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)
