from ase.units import Bohr
[docs]
def read_turbomole(fd):
"""Method to read turbomole coord file
coords in bohr, atom types in lowercase, format:
$coord
x y z atomtype
x y z atomtype f
$end
Above 'f' means a fixed atom.
"""
from ase import Atoms
from ase.constraints import FixAtoms
lines = fd.readlines()
atoms_pos = []
atom_symbols = []
myconstraints = []
# find $coord section;
# does not necessarily have to be the first $<something> in file...
for i, l in enumerate(lines):
if l.strip().startswith('$coord'):
start = i
break
for line in lines[start + 1:]:
if line.startswith('$'): # start of new section
break
else:
x, y, z, symbolraw = line.split()[:4]
symbolshort = symbolraw.strip()
symbol = symbolshort[0].upper() + symbolshort[1:].lower()
# print(symbol)
atom_symbols.append(symbol)
atoms_pos.append(
[float(x) * Bohr, float(y) * Bohr, float(z) * Bohr]
)
cols = line.split()
if (len(cols) == 5):
fixedstr = line.split()[4].strip()
if (fixedstr == "f"):
myconstraints.append(True)
else:
myconstraints.append(False)
else:
myconstraints.append(False)
# convert Turbomole ghost atom Q to X
atom_symbols = [element if element !=
'Q' else 'X' for element in atom_symbols]
atoms = Atoms(positions=atoms_pos, symbols=atom_symbols, pbc=False)
c = FixAtoms(mask=myconstraints)
atoms.set_constraint(c)
return atoms
class TurbomoleFormatError(ValueError):
default_message = ('Data format in file does not correspond to known '
'Turbomole gradient format')
def __init__(self, *args, **kwargs):
if args or kwargs:
ValueError.__init__(self, *args, **kwargs)
else:
ValueError.__init__(self, self.default_message)
[docs]
def read_turbomole_gradient(fd, index=-1):
""" Method to read turbomole gradient file """
# read entire file
lines = [x.strip() for x in fd.readlines()]
# find $grad section
start = end = -1
for i, line in enumerate(lines):
if not line.startswith('$'):
continue
if line.split()[0] == '$grad':
start = i
elif start >= 0:
end = i
break
if end <= start:
raise RuntimeError('File does not contain a valid \'$grad\' section')
# trim lines to $grad
del lines[:start + 1]
del lines[end - 1 - start:]
# Interpret $grad section
from ase import Atom, Atoms
from ase.calculators.singlepoint import SinglePointCalculator
from ase.units import Bohr, Hartree
images = []
while lines: # loop over optimization cycles
# header line
# cycle = 1 SCF energy = -267.6666811409 |dE/dxyz| = 0.157112 # noqa: E501
fields = lines[0].split('=')
try:
# cycle = int(fields[1].split()[0])
energy = float(fields[2].split()[0]) * Hartree
# gradient = float(fields[3].split()[0])
except (IndexError, ValueError) as e:
raise TurbomoleFormatError from e
# coordinates/gradient
atoms = Atoms()
forces = []
for line in lines[1:]:
fields = line.split()
if len(fields) == 4: # coordinates
# 0.00000000000000 0.00000000000000 0.00000000000000 c # noqa: E501
try:
symbol = fields[3].lower().capitalize()
# if dummy atom specified, substitute 'Q' with 'X'
if symbol == 'Q':
symbol = 'X'
position = tuple(Bohr * float(x) for x in fields[0:3])
except ValueError as e:
raise TurbomoleFormatError from e
atoms.append(Atom(symbol, position))
elif len(fields) == 3: # gradients
# -.51654903354681D-07 -.51654903206651D-07 0.51654903169644D-07 # noqa: E501
grad = []
for val in fields[:3]:
try:
grad.append(
-float(val.replace('D', 'E')) * Hartree / Bohr
)
except ValueError as e:
raise TurbomoleFormatError from e
forces.append(grad)
else: # next cycle
break
# calculator
calc = SinglePointCalculator(atoms, energy=energy, forces=forces)
atoms.calc = calc
# save frame
images.append(atoms)
# delete this frame from data to be handled
del lines[:2 * len(atoms) + 1]
return images[index]
[docs]
def write_turbomole(fd, atoms):
""" Method to write turbomole coord file
"""
from ase.constraints import FixAtoms
coord = atoms.get_positions()
symbols = atoms.get_chemical_symbols()
# convert X to Q for Turbomole ghost atoms
symbols = [element if element != 'X' else 'Q' for element in symbols]
fix_indices = set()
if atoms.constraints:
for constr in atoms.constraints:
if isinstance(constr, FixAtoms):
fix_indices.update(constr.get_indices())
fix_str = []
for i in range(len(atoms)):
if i in fix_indices:
fix_str.append('f')
else:
fix_str.append('')
fd.write('$coord\n')
for (x, y, z), s, fix in zip(coord, symbols, fix_str):
fd.write('%20.14f %20.14f %20.14f %2s %2s \n'
% (x / Bohr, y / Bohr, z / Bohr, s.lower(), fix))
fd.write('$end\n')