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
def parser(name, data):
""" Parse Lammps custom dump files
Preliminary implementation!
Needs to be 'custom' format with either:
'id element xs ys yz'
or
'id element x y z'
Only orthogonal cells for now
Assumes angstrom
"""
tmol = Molecule(name, steps=0)
i = 0
while i < len(data):
line = data[i]
if 'ITEM' in line:
if 'TIMESTEP' in line:
i += 2
tmol.newStep()
elif 'NUMBER OF ATOMS' in line:
nat = int(data[i + 1])
i += 2
elif 'BOX BOUNDS' in line:
tvec = [[0, 0, 0], [0, 0, 0], [0, 0, 0]]
tvec[0][0] = float(data[i + 1].split()[1]) -\
float(data[i + 1].split()[0])
tvec[1][1] = float(data[i + 2].split()[1]) -\
float(data[i + 2].split()[0])
tvec[2][2] = float(data[i + 3].split()[1]) -\
float(data[i + 3].split()[0])
tmol.setVec(tvec)
tmol.setCellDim(1, fmt='angstrom')
i += 4
elif 'ATOMS' in line:
line = line.split()
if 'id' not in line or 'element' not in line or\
('xs' not in line and 'x' not in line):
raise NotImplementedError("Lammps dump in not (yet) "
"recognized format")
# ididx = line.index('id') - 2
elidx = line.index('element') - 2
if 'xs' in line:
xidx = line.index('xs') - 2
yidx = line.index('ys') - 2
zidx = line.index('zs') - 2
fmt = 'crystal'
else:
xidx = line.index('x') - 2
yidx = line.index('y') - 2
zidx = line.index('z') - 2
fmt = 'angstrom'
if 'q' in line:
qidx = line.index('q') - 2
else:
qidx = False
tmol.newAtoms(nat)
for j in range(nat):
at = data[j + 1 + i].split()
if qidx:
tmol.setAtom(j, at[elidx],
[at[xidx], at[yidx], at[zidx]],
charge=float(at[qidx]))
else:
tmol.setAtom(j, at[elidx],
[at[xidx], at[yidx], at[zidx]])
tmol.setFmt(fmt, scale=True)
i += nat + 1
else:
i += 1
return tmol, None
def parser(name, data):
""" Parse PWScf output to trajectory """
tmol = Molecule(name, steps=0)
i = 0
vec = [[0, 0, 0], [0, 0, 0], [0, 0, 0]]
gamma = False
while i < len(data):
line = data[i].split()
# ignore empty lines
if not line:
pass
# read number of atoms
elif line[0:3] == ['number', 'of', 'atoms/cell']:
nat = int(line[4])
# read cell dimension
elif line[0] == 'celldm(1)=':
celldm = float(line[1])
# read initial cell vectors
elif line[0:2] == ['crystal', 'axes:']:
for j in [0, 1, 2]:
temp = data[i + 1 + j].split()
vec[j] = [float(x) for x in temp[3:6]]
# read initial positions:
elif line[0] == 'site':
tmol.newStep()
tmol.setCellDim(celldm)
tmol.setVec(vec)
tmol.newAtoms(nat)
for j in range(nat):
atom = data[j + i + 1].split()
tmol.setAtom(j, atom[1], atom[6:9])
tmol.setFmt('alat', scale=True)
i += nat
# read k-points:
elif line[0] == 'gamma-point':
gamma = True
elif line[0:3] == ['number', 'of', 'k'] and not gamma:
nk = int(line[4])
if nk < 100:
kpoints = []
for j in range(i + 2, i + nk + 2):
kp = data[j].split()
kpoints.append([kp[4], kp[5], kp[6].strip('), '), kp[9]])
tmol.setKpoints('discrete', kpoints)
tmol.setKpoints('active', 'discrete')
i += nk
# read step-vectors if cell is variable
elif line[0] == 'CELL_PARAMETERS':
for j in [0, 1, 2]:
temp = data[i + 1 + j].split()
vec[j] = [float(x) for x in temp[0:3]]
# read step-coordinates
elif line[0] == 'ATOMIC_POSITIONS':
tmol.newStep()
tmol.setCellDim(celldm)
tmol.setVec(vec)
tmol.newAtoms(nat)
for j in range(nat):
atom = data[j + i + 1].split()
tmol.setAtom(j, atom[0], atom[1:4],
fix=[not int(x) for x in atom[4:]])
tmol.setFmt(line[1].strip('()'), scale=True)
i += nat
# break on reaching final coordinates (duplicate)
elif line[0] == 'Begin':
break
# ignore everything else
else:
pass
i += 1
return tmol, None
