def wrapper(instance):
if fn.func_name in instance._done:
return
log.begin(self.description)
fn(instance)
log.end()
instance._done.add(fn.func_name)
def estimate_errors(atom_tables, fns_fchk):
from hipart.context import Context, Options
from hipart.schemes import HirshfeldScheme
from hipart.log import log
import numpy, time
configs = []
ref_config = None
# The loops below one jobs for each grid configuration, i.e. combination
# of radial and angular grid.
for size, atom_table in sorted(atom_tables.iteritems()):
for lebedev in 26, 50, 110, 230, 434, 770, 1454, 2702:
all_charges = []
start = time.clock()
for fn_fchk in fns_fchk:
log.begin("Config size=%i lebedev=%i fchk=%s" %
(size, lebedev, fn_fchk))
# Make a new working environment for every sample
options = Options(lebedev=lebedev,
do_work=False,
do_output=False,
do_random=True)
context = Context(fn_fchk, options)
scheme = HirshfeldScheme(context, atom_table)
scheme.do_charges()
all_charges.append(scheme.charges)
del scheme
log.end()
cost = time.clock() - start
log("cost=%.2e" % cost)
config = Config(size, lebedev, numpy.concatenate(all_charges),
cost)
configs.append(config)
if ref_config is None or (ref_config.size <= config.size and
ref_config.lebedev <= config.lebedev):
ref_config = config
# Compute the errors
ref_charges = configs[-1].charges
for config in configs:
config.error = (ref_charges - config.charges).std()
# Log all
log.begin("All configs")
for config in configs:
log(str(config))
log.end()
return configs
def __init__(self, filename, options):
log.set_verbose(options.verbose)
log.begin("Loading Electronic structure")
self.wavefn = load_wavefunction(filename)
self.wavefn.log()
log.end()
self.options = options
outdir = "%s.hipart" % self.wavefn.prefix
if options.do_output:
self.output = Output(outdir, self.wavefn.molecule.numbers)
else:
self.output = Output()
if options.do_work:
workdir = os.path.join(outdir, "work")
else:
workdir = None
self.work = Work(workdir, do_clean=options.do_clean)
def estimate_errors(atom_tables, fns_fchk):
from hipart.context import Context, Options
from hipart.schemes import HirshfeldScheme
from hipart.log import log
import numpy, time
configs = []
ref_config = None
# The loops below one jobs for each grid configuration, i.e. combination
# of radial and angular grid.
for size, atom_table in sorted(atom_tables.iteritems()):
for lebedev in 26, 50, 110, 230, 434, 770, 1454, 2702:
all_charges = []
start = time.clock()
for fn_fchk in fns_fchk:
log.begin("Config size=%i lebedev=%i fchk=%s" % (size, lebedev, fn_fchk))
# Make a new working environment for every sample
options = Options(lebedev=lebedev, do_work=False,
do_output=False, do_random=True)
context = Context(fn_fchk, options)
scheme = HirshfeldScheme(context, atom_table)
scheme.do_charges()
all_charges.append(scheme.charges)
del scheme
log.end()
cost = time.clock() - start
log("cost=%.2e" % cost)
config = Config(size, lebedev, numpy.concatenate(all_charges), cost)
configs.append(config)
if ref_config is None or (ref_config.size <= config.size and ref_config.lebedev <= config.lebedev):
ref_config = config
# Compute the errors
ref_charges = configs[-1].charges
for config in configs:
config.error = (ref_charges - config.charges).std()
# Log all
log.begin("All configs")
for config in configs:
log(str(config))
log.end()
return configs
def init_naturals(self, work):
log.begin("Natural orbitals")
def do_natural(dmat, label):
orbitals_name = "%s_orbitals" % label
occupations_name = "%s_occupations" % label
orbitals = work.load(orbitals_name,
(self.num_orbitals, self.num_orbitals))
occupations = work.load(occupations_name)
if orbitals is None or occupations is None:
log("Computing the %s orbitals and occupation numbers ..." %
label)
occupations, orbitals = compute_naturals(
dmat, self.num_orbitals)
work.dump(orbitals_name, orbitals)
work.dump(occupations_name, occupations)
num = get_num_filled(occupations)
return num, occupations, orbitals
if self.natural_orbitals is None or self.natural_occupations is None:
self.num_natural, self.natural_occupations, self.natural_orbitals = \
do_natural(self.density_matrix, "natural")
if self.alpha_orbitals is None or self.alpha_occupations is None:
if self.spin_density_matrix is None:
self.num_alpha = self.num_natural
self.alpha_orbitals = self.natural_orbitals
self.alpha_occupations = 0.5 * self.natural_occupations
else:
self.num_alpha, self.alpha_occupations, self.alpha_orbitals = \
do_natural((self.density_matrix + self.spin_density_matrix)/2, "alpha")
if self.beta_orbitals is None or self.beta_occupations is None:
if self.spin_density_matrix is None:
self.num_beta = self.num_natural
self.beta_orbitals = self.natural_orbitals
self.beta_occupations = 0.5 * self.natural_occupations
else:
self.num_beta, self.beta_occupations, self.beta_orbitals = \
do_natural((self.density_matrix - self.spin_density_matrix)/2, "beta")
log.end()
def pareto_front(configs):
