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Revision Author Date Message Commit Date
0591133 update cookbook8 with the manual 16 April 2009, 18:23:06 UTC
487eeea Add -DUSE_HDF5 to CPPFLAGS in module/Exchanger 16 April 2009, 18:22:22 UTC
075b734 change the viscosity section to be the same as that in cookbook3. 16 April 2009, 18:21:50 UTC
2c35d25 Removed domain extents, since they are determined by coor_file. 16 April 2009, 18:20:08 UTC
a7389af Removed instructions to 'make install', 'make clean' and 'make distclean'. Added dependencies. 16 April 2009, 18:07:53 UTC
a2a39ef Fixed a bug in cgrad solver introduced in r13270. 09 April 2009, 20:53:58 UTC
7dbc76c Left debugging output in, now cleaned up 09 April 2009, 20:39:24 UTC
d5b89ca Fixed file output issue which caused vtk log file I/O to bomb during Citcom finalize. 09 April 2009, 20:37:59 UTC
9d6cfb4 Sync'ing C and Pyre and adding comments 08 April 2009, 23:39:49 UTC
971856b Added a function citcom_finalize() to close files and MPI before exit. Return 0 when the code is finished normally. Rearrang post_processing and stokes_flow_only. 08 April 2009, 23:38:51 UTC
6e42502 Clean up. 08 April 2009, 23:34:43 UTC
811838a Removed multigrid-el option of stokes solver, which is broken for a long time and not used by anyone. 08 April 2009, 23:31:11 UTC
f482a84 Moved where to call read_rayleigh_from_file() earlier. I hope this doesn't break the ray_control stuff. 08 April 2009, 23:27:51 UTC
5ab6970 Fixed bug in vtop assignment. 08 April 2009, 20:24:59 UTC
c6a6fd7 Revert the unintended modification of examples/Makefile.am 07 April 2009, 22:50:02 UTC
c5e1db6 Change the viscosity option in cookbook3 and cookbook4 07 April 2009, 22:45:32 UTC
ce1c4ce Change the mesh size in cookbook2 07 April 2009, 22:44:24 UTC
02125c8 Renamed Seismic_model.c to Mineral_physics_models.c 04 April 2009, 00:59:32 UTC
1ff1990 Fixed a few bugs in seismic output * fixed errors in the coefficient table * fixed typos * normalized drho by reference density profile * more digits in the prem radius table * added two specfem flags in PREM calculation. * "dv" output for debugging purpose, disabled. 04 April 2009, 00:57:47 UTC
795f249 Inconsisent parameters with the manual 04 April 2009, 00:52:15 UTC
9de0f51 Modified the way the compositional init with ggrd tracer can now select either a range of layers (>0) or a specific layer (<0). 28 March 2009, 02:29:00 UTC
dc9672a limiting the number of multigrid cycles in solve_del2_u(). A new input parameter solver.vsolver.max_mg_cycles (default to 50) controls the max. number of multigrid cycles when solving the velocity. Without this parameter, when the stiffness matrix is near singular, the the multigrid solver may become an infinite loop. 20 March 2009, 23:36:56 UTC
25a7493 Remove mgunitx etc from pyre input. This restores the behavior in v3.0 and earlier version. In pyre version, the mesh size is always specified by nodex etc. In C version, the mesh size is specified by nodex if Solver=cgrad, and by mgunitx and levels if Solver=multigrid. 18 March 2009, 19:39:54 UTC
04c4125 Rollback the unintended change in velo output. 17 March 2009, 23:42:01 UTC
6e50c43 Check return values of sscanf/fscanf. This fixs issue265. 17 March 2009, 00:18:09 UTC
213f078 Removed obsolete function read_previous_field() 17 March 2009, 00:17:04 UTC
c1fbc1d remove angular momentum from stokes solution by setting solver.vsolver.remove_angular_mementum=1 17 March 2009, 00:16:11 UTC
e8525af Converting temperature/composition fields to seismic velocities, in a format that specfem3d portal and v4.1 can understand. * solver.param.mineral_physics_mode: default to 3, the model of Tramper, Vacher and Vlaar's PEPI 2001. * output_optional=seismic will write coordinates and seismic velocities in binary files for specfem comsumption. * domain bounds file "datafile.domain": binary file with nproc * 10 doubles. The 10 doubles are (rmin, rmax) and four (theta, phi) pairs for the four bottom corner nodes. This file is written by rank-0 processor only. 16 March 2009, 23:17:30 UTC
