def structure_to_gulp(iof,
struct,
runspec="single conp",
postcards=[],
potentials=None):
"""
Writes a file on gulp input format.
"""
iof = httk.IoAdapterFileWriter.use(iof)
f = iof.file
f.write(str(runspec) + "\n")
f.write("cell\n")
f.write(" " + str(struct.a) + " " + str(struct.b) + " " + str(struct.c) +
" ")
f.write(
str(struct.alpha) + " " + str(struct.beta) + " " + str(struct.gamma) +
"\n")
f.write("fractional\n")
for i in range(struct.N):
species = periodictable.atomic_symbol(struct.p1occupancies[i])
f.write(species + " ")
f.write(" ".join([str(float(x)) for x in struct.p1coords[i]]) + "\n")
#print("X",species+str(idx)+" "+" ".join([str(float(x)) for x in struct.coords[i]])+"\n")
for card in postcards:
f.write(card + "\n")
if potentials is None:
f.write(generate_fake_potentials(set(struct.p1assignments)))
f.write("\n")
iof.close()
def generate_fake_potentials_try2(species):
potentials = ""
potentials += "epsilon\n"
for s1 in species:
ss1 = periodictable.atomic_symbol(s1)
ns1 = periodictable.atomic_number(s1)
#potentials += "%s core %.4f %.4f 0 0\n" % (ss1,sqrt(0.5*ns1),pow(0.75*ns1,3.0/2.0))
# potentials += "%s core %.4f %.4f 0 0\n" % (ss1,pow(ns1,0.9783276738),pow(ns1,1.124243243))
potentials += "%s core %.4f %.4f 0 0\n" % (ss1, 0.1 * ns1, 0.1 * ns1)
potentials += "lennard zero epsilon combine all\n"
potentials += "0.0 12.0\n"
return potentials
def generate_fake_potentials(species):
potentials = ""
potentials += "atomab\n"
for s1 in species:
ss1 = periodictable.atomic_symbol(s1)
ns1 = periodictable.atomic_number(s1)
potentials += "%s core %.4f %.4f 0 0\n" % (ss1, sqrt(
0.5 * ns1), pow(0.75 * ns1, 3.0 / 2.0))
#potentials = "lennard combine 12 6\n"
potentials += "lennard 12 6 combine all\n"
potentials += "0.0 20.0\n"
#for s1 in species:
# ss1 = periodictable.atomic_symbol(s1)
# for s2 in species:
# ss2 = periodictable.atomic_symbol(s2)
# potentials += "%s core %s core %.4f %.4f\n" % (ss1, ss2,0.0,10.0)
return potentials
def symbol(self):
#if self.extended:
# raise Exception("SiteAssignment: cannot convert extended site assignment into just a symbol.")
return periodictable.atomic_symbol(self.atomic_number)
def uc_reduced_coordgroups_process_with_isotropy(coordgroup,
cell,
get_wyckoff=False):
#print("GURK",struct.formula,len(struct.uc_reduced_coords))
inputstr = httk.iface.isotropy_if.reduced_coordgroups_to_input(
coordgroup, cell)
out, err, completed = isotropy("./", [], inputstr)
if completed == 0:
cif = httk.iface.isotropy_if.out_to_cif(
IoAdapterString(string=out),
[atomic_symbol(x) for x in range(1,
len(coordgroup) + 1)])
#print("CIF",cif)
newstruct = cif_to_struct(IoAdapterString(string=cif),
backends=['cif2cell_reduce'])
checkstruct = cif_to_struct(IoAdapterString(string=cif),
backends=['cif2cell'])
only_rc_struct = cif_to_struct(
IoAdapterString(string=cif),
backends=['cif_reader_that_can_only_read_isotropy_cif'])
# This is an illeelegant hack
newstruct.rc_sites.wyckoff_symbols = only_rc_struct.rc_sites.wyckoff_symbols
# Cell basis can only be constructed from the cif approximately
cell_mismatch = sum(
sum((checkstruct.rc_cell.basis -
only_rc_struct.rc_cell.basis))).to_float()
#print("CELL MISMATCH:",sum(sum((newstruct.cell.maxnorm_basis - only_rc_struct.cell.maxnorm_basis))).to_float())
only_rc_struct._rc_cell = newstruct.rc_cell
# Make sure the hexhash is recomputed
only_rc_struct.rc_sites._hexhash = None
#print("CHECK THIS:", newstruct.rc_sites.hexhash, only_rc_struct.rc_sites.hexhash)
#print("CHECK THIS:", newstruct.cell.to_tuple(), only_rc_struct.cell.to_tuple())
if cell_mismatch > 1e-6 or newstruct.rc_sites.hexhash != only_rc_struct.rc_sites.hexhash:
print("Cell mismatch:", cell_mismatch)
print("Structure hashes:", newstruct.rc_sites.hexhash,
only_rc_struct.rc_sites.hexhash)
#print("Structures:", newstruct.rc_sites.to_tuple(), only_rc_struct.rc_sites.to_tuple())
raise Exception(
"isotropy_ext.struct_process_with_isotropy: internal error, structures that absolutely should be the same are not, sorry."
