def test_scale_structure_nine(self):
hcp = pymatgen.io.vaspio.Poscar.from_file("POSCAR_HCP").structure
sxtend = StructureExtensions(struc_work1=hcp, scaling_size="2 0 0,0 2 0,0 0 2", name=testdir)
scaled = sxtend.scale_structure()
self.assertEqual(scaled, pymatgen.io.vaspio.Poscar.from_file("POSCAR_HCP_222").structure)
self.assertEqual(scaled.lattice, pymatgen.io.vaspio.Poscar.from_file("POSCAR_HCP_222").structure.lattice)
self.assertEqual(scaled.sites.sort(), pymatgen.io.vaspio.Poscar.from_file("POSCAR_HCP_222").structure.sites.sort())
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 write_undefected_atom_indices(self):
"""Write undefected atom indices, including scaled indices.
Also write an undefected manifest file.
"""
scales = self.scaling.keys()
scales.append("")
for scaling_label in scales:
if scaling_label == "":
mySE=SE(struc_work1=self.startstr.copy())
mystruc=mySE.keywords['struc_work1']
else:
mySE=SE(struc_work1=self.startstr.copy(), scaling_size=self.scaling[scaling_label]["mast_size"])
mystruc=mySE.scale_structure()
alist=list()
manname=os.path.join(self.sdir,"manifest_%s__" % scaling_label)
for site in mystruc:
akey=self.get_new_key()
aname="atom_index_%s" % akey
aname = os.path.join(self.sdir, aname)
ameta = Metadata(metafile=aname)
ameta.write_data("atom_index",akey)
ameta.write_data("original_frac_coords", site.frac_coords)
ameta.write_data("element", site.species_string)
ameta.write_data("scaling_label", scaling_label)
alist.append(akey)
self.write_manifest_file(alist,manname)
return
def write_neb_phonon_sd_manifests(self):
"""Make NEB phonon manifests.
"""
neb_dict = self.input_options.get_item('neb', 'nebs')
if neb_dict == None:
return None
nlabels = neb_dict.keys()
scales = self.scaling.keys()
scales.append("")
for scaling_label in scales:
if scaling_label == "":
mySE = SE(struc_work1=self.startstr.copy())
else:
mySE = SE(
struc_work1=self.startstr.copy(),
scaling_size=self.scaling[scaling_label]["mast_size"])
for nlabel in nlabels:
pdict = dict(neb_dict[nlabel]["phonon"])
for phonon_label in pdict.keys():
pcoordsraw = pdict[phonon_label]['phonon_center_site']
pthresh = pdict[phonon_label]['threshold']
pcrad = pdict[phonon_label]['phonon_center_radius']
pcoords = np.array(pcoordsraw.split(), 'float')
if not (scaling_label == ""):
pcoords = mySE.get_scaled_coordinates(pcoords)
#pindices = self.find_orig_frac_coord_in_structure_dictionary(sdict, pcoords, pthresh+pcrad, True)
pindices = self.find_orig_frac_coord_in_atom_indices(
pcoords, "", scaling_label, True, 0.001 + pcrad)
manname = os.path.join(
self.sdir, "manifest_phonon_sd_%s_%s_%s" %
(nlabel, phonon_label, scaling_label))
self.write_manifest_file(pindices, manname)
return
def write_undefected_atom_indices(self):
"""Write undefected atom indices, including scaled indices.
Also write an undefected manifest file.
"""
scales = self.scaling.keys()
scales.append("")
for scaling_label in scales:
if scaling_label == "":
mySE = SE(struc_work1=self.startstr.copy())
mystruc = mySE.keywords['struc_work1']
else:
mySE = SE(
struc_work1=self.startstr.copy(),
scaling_size=self.scaling[scaling_label]["mast_size"])
mystruc = mySE.scale_structure()
alist = list()
manname = os.path.join(self.sdir, "manifest_%s__" % scaling_label)
for site in mystruc:
akey = self.get_new_key()
aname = "atom_index_%s" % akey
aname = os.path.join(self.sdir, aname)
ameta = Metadata(metafile=aname)
ameta.write_data("atom_index", akey)
ameta.write_data("original_frac_coords", site.frac_coords)
ameta.write_data("element", site.species_string)
ameta.write_data("scaling_label", scaling_label)
alist.append(akey)
self.write_manifest_file(alist, manname)
return
def write_neb_phonon_sd_manifests(self):
"""Make NEB phonon manifests.