ebff88c add test cases for the stokes solver under bousinessq approximation and truncated anelastic liquid approximation 16 March 2009, 22:52:08 UTC
e1f9320 seperate initialization and parameter input 16 March 2009, 22:50:06 UTC
ac6cb95 change the default of mgunit 16 March 2009, 22:44:42 UTC
8c586f0 Make the initialization step in pyre conforms to C version. This fixs a bug in r13270. 16 March 2009, 22:43:37 UTC
b655ef9 Disable HC related stuff if USE_GGRD is not set 10 March 2009, 00:58:34 UTC
aaec6e9 Changed ic flavors from 100 to 99 as per Eh's request 04 March 2009, 23:45:21 UTC
c7d458e Changed ggrd flavor init for tracers with checkpoint override from 2 to 100 as per Eh's request. 04 March 2009, 23:00:56 UTC
0085e63 Added ic_method_for_flavors=2, which works like the ggrd based tracer flavor init method ic_method_for_flavors=1 but overrides restart settings for tracers. This allows a compositional restart of a purely thermal run. 28 February 2009, 21:23:21 UTC
a9ab99d Partially back out r19268,r9272,r11215, since the AVM stuff is redesigned. 20 February 2009, 00:09:53 UTC
66ad9f1 Partially back out r11218, since the AVM stuff is redesigned. 19 February 2009, 23:46:52 UTC
c8a7398 Partially back out r11221, since the AVM stuff is redesigned. 19 February 2009, 23:41:16 UTC
edc858e Back out r11279, since the AVM stuff is redesigned. 19 February 2009, 23:35:07 UTC
f26ee7a Fixed minor bug exposed by C-to-C++ translation (r14045). 13 February 2009, 03:46:04 UTC
8e778fa Emit the warning message from a different place to get rid of static variables. Also, the macros TRUE and FALSE are undefined unless configured with GMT. 06 February 2009, 19:51:18 UTC
2dbb83a Fixed a bug in viscosity rheol=7. Bug reported by Laura Alisic. 22 December 2008, 18:48:50 UTC
e6414a7 Fixed two bugs in lg_pow(a, n), which computes a^n. One bug is when n=0, it returned a, instead of 1 Another bug is a^(n-1) was returned 19 November 2008, 06:49:04 UTC
00f2357 One more fix to zero geoid arrays 18 November 2008, 23:56:37 UTC
d11440a Zero'ed geoid arrays. 18 November 2008, 22:58:29 UTC
cd0f4b8 Patched up Ggrd_handling for velocity grids close to pole. Addded flag to suppress check of incompressibility and pressure convergence. Partially, this is because for kinematic BCs pressure will only be constrained up to a constant, partially because mixed density/plate flow models show very poor convergence, still to be checked. 18 November 2008, 06:55:46 UTC
b1d50c6 blob parameters were required even if tic_method != 2, changed such that the parameters were only read in if tic_method == 2 11 November 2008, 02:55:07 UTC
54a6331 Minor fix to allow compilation with USE_GGRD 11 November 2008, 02:48:36 UTC
3d888ba forget to check in module/setProperties.c 07 November 2008, 23:35:06 UTC
bcddb74 * Reserved 'tic_method=100' for user-defined initial temperature. * Read all parameters related to initial temperature regardless which tic_method is used. This will make the life easier when adding new tic_method. * Fixed a bug in 'tic_method=0' for regional model. The bug causes that the sinosoidal temperature perturbation is applied at 0th processor only. * Fixed a bug in 'tic_method=1' for regional model. 'tic_method=1' should generate a top TBL according to the input parameter 'half_space_age'. However, the code effectively multiply 25x to the age. Cookbook6 is using this tic_method, so its half_space_age needs to become 2500 to get the original temperature. * In 'tic_method=2', compute distance in Cartesian coordinate, instead of spherical coordinate. * Refactoring codes for temperature initial conditions. * Merged regional_construct_tic_from_input() and full_construct_tic_from_input() to construct_tic_from_input(). 07 November 2008, 23:32:20 UTC
ca13d76 Reserved 'rheol=100' for user-defined viscosity law. 07 November 2008, 23:32:00 UTC
a0d3b96 Added parameter 'use_cbf_topo' to pyre binding, default to off. 07 November 2008, 23:31:29 UTC
