Models: Classical MD: initial steps

[farhi]

inquire for MD using ASE couple with MDANSE python script to get Sqw, DOS, MSD...

[farhi]

May use either of:

• https://gitlab.com/materials-modeling/dynasor
• https://github.com/certik/dynsf

[farhi]

An example that runs with LAMMPS:

export LAMMPS_COMMAND="/usr/bin/mpirun -np 24 /usr/bin/lammps"

then: # ipython

from ase import Atoms, Atom
from ase.calculators.lammpsrun import LAMMPS
a = [6.5, 6.5, 7.7]
d = 2.3608
NaCl = Atoms([Atom('Na', [0, 0, 0]),
              Atom('Cl', [0, 0, d])],
             cell=a, pbc=True)
calc = LAMMPS()
NaCl.set_calculator(calc)
print(NaCl.get_stress()) # but LAMMPS remains active... ??

# now the MD
from ase.md.verlet import VelocityVerlet
import ase
dyn = VelocityVerlet(NaCl, dt=5.0 * ase.units.fs,trajectory='md.traj', logfile='md.log')
dyn.run(1000)  # take 1000 steps

[farhi]

MPI use does not seem to work properly, but

export LAMMPS_COMMAND="/usr/bin/lammps"

is OK. Execution time is:

• single core: 55 sec per 10000 steps
• OpenMP 24: it uses only 40% of total CPU resource (_export OMP_NUMTHREADS=24), and never ends !

[farhi]

Could use GROMACS-Matlab interfaces ? Use ASE to read e.g. CIF and export to Gromacs (only GRO file). Topology file will still be needed ?

• https://fr.mathworks.com/matlabcentral/fileexchange/47975-reading-gromacs-gro-file-in-matlab
• https://fr.mathworks.com/matlabcentral/fileexchange/33312-convert-gromacs-v-4-5-trajectory-files-into-matlab-matrix
• https://mdtoolbox.readthedocs.io/en/latest/alad_ksdensity.html
• https://bitbucket.org/BioSimVienna/gro-mex/src

then would run GROMACS externally, and finally read results. Can also use gmxdump to convert to text and process in Matlab.

[farhi]

We can run with any calculator with syntax:

• options.declaration = 'from ase.calculators.lammpsrun import LAMMPS';
• options.calculator='LAMMPS()';
• setenv('LAMMPS_COMMAND','/usr/bin/lammps');
• s=sqw_phonons('lattice', options)

this simplifies the integration of non supported calculators.

[farhi]

See also some additional LAMMPS/ASE examples with 'lammpsrun' as above.

• http://devonwa.com/2016/09/01/installing-and-using-LAMMPS-with-ASE/

[farhi]

GROMACS procedure to run MD is explained in the attached file

README.txt

using water as example. Could this be automated by coupling to e.g. ASE ?