ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
Example
Here is an example of how to calculate the total energy of a CO molecule:
#!/usr/bin/env python
from ase import *
from ase.calculators.jacapo import *
CO = data.molecules.molecule(’CO’)
CO.set_cell([6,6,6])
CO.center()
calc = Jacapo(nc=’CO.nc’,
atoms=CO,
pw=300,
nbands=8)
print CO.get_potential_energy()
Restarting from an old Calculation
With Jacapo it is very easy to restart an old calculation. All necessary information (including the constraints) is
stored in the out.nc file. To continue for example a geometry optimization do something like this:
calc = Jacapo(’old.nc’,stay_alive=True)
atoms = calc.get_atoms()
dyn = QuasiNewton(atoms,logfile=’qn.log’)
dyn.run(fmax=0.05)
Note, that the stay_alive flag is not stored in the .nc file and must be set when the calculator instance is created.
ABINIT
Introduction
ABINIT is a density-functional theory code based on pseudopotentials and a planewave basis.
Environment variables
Note: setting environment variables is necessary only if you configure your ABINIT/ASE environment from
scratch.
You need to write a script called abinit.py containing something like this:
import os
abinit = ’/usr/bin/abinis’ # full path to the abinit executable
exitcode = os.system(’%s < %s.files > %s.log’ % (abinit, label, label))
The environment variable ABINIT_SCRIPT must point to that file.
A directory containing the pseudopotential files (at least of .fhi type) is also needed, and it is to be put in the
environment variable ABINIT_PP_PATH. Abinit does not provide tarballs of pseduopotentials so the easiest way
is to download and unpack http://wiki.fysik.dtu.dk/abinit-files/abinit-pseudopotentials-2.tar.gz
Set the environment variables in your in your shell configuration file:
$ export ABINIT_SCRIPT=$HOME/bin/abinit.py
$ export ABINIT_PP_PATH=${HOME}/abinit-pseudopotentials-2/LDA_FHI
$ export ABINIT_PP_PATH=${HOME}/abinit-pseudopotentials-2/GGA_FHI:$ABINIT_PP_PATH
$ export ABINIT_PP_PATH=${HOME}/abinit-pseudopotentials-2/LDA_HGH:$ABINIT_PP_PATH
112 Chapter 7. Documentation for modules in ASE