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c2f28aa Merged revisions 8173-8193,8198,8200,8203,8208-8211,8216-8225,8229-8234,8238-8240,8246-8274,8276-8280 via svnmerge from svn+ssh://svn@geodynamics.org/cig/mc/3D/CitcomS/trunk ........ r8278 | tan2 | 2007-11-12 14:38:36 -0800 (Mon, 12 Nov 2007) | 1 line Added mishing header file to the makefile, also avoided compiling unused code. ........ r8279 | tan2 | 2007-11-12 14:42:56 -0800 (Mon, 12 Nov 2007) | 1 line Updated the version number and file NEWS ........ 12 November 2007, 22:50 UTC
4cab4ca Blocked revisions 8275 via svnmerge ........ r8275 | becker | 2007-11-11 12:37:22 -0800 (Sun, 11 Nov 2007) | 3 lines Synching with the new release, none of those changes should be relevant. ........ 12 November 2007, 22:49 UTC
0461d2e Merged revisions 8194-8245 via svnmerge from svn+ssh://svn@geodynamics.org/cig/mc/3D/CitcomS/trunk ........ r8194 | tan2 | 2007-10-30 14:49:58 -0700 (Tue, 30 Oct 2007) | 1 line Compute d(rho)/dr/rho from rho(r) ........ r8195 | tan2 | 2007-10-30 14:50:52 -0700 (Tue, 30 Oct 2007) | 1 line Fixed a bug in dimensionalizing density. Provided the formula of geoid calculation in the comments. Rearranged the order of functions. ........ r8196 | tan2 | 2007-10-30 14:53:50 -0700 (Tue, 30 Oct 2007) | 1 line A post-processing program to project geoid coefficents onto a regular (longitude, latitude) mesh ........ r8197 | tan2 | 2007-10-30 14:54:14 -0700 (Tue, 30 Oct 2007) | 1 line Added the C program project_geoid to the makefile ........ r8199 | tan2 | 2007-10-30 15:29:44 -0700 (Tue, 30 Oct 2007) | 1 line Minor modification ........ r8201 | tan2 | 2007-11-01 16:33:30 -0700 (Thu, 01 Nov 2007) | 1 line Print dv/v=dp/p=1.0 for the 1st Uzawa iteraion ........ r8202 | tan2 | 2007-11-01 16:33:50 -0700 (Thu, 01 Nov 2007) | 1 line Fixed an error in comment ........ r8204 | tan2 | 2007-11-05 17:03:35 -0800 (Mon, 05 Nov 2007) | 1 line Scaled topo with variable gravity. Fixed an error in comment. Rearranged computation. ........ r8205 | tan2 | 2007-11-05 17:03:55 -0800 (Mon, 05 Nov 2007) | 1 line Removed functions related sph. harm in lib/Regional_obsolete.c ........ r8206 | tan2 | 2007-11-05 17:04:20 -0800 (Mon, 05 Nov 2007) | 1 line Shrank the size of sph. harm arrays ........ r8207 | tan2 | 2007-11-05 17:04:43 -0800 (Mon, 05 Nov 2007) | 1 line Init'd some variables about vtk_io, which might be accessed with uninit'd values in output_finalize() ........ r8212 | tan2 | 2007-11-06 15:17:54 -0800 (Tue, 06 Nov 2007) | 1 line Fixed a few memory errors ........ r8213 | tan2 | 2007-11-06 15:18:12 -0800 (Tue, 06 Nov 2007) | 1 line Increase vlowstep to match the default value in pyre ........ r8214 | tan2 | 2007-11-06 15:18:35 -0800 (Tue, 06 Nov 2007) | 1 line Removed unused multigrid parameters ........ r8215 | tan2 | 2007-11-06 15:18:54 -0800 (Tue, 06 Nov 2007) | 1 line Added cgrad solver convergence parameters, increased buoyancy_ratio and lower the # of steps ........ r8226 | tan2 | 2007-11-07 11:51:56 -0800 (Wed, 07 Nov 2007) | 1 line Print a warning when matrix eqn solver not converging ........ r8227 | tan2 | 2007-11-07 11:52:17 -0800 (Wed, 07 Nov 2007) | 1 line Removed comp_el from default output, since it is not required for restart anymore. ........ r8228 | tan2 | 2007-11-07 11:52:39 -0800 (Wed, 07 Nov 2007) | 1 line Decreased the # of processors. This is the only way I can reproduce single-cell convection as in the manual. ........ r8235 | tan2 | 2007-11-08 11:18:26 -0800 (Thu, 08 Nov 2007) | 1 line Dereased the timestep size to reduce artifacts in advection ........ r8236 | tan2 | 2007-11-08 11:18:52 -0800 (Thu, 08 Nov 2007) | 1 line Update NEWS ........ r8237 | tan2 | 2007-11-08 11:19:12 -0800 (Thu, 08 Nov 2007) | 1 line Update the version number ........ r8241 | tan2 | 2007-11-08 13:17:14 -0800 (Thu, 08 Nov 2007) | 1 line Updated file ChangeLog to r8240 ........ r8242 | tan2 | 2007-11-08 13:36:55 -0800 (Thu, 08 Nov 2007) | 1 line Removed binary checkpoint files from makefile, as the file size is too big for distribution. ........ r8243 | tan2 | 2007-11-08 13:38:09 -0800 (Thu, 08 Nov 2007) | 1 line Updated file ChangeLog to r8242 ........ r8244 | tan2 | 2007-11-08 14:31:21 -0800 (Thu, 08 Nov 2007) | 1 line Replaced a system call by std C library remove() and disabled another system call (backup input file). Partially fixed issue130. All remaining system calls are in lib/Output_gzdir.c. ........ r8245 | tan2 | 2007-11-08 14:41:31 -0800 (Thu, 08 Nov 2007) | 1 line Updated file ChangeLog to r8244 ........ 08 November 2007, 23:28 UTC
