def test_force_value(self):
# set up TD force
vl = espressopp.VerletListAdress(self.system, cutoff=1.5, adrcut=1.5,
dEx=1.0, dHy=1.0, adrCenter=[5.0, 5.0, 5.0], sphereAdr=False)
thdforce = espressopp.integrator.TDforce(self.system,vl)
thdforce.addForce(itype=3,filename="table_tf.tab",type=1)
self.assertAlmostEqual(thdforce.getForce(1, 0.9), 1.52920, places=5)
def test_AdResS(self):
# set up AdResS domain decomposition
nodeGrid = espressopp.tools.decomp.nodeGrid(espressopp.MPI.COMM_WORLD.size)
cellGrid = espressopp.tools.decomp.cellGrid((10, 10, 10), nodeGrid, 1.5, 0.3)
self.system.storage = espressopp.storage.DomainDecompositionAdress(self.system, nodeGrid, cellGrid)
# add some particles (atomistic and coarse-grained particles now)
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, 0, 0, espressopp.Real3D(5.5, 5.0, 5.0), 1.0, 1),
(5, 0, 0, espressopp.Real3D(6.5, 5.0, 5.0), 1.0, 1),
(6, 0, 0, espressopp.Real3D(7.5, 5.0, 5.0), 1.0, 1),
]
tuples = [(1,4),(2,5),(3,6)]
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=1.0, dHy=1.0, adrCenter=[5.0, 5.0, 5.0], sphereAdr=False)
# integrator including AdResS
integrator = espressopp.integrator.VelocityVerlet(self.system)
integrator.dt = 0.01
adress = espressopp.integrator.Adress(self.system, vl, ftpl)
integrator.addExtension(adress)
# Langevin Thermostat
langevin = espressopp.integrator.LangevinThermostat(self.system)
langevin.gamma = 1.0
langevin.temperature = 1.0
langevin.adress = True
langevin.addExclusions([4])
integrator.addExtension(langevin)
# coordinates of particles before integration
before = [self.system.storage.getParticle(i).pos[j] for i in range(1,4) for j in range(3)]
# run ten steps
integrator.run(10)
# coordinates of particles after integration
after = [self.system.storage.getParticle(i).pos[j] for i in range(1,4) for j in range(3)]
# run checks (same as test before)
self.assertEqual(before[0], after[0])
self.assertEqual(before[1], after[1])
self.assertEqual(before[2], after[2])
self.assertNotEqual(before[3], after[3])
self.assertNotEqual(before[4], after[4])
self.assertNotEqual(before[5], after[5])
self.assertNotEqual(before[6], after[6])
self.assertNotEqual(before[7], after[7])
self.assertNotEqual(before[8], after[8])
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
# 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')
self.ftpl = espressopp.FixedTupleListAdress(self.system.storage)
self.ftpl.addTuples(tuples)
self.system.storage.setFixedTuplesAdress(self.ftpl)
self.system.storage.decompose()
# set up a verlet list
self.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)
# set up integrator
self.integrator = espressopp.integrator.VelocityVerletRESPA(
self.system)
self.integrator.dt = 0.01
self.integrator.multistep = 4
adress = espressopp.integrator.Adress(self.system,
self.vl,
self.ftpl,
multistep=4)
self.integrator.addExtension(adress)
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)
# 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)
# set up FEC
fec = espressopp.integrator.FreeEnergyCompensation(self.system, center=[5.0, 5.0, 5.0], sphereAdr=True)
fec.addForce(itype=3,filename="table_fec.tab",type=1)
integrator.addExtension(fec)
# y coordinates of particles before integration
before = [self.system.storage.getParticle(i).pos[1] for i in range(1,6)]
# run ten steps
integrator.run(10)
energy = fec.computeCompEnergy()
# y coordinates of particles after integration
after = [self.system.storage.getParticle(i).pos[1] for i in range(1,6)]
# run checks (as for test with slab-geometry, but check y-coordinates this time. Given the now spherical setup, particles should move as before but along the y-axis).
