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 (animated) XCrysDen structure files
Optionally contains datagrids/animations/forces
Parses multiple datagrids into multiple steps
"""
animated = False
periodic = False
pbcformats = ["MOLECULE", "POLYMER", "SLAB", "CRYSTAL"]
i = 0
while i < len(data):
if data[i][0] == '#':
pass
elif "ANIMSTEPS" in data[i]:
tmol = Molecule(name, steps=int(data[i].strip("ANIMSTEPS \r\n")))
animated = True
elif data[i].strip() in pbcformats:
periodic = True
# Parse coordinates of isolated molecule
elif not periodic and "ATOMS" in data[i]:
if animated:
tmol.changeStep(int(data[i].strip("ATOMS \r\n")) - 1)
else:
tmol = Molecule(name, steps=1)
j = 1
while i + j < len(data) and len(data[i + j].split()) in [4, 7]:
line = data[i + j].split()
tmol.newAtom(line[0], line[1:4])
j += 1
tmol.setFmt("angstrom", scale=True)
i += j - 1
# Parse periodic structure containing cell and coordinates
elif periodic and "PRIMVEC" in data[i]:
vec = [data[i + j].split() for j in range(1, 4)]
if animated and data[i].strip("PRIMVEC \r\n"):
tmol.changeStep(int(data[i].strip("PRIMVEC ")) - 1)
tmol.setVec(vec)
tmol.setCellDim(1, fmt='angstrom')
elif animated:
tmol.setVecAll(vec)
tmol.setCellDimAll(1, fmt='angstrom')
else:
tmol = Molecule(name, steps=1)
tmol.setVec(vec)
tmol.setCellDim(1, fmt='angstrom')
i += 3
elif periodic and "PRIMCOORD" in data[i]:
if animated:
tmol.changeStep(int(data[i].strip("PRIMCOORD \r\n")) - 1)
nat = int(data[i + 1].split()[0])
tmol.newAtoms(nat)
for j in range(nat):
line = data[j + 2 + i].split()
tmol.setAtom(j, line[0], line[1:4])
tmol.setFmt("angstrom", scale=True)
i += nat + 1
elif periodic and "CONVVEC" in data[i]:
# could be used, but not atm
pass
elif periodic and "CONVCOORD" in data[i]: # pragma: no cover
# should not even be there
pass
elif "BEGIN_" in data[i]:
datatype = data[i].strip("BEGIN_BLOCK_ \r\n")
endblock = "END_BLOCK_" + datatype
endgrid = "END_" + datatype
j = 1
grids = []
# only parse 3D datagrids
while endblock not in data[i + j]:
if datatype in data[i + j] and datatype == "DATAGRID_3D":
nvol = list(map(int, data[i + j + 1].split()))
vol = [[[0] * nvol[2] for y in range(nvol[1])]
for z in range(nvol[0])]
origin = list(map(float, data[i + j + 2].split()))
# assume spanning space equals cell
j += 6
line = data[i + j].split()
for z in range(nvol[2]):
for y in range(nvol[1]):
for x in range(nvol[0]):
while not (line or endgrid in data[i + j + 1]):
j += 1
line = data[i + j].split()
vol[x][y][z] = float(line.pop(0))
del vol[-1]
for n in vol:
del n[-1]
for m in n:
del m[-1]
grids.append((vol, origin))
j += 1
j += 1
if grids:
tmol.changeStep(0)
tmol.setVol(*grids[0])
if len(grids) > 1:
for k in range(1, len(grids)):
tmol.copyStep()
tmol.setVol(*grids[k])
i += j
i += 1
return tmol, None