a828fa9 Initialized merge tracking via "svnmerge" with revisions "1-8172" from svn+ssh://svn@geodynamics.org/cig/mc/3D/CitcomS/trunk 08 November 2007, 23:25 UTC
66cf530 Branch for v3.0 maintenance 22 October 2007, 20:59 UTC
8102449 Updated file ChangeLog to r8170 22 October 2007, 20:57 UTC
26c3d4a Updated NEWS 22 October 2007, 20:26 UTC
a05de44 Minor update 22 October 2007, 19:46 UTC
7823da3 Simpilify INSTALL 22 October 2007, 19:44 UTC
4832d3d Eliminated unnecessary computation 22 October 2007, 19:03 UTC
e8a9d98 Variable material properties in latent heat correction on adiabatic cooling 22 October 2007, 19:03 UTC
5b2e55b Added some comments 22 October 2007, 19:02 UTC
a27d3c6 Renamed control.width* -> control.inv_width* for clarity 19 October 2007, 19:24 UTC
88a2e23 Renamed coupler inventory: dimensional -> si_unit and transformational -> cartesian 18 October 2007, 18:53 UTC
f614f83 Minor change in the examples 17 October 2007, 22:44 UTC
25c9b53 Added comments on where C code is replaced by python code in Citcom.c 17 October 2007, 20:56 UTC
8d2bbbe Put the rest of r8111 back 17 October 2007, 20:55 UTC
9676e09 Fixed input diffusivity parameter in the examples, from r8111. 17 October 2007, 20:33 UTC
69e4ad8 Added back minor modification from r8111 17 October 2007, 20:32 UTC
7732890 Fixed a typo in the example 17 October 2007, 18:40 UTC
6a8e4b5 Fixed a bug in remove_rigid_rot() 17 October 2007, 18:36 UTC
93471fe Roll back r8111, reading velo files for init. temperature stays as tic_method=-1. Other changes in r8111 will be put back later. 17 October 2007, 18:35 UTC
1602d87 Fixed rigid rotation code bug. Added restart=2 option which will not use checkpoints, but tic_method=-1 style temperature input (formally realized via tic_method=-1, but this should be cleaner) fixed input diffusivity parameter in full example file. 13 October 2007, 19:07 UTC
334bd72 Turn off monitor_max_T in the test 12 October 2007, 20:24 UTC
fdf7f72 Boundary class is for regional model only, add a checking for it. 12 October 2007, 20:23 UTC
17b3276 Cookbook 9: nested solver coupling + coor_refine + tsolver tuning 11 October 2007, 01:23 UTC
0f0b81a Wiser now, commented in the E->fp output 11 October 2007, 00:03 UTC
4af480b Added coor=3 option for radial node spacing a la CitcomCU. Streamlined ggrd temperature init. Added file flush to heat flow output. 10 October 2007, 23:40 UTC
9c14928 Add an assertion 10 October 2007, 21:00 UTC
3c5bee2 Remove rigid body rotation from the velocity solution from global model. A input parameter 'solver.vsolver.remove_rigid_rotation', default to on, indicate whether to remove the rigid body rotation. For free-slip model, this parameter should be on. For model with imposed plate velocity, it is advised to turn off this parameter. 10 October 2007, 20:11 UTC
ee814bc Renamed excludeTop -> exclude_top, and excludeBottom -> exclude_bottom. (No other CitcomS parameter uses CamelCase.) Reworked the interaction of initial temperature and coupling. Created a new parameter exchange_initial_temperature. 05 October 2007, 20:02 UTC
b0f818a Strengthen the default convergence criterion for the 3rd iteration in compressible cg solver 05 October 2007, 20:00 UTC
72ad845 Disable a debugging output 05 October 2007, 19:58 UTC
4bcf0ad Add licence text to the multi-couplers 05 October 2007, 19:58 UTC
820d139 Turn off filter_temp by default since it's not in the energy equation 05 October 2007, 19:57 UTC
4e87245 Fxied material assignment bug in PDEPV (0 vs. 1 array issue...) 04 October 2007, 19:35 UTC