8ad1a60 * Added back parameters mgunitx/mgunity/mgunitz. This partly reverts r13256. * Under pyre, uses mgunitx/mgunity/mgunitz and levels to compute nodex/nodey/nodez in multigrid solver. * Merged regional_global_derived_values() and full_global_derived_values() to global_derived_values(). 07 November 2008, 23:14:19 UTC
70e5d7d Minor fix on node counting 05 November 2008, 00:19:05 UTC
00db2ff Added a missing import 04 November 2008, 22:50:02 UTC
3c39d9c zslice.py will slice opt files if present 04 November 2008, 21:02:08 UTC
629713a Removed input parameters "mgunitx", "mgunity" and "mgunitz". Their values are inferred from other parameters. Also, the code checks that "levels" > 1 when multigrid solver is used. 04 November 2008, 21:01:26 UTC
dc54393 Fixed a bug in outputting comp_el 04 November 2008, 21:00:01 UTC
4b191bb Fixed two typos, velocity norm function was called where pressure norm should have been called. This leads to core dumps, all seems to be working now. 01 November 2008, 18:37:20 UTC
f8e52fc Reporting correct nno and nel (number of nodes and elements) 31 October 2008, 20:18:13 UTC
ef7299c (for r13196) Fixing convergence criterion for Stokes solver. * New functions global_v_norm2(), global_p_norm2(), global_div_norm2() compute the L2 norm of velocity, pressure, and divergence. * The L2 norm of the vector f is defined as: \sum_{all elements} ( \int_{element} (f*f dA) ) / A where A is the volume of the domain. * The convergence criterion is controlled by parameter "accuracy" under "[CitcomS.solver.vsolver]". The iteration stops if (norm(div(rho*V))/norm(V) < accuracy) or ( (norm(dV)/norm(V) < accuracy) and (norm(dP)/norm(P) < accuracy) for the last two iterations ) * The default value of "accuracy" becomes 1e-4. * The input parameters "tole_compressibility" and "relative_err_accuracy" under "[CitcomS.solver.vsolver]" are gone. * The mass matrix E->MASS becomes double precision (was single precision). 29 October 2008, 23:22:10 UTC
2ba507e Fixed two bugs in vtk velocity output 29 October 2008, 23:17:11 UTC
f52d984 Initial test implementation of netcdf grd based assignment of designated Euler vectors based on a code grd. 23 October 2008, 23:35:27 UTC
f2bb425 multi-component chemical viscosity 04 September 2008, 22:46:39 UTC
fed8acd Fixed issue 158: incorrect E->control.fi_max with coor=1 04 September 2008, 20:18:53 UTC
e2213ae Some basic VTK parallel XML output * output in vts/pvts Structured VTK XML format * only these fields are available: coordinate, temperature, velocity and viscosity * coordinate and velocity are in Cartesian coordinates Some notes for future tasks: * adding other node- or element-based fields (pressure, stress, comp_nd, comp_el) is easy * tracer output should be in vtp format * surf, botm, and horiz_avg will be in vts format * geoid will still be as an ascii table 04 September 2008, 00:20:50 UTC
46cfb7a forgot to checkin this change in r12799 04 September 2008, 00:12:24 UTC
6ef0cc0 pyre input for "self_gravitation" 04 September 2008, 00:11:36 UTC
9eff47c self-gravitation geoid stuff * compute geoid due to internal buoyancy at the bottom * get rid of stress arrays * seperating topo effect on surface geoid into two part: surface topo and CMB topo. 04 September 2008, 00:10:51 UTC
867f7be E->viscosity.zbase_layer is not init'd in pyre version. This fixes issue 155. 24 July 2008, 18:42:45 UTC
972d8eb Both Eh and I were right and now the z_layer check should be finally fixed. 24 July 2008, 18:21:37 UTC
ccc8ab9 Fixed typo that provided assignment of zbase_layer thanks to Eh. 24 July 2008, 18:13:22 UTC
cc2e6d9 Added rheology option eight. The other merges are surprising. 24 July 2008, 01:00:16 UTC
55333fb Moved the stress computation into stress output subroutine, for consistency with the style of the Output...c files. 30 June 2008, 15:49:56 UTC
871fd84 Made CBF topography method and call to E->solver.parallel_communication_routs_s contingent on a "use_cbf_topo" parameter which is for now, by default, off, until the potential remaining memory bug (?) is tracked down. Made sure the stress tensor is computed before stress output, as CBF topo does not require the computation of the stress tensor. Added a z_layer input flag for zbase_layer other than the four layers used for the control of phase boundary depth. (Default is backward compatible.) 30 June 2008, 02:12:56 UTC
