def generate_inputs(db, name):
"""
Generates the input files in each sub-directory of the
distributed finite differences property calculation.
name: ( string ) method name passed to calling driver,
db: (database) The database object associated with this property
calculation. On exit this db['inputs_generated'] has been set True
Returns: nothing
Throws: Exception if the number of atomic displacements is not correct.
"""
molecule = core.get_active_molecule()
natom = molecule.natom()
# get list of displacements
displacement_geoms = core.atomic_displacements(molecule)
# Sanity Check
# there should be 3 cords * natoms *2 directions (+/-)
if not (6 * natom) == len(displacement_geoms):
raise Exception('The number of atomic displacements should be 6 times'
' the number of atoms!')
displacement_names = db['job_status'].keys()
for n, entry in enumerate(displacement_names):
if not os.path.exists(entry):
os.makedirs(entry)
# Setup up input file string
inp_template = 'molecule {molname}_{disp}'
inp_template += ' {{\n{molecule_info}\n}}\n{options}\n{jobspec}\n'
molecule.set_geometry(displacement_geoms[n])
molecule.fix_orientation(True)
molecule.fix_com(True)
inputfile = open('{0}/input.dat'.format(entry), 'w')
inputfile.write("# This is a psi4 input file auto-generated for"
"computing properties by finite differences.\n\n")
inputfile.write(
inp_template.format(
molname=molecule.name(),
disp=entry,
molecule_info=molecule.create_psi4_string_from_molecule(),
options=p4util.format_options_for_input(),
jobspec=db['prop_cmd']))
inputfile.close()
db['inputs_generated'] = True
def generate_inputs(db,name):
"""
Generates the input files in each sub-directory of the
distributed finite differences property calculation.
name: ( string ) method name passed to calling driver,
db: (database) The database object associated with this property
calculation. On exit this db['inputs_generated'] has been set True
Returns: nothing
Throws: Exception if the number of atomic displacements is not correct.
"""
molecule = core.get_active_molecule()
natom = molecule.natom()
# get list of displacements
displacement_geoms = core.atomic_displacements(molecule)
# Sanity Check
# there should be 3 cords * natoms *2 directions (+/-)
if not (6 * natom) == len(displacement_geoms):
raise Exception('The number of atomic displacements should be 6 times'
' the number of atoms!')
displacement_names = db['job_status'].keys()
for n, entry in enumerate(displacement_names):
if not os.path.exists(entry):
os.makedirs(entry)
# Setup up input file string
inp_template = 'molecule {molname}_{disp}'
inp_template += ' {{\n{molecule_info}\n}}\n{options}\n{jobspec}\n'
molecule.set_geometry(displacement_geoms[n])
molecule.fix_orientation(True)
molecule.fix_com(True)
inputfile = open('{0}/input.dat'.format(entry), 'w')
inputfile.write("# This is a psi4 input file auto-generated for"
"computing properties by finite differences.\n\n")
inputfile.write(
inp_template.format(
molname=molecule.name(),
disp=entry,
molecule_info=molecule.create_psi4_string_from_molecule(),
options=p4util.format_options_for_input(),
jobspec=db['prop_cmd']))
inputfile.close()
db['inputs_generated'] = True
