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)