def test_direc_and_neg_dims():
for dims in [(2, 3, 4), (-2, -3, -4), (-2, 3, 4), (2, -3, 4), (2, 3, -4)]:
m1 = crys.scell_mask(*dims, direc=1)[::-1, :]
m2 = crys.scell_mask(*dims, direc=-1)
assert (m1 == m2).all()
for direc in [1, -1]:
ref = crys.scell_mask(2, 3, 4, direc=direc)
assert ((ref + crys.scell_mask(-2, -3, -4, direc=direc)) == 0.0).all()
now = crys.scell_mask(-2, 3, 4, direc=direc)
assert ((ref[:, 0] + now[:, 0]) == 0.0).all()
assert (ref[:, 1:] == now[:, 1:]).all()
now = crys.scell_mask(2, -3, 4, direc=direc)
assert ((ref[:, 1] + now[:, 1]) == 0.0).all()
assert (ref[:, (0, 2)] == now[:, (0, 2)]).all()
now = crys.scell_mask(2, 3, -4, direc=direc)
assert ((ref[:, 2] + now[:, 2]) == 0.0).all()
assert (ref[:, :2] == now[:, :2]).all()
natoms = 20
coords_frac = rand(natoms, 3)
cell = rand(3, 3)
dims = (2, 3, 4)
symbols = [next(syms) for ii in range(natoms)]
struct = Structure(coords_frac=coords_frac, cell=cell, symbols=symbols)
# coords are offset by a constant shift if all dims and direc are < 0
s1 = crys.scell(struct, (2, 3, 4), direc=1)
s2 = crys.scell(struct, (-2, -3, -4), direc=-1)
d = s1.coords - s2.coords
assert np.abs(d - d[0, :][None, :]).sum() < 1e-12
def test_direc_and_neg_dims():
for dims in [(2,3,4), (-2,-3,-4), (-2,3,4), (2,-3,4), (2,3,-4)]:
m1 = crys.scell_mask(*dims, direc=1)[::-1,:]
m2 = crys.scell_mask(*dims, direc=-1)
assert (m1==m2).all()
for direc in [1,-1]:
ref = crys.scell_mask( 2, 3, 4, direc=direc)
assert ((ref + crys.scell_mask(-2,-3,-4, direc=direc)) == 0.0).all()
now = crys.scell_mask(-2, 3, 4, direc=direc)
assert ((ref[:,0] + now[:,0]) == 0.0).all()
assert (ref[:,1:] == now[:,1:]).all()
now = crys.scell_mask(2, -3, 4, direc=direc)
assert ((ref[:,1] + now[:,1]) == 0.0).all()
assert (ref[:,(0,2)] == now[:,(0,2)]).all()
now = crys.scell_mask(2, 3, -4, direc=direc)
assert ((ref[:,2] + now[:,2]) == 0.0).all()
assert (ref[:,:2] == now[:,:2]).all()
natoms = 20
coords_frac = rand(natoms,3)
cell = rand(3,3)
dims = (2,3,4)
symbols = [syms.next() for ii in range(natoms)]
struct = Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols)
# coords are offset by a constant shift if all dims and direc are < 0
s1 = crys.scell(struct, (2,3,4), direc=1)
s2 = crys.scell(struct, (-2,-3,-4), direc=-1)
d = s1.coords - s2.coords
assert np.abs(d - d[0,:][None,:]).sum() < 1e-12
def test_symmetry():
tools.skip_if_pkg_missing('pyspglib')
st_prim = crys.Structure(coords_frac=np.array([[0] * 3, [.5] * 3]),
cryst_const=np.array([3.5] * 3 + [60] * 3),
symbols=['Al', 'N'])
st_sc = crys.scell(st_prim, (2, 3, 4))
st_prim2 = symmetry.spglib_get_primitive(st_sc, symprec=1e-2)
# irreducible structs
assert symmetry.spglib_get_primitive(st_prim, symprec=1e-2) is None
assert symmetry.spglib_get_primitive(st_prim2, symprec=1e-2) is None
for st in [st_prim, st_sc, st_prim2]:
assert symmetry.spglib_get_spacegroup(st_prim,
symprec=1e-2) == (225, 'Fm-3m')
# this is redundant since we have is_same_struct(), but keep it anyway
tools.assert_dict_with_all_types_almost_equal(
