system = System.from_hdf5(f_res)
ff = ForceField.generate(system, 'pars.txt', rcut=15*angstrom, alpha_scale=3.2, gcut_scale=1.5, smooth_ei=True)
# Replace non-covalent part with LAMMPS
for part in ff.parts:
if part.name=='valence': part_valence = part
elif part.name=='pair_ei': part_ei = part
# Write LAMMPS system file
write_lammps_data(system)
nlist = BondedNeighborList(system)
pair_pot = PairPotEI(system.charges, 0.0, part_ei.pair_pot.rcut, tr=Switch3(part_ei.pair_pot.get_truncation().width), radii=system.radii)
scalings = Scalings(system, scale1=1.0, scale2=1.0, scale3=0.0)
pair_gauss = ForcePartPair(system,nlist,scalings,pair_pot)
pair_lammps = ForcePartLammps(system, pppm_accuracy=1e-6,fn_table='lammps_smoothei2.table', comm=comm, scalings=[0.0,0.0,1.0,0.0,0.0,1.0],fn_log='none')
ff = ForceField(system,[part_valence,pair_lammps,pair_gauss],nlist)
dof = StrainCellDOF(ff, gpos_rms=1e-8, dpos_rms=1e-6, gcell_rms=1e-8, dcell_rms=1e-6, do_frozen=False)
# Only write output from process 0
if rank==0:
f = h5py.File('traj_9.h5', mode='w')
hdf = HDF5Writer(f, step=1000, flush=10)
g = h5py.File('restart_9.h5',mode='w')
hdf_restart = RestartWriter(g, step=100000,flush=1)
vsl = VerletScreenLog(step=5000)
# Only write output from process 0
if rank==0:
log.set_level(log.medium)
def write_lammps_table_jelle(ff):
from yaff import NeighborList, PairPotEI, Switch3, ForcePartPair, Scalings,\
PairPotMM3
nffa = ff.system.ffatypes.shape[0]
numbers = []
for i in xrange(nffa):
index0 = np.where(ff.system.ffatype_ids == i)[0][0]
if np.sum(ff.system.ffatype_ids == i) > 1:
index1 = np.where(ff.system.ffatype_ids == i)[0][1]
numbers.append([index0, index1])
for j in xrange(i + 1, nffa):
index1 = np.where(ff.system.ffatype_ids == j)[0][0]
numbers.append([index0, index1])
part_names = [part.name for part in ff.parts]
print part_names
ftab = open('lammps_smoothei2.table', 'w')
ftab.write("# LAMMPS tabulated potential generated by Yaff\n")
ftab.write("# All quantities in atomic units\n")
ftab.write(
"# The names of the tables refer to the ffatypes that have to be used in the Yaff system\n"
)
ftab.write("#%4s %13s %21s %21s\n" % ("i", "d", "V", "F"))
for number in numbers:
pos = np.zeros((2, 3))
pos[1, 2] = 1.0
smallsys = System(system.numbers[number],
pos,
charges=system.charges[number],
radii=system.radii[number])
smallsys_noradii = System(system.numbers[number],
pos,
charges=system.charges[number])
idx_ei = -1
idx_mm3 = -1
for idx, part in enumerate(ff.parts):
if part.name == 'pair_ei': idx_ei = idx
elif part.name == 'pair_mm3': idx_mm3 = idx
tr = ff.parts[idx_ei].pair_pot.get_truncation()
rcut = ff.parts[idx_ei].pair_pot.rcut
alpha = ff.parts[idx_ei].pair_pot.alpha
nlist = NeighborList(smallsys)
pair_pot = PairPotEI(smallsys.charges,
alpha,
rcut,
tr=Switch3(tr.width),
radii=smallsys.radii)
# pair_pot = PairPotEI(smallsys.charges, 0.0, rcut, tr=None, radii=smallsys.radii)
scalings = Scalings(smallsys, scale1=1.0, scale2=1.0, scale3=1.0)
part0 = ForcePartPair(smallsys, nlist, scalings, pair_pot)
ff0 = ForceField(smallsys, [part0], nlist)
ff0.compute()
nlist1 = NeighborList(smallsys_noradii)
# pair_pot = PairPotEI(smallsys_noradii.charges, alpha, rcut, tr=Switch3(tr.width))
pair_pot = PairPotEI(smallsys_noradii.charges, alpha, rcut, tr=None)
scalings = Scalings(smallsys_noradii,
scale1=1.0,
scale2=1.0,
scale3=1.0)
part1 = ForcePartPair(smallsys_noradii, nlist1, scalings, pair_pot)
ff1 = ForceField(smallsys_noradii, [part1], nlist1)
ff1.compute()
tr = ff.parts[idx_mm3].pair_pot.get_truncation()
rcut = ff.parts[idx_mm3].pair_pot.rcut
nlist2 = NeighborList(smallsys)
pair_pot = PairPotMM3(ff.parts[idx_mm3].pair_pot.sigmas[number],
ff.parts[idx_mm3].pair_pot.epsilons[number],
ff.parts[idx_mm3].pair_pot.onlypaulis[number],
rcut, Switch3(tr.width))
scalings = Scalings(smallsys, scale1=1.0, scale2=1.0, scale3=1.0)
part2 = ForcePartPair(smallsys, nlist, scalings, pair_pot)
ff2 = ForceField(smallsys, [part2], nlist)
ff2.nlist.nneigh = 1
ff2.compute()
distances = np.linspace(0.5 * angstrom, rcut, 5000)
energies = []
toplot = []
for d in distances:
gposnn0 = np.zeros(ff0.system.pos.shape, float)
ff0.nlist.neighs[0] = (0, 1, d, 0.0, 0.0, d, 0, 0, 0)
energy0 = ff0.compute(gpos=gposnn0)
gposnn1 = np.zeros(ff1.system.pos.shape, float)
ff1.nlist.neighs[0] = (0, 1, d, 0.0, 0.0, d, 0, 0, 0)
energy1 = ff1.compute(gpos=gposnn1)
gposnn2 = np.zeros(ff2.system.pos.shape, float)
ff2.nlist.neighs[0] = (0, 1, d, 0.0, 0.0, d, 0, 0, 0)
energy2 = ff2.compute(gpos=gposnn2)
toplot.append([d, energy0, energy1, energy2])
row = [
d, energy0 - energy1 + energy2,
gposnn0[0, 2] - gposnn1[0, 2] + gposnn2[0, 2]
]
# row = [d, energy2, gposnn2[0,2]]
energies.append(row)
energies = np.asarray(energies)
toplot = np.asarray(toplot)
ffa0 = ff.system.ffatypes[ff.system.ffatype_ids[number[0]]]
ffa1 = ff.system.ffatypes[ff.system.ffatype_ids[number[1]]]
if ffa0 > ffa1:
name = '%s-%s' % (ffa0, ffa1)
else:
name = '%s-%s' % (ffa1, ffa0)
ftab.write("%s\nN %d R %f %f\n\n" %
(name, energies.shape[0], distances[0], distances[-1]))
for irow, row in enumerate(energies):
ftab.write("%05d %+13.8f %+21.12f %+21.12f\n" %
(irow + 1, row[0], row[1], row[2]))
print name