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Revision Author Date Message Commit Date
5e00adb Tag v3.0.2 19 June 2008, 22:48 UTC
d192381 Update ChangeLog upto r11290 07 March 2008, 19:48 UTC
d454520 Update NEWS and version number for v3.0.2 07 March 2008, 19:33 UTC
e62654f Merged revisions 11280 via svnmerge from svn+ssh://svn@geodynamics.org/cig/mc/3D/CitcomS/trunk ........ r11280 | tan2 | 2008-02-27 17:03:50 -0800 (Wed, 27 Feb 2008) | 4 lines Removed artificial tolerance of empty elements. This greatly decreases the minimal number of tracers per element required for a given mesh. This fixed issue140. ........ 28 February 2008, 20:53 UTC
7951892 Merged revisions 11219 via svnmerge from svn+ssh://svn@geodynamics.org/cig/mc/3D/CitcomS/trunk ........ r11219 | tan2 | 2008-02-20 17:01:09 -0800 (Wed, 20 Feb 2008) | 2 lines Fixed issue139. Bug for tracers near South pole. ........ 28 February 2008, 20:51 UTC
87c4530 Merged revisions 9216 via svnmerge from svn+ssh://svn@geodynamics.org/cig/mc/3D/CitcomS/trunk ........ r9216 | tan2 | 2008-02-04 12:40:45 -0800 (Mon, 04 Feb 2008) | 7 lines Fixed a regression reported by Lydia Dicaprio. The initial temperature should be constructured in this order: 1. if tic_method=-1, read from velo files. 2. if lith_age=1, read/constructed from lith_age files. 3. otherwise, call {full,regional}_construct_tic_from_input() ........ 28 February 2008, 20:46 UTC
87e7a0a Fixing Issue131: Compilation error in CitcomS-3.0.1 HDF5 support Merged revisions 8893 via svnmerge from svn+ssh://svn@geodynamics.org/cig/mc/3D/CitcomS/trunk ........ r8893 | tan2 | 2007-12-17 14:06:06 -0800 (Mon, 17 Dec 2007) | 1 line Fixed phase change width ........ 28 February 2008, 20:40 UTC
798eb0d Updated file ChangeLog to r8281. 12 November 2007, 23:03 UTC
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
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