def check_output(fn_h5, grp_name, overwrite):
'''Check if the output is already present in print a warning if --overwrite is not used
**Arguments:**
fn_h5
The output HDF5 file
grp_name
The HDF5 group in which the output is stored.
overwrite
Whether the user wants to overwrite contents that were already
present.
'''
if os.path.isfile(fn_h5):
with LockedH5File(fn_h5, 'r') as f:
if grp_name in f and len(f[grp_name]) > 0:
if overwrite:
if log.do_warning:
log.warn('Overwriting the contents of "%s" in the file "%s".' % (grp_name, fn_h5))
return False
else:
if log.do_warning:
log.warn('Skipping because the group "%s" is already present in the file "%s" and it is not empty.' % (grp_name, fn_h5))
return True
return False
def do_hartree_decomposition(self):
if not self.local:
if log.do_warning:
log.warn(
'Skipping hartree decomposition because no local grids were found.'
)
return
for index in xrange(self.natom):
key = ('hartree_decomposition', index)
if key not in self.cache:
self.do_density_decomposition()
if log.do_medium:
log('Computing hartree decomposition for atom %i' % index)
density_decomposition = self.cache.load(
'density_decomposition', index)
rho_splines = [
spline for foo, spline in sorted(
density_decomposition.iteritems())
]
v_splines = solve_poisson_becke(rho_splines)
hartree_decomposition = dict(
('spline_%05i' % j, spline)
for j, spline in enumerate(v_splines))
self.cache.dump(key, hartree_decomposition, tags='o')
def do_density_decomposition(self):
if not self.local:
if log.do_warning:
log.warn(
'Skipping density decomposition because no local grids were found.'
)
return
for index in xrange(self.natom):
atgrid = self.get_grid(index)
assert isinstance(atgrid, AtomicGrid)
key = ('density_decomposition', index)
if key not in self.cache:
moldens = self.get_moldens(index)
self.do_partitioning()
if log.do_medium:
log('Computing density decomposition for atom %i' % index)
at_weights = self.cache.load('at_weights', index)
splines = atgrid.get_spherical_decomposition(moldens,
at_weights,
lmax=self.lmax)
density_decomposition = dict(
('spline_%05i' % j, spline)
for j, spline in enumerate(splines))
self.cache.dump(key, density_decomposition, tags='o')
def check_output(fn_h5, grp_name, overwrite):
'''Check if the output is already present in print a warning if --overwrite is not used
**Arguments:**
fn_h5
The output HDF5 file
grp_name
The HDF5 group in which the output is stored.
overwrite
Whether the user wants to overwrite contents that were already
present.
'''
if os.path.isfile(fn_h5):
with LockedH5File(fn_h5, 'r') as f:
if grp_name in f and len(f[grp_name]) > 0:
if overwrite:
if log.do_warning:
log.warn(
'Overwriting the contents of "%s" in the file "%s".'
% (grp_name, fn_h5))
return False
else:
if log.do_warning:
log.warn(
'Skipping because the group "%s" is already present in the file "%s" and it is not empty.'
