testsuite/AdResS/HAdResS/test_HAdResS.py
#!/usr/bin/env python3
#
# Copyright (C) 2013-2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ESPResSo++ is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# -*- coding: utf-8 -*-
import sys
import time
import espressopp
import mpi4py.MPI as MPI
import unittest
class TestHAdResS(unittest.TestCase):
def setUp(self):
# set up system
system = espressopp.System()
box = (10, 10, 10)
system.bc = espressopp.bc.OrthorhombicBC(system.rng, box)
system.skin = 0.3
system.comm = MPI.COMM_WORLD
nodeGrid = espressopp.tools.decomp.nodeGrid(espressopp.MPI.COMM_WORLD.size,box,rc=1.5,skin=system.skin)
cellGrid = espressopp.tools.decomp.cellGrid(box, nodeGrid, rc=1.5, skin=system.skin)
system.storage = espressopp.storage.DomainDecompositionAdress(system, nodeGrid, cellGrid)
self.system = system
def test_slab(self):
# add some particles
particle_list = [
(1, 1, 0, espressopp.Real3D(5.5, 5.0, 5.0), 1.0, 0),
(2, 1, 0, espressopp.Real3D(6.5, 5.0, 5.0), 1.0, 0),
(3, 1, 0, espressopp.Real3D(7.5, 5.0, 5.0), 1.0, 0),
(4, 1, 0, espressopp.Real3D(8.5, 5.0, 5.0), 1.0, 0),
(5, 1, 0, espressopp.Real3D(9.5, 5.0, 5.0), 1.0, 0),
(6, 0, 0, espressopp.Real3D(5.5, 5.0, 5.0), 1.0, 1),
(7, 0, 0, espressopp.Real3D(6.5, 5.0, 5.0), 1.0, 1),
(8, 0, 0, espressopp.Real3D(7.5, 5.0, 5.0), 1.0, 1),
(9, 0, 0, espressopp.Real3D(8.5, 5.0, 5.0), 1.0, 1),
(10, 0, 0, espressopp.Real3D(9.5, 5.0, 5.0), 1.0, 1),
]
tuples = [(1,6),(2,7),(3,8),(4,9),(5,10)]
self.system.storage.addParticles(particle_list, 'id', 'type', 'q', 'pos', 'mass','adrat')
ftpl = espressopp.FixedTupleListAdress(self.system.storage)
ftpl.addTuples(tuples)
self.system.storage.setFixedTuplesAdress(ftpl)
self.system.storage.decompose()
# generate a verlet list
vl = espressopp.VerletListAdress(self.system, cutoff=1.5, adrcut=1.5,
dEx=2.0, dHy=1.0, adrCenter=[5.0, 5.0, 5.0], sphereAdr=False)
# add interaction
interNB = espressopp.interaction.VerletListHadressLennardJones2(vl, ftpl)
potWCA1 = espressopp.interaction.LennardJones(epsilon=1.0, sigma=1.0, shift='auto', cutoff=1.4)
potWCA2 = espressopp.interaction.LennardJones(epsilon=0.0, sigma=1.0, shift='auto', cutoff=1.4)
interNB.setPotentialAT(type1=0, type2=0, potential=potWCA1) # AT
interNB.setPotentialCG(type1=1, type2=1, potential=potWCA2) # CG
self.system.addInteraction(interNB)
# initialize lambda values
integrator = espressopp.integrator.VelocityVerlet(self.system)
integrator.dt = 0.01
adress = espressopp.integrator.Adress(self.system,vl,ftpl)
integrator.addExtension(adress)
espressopp.tools.AdressDecomp(self.system, integrator)
# coordinates and non-bonded energy of particles before integration
before = [self.system.storage.getParticle(i).pos[j] for i in range(1,6) for j in range(3)]
energy_before = interNB.computeEnergy()
# run ten steps and compute energy
integrator.run(10)
# coordinates and non-bonded energy of particles after integration
after = [self.system.storage.getParticle(i).pos[j] for i in range(1,6) for j in range(3)]
energy_after = interNB.computeEnergy()
# run checks (only particles in atomistic, hybrid and first part of coarse-grained region should move, i.e. the first 4 particles - as the WCA's epsilon is 0.0 in the coarse-grained region. Furthermore they should move along the x-axis only given their setup. Additionally, check energies)
self.assertAlmostEqual(after[0], 5.413650, places=5)
self.assertEqual(before[1], after[1])
self.assertEqual(before[2], after[2])
