def energy_i(self, posits):
params = self.params
cutoff = self.cutoff
#posits_ext = extend_structure(posits.copy(), self.pbc, self.cell)
#layer_indices = self.layer_indices
layer_neighbors = self.layer_neighbors
chem_symbs = self.chem_symbs
e_KC = np.zeros(len(posits))
for i, ri in enumerate(posits):
if chem_symbs[i] == 'C':
ni = local_normal(i, posits, layer_neighbors, accept_noneighbor = self.no_edge_neighbor)
ni = -1*ni
nj = np.array([0., 0., 1.])
neigh_orig = get_setOrig(ri, self.edge, self.bond)
neigh_pos = self.neigh_set + neigh_orig
for rj in neigh_pos:
e, new_maps = get_potential_ij(ri, rj, ni, nj, posits, i, params, \
cutoff)
if new_maps != None: self.map_seqs = new_maps
e_KC[i] += e
return e_KC
def energy_i(self, posits):
params = self.params
cutoff = self.cutoff
#posits_ext = extend_structure(posits.copy(), self.pbc, self.cell)
#layer_indices = self.layer_indices
layer_neighbors = self.layer_neighbors
chem_symbs = self.chem_symbs
e_KC = np.zeros(len(posits))
for i, ri in enumerate(posits):
if chem_symbs[i] == 'C':
ni = local_normal(i,
posits,
layer_neighbors,
accept_noneighbor=self.no_edge_neighbor)
ni = -1 * ni
nj = np.array([0., 0., 1.])
neigh_orig = get_setOrig(ri, self.edge, self.bond)
neigh_pos = self.neigh_set + neigh_orig
for rj in neigh_pos:
e, new_maps = get_potential_ij(ri, rj, ni, nj, posits, i, params, \
cutoff)
if new_maps != None: self.map_seqs = new_maps
e_KC[i] += e
return e_KC
def forces_on_posArr(self, split_beg, pos_arr, af1, af2, af3, dnGreat, \
posits, layer_neighbors, \
chem_symbs, params, cutoff, natoms):
nj = np.array([0., 0., 1.])
dnj = np.array([[0., 0., 0], [0., 0., 0], [0., 0., 0]])
for l, ri in enumerate(pos_arr):
i = l + split_beg
if chem_symbs[i] == 'C': # SHREAR ADD
ni_f = local_normal(i,
posits,
layer_neighbors,
accept_noneighbor=self.no_edge_neighbor)
dni_f = dnGreat[i]
ni = -1 * ni_f
dni = -dni_f
neigh_orig = get_setOrig(ri, self.edge, self.bond)
neigh_pos = self.neigh_set + neigh_orig
for rj in neigh_pos:
# Force due to atom j on atom i
fij = get_forces_ij(ri, rj, ni, nj, dni, dnj, \
posits, i, params, \
cutoff, no_edge_neighbor = self.no_edge_neighbor) #, layer_neighbors = layer_neighbors)
af1[i] += fij[0]
af2[i] += fij[1]
af3[i] += fij[2]
def nj(xi, *args):
i = args[0]
posits_use = positions.copy()
posits_use[ind, i] = xi
#posits_ext_use = extend_structure(posits_use.copy(), pbc, cell)
nj = local_normal(ind, posits_use, layer_neighbors, \
accept_noneighbor = no_edge_neighbor)
return nj
def nj(xi, *args):
i = args[0]
posits_use = positions.copy()
posits_use[ind, i] = xi
#posits_ext_use = extend_structure(posits_use.copy(), pbc, cell)
nj = local_normal(ind, posits_use, layer_neighbors, \
accept_noneighbor = no_edge_neighbor)
return nj
def e(rik, *args):
k = args[0]
posits_use = posits.copy()
posits_use[i,k] = rik
ri = posits_use[i]
#posits_ext = extend_structure(posits_use, pbc, cell)
ni = local_normal(i, posits, layer_neighbors, accept_noneighbor = no_edge_neighbor)*(-1)
nj = np.array([0.,0.,1.])
return get_potential_ij(ri, rj, ni, nj, posits_use, i, params, cutoff)
def e(rik, *args):
k = args[0]
posits_use = posits.copy()
posits_use[i, k] = rik
ri = posits_use[i]
#posits_ext = extend_structure(posits_use, pbc, cell)
ni = local_normal(
i, posits, layer_neighbors,
accept_noneighbor=no_edge_neighbor) * (-1)
nj = np.array([0., 0., 1.])
return get_potential_ij(ri, rj, ni, nj, posits_use, i, params, cutoff)
def energy_on_posArr(self, k, split_len, pos_arr, e_KCm, \
posits, layer_neighbors,
chem_symbs, params, cutoff, natoms):
nj = np.array([0., 0., 1.])
for l, ri in enumerate(pos_arr):
i = l + split_len
if chem_symbs[i] == 'C': # SHEAR ADD
ni = local_normal(i, posits, layer_neighbors, accept_noneighbor = self.no_edge_neighbor)
ni = -1*ni
neigh_orig = get_setOrig(ri, self.edge, self.bond)
neigh_pos = self.neigh_set + neigh_orig
for rj in neigh_pos:
e = get_potential_ij(ri, rj, ni, nj, posits, i, params, \
cutoff)
e_KCm[k] += e
def forces_on_posArr(self, split_beg, pos_arr, af1, af2, af3, dnGreat, \
posits, layer_neighbors, \
chem_symbs, params, cutoff, natoms):
nj = np.array([0., 0., 1.])
dnj = np.array([[0., 0., 0],
[0., 0., 0],
[0., 0., 0]])
for l, ri in enumerate(pos_arr):
i = l + split_beg
if chem_symbs[i] == 'C': # SHREAR ADD
ni_f = local_normal(i, posits, layer_neighbors, accept_noneighbor = self.no_edge_neighbor)
dni_f = dnGreat[i]
ni = -1*ni_f
dni = -dni_f
neigh_orig = get_setOrig(ri, self.edge, self.bond)
neigh_pos = self.neigh_set + neigh_orig
for rj in neigh_pos:
# Force due to atom j on atom i
fij = get_forces_ij(ri, rj, ni, nj, dni, dnj, \
posits, i, params, \
cutoff, no_edge_neighbor = self.no_edge_neighbor) #, layer_neighbors = layer_neighbors)
af1[i] += fij[0]
af2[i] += fij[1]
af3[i] += fij[2]
def energy_on_posArr(self, k, split_len, pos_arr, e_KCm, \
posits, layer_neighbors,
chem_symbs, params, cutoff, natoms):
nj = np.array([0., 0., 1.])
for l, ri in enumerate(pos_arr):
i = l + split_len
if chem_symbs[i] == 'C': # SHEAR ADD
ni = local_normal(i,
posits,
layer_neighbors,
accept_noneighbor=self.no_edge_neighbor)
ni = -1 * ni
neigh_orig = get_setOrig(ri, self.edge, self.bond)
neigh_pos = self.neigh_set + neigh_orig
for rj in neigh_pos:
e = get_potential_ij(ri, rj, ni, nj, posits, i, params, \
cutoff)
e_KCm[k] += e
