def make_density_profiles(program, num_lebedev, r_low, r_high, steps,
atom_numbers, max_ion, do_work, do_random):
# generate lebedev grid
lebedev_xyz, lebedev_weights = get_grid(num_lebedev)
# define radii
rgrid = RLogIntGrid(r_low, r_high, steps)
agrid = ALebedevIntGrid(num_lebedev, do_random)
f_pro = file("densities.txt", "w")
print >> f_pro, rgrid.get_description()
charges = []
# run over all directories, run cubegen, load cube data
pb = log.pb("Density profiles", len(atom_numbers) * (2 * max_ion + 1))
for number in atom_numbers:
symbol = periodic[number].symbol
for charge in xrange(-max_ion, max_ion + 1):
charge_label = charge_to_label(charge)
pb()
dirname = os.path.join("%03i%s" % (number, symbol), charge_label,
"gs")
# get the grid
if not os.path.isdir(dirname): continue
if do_work:
work = Work(dirname)
else:
work = Work()
grid = AtomicGrid.from_prefix("grid", work)
if grid is None:
center = numpy.zeros(3, float)
grid = AtomicGrid.from_parameters("grid", work, center, rgrid,
agrid)
# compute densities
program.compute_density(grid, dirname)
# this is spherical averaging, i.e. integral/(4*pi)
radrhos = agrid.integrate(grid.moldens) / (4 * numpy.pi)
print >> f_pro, "%3i %+2i" % (number, charge),
# leave out near zeros to save space and time
print >> f_pro, " ".join("%22.16e" % rho for rho in radrhos
if rho > 1e-100)
check = rgrid.integrate(4 * numpy.pi * rgrid.rs * rgrid.rs *
radrhos)
charges.append((number, symbol, charge, check))
pb()
f_pro.close()
counter = 0
for number, symbol, charge, real_charge in charges:
log("Total charge error: %3i %2s %+2i % 10.5e" %
(number, symbol, charge, -real_charge + number - charge))
counter += 1
def make_density_profiles(program, num_lebedev, r_low, r_high, steps, atom_numbers, max_ion, do_work, do_random):
# generate lebedev grid
lebedev_xyz, lebedev_weights = get_grid(num_lebedev)
# define radii
rgrid = RLogIntGrid(r_low, r_high, steps)
agrid = ALebedevIntGrid(num_lebedev, do_random)
f_pro = file("densities.txt", "w")
print >> f_pro, rgrid.get_description()
charges = []
# run over all directories, run cubegen, load cube data
pb = log.pb("Density profiles", len(atom_numbers)*(2*max_ion+1))
for number in atom_numbers:
symbol = periodic[number].symbol
for charge in xrange(-max_ion, max_ion+1):
charge_label = charge_to_label(charge)
pb()
dirname = os.path.join("%03i%s" % (number, symbol), charge_label, "gs")
# get the grid
if not os.path.isdir(dirname): continue
if do_work:
work = Work(dirname)
else:
work = Work()
grid = AtomicGrid.from_prefix("grid", work)
if grid is None:
center = numpy.zeros(3,float)
grid = AtomicGrid.from_parameters("grid", work, center, rgrid, agrid)
# compute densities
program.compute_density(grid, dirname)
# this is spherical averaging, i.e. integral/(4*pi)
radrhos = agrid.integrate(grid.moldens)/(4*numpy.pi)
print >> f_pro, "%3i %+2i" % (number, charge),
# leave out near zeros to save space and time
print >> f_pro, " ".join("%22.16e" % rho for rho in radrhos if rho > 1e-100)
check = rgrid.integrate(4*numpy.pi*rgrid.rs*rgrid.rs*radrhos)
charges.append((number, symbol, charge, check))
pb()
f_pro.close()
counter = 0
for number, symbol, charge, real_charge in charges:
log("Total charge error: %3i %2s %+2i % 10.5e" % (number, symbol, charge, -real_charge+number-charge))
counter += 1
def do_atgrids(self):
self.atgrids = []
pb = log.pb("Computing/Loading atomic grids and distances", self.molecule.size)
for i in xrange(self.molecule.size):
pb()
name = "atom%05i" % i
atgrid = AtomicGrid.from_prefix(name, self.work)
if atgrid is None:
center = self.molecule.coordinates[i]
atgrid = AtomicGrid.from_parameters(name, self.work, center, self.rgrid, self.agrid)
self.atgrids.append(atgrid)
# Compute and store all the distances from these grid points to the
# nuclei.
atgrid.distances = LazyDistances(self.molecule.coordinates, atgrid, self.context.options.save_mem)
pb()