st_prim.__dict__,
st_prim2.__dict__,
keys=['natoms', 'symbols', 'volume', 'cryst_const'])
assert symmetry.is_same_struct(st_prim, st_prim2)
def test_angle():
# CaCl struct, the supercell will have 0 and 180 degrees -> check corner
# cases
st = io.read_cif('files/angle/rs.cif')
st = crys.scell(st, (2,1,1))
nang = st.natoms*(st.natoms-1)*(st.natoms-2)
mask_val = 999.0
for deg in [True,False]:
for pbc in [True,False]:
agf = crys.angles(st, pbc=pbc, mask_val=mask_val)
agpy, aipy = angles(st, pbc=pbc, mask_val=mask_val)
eps = np.finfo(float).eps*5
assert np.allclose(agf, agpy)
assert aipy.shape[0] == nang
assert len((agf != mask_val).nonzero()[0]) == nang
angleidx = np.array(zip(*(agf != mask_val).nonzero()))
assert (angleidx == aipy).all()
assert not np.isnan(agpy).any(), "python angle nan"
assert not np.isnan(agf).any(), "fortran angle nan"
# do we have 0 and 180 degrees?
assert (agf < eps).any(), "no zero degree cases"
assert (agf - 180.0 < eps).any(), "no 180 degree cases"
assert (agf >= 0.0).all(), "negative angles"
def test_angle():
# CaCl struct, the supercell will have 0 and 180 degrees -> check corner
# cases
tools.skip_if_pkg_missing('CifFile')
st = io.read_cif('files/angle/rs.cif')
st = crys.scell(st, (2, 1, 1))
nang = st.natoms * (st.natoms - 1) * (st.natoms - 2)
mask_val = 999.0
for deg in [True, False]:
for pbc in [True, False]:
agf = crys.angles(st, pbc=pbc, mask_val=mask_val)
agpy, aipy = angles(st, pbc=pbc, mask_val=mask_val)
eps = np.finfo(float).eps * 5
assert np.allclose(agf, agpy)
assert aipy.shape[0] == nang
assert len((agf != mask_val).nonzero()[0]) == nang
angleidx = np.array(list(zip(*(agf != mask_val).nonzero())))
assert (angleidx == aipy).all()
assert not np.isnan(agpy).any(), "python angle nan"
assert not np.isnan(agf).any(), "fortran angle nan"
# do we have 0 and 180 degrees?
assert (agf < eps).any(), "no zero degree cases"
assert (agf - 180.0 < eps).any(), "no 180 degree cases"
assert (agf >= 0.0).all(), "negative angles"
run 1000
"""
assert len(sys.argv) == 2, "need one input arg: nvt or npt"
if sys.argv[1] == 'npt':
ens_txt = npt_txt
elif sys.argv[1] == 'nvt':
ens_txt = nvt_txt
else:
raise StandardError("only nvt / npt allowed")
# create structure file
st = crys.Structure(coords_frac=np.array([[0.0]*3, [.5]*3]),
cryst_const=np.array([2.85]*3 + [60]*3),
symbols=['Al','N'])
io.write_lammps('lmp.struct', crys.scell(st,(3,3,3)))
# write lmp.in for nvt or npt
common.file_write('lmp.in', lmp_in_templ.format(ensemble=ens_txt))
# run lammps
common.system("mpirun -np 2 lammps < lmp.in", wait=True)
# read trajectory
trtxt_orig = io.read_lammps_md_txt('log.lammps')
trdcd = io.read_lammps_md_dcd('log.lammps')
# plotting
plots = mpl.prepare_plots(['coords', 'coords_frac', 'velocity',
'cryst_const', 'cell'])
for name,pl in plots.iteritems():
run 1000
"""
assert len(sys.argv) == 2, "need one input arg: nvt or npt"
if sys.argv[1] == 'npt':
ens_txt = npt_txt
elif sys.argv[1] == 'nvt':
