testsuite/AdResS/RDFatomistic/test_RDFatomistic.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 espressopp
import mpi4py.MPI as MPI
import unittest
class TestRDFatomistic(unittest.TestCase):
def setUp(self):
# set up system
self.system = espressopp.System()
box = (10, 10, 10)
self.system.bc = espressopp.bc.OrthorhombicBC(self.system.rng, box)
self.system.rng = espressopp.esutil.RNG()
self.system.skin = 0.5
nodeGrid = espressopp.tools.decomp.nodeGrid(espressopp.MPI.COMM_WORLD.size,box,rc=1.5,skin=self.system.skin)
cellGrid = espressopp.tools.decomp.cellGrid(box, nodeGrid, rc=1.5, skin=self.system.skin)
self.system.storage = espressopp.storage.DomainDecompositionAdress(self.system, nodeGrid, cellGrid)
def test_span_true(self):
# add some particles
particle_list = [
(1, 1, 0, espressopp.Real3D(5.0, 5.0, 5.0), 1.0, 0),
(2, 1, 0, espressopp.Real3D(6.0, 5.0, 5.0), 1.0, 0),
(3, 1, 0, espressopp.Real3D(6.5, 5.0, 5.0), 1.0, 0),
(4, 1, 0, espressopp.Real3D(6.5, 5.5, 5.0), 1.0, 0),
(5, 0, 0, espressopp.Real3D(5.0, 5.0, 5.0), 1.0, 1),
(6, 0, 0, espressopp.Real3D(6.0, 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(6.5, 5.5, 5.0), 1.0, 1),
]
tuples = [(1,5),(2,6),(3,7),(4,8)]
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)
# initialize lambda values
integrator = espressopp.integrator.VelocityVerlet(self.system)
adress = espressopp.integrator.Adress(self.system,vl,ftpl)
integrator.addExtension(adress)
espressopp.tools.AdressDecomp(self.system, integrator)
# calculate rdfs
rdf_span = espressopp.analysis.RDFatomistic(system=self.system, type1=0, type2=0, span=1.0, spanbased=True)
rdf_span_array = rdf_span.compute(10)
# run checks
self.assertAlmostEqual(rdf_span_array[1], 0.0, places=5)
self.assertAlmostEqual(rdf_span_array[2], 33.506304, places=5)
def test_span_false(self):
# add some particles
particle_list = [
(1, 1, 0, espressopp.Real3D(5.0, 5.0, 5.0), 1.0, 0),
(2, 1, 0, espressopp.Real3D(6.0, 5.0, 5.0), 1.0, 0),
(3, 1, 0, espressopp.Real3D(6.5, 5.0, 5.0), 1.0, 0),
(4, 1, 0, espressopp.Real3D(6.5, 5.5, 5.0), 1.0, 0),
(5, 0, 0, espressopp.Real3D(5.0, 5.0, 5.0), 1.0, 1),
(6, 0, 0, espressopp.Real3D(6.0, 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(6.5, 5.5, 5.0), 1.0, 1),
]
tuples = [(1,5),(2,6),(3,7),(4,8)]
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)
# initialize lambda values
integrator = espressopp.integrator.VelocityVerlet(self.system)
adress = espressopp.integrator.Adress(self.system,vl,ftpl)
integrator.addExtension(adress)
espressopp.tools.AdressDecomp(self.system, integrator)
# calculate rdfs
rdf_nospan = espressopp.analysis.RDFatomistic(system=self.system, type1=0, type2=0, span=1.0, spanbased=False)
