def test_plot_atoms():
padb = ProAtomDB.from_refatoms(numbers=[8, 1], max_cation=1, max_anion=1)
with tmpdir('horton.scripts.test.test_atomdb.test_plot_atoms') as dn:
plot_atoms(padb, dn)
fns = [
'dens_001__h.png',
'rdens_001__h.png',
'fukui_001__h.png',
'rfukui_001__h.png',
'dens_008__o.png',
'rdens_008__o.png',
'fukui_008__o.png',
'rfukui_008__o.png',
]
check_files(dn, fns)
def test_plot_atoms():
padb = ProAtomDB.from_refatoms(numbers=[8, 1], max_cation=1, max_anion=1)
with tmpdir("horton.scripts.test.test_atomdb.test_plot_atoms") as dn:
plot_atoms(padb, dn)
fns = [
"dens_001__h.png",
"rdens_001__h.png",
"fukui_001__h.png",
"rfukui_001__h.png",
"dens_008__o.png",
"rdens_008__o.png",
"fukui_008__o.png",
"rfukui_008__o.png",
]
check_files(dn, fns)
def main_convert(args):
# The atomic grid specification
agspec = AtomicGridSpec(args.grid)
# The program is detected based on the run script that is present
run_scripts = glob("run_*.sh")
if len(run_scripts) != 1:
raise RuntimeError(
'Found %i run_*.sh scripts while exactly one is needed to know which program was used to run the atomic computations.'
% len(run_scripts))
program = atom_programs[run_scripts[0][4:-3]]
# Loop over all sensible directories
energy_table = EnergyTable()
records = []
for dn_state in sorted(glob("[01]??_??_[01]??_q[+-]??")):
number = int(dn_state[:3])
pop = int(dn_state[7:10])
cases = []
for dn_mult in sorted(glob('%s/mult??' % dn_state)):
if log.do_medium:
log('Loading from', dn_mult)
data, energy = program.load_atom(dn_mult)
if energy is None:
if log.do_medium:
log('No (sensible) results found: ', dn_mult)
continue
cases.append((energy, data))
if len(cases) == 0:
if log.do_medium:
log('Nothing found in: ', dn_state)
continue
# Get the lowest in energy and write to chk file
cases.sort()
energy, data = cases[0]
# Add case to energy table
energy_table.add(number, pop, energy)
# Write atom to HORTON file if possible
if data is not None:
data.to_file('%s/horton.h5' % dn_state)
# Construct a record for the proatomdb
records.append(ProAtomRecord.from_iodata(data, agspec))
# Release memory
data = None
del cases
# Let user know we are alive.
if log.do_medium:
log('Succesfull: ', dn_state)
# Report energies
if log.do_medium:
energy_table.log()
# Write out atoms file
proatomdb = ProAtomDB(records)
proatomdb.to_file('atoms.h5')
if log.do_medium:
log('Written atoms.h5')
# Make nice figures
plot_atoms(proatomdb)
def main_convert(args):
# The atomic grid specification
agspec = AtomicGridSpec(args.grid)
# The program is detected based on the run script that is present
run_scripts = glob("run_*.sh")
if len(run_scripts) != 1:
raise RuntimeError('Found %i run_*.sh scripts while exactly one is needed to know which program was used to run the atomic computations.' % len(run_scripts))
program = atom_programs[run_scripts[0][4:-3]]
# Loop over all sensible directories
energy_table = EnergyTable()
records = []
for dn_state in sorted(glob("[01]??_??_[01]??_q[+-]??")):
number = int(dn_state[:3])
pop = int(dn_state[7:10])
cases = []
for dn_mult in sorted(glob('%s/mult??' % dn_state)):
if log.do_medium:
log('Loading from', dn_mult)
data, energy = program.load_atom(dn_mult)
if energy is None:
if log.do_medium:
log('No (sensible) results found: ', dn_mult)
continue
cases.append((energy, data))
if len(cases) == 0:
if log.do_medium:
log('Nothing found in: ', dn_state)
continue
# Get the lowest in energy and write to chk file
cases.sort()
energy, data = cases[0]
# Add case to energy table
energy_table.add(number, pop, energy)
# Write atom to HORTON file if possible
if data is not None:
data.to_file('%s/horton.h5' % dn_state)
# Construct a record for the proatomdb
records.append(ProAtomRecord.from_iodata(data, agspec))
# Release memory
data = None
del cases
# Let user know we are alive.
if log.do_medium:
log('Succesfull: ', dn_state)
# Report energies
if log.do_medium:
energy_table.log()
# Write out atoms file
proatomdb = ProAtomDB(records)
proatomdb.to_file('atoms.h5')
if log.do_medium:
log('Written atoms.h5')
# Make nice figures
plot_atoms(proatomdb)
