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"
import sys
import numpy as np
from pwtools import crys, atomic_data, pwscf, io
from pwtools.common import str_arr, seq2str
from pwtools.constants import Bohr, Angstrom
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'
#!/usr/bin/env python # # cif2sgroup.py # # Extract information from a .cif file and print an input file for WIEN2k's # "sgroup" symmetry analysis tool. Note that the Cif reader assumes P1 # symmetry, i.e. symmetry information in the cif file is ignored. Use # ase.io.read(), which seems to parse symmetry information. # # usage:: # $ cif2sgroup.py foo.cif > foo.sgroup.in # # Find primitive cell # $ sgroup -prim [-set-TOL=1e-4] foo.sgroup.in # # See ``sgroup -help`` for more options. # # Notes # ----- # The unit of length of a,b,c is not important (Angstrom, Bohr,...). import sys from pwtools import io fn = sys.argv[1] struct = io.read_cif(fn) print io.wien_sgroup_input(struct, lat_symbol='P')
import sys
import numpy as np
from pwtools import crys, atomic_data, pwscf, io
from pwtools.common import str_arr, seq2str
from pwtools.constants import Bohr, Angstrom
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
#!/usr/bin/env python3 # # cif2sgroup.py # # Extract information from a .cif file and print an input file for WIEN2k's # "sgroup" symmetry analysis tool. Note that the Cif reader assumes P1 # symmetry, i.e. symmetry information in the cif file is ignored. Use # ase.io.read(), which seems to parse symmetry information. # # usage:: # $ cif2sgroup.py foo.cif > foo.sgroup.in # # Find primitive cell # $ sgroup -prim [-set-TOL=1e-4] foo.sgroup.in # # See ``sgroup -help`` for more options. # # Notes # ----- # The unit of length of a,b,c is not important (Angstrom, Bohr,...). import sys from pwtools import io fn = sys.argv[1] struct = io.read_cif(fn) print(io.wien_sgroup_input(struct, lat_symbol='P'))