"""
neb_dict=self.input_options.get_item('neb','nebs')
if neb_dict == None:
return None
nlabels=neb_dict.keys()
scales = self.scaling.keys()
scales.append("")
for scaling_label in scales:
if scaling_label == "":
mySE=SE(struc_work1=self.startstr.copy())
else:
mySE=SE(struc_work1=self.startstr.copy(), scaling_size=self.scaling[scaling_label]["mast_size"])
for nlabel in nlabels:
pdict = dict(neb_dict[nlabel]["phonon"])
for phonon_label in pdict.keys():
pcoordsraw = pdict[phonon_label]['phonon_center_site']
pthresh = pdict[phonon_label]['threshold']
pcrad = pdict[phonon_label]['phonon_center_radius']
pcoords = np.array(pcoordsraw.split(),'float')
if not (scaling_label == ""):
pcoords = mySE.get_scaled_coordinates(pcoords)
#pindices = self.find_orig_frac_coord_in_structure_dictionary(sdict, pcoords, pthresh+pcrad, True)
pindices = self.find_orig_frac_coord_in_atom_indices(pcoords,"",scaling_label,True,0.001+pcrad)
manname=os.path.join(self.sdir,"manifest_phonon_sd_%s_%s_%s" % (nlabel, phonon_label, scaling_label))
self.write_manifest_file(pindices, manname)
return
def test_strain_lattice(self):
perfect = pymatgen.io.vaspio.Poscar.from_file("POSCAR_unstrained").structure
sxtend = StructureExtensions(struc_work1=perfect)
strained = sxtend.strain_lattice(" 0.98 0.92 1.03 \n")
strain_compare = pymatgen.io.vaspio.Poscar.from_file("POSCAR_strained").structure
self.assertEqual(strained, strain_compare)
self.assertEqual(strained.lattice, strain_compare.lattice)
self.assertEqual(strained.sites, strain_compare.sites)
def test_scale_structure(self):
size = '1 1 0,-1 1 0,0 0 1'
perfect = pymatgen.io.vaspio.Poscar.from_file("POSCAR_perfect").structure
sxtend = StructureExtensions(struc_work1=perfect,scaling_size=size)
scaled = sxtend.scale_structure()
self.assertEqual(scaled, pymatgen.io.vaspio.Poscar.from_file("POSCAR_scaled").structure)
self.assertEqual(scaled.lattice, pymatgen.io.vaspio.Poscar.from_file("POSCAR_scaled").structure.lattice)
self.assertEqual(scaled.sites.sort(), pymatgen.io.vaspio.Poscar.from_file("POSCAR_scaled").structure.sites.sort())
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 test_get_sd_array_periodic_boundary(self):
perfect = pymatgen.io.vaspio.Poscar.from_file("POSCAR_perfect").structure
sxtend = StructureExtensions(struc_work1=perfect, name=testdir)
mysd = sxtend.get_sd_array("0.95 0.95 0.95", 1, 0.07)
#print mysd
myarr=np.zeros([40,3],bool)
for idx in [1]:
myarr[idx-1][0]=True
myarr[idx-1][1]=True
myarr[idx-1][2]=True
self.assertEqual(sum(np.fabs(sum(mysd-myarr))),0)
def test_get_sd_array(self):
perfect = pymatgen.io.vaspio.Poscar.from_file("POSCAR_perfect").structure
sxtend = StructureExtensions(struc_work1=perfect, name=testdir)
mysd = sxtend.get_sd_array("0.5 0.5 0.5", 3)
#print mysd
myarr=np.zeros([40,3],bool)
for idx in [8,20,25,26,28,30,32,33,36,37,38,39,40]:
myarr[idx-1][0]=True
myarr[idx-1][1]=True
myarr[idx-1][2]=True
self.assertEqual(sum(np.fabs(sum(mysd-myarr))),0)
def test_interpolation(self):
ep1 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_ep1").structure
ep2 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_ep2").structure
