def direct(script_str,
run_dir,
geoms,
grads,
hessians,
rotors_str='',
aux_dct=None,
input_name=INPUT_NAME,
output_names=OUTPUT_NAMES):
""" Generates an input file for a ProjRot job, runs it directly, and
obtains all of the possible output file strings
"""
input_str = projrot_io.writer.rpht_input(geoms,
grads,
hessians,
rotors_str=rotors_str)
output_strs = from_input_string(script_str,
run_dir,
input_str,
aux_dct=aux_dct,
input_name=input_name,
output_names=output_names)
return output_strs
def direct(script_str, run_dir, input_str, aux_dct=None,
input_name=INPUT_NAME,
output_names=OUTPUT_NAMES):
"""
:param aux_dct: auxiliary input strings dict[name: string]
:type aux_dct: dict[str: str]
:param script_str: string of bash script that contains
execution instructions electronic structure job
:type script_str: str
:param run_dir: name of directory to run electronic structure job
:type run_dir: str
"""
output_strs = from_input_string(
script_str, run_dir, input_str,
aux_dct=aux_dct,
input_name=input_name,
output_names=output_names)
return output_strs
def direct(script_str,
run_dir,
zma,
geo,
hess,
script_name=SCRIPT_NAME,
input_name=INPUT_NAME,
output_names=OUTPUT_NAMES):
""" Generates an input file for a ProjRot job, runs it directly, and
obtains all of the possible output file strings
"""
input_str = intder_io.writer.input_file(geo, zma)
aux_dct = {'file15': intder_io.writer.cartesian_hessian_file(hess)}
return from_input_string(script_str,
run_dir,
input_str,
aux_dct=aux_dct,
script_name=script_name,
input_name=input_name,
output_names=output_names)
def direct(script_str,
run_dir,
geo,
hess,
zma=None,
input_name=INPUT_NAME,
output_names=OUTPUT_NAMES):
""" Run INTDER
"""
input_str = intder_io.writer.input_file(geo, zma=zma)
hess_str = intder_io.writer.cart_hess_file(hess)
aux_dct = {'file15': hess_str}
output_strs = from_input_string(script_str,
run_dir,
input_str,
aux_dct=aux_dct,
input_name=input_name,
output_names=output_names)
return output_strs
def frame_oriented_structure(script_str, run_dir,
divsur_inp_str,
struct_inp_str,
divsur_name='divsur.inp',
tst_name='tst.inp',
struct_name='structure.inp',
output_names=('divsur.out',)):
""" get the divsur.out string containing divsur-frame geoms
"""
# Fill in the submission script
script_str.format(divsur_name, tst_name)
# Write some boilerplate tst.inp string to run script
tst_str = varecof_io.writer.input_file.tst(1, 1, .1, 1)
# Put the tst string in the aux dct
aux_dct = {tst_name: tst_str,
struct_name: struct_inp_str}
# Run the script to generate the divsur.out file
output_strs = from_input_string(
script_str, run_dir, divsur_inp_str,
aux_dct=aux_dct,
script_name=CONVSTRUCT_SCRIPT_NAME,
input_name=divsur_name,
output_names=output_names)
divsur_out_str = output_strs[0]
# Read the geometries and facial symmetries from divsur out file
if divsur_out_str is not None:
geos = varecof_io.reader.divsur.frame_geometries(
divsur_out_str)
faces, faces_symm = varecof_io.writer.assess_face_symmetries(
*geos)
else:
geos, faces, faces_symm = None, None, None
return geos, faces, faces_symm
def direct(script_str, run_dir, input_str, formula_str):
""" Generates an input file for a ThermP job runs it directly.
Need formula input to run the script
:param input_str: string of input file with .i97 suffix
"""
aux_dct = {NEW_GROUPS_NAME: _new_groups_str()}
input_name = INPUT_NAME.format(formula_str)
output_names = tuple(name.format(formula_str) for name in OUTPUT_NAMES)
output_strs = from_input_string(script_str,
run_dir,
input_str,
aux_dct=aux_dct,
input_name=input_name,
output_names=output_names)
if not _check(output_strs):
output_strs = None
return output_strs
def direct(script_str, run_dir,
pf_str, formula_str, hform0, temps,
enthalpyt=0.0, breakt=1000.0):
""" Generates an input file for a ThermP job runs it directly.
"""
input_str = thermp_io.writer.input_file(
ntemps=len(temps),
formula=formula_str,
delta_h=hform0,
enthalpy_temp=enthalpyt,
break_temp=breakt)
aux_dct = {'pf.dat': pf_str}
output_names = OUTPUT_NAMES.copy()
output_names[1] = output_names[1].format(formula_str)
output_strs = from_input_string(
script_str, run_dir, input_str,
aux_dct=aux_dct,
input_name=INPUT_NAME,
output_names=output_names)
return input_str, output_strs
