def parser(name, data):
""" Parse CPMD Input file """
tmol = Molecule(name)
tparam = deepcopy(param["default"])
tparam["name"] = name
i = 0
ibrav = '14'
symmetries = {'ISOLATED': '0',
'CUBIC': '1',
'FACE CENTERED CUBIC': '2',
'FCC': '2',
'BODY CENTERED CUBIC': '3',
'BCC': '3',
'HEXAGONAL': '4',
'TRIGONAL': '5',
'RHOMBOHEDRAL': '5',
'TETRAGONAL': '6',
'BODY CENTERED TETRAGONAL': '7',
'BCT': '7',
'ORTHORHOMBIC': '8',
'MONOCLINIC': '12',
'TRICLINIC': '14'}
fmt = 'bohr'
unitvec = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
scalevec = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
types = []
while i < len(data):
if data[i][0] == '!' or data[i].split() == []:
i += 1
elif '&' in data[i] and data[i].strip() != "&END":
# start recording namelist
nl = data[i].strip()
i += 1
while "&END" not in data[i]:
if nl == "&SYSTEM" and "ANGSTROM" in data[i]:
fmt = "angstrom"
elif nl == "&SYSTEM" and "KPOINTS" in data[i]:
if "MONKHORST" in data[i]:
kpoints = data[i + 1].split()
if "SHIFT=" in data[i]:
kpoints += data[i].split("SHIFT=")[1].split()[0:3]
else:
kpoints += ['0', '0', '0']
tmol.setKpoints('active', 'mpg')
tmol.setKpoints('mpg', kpoints)
i += 1
else:
kpoints = []
crystal = False
bands = False
if "SCALED" in data[i]:
crystal = True
if "BANDS" in data[i]:
bands = True
j = 1
line = data[i + j].split()
while not all([float(k) == 0 for k in line]):
kpoints.append(line[1:4] + [line[0]])
kpoints.append(line[4:] + ['0'])
j += 1
line = data[i + j].split()
i += j
else:
nk = int(data[i + 1])
for j in range(nk):
kpoints.append(data[i + j + 2].split())
i += 1 + nk
tmol.setKpoints('active', 'discrete')
tmol.setKpoints('discrete', kpoints)
tmol.setKpoints('options',
{'crystal': crystal, 'bands': bands})
elif nl == "&SYSTEM" and "SCALE" in data[i]:
if "CARTESIAN" in data[i]:
fmt = "alat"
else:
fmt = "crystal"
for token in data[i].strip().split():
if 'S=' in token:
scalevec[0][0] = 1 / float(token.strip('S='))
scalevec[1][1] = 1 / float(token.strip('S='))
scalevec[2][2] = 1 / float(token.strip('S='))
elif 'SX=' in token:
scalevec[0][0] = 1 / float(token.strip('SX='))
elif 'SY=' in token:
scalevec[1][1] = 1 / float(token.strip('SY='))
elif 'SZ=' in token:
scalevec[2][2] = 1 / float(token.strip('SZ='))
elif nl == "&SYSTEM" and "SYMMETRY" in data[i]:
arg = data[i + 1].strip()
if arg.isdigit():
ibrav = arg
else:
ibrav = symmetries[arg]
i += 1
elif nl == "&SYSTEM" and "CELL" in data[i]:
cell = list(map(float, data[i + 1].split()))
if "VECTORS" in data[i]:
while len(cell) < 9:
i += 1
cell += list(map(float, data[i + 1].split()))
ibrav = '-2'
else:
# cell = [a,b/a,c/a,cos(alpha),cos(beta),cos(gamma)]
a, b, c, alpha, beta, gamma = cell
tmol.setCellDim(a)
if "ABSOLUTE" in data[i]:
