def test_get_name_info(self): " Make sure we can get correct info from Name property. " filename = path + "/h_top_c_fcc_far_noname.xsd" xsd = XsdFile(filename) self.assertEqual(xsd.force, 0.0) self.assertEqual(xsd.energy, 0.0) self.assertEqual(xsd.magnetism, 0.0) self.assertTrue(hasattr(xsd, "path"))
def read_xsd(): # Get xsd file for filename in os.listdir('.'): name_list = filename.split('.') if name_list[-1] == 'xsd': xsdname = name_list[0] xsd = XsdFile(filename) break content = 'XSD -->\n' content += " The xsdfile is : \033[31;1;4m%s\033[0m \n" %filename return content, xsd, xsdname
def test_update_name(self): "Make sure we can update Name info." filename = path + "/h_top_c_fcc_far_noname.xsd" xsd = XsdFile(filename) xsd.update_name() for elem in xsd.tree.iter("SymmetrySystem"): name = elem.attrib["Name"] break self.assertTrue("E:" in name) self.assertTrue("F:" in name) self.assertTrue("M:" in name) self.assertTrue("P:" in name)
def test_construction_query(self): " Test OutCar construction and query functions. " filename = path + "/h_top_c_fcc_far.xsd" xsd = XsdFile(filename) # Check query functions. self.assertEqual(xsd.filename, filename) self.assertEqual(xsd.bases_const, 1.0) ref_bases = [[4.31035158, -2.48858265, 0.], [0., 4.97716529, 0.], [0., 0., 18.09575766]] self.assertListEqual(xsd.bases.tolist(), ref_bases) self.assertEqual(xsd.force, 0.048) self.assertEqual(xsd.energy, -100.896) self.assertEqual(xsd.magnetism, 8.25) self.assertTrue(hasattr(xsd, "path"))
def test_bulk_construction(self): " Test XsdFile construction for a bulk. " filename = path + "/bulk.xsd" xsd = XsdFile(filename) # Check the default coordinate value for the Atom3d tag without XYZ. ref_origin_coord = [0.0, 0.0, 0.0] ret_origin_coord = xsd.data[0].tolist() self.assertListEqual(ref_origin_coord, ret_origin_coord) # Check atom info update in new xsd file. temp_file = "{}/temp.xsd".format(path) xsd.tofile(temp_file) tree = ET.parse(temp_file) for atom3d in tree.iter('Atom3d'): break self.assertEqual(atom3d.get('XYZ'), '0.0,0.0,0.0') os.remove(temp_file)
force_info = outcar.atom_forces[max_num - 1, :] pos = force_info[:3].tolist() forces = force_info[3:].tolist() logging.info("{:<15s}: {}".format("max force atom", max_num)) logging.info("{:<15s}: ({}, {}, {})".format("atom position", *pos)) logging.info("{:<15s}: {}, {}, {}".format("forces", *forces)) logging.info("{:<15s}: {}\n".format("total-force", np.linalg.norm(forces))) # Get fort.188 info. if os.path.exists('./fort.188'): with open('fort.188', 'r') as f: atom_info = f.readlines()[5] logging.info("{:<10s}{:<10s}{:<15s}".format("Atom1", "Atom2", "DISTANCE")) logging.info("-" * 30) logging.info("{:<10s}{:<10s}{:<15s}\n".format(*str2list(atom_info))) # Create .xsd file. if args.xsd: status, output = commands.getstatusoutput('ls *.xsd | head -1') if not output.endswith('.xsd'): logging.info("No .xsd file in current directory.") sys.exit(1) xsd = XsdFile(filename=output) # modify atom color xsd.modify_color(atom_number=max_num) jobname = output.split('.')[0] filename = jobname + '-force.xsd' xsd.tofile(filename=filename) print filename + " has been created."
parser = argparse.ArgumentParser() parser.add_argument('-x', '--xsd', \ default='default.xsd', help='xsd File') parser.add_argument('-g', '--gen', \ default='geo_in.gen', help='Gen Format File Name') args = parser.parse_args() # read xsd and get fixes if args.xsd == 'default.xsd': for fname in os.listdir('.'): name_list = fname.split('.') if name_list[-1] == 'xsd': xsdname = name_list[0] xsd = XsdFile(fname) break else: xsd = XsdFile(args.xsd) symbol_dict = {} for i, symbol in enumerate(xsd.atom_types): symbol_dict[symbol] = i + 1 symbols = [] for num, sym in zip(xsd.atom_numbers, xsd.atom_types): symbols.extend([sym] * num) content = (' {:<8d} {:<s}\n').format(xsd.natom, 'F') content += ('{:>4s}' * len(xsd.atom_types) + '\n').format(*xsd.atom_types) for i, (sym, coord) in enumerate(zip(symbols, xsd.data)):