def displacement(system_0, system_1, box_reference='final'):
"""Compute the displacement vectors between all matching atoms for two systems."""
assert system_0.natoms == system_1.natoms, 'systems have different number of atoms'
if box_reference == 'final':
disp = dvect(system_0.atoms.view['pos'], system_1.atoms.view['pos'], system_1.box, system_1.pbc)
elif box_reference == 'initial':
disp = dvect(system_0.atoms.view['pos'], system_1.atoms.view['pos'], system_0.box, system_0.pbc)
elif box_reference is None:
disp = system_1.atoms.view['pos'] - system_0.atoms.view['pos']
else:
raise ValueError("box_reference must be 'final', 'initial', or None")
return disp
def displacement(system_0, system_1, box_reference='final'):
"""Compute the displacement vectors between all matching atoms for two systems."""
assert system_0.natoms == system_1.natoms, 'systems have different number of atoms'
if box_reference == 'final':
disp = dvect(system_0.atoms.view['pos'], system_1.atoms.view['pos'],
system_1.box, system_1.pbc)
elif box_reference == 'initial':
disp = dvect(system_0.atoms.view['pos'], system_1.atoms.view['pos'],
system_0.box, system_0.pbc)
elif box_reference is None:
disp = system_1.atoms.view['pos'] - system_0.atoms.view['pos']
else:
raise ValueError("box_reference must be 'final', 'initial', or None")
return disp
def displacement(system_0, system_1):
"""Compute the displacement vectors between all matching atoms for two systems."""
assert system_0.natoms == system_1.natoms, 'systems have different number of atoms'
disp = dvect(system_0.atoms.view['pos'], system_1.atoms.view['pos'], system_1.box, system_1.pbc)
return disp
def nlist(system, cutoff, cmult=1):
"""
Calculates a neighbor list for all atoms in a System taking periodic boundaries into account.
Keyword Arguments:
system -- System to calculate the neighbor list for.
cutoff -- radial cutoff distance for neighbors.
cmult -- parameter associated with the binning routine. Default value is most likely the fastest."""
natoms = system.natoms
vects = system.box.vects
origin = system.box.origin
pos = system.atoms.view['pos']
pbc = system.pbc
#Determine orthogonal superbox that fully encompases the system
corners = origin + np.array([[0,0,0], vects[0], vects[1], vects[2],
vects[0] + vects[1],
vects[0] + vects[2],
vects[1] + vects[2],
vects[0] + vects[1] + vects[2]])
supermin = corners.min(axis=0) - 2*cutoff
supermax = corners.max(axis=0) + 2*cutoff
#Construct bins
binsize = cutoff/cmult
xbins = np.arange(supermin[0], supermax[0], binsize)
ybins = np.arange(supermin[1], supermax[1], binsize)
zbins = np.arange(supermin[2], supermax[2], binsize)
#Create index lists for real atoms
x_index = np.digitize(pos[:, 0], xbins) - 1
y_index = np.digitize(pos[:, 1], ybins) - 1
z_index = np.digitize(pos[:, 2], zbins) - 1
xyz_index = np.hstack((x_index[:, np.newaxis], y_index[:, np.newaxis], z_index[:, np.newaxis]))
atom_index = np.arange(natoms, dtype=int)
real_bins = unique_rows(xyz_index)
#create iterators based on pbc
check = [xrange(1), xrange(1), xrange(1)]
for i in xrange(3):
if pbc[i]:
check[i] = xrange(-1, 2)
#construct list of ghost atoms in the superbox
ghost_pos = []
for x in check[0]:
for y in check[1]:
for z in check[2]:
if x == 0 and y == 0 and z == 0:
pass
else:
newpos = x*vects[0] + y*vects[1] + z*vects[2] + pos
bool_check = np.empty_like(newpos, dtype=bool)
for i in xrange(3):
bool_check[:, i] = np.all([newpos[:, i] > supermin[i], newpos[:, i] < supermax[i]], axis=0)
new_index = np.where(np.all(bool_check, axis=1))[0]
try:
ghost_pos = np.vstack((ghost_pos, newpos[new_index]))
ghost_index = np.hstack((ghost_index, new_index))
except:
ghost_pos = newpos[new_index]
ghost_index = new_index
#append index lists with ghost atoms
if len(ghost_pos) > 0:
x_index = np.digitize(ghost_pos[:, 0], xbins) - 1
y_index = np.digitize(ghost_pos[:, 1], ybins) - 1
z_index = np.digitize(ghost_pos[:, 2], zbins) - 1
xyz_g_index = np.hstack((x_index[:, np.newaxis], y_index[:, np.newaxis], z_index[:, np.newaxis]))
xyz_index = np.vstack((xyz_index, xyz_g_index))
atom_index = np.hstack((atom_index, ghost_index))
neighbors = np.zeros((natoms, 41), dtype=np.int)
#assign atoms and ghost atoms to xyz bins
xyz_bins = np.zeros((len(xbins), len(ybins), len(zbins), 41), dtype=np.int)
for i in xrange(len(atom_index)):
x,y,z = xyz_index[i]
xyz_bins[x,y,z,0] += 1
try:
xyz_bins[x,y,z, xyz_bins[x,y,z,0]] = atom_index[i]
except:
old_size = len(xyz_bins[0,0,0])
newbins = np.zeros((len(xbins), len(ybins), len(zbins), old_size + 10), dtype=np.int)
newbins[:, :, :, :old_size] = xyz_bins[:, :, :, :old_size]
xyz_bins = newbins
xyz_bins[x,y,z, xyz_bins[x,y,z,0]] = atom_index[i]
#iterate over all bins with real atoms
for bin in real_bins:
x,y,z = bin
#short = all atoms in current bin
short = xyz_bins[x,y,z, 1:xyz_bins[x,y,z,0]+1]
long = deepcopy(short)
#add all atoms in half of the nearby bins to long
for dx, dy, dz in box_iter(cmult):
try:
long = np.hstack((long, xyz_bins[x+dx,y+dy,z+dz, 1:xyz_bins[x+dx,y+dy,z+dz,0]+1]))
except:
long = xyz_bins[x+dx,y+dy,z+dz, 1:xyz_bins[x+dx,y+dy,z+dz,0]+1]
#compare all atoms in short to medium (which is long starting with u+1).
for u in xrange(len(short)):
u_pos = pos[short[u]]
u_index = short[u]
medium = long[u+1:]
v_pos = pos[medium]
try:
d = np.linalg.norm(dvect(u_pos, v_pos, system.box, system.pbc), axis=1)
except:
d = np.linalg.norm([dvect(u_pos, v_pos, system.box, system.pbc)], axis=1)
vlist = medium[np.where(d < cutoff)]
for v_index in vlist:
neighbors = __append_neighbor(neighbors, u_index, v_index)
#sort each atom's neighbors
for i in xrange(len(neighbors)):
neighbors[i][1 : neighbors[i][0]+1] = np.sort(neighbors[i][1 : neighbors[i][0]+1])
return neighbors