compare_im1 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_im1").structure
compare_im2 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_im2").structure
compare_im3 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_im3").structure
sxtend = StructureExtensions(struc_work1 = ep1, struc_work2 = ep2)
slist = sxtend.do_interpolation(3)
self.assertEqual(slist[0],ep1)
self.assertEqual(slist[1],compare_im1)
self.assertEqual(slist[2],compare_im2)
self.assertEqual(slist[3],compare_im3)
self.assertEqual(slist[4],ep2)
def test_multiple_sd_array(self):
perfect = pymatgen.io.vaspio.Poscar.from_file("POSCAR_perfect").structure
sxtend = StructureExtensions(struc_work1=perfect, name=testdir)
mysdlist = sxtend.get_multiple_sd_array("0.5 0.5 0.5", 1)
mylist=list()
mylist.append(np.zeros([40,3],bool))
mylist.append(np.zeros([40,3],bool))
mylist.append(np.zeros([40,3],bool))
mylist[0][8-1][0]=True
mylist[1][8-1][1]=True
mylist[2][8-1][2]=True
self.assertEqual(sum(np.fabs(sum(mysdlist[0]-mylist[0]))),0)
self.assertEqual(sum(np.fabs(sum(mysdlist[1]-mylist[1]))),0)
self.assertEqual(sum(np.fabs(sum(mysdlist[2]-mylist[2]))),0)
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 test_scale_structure(self):
size = '1 1 0,-1 1 0,0 0 1'
perfect = pymatgen.io.vaspio.Poscar.from_file(
"POSCAR_perfect").structure
sxtend = StructureExtensions(struc_work1=perfect, scaling_size=size)
scaled = sxtend.scale_structure()
self.assertEqual(
scaled,
pymatgen.io.vaspio.Poscar.from_file("POSCAR_scaled").structure)
self.assertEqual(
scaled.lattice,
pymatgen.io.vaspio.Poscar.from_file(
"POSCAR_scaled").structure.lattice)
self.assertEqual(
scaled.sites.sort(),
pymatgen.io.vaspio.Poscar.from_file(
"POSCAR_scaled").structure.sites.sort())
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
def test_sort_structure_and_neb_lines_really_scrambled(self):
raise SkipTest
neblines = list()
neblines.append(["Cr","0.0 0.9 0.8","0.0 0.8 0.7"])
neblines.append(["Cr","0.4 0.2 0.1","0.3 0.3 0.2"])
neblines.append(["Cr","0.29 0.05 0.05","0.01 0.01 0.98"])
neblines.append(["Ni","0.61 0.99 0.98","0.25 0.01 0.97"])
perfect3 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_defectgroup3_scrambled").structure
#print perfect3.get_sorted_structure()
#print perfect4.get_sorted_structure()
sxtend3 = StructureExtensions(struc_work1=perfect3)
sorted3 = sxtend3.sort_structure_and_neb_lines(neblines,"00",3)
compare_sorted3 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_sorted3").structure
self.assertEqual(sorted3, compare_sorted3)
self.assertEqual(sorted3.lattice, compare_sorted3.lattice)
self.assertEqual(sorted3.sites, compare_sorted3.sites)
perfect3 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_defectgroup3_really_scrambled").structure
#print perfect3.get_sorted_structure()
#print perfect4.get_sorted_structure()
sxtend3 = StructureExtensions(struc_work1=perfect3)
sorted3 = sxtend3.sort_structure_and_neb_lines(neblines,"00",3)
compare_sorted3 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_sorted3").structure
self.assertEqual(sorted3, compare_sorted3)