ens_txt = nvt_txt
else:
raise Exception("only nvt / npt allowed")
# create structure file
st = crys.Structure(coords_frac=np.array([[0.0]*3, [.5]*3]),
cryst_const=np.array([2.85]*3 + [60]*3),
symbols=['Al','N'])
io.write_lammps('lmp.struct', crys.scell(st,(3,3,3)))
# write lmp.in for nvt or npt
common.file_write('lmp.in', lmp_in_templ.format(ensemble=ens_txt))
# run lammps
common.system("mpirun -np 2 lammps < lmp.in", wait=True)
# read trajectory
trtxt_orig = io.read_lammps_md_txt('log.lammps')
trdcd = io.read_lammps_md_dcd('log.lammps')
# plotting
plots = mpl.prepare_plots(['coords', 'coords_frac', 'velocity',
'cryst_const', 'cell'])
for name,pl in plots.items():
np.array([[0.0, 0.0, 0.0],
[0.5, 0.0, 0.0],
[0.0, 0.5, 0.0],
[0.5, 0.5, 0.0],
[0.0, 0.0, 0.5],
[0.5, 0.0, 0.5],
[0.0, 0.5, 0.5],
[0.5, 0.5, 0.5],
])
symbols = ['Al', 'N', 'N', 'Al', 'N', 'Al', 'Al', 'N']
alat = 5.0
cell = np.identity(3) * alat
struct = crys.Structure(coords_frac=coords_frac,
symbols=symbols,
cell=cell)
sc = crys.scell(struct, (2,2,2))
name = 'aln_ibrav0_sc'
structs[name] = Struct(coords_frac=sc.coords_frac,
cell=sc.cell,
symbols=sc.symbols,
fnbase=name,
tgtdir=tgtdir)
print(structs[name].cryst_const)
## structs[name].write_cif()
## structs[name].write_axsf()
## structs[name].savetxt()
# AlN ibrav=2
# -----------
#
def test_scell():
cell = np.identity(3)
coords_frac = np.array([[0.5, 0.5, 0.5],
[1,1,1]])
symbols = ['Al', 'N']
sc = crys.scell(Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols), (2,2,2))
sc_coords_frac = \
np.array([[ 0.25, 0.25, 0.25],
[ 0.25, 0.25, 0.75],
[ 0.25, 0.75, 0.25],
[ 0.25, 0.75, 0.75],
[ 0.75, 0.25, 0.25],
[ 0.75, 0.25, 0.75],
[ 0.75, 0.75, 0.25],
[ 0.75, 0.75, 0.75],
[ 0.5 , 0.5 , 0.5 ],
[ 0.5 , 0.5 , 1. ],
[ 0.5 , 1. , 0.5 ],
[ 0.5 , 1. , 1. ],
[ 1. , 0.5 , 0.5 ],
[ 1. , 0.5 , 1. ],
[ 1. , 1. , 0.5 ],
[ 1. , 1. , 1. ]])
sc_symbols = ['Al']*8 + ['N']*8
sc_cell = \
np.array([[ 2., 0., 0.],
[ 0., 2., 0.],
[ 0., 0., 2.]])
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
# non-orthorhombic cell
cell = \
np.array([[ 1., 0.5, 0.5],
[ 0.25, 1., 0.2],
[ 0.2, 0.5, 1.]])
sc = crys.scell(Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols), (2,2,2))
sc_cell = \
np.array([[ 2. , 1. , 1. ],
[ 0.5, 2. , 0.4],
[ 0.4, 1. , 2. ]])
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
# crystal coords are cell-independent
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
# slab
#
# Test if old and new implementation behave for a tricky case: natoms == 2
# mask.shape[0], i.e. if reshape() behaves correctly.
# Reference generated with old implementation. Default is new.
cell = np.identity(3)
coords_frac = np.array([[0.5, 0.5, 0.5],
[1,1,1]])
symbols = ['Al', 'N']
sc = crys.scell(Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols), (1,1,2))
sc_coords_frac = \
np.array([[ 0.5 , 0.5 , 0.25],
[ 0.5 , 0.5 , 0.75],
[ 1. , 1. , 0.5 ],
[ 1. , 1. , 1. ]])
sc_cell = \
np.array([[ 1., 0., 0.],
[ 0., 1., 0.],
[ 0., 0., 2.]])
