def write_xyz(filename, obj, name='pwtools_dummy_mol_name'):
"""Write VMD-style [VMD] XYZ file.
length: Angstrom
Parameters
----------
filename : target file name
obj : Trajectory or Structure
name : str, optional
Molecule name.
References
----------
[VMD] http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html
"""
traj = crys.struct2traj(obj)
xyz_str = ""
for istep in range(traj.nstep):
xyz_str += "%i\n%s\n%s" %(traj.natoms,
name + '.%i' %(istep + 1),
pwscf.atpos_str_fast(traj.symbols,
traj.coords[istep,...]),
)
common.file_write(filename, xyz_str)
def write_xyz(filename, obj, name='pwtools_dummy_mol_name'):
"""Write VMD-style [VMD] XYZ file.
length: Angstrom
Parameters
----------
filename : target file name
obj : Trajectory or Structure
name : str, optional
Molecule name.
References
----------
[VMD] http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html
"""
traj = crys.struct2traj(obj)
xyz_str = ""
for istep in range(traj.nstep):
xyz_str += "%i\n%s\n%s" % (
traj.natoms,
name + '.%i' % (istep + 1),
pwscf.atpos_str_fast(traj.symbols, traj.coords[istep, ...]),
)
common.file_write(filename, xyz_str)
def write_axsf(filename, obj):
"""Write animated XSF file for Structure (only 1 step) or Trajectory.
Note that forces are converted eV / Ang -> Ha / Ang.
length: Angstrom
forces: Ha / Angstrom
Parameters
----------
filename : target file name
obj : Structure or Trajectory
References
----------
[XSF] http://www.xcrysden.org/doc/XSF.html
"""
# Notes
# -----
# XSF: The XSF spec [XSF] is a little fuzzy about what PRIMCOORD actually
# is (fractional or cartesian Angstrom). Only the latter case results
# in a correctly displayed structure in xcrsyden. So we use that.
#
# Speed: The only time-consuming step is calling atpos_str*() in the loop
# b/c that transforms *every* single float to a string, which
# effectively is a double loop over `ccf`. No way to get faster w/ pure
# Python.
#
traj = crys.struct2traj(obj)
# ccf = cartesian coords + forces (6 columns)
if traj.is_set_attr('forces'):
ccf = np.concatenate((traj.coords, traj.forces*eV/Ha), axis=-1)
else:
ccf = traj.coords
axsf_str = "ANIMSTEPS %i\nCRYSTAL" %traj.nstep
for istep in range(traj.nstep):
axsf_str += "\nPRIMVEC %i\n%s" %(istep+1,
common.str_arr(traj.cell[istep,...]))
axsf_str += "\nPRIMCOORD %i\n%i 1\n%s" %(istep+1,
traj.natoms,
pwscf.atpos_str_fast(traj.symbols,
ccf[istep,...]))
common.file_write(filename, axsf_str)
def write_axsf(filename, obj):
"""Write animated XSF file for Structure (only 1 step) or Trajectory.
Note that forces are converted eV / Ang -> Ha / Ang.
length: Angstrom
forces: Ha / Angstrom
Parameters
----------
filename : target file name
obj : Structure or Trajectory
References
----------
[XSF] http://www.xcrysden.org/doc/XSF.html
"""
# Notes
# -----
# XSF: The XSF spec [XSF] is a little fuzzy about what PRIMCOORD actually
# is (fractional or cartesian Angstrom). Only the latter case results
# in a correctly displayed structure in xcrsyden. So we use that.
#
# Speed: The only time-consuming step is calling atpos_str*() in the loop
# b/c that transforms *every* single float to a string, which
# effectively is a double loop over `ccf`. No way to get faster w/ pure
# Python.
#
traj = crys.struct2traj(obj)
# ccf = cartesian coords + forces (6 columns)
if traj.is_set_attr('forces'):
ccf = np.concatenate((traj.coords, traj.forces * eV / Ha), axis=-1)
else:
ccf = traj.coords
axsf_str = "ANIMSTEPS %i\nCRYSTAL" % traj.nstep
for istep in range(traj.nstep):
axsf_str += "\nPRIMVEC %i\n%s" % (
istep + 1, common.str_arr(traj.cell[istep, ...]))
axsf_str += "\nPRIMCOORD %i\n%i 1\n%s" % (
istep + 1, traj.natoms,
pwscf.atpos_str_fast(traj.symbols, ccf[istep, ...]))
common.file_write(filename, axsf_str)
def test_struct():
natoms = 10
cell = np.array([[3, 0, 0], [1.1, 5, -0.04], [-0.33, 1.5, 7]])
cryst_const = crys.cell2cc(cell)
coords_frac = rand(natoms, 3)
coords = crys.coord_trans(coords=coords_frac, old=cell, new=np.identity(3))
symbols = ['H'] * natoms
stress = rand(3, 3)
forces = rand(natoms, 3)
# Use ``cell`` instead of ``cryst_const` as input such that
# atoms.get_cell() test passes (see below for why -- cell orientation)
st = Structure(coords_frac=coords_frac,
symbols=symbols,
cell=cell,
stress=stress,
forces=forces,
etot=42)
