# type: ignore import numpy as np from ase import Atoms from ase.io import read, write import ase.io.rmc6f as rmc6f from ase.lattice.compounds import TRI_Fe2O3 rmc6f_input_text = """ (Version 6f format configuration file) Metadata owner: Joe Smith Metadata date: 31-01-1900 Metadata material: SF6 Metadata comment: Some comments go here... Metadata source: GSAS Number of moves generated: 89692 Number of moves tried: 85650 Number of moves accepted: 10074 Number of prior configuration saves: 0 Number of atoms: 7 Number density (Ang^-3): 0.068606 Supercell dimensions: 1 1 1 Cell (Ang/deg): 4.672816 4.672816 4.672816 90.0 90.0 90.0 Lattice vectors (Ang): 4.672816 0.000000 0.000000 0.000000 4.672816 0.000000 0.000000 0.000000 4.672816 Atoms: 1 S 0.600452 0.525100 0.442050 1 0 0 0 2 F 0.911952 0.450722 0.382733 2 0 0 0 3 F 0.283794 0.616712 0.500094 3 0 0 0 4 F 0.679823 0.854839 0.343915 4 0 0 0 5 F 0.531660 0.229024 0.535688 5 0 0 0 6 F 0.692514 0.584931 0.746683 6 0 0 0 7 F 0.509687 0.449350 0.111960 7 0 0 0 """ # Information for system positions = [ [0.600452, 0.525100, 0.442050], [0.911952, 0.450722, 0.382733], [0.283794, 0.616712, 0.500094], [0.679823, 0.854839, 0.343915], [0.531660, 0.229024, 0.535688], [0.692514, 0.584931, 0.746683], [0.509687, 0.449350, 0.111960]] symbols = ['S', 'F', 'F', 'F', 'F', 'F', 'F'] lat = 4.672816 # Intermediate data structures to test against symbol_xyz_list = [[s] + xyz for s, xyz in zip(symbols, positions)] symbol_xyz_dict = {i + 1: row for i, row in enumerate(symbol_xyz_list)} symbol_xyz_list_ext = [tuple([i + 1] + row + [0, 0, 0, 0]) for i, row in enumerate(symbol_xyz_list)] # Target Atoms system lat_positions = lat * np.array(positions) cell = [lat, lat, lat] rmc6f_atoms = Atoms(symbols, positions=lat_positions, cell=cell, pbc=[1, 1, 1]) def test_rmc6f_read(): """Test for reading rmc6f input file.""" with open('input.rmc6f', 'w') as rmc6f_input_f: rmc6f_input_f.write(rmc6f_input_text) rmc6f_input_atoms = read('input.rmc6f') assert len(rmc6f_input_atoms) == 7 assert rmc6f_input_atoms == rmc6f_atoms def test_rmc6f_write(): """Test for writing rmc6f input file.""" tol = 1e-5 write('output.rmc6f', rmc6f_atoms) readback = read('output.rmc6f') assert np.allclose(rmc6f_atoms.positions, readback.positions, rtol=tol) assert readback == rmc6f_atoms def test_rmc6f_write_with_order(): """Test for writing rmc6f input file with order passed in.""" tol = 1e-5 write('output.rmc6f', rmc6f_atoms, order=['F', 'S']) readback = read('output.rmc6f') reordered_positions = np.vstack( (rmc6f_atoms.positions[1:7], rmc6f_atoms.positions[0])) assert np.allclose(reordered_positions, readback.positions, rtol=tol) def test_rmc6f_write_with_triclinic_system(): """Test for writing rmc6f input file for triclinic system """ tol = 1e-5 fe4o6 = TRI_Fe2O3( symbol=('Fe', 'O'), latticeconstant={ 'a': 5.143, 'b': 5.383, 'c': 14.902, 'alpha': 90.391, 'beta': 90.014, 'gamma': 89.834}, size=(1, 1, 1)) # Make sure these are the returned cells (verified correct for rmc6f file) va = [5.143, 0.0, 0.0] vb = [0.015596, 5.382977, 0.0] vc = [-0.00364124, -0.101684, 14.901653] write('output.rmc6f', fe4o6) readback = read('output.rmc6f') assert np.allclose(fe4o6.positions, readback.positions, rtol=tol) assert np.allclose(va, readback.cell[0], rtol=tol) assert np.allclose(vb, readback.cell[1], rtol=tol) assert np.allclose(vc, readback.cell[2], rtol=tol) def test_rmc6f_read_construct_regex(): """Test for utility function that constructs rmc6f header regex.""" header_lines = [ "Number of atoms:", " Supercell dimensions: ", " Cell (Ang/deg): ", " Lattice vectors (Ang): "] result = rmc6f._read_construct_regex(header_lines) target = "(Number\\s+of\\s+atoms:|Supercell\\s+dimensions:|Cell\\s+\\(Ang/deg\\):|Lattice\\s+vectors\\s+\\(Ang\\):)" # noqa: E501 