用于与 GULP、LAMMPS 和 VASP 接口的结构和相位预测的遗传算法_python_代码_下载

# Copyright (c) Henniggroup. # Distributed under the terms of the MIT License. from __future__ import division, unicode_literals, print_function """ Test module: This module contains the unit tests for GASP. """ from gasp import general, development, variations, population, \ energy_calculators, organism_creators, objects_maker from gasp import geometry as geo from pymatgen.core.periodic_table import Element import unittest import random import copy import numpy as np import os import shutil import tempfile class TestIDGenerator(unittest.TestCase): def setUp(self): self.id_generator = general.IDGenerator() def test_initial_id_value(self): self.assertEqual(self.id_generator.id, 0) def test_incrementing_value(self): first_id = self.id_generator.make_id() second_id = self.id_generator.make_id() self.assertEqual(first_id + 1, second_id) class TestMating(unittest.TestCase): def setUp(self): mating_params = {'fraction': 0.1} self.mating = variations.Mating(mating_params) # get the current working directory and make a copy of it self.starting_cwd = copy.deepcopy(os.getcwd()) # make a temporary directory and move into it self.temp_dir = tempfile.mkdtemp() os.chdir(self.temp_dir) def tearDown(self): # move back to the original working directory os.chdir(self.starting_cwd) # delete the temporary directory shutil.rmtree(self.temp_dir) def test_double_parent(self): # make a cell to test species = [Element('Cu')] coords = [[0.5, 0.5, 0.5]] lattice = [[1, 0, 0], [0, 2, 0], [0, 0, 3]] cell = general.Cell(lattice, species, coords) old_lattice_lengths = copy.deepcopy(cell.lattice.abc) old_num_atoms = copy.deepcopy(cell.num_sites) old_volume = copy.deepcopy(cell.lattice.volume) # test with bulk geometry geometry = geo.Bulk() self.mating.double_parent(cell, geometry) self.assertEqual(round(cell.lattice.a, 5), round(2*old_lattice_lengths[0], 5)) self.assertEqual(round(cell.lattice.b, 5), round(old_lattice_lengths[1], 5)) self.assertEqual(round(cell.lattice.c, 5), round(old_lattice_lengths[2], 5)) self.assertEqual(round(cell.lattice.volume, 5), round(2*old_volume, 5)) self.assertEqual(cell.num_sites, 2*old_num_atoms) # test a cell with a different lattice lattice = [[3, 0, 0], [0, 1, 0], [0, 0, 2]] cell = general.Cell(lattice, species, coords) old_lattice_lengths = copy.deepcopy(cell.lattice.abc) old_num_atoms = copy.deepcopy(cell.num_sites) old_volume = copy.deepcopy(cell.lattice.volume) self.mating.double_parent(cell, geometry) self.assertEqual(round(cell.lattice.a, 5), round(old_lattice_lengths[0], 5)) self.assertEqual(round(cell.lattice.b, 5), round(2*old_lattice_lengths[1], 5)) self.assertEqual(round(cell.lattice.c, 5), round(old_lattice_lengths[2], 5)) self.assertEqual(round(cell.lattice.volume, 5), round(2*old_volume, 5)) self.assertEqual(cell.num_sites, 2*old_num_atoms) # test a cell with a different lattice lattice = [[3, 0, 0], [0, 2, 0], [0, 0, 1]] cell = general.Cell(lattice, species, coords) old_lattice_lengths = copy.deepcopy(cell.lattice.abc) old_num_atoms = copy.deepcopy(cell.num_sites) old_volume = copy.deepcopy(cell.lattice.volume) self.mating.double_parent(cell, geometry) self.assertEqual(round(cell.lattice.a, 5), round(old_lattice_lengths[0], 