self.assertEqual(before[0], after[0])
self.assertEqual(before[1], after[1])
self.assertAlmostEqual(after[2], 7.598165, places=5)
self.assertEqual(before[3], after[3])
self.assertEqual(before[4], after[4])
self.assertAlmostEqual(energy, 6.790157, places=5)
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)
# 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)
# set up FEC
fec = espressopp.integrator.FreeEnergyCompensation(self.system, center=[5.0, 5.0, 5.0])
fec.addForce(itype=3,filename="table_fec.tab",type=1)
integrator.addExtension(fec)
# x coordinates of particles before integration
before = [self.system.storage.getParticle(i).pos[0] for i in range(1,6)]
# run ten steps and compute energy
integrator.run(10)
energy = fec.computeCompEnergy()
# x coordinates of particles after integration
after = [self.system.storage.getParticle(i).pos[0] for i in range(1,6)]
# run checks (only one particle is in hybrid region and should feel the FEC. Also check that its FEC energy is correct)
self.assertEqual(before[0], after[0])
self.assertEqual(before[1], after[1])
self.assertAlmostEqual(after[2], 7.598165, places=5)
self.assertEqual(before[3], after[3])
self.assertEqual(before[4], after[4])
self.assertAlmostEqual(energy, 6.790157, places=5)
def test_single_moving_sphere(self):
# add some particles
particle_list = [
(1, 1, 0, espressopp.Real3D(5.0, 5.0, 5.0), espressopp.Real3D(0.0, 1.0, 0.0), 1.0, 0),
(2, 1, 0, espressopp.Real3D(5.0, 6.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 0),
(3, 1, 0, espressopp.Real3D(5.0, 7.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 0),
(4, 1, 0, espressopp.Real3D(5.0, 8.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 0),
(5, 1, 0, espressopp.Real3D(5.0, 9.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 0),
(6, 0, 0, espressopp.Real3D(5.0, 5.0, 5.0), espressopp.Real3D(0.0, 1.0, 0.0), 1.0, 1),
(7, 0, 0, espressopp.Real3D(5.0, 6.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 1),
(8, 0, 0, espressopp.Real3D(5.0, 7.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 1),
(9, 0, 0, espressopp.Real3D(5.0, 8.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 1),
(10, 0, 0, espressopp.Real3D(5.0, 9.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 1),
]
tuples = [(1,6),(2,7),(3,8),(4,9),(5,10)]
self.system.storage.addParticles(particle_list, 'id', 'type', 'q', 'pos', 'v', '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=1.0, dHy=1.0, pids=[1], sphereAdr=True)
# 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)
# set up TD force
thdforce = espressopp.integrator.TDforce(self.system,vl)
thdforce.addForce(itype=3,filename="table_tf.tab",type=1)
integrator.addExtension(thdforce)
# y coordinates of particles before integration
before = [self.system.storage.getParticle(i).pos[1] for i in range(1,6)]
# run ten steps
integrator.run(10)
# y coordinates of particles after integration
after = [self.system.storage.getParticle(i).pos[1] for i in range(1,6)]
# run checks (first particle moves and defines the AdResS region, second particle is in the corresponding hybrid region, others are in coarse-grained region)
self.assertAlmostEqual(after[0], 5.100000, places=5)
self.assertAlmostEqual(after[1], 6.618377, places=5)
self.assertEqual(before[2], after[2])
self.assertEqual(before[3], after[3])
self.assertEqual(before[4], after[4])
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=1.0, dHy=1.0, adrCenter=[5.0, 5.0, 5.0], sphereAdr=False)
# 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)
# set up TD force
thdforce = espressopp.integrator.TDforce(self.system,vl)
thdforce.addForce(itype=3,filename="table_tf.tab",type=1)
integrator.addExtension(thdforce)
# x coordinates of particles before integration
before = [self.system.storage.getParticle(i).pos[0] for i in range(1,6)]
# run ten steps
integrator.run(10)
# x coordinates of particles after integration
after = [self.system.storage.getParticle(i).pos[0] for i in range(1,6)]
# run checks (only one particle is in hybrid region, should feel the thermodynamic force, and should hence move along the x direction)
self.assertEqual(before[0], after[0])
self.assertAlmostEqual(after[1], 6.596913, places=5)
self.assertEqual(before[2], after[2])
self.assertEqual(before[3], after[3])
self.assertEqual(before[4], after[4])
def test_fixed_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=1.0, dHy=1.0, adrCenter=[5.0, 5.0, 5.0], sphereAdr=True)
# 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)
# set up TD force
thdforce = espressopp.integrator.TDforce(self.system,vl)
thdforce.addForce(itype=3,filename="table_tf.tab",type=1)
integrator.addExtension(thdforce)
# y coordinates of particles before integration
before = [self.system.storage.getParticle(i).pos[1] for i in range(1,6)]
