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potential_converter.py
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potential_converter.py
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#!/usr/bin/env python
import os
import sys
import argparse as ap
parser = ap.ArgumentParser(description='Potential Converter',
# epilog='something :-)',
usage='%(prog)s [options]',
fromfile_prefix_chars='@')
parser.add_argument('--version', action='version', version='%(prog)s 0.9')
parser.add_argument('-i', dest='inputfile', metavar='INPUT_FILE',
help='''Specify the name of the input file.''')
parser.add_argument('-o', dest='outputfile', metavar='OUTPUT_FILE',
help='''Specify the name of the output file.''')
parser.add_argument('--input-type', dest='inputtype', metavar='TYPE',
choices=['ancient', 'old', 'new'], default='ancient',
help='''Specify the format of the input file. Valid choices
are %(choices)s. [default: %(default)s]. "new" will
convert from new to ancient.''')
args = parser.parse_args()
pyver = sys.version_info
if pyver[0] < 2 or pyver[0] == 2 and pyver[1] < 7:
exit('ERROR: Python >= 2.7 required.')
if not args.inputfile:
exit('ERROR: no input file specified.')
elif not os.path.isfile(args.inputfile):
exit('ERROR: input file not found.')
elif not args.outputfile:
exit('ERROR: no outputfile specified.')
elif os.path.isfile(args.outputfile):
exit('ERROR: output file already exists.')
inputdir, inputfile = os.path.split(args.inputfile)
outputdir, outputfile = os.path.split(args.outputfile)
charge2elem = { 0: 'X', 1: 'H', 2: 'He', 3: 'Li', 4: 'Be', 5: 'B',
6: 'C', 7: 'N', 8: 'O', 9: 'F', 10: 'Ne', 11: 'Na',
12: 'Mg', 13: 'Al', 14: 'Si', 15: 'P', 16: 'S', 17: 'Cl',
18: 'Ar', 19: 'K', 20: 'Ca', 21: 'Sc', 22: 'Ti', 23: 'V',
24: 'Cr', 25: 'Mn', 26: 'Fe', 27: 'Co', 28: 'Ni', 29: 'Cu',
30: 'Zn', 31: 'Ga', 32: 'Ge', 33: 'As', 34: 'Se', 35: 'Br',
36: 'Kr', 37: 'Rb', 38: 'Sr', 39: 'Y', 40: 'Zr', 41: 'Nb',
42: 'Mo', 43: 'Tc', 44: 'Ru', 45: 'Rh', 46: 'Pd', 47: 'Ag',
48: 'Cd', 49: 'In', 50: 'Sn', 51: 'Sb', 52: 'Te', 53: 'I',
54: 'Xe', 55: 'Cs', 56: 'Ba', 57: 'La', 58: 'Ce', 59: 'Pr',
60: 'Nd', 61: 'Pm', 62: 'Sm', 63: 'Eu', 64: 'Gd', 65: 'Tb',
66: 'Dy', 67: 'Ho', 68: 'Er', 69: 'Tm', 70: 'Yb', 71: 'Lu',
72: 'Hf', 73: 'Ta', 74: 'W', 75: 'Re', 76: 'Os', 77: 'Ir',
78: 'Pt', 79: 'Au', 80: 'Hg', 81: 'Tl', 82: 'Pb', 83: 'Bi',
84: 'Po', 85: 'At', 86: 'Rn', 87: 'Fr', 88: 'Ra'}
elem2charge = {v:k for k, v in charge2elem.items()}
au2aa = 0.5291772108
if args.inputtype == 'ancient':
fin = open('{}'.format(args.inputfile), 'r')
line = fin.readline().split()
unit = line[0]
line = fin.readline().split()
nsites = int(line[0])
mulorder = int(line[1])
polorder = int(line[2])
lexlst = int(line[3])
if len(line) == 5:
lelems = 1
elif len(line) == 4:
lelems = 0
elems = []
coords = []
M0s = []
M1s = []
M2s = []
M3s = []
M4s = []
M5s = []
alphas = []
exclists = []
if mulorder == 5:
pad = 56
elif mulorder == 4:
pad = 35
