def __init__(self, molecule, forcefield=None):
if which('obabel') is None:
print('setup OBabel path')
sys.exit()
super(OBabel, self).__init__(molecule)
if not os.path.isfile(self.start_xyz_file):
molecule.mol_to_xyz(self.start_xyz_file)
self.optimized_coordinates = []
self.energy = 0.0
def __init__(self, molecule, qc_params):
if which('define') is None:
turbomole_logger.error('set Turbomole path')
sys.exit('Set turbomole path')
super(Turbomole, self).__init__(molecule)
self.start_coords = angstrom2bohr(molecule.coordinates)
self.atoms_in_fragments = molecule.fragments
self.energy = None
self.optimized_coordinates = None
self.basis = qc_params['basis']
self.method = qc_params['method']
def __init__(self, molecule, method):
if which('define') is None:
turbomole_logger.error('set Turbomole path')
sys.exit('Set turbomole path')
super(Turbomole, self).__init__(molecule)
self.charge = method['charge']
self.scf_type = method['scftype']
self.multiplicity = method['multiplicity']
self.start_coords = angstrom2bohr(molecule.coordinates)
self.atoms_in_fragments = molecule.fragments
self.energy = None
self.optimized_coordinates = None
def __init__(self, molecule, qc_params):
if which('mopac') is None:
print('set MOPAC path')
sys.exit()
super(Mopac, self).__init__(molecule)
self.inp_file = 'trial_' + self.job_name + '.mop'
self.arc_file = 'trial_' + self.job_name + '.arc'
self.start_coords = molecule.coordinates
self.optimized_coordinates = []
self.energy = 0.0
keyword = f'PM7 PRECISE LET DDMIN=0.0 CYCLES=10000 charge={molecule.charge}'
self.prepare_input(keyword=keyword)
def __init__(self, molecule, method):
if interface.which('define') is None:
print('set Turbomole path')
sys.exit()
if interface.which('xtb') is None:
print('set XTB path')
sys.exit()
super(XtbTurbo, self).__init__(molecule)
self.start_coords = angstrom2bohr(molecule.coordinates)
self.atoms_in_fragments = molecule.fragments
self.job_dir = '{}/job_{}'.format(os.getcwd(), self.job_name)
self.coord_file = 'coord'
self.energy_file = 'energy'
self.egrad_program = ['xtb', 'coord', '-grad']
if self.charge > 0:
self.egrad_program += ['-chrg', str(self.charge)]
if self.multiplicity != 1:
self.egrad_program += ['-uhf', str(self.multiplicity)]
self.energy = None
self.optimized_coordinates = None
def __init__(self, molecule, method):
if which('xtb') is None:
xtb_logger.error('set XTB path')
sys.exit()
super(Xtb, self).__init__(molecule)
self.cmd = "xtb {} -opt vtight".format(self.start_xyz_file)
if self.charge != 0:
self.cmd = "{} -chrg {}".format(self.cmd, self.charge)
if self.multiplicity != 1:
self.cmd = "{} -uhf {}".format(self.cmd, self.multiplicity)
if self.multiplicity == 1 and self.scftype is not 'rhf':
self.cmd = "{} -{}".format(self.cmd, self.scftype)
self.trajectory_xyz_file = 'traj_' + self.job_name + '.xyz'
def optimize(self, options):
"""
:return:This object will return the optimization status. It will
optimize a structure.
"""
# TODO: Add a return 'CycleExceeded'
max_cycles = options['opt_cycles']
gamma = options['gamma']
convergence = options['opt_threshold']
self.keyword = self.keyword + '!Opt'
self.prepare_input()
with open(self.out_file, 'w') as fopt:
out = subp.Popen([which("orca"), self.inp_file],
stdout=fopt,
stderr=fopt)
out.communicate()
out.poll()
exit_status = out.returncode
if exit_status == 0:
f = open(self.out_file, "r")
line = f.readlines()
if "****ORCA TERMINATED NORMALLY****" in line[-2]:
self.energy = self.get_energy()
self.optimized_coordinates = np.loadtxt(self.inp_file[:-4] +
".xyz",
dtype=float,
skiprows=2,
usecols=(1, 2, 3))
write_xyz(self.atoms_list,
self.optimized_coordinates,
self.result_xyz_file,
energy=self.energy)
f.close()
return True
else:
print("Error: OPTIMIZATION PROBABLY FAILED. "
"CHECK THE .out FILE FOR PARTIAL OPTIMIZTION ")
print("Check for partial optimization.")
print("Location: {}".format(os.getcwd()))
return False