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#! /usr/bin/python
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
from string import *
import re
import os
import sys
from math import sqrt
findBondNamePattern = re.compile(r"^(\S+)\s+(.*)$")
bondNamePattern = re.compile(r"(.*)([-=+@#])(.*)$")
parameterPattern = re.compile(r"^([^=]+)\s*\=\s*(\S+)\s*(.*)")
idPattern = re.compile(r"(\$Id\:.*\$)")
commentPattern = re.compile("#")
leadingWhitespacePattern = re.compile(r"^\s*")
trailingWhitespacePattern = re.compile(r"\s*$")
elmnts=[("H", 1, 1.6737),
("He", 2, 6.646),
("Li", 3, 11.525),
("Be", 4, 14.964),
("B", 5, 17.949),
("C", 6, 19.925),
("N", 7, 23.257),
("O", 8, 26.565),
("F", 9, 31.545),
("Ne", 10, 33.49),
("Na", 11, 38.1726),
("Mg", 12, 40.356),
("Al", 13, 44.7997),
("Si", 14, 46.6245),
("P", 15, 51.429),
("S", 16, 53.233),
("Cl", 17, 58.867),
("Ar", 18, 66.33),
("K", 19, 64.9256),
("Ca", 20, 66.5495),
("Sc", 21, 74.646),
("Ti", 22, 79.534),
("V", 23, 84.584),
("Cr", 24, 86.335),
("Mn", 25, 91.22),
("Fe", 26, 92.729),
("Co", 27, 97.854),
("Ni", 28, 97.483),
("Cu", 29, 105.513),
("Zn", 30, 108.541),
("Ga", 31, 115.764),
("Ge", 32, 120.53),
("As", 33, 124.401),
("Se", 34, 131.106),
("Br", 35, 132.674),
("Kr", 36, 134.429),
("Ax", 200, 0.000),
("Ss", 201, 0.000),
("Sp", 202, 0.000),
]
sym2num={}
for (sym, num, mass) in elmnts:
sym2num[sym] = num
bontyp = {'-':'1', '=':'2', '+':'3','@':'a', '#':'g'}
def printBond(a1, bond, a2, parameters):
ks = float(parameters['Ks'])
r0 = float(parameters['R0'])
de = float(parameters['De'])
quality = int(parameters['Quality'])
quadratic = int(parameters['Quadratic'])
bt=sqrt(ks/(2.0*de))/10.0
r0=r0*100.0
r=r0;
b = -1;
while b < 0:
a = (r * r - r0 * r0)
b = a * a / r - 4000000 * de * r0 / ks
r = r + 0.01
if sym2num[a1] > sym2num[a2]:
e2 = a1
e1 = a2
else:
e1 = a1
e2 = a2
print ' addInitialBondStretch(%7.2f,%7.2f,%7.4f,%7.4f,%7.2f,'%(ks,r0,de,bt,r),
print '%5d, %3d, "%s-%s-%s");'%(quality, quadratic, e1, bontyp[bond], e2)
if __name__ == "__main__":
f=open(sys.argv[1])
headerPrinted = False
for lin in f.readlines():
# remove leading and trailing whitespace
lin = leadingWhitespacePattern.sub('', lin)
lin = trailingWhitespacePattern.sub('', lin)
# find RCSID
m = idPattern.search(lin)
if m:
print '#define RCSID_BONDS_H "Generated from: ' + m.group(1) + '"'
continue
# ignore comments and blank lines
if commentPattern.match(lin): continue
if len(lin) == 0: continue
m = findBondNamePattern.match(lin)
if (m):
bond = m.group(1)
rest = m.group(2)
parameters = {}
parameters['bond'] = bond
# default values for particular parameters:
parameters['Quality'] = 9
parameters['Quadratic'] = 0
# extract parameters from rest of line into dictionary
m = parameterPattern.match(rest)
while m:
key = m.group(1)
value = m.group(2)
rest = m.group(3)
parameters[key] = value
m = parameterPattern.match(rest)
m = bondNamePattern.match(bond)
if m:
if not headerPrinted:
headerPrinted = True
print '// ks r0 de beta inflectionR qual quad bondName'
printBond(m.group(1), m.group(2), m.group(3), parameters)
else:
print >> sys.stderr, 'malformed bond: ' + bond
continue
else:
print >> sys.stderr, 'unrecognized line: "' + lin + '"'
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