def set_up_neb_folders(self, image_structures):
"""Set up NEB folders.
Args:
image_structures <list of Structure>: List
of image structures
"""
imct = 0
myname = self.keywords['name']
if 'mast_coordinates' in self.keywords['program_keys'].keys():
coordstrucs = self.get_coordinates_only_structure_from_input()
newstrucs = list()
sidx = 0 #ex. coordstrucs 0, 1, 2 for 3 images
while sidx < self.keywords['program_keys']['mast_neb_settings'][
'images']:
sxtend = StructureExtensions(
struc_work1=image_structures[sidx + 1].copy(),
name=self.keywords['name'])
newstrucs.append(
sxtend.graft_coordinates_onto_structure(coordstrucs[sidx]))
sidx = sidx + 1
while imct < len(image_structures):
imposcar = Poscar(image_structures[imct])
num_str = str(imct).zfill(2)
impath = os.path.join(myname, num_str)
impospath = os.path.join(myname, "POSCAR_" + num_str)
if 'mast_coordinates' in self.keywords['program_keys'].keys():
if imct == 0: #skip endpoint
pass
elif imct == len(image_structures) - 1: #skip other endpt
pass
else:
imposcar.structure = newstrucs[imct - 1].copy()
dirutil.lock_directory(myname)
self.write_poscar_with_zero_velocities(imposcar, impospath)
dirutil.unlock_directory(myname)
try:
os.makedirs(impath)
except OSError:
self.logger.warning("Directory at %s already exists." % impath)
return None
dirutil.lock_directory(impath)
self.write_poscar_with_zero_velocities(
imposcar, os.path.join(impath, "POSCAR"))
dirutil.unlock_directory(impath)
imct = imct + 1
return
def set_up_neb_folders(self, image_structures):
"""Set up NEB folders.
Args:
image_structures <list of Structure>: List
of image structures
"""
imct=0
myname = self.keywords['name']
if 'mast_coordinates' in self.keywords['program_keys'].keys():
coordstrucs=self.get_coordinates_only_structure_from_input()
newstrucs=list()
sidx = 0 #ex. coordstrucs 0, 1, 2 for 3 images
while sidx < self.keywords['program_keys']['mast_neb_settings']['images']:
sxtend = StructureExtensions(struc_work1=image_structures[sidx+1].copy(), name=self.keywords['name'])
newstrucs.append(sxtend.graft_coordinates_onto_structure(coordstrucs[sidx]))
sidx = sidx + 1
while imct < len(image_structures):
imposcar = Poscar(image_structures[imct])
num_str = str(imct).zfill(2)
impath = os.path.join(myname, num_str)
impospath = os.path.join(myname, "POSCAR_" + num_str)
if 'mast_coordinates' in self.keywords['program_keys'].keys():
if imct == 0: #skip endpoint
pass
elif imct == len(image_structures)-1: #skip other endpt
pass
else:
imposcar.structure=newstrucs[imct-1].copy()
dirutil.lock_directory(myname)
self.write_poscar_with_zero_velocities(imposcar, impospath)
dirutil.unlock_directory(myname)
try:
os.makedirs(impath)
except OSError:
self.logger.warning("Directory at %s already exists." % impath)
return None
dirutil.lock_directory(impath)
self.write_poscar_with_zero_velocities(imposcar, os.path.join(impath, "POSCAR"))
dirutil.unlock_directory(impath)
imct = imct + 1
return
