def success_list(prog):
""" Constructs a list of successes that be identified from the output file.
:param prog: the electronic structure program to use as a backend
:type prog: str
"""
return pm.call_module_function(prog, pm.Job.SUCCESS_LST)
def vpt2(prog, output_str):
""" Reads VPT2 information from the output string.
:param prog: electronic structure program to use as a backend
:type prog: str
:param output_str: string of the program's output file
:type output_str: str
"""
return pm.call_module_function(
prog,
pm.Job.VPT2,
# *args
output_str)
def program_version(prog, output_str):
""" Reads the version of the electronic structure code from the output file.
:param prog: electronic structure program to use as a backend
:type prog: str
:param output_str: string of the program's output file
:type output_str: str
"""
return pm.call_module_function(
prog,
pm.Job.PROG_VERS,
# *args
output_str)
def irc_path(prog, output_str):
""" read irc_path from the output string
:param prog: electronic structure program to use as a backend
:type prog: str
:param output_str: string of the program's output file
:type output_str: str
"""
return pm.call_module_function(
prog,
pm.Job.IRC_PATH,
# *args
output_str)
def has_normal_exit_message(prog, output_str):
""" Assess whether the output file string contains the
normal program exit message.
:param prog: electronic structure program to use as a backend
:type prog: str
:param output_str: string of the program's output file
:type output_str: str
"""
return pm.call_module_function(
prog,
pm.Job.EXIT_MSG,
# *args
output_str)
def polarizability(prog, output_str):
""" Reads the polarizability tensor from the output string.
Returns the dipole moment in _.
:param prog: electronic structure program to use as a backend
:type prog: str
:param output_str: string of the program's output file
:type output_str: str
"""
return pm.call_module_function(
prog,
pm.Job.POLAR,
# *args
output_str)
def normal_coordinates(prog, output_str):
""" Reads the displacement along the normal modes from the output string.
Returns the coordinates in Bohr.
:param prog: electronic structure program to use as a backend
:type prog: str
:param output_str: string of the program's output file
:type output_str: str
"""
return pm.call_module_function(
prog,
pm.Job.NORM_COORDS,
# *args
output_str)
def opt_zmatrix(prog, output_str):
""" Reads the optimized Z-Matrix from the output string.
Returns the geometry in Bohr+Radians.
:param prog: electronic structure program to use as a backend
:type prog: str
:param output_str: string of the program's output file
:type output_str: str
"""
return pm.call_module_function(
prog,
pm.Job.OPT_ZMA,
# *args
output_str)
def _opt_geometry(prog, output_str):
""" Reads the optimized geometry from the output string.
Returns the geometry in Bohr.
:param prog: electronic structure program to use as a backend
:type prog: str
:param output_str: string of the program's output file
:type output_str: str
"""
return pm.call_module_function(
prog,
pm.Job.OPT_GEO,
# *args
output_str)
def irc_points(prog, output_str):
""" Reads the geometries, gradients, and Hessians at each point along the
Intrinsic Reaction Coordinate from the output string.
:param prog: electronic structure program to use as a backend
:type prog: str
:param output_str: string of the program's output file
:type output_str: str
"""
return pm.call_module_function(
prog,
pm.Job.IRC_PTS,
# *args
output_str)
def dipole_moment(prog, output_str):
""" Reads the static dipole moment from the output string.
Returns the dipole moment in Debye.
:param prog: electronic structure program to use as a backend
:type prog: str
:param output_str: string of the program's output file
:type output_str: str
"""
return pm.call_module_function(
prog,
pm.Job.DIP_MOM,
# *args
output_str)
def has_error_message(prog, error, output_str):
""" Assess whether the output file string contains error messages
for any of the procedures in the job.
:param prog: electronic structure program to use as a backend
:type prog: str
:param error: a key indicating the type of error message
:type error: str
:param output_str: string of the program's output file
:type output_str: str
"""
return pm.call_module_function(
prog,
pm.Job.ERR_MSG,
# *args
error,
output_str)
def harmonic_frequencies(prog, output_str):
""" Reads the harmonic vibrational frequencies from the output string.
Returns the frequencies in cm-1.
:param prog: electronic structure program to use as a backend
:type prog: str
:param output_str: string of the program's output file
:type output_str: str
"""
harm_freqs = pm.call_module_function(
prog,
pm.Job.HARM_FREQS,
# *args
output_str)
if harm_freqs is not None:
assert all(isinstance(val, float) for val in harm_freqs)
assert numpy.shape(harm_freqs)[1] == 3
def hessian(prog, output_str):
""" Reads the Hessian from the output string.
Returns the Hessian in atomic units.
:param prog: electronic structure program to use as a backend
:type prog: str
:param output_str: string of the program's output file
:type output_str: str
"""
hess = pm.call_module_function(
prog,
pm.Job.HESSIAN,
# *args
output_str)
if hess is not None:
assert numpy.allclose(hess, numpy.transpose(hess))
return hess
def check_convergence_messages(prog, error, success, output_str):
""" Assess whether the output file string contains messages
denoting all of the requested procedures in the job have converged.
:param prog: electronic structure program to use as a backend
:type prog: str
:param error: a key indicating the type of error message
:type error: str
:param success: a key indicating the type of success message
:type success: str
:param output_str: string of the program's output file
:type output_str: str
"""
return pm.call_module_function(
prog,
pm.Job.CONV_MSG,
# *args
error,
success,
output_str)
def gradient(prog, output_str):
""" Reads the gradient from the output string.
Returns the gradient in atomic units.
:param prog: electronic structure program to use as a backend
:type prog: str
:param output_str: string of the program's output file
:type output_str: str
"""
grad = pm.call_module_function(
prog,
pm.Job.GRADIENT,
# *args
output_str)
# if grad is not None:
# assert all(isinstance(val, float) for val in grad)
# assert numpy.shape(grad)[1] == 3
return grad
def energy(prog, method, output_str):
""" Reads the electronic energy from the output string.
Returns the energy in Hartrees.
:param prog: electronic structure program to use as a backend
:type prog: str
:param method: electronic structure method
:type method: str
:param output_str: string of the program's output file
:type output_str: str
"""
ene = pm.call_module_function(
prog,
pm.Job.ENERGY,
# *args
method,
output_str)
if ene is not None:
assert isinstance(ene, float)
return ene