# run ten steps
integrator.run(10)
# y coordinates of particles after integration
after = [self.system.storage.getParticle(i).pos[1] for i in range(1,6)]
# run checks (as test before, just that particles should move in y-direction given the new setup and the spherical adaptive resolution geometry)
self.assertEqual(before[0], after[0])
self.assertAlmostEqual(after[1], 6.596913, places=5)
self.assertEqual(before[2], after[2])
self.assertEqual(before[3], after[3])
self.assertEqual(before[4], after[4])
def test_many_moving_spheres_fewupdates(self):
# add some particles
particle_list = [
(1, 1, 0, espressopp.Real3D(4.0, 5.0, 5.0), espressopp.Real3D(-1.0, 1.0, 0.0), 1.0, 0),
(2, 1, 0, espressopp.Real3D(6.0, 5.0, 5.0), espressopp.Real3D(1.0, 1.0, 0.0), 1.0, 0),
(3, 1, 0, espressopp.Real3D(5.0, 6.2, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 0),
(4, 1, 0, espressopp.Real3D(3.0, 8.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 0),
(5, 1, 0, espressopp.Real3D(7.0, 9.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 0),
(6, 0, 0, espressopp.Real3D(4.0, 5.0, 5.0), espressopp.Real3D(-1.0, 1.0, 0.0), 1.0, 1),
(7, 0, 0, espressopp.Real3D(6.0, 5.0, 5.0), espressopp.Real3D(1.0, 1.0, 0.0), 1.0, 1),
(8, 0, 0, espressopp.Real3D(5.0, 6.2, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 1),
(9, 0, 0, espressopp.Real3D(3.0, 8.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 1),
(10, 0, 0, espressopp.Real3D(7.0, 9.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 1),
]
tuples = [(1,6),(2,7),(3,8),(4,9),(5,10)]
self.system.storage.addParticles(particle_list, 'id', 'type', 'q', 'pos', 'v', '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=1.0, dHy=1.0, pids=[1,2], sphereAdr=True)
# initialize lambda values
integrator = espressopp.integrator.VelocityVerlet(self.system)
integrator.dt = 0.01
adress = espressopp.integrator.Adress(self.system,vl,ftpl,regionupdates = 5)
integrator.addExtension(adress)
espressopp.tools.AdressDecomp(self.system, integrator)
# set up TD force
thdforce = espressopp.integrator.TDforce(self.system, vl, startdist = 0.9, enddist = 2.1, edgeweightmultiplier = 20)
thdforce.addForce(itype=3,filename="table_tf.tab",type=1)
integrator.addExtension(thdforce)
# y coordinates of particles before integration
before = [self.system.storage.getParticle(i).pos[1] for i in range(1,6)]
# run ten steps
integrator.run(20)
# y coordinates of particles after integration (as test before, but more integration steps and the AdResS region is updated only every 5 steps)
after = [self.system.storage.getParticle(i).pos[1] for i in range(1,6)]
# run checks
self.assertAlmostEqual(after[0], 5.200000, places=5)
self.assertAlmostEqual(after[1], 5.200000, places=5)
self.assertAlmostEqual(after[2], 6.393199, places=5)
self.assertEqual(before[3], after[3])
self.assertEqual(before[4], after[4])
def setUp(self):
self.system = espressopp.System()
box = (10, 10, 10)
self.system.rng = espressopp.esutil.RNG()
self.system.bc = espressopp.bc.OrthorhombicBC(self.system.rng, box)
nodeGrid = espressopp.tools.decomp.nodeGrid(MPI.COMM_WORLD.size)
cellGrid = espressopp.tools.decomp.cellGrid(box,
nodeGrid,
rc=1.5,
skin=0.5)
self.system.storage = espressopp.storage.DomainDecompositionAdress(
self.system, nodeGrid, cellGrid)
particle_list = [(1, 1, espressopp.Real3D(3.0, 5.0, 5.0), 0, 0),
(2, 1, espressopp.Real3D(3.0, 4.9, 5.0), 1, 1),
(3, 1, espressopp.Real3D(3.0, 5.0, 4.9), 1, 2),
(4, 1, espressopp.Real3D(3.0, 5.1, 5.0), 1, 3),
(5, 1, espressopp.Real3D(3.0, 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)]
tuples = [(1, 2, 3, 4, 5), (6, 7, 8, 9, 10), (11, 12, 13, 14, 15),
(16, 17, 18, 19, 20)]
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)
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)
integrator = espressopp.integrator.PIAdressIntegrator(
system=self.system, verletlist=vl, nTrotter=4)
espressopp.tools.AdressDecomp(self.system, integrator)
def test_densitycalculation(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)
# 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 density profile
densityprofile = espressopp.analysis.AdressDensity(self.system, vl)
densityprofile.addExclusions([8])
density_array = densityprofile.compute(5)
# run checks
self.assertAlmostEqual(density_array[0], 31.250000, places=5)
self.assertAlmostEqual(density_array[1], 4.464286, places=5)
self.assertAlmostEqual(density_array[2], 0.0, places=5)
self.assertAlmostEqual(density_array[3], 0.844595, places=5)
self.assertAlmostEqual(density_array[4], 0.512295, 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 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)
cellGrid = espressopp.tools.decomp.cellGrid(box, nodeGrid, 1.5, 0.3)
system.storage = espressopp.storage.DomainDecompositionAdress(system, nodeGrid, cellGrid)
