Espresso/pp minimize energy

esmd_minimize_energy.py

#!/usr/bin/env python

import sys
import time
import espressomd


system = espressomd.System()
#gamma = 0.001, ftol=1.0, displa 0.001
system.minimize_energy.init(
    f_max=1.0,
    gamma=0.001,
    max_steps=2000,
    max_displacement=0.001)

system.skin = 0.3
system.time_step = 0.001
system.periodicity = [1, 1, 1]
system.box_l = (10.0, 10.0, 10.0)
system.non_bonded_inter[0, 0].lennard_jones.set_params(
    epsilon=1.0, sigma=1.0, cutoff=3.0, shift='auto')

system.part.add(id=1, pos=(2.0, 2.0, 2.0), mass=1.0, type=0)
system.part.add(id=2, pos=(2.1, 2.0, 2.0), mass=1.0, type=0)

energies0 = system.analysis.energy()
print 'before', energies0['total'], '1', system.part[1].pos, '2', system.part[2].pos

system.minimize_energy.minimize()

energies1 = system.analysis.energy()
print 'after', energies1['total'], '1', system.part[1].pos, '2', system.part[2].pos

# Set position and compute energy
# ESPP: 0.00547944174424
system.part[1].pos = (1.0, 2.0, 2.0)
system.part[2].pos = (2.0, 2.0, 2.0)
print 'after', system.analysis.energy()['total'], '1', system.part[1].pos, '2', system.part[2].pos
print 'espp ', 0.00547944174424

espp_minimize_energy.py

#!/usr/bin/env python

import sys
import time
import espressopp
import mpi4py.MPI as MPI

system = espressopp.System()
system.bc = espressopp.bc.OrthorhombicBC(system.rng, (10, 10, 10))
system.skin = 0.3
system.comm = MPI.COMM_WORLD
system.storage = espressopp.storage.DomainDecomposition(system)
system = system
particle_list = [
    (1, espressopp.Real3D(2.0, 2.0, 2.0), 1.0),
    (2, espressopp.Real3D(2.1, 2.0, 2.0), 1.0),
]
system.storage.addParticles(particle_list, 'id', 'pos', 'mass')
system.storage.decompose()
minimize_energy = espressopp.integrator.MinimizeEnergy(
    system, gamma=0.001, ftol=1.0, max_displacement=0.001)

vl = espressopp.VerletList(system, cutoff=3.0)
lj = espressopp.interaction.LennardJones(sigma=1.0, epsilon=1.0, cutoff=3.0, shift='auto')
interaction = espressopp.interaction.VerletListLennardJones(vl)
interaction.setPotential(type1=0, type2=0, potential=lj)
system.addInteraction(interaction)

energy_before = interaction.computeEnergy()

print 'before', energy_before, system.storage.getParticle(1).pos, system.storage.getParticle(2).pos

minimize_energy.run(2000)

print 'after', interaction.computeEnergy(), system.storage.getParticle(1).pos, system.storage.getParticle(2).pos

system.storage.modifyParticle(1, 'pos', espressopp.Real3D(1.0, 2.0, 2.0))
system.storage.modifyParticle(2, 'pos', espressopp.Real3D(2.0, 2.0, 2.0))
print 'after', interaction.computeEnergy(), system.storage.getParticle(1).pos, system.storage.getParticle(2).pos