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
