/usr/share/votca/scripts/inverse/density_symmetrize.py is in votca-csg-scripts 1.2.4-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 | #! /usr/bin/python
#
# Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
import sys
import getopt
import os
import math
firstx = []
firsty = []
secondx = []
secondy = []
outfile = ""
options = ["adressc=", "infile=", "outfile=","help"]
try:
opts, args = getopt.getopt(sys.argv[1:], "", options)
except getopt.GetoptError, err:
# print help information and exit:
print str(err) # will print something like "option -a not recognized"
print options
sys.exit(2)
for o, a in opts:
if o == "--help":
print """%(name)s, version %(ver)s
This script symmetrizes the density around --adressc for thermodynamic force iteration
Usage: %(name)s
Allowed options:
--adressc X.X center of the adress zone (x-value)
--infile FILE input file
--outfile FILE output file
""" % {'name': os.path.basename(sys.argv[0]),'ver': '%version%'}
sys.exit(0)
elif o == "-v":
verbose = True
elif o == "--adressc":
adressc = float(a)
elif o in ("--infile"):
infile = a
elif o in ("--outfile"):
outfile = a
else:
print options
assert False, "unhandled option"
for line in open(infile,"r").readlines():
if line[0] != "@" and line[0] != "#":
values = line.split()
if float(values[0]) <= adressc:
firstx.append(float(values[0]))
firsty.append(float(values[1]))
if float(values[0]) == adressc:
secondx.append(float(values[0]))
secondy.append(float(values[1]))
else:
if len(firstx)-1-len(secondx) >= 0 and (len(firstx)-1-len(secondx)) < len (firsty):
secondx.append(float(values[0]))
secondy.append( 0.5*(firsty[len(firstx)-len(secondx)]+(float(values[1]))) )
else:
print "Warning: symmetrize_density.pl : adressc not in center of data", line
print "index", len(firstx)-len(secondx)
f = open(outfile,"w")
i=0
for x in secondx:
f.write('%15.10e %15.10e i\n' % (x, secondy[i]))
i=i+1
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