cc73a80 Updated the cookbook scripts 01 October 2007, 20:38 UTC
f4f2b13 Added Cookbook8 for compressible model + geoid + checkpoint + vsolver tuning 01 October 2007, 19:26 UTC
ae31e95 Fixed restart I/O bug in Output_gzdir. 28 September 2007, 23:36 UTC
e429e26 Added function prototype and fixed a few errors 27 September 2007, 19:33 UTC
a79e4a9 Shrink the size of checkpoint files 27 September 2007, 19:07 UTC
02acf94 Enable coor_refine for regional model, only radial coordinate is refined 27 September 2007, 19:07 UTC
e29d3c2 Fixed a bug in vtkio 25 September 2007, 19:40 UTC
f392355 Introducing choice of reference state: When solver.param.reference_state=0, the reference state is read from a file (solver.param.refstate_file) When solver.param.reference_state=1 (default), the reference state is calculated using Adams-Williamson equation of state. 25 September 2007, 01:31 UTC
4170440 Detect the presence of libz and enable ascii-gz at configure time 24 September 2007, 21:29 UTC
95c453f Comment out varialbe thermal conductivity. Removed unused struct members. 24 September 2007, 21:28 UTC
e4cd242 Multiply rho*cp to DT/dt 24 September 2007, 21:28 UTC
6a4ff8e Don't write to log file, since only rank-0 proc can access it 19 September 2007, 20:34 UTC
37b7dd0 Set default value for tracer/composition flags earlier 19 September 2007, 20:34 UTC
a3387ca Shrink the size of arrays 19 September 2007, 20:33 UTC
3488a3f Shrink the size of arrays 19 September 2007, 20:31 UTC
37e37f8 Fixed uninit'd heat flux and geoid arrays bugs, as reported by valgrind 19 September 2007, 20:30 UTC
dec899b Minor bug fix in Output_gzidir, output_heating function didn't work. 19 September 2007, 00:28 UTC
c89da81 Fixed a memory bug in checkpoint 18 September 2007, 23:08 UTC
995fff8 Setup composition for regional model 18 September 2007, 23:07 UTC
f23ffbf Fix for Issue129: "CitcomS configured without exchanger still links with -lExchanger". Also, use CIT_HEADER_MPI so that configuring --with-exchanger using MPICH2 works (see Issue14 and Issue57). 18 September 2007, 01:52 UTC
a2fd2a4 Generalized init. composition from neighbors for multi-component composition 17 September 2007, 20:30 UTC
c10e388 Using neighboring elements to determine the initial composition, if only a few elements are empty. 17 September 2007, 19:07 UTC
e1af673 Revert accidental commit in part of r7957 15 September 2007, 00:17 UTC
94cd779 Rearranged computation of latent heat and the test condition of phase change 14 September 2007, 23:39 UTC
fedce4a Added the contribution of latent heat to the diffusion term 14 September 2007, 23:11 UTC
ffe1a6f Replace abs() by fabs() 14 September 2007, 23:11 UTC
d4bc483 Consevert energy (sum of rho*cp*T) instead of temperature (sum of T) in the Lenardic filter, also fixed a long-standing bug (abs -> fabs) 14 September 2007, 23:10 UTC
d13bdd5 Changed the magic numbers (0.0 and 1.0) to const variables, reindent the code. 14 September 2007, 23:09 UTC
9189bab Comment out adiabatic temperature profile for now, since it is not used in the code. 13 September 2007, 22:36 UTC
fcd95c8 Fixed a problem when the input string is empty 12 September 2007, 19:24 UTC
249d790 Added heating file to optional output 12 September 2007, 19:24 UTC
cb39951 Keep the load vector intact in the bicg solver 12 September 2007, 19:24 UTC
0b02b96 Using drand48() instead of rand() to improve the quality of random tracers. Added some debugging output if the tracer count is low. 12 September 2007, 19:23 UTC
f8219a2 Add new input boolean parameter 'itracer_warnings'. Default to on. When it is off, the exit condition of tracer is relaxed. 12 September 2007, 19:22 UTC
6b934e2 Removed the test for F=0 load vector bug. The bug was fixed in r7940. 12 September 2007, 19:19 UTC
d6e4a43 Fixed tsolver. Fixed a bug in TMass and another in convert element # to nz. 07 September 2007, 22:53 UTC
0d53949 Fixed a few memory problems. Shrink the size of several arrays related to Stokes eqn. Moved jacobi() to Obsolete.c 05 September 2007, 22:35 UTC
7273549 Forgot to update surfacee_tem 05 September 2007, 22:21 UTC
