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 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 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
def main():
args = parse_args()
fn_h5, grp_name = parse_h5(args.h5, 'h5')
with LockedH5File(fn_h5, 'r') as fin, open(args.csv, 'w') as fout:
w = csv.writer(fout)
w.writerow(['Converted data from %s' % args.h5])
w.writerow([])
for name, dset in iter_datasets(fin[grp_name]):
if len(dset.shape) > 3:
if log.do_warning:
log.warn(
'Skipping %s because it has more than three axes.' %
name)
else:
log('Converting %s' % name)
w.writerow(['Dataset', name])
w.writerow(['Shape'] + list(dset.shape))
if len(dset.shape) == 0:
w.writerow([dset[()]])
elif len(dset.shape) == 1:
for value in dset:
w.writerow([value])
elif len(dset.shape) == 2:
for row in dset:
w.writerow([value for value in row])
elif len(dset.shape) == 3:
for array in dset:
l = []
for col in array.T:
for value in col:
l.append(value)
l.append('')
del l[-1]
w.writerow(l)
else:
w.writerow(['Skipped because ndim=%i>3' % len(dset.shape)])
w.writerow([])
def main():
args = parse_args()
fn_h5, grp_name = parse_h5(args.h5, 'h5')
with LockedH5File(fn_h5, 'r') as fin, open(args.csv, 'w') as fout:
w = csv.writer(fout)
w.writerow(['Converted data from %s' % args.h5])
w.writerow([])
for name, dset in iter_datasets(fin[grp_name]):
if len(dset.shape) > 3:
if log.do_warning:
log.warn('Skipping %s because it has more than three axes.' % name)
else:
log('Converting %s' % name)
w.writerow(['Dataset', name])
w.writerow(['Shape'] + list(dset.shape))
if len(dset.shape) == 0:
w.writerow([dset[()]])
elif len(dset.shape) == 1:
for value in dset:
w.writerow([value])
elif len(dset.shape) == 2:
for row in dset:
w.writerow([value for value in row])
elif len(dset.shape) == 3:
for array in dset:
l = []
for col in array.T:
for value in col:
l.append(value)
l.append('')
del l[-1]
w.writerow(l)
else:
w.writerow(['Skipped because ndim=%i>3' % len(dset.shape)])
w.writerow([])
def plot_atoms(proatomdb):
try:
import matplotlib.pyplot as pt
except ImportError:
if log.do_warning:
log.warn('Skipping plots because matplotlib was not found.')
return
lss = {True: '-', False: ':'}
for number in proatomdb.get_numbers():
r = proatomdb.get_rgrid(number).radii
symbol = periodic[number].symbol
charges = proatomdb.get_charges(number)
suffix = '%03i_%s' % (number, symbol.lower().rjust(2, '_'))
# The density (rho)
pt.clf()
for i, charge in enumerate(charges):
record = proatomdb.get_record(number, charge)
y = record.rho
ls = lss[record.safe]
color = get_color(i)
label = 'q=%+i' % charge
pt.semilogy(r / angstrom, y, lw=2, ls=ls, label=label, color=color)
pt.xlim(0, 3)
pt.ylim(ymin=1e-5)
pt.xlabel('Distance from the nucleus [A]')
pt.ylabel('Spherically averaged density [Bohr**-3]')
pt.title('Proatoms for element %s (%i)' % (symbol, number))
pt.legend(loc=0)
fn_png = 'dens_%s.png' % suffix
pt.savefig(fn_png)
if log.do_medium:
log('Written', fn_png)
# 4*pi*r**2*rho
pt.clf()
for i, charge in enumerate(charges):
record = proatomdb.get_record(number, charge)
y = record.rho
ls = lss[record.safe]
color = get_color(i)
label = 'q=%+i' % charge
pt.plot(r / angstrom,
4 * np.pi * r**2 * y,
lw=2,
ls=ls,
label=label,
color=color)
pt.xlim(0, 3)
pt.ylim(ymin=0.0)
pt.xlabel('Distance from the nucleus [A]')
pt.ylabel('4*pi*r**2*density [Bohr**-1]')
pt.title('Proatoms for element %s (%i)' % (symbol, number))
pt.legend(loc=0)
fn_png = 'rdens_%s.png' % suffix
pt.savefig(fn_png)
if log.do_medium:
log('Written', fn_png)
fukui_data = []
if number - charges[0] == 1:
record0 = proatomdb.get_record(number, charges[0])
fukui_data.append((record0.rho, record0.safe, '%+i' % charges[0]))
for i, charge in enumerate(charges[1:]):
record0 = proatomdb.get_record(number, charge)
record1 = proatomdb.get_record(number, charges[i])
fukui_data.append(
(record0.rho - record1.rho, record0.safe
and record1.safe, '%+i-%+i' % (charge, charges[i])))
# The Fukui functions
pt.clf()
for i, (f, safe, label) in enumerate(fukui_data):
ls = lss[safe]
color = get_color(i)
pt.semilogy(r / angstrom,
f,
lw=2,
ls=ls,
label=label,
color=color,
alpha=1.0)
pt.semilogy(r / angstrom, -f, lw=2, ls=ls, color=color, alpha=0.2)
pt.xlim(0, 3)
pt.ylim(ymin=1e-5)
pt.xlabel('Distance from the nucleus [A]')
pt.ylabel('Fukui function [Bohr**-3]')
pt.title('Proatoms for element %s (%i)' % (symbol, number))
pt.legend(loc=0)
fn_png = 'fukui_%s.png' % suffix
pt.savefig(fn_png)
if log.do_medium:
log('Written', fn_png)
# 4*pi*r**2*Fukui
pt.clf()
for i, (f, safe, label) in enumerate(fukui_data):
ls = lss[safe]
color = get_color(i)
pt.plot(r / angstrom,
4 * np.pi * r**2 * f,
lw=2,
ls=ls,
label=label,
color=color)
pt.xlim(0, 3)
pt.xlabel('Distance from the nucleus [A]')
pt.ylabel('4*pi*r**2*Fukui [Bohr**-1]')
pt.title('Proatoms for element %s (%i)' % (symbol, number))
pt.legend(loc=0)
fn_png = 'rfukui_%s.png' % suffix
pt.savefig(fn_png)
if log.do_medium:
log('Written', fn_png)
def plot_atoms(proatomdb):
try:
import matplotlib.pyplot as pt
except ImportError:
if log.do_warning:
log.warn('Skipping plots because matplotlib was not found.')