eb573f1 Check in of proper version for elliptical net rotation correction. 27 June 2008, 00:53:30 UTC
9f7396f Reordered loop in get_buoyancy to speed up array access. Fixed omission of one elliptical correction, added a flag. 26 June 2008, 23:56:32 UTC
fa90e33 Replaced several trig function evaluations in Size_does_matter.c witht he precomputed SinCos arrays for speedup. Experimental ellipticity implementation has been improved somewhat, and made accessible only when -DALLOW_ELLIPTICAL is set. This was necessary to not slow the spherical version of the code down with if statements. 26 June 2008, 23:04:06 UTC
cc26d94 Modified net rotation computation for ellipticity. Minor additions (prototypes) to make the code compile smoothly under PGI. 25 June 2008, 01:13:32 UTC
6ada82f Modified routs_s for lines. Added some debugging output and updated comments. 24 June 2008, 21:18:37 UTC
a0ca2a8 Only top/bottom processors need to communicate 24 June 2008, 21:11:18 UTC
30e6081 Assignment of velocity boundary condition only called once at the top multigrid level during boundary condition assignment. Experimental implementation of mixed velocity/free slip boundary condition based on netcdf grids, in Ggrd_handling. 21 June 2008, 22:28:51 UTC
e6aaa4d Enable CBF topography 20 June 2008, 23:01:28 UTC
9cab369 Added back get_CBF_topo(), from Shijie Zhong, with some minor modifications. Minor modifications: * some double arrays -> float arrays * calling exchange_snode_d() -> calling *_exchange_snode_f() 20 June 2008, 22:51:56 UTC
1f78588 Resurrected full_parallel_communication_routs_s(), which is needed by CBF topo. Renamed exchange_snode_f() to full_exchange_snode_f() and regional_exchange_snode_f(). 20 June 2008, 22:50:51 UTC
b0228c2 Added get_global_1d_shape_fn_L() from Shijie Zhong 20 June 2008, 22:42:30 UTC
d98cafb Compute E->L and E->Lx 1d shape functions (1d is a misnomer, they are 2d actually). 20 June 2008, 22:41:57 UTC
2e17e1d The function declaration was put at a wrong place. 20 June 2008, 19:08:03 UTC
bf432bb Change back the order of input arguments to match the manual. 19 June 2008, 22:20:07 UTC
fff43af The comment in rheol=4 doesn't match the code and is removed. Added option rheol=7, with a complete temperature- and pressure-dependent Arrhenius law. This fixed issue152. 19 June 2008, 21:43:25 UTC
c3a51e5 Added debugging (but disabled) function for spherical harmonics expansion. 19 June 2008, 21:42:27 UTC
ab74087 Send geoid arrays to vertical columns of processors. After this fix, the geoid output is the same for nprocz=1 and nprocz>1. 19 June 2008, 01:05:12 UTC
08ab04b Compute E->surf_det (top surface area, ie. surface jacobian, of an element) on a unit sphere. Use E->surf_det, instead of the surface jacobian returned by get_global_1d_shape_fn(), to expand spherical harmonics. The surface jacobian returned by get_global_1d_shape_fn() is defined at the top radius of the current mesh. When nprocz>1, the top radius is not the same as the outer radius of the sphere for processors. As a result, the spherical harmonics expansion gave incorrect result when nprocz>1 in the previous revisions. 19 June 2008, 01:04:06 UTC
d3025a8 Speed up of computation by precomputing constants. 18 June 2008, 22:35:04 UTC
2d8894e Compute geoid with self gravitation. Code contributed by Shijie Zhong. 17 June 2008, 21:23:45 UTC
de569a3 Added a few more comments and made a few loops more efficient. 17 June 2008, 20:31:30 UTC
67ed449 Added a few comments on Rayleigh number netcdf control. 14 June 2008, 00:00:58 UTC
9735d41 update NEWS item 13 June 2008, 23:36:53 UTC
d5dc9d3 Replaced MPI_COMM_WORLD by E->parallel.world. MPI_COMM_WORLD is the global communicator. E->parallel.world is the communicator for the current solver. These two are different in a coupled run. Before this fix, full-regional coupling will dead lock. 13 June 2008, 23:35:38 UTC
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