self.system = system
# 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)
def test_PIAdResS(self):
print 'param =', self.param
constkinmass = self.param['constkinmass']
PILE = self.param['PILE']
realkinmass = self.param['realkinmass']
centroidthermostat = self.param['centroidthermostat']
KTI = self.param['KTI']
speedupInterAtom = self.param['speedupInterAtom']
speedupFreezeRings = self.param['speedupFreezeRings']
spherical_adress = self.param['spherical_adress']
nb_forcefield_setup = self.param['nb_forcefield_setup']
energy_before = self.param['energy_before']
energy_after = self.param['energy_after']
steps = 10
timestep_short = 0.001 / 16.0
multiplier_short_to_medium = 4
multiplier_medium_to_long = 4
interaction_cutoff = 0.84
potential_cutoff = 0.78
skin = 0.1
gamma = 0.0
temp = 2.50266751
if KTI:
ex_size = 100.0
else:
ex_size = 1.0
hy_size = 1.5
nTrotter = 4
clmassmultiplier = 100.0
PILElambda = 0.0
CMDparameter = 1.0
tabFEC_H = "FEC_H.dat"
tabFEC_O = "FEC_O.dat"
tabTHDF_H = "ThdForce_H.dat"
tabTHDF_O = "ThdForce_O.dat"
tabAngle = "tableESP_angle.dat"
tabBondHH = "tableESP_bondHH.dat"
tabBondOH = "tableESP_bondOH.dat"
tabHW_HW = "tableESP_HW_HW.dat"
tabHW_OW = "tableESP_HW_OW.dat"
tabOW_OW = "tableESP_OW_OW.dat"
pid, types, x, y, z, vx, vy, vz, Lx, Ly, Lz = espressopp.tools.readxyz(
"input_test.xyz")
masses = []
for item in types:
if item == 1:
masses.append(15.9994)
else:
masses.append(1.008)
num_Trotter_beads = len(x)
num_atoms = len(x) / nTrotter
size = (Lx, Ly, Lz)
system = espressopp.System()
system.bc = espressopp.bc.OrthorhombicBC(system.rng, size)
system.skin = skin
comm = MPI.COMM_WORLD
nodeGrid = decomp.nodeGrid(comm.size)
cellGrid = decomp.cellGrid(size, nodeGrid, interaction_cutoff, skin)
system.rng = espressopp.esutil.RNG()
system.storage = espressopp.storage.DomainDecompositionAdress(
system, nodeGrid, cellGrid)
props = ['id', 'pos', 'v', 'f', 'pib', 'type', 'mass', 'adrat']
allParticlesAT = []
allParticles = []
tuples = []
for pid_trotter in range(num_Trotter_beads):
allParticlesAT.append([
pid_trotter + 1,
Real3D(x[pid_trotter], y[pid_trotter], z[pid_trotter]),
Real3D(vx[pid_trotter], vy[pid_trotter], vz[pid_trotter]),
Real3D(0, 0, 0), pid_trotter % nTrotter + 1,
types[pid_trotter], masses[pid_trotter], 1
])
for pid_atom in range(num_atoms):
tmptuple = [pid_atom + num_Trotter_beads + 1]
for pid_trotter in range(nTrotter):
pid = pid_atom * nTrotter + pid_trotter
tmptuple.append((allParticlesAT[pid])[0])
firstParticleId = tmptuple[1]
cmp = allParticlesAT[firstParticleId - 1][1]
cmv = allParticlesAT[firstParticleId - 1][2]
allParticles.append([
pid_atom + num_Trotter_beads + 1,
Real3D(cmp[0], cmp[1], cmp[2]),
Real3D(cmv[0], cmv[1], cmv[2]),
Real3D(0, 0, 0), 0, types[pid_atom * nTrotter],
masses[pid_atom * nTrotter], 0
])
for pid_trotter in range(nTrotter):
pid = pid_atom * nTrotter + pid_trotter
allParticles.append([(allParticlesAT[pid])[0],
(allParticlesAT[pid])[1],
(allParticlesAT[pid])[2],
(allParticlesAT[pid])[3],
(allParticlesAT[pid])[4],
(allParticlesAT[pid])[5],
(allParticlesAT[pid])[6],
(allParticlesAT[pid])[7]])
tuples.append(tmptuple)
system.storage.addParticles(allParticles, *props)
ftpl = espressopp.FixedTupleListAdress(system.storage)
ftpl.addTuples(tuples)
system.storage.setFixedTuplesAdress(ftpl)
system.storage.decompose()
bondsOH = []
bondsHH = []
for part in range(num_atoms / 3):
bondsOH.append((num_Trotter_beads + 1 + 3 * part,
num_Trotter_beads + 1 + 3 * part + 1))
bondsOH.append((num_Trotter_beads + 1 + 3 * part,
num_Trotter_beads + 1 + 3 * part + 2))
bondsHH.append((num_Trotter_beads + 1 + 3 * part + 1,
num_Trotter_beads + 1 + 3 * part + 2))
fplOH = espressopp.FixedPairList(system.storage)
fplHH = espressopp.FixedPairList(system.storage)
fplOH.addBonds(bondsOH)
fplHH.addBonds(bondsHH)
angles = []
for part in range(num_atoms / 3):
angles.append((num_Trotter_beads + 1 + 3 * part + 1,
num_Trotter_beads + 1 + 3 * part,
num_Trotter_beads + 1 + 3 * part + 2))
ftl = espressopp.FixedTripleList(system.storage)
ftl.addTriples(angles)
vl = espressopp.VerletListAdress(system,
cutoff=interaction_cutoff,
adrcut=interaction_cutoff,
dEx=ex_size,
dHy=hy_size,
adrCenter=[Lx / 2, Ly / 2, Lz / 2],
exclusionlist=bondsOH + bondsHH,
sphereAdr=spherical_adress)
if nb_forcefield_setup == 1:
interNB = espressopp.interaction.VerletListPIadressTabulatedLJ(
vl, ftpl, nTrotter, speedupInterAtom)
elif nb_forcefield_setup == 2:
interNB = espressopp.interaction.VerletListPIadressNoDriftTabulated(
vl, ftpl, nTrotter, speedupInterAtom)
elif nb_forcefield_setup == 3:
interNB = espressopp.interaction.VerletListPIadressTabulated(
vl, ftpl, nTrotter, speedupInterAtom)
else:
raise ValueError(
"Wrong nb_forcefield_setup integer (only 1,2,3 accepted.")
