def test_atpos_str():
assert pwscf.atpos_str(['X'],
np.array([[0.1, 1, 1]]),
fmt='%g',
delim='_',
eps=0.0) == 'X_0.1_1_1'
assert pwscf.atpos_str(['X'],
np.array([[0.1, 1, 1]]),
fmt='%g',
delim='_',
eps=0.2) == 'X_0_1_1'
def write_input(self, atoms, properties=None, system_changes=None):
FileIOCalculator.write_input(self, atoms, properties,
system_changes)
struct = crys.atoms2struct(atoms)
self.cell = common.str_arr(struct.cell)
self.kpoints = pwscf.kpoints_str_pwin(kpts2mp(atoms, self.kpts))
if isinstance(self.pp, types.StringType):
pseudos = ["%s.%s" %(sym, self.pp) for sym in struct.symbols_unique]
else:
assert len(self.pp) == struct.ntypat
pseudos = []
for sym in struct.symbols_unique:
for ppi in self.pp:
if ppi.startswith(sym):
pseudos.append(ppi)
break
assert len(pseudos) == struct.ntypat
self.atspec = pwscf.atspec_str(symbols=struct.symbols_unique,
masses=struct.mass_unique,
pseudos=pseudos)
self.atpos = pwscf.atpos_str(symbols=struct.symbols,
coords=struct.coords_frac)
self.natoms = struct.natoms
self.ntyp = struct.ntypat
if self.backup:
for fn in [self.infile, self.outfile]:
if os.path.exists(fn):
common.backup(fn)
common.file_write(self.infile, self.fill_infile_templ())
def write_input(self, atoms, properties=None, system_changes=None):
FileIOCalculator.write_input(self, atoms, properties, system_changes)
struct = crys.atoms2struct(atoms)
self.cell = common.str_arr(struct.cell)
self.kpoints = pwscf.kpoints_str_pwin(kpts2mp(atoms, self.kpts))
if isinstance(self.pp, bytes):
pseudos = [
"%s.%s" % (sym, self.pp) for sym in struct.symbols_unique
]
else:
assert len(self.pp) == struct.ntypat
pseudos = []
for sym in struct.symbols_unique:
for ppi in self.pp:
if ppi.startswith(sym):
pseudos.append(ppi)
break
assert len(pseudos) == struct.ntypat
self.atspec = pwscf.atspec_str(symbols=struct.symbols_unique,
masses=struct.mass_unique,
pseudos=pseudos)
self.atpos = pwscf.atpos_str(symbols=struct.symbols,
coords=struct.coords_frac)
self.natoms = struct.natoms
self.ntyp = struct.ntypat
if self.backup:
for fn in [self.infile, self.outfile]:
if os.path.exists(fn):
common.backup(fn)
common.file_write(self.infile, self.fill_infile_templ())
templates = [batch.FileTemplate(basename='pw.in')]
# rs-AlN
st = crys.Structure(coords_frac=np.array([[0.0]*3, [0.5]*3]),
symbols=['Al','N'],
cryst_const=np.array([2.76]*3 + [60]*3))
params_lst = []
for ecutwfc in np.linspace(30,100,8):
params_lst.append([sql.SQLEntry(key='ecutwfc', sqlval=ecutwfc),
sql.SQLEntry(key='ecutrho', sqlval=4.0*ecutwfc),
sql.SQLEntry(key='cell', sqlval=common.str_arr(st.cell)),
sql.SQLEntry(key='natoms', sqlval=st.natoms),
sql.SQLEntry(key='atpos',
sqlval=pwscf.atpos_str(st.symbols,
st.coords_frac)),
])
calc = batch.ParameterStudy(machines=theo,
templates=templates,
params_lst=params_lst,
study_name='convergence_test_cutoff',
)
calc.write_input(sleep=0, backup=False, mode='w')
if not os.path.exists('calc'):
os.symlink('calc_theo', 'calc')
common.system("cp -r ../../../test/files/qe_pseudos calc_theo/pseudo; gunzip calc_theo/pseudo/*")
"""Indent text block by `num` white spaces."""
space = " "*num
return '\n'.join(space + line for line in txt.splitlines())
# All lengths in Bohr
struct = io.read_cif(sys.argv[1], units={'length': Angstrom/Bohr})
rcell = crys.recip_cell(struct.cell)
norms = np.sqrt((rcell**2.0).sum(axis=1))
bar = '-'*78
mass_unique = [atomic_data.pt[sym]['mass'] for sym in struct.symbols_unique]
atspec = pwscf.atspec_str(struct.symbols_unique,
mass_unique,
[sym + '.UPF' for sym in struct.symbols_unique])
celldm = crys.cc2celldm(struct.cryst_const)
atpos_frac = pwscf.atpos_str(struct.symbols, struct.coords_frac)
print("""\
Notes
-----
The .cif file is assumed to contain NO symmetry information:
_symmetry_space_group_name_H-M 'P 1'
_symmetry_Int_Tables_number 1
loop_
_symmetry_equiv_pos_as_xyz
x,y,z
Only a,b,c,alpha,beta,gamma and the fractional coords as found in the file are
used.
CPMD
----
def indent(txt, num=4):
"""Indent text block by `num` white spaces."""
space = " " * num
return '\n'.join(space + line for line in txt.splitlines())
# All lengths in Bohr
struct = io.read_cif(sys.argv[1], units={'length': Angstrom / Bohr})
rcell = crys.recip_cell(struct.cell)
norms = np.sqrt((rcell**2.0).sum(axis=1))
bar = '-' * 78
mass_unique = [atomic_data.pt[sym]['mass'] for sym in struct.symbols_unique]
atspec = pwscf.atspec_str(struct.symbols_unique, mass_unique,
[sym + '.UPF' for sym in struct.symbols_unique])
celldm = crys.cc2celldm(struct.cryst_const)
atpos_frac = pwscf.atpos_str(struct.symbols, struct.coords_frac)
print("""\
Notes
-----
The .cif file is assumed to contain NO symmetry information:
_symmetry_space_group_name_H-M 'P 1'
_symmetry_Int_Tables_number 1
loop_
_symmetry_equiv_pos_as_xyz
x,y,z
Only a,b,c,alpha,beta,gamma and the fractional coords as found in the file are
used.
CPMD
----
def test_atpos_str():
assert pwscf.atpos_str(["X"], np.array([[0.1, 1, 1]]), fmt="%g", delim="_", eps=0.0) == "X_0.1_1_1"
assert pwscf.atpos_str(["X"], np.array([[0.1, 1, 1]]), fmt="%g", delim="_", eps=0.2) == "X_0_1_1"