c77dfd0 Set the min of 2nd strain rate invariant to 1e-16 to prevent infinite viscosity when SDEPV=on 05 September 2007, 22:20 UTC
681786d Init'd timestep variables 05 September 2007, 22:20 UTC
e3ccb79 Added test for F=0 load vector bug, moved open_qfiles to after set_elapsed time. 04 September 2007, 23:09 UTC
e3f6845 Forgot to update the makefile 29 August 2007, 23:50 UTC
4b3831f Removed unused velocity bc files 29 August 2007, 23:39 UTC
f0d9ebe Restructing the repository layout for CitcomS documentation 29 August 2007, 23:18 UTC
e06f544 Forgot to update r7902 29 August 2007, 20:55 UTC
3711a41 Replaced output_open() with output_open_mode() Append the log and time files if restarting 29 August 2007, 20:48 UTC
a981bca Minor fix 29 August 2007, 20:47 UTC
d1f0b86 Missed to merge one modification after the conflict. 29 August 2007, 01:46 UTC
13492bf When checking in my changes, I had to resolve a conflict for lib/Instructions.c by hand, which I hope I did properly. Here are my changes: - renamed CONTOL structure members ORTHO and ORTHOZ to CITCOM_ORTHO and CITCOM_ORTHOZ Those were never used and conflicted with definitions in GMT gmt.h - Added a higher frequency heat flow output option like so: write_q_files=1 # option to write heat flux to files qt.dat and qb.dat # at intervals smaller than storage_spacing (0) - Added the capability to read in initial temperatures from netcdf grd files, if -USE_GGRD is used. Lot of options, like so: # # read initial temperature conditions from grd files (default values in parentheses) # tic_method=4 # read initial temperature from netcdf GRD files (off) ggrd_tinit_scale_with_prem=off # scale the temperature with PREM densities (off) ggrd_tinit_scale=1.0 # scaling factor to apply to read in scalars f (1.0) ggrd_tinit_offset=-0.5 # offset, T = f * scale + offset + tm (0.0) # where tm is the mean between top and bottom TBC values # if the bottom is flux, will use 1 for bottom TBC value ggrd_tinit_gfile="../../data/tomography/s20a_smean_new_age/t" # prefix of grd files, will # try to read t.1.grd, t.2.grd ... t.n.grd # where n is the number of layers in the depth file ggrd_tinit_dfile="../../data/tomography/s20a_smean_new_age/tdepth.dat" # file with layer depths in km from bottom up ggrd_tinit_prem_file="../../progs/src/hc-svn/prem/prem.dat" # PREM data file ggrd_tinit_override_tbc=on # override temperature boundary conditions (off) 29 August 2007, 00:51 UTC
3ba2a04 Defaulting datadir_old to the current directory 28 August 2007, 01:10 UTC
220393d Added various heating term to the energy equation. A new input parameter: solver.surfaceT for non-dimensional surface temperature. Removed old (and unused) input parameter: solver.const.surf_temp. 28 August 2007, 01:09 UTC
557acb3 Fixed a index bug in stokes solver 27 August 2007, 19:34 UTC
8347039 Add pyre input for new parameters introduced by TWB 27 August 2007, 19:34 UTC
1a41a1d Clean up the code and declared function prototypes to avoid compiler warnings 27 August 2007, 19:34 UTC
12591d6 Compute total visc and adi heating 23 August 2007, 20:20 UTC
fce4d3d Minor refactoring 23 August 2007, 20:19 UTC
4bc0ea7 Compute phase change wrt reference density and gravity profiles. 23 August 2007, 20:18 UTC
d0098c3 Avoid reading unused input parameters 23 August 2007, 20:18 UTC
1268a26 assert solver.tsolver.monitor_max_T is off in coupled run and remove debugging output 23 August 2007, 20:17 UTC
ae9b86a Renamed E->control.filter_temperature to E->advection.filter_temperature 23 August 2007, 20:16 UTC
8233668 Added new input parameter solver.tsolver.monitor_max_T When it is on (default), if the max temperature changes too much between timestep, the temperature field is restored at the tsolver is called using half of the timestep size. 23 August 2007, 20:16 UTC
447f924 Removed unused var. in struct advection 23 August 2007, 20:15 UTC
80a070b A new way to compute TMass 23 August 2007, 20:14 UTC
6d31d51 Minor refactoring: add comments, rename variables 23 August 2007, 20:14 UTC
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