% (grp_name, fn_h5))
return True
return False
def do_dispersion(self):
if self.lmax < 3:
if log.do_warning:
log.warn(
'Skipping the computation of dispersion coefficients because lmax=%i<3'
% self.lmax)
return
if log.do_medium:
log.cite(
'tkatchenko2009',
'the method to evaluate atoms-in-molecules C6 parameters')
log.cite('chu2004',
'the reference C6 parameters of isolated atoms')
log.cite('yan1996', 'the isolated hydrogen C6 parameter')
ref_c6s = { # reference C6 values in atomic units
1: 6.499, 2: 1.42, 3: 1392.0, 4: 227.0, 5: 99.5, 6: 46.6, 7: 24.2,
8: 15.6, 9: 9.52, 10: 6.20, 11: 1518.0, 12: 626.0, 13: 528.0, 14:
305.0, 15: 185.0, 16: 134.0, 17: 94.6, 18: 64.2, 19: 3923.0, 20:
2163.0, 21: 1383.0, 22: 1044.0, 23: 832.0, 24: 602.0, 25: 552.0, 26:
482.0, 27: 408.0, 28: 373.0, 29: 253.0, 30: 284.0, 31: 498.0, 32:
354.0, 33: 246.0, 34: 210.0, 35: 162.0, 36: 130.0, 37: 4769.0, 38:
3175.0, 49: 779.0, 50: 659.0, 51: 492.0, 52: 445.0, 53: 385.0,
}
volumes, new_volumes = self._cache.load('volumes',
alloc=self.natom,
tags='o')
volume_ratios, new_volume_ratios = self._cache.load('volume_ratios',
alloc=self.natom,
tags='o')
c6s, new_c6s = self._cache.load('c6s', alloc=self.natom, tags='o')
if new_volumes or new_volume_ratios or new_c6s:
self.do_moments()
radial_moments = self._cache.load('radial_moments')
if log.do_medium:
log('Computing atomic dispersion coefficients.')
for i in xrange(self.natom):
n = self.numbers[i]
volumes[i] = radial_moments[i, 3]
ref_volume = self.proatomdb.get_record(n, 0).get_moment(3)
volume_ratios[i] = volumes[i] / ref_volume
if n in ref_c6s:
c6s[i] = (volume_ratios[i])**2 * ref_c6s[n]
else:
c6s[i] = -1 # This is just to indicate that no value is available.
def do_hartree_decomposition(self):
if not self.local:
if log.do_warning:
log.warn('Skipping hartree decomposition because no local grids were found.')
return
for index in xrange(self.natom):
key = ('hartree_decomposition', index)
if key not in self.cache:
self.do_density_decomposition()
if log.do_medium:
log('Computing hartree decomposition for atom %i' % index)
density_decomposition = self.cache.load('density_decomposition', index)
rho_splines = [spline for foo, spline in sorted(density_decomposition.iteritems())]
v_splines = solve_poisson_becke(rho_splines)
hartree_decomposition = dict(('spline_%05i' % j, spline) for j, spline in enumerate(v_splines))
self.cache.dump(key, hartree_decomposition, tags='o')
def do_density_decomposition(self):
if not self.local:
if log.do_warning:
log.warn('Skipping density decomposition because no local grids were found.')
return
for index in xrange(self.natom):
atgrid = self.get_grid(index)
assert isinstance(atgrid, AtomicGrid)
key = ('density_decomposition', index)
if key not in self.cache:
moldens = self.get_moldens(index)
self.do_partitioning()
if log.do_medium:
log('Computing density decomposition for atom %i' % index)
at_weights = self.cache.load('at_weights', index)
splines = atgrid.get_spherical_decomposition(moldens, at_weights, lmax=self.lmax)
density_decomposition = dict(('spline_%05i' % j, spline) for j, spline in enumerate(splines))
self.cache.dump(key, density_decomposition, tags='o')
def do_dispersion(self):
if self.lmax < 3:
if log.do_warning:
log.warn('Skipping the computation of dispersion coefficients because lmax=%i<3' % self.lmax)
return
if log.do_medium:
log.cite('tkatchenko2009', 'the method to evaluate atoms-in-molecules C6 parameters')
log.cite('chu2004', 'the reference C6 parameters of isolated atoms')
log.cite('yan1996', 'the isolated hydrogen C6 parameter')
ref_c6s = { # reference C6 values in atomic units
1: 6.499, 2: 1.42, 3: 1392.0, 4: 227.0, 5: 99.5, 6: 46.6, 7: 24.2,
8: 15.6, 9: 9.52, 10: 6.20, 11: 1518.0, 12: 626.0, 13: 528.0, 14:
305.0, 15: 185.0, 16: 134.0, 17: 94.6, 18: 64.2, 19: 3923.0, 20:
2163.0, 21: 1383.0, 22: 1044.0, 23: 832.0, 24: 602.0, 25: 552.0, 26:
482.0, 27: 408.0, 28: 373.0, 29: 253.0, 30: 284.0, 31: 498.0, 32:
354.0, 33: 246.0, 34: 210.0, 35: 162.0, 36: 130.0, 37: 4769.0, 38:
3175.0, 49: 779.0, 50: 659.0, 51: 492.0, 52: 445.0, 53: 385.0,
}
volumes, new_volumes = self._cache.load('volumes', alloc=self.natom, tags='o')
volume_ratios, new_volume_ratios = self._cache.load('volume_ratios', alloc=self.natom, tags='o')
c6s, new_c6s = self._cache.load('c6s', alloc=self.natom, tags='o')
if new_volumes or new_volume_ratios or new_c6s:
self.do_populations()
self.do_moments()
radial_moments = self._cache.load('radial_moments')
populations = self._cache.load('populations')
if log.do_medium:
log('Computing atomic dispersion coefficients.')