elif mulorder == 3:
pad = 20
elif mulorder == 2:
pad = 10
elif mulorder == 1:
pad = 4
elif mulorder == 0:
pad = 1
for line in fin:
line = line.split()
if not line:
continue
exclists.append(map(int, line[0:lexlst]))
coords.append(map(float, line[lexlst+lelems:lexlst+lelems+3]))
if lelems == 1:
elems.append(int(line[lexlst]))
elif lelems == 0:
elems.append(0)
if mulorder >= 0:
M0s.append(float(line[lexlst+lelems+3]))
if mulorder >= 1:
M1s.append(map(float, line[lexlst+lelems+4:lexlst+lelems+7]))
if mulorder >= 2:
M2s.append(map(float, line[lexlst+lelems+7:lexlst+lelems+13]))
if mulorder >= 3:
M3s.append(map(float, line[lexlst+lelems+13:lexlst+lelems+23]))
if mulorder >= 4:
M4s.append(map(float, line[lexlst+lelems+23:lexlst+lelems+38]))
if mulorder >= 5:
M5s.append(map(float, line[lexlst+lelems+38:lexlst+lelems+59]))
if polorder == 1:
isoalpha = float(line[lexlst+lelems+3+pad])
alphas.append([isoalpha, 0.0, 0.0, isoalpha, 0.0, isoalpha])
elif polorder == 2:
start = lexlst+lelems+pad+3
end = lexlst+lelems+pad+9
alphas.append(map(float, line[start:end]))
fin.close()
if unit == 'AU':
coords = [[elem * au2aa for elem in coord] for coord in coords]
ndec = len(str(nsites))
body = '@COORDINATES\n'
body += '{}\n'.format(nsites)
body += 'AA\n'
for i, coord in enumerate(coords):
body += '{0} {1[0]:14.8f} {1[1]:14.8f} {1[2]:14.8f}\n'.format(charge2elem[elems[i]], coord)
if mulorder >= 0:
body += '@MULTIPOLES\n'
if mulorder >= 0:
body += 'ORDER 0\n'
body += '{0}\n'.format(nsites)
for i, M0 in enumerate(M0s):
body += '{0:{1}d} {2:14.8f}\n'.format(i+1, ndec, M0)
if mulorder >= 1:
body += 'ORDER 1\n'
body += '{0}\n'.format(nsites)
for i, M1 in enumerate(M1s):
body += '{0:{1}d}'.format(i+1, ndec)
for j in range(3):
body += ' {0:14.8f}'.format(M1[j])
body += '\n'
if mulorder >= 2:
body += 'ORDER 2\n'
body += '{0}\n'.format(nsites)
for i, M2 in enumerate(M2s):
body += '{0:{1}d}'.format(i+1, ndec)
for j in range(6):
body += ' {0:14.8f}'.format(M2[j])
body += '\n'
if mulorder >= 3:
body += 'ORDER 3\n'
body += '{0}\n'.format(nsites)
for i, M3 in enumerate(M3s):
body += '{0:{1}d}'.format(i+1, ndec)
for j in range(10):
body += ' {0:14.8f}'.format(M3[j])
body += '\n'
if mulorder >= 4:
body += 'ORDER 4\n'
body += '{0}\n'.format(nsites)
for i, M4 in enumerate(M4s):
body += '{0:{1}d}'.format(i+1, ndec)
for j in range(15):
body += ' {0:14.8f}'.format(M4[j])
body += '\n'
if mulorder >= 5:
body += 'ORDER 5\n'
body += '{0}\n'.format(nsites)
for i, M5 in enumerate(M5s):
body += '{0:{1}d}'.format(i+1, ndec)
for j in range(21):
body += ' {0:14.8f}'.format(M5[j])
body += '\n'
if polorder >= 1:
body += '@POLARIZABILITIES\n'
body += 'ORDER 1 1\n'
body += '{0}\n'.format(nsites)
for i, alpha in enumerate(alphas):
body += '{0:{1}d}'.format(i+1, ndec)
for j in range(6):
body += ' {0:14.8f}'.format(alpha[j])
body += '\n'
if exclists:
body += 'EXCLISTS\n'
body += '{0} {1}\n'.format(nsites, lexlst)
for i, exclist in enumerate(exclists):
for ex in exclist:
body += ' {0:{1}}'.format(ex, ndec)
body += '\n'
body += '\n'
elif args.inputtype == 'old':
fin = open('{}'.format(args.inputfile), 'r')
oldpot = fin.readlines()
fin.close()
body = ""
read_num_atoms = False
exclist_nums = False
for i in oldpot:
if i[0] == "!":
body += i
elif "coordinates" in i:
body += "@COORDINATES\n"
read_num_atoms = True
elif "monopoles" in i:
body += "@MULTIPOLES\nORDER 0\n"
elif "dipoles" in i:
body += "ORDER 1\n"
elif "quadrupoles" in i:
body += "ORDER 2\n"
elif "alphas" in i:
body += "@POLARIZABILITIES\nORDER 1 1\n"
elif "exclists" in i or "exlists" in i:
exclist_nums = True
body += "EXCLISTS\n"
elif read_num_atoms:
num_atoms = i.split()[0]
body += i
read_num_atoms = False
elif exclist_nums:
body += "{0} {1}\n".format(num_atoms, i.split()[0])
exclist_nums = False
else:
body += i
elif args.inputtype == "new":
# at the moment rather stupid.
# will only work if all sites have all properties.
fin = open('{}'.format(args.inputfile), 'r')
newpot = fin.readlines()
fin.close()
exclist , read_exclist = [], False
coord , read_coord = [], False
monopoles , read_monopoles = [], False
dipoles , read_dipoles = [], False
quadrupoles , read_quadrupoles = [], False
alphas , read_alphas = [], False
skip_one, skip_two, read_num, read_excnum = False, False, False, False
for i in newpot:
if skip_one:
skip_one = False
elif skip_two:
skip_two = False
skip_one = True
elif read_exclist:
exclist.append(i)
k += 1
if k == num_atoms:
read_exclist = False
k = 0
elif read_coord:
coord.append(i)
k += 1
if k == num_atoms:
read_coord = False
k = 0
elif read_monopoles:
monopoles.append(i)
k += 1
if k == num_atoms:
read_monopoles = False
k = 0
elif read_dipoles:
dipoles.append(i)
k += 1
if k == num_atoms:
read_dipoles = False
k = 0
elif read_quadrupoles:
quadrupoles.append(i)
k += 1
if k == num_atoms:
read_quadrupoles = False
k = 0
elif read_alphas:
alphas.append(i)
k += 1
if k == num_atoms:
read_alphas = False
k = 0
elif "@COORDINATES" in i:
read_num = True
elif "EXCLISTS" in i:
read_excnum = True
k = 0
elif "@POLARIZABILITIES" in i:
skip_two = True
read_alphas = True
elif "ORDER 2" in i:
skip_one = True
read_quadrupoles = True
elif "ORDER 1" in i:
skip_one = True
read_dipoles = True
elif "ORDER 0" in i:
skip_one = True
read_monopoles = True
elif read_num:
num_atoms = int(i.split()[0])
skip_one = True
read_coord = True
read_num = False
k = 0
elif read_excnum:
exc_num = int(i.split()[1])
read_excnum = False
read_exclist = True
body = "AA\n {0} 2 2 {1} 1\n".format(num_atoms,exc_num)
for i in range(len(coord)):
a = exclist[i].replace('\n','')
b = "{0}".format(elem2charge[coord[i].split()[0]])
c = " ".join(coord[i].split()[1:])
d = " ".join(monopoles[i].split()[1:])
e = " ".join(dipoles[i].split()[1:])
f = " ".join(quadrupoles[i].split()[1:])
g = " ".join(alphas[i].split()[1:])
line = " ".join([a,b,c,d,e,f,g])
body += line + "\n"
fout = open('{}'.format(args.outputfile), 'w')
fout.write(body)
fout.close()