def setBondedInteractions(system, input_conf, ftpl):
ret_list = {}
bonds = input_conf.bondtypes
bondtypeparams = input_conf.bondtypeparams
for (bid, cross_bonds), bondlist in bonds.iteritems():
if ftpl:
fpl = espressopp.FixedPairListAdress(system.storage, ftpl)
else:
fpl = espressopp.FixedPairList(system.storage)
fpl.addBonds(bondlist)
bdinteraction = bondtypeparams[bid].createEspressoInteraction(system, fpl)
if bdinteraction:
system.addInteraction(bdinteraction, 'bond_{}{}'.format(
bid, '_cross' if cross_bonds else ''))
ret_list.update({(bid, cross_bonds): bdinteraction})
return ret_list
# append tuple to tuplelist
tuples.append(tmptuple)
# add particles to system
system.storage.addParticles(allParticles, "id", "pos", "v", "f", "type", "mass", "adrat")
# create FixedTupleList object
ftpl = espressopp.FixedTupleListAdress(system.storage)
# and add the tuples
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
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)
lj14interaction=gromacs.setLennardJones14Interactions(system, defaults, atomtypeparameters, onefourlist, nbCutoff)
# set up coulomb 1-4 interactions
qq14_interactions=gromacs.setCoulomb14Interactions(system, defaults, onefourlist, nbCutoff, atTypes)
## set up bond interactions according to the parameters read from the .top file
bondedinteractions=gromacs.setBondedInteractionsAdress(system, atBondtypes, bondtypeparams,ftpl)
# set up angle interactions according to the parameters read from the .top file
angleinteractions=gromacs.setAngleInteractionsAdress(system, atAngletypes, angletypeparams,ftpl)
# set up dihedral interactions according to the parameters read from the .top file
dihedralinteractions=gromacs.setDihedralInteractionsAdress(system, atDihedraltypes, dihedraltypeparams,ftpl)
def setPairInteractions(system, input_conf, cutoff, coulomb_cutoff, ftpl=None):
pairs = input_conf.pairtypes
fudgeQQ = float(input_conf.defaults['fudgeQQ'])
pref = 138.935485 * fudgeQQ # we want gromacs units, so this is 1/(4 pi eps_0) ins units of kJ mol^-1 e^-2, scaled by fudge factor
pairtypeparams = input_conf.pairtypeparams
static_14_pairs = []
cross_14_pairs_cg = []
cross_14_pairs_at = []
for (pid, cross_bonds), pair_list in pairs.iteritems():
params = pairtypeparams[pid]
is_cg = input_conf.atomtypeparams[
input_conf.types[pair_list[0][0] - 1]]['particletype'] == 'V'
if is_cg or ftpl is None:
fpl = espressopp.FixedPairList(system.storage)
else:
fpl = espressopp.FixedPairListAdress(system.storage, ftpl)
fpl.addBonds(pair_list)
if cross_bonds or is_cg:
if is_cg:
cross_14_pairs_cg.extend(pair_list)
else:
cross_14_pairs_at.extend(pair_list)
else:
static_14_pairs.extend(pair_list)
if not cross_bonds:
is_cg = None
if params['sig'] > 0.0 and params['eps'] > 0.0:
print('Pair interaction {} num pairs: {} sig={} eps={} cutoff={} is_cg={}'.format(
params, len(pair_list), params['sig'], params['eps'], cutoff, is_cg))
pot = espressopp.interaction.LennardJones(
sigma=params['sig'],
epsilon=params['eps'],
shift='auto',
cutoff=cutoff)
if is_cg is None:
interaction = espressopp.interaction.FixedPairListLennardJones(system, fpl, pot)
else:
interaction = espressopp.interaction.FixedPairListAdressLennardJones(
system, fpl, pot, is_cg)
system.addInteraction(interaction, 'lj-14_{}{}'.format(pid, '_cross' if cross_bonds else ''))
# Set Coulomb14
if static_14_pairs or cross_14_pairs_cg or cross_14_pairs_at:
type_pairs = set()
for type_1, pi in input_conf.atomtypeparams.iteritems():
for type_2, pj in input_conf.atomtypeparams.iteritems():
if pi['particletype'] != 'V' and pj['particletype'] != 'V':
type_pairs.add(tuple(sorted([type_1, type_2])))
type_pairs = sorted(type_pairs)
print('Using fudgeQQ: {}, type_pairs: {}'.format(fudgeQQ, len(type_pairs)))
potQQ = espressopp.interaction.CoulombTruncated(prefactor=pref, cutoff=coulomb_cutoff)
if static_14_pairs:
print('Defined {} of static coulomb 1-4 pairs'.format(len(static_14_pairs)))
fpl_static = espressopp.FixedPairList(system.storage)
fpl_static.addBonds(static_14_pairs)
interaction_static = espressopp.interaction.FixedPairListTypesCoulombTruncated(system, fpl_static)
for type_1, type_2 in type_pairs:
interaction_static.setPotential(type1=type_1, type2=type_2, potential=potQQ)
system.addInteraction(interaction_static, 'coulomb14')
if cross_14_pairs_cg:
print('Defined {} of cross coulomb CG 1-4 pairs'.format(len(cross_14_pairs_cg)))
fpl_cross = espressopp.FixedPairList(system.storage)
fpl_cross.addBonds(cross_14_pairs_cg)
# Now set cross potential.
interaction_dynamic = espressopp.interaction.FixedPairListAdressTypesCoulombTruncated(
system, fpl_cross, True)
for type_1, type_2 in type_pairs:
interaction_dynamic.setPotential(type1=type_1, type2=type_2, potential=potQQ)
system.addInteraction(interaction_dynamic, 'coulomb14_cg_cross')
if cross_14_pairs_at:
print('Defined {} of cross coulomb AT 1-4 pairs'.format(len(cross_14_pairs_at)))
fpl_cross = espressopp.FixedPairList(system.storage)
fpl_cross.addBonds(cross_14_pairs_at)
# Now set cross potential.
interaction_dynamic = espressopp.interaction.FixedPairListAdressTypesCoulombTruncated(
system, fpl_cross, False)
for type_1, type_2 in type_pairs:
interaction_dynamic.setPotential(type1=type_1, type2=type_2, potential=potQQ)
system.addInteraction(interaction_dynamic, 'coulomb14_at_cross')
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)
