def makeNnzDist():
import parseXYZ
matD = getAtomMatrix("/Volumes/s/matrices/matrixmarket/diamond-2r_P2_A.mm")
matW = getAtomMatrix("/Volumes/s/matrices/matrixmarket/nanowire25-2r_P2_A.mm")
nnzD = matD.nnz
nnzW = matW.nnz
distD = np.array([0.0] * nnzD)
distW = np.array([0.0] * nnzW)
xyzD = parseXYZ.getXYZ("diamond-2r_P2.xyz")
xyzW = parseXYZ.getXYZ("nanowire25-2r_P2.xyz")
for i in range(matW.nnz):
if i < matD.nnz:
atom1 = matD.row[i]
atom2 = matD.col[i]
distD[i] = parseXYZ.getdistance(
xyzD[1][atom1], xyzD[2][atom1], xyzD[3][atom1], xyzD[1][atom2], xyzD[2][atom2], xyzD[3][atom2]
)
atom1 = matW.row[i]
atom2 = matW.col[i]
distW[i] = parseXYZ.getdistance(
xyzW[1][atom1], xyzW[2][atom1], xyzW[3][atom1], xyzW[1][atom2], xyzW[2][atom2], xyzW[3][atom2]
)
print "done"
plt.figure()
plt.hist(distD, bins=1000, cumulative=False, normed=True, histtype=u"step", color="red", edgecolor="red", alpha=0.7)
plt.hist(
distW, bins=1000, cumulative=False, normed=True, histtype=u"step", color="green", edgecolor="green", alpha=0.7
)
plt.show()
return
def makeNnzHist(mat, xyz):
import parseXYZ
nnz = mat.nnz
dist = np.array([0.0] * nnz)
for i in range(nnz):
atom1 = mat.row[i]
atom2 = mat.col[i]
dist[i] = parseXYZ.getdistance(
xyz[1][atom1], xyz[2][atom1], xyz[3][atom1], xyz[1][atom2], xyz[2][atom2], xyz[3][atom2]
)
plt.figure()
plt.hist(dist, bins=1000, cumulative=False, normed=True, histtype=u"step", color="red", edgecolor="red", alpha=0.7)
return
def getDistMat(xyz, thresh):
import parseXYZ
natoms = len(xyz[1])
mat = np.zeros((natoms, natoms), dtype=np.int)
centerlist = []
for i in range(natoms - 1):
for j in range(i + 1, natoms):
tmp = parseXYZ.getdistance(xyz[1][i], xyz[2][i], xyz[3][i], xyz[1][j], xyz[2][j], xyz[3][j])
if tmp < thresh:
mat[i][j] = tmp
if abs(i - j) < 152 and abs(i - j) > 148:
centerlist.append(i)
centerlist.append(j)
print "jmol command:", str(["C" + str(centerlist[i] + 1) for i in range(len(centerlist))]).replace("[", "").replace(
"]", ""
).replace("'", "")
return spa.coo_matrix(mat)
