/usr/share/pyshared/ase/data/tmxr200x.py is in python-ase 3.6.0.2515-1.
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import pprint
import re
from urllib import urlretrieve
import zipfile
import datetime
try:
from subprocess import Popen, PIPE
except ImportError:
from os import popen3
else:
def popen3(cmd):
p = Popen(cmd, shell=True, close_fds=True,
stdin=PIPE, stdout=PIPE, stderr=PIPE)
return p.stdin, p.stdout, p.stderr
import numpy as np
import ase.io
from ase.atom import Atom
from ase.atoms import Atoms
from ase.data import atomic_numbers, chemical_symbols
from ase.data import ground_state_magnetic_moments
# Transition Metals First-row (TM1R): 10.1021/ct6001187 # 32 compounds
# Transition Metals Second-row (TM2R): 10.1021/ct700178y # 19 compounds
# Transition Metals Third-row (TM3R): 10.1021/ct800172j # 25 compounds
#http://pubs.acs.org/doi/suppl/10.1021/ct6001187/suppl_file/ct6001187-file002.pdf
#http://pubs.acs.org/doi/suppl/10.1021/ct700178y/suppl_file/ct700178y-file002.pdf
#http://pubs.acs.org/doi/suppl/10.1021/ct800172j/suppl_file/ct800172j_si_001.pdf
url_root = 'http://pubs.acs.org/doi/suppl/'
journal = '10.1021'
database_files = {
'TM1R2006': {'doi': journal + '/ct6001187', 'module': 'TMXR200X_TM1R2006'},
'TM2R2007': {'doi': journal + '/ct700178y', 'module': 'TMXR200X_TM2R2007'},
'TM3R2008': {'doi': journal + '/ct800172j', 'module': 'TMXR200X_TM3R2008'},
}
database_files['TM1R2006']['pdf'] = database_files['TM1R2006']['doi'] + '/suppl_file/ct6001187-file002.pdf'
database_files['TM2R2007']['pdf'] = database_files['TM2R2007']['doi'] + '/suppl_file/ct700178y-file002.pdf'
database_files['TM3R2008']['pdf'] = database_files['TM3R2008']['doi'] + '/suppl_file/ct800172j_si_001.pdf'
def download_file(url, filename, dir='.'):
# do not mirror subdirectory structure of url
outfile = os.path.join(dir, os.path.basename(filename))
if 0: # fails, use files from disk
urlretrieve(os.path.join(url, filename), outfile)
return outfile
def read_geometries(filename, dir='.'):
txt = os.path.join(dir, filename)
fh = open(txt, 'rb')
table = fh.read()
firstsplit = '(in xyz format):' # TM1R2006 and TM2R2007
dataformat = 'xyz'
if table.find('(Gaussian archive entries):') != -1:
firstsplit = '(Gaussian archive entries):' # TM3R2008
dataformat = 'gaussian'
table = table.split(firstsplit)
table = table[1]
# remove one or two digit numbers (page numbers/numbers of atoms in xyz format)
table = re.sub('\n\d\d\n', '\n', table)
table = re.sub('\n\d\n', '\n', table)
# remove S + two digit numbers (page numbers)
table = re.sub('\nS\d\d\n', '\n', table)
# remove S + one digit (page numbers)
table = re.sub('\nS\d\n', '\n', table)
# remove empty lines
# http://stackoverflow.com/questions/1140958/whats-a-quick-one-liner-to-remove-empty-lines-from-a-python-string
table = os.linesep.join([s for s in table.splitlines() if s])
geometries = []
if dataformat == 'xyz':
# split on new lines
table = table.split('\n')
# mark compound names with ':' tags
for n, line in enumerate(table):
if not (line.find('.') != -1):
# remove method/basis set information
table[n] = table[n].replace(' BP86/qzvp', '')
table[n] = ':' + table[n] + ':'
table = '\n'.join([s for s in table])
# split into compounds
# http://simonwillison.net/2003/Oct/26/reSplit/
# http://stackoverflow.com/questions/647655/python-regex-split-and-special-character
table = re.compile('(:.*:)').split(table)
# remove empty elements
table = [l.strip() for l in table]
table = [l for l in table if len(l) > 1]
# extract compounds
for n in range(0, len(table), 2):
compound = table[n].replace(':', '').replace(' ', '_')
geometry = []
for atom in table[n+1].split('\n'):
geometry.append(Atom(symbol=atom.split()[0], position=atom.split()[1:]))
atoms = Atoms(geometry)