sc_symbols = ['Al', 'Al', 'N', 'N']
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
sc = crys.scell(Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols), (1,2,1))
sc_coords_frac = \
np.array([[ 0.5 , 0.25, 0.5 ],
[ 0.5 , 0.75, 0.5 ],
[ 1. , 0.5 , 1. ],
[ 1. , 1. , 1. ]])
sc_cell = \
np.array([[ 1., 0., 0.],
[ 0., 2., 0.],
[ 0., 0., 1.]])
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
sc = crys.scell(Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols), (2,1,1))
sc_coords_frac = \
np.array([[ 0.25, 0.5 , 0.5 ],
[ 0.75, 0.5 , 0.5 ],
[ 0.5 , 1. , 1. ],
[ 1. , 1. , 1. ]])
sc_cell = \
np.array([[ 2., 0., 0.],
[ 0., 1., 0.],
[ 0., 0., 1.]])
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
# symbols = None
sc = crys.scell(Structure(coords_frac=coords_frac,
cell=cell,
symbols=None), (2,2,2))
assert sc.symbols is None
# Trajectory
natoms = 4
nstep = 100
symbols = [syms.next() for ii in range(natoms)]
# cell 2d
coords_frac = rand(nstep,natoms,3)
cell = rand(3,3)
dims = (2,3,4)
nmask = np.prod(dims)
sc = crys.scell(Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols),
dims=dims)
assert sc.coords_frac.shape == (nstep, nmask*natoms, 3)
assert sc.symbols == common.flatten([[sym]*nmask for sym in symbols])
assert sc.cell.shape == (nstep,3,3)
np.testing.assert_array_almost_equal(sc.cell,
num.extend_array(cell * np.asarray(dims)[:,None],
sc.nstep,
axis=0))
# cell 3d
cell = rand(nstep,3,3)
sc = crys.scell(Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols),
dims=dims)
assert sc.coords_frac.shape == (nstep, nmask*natoms, 3)
coords_frac2 = np.array([crys.scell(Structure(coords_frac=coords_frac[ii,...,],
cell=cell[ii,...],
symbols=symbols), dims=dims).coords_frac \
for ii in range(nstep)])
np.testing.assert_array_almost_equal(sc.coords_frac, coords_frac2)
assert sc.symbols == common.flatten([[sym]*nmask for sym in symbols])
assert sc.cell.shape == (nstep,3,3)
np.testing.assert_array_almost_equal(sc.cell,
cell * np.asarray(dims)[None,:,None])
# methods
natoms = 20
coords_frac = rand(natoms,3)
cell = rand(3,3)
dims = (2,3,4)
symbols = [syms.next() for ii in range(natoms)]
struct = Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols)
sc1 = crys.scell(struct, dims=dims, method=1)
sc2 = crys.scell(struct, dims=dims, method=2)
d1 = dict([(key, getattr(sc1, key)) for key in sc1.attr_lst])
d2 = dict([(key, getattr(sc2, key)) for key in sc2.attr_lst])
tools.assert_dict_with_all_types_almost_equal(d1, d2)
pair_coeff * * ../AlN.tersoff Al N
### IO
dump dump_txt all custom 1 lmp.out.dump id type xu yu zu fx fy fz &
vx vy vz xsu ysu zsu
dump_modify dump_txt sort id
dump dump_dcd all dcd 1 lmp.out.dcd
dump_modify dump_dcd sort id unwrap yes