self.assertEqual(sorted3.lattice, compare_sorted3.lattice)
self.assertEqual(sorted3.sites, compare_sorted3.sites)
def test_scale_defect(self):
perfect = pymatgen.io.vaspio.Poscar.from_file("POSCAR_perfect").structure
scalingsize = "2,2,2"
sxtend = StructureExtensions(struc_work1=perfect, scaling_size=scalingsize, name=testdir)
scaled = sxtend.scale_structure()
sxtend2 = StructureExtensions(struc_work1=scaled, struc_work2=perfect, scaling_size=scalingsize, name=testdir)
vac1={'symbol':'O', 'type': 'vacancy', 'coordinates': np.array([0.25, 0.75, 0.25])}
defected = sxtend2.scale_defect(vac1,'fractional',0.0001)
int1={'symbol':'Ni', 'type': 'interstitial', 'coordinates': np.array([0.3, 0.3, 0.3])}
sxtend3 = StructureExtensions(struc_work1=defected, struc_work2=perfect, scaling_size=scalingsize, name=testdir)
defected2 = sxtend3.scale_defect(int1,'fractional',0.0001)
sub1={'symbol':'Fe', 'type': 'substitution','coordinates':np.array([0.25, 0.25,0.75])}
sxtend4 = StructureExtensions(struc_work1=defected2, struc_work2=perfect, scaling_size=scalingsize, name=testdir)
defected3 = sxtend4.scale_defect(sub1,'fractional',0.0001)
self.assertEqual(pymatgen.io.vaspio.Poscar.from_file("POSCAR_scaled_defected").structure, defected3)
def test_induce_defect_frac(self):
perfect = pymatgen.io.vaspio.Poscar.from_file("POSCAR_perfect").structure
compare_vac1 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_vac1").structure
compare_int1 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_int1").structure
compare_sub1 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_sub1").structure
coord_type='fractional'
threshold=1.e-4
vac1={'symbol':'O', 'type': 'vacancy', 'coordinates': np.array([0.25, 0.75, 0.25])}
int1={'symbol':'Ni', 'type': 'interstitial', 'coordinates': np.array([0.3, 0.3, 0.3])}
sub1={'symbol':'Fe', 'type': 'substitution','coordinates':np.array([0.25, 0.25,0.75])}
sxtend = StructureExtensions(struc_work1=perfect)
struc_vac1 = sxtend.induce_defect(vac1, coord_type, threshold)
struc_int1 = sxtend.induce_defect(int1, coord_type, threshold)
struc_sub1 = sxtend.induce_defect(sub1, coord_type, threshold)
self.assertEqual(struc_vac1,compare_vac1)
self.assertEqual(struc_int1,compare_int1)
self.assertEqual(struc_sub1,compare_sub1)
self.assertEqual(struc_vac1.lattice,compare_vac1.lattice)
self.assertEqual(struc_int1.lattice,compare_int1.lattice)
self.assertEqual(struc_sub1.lattice,compare_sub1.lattice)
self.assertEqual(struc_vac1.sites,compare_vac1.sites)
self.assertEqual(struc_int1.sites,compare_int1.sites)
self.assertEqual(struc_sub1.sites,compare_sub1.sites)
def write_neb_endpoint_manifests(self):
"""Make NEB endpoint manifests.
"""
neb_dict = self.input_options.get_item('neb', 'nebs')
if neb_dict == None:
return None
nlabels = neb_dict.keys()
scales = self.scaling.keys()
scales.append("")
for scaling_label in scales:
if scaling_label == "":
mySE = SE(struc_work1=self.startstr.copy())
else:
mySE = SE(
struc_work1=self.startstr.copy(),
scaling_size=self.scaling[scaling_label]["mast_size"])
for nlabel in nlabels:
def1 = nlabel.split("-")[0].strip()
