662 lines
20 KiB
Python
662 lines
20 KiB
Python
from diceplayer import logger
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from diceplayer.config.player_config import PlayerConfig
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from diceplayer.shared.environment.atom import Atom
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from diceplayer.shared.environment.molecule import Molecule
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from diceplayer.shared.environment.system import System
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from diceplayer.shared.interface.dice_interface import DiceInterface
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from tests.mocks.mock_inputs import get_config_example
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from tests.mocks.mock_proc import MockConnection, MockProc
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import yaml
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import io
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import unittest
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from unittest import mock
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class TestDiceInterface(unittest.TestCase):
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def setUp(self):
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logger.set_logger(stream=io.StringIO())
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config = yaml.load(get_config_example(), Loader=yaml.Loader)
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self.config = PlayerConfig.from_dict(config["diceplayer"])
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def test_class_instantiation(self):
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dice = DiceInterface()
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self.assertIsInstance(dice, DiceInterface)
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def test_configure(self):
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dice = DiceInterface()
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self.assertIsNone(dice.step)
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self.assertIsNone(dice.system)
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# Ignoring the types for testing purposes
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dice.configure(self.config, System())
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self.assertIsNotNone(dice.step)
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self.assertIsNotNone(dice.system)
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def test_reset(self):
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dice = DiceInterface()
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dice.configure(self.config, System())
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self.assertTrue(hasattr(dice, "step"))
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self.assertTrue(hasattr(dice, "system"))
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dice.reset()
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self.assertFalse(hasattr(dice, "step"))
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self.assertFalse(hasattr(dice, "system"))
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@mock.patch("diceplayer.shared.interface.dice_interface.Process", MockProc())
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@mock.patch("diceplayer.shared.interface.dice_interface.connection", MockConnection)
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def test_start(self):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.start(1)
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@mock.patch("diceplayer.shared.interface.dice_interface.connection", MockConnection)
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@mock.patch(
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"diceplayer.shared.interface.dice_interface.Process", MockProc(exitcode=1)
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)
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def test_start_with_process_error(self):
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dice = DiceInterface()
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dice.configure(self.config, System())
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with self.assertRaises(SystemExit):
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dice.start(1)
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def test_simulation_process_raises_exception(self):
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dice = DiceInterface()
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with self.assertRaises(SystemExit):
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dice._simulation_process(1, 1)
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@mock.patch(
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"diceplayer.shared.interface.dice_interface.DiceInterface._make_proc_dir"
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)
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@mock.patch(
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"diceplayer.shared.interface.dice_interface.DiceInterface._make_dice_inputs"
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)
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@mock.patch("diceplayer.shared.interface.dice_interface.DiceInterface._run_dice")
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def test_simulation_process(
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self, mock_run_dice, mock_make_dice_inputs, mock_make_proc_dir
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):
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dice = DiceInterface()
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dice._simulation_process(1, 1)
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self.assertTrue(dice._make_proc_dir.called)
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self.assertTrue(dice._make_dice_inputs.called)
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self.assertTrue(dice._run_dice.called)
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@mock.patch("diceplayer.shared.interface.dice_interface.Path.mkdir")
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@mock.patch("diceplayer.shared.interface.dice_interface.Path.exists")
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def test_make_proc_dir_if_simdir_exists(self, mock_path_exists, mock_path_mkdir):
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dice = DiceInterface()
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dice.configure(self.config, System())
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mock_path_exists.return_value = False
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dice._make_proc_dir(1, 1)
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self.assertEqual(mock_path_mkdir.call_count, 2)
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@mock.patch("diceplayer.shared.interface.dice_interface.Path.mkdir")
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@mock.patch("diceplayer.shared.interface.dice_interface.Path.exists")
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def test_make_proc_dir_if_simdir_doesnt_exists(
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self, mock_path_exists, mock_path_mkdir
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):
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dice = DiceInterface()
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dice.configure(self.config, System())
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mock_path_exists.return_value = False
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dice._make_proc_dir(1, 1)
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self.assertEqual(mock_path_mkdir.call_count, 2)
