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Revision Author Date Message Commit Date
3654872 Tag for v2.2.1 27 March 2007, 04:40 UTC
78e36d1 Regenerated ChangeLog upto r6417 27 March 2007, 04:39 UTC
190e4e8 Updated NEWS for the upcoming 2.2.1 27 March 2007, 04:37 UTC
1ab1ba9 Forgot to add cookbook7.cfg to the file list 27 March 2007, 04:20 UTC
d1623a6 Regenerated ChangeLog upto r6409 26 March 2007, 18:48 UTC
074e8d9 Forgot to add a header file to the file list 26 March 2007, 18:45 UTC
585244b Regenerated ChangeLog upto r6403 26 March 2007, 18:25 UTC
e8056e6 Set the length unit to cm to fit within the page 26 March 2007, 18:20 UTC
c7236d2 Changed the size of gmt plots to fit within the page 26 March 2007, 18:11 UTC
8ccaa32 restored edits to stable copy; regen pdf, images showing 26 March 2007, 18:05 UTC
3b056f3 Enlarged the figure of cookbook7. Rephrased the description of the low-viscosity-zone parameters, per Sue's suggestion. 26 March 2007, 06:01 UTC
d79404c chasing down image problem 26 March 2007, 00:23 UTC
6f388ea changed 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 \c 25 March 2007, 23:07 UTC
723f757 edits of new copy; attempt to fix an image that is not displaying, still unresolved 25 March 2007, 22:55 UTC
8688ee2 Finished Cookbook7 24 March 2007, 23:05 UTC
0a6d3bd Changed the version number to 2.2 24 March 2007, 23:03 UTC
1af6a2d Added new cookbook7 24 March 2007, 00:02 UTC
3cd5331 Updated the NEWS for v2.2.0 23 March 2007, 22:21 UTC
5fc07c2 Added new parameter 'adv_gamme' to the manual and input samples. Documented a new tic_method=3 23 March 2007, 22:21 UTC
1e70a61 Added description to the tracer and composition input/output files 23 March 2007, 21:06 UTC
c0753b2 Added the tracer parameters to the manual and sample input files 23 March 2007, 20:40 UTC
c50ae40 Disable the parameter "analytical_tracer_test", and make "chemical_buoyancy" a boolean 23 March 2007, 20:39 UTC
2678c56 Added the low-visc-zone parameters to the manual and the sample input files 23 March 2007, 19:37 UTC
b4b5b1c Added the image for cookbook7 (thermo-chemical convection 23 March 2007, 05:31 UTC
130bee2 When 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 UTC
a2482bb These two EPS files are the leftover of an old cookbook 23 March 2007, 05:25 UTC
801b1bb Gather theta and phi only in get_neighboring_caps() 23 March 2007, 05:22 UTC
6bef184 Changed the header format of comp_* output to be consistent with other data files 23 March 2007, 05:21 UTC
da31e1c added bib entry per eh, changed cover to citcoms (rem .py), changed to 2.2.0, todo notation removed; regen pdf 22 March 2007, 22:11 UTC
3339bf3 Make the output of 1st iteration consistent with later iterations 22 March 2007, 19:58 UTC
8f757ca 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 UTC
1d3cb93 Renamed initialize_tracer_arrays() to allocate_tracer_arrays() 22 March 2007, 19:55 UTC
34b83e1 Updated the version number to 2.2.0 21 March 2007, 22:46 UTC
f1b0e00 Updated the dependency information 21 March 2007, 22:46 UTC
c03947b Added chemical Rayleigh number to the equations 21 March 2007, 22:46 UTC
ed136d5 Added history of v2.2 release 21 March 2007, 22:45 UTC
9bf807f Added citation to McNamara & Zhong 2004 21 March 2007, 22:45 UTC
42b79b0 Added a safeguard against nprocx or nprocy greater than 1 21 March 2007, 19:30 UTC
064cf26 full_lost_souls() now works for nprocz>1 as well 20 March 2007, 06:34 UTC
585d503 Removed the 'tracer_interpolation_scheme' and 'tracer_advection_scheme' parameters 20 March 2007, 06:27 UTC
0860212 Reporting error if low viscosity channel/wedge is turned on, but tracer is turned off 20 March 2007, 06:26 UTC
5812fbe 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 UTC
7c2622b Init'd E->composition.icompositional_rheology to 0 19 March 2007, 23:44 UTC
086ba84 * 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 UTC
3d926d3 Removing read_comp(), which is not used anymore 19 March 2007, 23:29 UTC
4c3acc7 Advect the tracers right after temperature advection, before solving velocity 19 March 2007, 23:25 UTC
0bf6d88 Replaced for-loop by an if, which matchs the intention better 19 March 2007, 23:08 UTC
71b53f2 Init'd advection.timestep and advection.timesteps earlier. The time output uses these parameters. 19 March 2007, 22:53 UTC
