def run(pos, nbrs): num_atoms = len(pos) result = np.zeros(num_atoms, int) strains = np.zeros(num_atoms).astype(np.double) rmsds = np.zeros(num_atoms).astype(np.double) if 1: for i in range(num_atoms): positions = np.concatenate(([pos[i]], pos[nbrs[i][:18]])) (struct, alloy, rmsd, scale, rot, F, F_res, P, U, lattice_constant) = ptmmodule.index_structure(positions, calculate_strains=1, topological_ordering=1) if 0 and struct == 0 and all([e > 1000 for e in nbrs[i]]): print nbrs[i] print positions positions -= pos[i] plot_points(positions[:15]) #(struct, alloy, rmsd, scale, rot, lattice_constant) = ptmmodule.index_structure(positions) #if struct == 2: # vm, r = calc_fcc_strain(F, F_res, P, U, positions[:13]) # strains[i] = vm result[i] = struct rmsds[i] = rmsd indices = np.where(rmsds < 0.12)[0] kept = np.bincount(result[indices]) kept[0] += num_atoms - len(indices) print "rmsd < 0.12:", kept, sum(kept) return result, rmsds indices = np.where(result == 2)[0] plt.hist(strains[indices], bins=200) plt.show()
def PTM(atoms, target_structures=None, calculate_strains=False, cutoff=10.0):
"""Run Complex Hull Analysis on an Atoms object.
Parameters:
atoms: The atoms object
target_structures=None: A tuple of structures to be investigated.
It defaults to ('sc', 'fcc', 'hcp', 'ico', 'bcc').
It MUST be a tuple, not a list or other sequence (bug?).
calculate_strains=False: Set to True to calculate strains.
cutoff: A cutoff used for the neighborlist. Must be large enough that all
nearest neighbors are returned (second-nearest for BCC). Using a too
large value may impact performance, but not results.
Returns:
(structures, alloytypes, rmsds, scales, rotations, [strains])
Each of these are a NumPy array of the same length as the number of atoms.
For each atom, the data returned is
structures[i]: The local crystal structure around atom i, if any.
0 = none; 1 = SC; 2 = FCC; 3 = HCP; 4 = Icosahedral; 5 = BCC.
alloytypes[i]: The alloy structure identified.
0 = unidentified; 1 = pure element; 2 = L1_0;
3 = L1_2 majority atom; 4 = L1_2 minority atom.
(0 is returned if structures[i] != 2 or if no known alloy structure
is recognized)
rmsds[i]: The RMSD error in the fitting to the template, or INF if
no structure was identified.
scales[i]: The average distance to the nearest neighbors for
structures 1-4; or the average distance to nearest and
next-nearest neighbors for structure 5 (BCC); or INF if no
structure was identified.
rotations[i]: The rotation of the crystal lattice, expressed as a
unit quaternion. If no structure was found, the illegal
value (0, 0, 0, 0) is returned.
strains[i] (only returned if calculate_strains=True). The strain
tensor as a symmetric 3x3 matrix. The trace of the matrix is
1.0, since a hydrostatic component of the strain cannot be
determined without a-priori knowledge of the reference
lattice parameter. If such knowledge is available, the
hydrostatic component of the strain can be calculated from
scales[i].
"""
numnb = 18 # Plus central atom
nblist = asap3.FullNeighborList(cutoff, atoms)
structures = np.zeros(len(atoms), int)
alloys = np.zeros(len(atoms), int)
rmsds = np.zeros(len(atoms))
scales = np.zeros(len(atoms))
rotations = np.zeros((len(atoms), 4))
if calculate_strains:
strains = np.zeros((len(atoms), 3, 3))
z_all = atoms.get_atomic_numbers()
for i in range(len(atoms)):
indices, relative_positions, sqdist = nblist.get_neighbors(i)
assert(len(indices) >= numnb)
nearest = np.argsort(sqdist)[:numnb]
positions = np.zeros((numnb+1,3))
positions[1:] = relative_positions[nearest]
z = np.zeros(numnb+1, np.int32)
z[0] = z_all[i]
z[1:] = z_all[indices[nearest]]
data = ptmmodule.index_structure(positions, z,
calculate_strains=calculate_strains,
topological_ordering=True)
# data = (struct, alloy, rmsd, scale, rotation)
structures[i], alloys[i], rmsds[i], scales[i] = data[:4]
if structures[i]:
rotations[i] = data[4]
if calculate_strains:
strains[i] = data[7]
if calculate_strains:
return structures, alloys, rmsds, scales, rotations, strains
else:
return structures, alloys, rmsds, scales, rotations
