def read(self, filename='trajectory.vmol', position=0):
"""Read atom configurations of step position"""
self.file = None
f = open(filename)
# find coordinates
loa = Cluster([])
coords = False
for l in f.readlines():
if coords:
w = l.split()
loa.append(Atom(w[3].replace ("\n", "" ),
(float(w[0]), float(w[1]), float(w[2]))))
def read(self, filename='trajectory.vmol', position=0):
"""Read atom configurations of step position"""
self.file = None
f = open(filename)
# find coordinates
loa = Cluster([])
coords = False
for l in f.readlines():
if coords:
w = l.split()
loa.append(Atom(w[3].replace("\n", ""),
(float(w[0]), float(w[1]), float(w[2]))))
def read_viewmol(self, filename):
f = open(filename)
# read the definition first
definition=False
for line in f:
w = line.split()
if not definition:
if w[0] == '$coord':
definition=True
self.scale = float(w[1])
loa = Cluster([])
else:
if w[0] == '$grad':
# definition ends here
self.definition = loa
break
else:
# we assume this is a coordinate entry
coo = (float(w[0]), float(w[1]), float(w[2]))
loa.append(Atom(w[3], coo))
# get the iterations
cycle = False
for line in f:
w = line.split()
if not cycle:
# search for the cycle keyword
if w[0] == 'cycle=':
cycle=True
n_coo=0
n_F=0
self.images.append(Cluster([]))
else:
if n_coo < len(self.definition):
n_coo += 1
coo = (float(w[0]), float(w[1]), float(w[2]))
self[-1].append(Atom(w[3], coo))
elif n_F < len(self.definition):
F = (float(w[0]), float(w[1]), float(w[2]))
self[-1][n_F].F = F
n_F += 1
if n_F == len(self.definition):
cycle=False
def read_viewmol(self, filename):
f = open(filename)
# read the definition first
definition = False
for line in f:
w = line.split()
if not definition:
if w[0] == '$coord':
definition = True
self.scale = float(w[1])
loa = Cluster([])
else:
if w[0] == '$grad':
# definition ends here
self.definition = loa
break
else:
# we assume this is a coordinate entry
coo = (float(w[0]), float(w[1]), float(w[2]))
loa.append(Atom(w[3], coo))
# get the iterations
cycle = False
for line in f:
w = line.split()
if not cycle:
# search for the cycle keyword
if w[0] == 'cycle=':
cycle = True
n_coo = 0
n_F = 0
self.images.append(Cluster([]))
else:
if n_coo < len(self.definition):
n_coo += 1
coo = (float(w[0]), float(w[1]), float(w[2]))
self[-1].append(Atom(w[3], coo))
elif n_F < len(self.definition):
F = (float(w[0]), float(w[1]), float(w[2]))
self[-1][n_F].F = F
n_F += 1
if n_F == len(self.definition):
cycle = False
"""Test Hirshfeld for spin/no spin consitency"""
from ase import Atom
from gpaw import GPAW
from ase.parallel import parprint
from gpaw.analyse.hirshfeld import HirshfeldPartitioning
from gpaw import FermiDirac
from gpaw.cluster import Cluster
from gpaw.test import equal
h = 0.25
box = 3
atoms = Cluster()
atoms.append(Atom('H'))
atoms.minimal_box(box)
volumes = []
for spinpol in [False, True]:
calc = GPAW(h=h,
occupations=FermiDirac(0.1, fixmagmom=True),
experimental={'niter_fixdensity': 2},
spinpol=spinpol)
calc.calculate(atoms)
volumes.append(HirshfeldPartitioning(calc).get_effective_volume_ratios())
parprint(volumes)
equal(volumes[0][0], volumes[1][0], 4e-9)