return
lss = {True: '-', False: ':'}
for number in proatomdb.get_numbers():
r = proatomdb.get_rgrid(number).radii
symbol = periodic[number].symbol
charges = proatomdb.get_charges(number)
suffix = '%03i_%s' % (number, symbol.lower().rjust(2, '_'))
# The density (rho)
pt.clf()
for i, charge in enumerate(charges):
record = proatomdb.get_record(number, charge)
y = record.rho
ls = lss[record.safe]
color = get_color(i)
label = 'q=%+i' % charge
pt.semilogy(r/angstrom, y, lw=2, ls=ls, label=label, color=color)
pt.xlim(0, 3)
pt.ylim(ymin=1e-5)
pt.xlabel('Distance from the nucleus [A]')
pt.ylabel('Spherically averaged density [Bohr**-3]')
pt.title('Proatoms for element %s (%i)' % (symbol, number))
pt.legend(loc=0)
fn_png = 'dens_%s.png' % suffix
pt.savefig(fn_png)
if log.do_medium:
log('Written', fn_png)
# 4*pi*r**2*rho
pt.clf()
for i, charge in enumerate(charges):
record = proatomdb.get_record(number, charge)
y = record.rho
ls = lss[record.safe]
color = get_color(i)
label = 'q=%+i' % charge
pt.plot(r/angstrom, 4*np.pi*r**2*y, lw=2, ls=ls, label=label, color=color)
pt.xlim(0, 3)
pt.ylim(ymin=0.0)
pt.xlabel('Distance from the nucleus [A]')
pt.ylabel('4*pi*r**2*density [Bohr**-1]')
pt.title('Proatoms for element %s (%i)' % (symbol, number))
pt.legend(loc=0)
fn_png = 'rdens_%s.png' % suffix
pt.savefig(fn_png)
if log.do_medium:
log('Written', fn_png)
fukui_data = []
if number - charges[0] == 1:
record0 = proatomdb.get_record(number, charges[0])
fukui_data.append((record0.rho, record0.safe, '%+i' % charges[0]))
for i, charge in enumerate(charges[1:]):
record0 = proatomdb.get_record(number, charge)
record1 = proatomdb.get_record(number, charges[i])
fukui_data.append((
record0.rho - record1.rho,
record0.safe and record1.safe,
'%+i-%+i' % (charge, charges[i])
))
# The Fukui functions
pt.clf()
for i, (f, safe, label) in enumerate(fukui_data):
ls = lss[safe]
color = get_color(i)
pt.semilogy(r/angstrom, f, lw=2, ls=ls, label=label, color=color, alpha=1.0)
pt.semilogy(r/angstrom, -f, lw=2, ls=ls, color=color, alpha=0.2)
pt.xlim(0, 3)
pt.ylim(ymin=1e-5)
pt.xlabel('Distance from the nucleus [A]')
pt.ylabel('Fukui function [Bohr**-3]')
pt.title('Proatoms for element %s (%i)' % (symbol, number))
pt.legend(loc=0)
fn_png = 'fukui_%s.png' % suffix
pt.savefig(fn_png)
if log.do_medium:
log('Written', fn_png)
# 4*pi*r**2*Fukui
pt.clf()
for i, (f, safe, label) in enumerate(fukui_data):
ls = lss[safe]
color = get_color(i)
pt.plot(r/angstrom, 4*np.pi*r**2*f, lw=2, ls=ls, label=label, color=color)
pt.xlim(0, 3)
pt.xlabel('Distance from the nucleus [A]')
pt.ylabel('4*pi*r**2*Fukui [Bohr**-1]')
pt.title('Proatoms for element %s (%i)' % (symbol, number))
pt.legend(loc=0)
fn_png = 'rfukui_%s.png' % suffix
pt.savefig(fn_png)
if log.do_medium:
log('Written', fn_png)