def2 = nlabel.split("-")[1].strip()
manname1 = os.path.join(
self.sdir,
"manifest_%s_%s_%s" % (scaling_label, def1, nlabel))
manname2 = os.path.join(
self.sdir,
"manifest_%s_%s_%s" % (scaling_label, def2, nlabel))
mlist1raw = list(
self.read_manifest_file("%s/manifest_%s_%s_" %
(self.sdir, scaling_label, def1)))
mlist2raw = list(
self.read_manifest_file("%s/manifest_%s_%s_" %
(self.sdir, scaling_label, def2)))
mlist1 = list()
mlist2 = list()
for mitem in mlist1raw: #clean up leftover semicolons from defect manifests
if ";" in mitem:
mlist1.append(mitem.split(";")[0])
else:
mlist1.append(mitem)
for mitem in mlist2raw: #clean up leftover semicolons from defect manifests
if ";" in mitem:
mlist2.append(mitem.split(";")[0])
else:
mlist2.append(mitem)
maddtoend1 = list()
maddtoend2 = list()
nlines = list(neb_dict[nlabel]["lines"])
for nline in nlines:
ncoord1 = np.array(nline[1].split(), 'float')
ncoord2 = np.array(nline[2].split(), 'float')
if not (scaling_label == ""):
ncoord1 = mySE.get_scaled_coordinates(ncoord1)
ncoord2 = mySE.get_scaled_coordinates(ncoord2)
nelem = nline[0]
nidx1 = self.find_orig_frac_coord_in_atom_indices(
ncoord1, nelem, scaling_label, False, 0.001)
nidx2 = self.find_orig_frac_coord_in_atom_indices(
ncoord2, nelem, scaling_label, False, 0.001)
try:
mlist1.remove(nidx1)
except ValueError:
raise MASTError(
self.__class__.__name__,
"For neb %s, cannot remove atom index %s from mlist1: %s"
% (nlabel, nidx1, mlist1))
maddtoend1.append(nidx1) #resort matches to the bottom
try:
mlist2.remove(nidx2)
except ValueError:
raise MASTError(
self.__class__.__name__,
"For neb %s, cannot remove atom index %s from mlist2: %s"
% (nlabel, nidx2, mlist2))
maddtoend2.append(nidx2)
if not (mlist1 == mlist2):
raise MASTError(
"NEB %s truncated manifests do not match: %s, %s" %
(nlabel, mlist1, mlist2))
mlist1.extend(maddtoend1)
mlist2.extend(maddtoend2)
self.write_manifest_file(mlist1, manname1)
self.write_manifest_file(mlist2, manname2)
return
def test_scale_defect(self):
size = '1 1 0,-1 1 0,0 0 1'
perfect = pymatgen.io.vaspio.Poscar.from_file(
"POSCAR_perfect").structure
sxtend = StructureExtensions(struc_work1=perfect, scaling_size=size)
scaled = sxtend.scale_structure()
sxtend2 = StructureExtensions(struc_work1=scaled, scaling_size=size)
vac1 = {
'symbol': 'O',
'type': 'vacancy',
'coordinates': np.array([0.25, 0.75, 0.25])
}
defected = sxtend2.scale_defect(vac1, 'fractional', 0.0001)
int1 = {
'symbol': 'Ni',
'type': 'interstitial',
'coordinates': np.array([0.3, 0.3, 0.3])
}
sxtend3 = StructureExtensions(struc_work1=defected, scaling_size=size)
defected2 = sxtend3.scale_defect(int1, 'fractional', 0.0001)
sub1 = {
'symbol': 'Fe',
'type': 'substitution',
'coordinates': np.array([0.25, 0.25, 0.75])
}
sxtend4 = StructureExtensions(struc_work1=defected2, scaling_size=size)
defected3 = sxtend4.scale_defect(sub1, 'fractional', 0.0001)
self.assertEqual(
pymatgen.io.vaspio.Poscar.from_file(
"POSCAR_scaled_defected").structure, defected3)
def write_defected_atom_indices(self):
"""Write any additional defect atom indices and make manifests.
