[ase-users] Installing ASE to compute Nudged elastic band using MOPAC ASE_MOPAC_COMMAND

[Lystrom, Levi]

Hello,


I recently found that ASE is able to perform Nudged elastic band using MOPAC to compute the geometries. I would like to use ase for Nudged elastic band to find the minimal path between configurational isomers and the transition state between them. I tried to optimize my structures using MOPAC but I get errors, I will attach the script I used below and the error I got. I looked into the ase.calculators.mopac and found that I should set the ASE_MOPAC_COMMAND but I do not understand how to set one variable to multiple values except appending or perpending. My MOPAC_2016.exe was set in my local directories because the admin of the cluster has not installed MOPAC.


Here is what the ase.calculators.mopac states:

"""This module defines an ASE interface to MOPAC.

Set $ASE_MOPAC_COMMAND to something like::

LD_LIBRARY_PATH=/path/to/lib/ \

MOPAC_LICENSE=/path/to/license \

/path/to/MOPAC2012.exe PREFIX.mop 2> /dev/null

"""


I have in my ~/.bashrc file the following:

## Setting Mopca
export MOPAC_LICENSE=/home/lystrom/opt/mopac/
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/lystrom/opt/mopac; export LD_LIBRARY_PATH
PATH=$PATH:/home/lystrom/opt/mopac; export PATH
alias mopac='/home/lystrom/opt/mopac/MOPAC2016.exe'


Here is the error I get when I try to use MOPAC to optimize my structures:
[lystrom at cluster3-0 C18H15N1]$ python MOPAC.py
Traceback (most recent call last):
  File "MOPAC.py", line 44, in <module>
    dyn.run(fmax=0.001)
  File "/home/lystrom/bin/python/ase/ase/optimize/optimize.py", line 174, in run
    f = self.atoms.get_forces()
  File "/home/lystrom/bin/python/ase/ase/atoms.py", line 735, in get_forces
    forces = self._calc.get_forces(self)
  File "/home/lystrom/bin/python/ase/ase/calculators/calculator.py", line 460, in get_forces
    return self.get_property('forces', atoms)
  File "/home/lystrom/bin/python/ase/ase/calculators/calculator.py", line 493, in get_property
    self.calculate(atoms, [name], system_changes)
  File "/home/lystrom/bin/python/ase/ase/calculators/calculator.py", line 656, in calculate
    .format(self.name, self.directory, errorcode))
RuntimeError: mopac in . returned an error: 127
[lystrom at cluster3-0 C18H15N1]$


Here is my script:
from ase import Atoms
from ase.optimize import BFGS
from ase.calculators.mopac import MOPAC
from ase.io import read, write
import numpy as np

atoms = Atoms('C18H15N1',
     positions=[( 0.15624900,   -1.78811500,   -0.04509800),
                ( 0.28109400,    0.44850700,   -0.92241700),
                (-0.32156400,    1.75582700,   -0.87207700),
                (-0.51110200,   -0.65785900,   -0.46731500),
                ( 1.54480000,   -1.90763700,   -0.42144500),
                ( 1.61597411,   -3.83002555,    1.03226598),
                (-1.90644800,   -0.40547500,   -0.15348300),
                ( 2.22437426,   -3.03683036,   -0.00372979),
                (-2.37594600,    0.93996100,   -0.15895200),
                ( 2.44339172,   -4.68009707,    1.81540021),
                (-2.79358600,   -1.45076500,    0.15280900),
                ( 3.62009399,   -3.23619310,   -0.28886688),
                (-3.73332000,    1.18878400,    0.17319700),
                ( 3.78537184,   -4.78372920,    1.56656205),
                (-4.11612500,   -1.18307300,    0.46527800),
                ( 4.23097277,   -2.46135055,   -1.47125690),
                ( 4.37455627,   -4.07187920,    0.47950947),
                (-4.58109300,    0.13957700,    0.47946700),
                (-0.24947600,   -2.44795800,    0.73202600),
                ( 0.29543500,    2.62677100,   -1.16773900),
                ( 0.52835857,   -3.99897057,    1.04168525),
                ( 1.16173900,    0.30318400,   -1.55971300),
                ( 1.97295568,   -5.26254600,    2.62284032),
                ( 2.07846004,   -1.03020986,   -0.81253135),
                (-2.42821000,   -2.48908700,    0.13520000),
                ( 3.57462212,   -2.52128715,   -2.31417528),
                (-4.10652100,    2.22499800,    0.18181200),
                ( 4.36422602,   -1.43621033,   -1.19515707),
                ( 4.42683485,   -5.43459085,    2.17926994),
                (-4.80603300,   -2.00620700,    0.70192900),
                ( 5.17851177,   -2.88818979,   -1.72596869),
                ( 5.44512012,   -4.21957985,    0.27336622),
                (-5.63251000,    0.34153900,    0.73416700),
                (-1.54626800,    2.01782300,   -0.49355400)],
                calculator=MOPAC(method='AM1',task='OPT'))
dyn = BFGS(atoms, 'C18H15N1.traj')
dyn.run(fmax=0.001)
print(atoms)
print(atoms.read(label='C18H15N1'))

write('C18H15N1.xyz', read('C18H15N1.traj'))


Any help would be very much appreciate,


Levi Lystrom

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