potOOqm = espressopp.interaction.Tabulated(itype=3,
filename=tabOW_OW,
cutoff=potential_cutoff)
potHOqm = espressopp.interaction.Tabulated(itype=3,
filename=tabHW_OW,
cutoff=potential_cutoff)
potHHqm = espressopp.interaction.Tabulated(itype=3,
filename=tabHW_HW,
cutoff=potential_cutoff)
if nb_forcefield_setup == 1:
interNB.setPotentialQM(type1=1, type2=1, potential=potOOqm)
interNB.setPotentialQM(type1=1, type2=0, potential=potHOqm)
interNB.setPotentialQM(type1=0, type2=0, potential=potHHqm)
potOOcl = espressopp.interaction.LennardJones(
epsilon=temp,
sigma=0.25,
shift='auto',
cutoff=1.122462048309373 * 0.25)
interNB.setPotentialCL(type1=1, type2=1, potential=potOOcl)
elif nb_forcefield_setup == 2:
interNB.setPotential(type1=1, type2=1, potential=potOOqm)
interNB.setPotential(type1=1, type2=0, potential=potHOqm)
interNB.setPotential(type1=0, type2=0, potential=potHHqm)
elif nb_forcefield_setup == 3:
interNB.setPotentialQM(type1=1, type2=1, potential=potOOqm)
interNB.setPotentialQM(type1=1, type2=0, potential=potHOqm)
interNB.setPotentialQM(type1=0, type2=0, potential=potHHqm)
interNB.setPotentialCL(type1=1, type2=1, potential=potOOqm)
interNB.setPotentialCL(type1=1, type2=0, potential=potHOqm)
interNB.setPotentialCL(type1=0, type2=0, potential=potHHqm)
system.addInteraction(interNB)
potBondHH = espressopp.interaction.Tabulated(itype=3,
filename=tabBondHH)
potBondOH = espressopp.interaction.Tabulated(itype=3,
filename=tabBondOH)
interBondedHH = espressopp.interaction.FixedPairListPIadressTabulated(
system, fplHH, ftpl, potBondHH, nTrotter, speedupInterAtom)
interBondedOH = espressopp.interaction.FixedPairListPIadressTabulated(
system, fplOH, ftpl, potBondOH, nTrotter, speedupInterAtom)
system.addInteraction(interBondedHH)
system.addInteraction(interBondedOH)
potAngle = espressopp.interaction.TabulatedAngular(itype=3,
filename=tabAngle)
interAngle = espressopp.interaction.FixedTripleListPIadressTabulatedAngular(
system, ftl, ftpl, potAngle, nTrotter, speedupInterAtom)
system.addInteraction(interAngle)
integrator = espressopp.integrator.PIAdressIntegrator(
system=system,
verletlist=vl,
timestep=timestep_short,
sSteps=multiplier_short_to_medium,
mSteps=multiplier_medium_to_long,
nTrotter=nTrotter,
realKinMass=realkinmass,
constKinMass=constkinmass,
temperature=temp,
gamma=gamma,
centroidThermostat=centroidthermostat,
CMDparameter=CMDparameter,
PILE=PILE,
PILElambda=PILElambda,
CLmassmultiplier=clmassmultiplier,
speedup=speedupFreezeRings,
KTI=KTI)
if not KTI:
fec = espressopp.integrator.FreeEnergyCompensation(
system, center=[Lx / 2, Ly / 2, Lz / 2], ntrotter=nTrotter)
fec.addForce(itype=3, filename=tabFEC_O, type=1)
fec.addForce(itype=3, filename=tabFEC_H, type=0)
integrator.addExtension(fec)
thdf = espressopp.integrator.TDforce(system, vl)
thdf.addForce(itype=3, filename=tabTHDF_O, type=1)
thdf.addForce(itype=3, filename=tabTHDF_H, type=0)
integrator.addExtension(thdf)
if KTI:
for i in range(1, num_Trotter_beads + num_atoms + 1):
system.storage.modifyParticle(i, 'lambda_adrd', 0.0)
system.storage.modifyParticle(i, 'lambda_adr', 0.0)
system.storage.modifyParticle(
i, 'varmass',
clmassmultiplier * system.storage.getParticle(i).mass)
system.storage.decompose()
espressopp.tools.AdressDecomp(system, integrator)
Eb = interBondedOH.computeEnergy() + interBondedHH.computeEnergy()
EAng = interAngle.computeEnergy()
ELj = interNB.computeEnergy()
Ek = integrator.computeKineticEnergy()
EPI = integrator.computeRingEnergy()
if KTI == False:
Ecorr = fec.computeCompEnergy() + thdf.computeTDEnergy()
else:
Ecorr = 0.0
energy_before_thistest = Ek + Eb + EAng + ELj + EPI + Ecorr
integrator.run(steps)
Eb = interBondedOH.computeEnergy() + interBondedHH.computeEnergy()
EAng = interAngle.computeEnergy()
ELj = interNB.computeEnergy()
Ek = integrator.computeKineticEnergy()
EPI = integrator.computeRingEnergy()
if KTI == False:
Ecorr = fec.computeCompEnergy() + thdf.computeTDEnergy()
else:
Ecorr = 0.0
energy_after_thistest = Ek + Eb + EAng + ELj + EPI + Ecorr
self.assertAlmostEqual(energy_before_thistest, energy_before, places=5)
self.assertAlmostEqual(energy_after_thistest, energy_after, 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)
bondsOH.append((num_Trotter_beads + 1 + 3 * part,
num_Trotter_beads + 1 + 3 * part + 2))
bondsHH.append((num_Trotter_beads + 1 + 3 * part + 1,
num_Trotter_beads + 1 + 3 * part + 2))
# add bonds between atoms
fplOH = espressopp.FixedPairList(system.storage)
fplHH = espressopp.FixedPairList(system.storage)
fplOH.addBonds(bondsOH)
fplHH.addBonds(bondsHH)
# create the adaptive resolution verlet list
vl = espressopp.VerletListAdress(system,
cutoff=interaction_cutoff,
adrcut=interaction_cutoff,
dEx=ex_size,
dHy=hy_size,
adrCenter=[Lx / 2, Ly / 2, Lz / 2],
exclusionlist=bondsOH + bondsHH)
# create angle list between atoms
angles = []
for part in range(num_atoms / 3):
angles.append((num_Trotter_beads + 1 + 3 * part + 1,
num_Trotter_beads + 1 + 3 * part,
num_Trotter_beads + 1 + 3 * part + 2))
# add angles between atoms
ftl = espressopp.FixedTripleList(system.storage)
ftl.addTriples(angles)
integrator.addExtension(thermostat)
else:
print "#No thermostat"
########################################################################
# 6. define atomistic and adres interactions
########################################################################
## adres interactions ##
print '# moving atomistic region composed of multiple spheres centered on each protein cg particle'
particlePIDsADR = [mapAtToCgIndex[pid] for pid in particlePIDsADR]
verletlist = espressopp.VerletListAdress(system,
cutoff=nbCutoff,
adrcut=nbCutoff,
dEx=ex_size,
dHy=hy_size,
pids=particlePIDsADR,
sphereAdr=True)
# set up LJ interaction according to the parameters read from the .top file
lj_adres_interaction = gromacs.setLennardJonesInteractions(system,
defaults,
atomtypeparameters,
verletlist,
intCutoff,
adress=True,
ftpl=ftpl)
# set up coulomb interactions according to the parameters read from the .top file
print '#Note: Reaction Field method is used for Coulomb interactions'
system.storage.setFixedTuplesAdress(ftpl)
# add bonds between AT particles
fpl = espressopp.FixedPairListAdress(system.storage, ftpl)
fpl.addBonds(bonds)
# decompose after adding tuples and bonds
print "Added tuples and bonds, decomposing now ..."
