def parser(name, data):
""" Parse Empire specific xyz file """
tmol = Molecule(name)
nat = int(data[0])
tmol.comment = data[1].strip()
tmol.newAtoms(nat)
for j in range(nat):
line = data[j + 2].split()
tmol.setAtom(j, line[0], line[1:4])
tmol.setFmt("angstrom", scale=True)
vec = [0, 0, 0]
for i in range(3):
vec[i] = [float(x) for x in data[nat + 3 + i].split()]
tmol.setVec(vec)
tmol.setCellDim(1, fmt="angstrom")
return tmol, None
def parser(name, data):
""" Parse Gaussian Cube file """
tmol = Molecule(name)
fmt = "bohr"
# two lines of comments, combine
tmol.comment = data[0] + ";" + data[1]
# nat, origin[3]
nat = int(data[2].split()[0])
origin = [float(data[2].split()[i]) for i in [1, 2, 3]]
# n of datapoints(dir), cell_vec[3]
nvol = [0, 0, 0]
tvec = [0, 0, 0]
for i in [0, 1, 2]:
line = data[i + 3].split()
nvol[i] = int(line[0])
if nvol[i] < 0:
nvol[i] = -nvol[i]
fmt = "angstrom"
tvec[i] = [float(line[j]) * nvol[i] for j in [1, 2, 3]]
tmol.setVec(tvec)
pse = list(glob_pse.keys())
tmol.newAtoms(nat)
for i in range(nat):
# line = Z, charge, coord(x, y, z)
line = data[i + 6].split()
tmol.setAtom(i, pse[int(line[0])], line[2:5], charge=float(line[1]))
tmol.setFmt(fmt, scale=False)
tmol.setCellDim(1, fmt=fmt)
# rest of file has datagrid, x is outer loop, z inner
vol = [[[0] * nvol[2] for i in range(nvol[1])] for j in range(nvol[0])]
i = 6 + nat
line = data[i].split()
for x in range(nvol[0]):
for y in range(nvol[1]):
for z in range(nvol[2]):
while not line and i < (len(data) - 1):
i += 1
line = data[i].split()
vol[x][y][z] = float(line.pop(0))
tmol.setVol(vol, origin)
return tmol, None
def parser(name, data):
""" Parse xyz files (angstrom) """
# create list of mol, trajectory support
tmol = Molecule(name, steps=0)
i = 0
while i < len(data):
# handle empty lines at eof or between molecules
if not data[i].strip().isdigit():
i += 1
continue
# fixed format nat and comment
tmol.newStep()
nat = int(data[i])
tmol.comment = data[i + 1].strip()
# read coordinates and types
tmol.newAtoms(nat)
for j in range(nat):
line = data[j + i + 2].split()
tmol.setAtom(j, line[0], line[1:4])
tmol.setFmt('angstrom', scale=True)
i += nat + 2
return tmol, None
