def write_surf_matrix(surf_matrix, output):
xlen = len(surf_matrix)
ylen = len(surf_matrix[0])
surf_array = numpy.empty((xlen*ylen, 3))
for x_index in xrange(xlen):
for y_index in xrange(ylen):
surf_index = x_index*xlen+y_index
surf_array[surf_index][0] = x_index
surf_array[surf_index][1] = y_index
surf_array[surf_index][2] = surf_matrix[x_index][y_index]
write.xyz(output).write(['H']*len(surf_array), surf_array)
def test_type(ltype):
lat = create.Lattice(lattice_system=ltype)
mol = create.Molecule(["Ag"], numpy.array([[0,0,0]]))
cry = create.Crystal(mol, lat)
k = cry.get_crystal()
wri = write.xyz("out.xyz")
wri.write(k[0], k[1])
def test_rotate(axis, theta):
lat = create.Lattice()
lat.set_lattice_miller(5, [1,1,0], math.radians(45))
mol = create.Molecule(["Ag", "Ag"], numpy.array([[0,0,0],[0,0,1]],dtype=float))
mol.rotate(axis, theta)
cry = create.Crystal(mol, lat)
k = cry.get_crystal()
wri = write.xyz("out.xyz")
wri.write(k[0], k[1])
def write_surf_array(surf_array, output):
write.xyz(output).write(['Si']*len(surf_array), surf_array)
def single(types, coords):
wr = write.xyz('single.xyz')
wr.write(types, coords)
wr.close()
def test_read_write(ifile_name, ofile_name):
traj = analyze.Traj(ifile_name, "lammpstrj")
frame = traj.read()
wxyz = write.xyz(ofile_name, 0)
wxyz.write(frame)
