[ase-users] Save results of dynamic simulation of atoms position, energy, forces

[Dong gi Kang]

Dear James,

Thank you for the prompt reply.

May I ask you again the same question?
Sorry for asking again even though you gave me a clear advice. I only have few days of experience in ase.

So, I have to append the results not with atoms.copy() command which only pass the atom positions and momenta.

##################
# store position/E/F  #
##################
db = []
def collect_data():
    #db.append(atoms.copy())

dynamics.attach(collect_data, interval=10)
dynamics.run(steps=500)
write(‘./tmp/atoms_db.xyz’, db, write_results=True)


I attempted with below script which gives an error :TypeError: 'Potential' object is not callable
Def collect_data():
    atoms_copy.calc = SinglePointCalculator(atoms)
    db.append(atoms_copy.calc)

and I am not where to place and use the commands:
atoms_copy = atoms.calc()
atoms_copy.calc = atoms.calc

If you do not mind may I ask you to show how to write the script to save the results of the MD calc?

Sorry for asking again even though you gave me a clear advice.

I appreciate your time and help.

Dong-gi Kang




From: james.kermode at gmail.com <james.kermode at gmail.com>
Date: Thursday, 10 December 2020 at 11:00
To: Dong gi Kang <kdg4206 at gmail.com>, ase-users at listserv.fysik.dtu.dk <ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] Save results of dynamic simulation of atoms position, energy, forces
Hi Dong,

atoms.copy() does not copy the calculator – either do this by hand, with

atoms_copy = atoms.calc()
atoms_copy.calc = atoms.calc

or make a SinglePointCalculator with the results:

from ase.calculators.singlepoint import SinglePointCalculator
atoms_copy.calc = SinglePointCalculator(**atoms.calc.results)

James

From: ase-users-bounces at listserv.fysik.dtu.dk <ase-users-bounces at listserv.fysik.dtu.dk>
Date: Thursday, 10 December 2020 at 10:46
To: ase-users at listserv.fysik.dtu.dk <ase-users at listserv.fysik.dtu.dk>
Subject: [ase-users] Save results of dynamic simulation of atoms position, energy, forces
Hi all,

I would like to store as an extended xyz file the results of dynamic simulations (atoms position, energy, forces).
This is the script that I ran MD calcs for Si slab. The end of the script (where is marked) only stores atom position and momenta instead of position/energy/force (atoms.copy() does not copy force/energy)

Could you please give any advice?

` ` `
import os
import sys
import numpy as np
import matplotlib.pylab as plt
from quippy.potential import Potential
from quippy.descriptors import Descriptor
from ase import Atoms, units
from ase.build import add_vacuum
from ase.lattice.cubic import Diamond
from ase.io import write
from ase.constraints import FixAtoms
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.md.verlet import VelocityVerlet
from ase.md.langevin import Langevin
from ase.optimize.precon import PreconLBFGS, Exp
sys.path.append('/home/{user}/software/QUIP/src/GAP/doc_src/gap_si_surface/')
from visualise import ViewStructure

T = 1000.0 # Temperature [Kelvin]
timestep = 1.0 * units.fs

##############
# building struc #
##############
def build_slab(size=(1,2,2), vacuum=10.):
    # Build Si lattice.
    # lattice = Diamond('Si', directions=([1, 0, 0], [0, 1, 0], [0, 0, 1]), latticeconstant=5.44, size=size)
    lattice = Diamond('Si', latticeconstant=5.44, size=size)
    atoms = Atoms(lattice)

    # Fixing the bottom layer
    bottom = atoms.positions[:,2].min()
    fixed_mask = (abs(atoms.positions[:,2] - bottom) < 2.0)
    atoms.set_constraint(FixAtoms(mask=fixed_mask))

    # build surface by adding space to z direction
    add_vacuum(atoms, vacuum)
    # atoms.center(vacuum=10.0, axis=2)

    return atoms

atoms = build_slab()
print('Number of atoms:', len(atoms))

############
# Setting Calc #
############
# attach tight binding calculator
qm_pot = Potential('TB DFTB', param_filename='/home/uccatka/software/QUIP/share/Parameters/tightbind.parms.DFTB.pbc-0-1.xml')
atoms.set_calculator(qm_pot)  # Set the potential

# Thermalize atoms
MaxwellBoltzmannDistribution(atoms, 2.0 * T * units.kB)
# dynamics = VelocityVerlet(atoms, timestep)
dynamics = Langevin(atoms, timestep, T * units.kB, 0.002)

#attach observer to dynamics to track quantity of interest (temperature)
def print_status():
    print('Step = {}, time = {} [fs], T = {} [K]'.format(
        dynamics.nsteps,
        dynamics.nsteps * dynamics.dt / units.fs,
        atoms.get_kinetic_energy() / (1.5 * units.kB * len(atoms))
    ))

def print_energy(a=atoms):  # store a reference to atoms in the definition.
    """Function to print the potential, kinetic and total energy."""
    epot = a.get_potential_energy() / len(a)
    ekin = a.get_kinetic_energy() / len(a)
    force = a.get_forces()
    print('Energy per atom: Epot = %.3feV  Ekin = %.3feV (T=%3.0fK)  '
          'Etot = %.3feV force = %.3f'% (epot, ekin, ekin / (1.5 * units.kB), epot + ekin, force))

dynamics.attach(print_status, interval=10)
dynamics.attach(print_energy, interval=1)
dynamics.run(steps=100)

##################
# store position/E/F  #
##################
db = []
def collect_data():
    db.append(atoms.copy())

dynamics.attach(collect_data, interval=10)
dynamics.run(steps=500)

write(‘./tmp/atoms_db.xyz’, db, write_results=True)
` ` `
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