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def test_make_dice_seed(self):
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seed = DiceInterface._make_dice_seed()
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self.assertIsInstance(seed, int)
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def test_make_dice_inputs_nstep_len_two_with_randoninit_first_cycle_one(self):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.step.dice.nstep = [1, 1]
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dice._make_potentials = mock.Mock()
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dice._make_init_file = mock.Mock()
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dice._new_density = mock.Mock()
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dice._make_nvt_ter = mock.Mock()
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dice._make_nvt_eq = mock.Mock()
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dice._make_npt_ter = mock.Mock()
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dice._make_npt_eq = mock.Mock()
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dice._make_dice_inputs(1, 1)
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self.assertTrue(dice._make_potentials.called)
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self.assertFalse(dice._make_init_file.called)
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self.assertFalse(dice._new_density.called)
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self.assertTrue(dice._make_nvt_ter.called)
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self.assertTrue(dice._make_nvt_eq.called)
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self.assertFalse(dice._make_npt_ter.called)
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self.assertFalse(dice._make_npt_eq.called)
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@mock.patch("builtins.open", new_callable=mock.mock_open, read_data="test")
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@mock.patch(
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"diceplayer.shared.interface.dice_interface.Path.exists", return_value=True
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)
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def test_make_dice_inputs_nstep_len_two_with_randoninit_first_cycle_two(
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self, mock_path_exists, mock_open
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):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.step.dice.nstep = [1, 1]
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dice._make_potentials = mock.Mock()
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dice._make_init_file = mock.Mock()
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dice._new_density = mock.Mock()
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dice._make_nvt_ter = mock.Mock()
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dice._make_nvt_eq = mock.Mock()
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dice._make_npt_ter = mock.Mock()
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dice._make_npt_eq = mock.Mock()
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dice._make_dice_inputs(2, 1)
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self.assertTrue(dice._make_potentials.called)
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self.assertTrue(dice._make_init_file.called)
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self.assertTrue(dice._new_density.called)
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self.assertFalse(dice._make_nvt_ter.called)
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self.assertTrue(dice._make_nvt_eq.called)
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self.assertFalse(dice._make_npt_ter.called)
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self.assertFalse(dice._make_npt_eq.called)
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@mock.patch(
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"diceplayer.shared.interface.dice_interface.Path.exists", return_value=False
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)
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def test_make_dice_inputs_raises_exception_on_last_not_found(
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self, mock_path_exists
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):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.step.dice.nstep = [1, 1]
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dice._make_potentials = mock.Mock()
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dice._make_init_file = mock.Mock()
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dice._new_density = mock.Mock()
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dice._make_nvt_ter = mock.Mock()
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dice._make_nvt_eq = mock.Mock()
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dice._make_npt_ter = mock.Mock()
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dice._make_npt_eq = mock.Mock()
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with self.assertRaises(FileNotFoundError):
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dice._make_dice_inputs(2, 1)
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def test_make_dice_inputs_nstep_len_three_with_randoninit_first_cycle_one(self):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice._make_potentials = mock.Mock()
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dice._make_init_file = mock.Mock()
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dice._new_density = mock.Mock()
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dice._make_nvt_ter = mock.Mock()
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dice._make_nvt_eq = mock.Mock()
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dice._make_npt_ter = mock.Mock()
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dice._make_npt_eq = mock.Mock()
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dice._make_dice_inputs(1, 1)
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self.assertTrue(dice._make_potentials.called)
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self.assertFalse(dice._make_init_file.called)
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self.assertFalse(dice._new_density.called)
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self.assertTrue(dice._make_nvt_ter.called)
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self.assertFalse(dice._make_nvt_eq.called)
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self.assertTrue(dice._make_npt_ter.called)
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self.assertTrue(dice._make_npt_eq.called)
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@mock.patch("diceplayer.shared.interface.dice_interface.os")
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@mock.patch("diceplayer.shared.interface.dice_interface.shutil")
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@mock.patch(
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"diceplayer.shared.interface.dice_interface.Path.exists", return_value=True
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)
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def test_run_dice_on_first_cycle_run_successful(
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self, mock_path_exists, mock_shutils, mock_os
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):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.step.dice.nstep = [1, 1, 1]
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dice.run_dice_file = mock.Mock()
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dice._run_dice(1, 1)