thermo_style custom step temp vol cella cellb cellc cellalpha cellbeta cellgamma &
ke pe etotal &
press pxx pyy pzz pxy pxz pyz cpu press
thermo_modify flush yes
thermo 1
fix 1 all box/relax tri 0.0
minimize 1e-8 1e-8 5000 10000
"""
st = crys.Structure(coords_frac=np.array([[0.0]*3, [.5]*3]),
cryst_const=np.array([2.85]*3 + [60]*3),
symbols=['Al','N'])
for dr in ['md-nvt', 'md-npt', 'vc-relax']:
common.system("rm -rfv {dr}; mkdir -v {dr}".format(dr=dr))
io.write_lammps('vc-relax/lmp.struct', st)
io.write_lammps('md-nvt/lmp.struct', crys.scell(st,(2,2,2)))
io.write_lammps('md-npt/lmp.struct', crys.scell(st,(2,2,2)))
for dr,txt in lmp_in.iteritems():
common.file_write('%s/lmp.in' %dr, txt)
def test_scell():
cell = np.identity(3)
coords_frac = np.array([[0.5, 0.5, 0.5], [1, 1, 1]])
symbols = ['Al', 'N']
sc = crys.scell(
Structure(coords_frac=coords_frac, cell=cell, symbols=symbols),
(2, 2, 2))
sc_coords_frac = \
np.array([[ 0.25, 0.25, 0.25],
[ 0.25, 0.25, 0.75],
[ 0.25, 0.75, 0.25],
[ 0.25, 0.75, 0.75],
[ 0.75, 0.25, 0.25],
[ 0.75, 0.25, 0.75],
[ 0.75, 0.75, 0.25],
[ 0.75, 0.75, 0.75],
[ 0.5 , 0.5 , 0.5 ],
[ 0.5 , 0.5 , 1. ],
[ 0.5 , 1. , 0.5 ],
[ 0.5 , 1. , 1. ],
[ 1. , 0.5 , 0.5 ],
[ 1. , 0.5 , 1. ],
[ 1. , 1. , 0.5 ],
[ 1. , 1. , 1. ]])
sc_symbols = ['Al'] * 8 + ['N'] * 8
sc_cell = \
np.array([[ 2., 0., 0.],
[ 0., 2., 0.],
[ 0., 0., 2.]])
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
# non-orthorhombic cell
cell = \
np.array([[ 1., 0.5, 0.5],
[ 0.25, 1., 0.2],
[ 0.2, 0.5, 1.]])
sc = crys.scell(
Structure(coords_frac=coords_frac, cell=cell, symbols=symbols),
(2, 2, 2))
sc_cell = \
np.array([[ 2. , 1. , 1. ],
[ 0.5, 2. , 0.4],
[ 0.4, 1. , 2. ]])
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
# crystal coords are cell-independent
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
# slab
#
# Test if old and new implementation behave for a tricky case: natoms == 2
# mask.shape[0], i.e. if reshape() behaves correctly.
# Reference generated with old implementation. Default is new.
cell = np.identity(3)
coords_frac = np.array([[0.5, 0.5, 0.5], [1, 1, 1]])
symbols = ['Al', 'N']
sc = crys.scell(
Structure(coords_frac=coords_frac, cell=cell, symbols=symbols),
(1, 1, 2))
sc_coords_frac = \
np.array([[ 0.5 , 0.5 , 0.25],
[ 0.5 , 0.5 , 0.75],
[ 1. , 1. , 0.5 ],
[ 1. , 1. , 1. ]])
sc_cell = \
np.array([[ 1., 0., 0.],
[ 0., 1., 0.],
[ 0., 0., 2.]])
sc_symbols = ['Al', 'Al', 'N', 'N']
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
sc = crys.scell(
Structure(coords_frac=coords_frac, cell=cell, symbols=symbols),
(1, 2, 1))
sc_coords_frac = \
np.array([[ 0.5 , 0.25, 0.5 ],
[ 0.5 , 0.75, 0.5 ],
[ 1. , 0.5 , 1. ],
[ 1. , 1. , 1. ]])
sc_cell = \
np.array([[ 1., 0., 0.],
[ 0., 2., 0.],
[ 0., 0., 1.]])
