def copy(cls, lot, options, copy_wavefunction=True):
# Get node id for new struct
node_id = options.get('node_id', 1)
print(" making folder scratch/{}".format(node_id))
os.system('mkdir -p scratch/{}'.format(node_id))
file_options = File_Options.copy(lot.file_options)
options['file_options'] = file_options
if node_id != lot.node_id and copy_wavefunction:
old_path = 'scratch/{}/orbs.archive'.format(lot.node_id)
new_path = 'scratch/{}/orbs.archive'.format(node_id)
cmd = 'cp -r ' + old_path + ' ' + new_path
print(" copying scr files\n {}".format(cmd))
os.system(cmd)
os.system('wait')
return cls(lot.options.copy().set_values(options))
def copy(cls, lot, options, copy_wavefunction=True):
node_id = options.get('node_id', lot.node_id)
file_options = File_Options.copy(lot.file_options)
options['file_options'] = file_options
if node_id != lot.node_id and copy_wavefunction:
if "casscf" in lot.file_options.ActiveOptions:
old_path = 'scratch/{:03}/{}/c0.casscf'.format(
lot.ID, lot.node_id)
new_path = 'scratch/{:03}/{}/c0.casscf'.format(lot.ID, node_id)
copy_file(old_path, new_path)
else:
if lot.unrestricted:
old_path = 'scratch/{:03}/{}/ca0'.format(
lot.ID, lot.node_id)
new_path = 'scratch/{:03}/{}/'.format(lot.ID, node_id)
if os.path.isfile(old_path):
copy_file(old_path, new_path)
else:
print(" no file to copy")
old_path = 'scratch/{:03}/{}/cb0'.format(
lot.ID, lot.node_id)
new_path = 'scratch/{:03}/{}/'.format(lot.ID, node_id)
if os.path.isfile(old_path):
copy_file(old_path, new_path)
else:
print(" no file to copy")
else:
old_path = 'scratch/{:03}/{}/c0'.format(
lot.ID, lot.node_id)
new_path = 'scratch/{:03}/{}/'.format(lot.ID, node_id)
if os.path.isfile(old_path):
copy_file(old_path, new_path)
else:
print(" no file to copy")
# cmd = 'cp -r ' + old_path +' ' + new_path
# print(" copying scr files\n {}".format(cmd))
# os.system(cmd)
# os.system('wait')
return cls(lot.options.copy().set_values(options))
def copy(cls, lot, options, copy_wavefunction=True):
node_id = options.get('node_id', 1)
print(" making folder scratch/{}".format(node_id))
os.system('mkdir -p scratch/{}'.format(node_id))
file_options = File_Options.copy(lot.file_options)
options['file_options'] = file_options
if node_id != lot.node_id and copy_wavefunction:
if "casscf" in lot.file_options.ActiveOptions:
old_path = 'scratch/{}/c0.casscf'.format(lot.node_id)
new_path = 'scratch/{}/'.format(node_id)
else:
old_path = 'scratch/{}/c0'.format(lot.node_id)
new_path = 'scratch/{}/'.format(node_id)
cmd = 'cp -r ' + old_path + ' ' + new_path
print(" copying scr files\n {}".format(cmd))
os.system(cmd)
os.system('wait')
return cls(lot.options.copy().set_values(options))
def copy(cls, lot, options, copy_wavefunction=True):
node_id = options.get('node_id', lot.node_id)
file_options = File_Options.copy(lot.file_options)
options['file_options'] = file_options
if node_id != lot.node_id and copy_wavefunction:
if "casscf" in lot.file_options.ActiveOptions:
old_path = 'scratch/{:03}/{}/c0.casscf'.format(
lot.ID, lot.node_id)
new_path = 'scratch/{:03}/{}/c0.casscf'.format(lot.ID, node_id)
copy_file(old_path, new_path)
else:
use_alpha = False
for state in lot.states:
if state[0] == 2:
use_alpha = True
if use_alpha:
old_path = 'scratch/{:03}/{}/ca0'.format(
lot.ID, lot.node_id)
new_path = 'scratch/{:03}/{}/'.format(lot.ID, node_id)
