def optimize(self,
max_cycles=350,
gamma=0.0,
restart=False,
convergence='normal'):
"""
:return:This object will return the optimization status. It will
optimize a structure.
"""
# TODO: Add a return 'CycleExceeded'
logfile = "trial_{}.log".format(self.job_name)
with open(logfile, 'w') as fopt:
out = subp.Popen(["mopac", self.inp_file],
stdout=fopt,
stderr=fopt)
out.communicate()
out.poll()
exit_status = out.returncode
if exit_status == 0:
if os.path.exists(self.arc_file):
self.energy = self.get_energy()
self.optimized_coordinates = self.get_coords()
interface.write_xyz(self.atoms_list,
self.optimized_coordinates,
self.result_xyz_file,
self.job_name,
energy=self.energy)
return True
else:
print("Error: File ", self.arc_file, "was not found.")
print("Check for partial optimization.")
print("Location: {}".format(os.getcwd()))
return False
def optimize(self,
max_cycles=350,
gamma=0.0,
restart=False,
convergence='normal'):
"""
:return:This object will return the optimization status. It will
optimize a structure.
"""
# TODO: Add a return 'CycleExceeded'
with open(self.out_file, 'w') as fopt:
out = subp.Popen(["psi4", 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")
if " **** Optimization is complete!" in f.read():
print("Optimized")
self.energy = self.get_energy()
self.optimized_coordinates = self.get_coordinates()
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
def run_turbomole_jobex(self, max_cycles=350):
"""
return one of the following:
True: converged
SCFFailed
GradFailed
UpdateFailed
CycleExceeded
False: unknown error or jebex excution error
:rtype: string or boolean
"""
with open('jobex.out', 'w') as fj:
try:
subp.check_call(['jobex', '-ri', '-c', str(max_cycles)], stdout=fj,
stderr=fj)
except subp.CalledProcessError as e:
turbomole_logger.error('jobex failed, check %s/jobex.out'
% os.getcwd())
return False
if os.path.isfile('GEO_OPT_FAILED'):
message = open('GEO_OPT_FAILED').read()
if 'ERROR: Module' in message:
turbomole_logger.error('Error in module!\n chcek %s/GEO_OPT_FAILED' % os.getcwd())
return False
elif 'ERROR in statpt step,' in message:
turbomole_logger.error('Statpt failed!\n chcek %s/GEO_OPT_FAILED' % os.getcwd())
return 'UpdateFailed'
elif 'ERROR in relax step,' in message:
turbomole_logger.error('Relax failed!\n chcek %s/GEO_OPT_FAILED' % os.getcwd())
return 'UpdateFailed'
elif 'ERROR: your energy calculation did not converge !!,' in message:
turbomole_logger.error('SCF failed!\n chcek %s/GEO_OPT_FAILED' % os.getcwd())
return 'SCFFailed'
elif 'ERROR in dscf step' in message:
turbomole_logger.error('SCF failed!\n chcek %s/GEO_OPT_FAILED' % os.getcwd())
return 'SCFFailed'
elif 'ERROR in gradient step' in message:
turbomole_logger.error('Gradient failed!\n chcek %s/GEO_OPT_FAILED' % os.getcwd())
return 'GradientFailed'
elif 'OPTIMIZATION DID NOT CONVERGE' in message:
turbomole_logger.error('Geometry did not converge in %d cycles.\ncheck %s' % (max_cycles, os.getcwd()))
self.energy = get_energy()
self.optimized_coordinates = bohr2angstrom(get_coords())
return 'CycleExceeded'
else:
turbomole_logger.error('Unknown Error!\n chcek the files in %s' % os.getcwd())
return False
elif os.path.isfile('GEO_OPT_CONVERGED'):
turbomole_logger.debug('jobex done')
self.energy = get_energy()
self.optimized_coordinates = bohr2angstrom(get_coords())
interface.write_xyz(self.atoms_list, self.optimized_coordinates,
self.result_xyz_file,
self.job_name,
energy=self.energy)
return True
def optimize(self, options):
"""
:return:This object will return the optimization status. It will
optimize a structure.
