def xyz2gen(args):
'''Converts the given INPUT file in XYZ format to DFTB+ GEN format.
Args:
args: Namespace of command line arguments
'''
infile = args.infile
try:
xyz = Xyz.fromfile(infile)
except OSError:
raise ScriptError('You must enter a valid path to the input file.')
geo = xyz.geometry
if args.lattfile:
fp = open(args.lattfile, "r")
tmp = np.fromfile(fp, count=9, dtype=float, sep=" ")
latvecs = tmp.reshape((3, 3))
fp.close()
geo.setlattice(latvecs)
gen = Gen(geo, fractional=args.fractional)
if args.output:
if args.output == "-":
outfile = sys.stdout
else:
outfile = args.output
else:
if infile.endswith(".xyz"):
outfile = infile[:-4] + ".gen"
else:
outfile = infile + ".gen"
gen.tofile(outfile)
def repeatgen(infile, repeats, options):
'''Repeats geometry from gen files.
Args:
infile: File containing the gen-formatted geometry.
repeats: (n1, n2, n3) integer tuple containing the repetitions along
each lattice vector.
options: Options (e.g. as returned by the command line parser).
'''
gen = Gen.fromfile(infile)
geo = gen.geometry
latvecs = geo.latvecs
if options.latticefile:
latvecs = np.fromfile(options.latticefile, sep=' ')
if len(latvecs) != 9:
msg = ('Invalid number of lattice vector components in '
+ options.latticefile)
raise ScriptError(msg)
latvecs.shape = (3, 3)
if latvecs is None:
msg = 'No lattice vectors found (neither in gen nor in external file)'
raise ScriptError(msg)
newgeo = _repeatgeo(geo, latvecs, repeats)
newgen = Gen(newgeo, gen.fractional)
outfile = options.output
if outfile == '-':
outfile = sys.stdout
newgen.tofile(outfile)
def straingen(args, strain):
'''Strains a geometry from a gen file.
Args:
args: Namespace of command line arguments
strain: Strain to apply
'''
infile = args.infile
try:
gen = Gen.fromfile(infile)
except OSError:
raise ScriptError('You must enter a valid path to the input file.')
geometry = gen.geometry
strainmtx = np.zeros((3, 3), dtype=float)
for jj in range(3):
strainmtx[jj][jj] = 1.0
components = LABELS[args.component.lower()]
for ii in components:
strainmtx[VOIGHT[ii][0]][VOIGHT[ii][1]] += 0.005 * strain
strainmtx[VOIGHT[ii][1]][VOIGHT[ii][0]] += 0.005 * strain
if geometry.latvecs is not None:
geometry.latvecs = np.dot(geometry.latvecs, strainmtx)
geometry.coords = np.dot(geometry.coords, strainmtx)
if args.output:
if args.output == "-":
outfile = sys.stdout
else:
outfile = args.output
else:
if infile.endswith(".gen"):
outfile = infile
else:
outfile = infile + ".gen"
gen = Gen(geometry, fractional=gen.fractional)
gen.tofile(outfile)
def straingen(infile, strain, options):
'''Strains a geometry from a gen file.
Args:
infile: File containing the gen-formatted geometry
strain: Strain to apply
options: Options (e.g. as returned by the command line parser)
'''
gen = Gen.fromfile(infile)
geometry = gen.geometry
strainmtx = np.zeros((3, 3), dtype=float)
for jj in range(3):
strainmtx[jj][jj] = 1.0
components = LABELS[options.component.lower()]
for ii in components:
strainmtx[VOIGHT[ii][0]][VOIGHT[ii][1]] += 0.005 * strain
strainmtx[VOIGHT[ii][1]][VOIGHT[ii][0]] += 0.005 * strain
if geometry.latvecs is not None:
geometry.latvecs = np.dot(geometry.latvecs, strainmtx)
geometry.coords = np.dot(geometry.coords, strainmtx)
if options.output:
if options.output == "-":
outfile = sys.stdout
else:
outfile = options.output
else:
if infile.endswith(".gen"):
outfile = infile
else:
outfile = infile + ".gen"
gen = Gen(geometry, fractional=gen.fractional)
gen.tofile(outfile)
def repeatgen(args):
'''Repeats geometry from gen files.
Args:
args: Namespace of command line arguments
'''
infile = args.infile
repeats = [args.n1, args.n2, args.n3]
try:
gen = Gen.fromfile(infile)
except OSError:
raise ScriptError('You must enter a valid path to the input file.')
geo = gen.geometry
latvecs = geo.latvecs
if args.latticefile:
latvecs = np.fromfile(args.latticefile, sep=' ')
if len(latvecs) != 9:
msg = ('Invalid number of lattice vector components in ' +
args.latticefile)
raise ScriptError(msg)
latvecs.shape = (3, 3)
if latvecs is None:
msg = 'No lattice vectors found (neither in gen nor in external file)'
raise ScriptError(msg)
if args.phonons:
newgeo = _repeatgeo2(geo, latvecs, repeats)
else:
newgeo = _repeatgeo(geo, latvecs, repeats)
newgen = Gen(newgeo, gen.fractional)
outfile = args.output
if outfile == '-':
outfile = sys.stdout
newgen.tofile(outfile)