self.assertAlmostEqual(after[3], 6.507075, places=5)
self.assertEqual(before[4], after[4])
self.assertEqual(before[5], after[5])
self.assertAlmostEqual(after[6], 7.551088, places=5)
self.assertEqual(before[7], after[7])
self.assertEqual(before[8], after[8])
self.assertAlmostEqual(after[9], 8.531737, places=5)
self.assertEqual(before[10], after[10])
self.assertEqual(before[11], after[11])
self.assertEqual(before[12], after[12])
self.assertEqual(before[13], after[13])
self.assertEqual(before[14], after[14])
self.assertAlmostEqual(energy_before,0.921374, places=5)
self.assertAlmostEqual(energy_after, -0.468436, places=5)
def test_sphere(self):
# add some particles
particle_list = [
(1, 1, 0, espressopp.Real3D(5.0, 5.5, 5.0), 1.0, 0),
(2, 1, 0, espressopp.Real3D(5.0, 6.5, 5.0), 1.0, 0),
(3, 1, 0, espressopp.Real3D(5.0, 7.5, 5.0), 1.0, 0),
(4, 1, 0, espressopp.Real3D(5.0, 8.5, 5.0), 1.0, 0),
(5, 1, 0, espressopp.Real3D(5.0, 9.5, 5.0), 1.0, 0),
(6, 0, 0, espressopp.Real3D(5.0, 5.5, 5.0), 1.0, 1),
(7, 0, 0, espressopp.Real3D(5.0, 6.5, 5.0), 1.0, 1),
(8, 0, 0, espressopp.Real3D(5.0, 7.5, 5.0), 1.0, 1),
(9, 0, 0, espressopp.Real3D(5.0, 8.5, 5.0), 1.0, 1),
(10, 0, 0, espressopp.Real3D(5.0, 9.5, 5.0), 1.0, 1),
]
tuples = [(1,6),(2,7),(3,8),(4,9),(5,10)]
self.system.storage.addParticles(particle_list, 'id', 'type', 'q', 'pos', 'mass','adrat')
ftpl = espressopp.FixedTupleListAdress(self.system.storage)
ftpl.addTuples(tuples)
self.system.storage.setFixedTuplesAdress(ftpl)
self.system.storage.decompose()
# generate a verlet list
vl = espressopp.VerletListAdress(self.system, cutoff=1.5, adrcut=1.5,
dEx=2.0, dHy=1.0, adrCenter=[5.0, 5.0, 5.0], sphereAdr=True)
# add interaction
interNB = espressopp.interaction.VerletListHadressLennardJones2(vl, ftpl)
potWCA1 = espressopp.interaction.LennardJones(epsilon=1.0, sigma=1.0, shift='auto', cutoff=1.4)
potWCA2 = espressopp.interaction.LennardJones(epsilon=0.0, sigma=1.0, shift='auto', cutoff=1.4)
interNB.setPotentialAT(type1=0, type2=0, potential=potWCA1) # AT
interNB.setPotentialCG(type1=0, type2=0, potential=potWCA2) # CG
self.system.addInteraction(interNB)
# initialize lambda values
integrator = espressopp.integrator.VelocityVerlet(self.system)
integrator.dt = 0.01
adress = espressopp.integrator.Adress(self.system,vl,ftpl)
integrator.addExtension(adress)
espressopp.tools.AdressDecomp(self.system, integrator)
# coordinates and non-bonded energy of particles before integration
before = [self.system.storage.getParticle(i).pos[j] for i in range(1,6) for j in range(3)]
energy_before = interNB.computeEnergy()
# run ten steps and compute energy
integrator.run(10)
# coordinates and non-bonded energy of particles after integration
after = [self.system.storage.getParticle(i).pos[j] for i in range(1,6) for j in range(3)]
energy_after = interNB.computeEnergy()
# run checks (as before, just that particles should now move along the y-axis only, given their setup and the spherical adaptive resolution geometry)
self.assertEqual(before[0], after[0])
self.assertAlmostEqual(after[1], 5.413650, places=5)
self.assertEqual(before[2], after[2])
self.assertEqual(before[3], after[3])
self.assertAlmostEqual(after[4], 6.507075, places=5)
self.assertEqual(before[5], after[5])
self.assertEqual(before[6], after[6])
self.assertAlmostEqual(after[7], 7.551088, places=5)
self.assertEqual(before[8], after[8])
self.assertEqual(before[9], after[9])
self.assertAlmostEqual(after[10], 8.531737, places=5)
self.assertEqual(before[11], after[11])