)
#order = [x.as_integer-1 for x in newstruct.assignments]
#print("ORDER:",order)
if get_wyckoff:
return newstruct.rc_reduced_coordgroups, newstruct.rc_sites.wyckoff_symbols, [
[atomic_number(x) for x in y]
for y in newstruct.assigments.symbols_list()
]
else:
return newstruct.rc_reduced_coordgroups
else:
print("ISOTROPY STDERR:")
#print(inputstr)
print("========")
#print(out)
#print("========")
print(err)
print("========")
raise Exception("isotropy_ext: isotropy did not complete.")
def prepare_single_run(dirpath,
struct,
poscarspath=None,
template='t:/vasp/single/static',
overwrite=False):
if overwrite:
mkdir_p(dirpath)
else:
os.mkdir(dirpath)
structure_to_poscar(os.path.join(dirpath, "POSCAR"),
struct,
fix_negative_determinant=True)
#write_generic_kpoints_file(os.path.join(dirpath,"KPOINTS"),comment=structure_to_comment(struct))
kpoints = calculate_kpoints(struct)
write_kpoints_file(os.path.join(dirpath, "KPOINTS"),
kpoints,
comment=structure_to_comment(struct))
ioa = IoAdapterFileWriter.use(os.path.join(dirpath, "POTCAR"))
f = ioa.file
spieces_counts = []
magmomlist = get_magnetizations(struct.symbols, 5, 1)
magmom_per_ion = magmomlist[0]
magmoms = []
nelect = 0
natoms = 0
nmag = 0
for i in range(len(struct.assignments)):
assignment = struct.assignments[i]
count = struct.uc_counts[i]
symbol = periodictable.atomic_symbol(assignment.symbol)
pp = get_pseudopotential(symbol, poscarspath)
f.write(pp)
spieces_counts.append(count)
#magmoms.append(str(count)+"*"+str(get_magmom(symbol)))
magmom = magmom_per_ion[i]
magmoms.append(str(count) + "*" + str(magmom))
def zval(results, match):
results['zval'] = float(match.group(1))
results = micro_pyawk(IoAdapterString(pp),
[["^ *POMASS.*; *ZVAL *= *([^ ]+)", None, zval]])
if not 'zval' in results:
raise Exception(
"vasp_if.prepare_simple_static_run: Could not read ZVAL from potcar file"
)
nelect += results['zval'] * count
natoms += count
nmag += count * magmom
ioa.close()
nbands1 = int(0.6 * nelect + 1.0) + int(math.ceil(natoms / 2.0) + 0.1)
nbands2 = int(0.6 * nelect + 1.0) + int(math.ceil(nmag / 2.0) + 0.1)
nbands3 = int(0.6 * nelect + 1.0) + 20
nbands_spin = max(1, nbands1, nbands2, nbands3)
nbands_spin += nbands_spin % 2
nbands1 = int(nelect / 2.0 + 2) + int(math.ceil(natoms / 2.0) + 0.1)
nbands2 = int(math.ceil(nelect / 2.0) + 20 + 0.1)
nbands_nospin = max(1, nbands1, nbands2)
nbands_nospin += nbands_spin % 2
data = {}
data['VASP_SPIECES_COUNTS'] = " ".join(list(map(str, spieces_counts)))
data['VASP_MAGMOM'] = " ".join(list(map(str, magmoms)))
data['VASP_NBANDS_SPIN'] = str(nbands_spin)
data['VASP_NBANDS_NOSPIN'] = str(nbands_nospin)
if template.startswith('t:'):
template = os.path.join(httk.httk_root, 'Execution', 'tasks-templates',
template[2:])
apply_templates(template, dirpath, envglobals=data, mkdir=False)