def geo_from_output(fname):
import re
from PyQuante.Util import parseline, cleansym
from PyQuante.Element import sym2no
from PyQuante.Molecule import Molecule
igeo = re.compile('Input geometry')
sgeo = re.compile('Symmetrized geometry')
# Double check the syntax of these last two
ngeo = re.compile('new geometry')
fgeo = re.compile('final geometry')
geo = []
file = open(fname)
while 1:
line = file.readline()
if not line: break
if igeo.search(line) or sgeo.search(line) or ngeo.search(line) \
or fgeo.search(line):
geo = []
line = file.readline()
line = file.readline()
while 1:
line = file.readline()
if len(line.split()) < 4: break
sym, x, y, z = parseline(line, 'sfff')
atno = sym2no[cleansym(sym)]
geo.append((atno, (x, y, z)))
return Molecule('jaguar molecule', geo)
def geo_from_output(fname):
import re
from PyQuante.Util import parseline,cleansym
from PyQuante.Element import sym2no
from PyQuante.Molecule import Molecule
igeo = re.compile('Input geometry')
sgeo = re.compile('Symmetrized geometry')
# Double check the syntax of these last two
ngeo = re.compile('new geometry')
fgeo = re.compile('final geometry')
geo = []
file = open(fname)
while 1:
line = file.readline()
if not line: break
if igeo.search(line) or sgeo.search(line) or ngeo.search(line) \
or fgeo.search(line):
geo = []
line = file.readline()
line = file.readline()
while 1:
line = file.readline()
if len(line.split()) < 4: break
sym,x,y,z = parseline(line,'sfff')
atno = sym2no[cleansym(sym)]
geo.append((atno,(x,y,z)))
return Molecule('jaguar molecule',geo)
def parse_atoms(atom_lines,**opts):
from PyQuante.Molecule import Molecule
atomlist = []
for line in atom_lines[1:]:
atno,x,y,z = parseline(line,'xxdfff')
atomlist.append((atno,(x,y,z)))
molopts = {}
if re.search("Angs",atom_lines[0]): molopts['units'] = 'angs'
atoms = Molecule('Molf',atomlist,**molopts)
return atoms
def split_guess_lines(guess_lines):
from PyQuante.Util import parseline
from PyQuante.NumWrap import transpose, array
import re
orbpat = re.compile('Orbital Energy')
orb = []
orbe = []
occs = []
orbs = []
for line in guess_lines:
if orbpat.search(line):
orbei, occi = parseline(line, 'xxxfxf')
orbe.append(orbei)
occs.append(occi)
orb = []
orbs.append(orb)
else:
orb.extend(map(float, line.split()))
orbs = transpose(array(orbs))
return occs, orbe, orbs
def split_guess_lines(guess_lines):
from PyQuante.Util import parseline
from PyQuante.NumWrap import transpose,array
import re
orbpat = re.compile('Orbital Energy')
orb = []
orbe = []
occs = []
orbs = []
for line in guess_lines:
if orbpat.search(line):
orbei,occi = parseline(line,'xxxfxf')
orbe.append(orbei)
occs.append(occi)
orb = []
orbs.append(orb)
else:
orb.extend(map(float,line.split()))
orbs = transpose(array(orbs))
return occs,orbe,orbs