre counterpart | 25 January 2007, 00:57:21 UTC |
f727da9 | Eh Tan | 17 January 2007, 20:02:37 UTC | Fixed a bug in locating elements right above tracers | 17 January 2007, 20:02:37 UTC |
495961c | Eh Tan | 17 January 2007, 01:54:39 UTC | Replaced 'exit(0)' with correct MPI exit, related to issue69 | 17 January 2007, 01:54:39 UTC |
ccfc46d | Eh Tan | 16 January 2007, 20:37:14 UTC | Fixed issue77 - velocity b.c not scaled correctly when age becomes negative | 16 January 2007, 20:37:14 UTC |
2ca42ed | Eh Tan | 16 January 2007, 19:49:51 UTC | Read input parameter 'half_space_age' when tic_method=1 | 16 January 2007, 19:49:51 UTC |
efe5b97 | Eh Tan | 16 January 2007, 18:50:16 UTC | Fixed incorrect prototype | 16 January 2007, 18:50:16 UTC |
cada3c8 | Eh Tan | 16 January 2007, 18:43:28 UTC | 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 | Eh Tan | 16 January 2007, 17:41:55 UTC | Tracer-defined rheology -- low viscosity channel/wedge | 16 January 2007, 17:41:55 UTC |
3aef1cf | Eh Tan | 15 January 2007, 21:42:04 UTC | Added regional (passive) tracers | 15 January 2007, 21:42:04 UTC |
e7950e5 | Eh Tan | 09 January 2007, 21:11:58 UTC | Fix for time-invariant velocity boundary conditions, issue75 | 09 January 2007, 21:11:58 UTC |
1be8307 | Eh Tan | 08 January 2007, 23:09:47 UTC | Another document fix for issue75, related to "how to specify time-invariant velocity boundary conditions?" | 08 January 2007, 23:09:47 UTC |
0bfa938 | Eh Tan | 08 January 2007, 22:19:35 UTC | 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 | Eh Tan | 08 January 2007, 22:19:14 UTC | 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 | Eh Tan | 05 January 2007, 22:33:03 UTC | 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 | Leif Strand | 05 January 2007, 00:06:11 UTC | Fix for issue72: "'make install' broken for non-pyred CitcomS". | 05 January 2007, 00:06:11 UTC |
9b67fc5 | Sue Kientz | 20 December 2006, 22:13:44 UTC | added note about updating to 2.10.3 | 20 December 2006, 22:13:44 UTC |
0b9c4d2 | Eh Tan | 09 December 2006, 00:26:38 UTC | Regenerated ChangeLog upto r5565 | 09 December 2006, 00:26:38 UTC |
545c4df | Sue Kientz | 09 December 2006, 00:22:28 UTC | gurnis final changes; image resize; ready for release | 09 December 2006, 00:22:28 UTC |
47bdc2d | Sue Kientz | 08 December 2006, 23:50:10 UTC | small text changes; image resize | 08 December 2006, 23:50:10 UTC |
7da60aa | Eh Tan | 08 December 2006, 23:45:26 UTC | Added "created by OpenDX" on several figure captions | 08 December 2006, 23:45:26 UTC |
03df21a | Eh Tan | 08 December 2006, 23:36:57 UTC | Updated MayaVi2 section | 08 December 2006, 23:36:57 UTC |
8f5c823 | Eh Tan | 08 December 2006, 23:30:39 UTC | Renamed the MayaVi launching script and move it to visual/ | 08 December 2006, 23:30:39 UTC |
dd70690 | Eh Tan | 08 December 2006, 23:26:02 UTC | Added executable bit to file permission | 08 December 2006, 23:26:02 UTC |
742ed51 | Luis Armendariz | 08 December 2006, 22:44:00 UTC | Add plugins for MayaVi2 to installation | 08 December 2006, 22:44:00 UTC |
92235c0 | Luis Armendariz | 08 December 2006, 22:27:26 UTC | Added README files | 08 December 2006, 22:27:26 UTC |
c60971f | Sue Kientz | 08 December 2006, 22:00:21 UTC | fixed image size, text size and other small text changes | 08 December 2006, 22:00:21 UTC |
8c92de8 | Luis Armendariz | 08 December 2006, 21:16:47 UTC | Removing reduce filter from comments, as it is currently obsolete. | 08 December 2006, 21:16:47 UTC |
4511a3d | Luis Armendariz | 08 December 2006, 21:15:17 UTC | Added MayaVi screenshot to manual, along with a couple of other fixes. | 08 December 2006, 21:15:17 UTC |
13061f6 | Luis Armendariz | 08 December 2006, 20:03:11 UTC | 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 | Luis Armendariz | 08 December 2006, 19:47:43 UTC | Forgot to rename data filters. | 08 December 2006, 19:47:43 UTC |
de6f70d | Luis Armendariz | 08 December 2006, 17:53:20 UTC | Added MayaVi2 screenshot for the manual. | 08 December 2006, 17:53:20 UTC |
75bb12b | Luis Armendariz | 08 December 2006, 17:44:47 UTC | Various patches. | 08 December 2006, 17:44:47 UTC |
b3423fa | Luis Armendariz | 08 December 2006, 17:40:08 UTC | Forking original plugins | 08 December 2006, 17:40:08 UTC |
9c83a26 | Luis Armendariz | 08 December 2006, 17:32:25 UTC | Archiving original plugins. | 08 December 2006, 17:32:25 UTC |
42b3b3e | Luis Armendariz | 08 December 2006, 17:31:25 UTC | Modify plugins directory | 08 December 2006, 17:31:25 UTC |
3c488f3 | Luis Armendariz | 08 December 2006, 17:29:46 UTC | Explain contents of each directory. | 08 December 2006, 17:29:46 UTC |