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 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 gen_file_equals(current, reference):
'''Checks whether contents of a gen file equals another one.
Args:
current (str): Name of gen file to check.
reference (str): Name of reference gen file.
'''
curgen = Gen.fromfile(current)
refgen = Gen.fromfile(reference)
return curgen.equals(refgen)
def gen2cif(args):
'''Converts the given INPUT file in DFTB+ GEN format to CIF 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.')
geometry = gen.geometry
if not geometry.periodic:
geometry.setlattice(args.cellsize * np.eye(3))
cif = Cif(gen.geometry)
if args.output:
if args.output == "-":
outfile = sys.stdout
else:
outfile = args.output
else:
if infile.endswith(".gen"):
outfile = infile[:-4] + ".cif"
else:
outfile = infile + ".cif"
cif.tofile(outfile)
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 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 test_interaction(filename, i_contacts, r_interactions, principle_layers):
'''Tests if every principle layer only interacts with adjacent layers.
Also checks that contacts only interact with one layer. Does not check if
contacts are interacting.'''
geo = Gen.fromfile(filename).geometry
interaction_mtrx = _create_interaction_mtrx(r_interactions)
test_passed = True
# Check layers
print('Starting interaction test:')
for layer_index, layer in enumerate(principle_layers):
interacting_layers = set()
for currentlayeratom in layer:
for otherlayer_index, otherlayer in enumerate(principle_layers):
for otheratom in otherlayer:
distance = np.linalg.norm(geo.coords[otheratom] -
geo.coords[currentlayeratom])
species = (geo.indexes[currentlayeratom],
geo.indexes[otheratom])
if distance <= interaction_mtrx[species[0]][species[1]]:
interacting_layers.add(otherlayer_index)
if (min(interacting_layers) < layer_index - 1
or max(interacting_layers) > layer_index + 1):
shifted_layers = {elem + 1 for elem in interacting_layers}
print('Principle layers were not sorted right! Atom ' +
str(currentlayeratom + 1) + ' in layer ' +
str(layer_index + 1) +
' might be interacting with non adjacent layer: ' +
str(shifted_layers))
test_passed = False
# Checks if every contact only interacts with one layer
i_contacts.append(geo.natom)
for contact in range(len(i_contacts) - 1):
contactatoms = set(range(i_contacts[contact], i_contacts[contact + 1]))
interacting_layers = set()
for atom in contactatoms:
for layerindex, layer in enumerate(principle_layers):
for layeratom in layer:
distance = np.linalg.norm(geo.coords[atom] -
geo.coords[layeratom])
species = (geo.indexes[atom], geo.indexes[layeratom])
if distance <= interaction_mtrx[species[0]][species[1]]:
interacting_layers.add(layerindex)
if len(interacting_layers) > 1:
shifted_layers = {elem + 1 for elem in interacting_layers}
print('Principle layers were not sorted right! Atom ' +
str(atom + 1) + ' in contact ' + str(contact + 1) +
' is interacting with more than one layer: ' +
str(shifted_layers))
test_passed = False
if test_passed:
print('Principle layers passed interaction test')
return test_passed
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)
def partition(filename, i_contacts, r_interactions, maxiterations):
'''Creates principle layers. Atom indexes starting with 0. Algorithm first
creates chains starting from every contact. Each chain element is called a
bin and every bin only interacts with adjacent bins or contacts (Not a
principle layer yet). Chains (and also dead ends) are merged until only
two chains are left. Those two chains will be resorted to create the
principle layers.'''
bin_index = 0
geo = Gen.fromfile(filename).geometry
interaction_mtrx = _create_interaction_mtrx(r_interactions)
allchains = _create_starting_chains(i_contacts, geo.natom)
unsorted_atoms = set(range(min(i_contacts)))
print('Starting to create chains from every contact:')
while unsorted_atoms:
if bin_index >= maxiterations:
print('Maximum iterations reached:', maxiterations)
print('Exiting program')
sys.exit()
bin_index += 1
_create_next_bins(allchains, unsorted_atoms, geo, interaction_mtrx)
chains_merged = False
if len(allchains) > 2:
chains_merged = _merge_interacting_chains(allchains, geo,
interaction_mtrx)
print('Bins for iteration', bin_index, 'created. Chains merged:',
chains_merged)
if (len(allchains) == 2 and _chains_interact(
allchains[0], allchains[1], geo, interaction_mtrx)):
if len(allchains[1]) > 1 and _bins_interact(
allchains[0][-1], allchains[1][-2], geo, interaction_mtrx):
allchains[0][-1] = allchains[0][-1].union(allchains[1][-1])
del allchains[1][-1]
print('Merged last bin of chain1 and chain2')
if unsorted_atoms:
_sort_remaining(allchains, unsorted_atoms, geo,
interaction_mtrx)
print('Sorted remaining atoms')
print('All atoms sorted')
principle_layers = _create_finalchain(allchains)
print('Principle layers created (Last two chains combined)')
return principle_layers