rdf_nospan_array = rdf_nospan.compute(10)
# run checks
self.assertAlmostEqual(rdf_nospan_array[1], 136.418523, places=5)
self.assertAlmostEqual(rdf_nospan_array[2], 16.753152, places=5)
def test_path_integral(self):
# add some particles
particle_list = [
(1, 1, espressopp.Real3D(1.0, 5.0, 5.0), 0, 0),
(2, 1, espressopp.Real3D(1.0, 4.9, 5.0), 1, 1),
(3, 1, espressopp.Real3D(1.0, 5.0, 4.9), 1, 2),
(4, 1, espressopp.Real3D(1.0, 5.1, 5.0), 1, 3),
(5, 1, espressopp.Real3D(1.0, 5.0, 5.1), 1, 4),
(6, 1, espressopp.Real3D(6.0, 5.0, 5.0), 0, 0),
(7, 1, espressopp.Real3D(6.0, 4.8, 5.0), 1, 1),
(8, 1, espressopp.Real3D(6.0, 5.0, 4.8), 1, 2),
(9, 1, espressopp.Real3D(6.0, 5.2, 5.0), 1, 3),
(10, 1, espressopp.Real3D(6.0, 5.0, 5.2), 1, 4),
(11, 1, espressopp.Real3D(7.0, 5.0, 5.0), 0, 0),
(12, 1, espressopp.Real3D(7.0, 4.8, 5.0), 1, 1),
(13, 1, espressopp.Real3D(7.0, 5.0, 4.8), 1, 2),
(14, 1, espressopp.Real3D(7.0, 5.2, 5.0), 1, 3),
(15, 1, espressopp.Real3D(7.0, 5.0, 5.2), 1, 4),
(16, 0, espressopp.Real3D(9.0, 5.0, 5.0), 0, 0),
(17, 0, espressopp.Real3D(9.0, 4.8, 5.0), 1, 1),
(18, 0, espressopp.Real3D(9.0, 5.0, 4.8), 1, 2),
(19, 0, espressopp.Real3D(9.0, 5.2, 5.0), 1, 3),
(20, 0, espressopp.Real3D(9.0, 5.0, 5.2), 1, 4),
(21, 0, espressopp.Real3D(5.0, 5.0, 5.0), 0, 0),
(22, 0, espressopp.Real3D(5.0, 4.8, 5.0), 1, 1),
(23, 0, espressopp.Real3D(5.0, 5.0, 4.8), 1, 2),
(24, 0, espressopp.Real3D(5.0, 5.2, 5.0), 1, 3),
(25, 0, espressopp.Real3D(5.0, 5.0, 5.2), 1, 4),
(26, 1, espressopp.Real3D(5.0, 5.0, 5.0), 0, 0),
(27, 1, espressopp.Real3D(5.5, 4.5, 5.0), 1, 2),
(28, 1, espressopp.Real3D(5.5, 5.0, 4.5), 1, 3),
(29, 1, espressopp.Real3D(5.5, 5.5, 5.0), 1, 4),
(30, 1, espressopp.Real3D(5.5, 5.0, 5.5), 1, 1)
]
tuples = [(1,2,3,4,5),(6,7,8,9,10),(11,12,13,14,15),(16,17,18,19,20),(21,22,23,24,25),(26,27,28,29,30)]
self.system.storage.addParticles(particle_list, 'id', 'type', 'pos', 'adrat', 'pib')
ftpl = espressopp.FixedTupleListAdress(self.system.storage)
ftpl.addTuples(tuples)
self.system.storage.setFixedTuplesAdress(ftpl)
# 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)
# initialize lambda values
integrator = espressopp.integrator.PIAdressIntegrator(system=self.system, verletlist=vl, nTrotter=4)
espressopp.tools.AdressDecomp(self.system, integrator)
# calculate rdfs
rdf_pi = espressopp.analysis.RDFatomistic(system=self.system, type1=1, type2=1, span=2.5)
rdf_pi_array = rdf_pi.computePathIntegral(10)
# run checks
self.assertAlmostEqual(rdf_pi_array[1], 49.121896, places=5)
self.assertAlmostEqual(rdf_pi_array[2], 26.525824, places=5)
self.assertAlmostEqual(rdf_pi_array[3], 15.898631, places=5)
self.assertAlmostEqual(rdf_pi_array[4], 0.0, places=5)
if __name__ == '__main__':
unittest.main()