system.storage.decompose()
print "done decomposing"
# AdResS Verlet list
vl = espressopp.VerletListAdress(system,
cutoff=rc + skin,
adrcut=rc + skin,
dEx=ex_size,
dHy=hy_size,
adrCenter=[18.42225, 18.42225, 18.42225])
# non-bonded potentials
# LJ Capped WCA between AT and tabulated Morse between CG particles
interNB = espressopp.interaction.VerletListAdressLennardJonesCapped(vl, ftpl)
potWCA = espressopp.interaction.LennardJonesCapped(epsilon=1.0,
sigma=1.0,
shift=True,
caprad=0.27,
cutoff=rca)
potMorse = espressopp.interaction.Tabulated(itype=2,
filename=tabMorse,
cutoff=rc) # CG
interNB.setPotentialAT(type1=1, type2=1, potential=potWCA) # AT
print "# thermostat temperature = ", temperature*temperatureConvFactor
# tell the integrator to use this thermostat
integrator.addExtension(thermostat)
else:
print "#No thermostat"
########################################################################
# 6. define atomistic and adres interactions
########################################################################
## adres interactions ##
cm = adresRegionCentreAtIndex
print '# spherical moving atomistic region for adres centred on atom ',cm,' i.e. cg particle ',mapAtToCgIndex[cm]
verletlist = espressopp.VerletListAdress(system, cutoff=nbCutoff, adrcut=nbCutoff,
dEx=ex_size, dHy=hy_size,
pids=[mapAtToCgIndex[cm]], sphereAdr=True)
# set up LJ interaction according to the parameters read from the .top file
lj_adres_interaction = gromacs.setLennardJonesInteractionsTI(system, defaults, atomtypeparameters, verletlist, nbCutoff, epsilonB=0.0, sigmaSC=sigmaSC, alphaSC=alphaSC, powerSC=powerSC, lambdaTI=lambdaTIVdwl, pidlist=stateBIndices, annihilate=False, adress=True, ftpl=ftpl)
# set up coulomb interactions according to the parameters read from the .top file
# !! Warning: this only works for reaction-field now!
qq_adres_interaction = gromacs.setCoulombInteractionsTI(system, verletlist, nbCutoff, atTypes, epsilon1=1, epsilon2=80, kappa=0, lambdaTI=lambdaTICoul, pidlist=stateBIndices, annihilate=False, adress=True, ftpl=ftpl)
# bonded (fixed list) interactions in solute (between atomistic particles, solute is one coarse-grained particle)
# only for solute, no bonded interactions for water
# set up LJ 1-4 interactions
onefourlist = espressopp.FixedPairListAdress(system.storage,ftpl)
onefourlist.addBonds(atOnefourpairslist)
def test_potential_decoupling(self):
#add particles
particle_list = [
(4, 1, 0, espressopp.Real3D(2.0, 2.0, 2.0), 1.0, 0),
(5, 1, 0, espressopp.Real3D(2.3, 2.0, 2.0), 1.0, 0),
(6, 1, 0, espressopp.Real3D(2.6, 2.0, 2.0), 1.0, 0),
(1, 0, 1, espressopp.Real3D(2.0, 2.0, 2.0), 1.0, 1),
(2, 0, -1, espressopp.Real3D(2.3, 2.0, 2.0), 1.0, 1),
(3, 0, -1, espressopp.Real3D(2.6, 2.0, 2.0), 1.0, 1),
]
tuples = [(4, 1), (5, 2), (6, 3)]
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()
vl = espressopp.VerletListAdress(self.system,
cutoff=1.5,
adrcut=1.5,
dEx=2.0,
dHy=1.0,
pids=[4],
sphereAdr=True)
#add LJ interaction
interactionLJ = espressopp.interaction.VerletListAdressLennardJonesSoftcoreTI(
vl, ftpl)
potLJ = espressopp.interaction.LennardJonesSoftcoreTI(epsilonA=1.0,
sigmaA=0.2,
epsilonB=0.0,
sigmaB=0.2,
alpha=0.5,
power=1.0,
cutoff=1.5,
lambdaTI=0.3,
annihilate=False)
potLJ.addPids([1, 2])
interactionLJ.setPotentialAT(type1=0, type2=0, potential=potLJ)
self.system.addInteraction(interactionLJ)
#add electrostatic interaction
interactionQQ = espressopp.interaction.VerletListAdressReactionFieldGeneralizedTI(
vl, ftpl)
potQQ = espressopp.interaction.ReactionFieldGeneralizedTI(
prefactor=1.0,
kappa=0.0,
epsilon1=1,
epsilon2=80,
cutoff=1.5,
lambdaTI=0.3,
annihilate=False)
potQQ.addPids([1, 2])
interactionQQ.setPotentialAT(type1=0, type2=0, potential=potQQ)
self.system.addInteraction(interactionQQ)
#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)
self.assertAlmostEqual(interactionQQ.computeEnergyDeriv(),
-1.627412,
places=5)
self.assertAlmostEqual(interactionLJ.computeEnergyDeriv(),
0.330739,
places=5)
self.assertAlmostEqual(interactionQQ.computeEnergy(),
-1.213441,
places=5)
self.assertAlmostEqual(interactionLJ.computeEnergy(),
-0.545769,
places=5)
def test_gromacs_adress(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)]
#tuples = [(1,2),(3,4),(5,6),(7,8),(9,10)]
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)
file_gro_adress = "test_standard_dumpGROAdress_type_not_hardcoded.gro"
dump_gro_adress = espressopp.io.DumpGROAdress(self.system,
ftpl,
integrator,
filename=file_gro_adress)
dump_gro_adress.dump()
self.assertTrue(
filecmp.cmp(file_gro_adress, expected_files[0], shallow=False),
"!!! Error! Files are not equal!! They should be equal!")