"""
# TODO: Add a return 'CycleExceeded'
logfile = "trial_{}.out".format(self.job_name)
max_opt_cycles = options['opt_cycles']
gamma = options['gamma']
opt_keywords = f"maxcycles={max_opt_cycles}"
convergence = options['opt_threshold']
if convergence != 'normal':
opt_keywords += f", {convergence}"
self.keyword += f" opt=({opt_keywords})"
self.prepare_input()
with open(self.out_file, 'w') as fopt:
out = subp.Popen(["g16", self.inp_file], stdout=fopt, stderr=fopt)
out.communicate()
out.poll()
exit_status = out.returncode
if exit_status == 0:
file_pointer = open(self.out_file, "r")
this_line = file_pointer.readlines()
check_1 = 0
check_2 = 0
for j in this_line:
if "Optimization completed" in j:
check_1 = 1
if "SCF Done" in j:
check_2 = 1
if ("Normal termination"
in this_line[-1]) and check_1 == 1 and check_2 == 1:
self.energy = self.get_energy()
self.optimized_coordinates = self.get_coords()
interface.write_xyz(self.atoms_list,
self.optimized_coordinates,
self.result_xyz_file,
self.job_name,
energy=self.energy)
file_pointer.close()
return True
else:
print("Error: OPTIMIZATION PROBABLY FAILED.")
print("Location: {}".format(os.getcwd()))
return False
def optimize(self, options):
max_cycles = options['opt_cycles']
gamma = options['gamma']
convergence = options['opt_threshold']
pyar.interface.turbomole.make_coord(self.atoms_list, self.start_coords, self.coord_file)
pyar.interface.turbomole.prepare_control()
for cycle in range(max_cycles):
xtb_turbo_logger.debug("Optimization Cycle {}".format(cycle))
# Calculate energy and gradient
status, message, energy, gradients = self.calc_engrad
if status is False:
xtb_turbo_logger.critical('Energy/Gradient evaluation failed')
return 'SCFFailed'
# Calculate afir gradient if gamma is greater than zero
afir_energy, afir_gradient = restraints.isotropic(self.atoms_in_fragments, self.atoms_list,
pyar.interface.turbomole.get_coords(), gamma)
pyar.interface.turbomole.rewrite_turbomole_energy_and_gradient_files(self.number_of_atoms, afir_energy,
afir_gradient)
# Update coordinates and check convergence.
status = pyar.interface.turbomole.update_coord()
if status is False:
xtb_turbo_logger.critical('Coordinate update failed in cycle %d' % cycle)
xtb_turbo_logger.critical('Check the job in %s' % os.getcwd())
return 'UpdateFailed'
convergence_status = pyar.interface.turbomole.check_geometry_convergence()
if convergence_status is True:
xtb_turbo_logger.info('converged at {}'.format(cycle))
self.energy = pyar.interface.turbomole.get_energy()
self.optimized_coordinates = bohr2angstrom(pyar.interface.turbomole.get_coords())
interface.write_xyz(self.atoms_list, self.optimized_coordinates,
self.result_xyz_file,
self.job_name,
energy=self.energy)
return True
with open('energy.dat', 'a') as fe:
fe.writelines("{:3d} {:15.8f} {:15.8f}\n".format(cycle, energy, energy + afir_energy))
else:
xtb_turbo_logger.info("cycle exceeded")
status = 'cycle_exceeded'
self.energy = pyar.interface.turbomole.get_energy()
self.optimized_coordinates = bohr2angstrom(pyar.interface.turbomole.get_coords())
return status
def optimize(self,
max_cycles=350,
gamma=None,
restart=False,
convergence='normal'):
"""
:returns: True,
'SCFFailed',
'GradFailed',
'UpdateFailed',
'CycleExceeded',
False
"""
if gamma is not None:
xtb_logger.error('not implemented in this module. Use xtb_turbo')
with open('xtb.out', 'w') as output_file_pointer:
try:
out = subp.check_call(self.cmd.split(),
stdout=output_file_pointer,
stderr=output_file_pointer)
except Exception as e:
xtb_logger.info(' Optimization failed')
xtb_logger.error(f" {e}")
return False
if os.path.isfile('.xtboptok'):
write_xyz(self.atoms_list,
self.optimized_coordinates,
self.result_xyz_file,
job_name=self.job_name,
energy=self.energy)
os.rename('xtbopt.log', self.trajectory_xyz_file)
os.remove('.xtboptok')
return True
elif os.path.isfile('.sccnotconverged') or os.path.isfile(
'NOT_CONVERGED'):
xtb_logger.info(
' SCF Convergence failure in {} run in {}'.format(
self.start_xyz_file, os.getcwd()))
return 'SCFFailed'
else:
xtb_logger.info(
' Something went wrong with {} run in {}'.format(
self.start_xyz_file, os.getcwd()))