self.assertEqual(before[12], after[12])
self.assertEqual(before[13], after[13])
self.assertEqual(before[14], after[14])
self.assertAlmostEqual(energy_before,0.921374, places=5)
self.assertAlmostEqual(energy_after, -0.468436, places=5)
def test_ATATCG_template(self):
# add some particles
particle_list = [
(1, 1, 0, espressopp.Real3D(5.5, 5.0, 5.0), 1.0, 0),
(2, 1, 0, espressopp.Real3D(6.5, 5.0, 5.0), 1.0, 0),
(3, 1, 0, espressopp.Real3D(7.5, 5.0, 5.0), 1.0, 0),
(4, 1, 0, espressopp.Real3D(8.5, 5.0, 5.0), 1.0, 0),
(5, 1, 0, espressopp.Real3D(9.5, 5.0, 5.0), 1.0, 0),
(6, 0, 1.0, espressopp.Real3D(5.5, 5.0, 5.0), 1.0, 1),
(7, 0, 1.0, espressopp.Real3D(6.5, 5.0, 5.0), 1.0, 1),
(8, 0, 1.0, espressopp.Real3D(7.5, 5.0, 5.0), 1.0, 1),
(9, 0, 1.0, espressopp.Real3D(8.5, 5.0, 5.0), 1.0, 1),
(10, 0, 1.0, espressopp.Real3D(9.5, 5.0, 5.0), 1.0, 1),
]
tuples = [(1,6),(2,7),(3,8),(4,9),(5,10)]
self.system.storage.addParticles(particle_list, 'id', 'type', 'q', 'pos', 'mass','adrat')
ftpl = espressopp.FixedTupleListAdress(self.system.storage)
ftpl.addTuples(tuples)
self.system.storage.setFixedTuplesAdress(ftpl)
self.system.storage.decompose()
# generate a verlet list
vl = espressopp.VerletListAdress(self.system, cutoff=1.5, adrcut=1.5,
dEx=2.0, dHy=1.0, adrCenter=[5.0, 5.0, 5.0], sphereAdr=False)
# add interactions
interNB = espressopp.interaction.VerletListHadressATLJReacFieldGenHarmonic(vl, ftpl)
potLJ = espressopp.interaction.LennardJones(epsilon=0.650299305951, sigma=0.316549165245, shift='auto', cutoff=1.4)
potQQ = espressopp.interaction.ReactionFieldGeneralized(prefactor=138.935485, kappa=0.0, epsilon1=1.0, epsilon2=80.0, cutoff= 1.4, shift="auto")
potCG = espressopp.interaction.Harmonic(K=500.0, r0=1.4, cutoff=1.4)
interNB.setPotentialAT1(type1=0, type2=0, potential=potLJ)
interNB.setPotentialAT2(type1=0, type2=0, potential=potQQ)
interNB.setPotentialCG(type1=1, type2=1, potential=potCG)
self.system.addInteraction(interNB)
# set up integrator
integrator = espressopp.integrator.VelocityVerlet(self.system)
integrator.dt = 0.01
adress = espressopp.integrator.Adress(self.system, vl, ftpl)
integrator.addExtension(adress)
espressopp.tools.AdressDecomp(self.system, integrator)
# coordinates and non-bonded energy of particles before integration
before = [self.system.storage.getParticle(i).pos[j] for i in range(1,6) for j in range(3)]
energy_before = interNB.computeEnergy()
# run ten steps and compute energy
integrator.run(10)
# coordinates and non-bonded energy of particles after integration
after = [self.system.storage.getParticle(i).pos[j] for i in range(1,6) for j in range(3)]
energy_after = interNB.computeEnergy()
# run checks
self.assertAlmostEqual(after[0], 5.060715, places=5)
self.assertEqual(before[1], after[1])
self.assertEqual(before[2], after[2])
self.assertAlmostEqual(after[3], 6.063541, places=5)
self.assertEqual(before[4], after[4])
self.assertEqual(before[5], after[5])
self.assertAlmostEqual(after[6], 6.956633, places=5)
self.assertEqual(before[7], after[7])
self.assertEqual(before[8], after[8])
self.assertAlmostEqual(after[9], 8.530581, places=5)
self.assertEqual(before[10], after[10])
self.assertEqual(before[11], after[11])
self.assertAlmostEqual(after[12], 0.482246, places=5)
self.assertEqual(before[13], after[13])
self.assertEqual(before[14], after[14])
self.assertAlmostEqual(energy_before, 191.685729, places=5)
self.assertAlmostEqual(energy_after, 43.035403, places=5)
if __name__ == '__main__':
unittest.main()