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.VerletListAdressATLJReacFieldGenHarmonic(
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], 5.004574, places=5)
self.assertEqual(before[1], after[1])
self.assertEqual(before[2], after[2])
self.assertAlmostEqual(after[3], 6.009012, places=5)
self.assertEqual(before[4], after[4])
self.assertEqual(before[5], after[5])
self.assertAlmostEqual(after[6], 7.129601, places=5)
self.assertEqual(before[7], after[7])
self.assertEqual(before[8], after[8])
self.assertAlmostEqual(after[9], 8.787093, places=5)
self.assertEqual(before[10], after[10])
self.assertEqual(before[11], after[11])
self.assertAlmostEqual(after[12], 0.569719, places=5)
self.assertEqual(before[13], after[13])
self.assertEqual(before[14], after[14])
self.assertAlmostEqual(energy_before, 223.764297, places=5)
self.assertAlmostEqual(energy_after, 23.995610, places=5)
def test_slab(self):
# add some particles
particle_list = [
(1, 1, espressopp.Real3D(5.5, 5.0, 5.0), 1.0, 0),
(2, 1, espressopp.Real3D(6.5, 5.0, 5.0), 1.0, 0),
(3, 1, espressopp.Real3D(7.5, 5.0, 5.0), 1.0, 0),
(4, 1, espressopp.Real3D(8.5, 5.0, 5.0), 1.0, 0),
(5, 1, espressopp.Real3D(9.5, 5.0, 5.0), 1.0, 0),
(6, 0, espressopp.Real3D(5.5, 5.0, 5.0), 1.0, 1),
(7, 0, espressopp.Real3D(6.5, 5.0, 5.0), 1.0, 1),
(8, 0, espressopp.Real3D(7.5, 5.0, 5.0), 1.0, 1),
(9, 0, espressopp.Real3D(8.5, 5.0, 5.0), 1.0, 1),
(10, 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', '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.VerletListAdressLennardJones2(
vl, ftpl)
potWCA1 = espressopp.interaction.LennardJones(epsilon=1.0,
sigma=1.0,
shift='auto',
cutoff=1.4)
potWCA2 = espressopp.interaction.LennardJones(epsilon=0.5,
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
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 (Particles should move along the x-axis only given their initial configuration. Additionally, check energies)
self.assertAlmostEqual(after[0], 5.413171, places=5)
self.assertEqual(before[1], after[1])
self.assertEqual(before[2], after[2])
self.assertAlmostEqual(after[3], 6.500459, places=5)
self.assertEqual(before[4], after[4])
self.assertEqual(before[5], after[5])
self.assertAlmostEqual(after[6], 7.522099, places=5)
self.assertEqual(before[7], after[7])
self.assertEqual(before[8], after[8])
self.assertAlmostEqual(after[9], 8.512569, places=5)
self.assertEqual(before[10], after[10])
self.assertEqual(before[11], after[11])
self.assertAlmostEqual(after[12], 9.551701, places=5)
self.assertEqual(before[13], after[13])
self.assertEqual(before[14], after[14])
self.assertAlmostEqual(energy_before, 1.266889, places=5)
self.assertAlmostEqual(energy_after, -0.209015, 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)
def test_rattle(self):
#add particles
# 4-3-5
# |
# |
# 2-1
particle_list = [(6, 1, espressopp.Real3D(3.2, 3.3, 3.0),
espressopp.Real3D(0, 0, 0), 9.0, 0),
(1, 0, espressopp.Real3D(3.2, 3.1, 3.0),
espressopp.Real3D(0.27, -0.07, 0.10), 3.0, 1),
(2, 0, espressopp.Real3D(3.1, 3.1, 3.0),
espressopp.Real3D(0.23, 0.22, 0.00), 1.0, 1),
(3, 0, espressopp.Real3D(3.2, 3.3, 3.0),
espressopp.Real3D(0.24, -0.37, -0.10), 3.0, 1),
(4, 0, espressopp.Real3D(3.1, 3.3, 3.0),
espressopp.Real3D(0.14, 0.20, -0.05), 1.0, 1),
(5, 0, espressopp.Real3D(3.3, 3.3, 3.0),
espressopp.Real3D(0.04, 0.17, -0.20), 1.0, 1)]
tuples = [(6, 1, 2, 3, 4, 5)]
constrainedBondsList = [[1, 2, 0.1, 3.0, 1.0], [3, 4, 0.1, 3.0, 1.0],
[3, 5, 0.1, 3.0,
1.0]] #pid1,pid2,constraintDist,mass1,mass2
constraintDist2 = []
for bond in constrainedBondsList:
constraintDist2.append(bond[2] * bond[2])
self.system.storage.addParticles(particle_list, 'id', 'type', 'pos',
'v', 'mass', 'adrat')
ftpl = espressopp.FixedTupleListAdress(self.system.storage)
ftpl.addTuples(tuples)
self.system.storage.setFixedTuplesAdress(ftpl)
self.system.storage.decompose()
