Revision 0461d2e117ce88704a56dd8bcbf6bf7787991b15 authored by Eh Tan on 08 November 2007, 23:28:46 UTC, committed by Eh Tan on 08 November 2007, 23:28:46 UTC
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)
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  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.
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  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
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  r8197 | tan2 | 2007-10-30 14:54:14 -0700 (Tue, 30 Oct 2007) | 1 line
  
  Added the C program project_geoid to the makefile
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  r8199 | tan2 | 2007-10-30 15:29:44 -0700 (Tue, 30 Oct 2007) | 1 line
  
  Minor modification
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  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
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  r8202 | tan2 | 2007-11-01 16:33:50 -0700 (Thu, 01 Nov 2007) | 1 line
  
  Fixed an error in comment
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  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.
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  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
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  r8206 | tan2 | 2007-11-05 17:04:20 -0800 (Mon, 05 Nov 2007) | 1 line
  
  Shrank the size of sph. harm arrays
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  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()
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  r8212 | tan2 | 2007-11-06 15:17:54 -0800 (Tue, 06 Nov 2007) | 1 line
  
  Fixed a few memory errors
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  r8213 | tan2 | 2007-11-06 15:18:12 -0800 (Tue, 06 Nov 2007) | 1 line
  
  Increase vlowstep to match the default value in pyre
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  r8214 | tan2 | 2007-11-06 15:18:35 -0800 (Tue, 06 Nov 2007) | 1 line
  
  Removed unused multigrid parameters
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  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
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  r8226 | tan2 | 2007-11-07 11:51:56 -0800 (Wed, 07 Nov 2007) | 1 line
  
  Print a warning when matrix eqn solver not converging
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  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.
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  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.
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  r8235 | tan2 | 2007-11-08 11:18:26 -0800 (Thu, 08 Nov 2007) | 1 line
  
  Dereased the timestep size to reduce artifacts in advection
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  r8236 | tan2 | 2007-11-08 11:18:52 -0800 (Thu, 08 Nov 2007) | 1 line
  
  Update NEWS
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  r8237 | tan2 | 2007-11-08 11:19:12 -0800 (Thu, 08 Nov 2007) | 1 line
  
  Update the version number
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  r8241 | tan2 | 2007-11-08 13:17:14 -0800 (Thu, 08 Nov 2007) | 1 line
  
  Updated file ChangeLog to r8240
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  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.
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  r8243 | tan2 | 2007-11-08 13:38:09 -0800 (Thu, 08 Nov 2007) | 1 line
  
  Updated file ChangeLog to r8242
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  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.
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  r8245 | tan2 | 2007-11-08 14:41:31 -0800 (Thu, 08 Nov 2007) | 1 line
  
  Updated file ChangeLog to r8244
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Raw File
autocombine.py
#!/usr/bin/env python
#
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#<LicenseText>
#
# CitcomS.py by Eh Tan, Eun-seo Choi, and Pururav Thoutireddy.
# Copyright (C) 2002-2005, California Institute of Technology.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
#
#</LicenseText>
#
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

'''Automatically find the input parameters from CitcomS input file and run
'batchcombine.py'

usage: autocombine.py machinefile inputfile step1 [step2 [...] ]
'''

# default values for CitcomS input
defaults = {'output_format': 'ascii',
            'output_optional': 'surf,botm',
            'buoy_type': 1,
            'tracer_flavors': 2,
            'nprocx': 1,
            'nprocy': 1,
            'nprocz': 1,
            'nodex': 9,
            'nodey': 9,
            'nodez': 9}



def normalize_optional(output_optional):
    fields = []

    for opt in output_optional.split(','):
        ## remove the leading/trailing whitespaces
        opt = opt.strip()

        ## retain fields that are node-based
        if opt in ('pressure', 'stress', 'comp_nd'):
            fields.append(opt)


    return ','.join(fields)



if __name__ == '__main__':

    import sys
    import batchcombine as bc

    if len(sys.argv) < 4:
        print __doc__
        sys.exit(1)

    machinefile = sys.argv[1]
    inputfile = sys.argv[2]
    timesteps = [int(i) for i in sys.argv[3:]]

    # parse input
    from parser import Parser
    parser = Parser(defaults)
    parser.read(inputfile)

    datadir = parser.getstr('datadir')
    datafile = parser.getstr('datafile')
    output_format = parser.getstr('output_format')

    if output_format != 'ascii':
        print "Error: don't know how to combine the output", \
              "(output_format=%s)" % output_format
        sys.exit(1)

    output_optional = parser.getstr('output_optional')
    optional_fields = normalize_optional(output_optional)

    buoy_type = parser.getint('buoy_type')
    nflavors = parser.getint('tracer_flavors')
    if buoy_type == 0:
        ncompositions = nflavors
    elif buoy_type == 1:
        ncompositions = nflavors - 1
    else:
        print "Error: don't know how to combine the output", \
              "(buoy_type=%d)" % buoy_type
        sys.exit(1)



    nodex = parser.getint('nodex')
    nodey = parser.getint('nodey')
    nodez = parser.getint('nodez')
    ncap = parser.getint('nproc_surf')
    nprocx = parser.getint('nprocx')
    nprocy = parser.getint('nprocy')
    nprocz = parser.getint('nprocz')

    totalnodes = nprocx * nprocy * nprocz * ncap
    nodelist = bc.machinefile2nodelist(machinefile, totalnodes)

    for timestep in timesteps:
        # combining coord, velo, temp, and visc
        bc.batchcombine(nodelist, datadir, datafile, timestep,
                        nodex, nodey, nodez,
                        ncap, nprocx, nprocy, nprocz,
                        'coord,velo,visc', 0)

        # combining optional fields, if necessary
        if optional_fields:
            bc.batchcombine(nodelist, datadir, datafile, timestep,
                            nodex, nodey, nodez,
                            ncap, nprocx, nprocy, nprocz,
                            optional_fields, ncompositions)



# version
# $Id$

# End of file
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