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 = psi4.get_active_molecule()
natom = molecule.natom()
# get list of displacements
displacement_geoms = psi4.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(name, db):
molecule = psi4.get_active_molecule()
natom = molecule.natom()
# Get list of displacements
displacement_geoms = psi4.atomic_displacements()
# Sanity check!
# Until we append the original geometry
if not (6 * natom) == len(displacement_geoms):
raise Exception('The number displacements should be 6 times the number'
'of atoms!')
# List of displacements for iterating
displacement_names = db['job_status'].keys()
for n, entry in enumerate(displacement_names):
if not os.path.exists(entry):
os.makedirs(entry)
# Set up
mol_open = 'molecule ' + molecule.name() + '_' + entry + ' {\n'
mol_close = '}'
molecule.set_geometry(displacement_geoms[n])
molecule.fix_orientation(True)
molecule.fix_com(True)
# Write input file
inputfile = open('{0}/input.dat'.format(entry), 'w')
inputfile.write("# This is a psi4 input file auto-generated for "
"computing Raman Optical Activity.\n\n")
#inputfile.write(basic_molecule_for_input(molecule))
inputfile.write("{}{}{}".format(
mol_open, molecule.create_psi4_string_from_molecule(), mol_close))
#.format(mol_open,molecule.save_string_xyz(),mol_close))
inputfile.write('\n')
inputfile.write(p4util.format_options_for_input())
inputfile.write('\n')
inputfile.write(
"property('{0}', properties=['roa_tensor'])".format(name))
inputfile.close()
def generate_inputs(name,db):
molecule = psi4.get_active_molecule()
natom = molecule.natom()
# Get list of displacements
displacement_geoms = psi4.atomic_displacements(molecule)
# Sanity check!
# Until we append the original geometry
if not (6*natom) == len(displacement_geoms):
raise Exception('The number displacements should be 6 times the number'
'of atoms!')
# List of displacements for iterating
displacement_names = db['job_status'].keys()
for n,entry in enumerate(displacement_names):
if not os.path.exists(entry):
os.makedirs(entry)
# Set up
mol_open = 'molecule ' + molecule.name() + '_' + entry + ' {\n'
mol_close = '}'
molecule.set_geometry(displacement_geoms[n])
molecule.fix_orientation(True)
molecule.fix_com(True)
# Write input file
inputfile = open('{0}/input.dat'.format(entry), 'w')
inputfile.write("# This is a psi4 input file auto-generated for "
"computing Raman Optical Activity.\n\n")
#inputfile.write(basic_molecule_for_input(molecule))
inputfile.write("{}{}{}"
.format(mol_open,molecule.create_psi4_string_from_molecule(),mol_close))
#.format(mol_open,molecule.save_string_xyz(),mol_close))
inputfile.write('\n')
inputfile.write(p4util.format_options_for_input())
inputfile.write('\n')
inputfile.write("property('{0}', properties=['roa_tensor'])".format(name))
inputfile.close()