assert result == target def test_rmc6f_read_line_of_atoms_section_style_no_labels(): """Test for reading a line of atoms section w/ 'no labels' style for rmc6f """ atom_line = "1 S 0.600452 0.525100 0.442050 1 0 0 0" atom_id, props = rmc6f._read_line_of_atoms_section(atom_line.split()) target_id = 1 target_props = ['S', 0.600452, 0.5251, 0.44205] assert atom_id == target_id assert props == target_props def test_rmc6f_read_line_of_atoms_section_style_labels(): """Test for reading a line of atoms section w/ 'labels'-included style for rmc6f """ atom_line = "1 S [1] 0.600452 0.525100 0.442050 1 0 0 0" atom_id, props = rmc6f._read_line_of_atoms_section(atom_line.split()) target_id = 1 target_props = ['S', 0.600452, 0.5251, 0.44205] assert atom_id == target_id assert props == target_props def test_rmc6f_read_line_of_atoms_section_style_magnetic(): """Test for reading a line of atoms section w/ 'magnetic' style for rmc6f """ atom_line = "1 S 0.600452 0.525100 0.442050 1 0 0 0 M: 0.1" atom_id, props = rmc6f._read_line_of_atoms_section(atom_line.split()) target_id = 1 target_props = ['S', 0.600452, 0.5251, 0.44205, 0.1] assert atom_id == target_id assert props == target_props def test_rmc6f_read_process_rmc6f_lines_to_pos_and_cell(): """Test for utility function that processes lines of rmc6f using regular expressions to capture atom properties and cell information """ tol = 1e-5 lines = rmc6f_input_text.split('\n') props, cell = rmc6f._read_process_rmc6f_lines_to_pos_and_cell(lines) target_cell = np.zeros((3, 3), float) np.fill_diagonal(target_cell, 4.672816) assert props == symbol_xyz_dict assert np.allclose(cell, target_cell, rtol=tol) def test_rmc6f_read_process_rmc6f_lines_to_pos_and_cell_padded_whitespace(): """Test for utility function that processes lines of rmc6f using regular expressions to capture atom properties and cell information with puposeful whitespace padded on one line """ tol = 1e-5 lines = rmc6f_input_text.split('\n') lines[14] = " {} ".format(lines[14]) # intentional whitespace props, cell = rmc6f._read_process_rmc6f_lines_to_pos_and_cell(lines) target_cell = np.zeros((3, 3), float) np.fill_diagonal(target_cell, 4.672816) assert props == symbol_xyz_dict assert np.allclose(cell, target_cell, rtol=tol) def test_rmc6f_write_output_column_format(): """Test for utility function that processes the columns in array and gets back out formatting information. """ cols = ['id', 'symbols', 'scaled_positions', 'ref_num', 'ref_cell'] arrays = {} arrays['id'] = np.array([1, 2, 3, 4, 5, 6, 7]) arrays['symbols'] = np.array(symbols) arrays['ref_num'] = np.zeros(7, int) arrays['ref_cell'] = np.zeros((7, 3), int) arrays['scaled_positions'] = lat_positions / lat ncols, dtype_obj, fmt = rmc6f._write_output_column_format(cols, arrays) target_ncols = [1, 1, 3, 1, 3] target_fmt = "%8d %s%14.6f %14.6f %14.6f %8d %8d %8d %8d \n" assert ncols == target_ncols assert fmt == target_fmt def test_rmc6f_write_output(): """Test for utility function for writing rmc6f output """ fileobj = "output.rmc6f" header_lines = [ '(Version 6f format configuration file)', '(Generated by ASE - Atomic Simulation Environment https://wiki.fysik.dtu.dk/ase/ )', # noqa: E501 "Metadata date:18-007-'2019", 'Number of types of atoms: 2 ', 'Atom types present: S F', 'Number of each atom type: 1 6', 'Number of moves generated: 0', 'Number of moves tried: 0', 'Number of moves accepted: 0', 'Number of prior configuration saves: 0', 'Number of atoms: 7', 'Supercell dimensions: 1 1 1', 'Number density (Ang^-3): 0.06860598423060468', 'Cell (Ang/deg): 4.672816 4.672816 4.672816 90.0 90.0 90.0', 'Lattice vectors (Ang):', ' 4.672816 0.000000 0.000000', ' 0.000000 4.672816 0.000000', ' 0.000000 0.000000 4.672816', 'Atoms:'] data_array = symbol_xyz_list_ext data_dtype = [ ('id', '