def gen2xyz(args):
'''Converts the given INPUT file in DFTB+ GEN format to XYZ format.
Args:
args: Namespace of command line arguments
'''
infile = args.infile
try:
gen = Gen.fromfile(infile)
except OSError:
raise ScriptError('You must enter a valid path to the input file.')
xyz = Xyz(gen.geometry, args.comment)
if args.output:
if args.output == "-":
outfile = sys.stdout
else:
outfile = args.output
else:
if infile.endswith(".gen"):
outfile = infile[:-4] + ".xyz"
else:
outfile = infile + ".xyz"
xyz.tofile(outfile)
if gen.geometry.periodic and args.lattfile:
fp = open(args.lattfile, "w")
for vec in gen.geometry.latvecs:
fp.write("{0:18.10E} {1:18.10E} {2:18.10E}\n".format(*vec))
fp.close()
def xyz_file_equals(current, reference, check_comment=False):
'''Checks whether contents of an xyz file equals another one.
Args:
current (str): Name of xyz file to check.
reference (str): Name of reference xyz file.
'''
curxyz = Xyz.fromfile(current)
refxyz = Xyz.fromfile(reference)
return curxyz.equals(refxyz, check_comment=check_comment)
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)