f4292ca Reimplemented my version of low_viscosity_channel_factor() and low_viscosity_wedge_factor() 19 March 2007, 22:51 UTC
b9a5f9d Clean up the function prototype declaration 19 March 2007, 22:50 UTC
6ad7c85 Moving tracer initialization code to a function 19 March 2007, 22:48 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 UTC
a95684d Apply chemical buoyancy only when using tracer 17 March 2007, 00:38 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 UTC
a9782f6 Removed broken usage() method. (Pythia v0.8.1.3 will have a reasonable default for this method.) 15 March 2007, 02:51 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 UTC
14d3b40 Commented out code about compositional_rheology, which is not implemented 12 March 2007, 23:27 UTC
132480a Removed static variables, added some code documentation 12 March 2007, 23:11 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 UTC
1f8c67a Initial bulk composition 12 March 2007, 22:07 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 UTC
beb0afe Compute the Cartesian velocity on the fly, not storing it in a seperated array 12 March 2007, 22:05 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 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 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 UTC
a8d1a1b Add Vlad to the author list 09 March 2007, 00:26 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 UTC
068a4d5 Minor Makefile fix I made while working on Nemesis (i.e. with embedding disabled). 08 March 2007, 00:35 UTC
b233c5a * Simplified checking in the radial direction * Removed obsolete variables in trace struct 02 March 2007, 00:09 UTC
8467ab6 Finally, exchanging tracers between processors works, at least in 12-proc cases 01 March 2007, 21:23 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 UTC
513bb8e Fixed two errors reported by icc 01 March 2007, 21:17 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 UTC
30792de Migrating the tracer code (not finished) 01 March 2007, 21:15 UTC
7f019a8 Copied from Allen McNamara's tracer code. The code will fail to compile 01 March 2007, 21:02 UTC
5e312c7 Resurrected Exchanger source. 16 February 2007, 17:44 UTC
734c621 Spherical version of the temperature solver 08 February 2007, 00:15 UTC
4f896c0 Removed the use of a new feature in python 2.4 ("substring" in "string") 08 February 2007, 00:14 UTC
9248203 Added input parameters that controlling the predictor-corrector scheme 06 February 2007, 02:23 UTC
06c809e Fixed a bug when reading coor_file in full CitcomS 06 February 2007, 02:22 UTC
d6b6188 Changed smoothing method for viscosity to be consistent with CitcomCU 06 February 2007, 02:22 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-> - E->sphere.ri)) 02 February 2007, 23:30 UTC
7350e59 Disable pid output for processors of rank>0 02 February 2007, 20:10 UTC
fdbac82 Removed spaces around the equal sign when writing pid file, which confused 31 January 2007, 20:46 UTC
c009c18 Moved Python egg stuff into our Autoconf macro library. 30 January 2007, 21:16 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 UTC
1f34cc0 Compute the 2nd invariant of strain rate tensor in spherical coordinate 30 January 2007, 19:04 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 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 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 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 UTC
fe3fb9f Write controller inventory to pid file. This is a heck! 26 January 2007, 21:32 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 UTC
8734680 Get rid of static variables 25 January 2007, 01:38 UTC
3cf8bd1 Refactoring various functions to simplify their pyre counterpart 25 January 2007, 00:57 UTC
f727da9 Fixed a bug in locating elements right above tracers 17 January 2007, 20:02 UTC
495961c Replaced 'exit(0)' with correct MPI exit, related to issue69 17 January 2007, 01:54 UTC
ccfc46d Fixed issue77 - velocity b.c not scaled correctly when age becomes negative 16 January 2007, 20:37 UTC
2ca42ed Read input parameter 'half_space_age' when tic_method=1 16 January 2007, 19:49 UTC
efe5b97 Fixed incorrect prototype 16 January 2007, 18:50 UTC
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