def test_get_ase_atoms():
natoms = 10
st = crys.Structure(coords_frac=rand(natoms,3),
symbols=['H']*10,
cell=rand(3,3))
try:
import ase
st2 = crys.atoms2struct(crys.struct2atoms(st))
keys = ['natoms', 'coords', 'coords_frac', 'symbols', 'cryst_const',
'cell', 'volume', 'mass']
tools.assert_dict_with_all_types_almost_equal(\
st.__dict__,
st2.__dict__,
keys=keys,
strict=True)
# in case the test fails, use this to find out which key failed
## for kk in keys:
## print("testing: %s ..." %kk)
## tools.assert_all_types_almost_equal(st.__dict__[kk], st2.__dict__[kk])
for pbc in [True,False]:
at = st.get_ase_atoms(pbc=pbc)
assert (at.pbc == np.array([pbc]*3)).all()
at = crys.struct2atoms(st, pbc=pbc)
assert (at.pbc == np.array([pbc]*3)).all()
except ImportError:
tools.skip("cannot import ase, skipping test get_ase_atoms()")
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 test_get_ase_atoms():
natoms = 10
st = crys.Structure(coords_frac=rand(natoms, 3),
symbols=['H'] * 10,
cell=rand(3, 3))
try:
import ase
st2 = crys.atoms2struct(crys.struct2atoms(st))
keys = [
'natoms', 'coords', 'coords_frac', 'symbols', 'cryst_const',
'cell', 'volume', 'mass'
]
tools.assert_dict_with_all_types_almost_equal(\
st.__dict__,
st2.__dict__,
keys=keys,
strict=True)
# in case the test fails, use this to find out which key failed
## for kk in keys:
## print("testing: %s ..." %kk)
## tools.assert_all_types_almost_equal(st.__dict__[kk], st2.__dict__[kk])
for pbc in [True, False]:
at = st.get_ase_atoms(pbc=pbc)
assert (at.pbc == np.array([pbc] * 3)).all()
at = crys.struct2atoms(st, pbc=pbc)
assert (at.pbc == np.array([pbc] * 3)).all()
except ImportError:
tools.skip("cannot import ase, skipping test get_ase_atoms()")
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())
def write_input(self, atoms, properties=None, system_changes=None):
FileIOCalculator.write_input(self, atoms, properties,
system_changes)
if self.backup:
for fn in [self.infile, self.outfile, self.dumpfile,
self.structfile, self.logfile]:
if os.path.exists(fn):
common.backup(fn)
common.file_write(self.infile, self.fill_infile_templ())
io.write_lammps(self.structfile,
crys.atoms2struct(atoms),
symbolsbasename=os.path.basename(self.structfile) + \
'.symbols')
def write_input(self, atoms, properties=None, system_changes=None):
FileIOCalculator.write_input(self, atoms, properties, system_changes)
if self.backup:
for fn in [
self.infile, self.outfile, self.dumpfile, self.structfile,
self.logfile
]:
if os.path.exists(fn):
common.backup(fn)
common.file_write(self.infile, self.fill_infile_templ())
io.write_lammps(self.structfile,
crys.atoms2struct(atoms),
symbolsbasename=os.path.basename(self.structfile) + \
'.symbols')
