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 makeCouplingAtomPlot(n, tag):
import parseXYZ
from mpl_toolkits.mplot3d import Axes3D
mmdir = "/Volumes/s/matrices/matrixmarket/"
mmfile = mmdir + tag + "_A.mm"
xyzdir = "/Volumes/s/keceli/Dropbox/work/SEMO/xyz/"
xyzfile = xyzdir + tag + ".xyz"
mat = getAtomMatrix(mmfile)
nnz = mat.nnz
distW = np.array([0.0] * nnz)
xyz = parseXYZ.getXYZ(xyzfile)
matD = getDistMat(xyz, 5.6)
makeNnzHist(mat, xyz)
xyzW = np.asarray(xyz[1:4])
myrow = np.asarray(mat.row)
mycol = np.asarray(mat.col)
listofAtoms1 = myrow[mycol == n]
listofAtoms2 = mycol[myrow == n]
listofAtoms = np.unique(np.concatenate((listofAtoms1, listofAtoms2)))
print "focused atom number and its coordinates:", n + 1, xyzW[:, n]
print "number of atoms interacting with this atom:", len(listofAtoms)
print "list of interacting atoms:", listofAtoms + 1
print "jmol command:", str(["C" + str(listofAtoms[i] + 1) for i in range(len(listofAtoms))]).replace(
"[", ""
).replace("]", "").replace("'", "")
print "coordinates of interacting atoms", xyzW[:, listofAtoms]
fig = plt.figure()
plt.spy(mat, markersize=1)
fig = plt.figure()
plt.spy(matD, markersize=1)
fig = plt.figure()
plt.plot(listofAtoms, linestyle="None", marker="s")
fig = plt.figure()
ax = fig.add_subplot(111, projection="3d")
plt.plot(xyzW[0, :], xyzW[1, :], xyzW[2, :], linestyle="None", marker=".", color="black", markersize=2)
plt.plot(
xyzW[0, listofAtoms],
xyzW[1, listofAtoms],
xyzW[2, listofAtoms],
linestyle="None",
marker="o",
color="red",
markersize=3,
)
plt.plot([xyzW[0, n]], [xyzW[1, n]], [xyzW[2, n]], linestyle="None", marker="s", color="blue", markersize=4)
plt.grid(which="major", axis="all")
plt.gca().set_aspect("equal", adjustable="box")
# ax.auto_scale_xyz()
# plt.axis('equal')
ax.set_xlim([-5, 25])
ax.set_ylim([-5, 25])
ax.set_zlim([0, 45])
ax.set_xlabel("x")
ax.set_ylabel("y")
ax.set_zlabel("z")
return