"""
defect_dict = self.input_options.get_item('defects', 'defects')
if defect_dict == None:
return None
dlabels = defect_dict.keys()
scales = self.scaling.keys()
scales.append("")
for scaling_label in scales:
alist = list(
self.read_manifest_file("%s/manifest_%s__" %
(self.sdir, scaling_label)))
if scaling_label == "":
mySE = SE(struc_work1=self.startstr.copy())
else:
mySE = SE(
struc_work1=self.startstr.copy(),
scaling_size=self.scaling[scaling_label]["mast_size"])
for dlabel in dlabels:
dlist = list(alist)
manname = os.path.join(
self.sdir, "manifest_%s_%s_" % (scaling_label, dlabel))
dsubkeys = defect_dict[dlabel].keys()
for dsubkey in dsubkeys:
if "subdefect_" in dsubkey:
dtype = defect_dict[dlabel][dsubkey]['type']
dcoords = defect_dict[dlabel][dsubkey]['coordinates']
delement = defect_dict[dlabel][dsubkey]['symbol']
if not (scaling_label == ""):
dcoords = mySE.get_scaled_coordinates(dcoords)
if dtype == "interstitial":
didx = self.find_orig_frac_coord_in_atom_indices(
dcoords, delement, scaling_label, False, 0.001)
if didx == None:
akey = self.get_new_key()
aname = "atom_index_%s" % akey
aname = os.path.join(self.sdir, aname)
ameta = Metadata(metafile=aname)
ameta.write_data("atom_index", akey)
ameta.write_data("original_frac_coords",
dcoords)
ameta.write_data("element", delement)
ameta.write_data("scaling_label",
scaling_label)
dlist.append("%s;int" %
akey) #interstitial label
else:
dlist.append("%s;int" % didx)
elif dtype == "vacancy":
didx = self.find_orig_frac_coord_in_atom_indices(
dcoords, delement, scaling_label, False, 0.001)
try:
dlist.remove(didx)
except ValueError:
raise MASTError(
self.__class__.__name__,
"For defect %s, cannot remove atom index %s from list: %s"
% (dlabel, didx, dlist))
elif dtype in ["substitution", "antisite"]:
didxlist = self.find_orig_frac_coord_in_atom_indices(
dcoords, "", scaling_label, True, 0.001
) #leave element empty; just search coords
idxtorepl = list()
for didx in didxlist:
dmeta = Metadata(metafile="%s/atom_index_%s" %
(self.sdir, didx))
dmetaelem = dmeta.read_data("element")
if not (delement == dmetaelem):
if didx in dlist:
dlist.remove(didx)
idxtorepl.append(didx)
if len(idxtorepl) > 1:
raise MASTError(
self.__class__.__name__,
"Interstitial %s is attempting to replace more than one atom: %s"
% (dlabel, idxtorepl))
didxsub = self.find_orig_frac_coord_in_atom_indices(
dcoords, delement, scaling_label, False, 0.001
) #leave element empty; just search coords
if didxsub == None:
akey = self.get_new_key()
aname = "atom_index_%s" % akey
aname = os.path.join(self.sdir, aname)
ameta = Metadata(metafile=aname)
ameta.write_data("atom_index", akey)
ameta.write_data("original_frac_coords",
dcoords)
ameta.write_data("element",
delement) #sub element here
ameta.write_data("scaling_label",
scaling_label)
dlist.append("%s;%s" % (akey, idxtorepl[0]))
else:
dlist.append("%s;%s" % (didxsub, idxtorepl[0]))
self.write_manifest_file(dlist, manname)
return
def test_sort_structure_and_neb_lines(self):
perfect1 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_defectgroup1").structure
compare_sorted1 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_sorted1").structure
perfect2 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_defectgroup2").structure
compare_sorted2 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_sorted2").structure
neblines = list()
neblines.append(["Cr","0.3 0 0","0 0 0"])
neblines.append(["Ni","0.6 0 0","0.3 0 0"])
sxtend1 = StructureExtensions(struc_work1=perfect1, name=testdir)
sorted1 = sxtend1.sort_structure_and_neb_lines(neblines,"00",3)
sxtend2 = StructureExtensions(struc_work1=perfect2, name=testdir)
sorted2 = sxtend2.sort_structure_and_neb_lines(neblines,"04",3)
self.assertEqual(sorted1, compare_sorted1)
self.assertEqual(sorted2, compare_sorted2)
self.assertEqual(sorted1.lattice, compare_sorted1.lattice)
self.assertEqual(sorted2.lattice, compare_sorted2.lattice)
self.assertEqual(sorted1.sites, compare_sorted1.sites)
self.assertEqual(sorted2.sites, compare_sorted2.sites)
neblines = list()
neblines.append(["Cr","0.29 0.05 0.05","0.01 0.01 0.98"])
neblines.append(["Ni","0.61 0.99 0.98","0.25 0.01 0.97"])
sxtend1 = StructureExtensions(struc_work1=perfect1, name=testdir)
sorted1 = sxtend1.sort_structure_and_neb_lines(neblines,"00",3)
sxtend2 = StructureExtensions(struc_work1=perfect2, name=testdir)
sorted2 = sxtend2.sort_structure_and_neb_lines(neblines,"04",3)
self.assertEqual(sorted1, compare_sorted1)
self.assertEqual(sorted2, compare_sorted2)
self.assertEqual(sorted1.lattice, compare_sorted1.lattice)
