/usr/share/pyshared/ase/io/turbomole.py is in python-ase 3.6.0.2515-1.1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 | from ase.atoms import Atoms
from ase.units import Bohr
def read_turbomole(filename='coord'):
"""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, Atom
from ase.constraints import FixAtoms
if isinstance(filename, str):
f = open(filename)
lines = f.readlines()
atoms_pos = []
atom_symbols = []
myconstraints=[]
# find $coord section;
# does not necessarily have to be the first $<something> in file...
start = lines.index('$coord') # raises ValueError if not found
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)
if type(filename) == str:
f.close()
atoms = Atoms(positions = atoms_pos, symbols = atom_symbols, pbc = False)
c = FixAtoms(mask = myconstraints)
atoms.set_constraint(c)
#print c
return atoms
def read_turbomole_gradient(filename='gradient', index=-1):
""" Method to read turbomole gradient file """
if isinstance(filename, str):
f = open(filename)
# read entire file
lines = [x.strip() for x in f.readlines()]
# find $grad section
start = end = -1
for i, line in enumerate(lines):
if not line.startswith('$'):
continue
if line.split()[0] == '$grad':
start = i
elif start >= 0:
end = i
break
if end <= start:
raise RuntimeError('File %s does not contain a valid \'$grad\' section' % (filename))
def formatError():
raise RuntimeError('Data format in file %s does not correspond to known Turbomole gradient format' % (filename))
# trim lines to $grad
del lines[:start+1]
del lines[end-1-start:]
# Interpret $grad section
from ase import Atoms, Atom
from ase.calculators.singlepoint import SinglePointCalculator
from ase.units import Bohr
images = []
while len(lines): # loop over optimization cycles
# header line
# cycle = 1 SCF energy = -267.6666811409 |dE/dxyz| = 0.157112
fields = lines[0].split('=')
try:
cycle = int(fields[1].split()[0])
energy = float(fields[2].split()[0])
gradient = float(fields[3].split()[0])
except (IndexError, ValueError):
formatError()
# coordinates/gradient
atoms = Atoms()
forces = []
for line in lines[1:]:
fields = line.split()
if len(fields) == 4: # coordinates
# 0.00000000000000 0.00000000000000 0.00000000000000 c
try:
symbol = fields[3].lower().capitalize()
position = tuple([bohr2angstrom(float(x)) for x in fields[0:3] ])
except ValueError:
formatError()
atoms.append(Atom(symbol, position))
elif len(fields) == 3: # gradients
# -.51654903354681D-07 -.51654903206651D-07 0.51654903169644D-07
try:
grad = [float(x.replace('D', 'E')) * Bohr for x in fields[0:3] ]
except ValueError:
formatError()
forces.append(grad)
else: # next cycle
break
# calculator
calc = SinglePointCalculator(energy, forces, None, None, atoms)
atoms.set_calculator(calc)
# save frame
images.append(atoms)
# delete this frame from data to be handled
del lines[:2*len(atoms)+1]
return images[index]
def write_turbomole(filename, atoms):
"""Method to write turbomole coord file
"""
import numpy as np
from ase.constraints import FixAtoms
if isinstance(filename, str):
f = open(filename, 'w')
else: # Assume it's a 'file-like object'
f = filename
coord = atoms.get_positions()
symbols = atoms.get_chemical_symbols()
printfixed = False
if atoms.constraints:
for constr in atoms.constraints:
if isinstance(constr, FixAtoms):
fix_index=constr.index
printfixed=True
#print sflags
if (printfixed):
fix_str=[]
for i in fix_index:
if i == 1:
fix_str.append("f")
else:
fix_str.append(" ")
f.write("$coord\n")
if (printfixed):
for (x, y, z), s, fix in zip(coord,symbols,fix_str):
f.write('%20.14f %20.14f %20.14f %2s %2s \n'
% (x/Bohr, y/Bohr, z/Bohr, s.lower(), fix))
else:
for (x, y, z), s in zip(coord,symbols):
f.write('%20.14f %20.14f %20.14f %2s \n'
% (x/Bohr, y/Bohr, z/Bohr, s.lower()))
f.write("$end\n")
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