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_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_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 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
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