self.assertEqual(sorted2.lattice, compare_sorted2.lattice)
self.assertEqual(sorted1.sites, compare_sorted1.sites)
self.assertEqual(sorted2.sites, compare_sorted2.sites)
neblines = list()
neblines.append(["Cr","0.0 0.9 0.8","0.0 0.8 0.7"])
neblines.append(["Cr","0.4 0.2 0.1","0.3 0.3 0.2"])
neblines.append(["Cr","0.29 0.05 0.05","0.01 0.01 0.98"])
neblines.append(["Ni","0.61 0.99 0.98","0.25 0.01 0.97"])
perfect3 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_defectgroup3").structure
#print perfect3.get_sorted_structure()
perfect4 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_defectgroup4").structure
#print perfect4.get_sorted_structure()
sxtend3 = StructureExtensions(struc_work1=perfect3, name=testdir)
sorted3 = sxtend3.sort_structure_and_neb_lines(neblines,"00",3)
#print sorted3
sxtend4 = StructureExtensions(struc_work1=perfect4, name=testdir)
sorted4 = sxtend4.sort_structure_and_neb_lines(neblines,"04",3)
#print sorted4
compare_sorted3 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_sorted3").structure
#print compare_sorted3
compare_sorted4 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_sorted4").structure
#print compare_sorted4
self.assertEqual(sorted3, compare_sorted3)
self.assertEqual(sorted4, compare_sorted4)
self.assertEqual(sorted3.lattice, compare_sorted3.lattice)
self.assertEqual(sorted4.lattice, compare_sorted4.lattice)
self.assertEqual(sorted3.sites, compare_sorted3.sites)
self.assertEqual(sorted4.sites, compare_sorted4.sites)
def write_defected_atom_indices(self):
"""Write any additional defect atom indices and make manifests.
"""
defect_dict=self.input_options.get_item('defects','defects')
if defect_dict == None:
return None
dlabels=defect_dict.keys()
scales = self.scaling.keys()
scales.append("")
for scaling_label in scales:
alist=list(self.read_manifest_file("%s/manifest_%s__" % (self.sdir, scaling_label)))
if scaling_label == "":
mySE=SE(struc_work1=self.startstr.copy())
else:
mySE=SE(struc_work1=self.startstr.copy(), scaling_size=self.scaling[scaling_label]["mast_size"])
for dlabel in dlabels:
dlist = list(alist)
manname=os.path.join(self.sdir,"manifest_%s_%s_" % (scaling_label, dlabel))
dsubkeys=defect_dict[dlabel].keys()
for dsubkey in dsubkeys:
if "subdefect_" in dsubkey:
dtype=defect_dict[dlabel][dsubkey]['type']
dcoords=defect_dict[dlabel][dsubkey]['coordinates']
delement=defect_dict[dlabel][dsubkey]['symbol']
if not (scaling_label == ""):
dcoords = mySE.get_scaled_coordinates(dcoords)
if dtype == "interstitial":
didx=self.find_orig_frac_coord_in_atom_indices(dcoords, delement, scaling_label, False, 0.001)
if didx == None:
akey=self.get_new_key()
aname="atom_index_%s" % akey
aname = os.path.join(self.sdir, aname)
ameta = Metadata(metafile=aname)
ameta.write_data("atom_index",akey)
ameta.write_data("original_frac_coords", dcoords)
ameta.write_data("element", delement)
ameta.write_data("scaling_label", scaling_label)
dlist.append("%s;int" % akey) #interstitial label
else:
dlist.append("%s;int" % didx)
elif dtype == "vacancy":
didx=self.find_orig_frac_coord_in_atom_indices(dcoords, delement, scaling_label, False, 0.001)
try:
dlist.remove(didx)
except ValueError:
raise MASTError(self.__class__.__name__, "For defect %s, cannot remove atom index %s from list: %s" % (dlabel, didx, dlist))
elif dtype in ["substitution","antisite"]:
didxlist=self.find_orig_frac_coord_in_atom_indices(dcoords, "", scaling_label, True, 0.001) #leave element empty; just search coords
idxtorepl=list()
for didx in didxlist:
dmeta = Metadata(metafile="%s/atom_index_%s" % (self.sdir, didx))
dmetaelem = dmeta.read_data("element")
if not (delement == dmetaelem):
if didx in dlist:
dlist.remove(didx)
idxtorepl.append(didx)
if len(idxtorepl) > 1:
raise MASTError(self.__class__.__name__, "Interstitial %s is attempting to replace more than one atom: %s" % (dlabel, idxtorepl))
didxsub=self.find_orig_frac_coord_in_atom_indices(dcoords, delement, scaling_label, False, 0.001) #leave element empty; just search coords
if didxsub == None:
akey=self.get_new_key()
aname="atom_index_%s" % akey
aname = os.path.join(self.sdir, aname)
ameta = Metadata(metafile=aname)
ameta.write_data("atom_index",akey)
ameta.write_data("original_frac_coords", dcoords)
ameta.write_data("element", delement) #sub element here
ameta.write_data("scaling_label", scaling_label)
dlist.append("%s;%s" % (akey, idxtorepl[0]))
else:
dlist.append("%s;%s" % (didxsub, idxtorepl[0]))
self.write_manifest_file(dlist, manname)
return
def write_neb_endpoint_manifests(self):
"""Make NEB endpoint manifests.