# Test if all getters work.
for name in st.attr_lst:
print(name)
st.try_set_attr(name)
assert getattr(st, name) is not None, "attr None: %s" % name
assert eval('st.get_%s()' %
name) is not None, "getter returns None: %s" % name
aaae(coords_frac, st.coords_frac)
aaae(cryst_const, st.cryst_const)
aaae(coords, st.coords)
assert st.natoms == natoms
st = Structure(coords_frac=coords_frac, symbols=symbols, cell=cell)
aaae(coords, st.get_coords())
# Cell calculated from cryst_const has defined orientation in space which may be
# different from the original `cell`, but the volume and underlying cryst_const
# must be the same.
st = Structure(coords_frac=coords_frac,
symbols=symbols,
cryst_const=cryst_const)
assert st.get_cell() is not None
np.testing.assert_almost_equal(crys.volume_cell(cell),
crys.volume_cell(st.get_cell()))
aaae(cryst_const, crys.cell2cc(st.get_cell()))
# units
st = Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols,
stress=stress,
forces=forces,
units={
'length': 2,
'forces': 3,
'stress': 4
})
aaae(2 * coords, st.coords)
aaae(3 * forces, st.forces)
aaae(4 * stress, st.stress)
traj = crys.struct2traj(st)
assert traj.is_traj
# copy(): Assert everything has another memory location = is a new copy of
# the object. IntTypes are NOT copied by copy.deepcopy(), which we use in
# Structure.copy(), apparently b/c they are always automatically copied
# before in-place operations. Same for float type.
#
# >>> a=10; b=a; print id(a); print id(b)
# 36669152
# 36669152
# >>> a*=100; print id(a); print id(b)
# 72538264
# 36669152
# >>> a
# 100
# >>> b
# 10
#
# >>> a=[1,2,3]; b=a; print id(a); print id(b)
# 72624320
# 72624320
# >>> a[0] = 44; print id(a); print id(b)
# 72624320
# 72624320
# >>> a
# [44, 2, 3]
# >>> b
# [44, 2, 3]
st2 = st.copy()
for name in st.attr_lst:
val = getattr(st, name)
if val is not None and not (isinstance(val, int) or \
isinstance(val, float)):
val2 = getattr(st2, name)
assert id(val2) != id(val)
assert_all_types_equal(val2, val)
def test_struct():
natoms = 10
cell = np.array([[3,0,0],
[1.1,5,-0.04],
[-0.33,1.5,7]])
cryst_const = crys.cell2cc(cell)
coords_frac = rand(natoms,3)
coords = crys.coord_trans(coords=coords_frac,
old=cell,
new=np.identity(3))
symbols = ['H']*natoms
stress = rand(3,3)
forces = rand(natoms,3)
# Use ``cell`` instead of ``cryst_const` as input such that
# atoms.get_cell() test passes (see below for why -- cell orientation)
st = Structure(coords_frac=coords_frac,
symbols=symbols,
cell=cell,
stress=stress,
forces=forces,
etot=42)
# Test if all getters work.
for name in st.attr_lst:
print name
st.try_set_attr(name)
assert getattr(st, name) is not None, "attr None: %s" %name
assert eval('st.get_%s()'%name) is not None, "getter returns None: %s" %name
aaae(coords_frac, st.coords_frac)
aaae(cryst_const, st.cryst_const)
aaae(coords, st.coords)
assert st.natoms == natoms
st = Structure(coords_frac=coords_frac,
symbols=symbols,
cell=cell)
aaae(coords, st.get_coords())
# Cell calculated from cryst_const has defined orientation in space which may be
# different from the original `cell`, but the volume and underlying cryst_const
# must be the same.
st = Structure(coords_frac=coords_frac,
symbols=symbols,
cryst_const=cryst_const)
assert st.get_cell() is not None
np.testing.assert_almost_equal(crys.volume_cell(cell),
crys.volume_cell(st.get_cell()))
aaae(cryst_const, crys.cell2cc(st.get_cell()))
# units
st = Structure(coords_frac=coords_frac,
cell=cell,
symbols=symbols,
stress=stress,
forces=forces,
units={'length': 2, 'forces': 3, 'stress': 4})
aaae(2*coords, st.coords)
aaae(3*forces, st.forces)
aaae(4*stress, st.stress)
traj = crys.struct2traj(st)
assert traj.is_traj
# copy(): Assert everything has another memory location = is a new copy of
# the object. IntTypes are NOT copied by copy.deepcopy(), which we use in
# Structure.copy(), apparently b/c they are always automatically copied
# before in-place operations. Same for float type.
#
# >>> a=10; b=a; print id(a); print id(b)
# 36669152
# 36669152
# >>> a*=100; print id(a); print id(b)
# 72538264
# 36669152
# >>> a
# 100
# >>> b
# 10
#
# >>> a=[1,2,3]; b=a; print id(a); print id(b)
# 72624320
# 72624320
# >>> a[0] = 44; print id(a); print id(b)
# 72624320
# 72624320
# >>> a
# [44, 2, 3]
# >>> b
# [44, 2, 3]
st2 = st.copy()
for name in st.attr_lst:
val = getattr(st,name)
if val is not None and not (isinstance(val, types.IntType) or \
isinstance(val, types.FloatType)):
val2 = getattr(st2,name)
assert id(val2) != id(val)
assert_all_types_equal(val2, val)