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
sc = crys.scell(
Structure(coords_frac=coords_frac, cell=cell, symbols=symbols),
(2, 1, 1))
sc_coords_frac = \
np.array([[ 0.25, 0.5 , 0.5 ],
[ 0.75, 0.5 , 0.5 ],
[ 0.5 , 1. , 1. ],
[ 1. , 1. , 1. ]])
sc_cell = \
np.array([[ 2., 0., 0.],
[ 0., 1., 0.],
[ 0., 0., 1.]])
assert sc.symbols == sc_symbols
np.testing.assert_array_almost_equal(sc.cell, sc_cell)
np.testing.assert_array_almost_equal(sc.coords_frac, sc_coords_frac)
# symbols = None
sc = crys.scell(
Structure(coords_frac=coords_frac, cell=cell, symbols=None), (2, 2, 2))
assert sc.symbols is None
# Trajectory
natoms = 4
nstep = 100
symbols = [next(syms) for ii in range(natoms)]
# cell 2d
coords_frac = rand(nstep, natoms, 3)
cell = rand(3, 3)
dims = (2, 3, 4)
nmask = np.prod(dims)
sc = crys.scell(Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols),
dims=dims)
assert sc.coords_frac.shape == (nstep, nmask * natoms, 3)
assert sc.symbols == common.flatten([[sym] * nmask for sym in symbols])
assert sc.cell.shape == (nstep, 3, 3)
np.testing.assert_array_almost_equal(
sc.cell,
num.extend_array(cell * np.asarray(dims)[:, None], sc.nstep, axis=0))
# cell 3d
cell = rand(nstep, 3, 3)
sc = crys.scell(Trajectory(coords_frac=coords_frac,
cell=cell,
symbols=symbols),
dims=dims)
assert sc.coords_frac.shape == (nstep, nmask * natoms, 3)
coords_frac2 = np.array([crys.scell(Structure(coords_frac=coords_frac[ii,...,],
cell=cell[ii,...],
symbols=symbols), dims=dims).coords_frac \
for ii in range(nstep)])
np.testing.assert_array_almost_equal(sc.coords_frac, coords_frac2)
assert sc.symbols == common.flatten([[sym] * nmask for sym in symbols])
assert sc.cell.shape == (nstep, 3, 3)
np.testing.assert_array_almost_equal(
sc.cell,
cell * np.asarray(dims)[None, :, None])
# methods
natoms = 20
coords_frac = rand(natoms, 3)
cell = rand(3, 3)
dims = (2, 3, 4)
symbols = [next(syms) for ii in range(natoms)]
struct = Structure(coords_frac=coords_frac, cell=cell, symbols=symbols)
sc1 = crys.scell(struct, dims=dims, method=1)
sc2 = crys.scell(struct, dims=dims, method=2)
d1 = dict([(key, getattr(sc1, key)) for key in sc1.attr_lst])
d2 = dict([(key, getattr(sc2, key)) for key in sc2.attr_lst])
tools.assert_dict_with_all_types_almost_equal(d1, d2)
np.array([[0.0, 0.0, 0.0],
[0.5, 0.0, 0.0],
[0.0, 0.5, 0.0],
[0.5, 0.5, 0.0],
[0.0, 0.0, 0.5],
[0.5, 0.0, 0.5],
[0.0, 0.5, 0.5],
[0.5, 0.5, 0.5],
])
symbols = ['Al', 'N', 'N', 'Al', 'N', 'Al', 'Al', 'N']
alat = 5.0
cell = np.identity(3) * alat
struct = crys.Structure(coords_frac=coords_frac,
symbols=symbols,
cell=cell)
sc = crys.scell(struct, (2,2,2))
name = 'aln_ibrav0_sc'
structs[name] = Struct(coords_frac=sc.coords_frac,
cell=sc.cell,
symbols=sc.symbols,
fnbase=name,
tgtdir=tgtdir)
print structs[name].cryst_const
## structs[name].write_cif()
## structs[name].write_axsf()
## structs[name].savetxt()
# AlN ibrav=2
# -----------
#