"""
neb_dict=self.input_options.get_item('neb','nebs')
if neb_dict == None:
return None
nlabels=neb_dict.keys()
scales = self.scaling.keys()
scales.append("")
for scaling_label in scales:
if scaling_label == "":
mySE=SE(struc_work1=self.startstr.copy())
else:
mySE=SE(struc_work1=self.startstr.copy(), scaling_size=self.scaling[scaling_label]["mast_size"])
for nlabel in nlabels:
def1 = nlabel.split("-")[0].strip()
def2 = nlabel.split("-")[1].strip()
manname1=os.path.join(self.sdir,"manifest_%s_%s_%s" % (scaling_label, def1, nlabel))
manname2=os.path.join(self.sdir,"manifest_%s_%s_%s" % (scaling_label, def2, nlabel))
mlist1raw=list(self.read_manifest_file("%s/manifest_%s_%s_" % (self.sdir, scaling_label, def1)))
mlist2raw=list(self.read_manifest_file("%s/manifest_%s_%s_" % (self.sdir, scaling_label, def2)))
mlist1=list()
mlist2=list()
for mitem in mlist1raw: #clean up leftover semicolons from defect manifests
if ";" in mitem:
mlist1.append(mitem.split(";")[0])
else:
mlist1.append(mitem)
for mitem in mlist2raw: #clean up leftover semicolons from defect manifests
if ";" in mitem:
mlist2.append(mitem.split(";")[0])
else:
mlist2.append(mitem)
maddtoend1=list()
maddtoend2=list()
nlines=list(neb_dict[nlabel]["lines"])
for nline in nlines:
ncoord1 = np.array(nline[1].split(), 'float')
ncoord2 = np.array(nline[2].split(), 'float')
if not (scaling_label == ""):
ncoord1 = mySE.get_scaled_coordinates(ncoord1)
ncoord2 = mySE.get_scaled_coordinates(ncoord2)
nelem = nline[0]
nidx1 = self.find_orig_frac_coord_in_atom_indices(ncoord1, nelem, scaling_label, False, 0.001)
nidx2 = self.find_orig_frac_coord_in_atom_indices(ncoord2, nelem, scaling_label, False, 0.001)
try:
mlist1.remove(nidx1)
except ValueError:
raise MASTError(self.__class__.__name__, "For neb %s, cannot remove atom index %s from mlist1: %s" % (nlabel, nidx1, mlist1))
maddtoend1.append(nidx1) #resort matches to the bottom
try:
mlist2.remove(nidx2)
except ValueError:
raise MASTError(self.__class__.__name__, "For neb %s, cannot remove atom index %s from mlist2: %s" % (nlabel, nidx2, mlist2))
maddtoend2.append(nidx2)
if not (mlist1==mlist2):
raise MASTError("NEB %s truncated manifests do not match: %s, %s" % (nlabel, mlist1, mlist2))
mlist1.extend(maddtoend1)
mlist2.extend(maddtoend2)
self.write_manifest_file(mlist1, manname1)
self.write_manifest_file(mlist2, manname2)
return