for i in xrange(self.natom):
n = self.numbers[i]
volumes[i] = radial_moments[i,2]/populations[i]
ref_volume = self.proatomdb.get_record(n, 0).get_moment(3)/n
volume_ratios[i] = volumes[i]/ref_volume
if n in ref_c6s:
c6s[i] = (volume_ratios[i])**2*ref_c6s[n]
else:
c6s[i] = -1 # This is just to indicate that no value is available.
def write_input(self, number, charge, mult, template, do_overwrite):
# Directory stuff
nel = number - charge
dn_mult = '%03i_%s_%03i_q%+03i/mult%02i' % (
number, periodic[number].symbol.lower().rjust(
2, '_'), nel, charge, mult)
# Figure out if we want to write
fn_inp = '%s/atom.in' % dn_mult
exists = os.path.isfile(fn_inp)
do_write = not exists or do_overwrite
if do_write:
try:
subs = template.get_subs(number, nel, mult)
except KeyError:
if log.do_warning:
log.warn(
'Could not find all subs for %03i.%03i.%03i. Skipping.'
% (number, nel, mult))
return dn_mult, False
if not os.path.isdir(dn_mult):
os.makedirs(dn_mult)
with open(fn_inp, 'w') as f:
f.write(
template.substitute(
subs,
charge=str(charge),
mult=str(mult),
number=str(number),
element=periodic[number].symbol,
))
if log.do_medium:
if exists:
log('Overwritten: ', fn_inp)
else:
log('Written new: ', fn_inp)
elif log.do_medium:
log('Not overwriting: ', fn_inp)
return dn_mult, do_write
def write_input(self, number, charge, mult, template, do_overwrite):
# Directory stuff
nel = number - charge
dn_mult = '%03i_%s_%03i_q%+03i/mult%02i' % (
number, periodic[number].symbol.lower().rjust(2, '_'), nel, charge, mult)
# Figure out if we want to write
fn_inp = '%s/atom.in' % dn_mult
exists = os.path.isfile(fn_inp)
do_write = not exists or do_overwrite
if do_write:
try:
subs = template.get_subs(number, nel, mult)
except KeyError:
if log.do_warning:
log.warn('Could not find all subs for %03i.%03i.%03i. Skipping.' % (number, nel, mult))
return dn_mult, False
if not os.path.isdir(dn_mult):
os.makedirs(dn_mult)
with open(fn_inp, 'w') as f:
f.write(template.substitute(
subs,
charge=str(charge),
mult=str(mult),
number=str(number),
element=periodic[number].symbol,
))
if log.do_medium:
if exists:
log('Overwritten: ', fn_inp)
else:
log('Written new: ', fn_inp)
elif log.do_medium:
log('Not overwriting: ', fn_inp)
return dn_mult, do_write