copy_file(old_path, new_path)
old_path = 'scratch/{:03}/{}/cb0'.format(
lot.ID, lot.node_id)
new_path = 'scratch/{:03}/{}/'.format(lot.ID, node_id)
copy_file(old_path, new_path)
else:
old_path = 'scratch/{:03}/{}/c0'.format(
lot.ID, lot.node_id)
new_path = 'scratch/{:03}/{}/'.format(lot.ID, node_id)
copy_file(old_path, new_path)
#cmd = 'cp -r ' + old_path +' ' + new_path
#print(" copying scr files\n {}".format(cmd))
#os.system(cmd)
#os.system('wait')
return cls(lot.options.copy().set_values(options))
def __init__(
self,
options,
):
""" Constructor """
self.options = options
# properties
self.Energy = namedtuple('Energy', 'value unit')
self.Gradient = namedtuple('Gradient', 'value unit')
self.Coupling = namedtuple('Coupling', 'value unit')
self._Energies = {}
self._Gradients = {}
self._Couplings = {}
# count number of states
singlets = self.search_tuple(self.states, 1)
doublets = self.search_tuple(self.states, 2)
triplets = self.search_tuple(self.states, 3)
quartets = self.search_tuple(self.states, 4)
quintets = self.search_tuple(self.states, 5)
#TODO do this for all states, since it catches if states are put in lazy e.g [(1,1)]
if singlets:
len_singlets = max(singlets, key=lambda x: x[1])[1] + 1
else:
len_singlets = 0
len_doublets = len(doublets)
len_triplets = len(triplets)
len_quartets = len(quartets)
len_quintets = len(quintets)
# DO this before fixing states if put in lazy
if self.options['gradient_states'] == None and self.calc_grad:
print(" Assuming gradient states are ", self.states)
self.options['gradient_states'] = self.options['states']
if len(
self.states
) < len_singlets + len_doublets + len_triplets + len_quartets + len_quintets:
print('fixing states to be proper length')
tmp = []
# TODO put in rest of fixed states
for i in range(len_singlets):
tmp.append((1, i))
for i in range(len_triplets):
tmp.append((3, i))
self.states = tmp
print(' New states ', self.states)
self.geom = self.options['geom']
if self.geom is not None:
print(" initializing LOT from geom")
elif self.options['fnm'] is not None:
print(" initializing LOT from file")
if not os.path.exists(self.options['fnm']):
logger.error(
'Tried to create LOT object from a file that does not exist: %s\n'
% self.options['fnm'])
raise IOError
self.geom = manage_xyz.read_xyz(self.options['fnm'], scale=1.)
else:
raise RuntimeError("Need to initialize LOT object")
# Cache some useful atributes - other useful attributes are properties
self.currentCoords = manage_xyz.xyz_to_np(self.geom)
self.atoms = manage_xyz.get_atoms(self.geom)
self.ID = self.options['ID']
self.nproc = self.options['nproc']
self.charge = self.options['charge']
self.node_id = self.options['node_id']
self.lot_inp_file = self.options['lot_inp_file']
# Bools for running
self.hasRanForCurrentCoords = False
self.has_nelectrons = False
# Read file options if they exist and not already set
if self.file_options is None:
self.file_options = File_Options(self.lot_inp_file)
#package specific implementation
#TODO MOVE to specific package !!!
# tc cloud
self.options['job_data']['orbfile'] = self.options['job_data'].get(
'orbfile', '')
# pytc? TODO
self.options['job_data']['lot'] = self.options['job_data'].get(
'lot', None)
print(" making folder scratch/{:03}/{}".format(self.ID, self.node_id))
os.system('mkdir -p scratch/{:03}/{}'.format(self.ID, self.node_id))