vl = espressopp.VerletListAdress(self.system,
cutoff=1.5,
adrcut=1.5,
dEx=2.0,
dHy=1.0,
pids=[6],
sphereAdr=True)
#one unconstrained bond
fpl = espressopp.FixedPairListAdress(self.system.storage, ftpl)
fpl.addBonds([(1, 3)])
pot = espressopp.interaction.Harmonic(K=5.0, r0=0.2)
interB = espressopp.interaction.FixedPairListHarmonic(
self.system, fpl, pot)
self.system.addInteraction(interB)
#some angles
ftl = espressopp.FixedTripleListAdress(self.system.storage, ftpl)
ftl.addTriples([(2, 1, 3), (1, 3, 4), (1, 3, 5)])
pot = espressopp.interaction.AngularHarmonic(K=5.0,
theta0=math.pi / 2.0)
interA = espressopp.interaction.FixedTripleListAngularHarmonic(
self.system, ftl, pot)
self.system.addInteraction(interA)
#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)
rattle = espressopp.integrator.Rattle(self.system,
maxit=1000,
tol=1e-6,
rptol=1e-6)
rattle.addConstrainedBonds(constrainedBondsList)
integrator.addExtension(rattle)
integrator.run(5)
#check if bond lengths are the same as constraint lengths
for i, bond in enumerate(constrainedBondsList):
pid1 = bond[0]
pid2 = bond[1]
dist2 = sqrlen(
self.system.bc.getMinimumImageVector(
self.system.storage.getParticle(pid1).pos,
self.system.storage.getParticle(pid2).pos))
self.assertAlmostEqual(constraintDist2[i], dist2, places=6)
#check velocities after 5 steps of deterministic simulation
vsum = 0.0
for pid in xrange(1, 6):
part = self.system.storage.getParticle(pid)
vsum += sqrlen(part.v)
self.assertAlmostEqual(vsum, 0.3842668659, places=6)
ftpl.addTuples(tuples)
system.storage.setFixedTuplesAdress(ftpl)
# add bonds between AT particles
fpl = espressopp.FixedPairListAdress(system.storage, ftpl)
bonds = Tetracryst.makebonds(len(x))
fpl.addBonds(bonds)
# decompose after adding tuples and bonds
print "Added tuples and bonds, decomposing now ..."
system.storage.decompose()
print "done decomposing"
# AdResS Verlet list
vl = espressopp.VerletListAdress(system, cutoff=rc, adrcut=rc,
dEx=ex_size, dHy=hy_size,
adrCenter=[Lx/2, Ly/2, Lz/2])
# non-bonded potentials
# LJ capped WCA between AT and tabulated potential between CG particles
interNB = espressopp.interaction.VerletListHadressLennardJones(vl, ftpl) # Here we need specific (H-)AdResS interaction type
potWCA = espressopp.interaction.LennardJones(epsilon=1.0, sigma=1.0, shift='auto', cutoff=rca)
potCG = espressopp.interaction.Tabulated(itype=3, filename=tabCG, cutoff=rc) # CG
interNB.setPotentialAT(type1=1, type2=1, potential=potWCA) # AT
interNB.setPotentialCG(type1=0, type2=0, potential=potCG) # CG
system.addInteraction(interNB)
# bonded potentials
# quartic potential between AT particles
potQuartic = espressopp.interaction.Quartic(K=75.0, r0=1.0)
interQuartic = espressopp.interaction.FixedPairListQuartic(system, fpl, potQuartic)
ftpl.addTuples(tuples)
system.storage.setFixedTuplesAdress(ftpl)
# decompose to distribute the particles correctly before adding interactions
system.storage.decompose()
###########################################
# 5. set up structure, interactions, and force field #
###########################################
print('Setting up interactions and force field...')
# create the adaptive resolution verlet list
verletlist = espressopp.VerletListAdress(
system,
cutoff=interaction_cutoff_cg,
adrcut=interaction_cutoff_verletlist_at,
dEx=ex_size,
dHy=hy_size,
adrCenter=[Lx / 2, Ly / 2, Lz / 2])
# set up atomistic nonbonded interactions. This interaction template handles both the Lannard Jones and the Reaction Field within AdResS
interNBat = espressopp.interaction.VerletListAdressATLenJonesReacFieldGen(
verletlist, ftpl)
potLJ = espressopp.interaction.LennardJones(epsilon=0.650299305951,
sigma=0.316549165245,
shift='auto',
cutoff=interaction_cutoff_at)
interNBat.setPotential1(type1=1, type2=1, potential=potLJ)
potQQ = espressopp.interaction.ReactionFieldGeneralized(
prefactor=138.935485,
kappa=0.0,