return False
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
def optimize(self, options):
"""This is the python implementation of jobex of turbomole
:returns: Union(True,
'SCFFailed',
'GradFailed',
'UpdateFailed',
'CycleExceeded',
False)
"""
max_cycles = options['opt_cycles']
gamma = options['gamma']
convergence = options['opt_threshold']
if convergence == 'loose':
scf_conv = 6
elif convergence == 'tight':
scf_conv = 8
else:
scf_conv = 7
basis_set = self.basis
functional = 'bp'
if self.method.lower() == 'bp86':
functional = 'bp'
if self.method.lower() == 'b3lyp':
functional = 'b3-lyp'
make_coord(self.atoms_list, self.start_coords)
define_status = prepare_control(scf_conv=scf_conv,
charge=self.charge,
multiplicity=self.multiplicity,
basis=basis_set,
func=functional)
if define_status is False:
turbomole_logger.debug(
'Initial Define failed, converting to cartesian coordinate')
remove('control')
define_status = prepare_control(scf_conv=scf_conv,
coordinates='cartesian',
charge=self.charge,
multiplicity=self.multiplicity)
if define_status is False:
turbomole_logger.debug('Initial Define failed again. Quit')
return 'UpdateFailed'
if gamma is None:
return self.run_turbomole_jobex(max_cycles=max_cycles)
# Test for Turbomole input
if not os.path.isfile('control'):
turbomole_logger.critical("Turbomole control file should exist")
return False
with open('not.converged', 'w') as fp:
fp.write('$convcrit\n')
fp.write(' energy 6\n')
fp.write(' cartesian gradient 3\n')
fp.write(' basis set gradient 3\n')
fp.write(' cycles 1\n')
fp.write('$convergence not reached\n')
fp.write('$end\n')
remove('statistics')
remove('dscf_problem')
turbomole_logger.info("Turbomole Optimization started\n")
turbomole_logger.info(" at %s\n" % datetime.datetime.now())
turbomole_logger.info(" on machine %s\n" % socket.gethostname())
turbomole_logger.info(" by user %s\n" % os.getlogin())
turbomole_logger.info(" in directory %s\n" % os.getcwd())
initial_status, initial_energy = calc_energy()
if initial_status is False:
turbomole_logger.warning('Initial energy evaluation failed.')
return 'SCFFailed'
turbomole_logger.debug('First step: %s, %f' %
(initial_status, initial_energy))
for cycle in range(max_cycles):
# Calculate Gradients
gradient_status = calc_gradients()
if gradient_status is False:
turbomole_logger.error(
'Gradient evaluation failed in cycle %d' % cycle)
return 'GradFailed'
for line in open('gradient').readlines():
if 'cycle' in line:
turbomole_logger.debug(line.strip())
# Calculate afir gradient if gamma is greater than zero
# if gamma > 0.0:
afir_energy, afir_gradients = restraints.isotropic(
self.atoms_in_fragments, self.atoms_list, get_coords(), gamma)
rewrite_turbomole_energy_and_gradient_files(
self.number_of_atoms, afir_energy, afir_gradients)
turbomole_logger.debug(f'restraint energy = {afir_energy:f}')
# Update coordinates and check convergence.
update_status = update_coord()
if update_status is False:
turbomole_logger.critical(
'Coordinate update failed in cycle %d' % cycle)
turbomole_logger.critical('Check the job in %s' % os.getcwd())
return 'UpdateFailed'
convergence_status = check_geometry_convergence()
if convergence_status is True:
turbomole_logger.info('converged at %d' % cycle)
self.energy = get_energy()
self.optimized_coordinates = bohr2angstrom(get_coords())
interface.write_xyz(self.atoms_list,
self.optimized_coordinates,
self.result_xyz_file,
self.job_name,
energy=self.energy)
return True
# Calculate energy
scf_status, energy = calc_energy()
if scf_status is False:
turbomole_logger.critical(
'Energy evaluation failed in cycle %d' % cycle)
return 'SCFFailed'
with open('energy.dat', 'a') as fe:
# if gamma > 0.0:
fe.writelines("{:3d} {:15.8f} {:15.8f}\n".format(
cycle, energy, energy + afir_energy))
# else:
# fe.writelines("{:3d} {:15.8f}\n".format(cycle, energy))
else:
turbomole_logger.info(
"OPTIMIZATION DID NOT CONVERGE WITHIN "
"%d CYCLES\n Restarting it after checking "
"the gradient norms\n might be a good idea..."
" (grep cycle gradient)" % max_cycles)
self.energy = get_energy()
self.optimized_coordinates = bohr2angstrom(get_coords())
return 'CycleExceeded'