def main():
import glob
from molmod import angstrom
from hipart.atoms import AtomTable
from hipart.context import Context, Options
from hipart.schemes import HirshfeldScheme
# load the atom table from the first example
atom_table = AtomTable("../001-usage/atoms/densities.txt")
# select formatted checkpoint files from the first example
fns_fchk = glob.glob("../001-usage/*.fchk")
f = file("all.txt", "w")
# loop over all formatted checkpoint files
for fn_fchk in fns_fchk:
# setup a HiPart computation
options = Options(lebedev=266, do_work=False, do_output=False)
context = Context(fn_fchk, options)
scheme = HirshfeldScheme(context, atom_table)
# the following line does the computation
scheme.do_charges()
# print output to the file all.txt
m = scheme.molecule
print >> f, "XXX", m.size
for i in xrange(m.size):
print >> f, "%3i % 15.10f % 15.10f % 15.10f % 9.5f" % (
m.numbers[i], m.coordinates[i,0]/angstrom,
m.coordinates[i,1]/angstrom, m.coordinates[i,2]/angstrom,
scheme.charges[i]
)
f.close()
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 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 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