# cell = [a, b, c, ...]
b = b / a
c = c / a
if "DEGREE" in data[i]:
# cell = [..., alpha, beta, gamma]
alpha, beta, gamma =\
map(cos, map(deg2rad, [alpha, beta, gamma]))
i += 1
elif nl == "&ATOMS" and data[i][0] == '*':
atype = regex('[-_.]', data[i][1:].strip())[0]
while atype in types:
if not atype[-1].isdigit():
atype += "1"
else:
atype = atype[:-1] + str(int(atype[-1]) + 1)
types.append(atype)
tmol.pse[atype]['CPPP'] = data[i][1:].strip()
tmol.pse[atype]['CPNL'] = data[i + 1].strip()
nat = int(data[i + 2])
for j in range(nat):
tmol.newAtom(atype, data[i + 3 + j].split()[:3])
i += 2 + nat
elif nl == "&ATOMS" and "CONSTRAINTS" in data[i]:
# parse coordinate-fixes
j = 1
constraints = ""
line = data[i + j]
while "END" not in line:
if "FIX" in line and ("ALL" in line or "QM" in line):
for at in range(tmol.nat):
tmol.setAtom(at, fix=[True, True, True])
elif "FIX" in line and "ELEM" in line:
j += 1
vals = data[i + j].split()
Z = int(vals.pop(0))
if "SEQ" in line:
beg = int(vals.pop(0)) - 1
end = int(vals.pop(0))
r = range(beg, end)
else:
r = range(tmol.nat)
for at in r:
if tmol.pse[tmol.getAtom(at)[0]]["Z"] == Z:
tmol.setAtom(at, fix=[True, True, True])
elif "FIX" in line and "PPTY" in line:
j += 1
vals = data[i + j].split()
PP = int(vals.pop(0)) - 1
if "SEQ" in line:
beg = int(vals.pop(0)) - 1
end = int(vals.pop(0))
r = range(beg, end)
else:
r = range(tmol.nat)
for at in r:
if tmol.getAtom(at)[0] == types[PP]:
tmol.setAtom(at, fix=[True, True, True])
elif "FIX" in line and "SEQ" in line:
j += 1
vals = data[i + j].split()
for at in range(int(vals[0]) - 1, int(vals[1])):
tmol.setAtom(at, fix=[True, True, True])
elif "FIX" in line and "ATOM" in line:
j += 1
vals = data[i + j].split()
count = int(vals.pop(0))
for k in range(count):
if not vals:
j += 1
vals = data[i + j].split()
tmol.setAtom(int(vals.pop(0)) - 1,
fix=[True, True, True])
elif "FIX" in line and "COOR" in line:
j += 1
vals = data[i + j].split()
count = int(vals.pop(0))
for k in range(count):
j += 1
fixcoord = list(map(int, data[i + j].split()))
tmol.setAtom(fixcoord[0] - 1, fix=[
bool(not fixcoord[1]),
bool(not fixcoord[2]),
bool(not fixcoord[3])])
elif line.strip():
constraints += line
j += 1
line = data[i + j]
if constraints:
tparam[nl] += "CONSTRAINTS\n" + constraints +\
"END CONSTRAINTS\n"
i += j
elif nl == "&ATOMS" and "ISOTOPE" in data[i]:
j = 0
for t in types:
j += 1
mass = data[i + j].strip()
tmol.pse[t]['m'] = float(mass)
i += j
else:
tparam[nl] += data[i]
i += 1
else:
i += 1
# apply cell vec (scale SX etc.)
if scalevec != unitvec:
tmol.setVec(scalevec, scale=True)
tmol.setVec(unitvec)
# parse cell parameters
if ibrav == '-2':
tmol.setVec([cell[0:3], cell[3:6], cell[6:9]])
elif ibrav == '1':
# simple cubic
pass
elif ibrav == '2':
# face centered cubic
tmol.setVec([[-0.5, 0, 0.5], [0, 0.5, 0.5], [-0.5, 0.5, 0]])
elif ibrav == '3':
# body centered cubic
tmol.setVec([[0.5, 0.5, 0.5], [-0.5, 0.5, 0.5], [-0.5, -0.5, 0.5]])
elif ibrav == '4':
# hexagonal
tmol.setVec([[1, 0, 0], [-0.5, sqrt(3) * 0.5, 0], [0, 0, c]])
elif ibrav == '5':
# trigonal
tx = sqrt((1 - alpha) / 2)
ty = sqrt((1 - alpha) / 6)
tz = sqrt((1 + 2 * alpha) / 3)
tmol.setVec([[tx, -ty, tz], [0, 2 * ty, tz], [-tx, -ty, tz]])
elif ibrav == '6':
# simple tetragonal
tmol.setVec([[1, 0, 0], [0, 1, 0], [0, 0, c]])
elif ibrav == '7':
# body centered tetragonal
tmol.setVec([[0.5, -0.5, c * 0.5],
[0.5, 0.5, c * 0.5],
[-0.5, -0.5, c * 0.5]])
elif ibrav == '0' or ibrav == '8':
# simple orthorhombic
tmol.setVec([[1, 0, 0], [0, b, 0], [0, 0, c]])
elif ibrav == '12':
# simple monoclinic
tmol.setVec([[1, 0, 0],
[b * alpha, b * sqrt(1 - alpha**2), 0],
[0, 0, c]])
elif ibrav == '14':
# triclinic
singam = sqrt(1 - gamma**2)
tmol.setVec([[1, 0, 0], [b * gamma, b * singam, 0],
[c * beta, c * (alpha - beta * gamma) / singam,
c * sqrt(1 + 2 * alpha * beta * gamma - alpha * alpha -
beta * beta - gamma * gamma) / singam]])
# scale alat with explicit vectors
if fmt == 'alat' and ibrav == '-2':
vec = tmol.getVec()
a = sqrt(vec[0][0] * vec[0][0] + vec[0][1] *
vec[0][1] + vec[0][2] * vec[0][2])
b = sqrt(vec[1][0] * vec[1][0] + vec[1][1] *
vec[1][1] + vec[1][2] * vec[1][2])
c = sqrt(vec[2][0] * vec[2][0] + vec[2][1] *
vec[2][1] + vec[2][2] * vec[2][2])
tmol.setVec([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
tmol.setVec([[a, 0, 0], [0, b, 0], [0, 0, c]], scale=True)
tmol.setVec(vec)
# scale crystal, alat /w symmetry, angstrom-atoms
tmol.setFmt(fmt, scale=True)
# scale angstrom-cell
tmol.setCellDim(tmol.getCellDim(fmt='bohr'), fmt=fmt)
return tmol, tparam