# set the charge and magnetic moment on the heaviest atom (better ideas?)
heaviest = max([a.get_atomic_number() for a in atoms])
heaviest_index = [a.get_atomic_number() for a in atoms].index(heaviest)
charge = 0.0
if abs(charge) > 0.0:
charges = [0.0 for a in atoms]
charges[heaviest_index] = charge
atoms.set_charges(charges)
if compound in [ # see corresponding articles
'Ti(BH4)3', # TM1R2006
'V(NMe2)4', # TM1R2006
'Cu(acac)2', # TM1R2006
'Nb(Cp)(C7H7)_Cs', # TM2R2007
'CdMe_C3v', # TM2R2007
]:
multiplicity = 2.0
else:
multiplicity = 1.0
if multiplicity > 1.0:
magmoms = [0.0 for a in atoms]
magmoms[heaviest_index] = multiplicity - 1
atoms.set_initial_magnetic_moments(magmoms)
geometries.append((compound, atoms))
elif dataformat == 'gaussian':
# remove new lines
table = table.replace('\n', '')
# fix: MeHg(Cl) written as MeHg(CN)
table = table.replace(
'MeHg(CN), qzvp (SDD/def-qzvp for metal)\\\\0,1\\Hg,0.,0.,0.1975732257',
'MeHg(Cl), qzvp (SDD/def-qzvp for metal)\\\\0,1\\Hg,0.,0.,0.1975732257')
# split on compound end marks
table = table.split('\\\@')
# remove empty elements
table = [l.strip() for l in table]
table = [l for l in table if len(l) > 1]
# extract compounds
for n, line in enumerate(table):
# split on gaussian separator '\\'
entries = line.split('\\\\')
compound = entries[2].split(',')[0].split(' ')[0]
# charge and multiplicity from gaussian archive
charge, multiplicity = entries[3].split('\\')[0].split(',')
charge = float(charge)
multiplicity = float(multiplicity)
if compound in ['Au(Me)PMe3']: # in gzmat format!
# check openbabel version (babel >= 2.2 needed)
cmd = popen3('babel -V')[1]
output = cmd.read().strip()
cmd.close()
v1, v2, v3 = output.split()[2].split('.')
v1, v2, v3 = int(v1), int(v2), int(v3)
if not (v1 > 2 or ((v1 == 2) and (v2 >= 2))):
print compound + ': skipped - version of babel does not support gzmat format'
continue # this one is given in z-matrix format
finame = compound.replace('(', '').replace(')', '') + '.orig'
foname = finame.split('.')[0] + '.xyz'
fi = open(finame, 'w')
fo = open(foname, 'w')
if 1: # how to extract zmat by hand
zmat = ['#'] # must start with gaussian input start
zmat.extend('@') # separated by newline
zmat.extend([compound])
zmat.extend('@') # separated by newline
zmat.extend([str(int(charge)) + ' ' + str(int(multiplicity))])
zmat.extend(entries[3].replace(',', ' ').split('\\')[1:])
zmat.extend('@') # atom and variable definitions separated by newline
zmat.extend(entries[4].split('\\'))
zmat.extend('@') # end with newline
for l in zmat:
fi.write(l.replace('@', '').replace('=', ' ') + '\n')
fi.close()
if 0:
# or use the whole gausian archive entry
entries = ''.join(entries)
fi.write(entries)
# convert gzmat into xyz using openbabel (babel >= 2.2 needed)
cmd = popen3('babel -i gzmat ' + finame + ' -o xyz ' + foname)[2]
error = cmd.read().strip()
cmd.close()
fo.close()
if not (error.find('0 molecules') != -1):
atoms = ase.io.read(foname)
else:
print compound + ': babel conversion failed'
continue # conversion failed
else:
positions = entries[3].replace(',', ' ').split('\\')[1:]
geometry = []
for k, atom in enumerate(positions):
geometry.append(Atom(symbol=atom.split()[0],
position=[float(p) for p in atom.split()[1:]]))
atoms = Atoms(geometry)
#
# set the charge and magnetic moment on the heaviest atom (better ideas?)
heaviest = max([a.get_atomic_number() for a in atoms])
heaviest_index = [a.get_atomic_number() for a in atoms].index(heaviest)
if abs(charge) > 0.0:
charges = [0.0 for a in atoms]
charges[heaviest_index] = charge
atoms.set_charges(charges)
if multiplicity > 1.0:
magmoms = [0.0 for a in atoms]
magmoms[heaviest_index] = multiplicity - 1
atoms.set_initial_magnetic_moments(magmoms)
geometries.append((compound, atoms))
return geometries
def pdftotext(filename):
os.system('pdftotext -raw -nopgbrk '+ filename)
return os.path.splitext(filename)[0] + '.txt'
from ase.data.gmtkn30 import format_data
def main():
if not os.path.isdir('TMXR200X'):
os.makedirs('TMXR200X')
#for database in ['TM1R2006']:
for database in database_files.keys():
fh = open(database_files[database]['module'].lower() + '.py', 'w')
fh.write('# Computer generated code! Hands off!\n')
fh.write('# Generated: ' + str(datetime.date.today()) + '\n')
fh.write('from numpy import array\n')
fh.write('data = ')
data = {} # specification of molecules
info = {} # reference/calculation info
# download structures
file = database_files[database]['pdf']
f = os.path.abspath(download_file(url_root, file, dir='TMXR200X'))
f = pdftotext(f)
geometries = read_geometries(f)
# set number of unpaired electrons and charges
no_unpaired_electrons = []
charges = []
for a in geometries:
magmom = sum(a[1].get_initial_magnetic_moments())
if magmom > 0.0:
no_unpaired_electrons.append((a[0], magmom))
charge = sum(a[1].get_charges())
if abs(charge) > 0.0:
charges.append((a[0], charge))
data = format_data(database, geometries, no_unpaired_electrons, charges)
# all constituent atoms
atoms = []
for formula, geometry in geometries:
atoms.extend(list(set(geometry.get_chemical_symbols())))
atoms=list(set(atoms))
atoms.sort()
for atom in atoms:
magmom=ground_state_magnetic_moments[atomic_numbers[atom]]
data[atom] = {
'database': database,
'name': atom,
'symbols': atom,
'magmoms': [magmom], # None or list
'charges': None, # None or list
'positions': np.array([[0.0]*3]),
}
Atom(atom, magmom=magmom)
pprint.pprint(data, stream=fh)
fh.close()
if __name__ == '__main__':
main()
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