def _vasp_poscar_setup(self):
"""Set up the POSCAR file for a single VASP run.
"""
name = self.keywords['name']
pospath = os.path.join(name, "POSCAR")
if os.path.isfile(pospath):
my_poscar = Poscar.from_file(pospath)
#parent should have given a structure
else: #this is an originating run; mast should give it a structure
if self.keywords['structure'] is not None:
my_poscar = Poscar(self.keywords['structure'])
else:
pf = os.path.join(os.path.dirname(name),'POSCAR_%s'%os.path.basename(name))
if os.path.isfile(pf):
my_poscar = Poscar.from_file(pf)
workdir=os.path.dirname(name)
sdir=os.path.join(workdir,"structure_index_files")
if os.path.exists(sdir):
mystr=my_poscar.structure
manname="manifest___"
myatomindex=AtomIndex(structure_index_directory=sdir)
newstr=myatomindex.graft_new_coordinates_from_manifest(mystr, manname, "")
self.logger.info("Getting original coordinates from manifest.")
new_pos=Poscar(newstr)
my_poscar=new_pos
self.logger.info("No POSCAR found from a parent; base structure used for %s" % self.keywords['name'])
if 'mast_coordinates' in self.keywords['program_keys'].keys():
sxtend = StructureExtensions(struc_work1=my_poscar.structure, name=self.keywords['name'])
coordstrucs=self.get_coordinates_only_structure_from_input()
newstruc = sxtend.graft_coordinates_onto_structure(coordstrucs[0])
my_poscar.structure=newstruc.copy()
dirutil.lock_directory(name)
my_poscar.write_file(pospath)
dirutil.unlock_directory(name)
return my_poscar
def test_graft_coordinates(self):
perfect = pymatgen.io.vaspio.Poscar.from_file("POSCAR_perfect").structure
coordsonly = pymatgen.io.vaspio.Poscar.from_file("POSCAR_coordinates").structure
compare_grafted = pymatgen.io.vaspio.Poscar.from_file("POSCAR_grafted").structure
sxtend = StructureExtensions(struc_work1=perfect)
grafted = sxtend.graft_coordinates_onto_structure(coordsonly)
self.assertEqual(grafted, compare_grafted)
self.assertEqual(grafted.lattice, compare_grafted.lattice)
self.assertEqual(grafted.sites, compare_grafted.sites)
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)
imposcar.write_file(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)
imposcar.write_file(os.path.join(impath, "POSCAR"))
dirutil.unlock_directory(impath)
imct = imct + 1
return
