Révision 5 ase/calculators/turbomole.py
| turbomole.py (revision 5) | ||
|---|---|---|
| 1 | 1 |
"""This module defines an ASE interface to Turbomole |
| 2 |
|
|
| 3 | 2 |
http://www.turbomole.com/ |
| 4 | 3 |
""" |
| 5 | 4 |
import os, sys, string |
| ... | ... | |
| 11 | 10 |
import numpy as np |
| 12 | 11 |
|
| 13 | 12 |
class Turbomole(Calculator): |
| 14 |
"""Class for doing Turbomole calculations. |
|
| 15 |
""" |
|
| 16 | 13 |
def __init__(self, label='turbomole', calculate_energy="dscf", calculate_forces="grad", post_HF = False): |
| 17 |
"""Construct TURBOMOLE-calculator object. |
|
| 18 |
|
|
| 19 |
Parameters |
|
| 20 |
========== |
|
| 21 |
label: str |
|
| 22 |
Prefix to use for filenames (label.txt, ...). |
|
| 23 |
Default is 'turbomole'. |
|
| 24 |
|
|
| 25 |
Examples |
|
| 26 |
======== |
|
| 27 |
This is poor man's version of ASE-Turbomole: |
|
| 28 |
|
|
| 29 |
First you do a normal turbomole preparation using turbomole's |
|
| 30 |
define-program for the initial and final states. |
|
| 31 |
|
|
| 32 |
(for instance in subdirectories Initial and Final) |
|
| 33 |
|
|
| 34 |
Then relax the initial and final coordinates with desired constraints |
|
| 35 |
using standard turbomole. |
|
| 36 |
|
|
| 37 |
Copy the relaxed initial and final coordinates |
|
| 38 |
(initial.coord and final.coord) |
|
| 39 |
and the turbomole related files (from the subdirectory Initial) |
|
| 40 |
control, coord, alpha, beta, mos, basis, auxbasis etc to the directory |
|
| 41 |
you do the diffusion run. |
|
| 42 |
|
|
| 43 |
For instance: |
|
| 44 |
cd $My_Turbomole_diffusion_directory |
|
| 45 |
cd Initial; cp control alpha beta mos basis auxbasis ../; |
|
| 46 |
cp coord ../initial.coord; |
|
| 47 |
cd ../; |
|
| 48 |
cp Final/coord ./final.coord; |
|
| 49 |
mkdir Gz ; cp * Gz ; gzip -r Gz |
|
| 50 |
|
|
| 51 |
from ase.io import read |
|
| 52 |
from ase.calculators.turbomole import Turbomole |
|
| 53 |
a = read('coord', index=-1, format='turbomole')
|
|
| 54 |
calc = Turbomole() |
|
| 55 |
a.set_calculator(calc) |
|
| 56 |
e = a.get_potential_energy() |
|
| 57 |
|
|
| 58 |
""" |
|
| 59 |
|
|
| 60 | 14 |
self.label = label |
| 61 | 15 |
self.converged = False |
| 62 | 16 |
|
| ... | ... | |
| 88 | 42 |
def execute(self, command): |
| 89 | 43 |
from subprocess import Popen, PIPE |
| 90 | 44 |
try: |
| 45 |
# the sub process gets started here |
|
| 91 | 46 |
proc = Popen([command], shell=True, stderr=PIPE) |
| 92 | 47 |
error = proc.communicate()[1] |
| 93 |
if "abnormally" in error: |
|
| 48 |
# check the error output |
|
| 49 |
if not " ended normally" in error: |
|
| 94 | 50 |
raise OSError(error) |
| 95 | 51 |
print "TM command: ", command, "successfully executed" |
| 96 | 52 |
except OSError, e: |
| 97 |
print >>sys.stderr, "Execution failed:", e |
|
| 53 |
print >>sys.stderr, "Execution failed: ", e
|
|
| 98 | 54 |
sys.exit(1) |
| 99 | 55 |
|
| 100 | 56 |
def get_potential_energy(self, atoms): |
| ... | ... | |
| 134 | 90 |
return self.forces.copy() |
| 135 | 91 |
|
| 136 | 92 |
def get_stress(self, atoms): |
| 137 |
return self.stress.copy()
|
|
| 93 |
return self.stress |
|
| 138 | 94 |
|
| 139 | 95 |
def set_atoms(self, atoms): |
| 140 | 96 |
if self.atoms == atoms: |
| ... | ... | |
| 162 | 118 |
energy_tmp = float(line.split()[1]) |
| 163 | 119 |
if self.post_HF: |
| 164 | 120 |
energy_tmp += float(line.split()[4]) |
| 121 |
# update energy units |
|
| 165 | 122 |
self.e_total = energy_tmp * Hartree |
| 166 | 123 |
|
| 167 | 124 |
|
| ... | ... | |
| 184 | 141 |
print 'Gradients not found' |
| 185 | 142 |
raise RuntimeError("Please check TURBOMOLE gradients")
|
| 186 | 143 |
|
| 144 |
# next line |
|
| 187 | 145 |
iline += len(self.atoms) + 1 |
| 146 |
# $end line |
|
| 188 | 147 |
nline -= 1 |
| 148 |
# read gradients |
|
| 189 | 149 |
for i in xrange(iline, nline): |
| 190 | 150 |
line = string.replace(lines[i],'D','E') |
| 191 | 151 |
#tmp=np.append(forces_tmp,np.array\ |
Formats disponibles : Unified diff