https://github.com/geodynamics/citcoms
Tip revision: 0473ed5e226f2a1bc702fb1c6f1210ee721ddc33 authored by Rene Gassmoeller on 03 November 2022, 16:37:30 UTC
Merge pull request #10 from ljhwang/patch-1
Merge pull request #10 from ljhwang/patch-1
Tip revision: 0473ed5
pasteCitcomData.py
#!/usr/bin/env python
#
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#<LicenseText>
#
# CitcomS.py by Eh Tan, Eun-seo Choi, and Pururav Thoutireddy.
# Copyright (C) 2007, 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>
#
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
'''
Paste CitcomS data together
Usage: pasteCitcomData.py datadir datafile field1,field2[,...] rank step save_dir
datadir: directory of the output files
datafile: prefix of the output files
field1, field2, ...: the fields to be pasted (e.g.: coord, velo)
rank: MPI rank of the output
step: time step of the output
save_dir: directory for the pasted file
'''
import os
def run(datadir, datafile, fields, rank, step, save_dir):
datadir = expand_datadir(datadir, rank)
outfile = '%s/%s.%s.%d.%d.pasted' % (save_dir, datafile, fields,
rank, step)
f = open(outfile, 'w')
try:
paste(datadir, datafile, fields, rank, step, f)
finally:
f.close()
return
def paste(datadir, datafile, fields, rank, step, stream=None):
if stream is None:
import sys
stream = sys.stdout
files = []
for infix in fields.split(','):
f = open_file(datadir, datafile, infix, rank, step)
strip_headerlines(f, infix)
files.append(f)
paste_files_and_write(stream, *files)
return
def expand_datadir(datadir, rank):
'''Expand the special strings in datadir
'''
##
s = "%HOSTNAME"
try:
datadir.index(s)
except: pass
else:
from socket import gethostname
datadir = datadir.replace(s, gethostname())
##
s = "%RANK"
try:
datadir.index(s)
except: pass
else:
datadir = datadir.replace(s, str(rank))
##
if datadir == "%DATADIR":
fp = os.popen("citcoms_datadir", "r")
datadir = fp.readline().strip()
fp.close()
return datadir
def open_file(datadir, datafile, infix, rank, step):
if infix == 'coord':
filename = '%s/%s.%s.%d' % (datadir, datafile, infix, rank)
else:
filename = '%s/%s.%s.%d.%d' % (datadir, datafile, infix, rank, step)
f = open(filename, 'r')
return f
def strip_headerlines(f, infix):
'''Remove the header lines from f
'''
# how many header lines for each infix
headers = {'coord': 1,
'botm': 1,
'comp_nd': 2,
'pressure': 2,
'stress': 2,
'surf': 1,
'velo': 2,
'visc': 1}
nlines = headers[infix]
for i in range(nlines):
f.readline()
return
def paste_files_and_write(stream, *files):
# zip all file iterators in one
from itertools import izip
lines = izip(*files)
# read all files simulataneously
for line in lines:
line = ' '.join([x.strip() for x in line]) + '\n'
stream.write(line)
return
if __name__ == '__main__':
import sys
if len(sys.argv) < 6:
print __doc__
sys.exit()
datadir = sys.argv[1]
datafile = sys.argv[2]
fields = sys.argv[3]
rank = int(sys.argv[4])
step = int(sys.argv[5])
save_dir = sys.argv[6]
run(datadir, datafile, fields, rank, step, save_dir)
# End of file