root / ase / io / turbomole.py @ 1
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| 1 | 1 | tkerber | from ase.atoms import Atoms |
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| 2 | 1 | tkerber | from ase.units import Bohr |
| 3 | 1 | tkerber | |
| 4 | 1 | tkerber | |
| 5 | 1 | tkerber | def read_turbomole(filename='coord'): |
| 6 | 1 | tkerber | """Method to read turbomole coord file
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| 7 | 1 | tkerber |
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| 8 | 1 | tkerber | coords in bohr, atom types in lowercase, format:
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| 9 | 1 | tkerber | $coord
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| 10 | 1 | tkerber | x y z atomtype
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| 11 | 1 | tkerber | x y z atomtype f
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| 12 | 1 | tkerber | $end
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| 13 | 1 | tkerber | Above 'f' means a fixed atom.
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| 14 | 1 | tkerber | """
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| 15 | 1 | tkerber | from ase import Atoms, Atom |
| 16 | 1 | tkerber | from ase.constraints import FixAtoms |
| 17 | 1 | tkerber | |
| 18 | 1 | tkerber | if isinstance(filename, str): |
| 19 | 1 | tkerber | f = open(filename)
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| 20 | 1 | tkerber | |
| 21 | 1 | tkerber | lines = f.readlines() |
| 22 | 1 | tkerber | atoms_pos = [] |
| 23 | 1 | tkerber | atom_symbols = [] |
| 24 | 1 | tkerber | dollar_count=0
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| 25 | 1 | tkerber | myconstraints=[] |
| 26 | 1 | tkerber | for line in lines: |
| 27 | 1 | tkerber | if ('$' in line): |
| 28 | 1 | tkerber | dollar_count = dollar_count + 1
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| 29 | 1 | tkerber | if (dollar_count >= 2): |
| 30 | 1 | tkerber | break
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| 31 | 1 | tkerber | else:
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| 32 | 1 | tkerber | x, y, z, symbolraw = line.split()[:4]
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| 33 | 1 | tkerber | symbolshort=symbolraw.strip() |
| 34 | 1 | tkerber | symbol=symbolshort[0].upper()+symbolshort[1:].lower() |
| 35 | 1 | tkerber | #print symbol
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| 36 | 1 | tkerber | atom_symbols.append(symbol) |
| 37 | 1 | tkerber | atoms_pos.append([float(x)*Bohr, float(y)*Bohr, float(z)*Bohr]) |
| 38 | 1 | tkerber | cols = line.split() |
| 39 | 1 | tkerber | if (len(cols) == 5): |
| 40 | 1 | tkerber | fixedstr = line.split()[4].strip()
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| 41 | 1 | tkerber | if (fixedstr == "f"): |
| 42 | 1 | tkerber | myconstraints.append(True)
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| 43 | 1 | tkerber | else:
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| 44 | 1 | tkerber | myconstraints.append(False)
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| 45 | 1 | tkerber | else:
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| 46 | 1 | tkerber | myconstraints.append(False)
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| 47 | 1 | tkerber | |
| 48 | 1 | tkerber | if type(filename) == str: |
| 49 | 1 | tkerber | f.close() |
| 50 | 1 | tkerber | |
| 51 | 1 | tkerber | atoms = Atoms(positions = atoms_pos, symbols = atom_symbols, pbc = False)
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| 52 | 1 | tkerber | c = FixAtoms(myconstraints) |
| 53 | 1 | tkerber | atoms.set_constraint(c) |
| 54 | 1 | tkerber | #print c
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| 55 | 1 | tkerber | |
| 56 | 1 | tkerber | |
| 57 | 1 | tkerber | return atoms
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| 58 | 1 | tkerber | |
| 59 | 1 | tkerber | def write_turbomole(filename, atoms): |
| 60 | 1 | tkerber | """Method to write turbomole coord file
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| 61 | 1 | tkerber | """
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| 62 | 1 | tkerber | |
| 63 | 1 | tkerber | import numpy as np |
| 64 | 1 | tkerber | from ase.constraints import FixAtoms |
| 65 | 1 | tkerber | |
| 66 | 1 | tkerber | if isinstance(filename, str): |
| 67 | 1 | tkerber | f = open(filename, 'w') |
| 68 | 1 | tkerber | else: # Assume it's a 'file-like object' |
| 69 | 1 | tkerber | f = filename |
| 70 | 1 | tkerber | |
| 71 | 1 | tkerber | coord = atoms.get_positions() |
| 72 | 1 | tkerber | symbols = atoms.get_chemical_symbols() |
| 73 | 1 | tkerber | printfixed = False
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| 74 | 1 | tkerber | |
| 75 | 1 | tkerber | if atoms.constraints:
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| 76 | 1 | tkerber | for constr in atoms.constraints: |
| 77 | 1 | tkerber | if isinstance(constr, FixAtoms): |
| 78 | 1 | tkerber | fix_index=constr.index |
| 79 | 1 | tkerber | printfixed=True
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| 80 | 1 | tkerber | #print sflags
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| 81 | 1 | tkerber | |
| 82 | 1 | tkerber | if (printfixed):
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| 83 | 1 | tkerber | fix_str=[] |
| 84 | 1 | tkerber | for i in fix_index: |
| 85 | 1 | tkerber | if i == 1: |
| 86 | 1 | tkerber | fix_str.append("f")
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| 87 | 1 | tkerber | else:
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| 88 | 1 | tkerber | fix_str.append(" ")
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| 89 | 1 | tkerber | |
| 90 | 1 | tkerber | |
| 91 | 1 | tkerber | f.write("$coord\n")
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| 92 | 1 | tkerber | if (printfixed):
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| 93 | 1 | tkerber | for (x, y, z), s, fix in zip(coord,symbols,fix_str): |
| 94 | 1 | tkerber | f.write('%20.14f %20.14f %20.14f %2s %2s \n'
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| 95 | 1 | tkerber | % (x/Bohr, y/Bohr, z/Bohr, s.lower(), fix)) |
| 96 | 1 | tkerber | |
| 97 | 1 | tkerber | else:
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| 98 | 1 | tkerber | for (x, y, z), s in zip(coord,symbols): |
| 99 | 1 | tkerber | f.write('%20.14f %20.14f %20.14f %2s \n'
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| 100 | 1 | tkerber | % (x/Bohr, y/Bohr, z/Bohr, s.lower())) |
| 101 | 1 | tkerber | f.write("$end\n")
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