Exemplo n.º 1
0
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
Exemplo n.º 2
0
Arquivo: roa.py Projeto: xwang862/psi4
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()
Exemplo n.º 3
0
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()