5)) self.assertEqual(round(cell.lattice.b, 5), round(old_lattice_lengths[1], 5)) self.assertEqual(round(cell.lattice.c, 5), round(2*old_lattice_lengths[2], 5)) self.assertEqual(round(cell.lattice.volume, 5), round(2*old_volume, 5)) self.assertEqual(cell.num_sites, 2*old_num_atoms) # test a cell with a random lattice lattice = [ [random.uniform(-5, 5), random.uniform(-5, 5), random.uniform(-5, 5)], [random.uniform(-5, 5), random.uniform(-5, 5), random.uniform(-5, 5)], [random.uniform(-5, 5), random.uniform(-5, 5), random.uniform(-5, 5)]] cell = general.Cell(lattice, species, coords) old_num_atoms = copy.deepcopy(cell.num_sites) old_volume = copy.deepcopy(cell.lattice.volume) self.mating.double_parent(cell, geometry) self.assertEqual(round(cell.lattice.volume, 5), round(2*old_volume, 5)) self.assertEqual(cell.num_sites, 2*old_num_atoms) # test with sheet geometry geometry = geo.Sheet({'shape': 'sheet'}) lattice = [[1, 0, 0], [0, 2, 0], [0, 0, 3]] cell = general.Cell(lattice, species, coords) old_lattice_lengths = copy.deepcopy(cell.lattice.abc) old_num_atoms = copy.deepcopy(cell.num_sites) old_volume = cell.lattice.volume self.mating.double_parent(cell, geometry) self.assertEqual(round(cell.lattice.a, 5), round(2*old_lattice_lengths[0], 5)) self.assertEqual(round(cell.lattice.b, 5), round(old_lattice_lengths[1], 5)) self.assertEqual(round(cell.lattice.c, 5), round(old_lattice_lengths[2], 5)) self.assertEqual(round(cell.lattice.volume, 5), round(2*old_volume, 5)) self.assertEqual(cell.num_sites, 2*old_num_atoms) # test a cell with a different lattice lattice = [[3, 0, 0], [0, 1, 0], [0, 0, 2]] cell = general.Cell(lattice, species, coords) old_lattice_lengths = copy.deepcopy(cell.lattice.abc) old_num_atoms = copy.deepcopy(cell.num_sites) old_volume = cell.lattice.volume self.mating.double_parent(cell, geometry) self.assertEqual(round(cell.lattice.a, 5), round(old_lattice_lengths[0], 5)) self.assertEqual(round(cell.lattice.b, 5), round(2*old_lattice_lengths[1], 5)) self.assertEqual(round(cell.lattice.c, 5), round(old_lattice_lengths[2], 5)) self.assertEqual(round(cell.lattice.volume, 5), round(2*old_volume, 5)) self.assertEqual(cell.num_sites, 2*old_num_atoms) # test a cell with a different lattice lattice = [[3, 0, 0], [0, 2, 0], [0, 0, 1]] cell = general.Cell(lattice, species, coords) old_lattice_lengths = copy.deepcopy(cell.lattice.abc) old_num_atoms = copy.deepcopy(cell.num_sites) old_volume = cell.lattice.volume self.mating.double_parent(cell, geometry) self.assertEqual(round(cell.lattice.a, 5), round(old_lattice_lengths[0], 5)) self.assertEqual(round(cell.lattice.b, 5), round(2*old_lattice_lengths[1], 5)) self.assertEqual(round(cell.lattice.c, 5), round(old_lattice_lengths[2], 5)) self.assertEqual(round(cell.lattice.volume, 5), round(2*old_volume, 5)) self.assertEqual(cell.num_sites, 2*old_num_atoms) # test a cell with a random lattice lattice = [ [random.uniform(-5, 5), random.uniform(-5, 5), random.uniform(-5, 5)], [random.uniform(-5, 5), random.uniform(-5, 5), random.uniform(-5, 5)], [random.uniform(-5, 5), random.uniform(-5, 5), random.uniform(-5, 5)]] cell = general.Cell(lattice, species, coords) old_num_atoms = copy.deepcopy(cell.num_sites) old_volume = copy.deepcopy(cell.lattice.volume) self.mating.double_parent(cell, geometr