def test_hdf5_simple():
# This test does not write all possible outputs
sys = get_system_water()
ff = ForceField.generate(sys, pkg_resources.resource_filename(__name__, '../../data/test/parameters_water_bondharm.txt'))
with h5.File('yaff.sampling.test.test_verlet.test_hdf5_simple.h5', driver='core', backing_store=False) as f:
hdf5 = HDF5Writer(f)
nve = VerletIntegrator(ff, 1.0*femtosecond, hooks=hdf5)
nve.run(15)
assert nve.counter == 15
check_hdf5_common(hdf5.f, isolated=True)
assert get_last_trajectory_row(f['trajectory']) == 16
assert f['trajectory/counter'][15] == 15
def test_hdf5_simple():
# This test does not write all possible outputs
sys = get_system_water()
ff = ForceField.generate(sys, context.get_fn('test/parameters_water_bondharm.txt'))
f = h5.File('yaff.sampling.test.test_verlet.test_hdf5_simple.h5', driver='core', backing_store=False)
try:
hdf5 = HDF5Writer(f)
nve = VerletIntegrator(ff, 1.0*femtosecond, hooks=hdf5)
nve.run(15)
assert nve.counter == 15
check_hdf5_common(hdf5.f, isolated=True)
assert get_last_trajectory_row(f['trajectory']) == 16
assert f['trajectory/counter'][15] == 15
finally:
f.close()
def test_pair_pot_eidip_water_setdipoles():
# '''Test if we can modify dipoles of PairPotEIDip object'''
#Setup simple system
system = get_system_water()
rcut = 50.0*angstrom
#Some arrays representing dipoles
dipoles0 = np.array( [[1.0,2.0,3.0],[4.0,5.0,6.0],[7.0,8.0,9.0 ]] ) # natom x 3
dipoles1 = np.array( [[9.0,8.0,7.0],[6.0,5.0,4.0],[3.0,2.0,1.0 ]] ) # natom x 3
dipoles2 = np.array( [[9.0,8.0],[6.0,5.0],[3.0,2.0 ]] ) # natom x 2
dipoles3 = np.array( [[9.0,8.0,7.0],[6.0,5.0,4.0]] ) # natom x 2
#Array representing atomic polarizability tensors
poltens_i = np.tile( np.diag([1.0,1.0,1.0]) , np.array([system.natom, 1]) )
system.dipoles = dipoles0
#Initialize pair potential
pair_pot = PairPotEIDip(system.charges, system.dipoles, poltens_i, 0.0, rcut)
#Check if dipoles are initialized correctly
assert np.all( pair_pot.dipoles == dipoles0 )
#Update the dipoles to new values
system.dipoles[:] = dipoles1
assert np.all( pair_pot.dipoles == dipoles1 )
#Try to update dipoles of PairPot directly, this should raise an attribute error
with assert_raises(AttributeError):
pair_pot.dipoles = dipoles1
def get_ff_water():
system = get_system_water()
fn_pars = context.get_fn('test/parameters_water.txt')
return ForceField.generate(system, fn_pars)
def get_ff_water():
system = get_system_water()
fn_pars = pkg_resources.resource_filename(
__name__, '../../data/test/parameters_water.txt')
return ForceField.generate(system, fn_pars)
def get_ff_water():
system = get_system_water()
fn_pars = context.get_fn('test/parameters_water.txt')
return ForceField.generate(system, fn_pars)
def get_part_water_eidip(scalings = [0.5,1.0,1.0],rcut=14.0*angstrom,switch_width=0.0*angstrom, finite=False, alpha=0.0, do_radii=False):
'''
Make a system with one water molecule with a point dipole on every atom,
setup a ForcePart...
'''
# Set dipoles
dipoles = np.array( [[1.0,2.0,3.0],[4.0,5.0,6.0],[7.0,8.0,9.0 ]] ) # natom x 3
# Initialize system, nlist and scaling
system = get_system_water()
#TODO make radii2 system attribute
system.radii = np.array( [ 1.5,1.2,1.2] ) * angstrom
system.radii2 = np.array( [1.6,1.3,1.2] ) * angstrom
if finite:
#Make a system with point dipoles approximated by two charges
system = make_system_finite_dipoles(system, dipoles, eps=0.0001*angstrom)
if not do_radii:
system.radii *= 0.0
if not finite:system.radii2 *= 0.0
nlist = NeighborList(system)
scalings = Scalings(system, scalings[0], scalings[1], scalings[2])
# Set poltens
poltens_i = np.tile( 0.0*np.diag([1.0,1.0,1.0]) , np.array([system.natom, 1]) )
# Create the pair_pot and part_pair
if finite:
pair_pot = PairPotEI(system.charges,alpha, rcut, tr=Switch3(switch_width), radii=system.radii)
else:
pair_pot = PairPotEIDip(system.charges, dipoles, poltens_i, alpha, rcut, tr=Switch3(switch_width), radii=system.radii, radii2=system.radii2)
part_pair = ForcePartPair(system, nlist, scalings, pair_pot)
nlist.update()
#Make a different nlist in case we approximate the point dipoles with charges
#Interactions between charges at the same site should be excluded
if finite:
neigh_dtype = [
('a', int), ('b', int), ('d', float), # a & b are atom indexes, d is the distance
('dx', float), ('dy', float), ('dz', float), # relative vector (includes cell vectors of image cell)
('r0', int), ('r1', int), ('r2', int) # position of image cell.
]
nneigh = np.sum( nlist.neighs[0:nlist.nneigh]['d'] > 0.2*angstrom )
new_neighs = np.zeros(nneigh, dtype=neigh_dtype)
counter = 0
for n in nlist.neighs[0:nlist.nneigh]:
if n['d']>0.2*angstrom:
new_neighs[counter] = n
counter += 1
nlist.neighs = new_neighs
nlist.nneigh = nneigh
# The pair function
def pair_fn(i, j, d, delta):
energy = 0.0
#Charge-Charge
energy += system.charges[i]*system.charges[j]/d
if not finite:
#Charge-Dipole
energy += system.charges[i]*np.dot(delta, pair_pot.dipoles[j,:])/d**3
#Dipole-Charge
energy -= system.charges[j]*np.dot(delta, pair_pot.dipoles[i,:])/d**3
#Dipole-Dipole
energy += np.dot( pair_pot.dipoles[i,:] , pair_pot.dipoles[j,:] )/d**3 - \
3*np.dot(pair_pot.dipoles[i,:],delta)*np.dot(delta,pair_pot.dipoles[j,:])/d**5
if d > rcut - switch_width:
x = (rcut - d)/switch_width
energy *= (3-2*x)*x*x
return energy
return system, nlist, scalings, part_pair, pair_pot, pair_fn
def get_ff_water():
system = get_system_water()
fn_pars = pkg_resources.resource_filename(__name__, '../../data/test/parameters_water.txt')
return ForceField.generate(system, fn_pars)