from hipart.log import log
# take a copy of the list, so that we can modify locally.
configs = list(configs)
# eliminate all configs that are not pareto-optimal
configs.sort(key=(lambda c: c.error))
i = 0
while i < len(configs):
ref_cost = configs[i].cost
j = len(configs) - 1
while j > i:
if configs[j].cost >= configs[i].cost:
del configs[j]
j -= 1
i += 1
# print the pareto front.
log.begin("Pareto front")
for config in configs:
log(str(config))
config.optimal = True
log.end()
def pareto_front(configs):
from hipart.log import log
# take a copy of the list, so that we can modify locally.
configs = list(configs)
# eliminate all configs that are not pareto-optimal
configs.sort(key=(lambda c: c.error))
i = 0
while i < len(configs):
ref_cost = configs[i].cost
j = len(configs) -1
while j > i:
if configs[j].cost >= configs[i].cost:
del configs[j]
j -= 1
i += 1
# print the pareto front.
log.begin("Pareto front")
for config in configs:
log(str(config))
config.optimal = True
log.end()
def init_naturals(self, work):
log.begin("Natural orbitals")
def do_natural(dmat, label):
orbitals_name = "%s_orbitals" % label
occupations_name = "%s_occupations" % label
orbitals = work.load(orbitals_name, (self.num_orbitals, self.num_orbitals))
occupations = work.load(occupations_name)
if orbitals is None or occupations is None:
log("Computing the %s orbitals and occupation numbers ..." % label)
occupations, orbitals = compute_naturals(dmat, self.num_orbitals)
work.dump(orbitals_name, orbitals)
work.dump(occupations_name, occupations)
num = get_num_filled(occupations)
return num, occupations, orbitals
if self.natural_orbitals is None or self.natural_occupations is None:
self.num_natural, self.natural_occupations, self.natural_orbitals = \
do_natural(self.density_matrix, "natural")
if self.alpha_orbitals is None or self.alpha_occupations is None:
if self.spin_density_matrix is None:
self.num_alpha = self.num_natural
self.alpha_orbitals = self.natural_orbitals
self.alpha_occupations = 0.5*self.natural_occupations
else:
self.num_alpha, self.alpha_occupations, self.alpha_orbitals = \
do_natural((self.density_matrix + self.spin_density_matrix)/2, "alpha")
if self.beta_orbitals is None or self.beta_occupations is None:
if self.spin_density_matrix is None:
self.num_beta = self.num_natural
self.beta_orbitals = self.natural_orbitals
self.beta_occupations = 0.5*self.natural_occupations
else:
self.num_beta, self.beta_occupations, self.beta_orbitals = \
do_natural((self.density_matrix - self.spin_density_matrix)/2, "beta")
log.end()
def estimate_errors(atom_tables, fn_fchk):
from hipart.context import Context, Options
from hipart.schemes import HirshfeldScheme
from hipart.log import log
import numpy, time
configs = []
# The loops below run 40 jobs for each grid configuration, i.e. combination
# of radial and angular grid. Due to the random rotations of the angular
# integration grids, the resulting charges will differ in each run. The
# standard devation on each charge over the 40 runs is computed, and then
# the error over all atoms is averaged. This error is used as 'the' error on
# the charges. The cost is the cpu time consumed for computing this error.
for size, atom_table in sorted(atom_tables.iteritems()):
for lebedev in 26, 50, 110, 170, 266, 434:
log.begin("Config size=%i lebedev=%i" % (size, lebedev))
start = time.clock()
all_charges = []
for counter in xrange(40):
log.begin("Sample counter=%i" % counter)
# Make a new working environment for every sample
options = Options(lebedev=lebedev,
do_work=False,
do_output=False)
context = Context(fn_fchk, options)
scheme = HirshfeldScheme(context, atom_table)
scheme.do_charges()
all_charges.append(scheme.charges)
del scheme
log.end()
all_charges = numpy.array(all_charges)
error = all_charges.std(axis=0).mean()
cost = time.clock() - start
log("error=%.2e cost=%.2e" % (error, cost))
configs.append(Config(size, lebedev, error, cost))
log.end()
log.begin("All configs")
for config in configs:
log(str(config))
log.end()
return configs
def estimate_errors(atom_tables, fn_fchk):
from hipart.context import Context, Options
from hipart.schemes import HirshfeldScheme
from hipart.log import log
import numpy, time
configs = []
# The loops below run 40 jobs for each grid configuration, i.e. combination
# of radial and angular grid. Due to the random rotations of the angular
# integration grids, the resulting charges will differ in each run. The
# standard devation on each charge over the 40 runs is computed, and then
# the error over all atoms is averaged. This error is used as 'the' error on
# the charges. The cost is the cpu time consumed for computing this error.
for size, atom_table in sorted(atom_tables.iteritems()):
for lebedev in 26, 50, 110, 170, 266, 434:
log.begin("Config size=%i lebedev=%i" % (size, lebedev))
start = time.clock()
all_charges = []
for counter in xrange(40):
log.begin("Sample counter=%i" % counter)
# Make a new working environment for every sample
options = Options(lebedev=lebedev, do_work=False,
do_output=False)
context = Context(fn_fchk, options)
scheme = HirshfeldScheme(context, atom_table)
scheme.do_charges()
all_charges.append(scheme.charges)
del scheme
log.end()
all_charges = numpy.array(all_charges)
error = all_charges.std(axis=0).mean()
cost = time.clock() - start
log("error=%.2e cost=%.2e" % (error, cost))
configs.append(Config(size, lebedev, error, cost))
log.end()
log.begin("All configs")
for config in configs:
log(str(config))
log.end()
return configs