ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
# Set and clear and reset settings (just for shows)
calc.param.task = ’SinglePoint’
# Reset to CASTEP default
calc.param.task.clear()
# all of the following are identical
calc.param.task = ’GeometryOptimization’
calc.task = ’GeometryOptimization’
calc.TASK = ’GeometryOptimization’
calc.Task = ’GeometryOptimization’
# Prepare atoms
mol = ase.atoms.Atoms(’CO’, [[0, 0, 0], [0, 0, 1.2]], cell=[10, 10, 10])
mol.set_calculator(calc)
# Check for correct input
if calc.dryrun_ok():
print(’%s : %s ’ % (mol.calc._label, mol.get_potential_energy()))
else:
print("Found error in input")
print(calc._error)
# Read all settings from previous calculation
mol = ase.io.castep.read_seed(’%s/CO_LDA’ % directory)
# Use the OTF pseudo-potential we have just generated
mol.calc.set_pspot(’OTF’)
# Change some settings
mol.calc.param.xc_functional = ’PBE’
# don’t forget to set an appropriate label
mol.calc._label = ’CO_PBE’
# Recalculate the potential energy
print(’%s : %s ’ % (mol.calc._label, mol.get_potential_energy()))
Gromacs
Introduction
Gromacs is a free classical molecular dynamics package. It is mainly used in modeling of biological systems. It
is part of the ubuntu-linux distribution.
Gromacs Calculator
This ASE-interface is a preliminary one and it is VERY SLOW so do not use it for production runs. It is here
because of hopefully we’ll get a QM/MM calculator which is using gromacs as the MM part.
For example:
calc = Gromacs( init_structure_file=infilename, force_field=’oplsaa’, water_model=’tip3p’, define = ‘-
DFLEXIBLE’, integrator = ‘md’, nsteps = ‘0’, nstfout = ‘1’, nstlog = ‘1’, nstenergy = ‘1’, energygrps =
‘System’, nstlist = ‘1’, ns_type = ‘grid’, pbc = ‘xyz’, rlist = ‘1.15’, coulombtype = ‘PME-Switch’, rcoulomb
= ‘0.8’, vdwtype = ‘shift’, rvdw = ‘0.8’, rvdw_switch = ‘0.75’, DispCorr = ‘Ener’)
134 Chapter 7. Documentation for modules in ASE