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self.assertTrue(mock_os.getcwd.called)
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self.assertTrue(mock_os.chdir.called)
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self.assertEqual(dice.run_dice_file.call_count, 3)
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self.assertTrue(mock_shutils.copy.called)
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.step.dice.nstep = [1, 1]
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dice.run_dice_file = mock.Mock()
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dice._run_dice(1, 1)
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self.assertTrue(mock_os.getcwd.called)
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self.assertTrue(mock_os.chdir.called)
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self.assertEqual(dice.run_dice_file.call_count, 2)
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self.assertTrue(mock_shutils.copy.called)
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@mock.patch("diceplayer.shared.interface.dice_interface.os")
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@mock.patch("diceplayer.shared.interface.dice_interface.shutil")
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@mock.patch(
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"diceplayer.shared.interface.dice_interface.Path.exists", return_value=True
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)
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def test_run_dice_on_second_cycle_run_successful(
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self, mock_path_exists, mock_shutils, mock_os
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):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.run_dice_file = mock.Mock()
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dice._run_dice(2, 1)
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self.assertTrue(mock_os.getcwd.called)
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self.assertTrue(mock_os.chdir.called)
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self.assertEqual(dice.run_dice_file.call_count, 2)
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self.assertTrue(mock_shutils.copy.called)
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.run_dice_file = mock.Mock()
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dice._run_dice(2, 1)
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self.assertTrue(mock_os.getcwd.called)
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self.assertTrue(mock_os.chdir.called)
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self.assertEqual(dice.run_dice_file.call_count, 1)
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self.assertTrue(mock_shutils.copy.called)
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@mock.patch("diceplayer.shared.interface.dice_interface.os")
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@mock.patch("diceplayer.shared.interface.dice_interface.shutil")
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@mock.patch(
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"diceplayer.shared.interface.dice_interface.Path.exists", return_value=False
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)
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def test_run_dice_on_second_cycle_run_successful(
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self, mock_path_exists, mock_shutils, mock_os
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):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.run_dice_file = mock.Mock()
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with self.assertRaises(FileNotFoundError):
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dice._run_dice(1, 1)
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@mock.patch("builtins.open", new_callable=mock.mock_open)
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def test_make_init_file(self, mock_open):
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example_atom = Atom(
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lbl=1,
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na=1,
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rx=1.0,
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ry=1.0,
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rz=1.0,
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chg=1.0,
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eps=1.0,
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sig=1.0,
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)
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main_molecule = Molecule("main_molecule")
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main_molecule.add_atom(example_atom)
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secondary_molecule = Molecule("secondary_molecule")
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secondary_molecule.add_atom(example_atom)
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system = System()
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system.add_type(main_molecule)
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system.add_type(secondary_molecule)
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dice = DiceInterface()
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dice.configure(self.config, system)
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dice.step.dice.nmol = [1, 1]
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last_xyz_file = io.StringIO()
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last_xyz_file.writelines(
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[
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" TEST\n",
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" Configuration number : TEST = TEST TEST TEST\n",
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" H 1.00000 1.00000 1.00000\n",
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" H 1.00000 1.00000 1.00000\n",
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]
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)
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last_xyz_file.seek(0)
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dice._make_init_file("test", last_xyz_file)
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mock_handler = mock_open()
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calls = mock_handler.write.call_args_list
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lines = list(map(lambda x: x[0][0], calls))
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expected_lines = [
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" 1.000000 1.000000 1.000000\n",
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" 1.000000 1.000000 1.000000\n",
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"$end",
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]
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self.assertEqual(lines, expected_lines)
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@mock.patch("builtins.open", new_callable=mock.mock_open)
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def test_new_density(self, mock_open):
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example_atom = Atom(
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lbl=1,
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na=1,
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rx=1.0,
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ry=1.0,
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rz=1.0,
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chg=1.0,
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eps=1.0,
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sig=1.0,
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)
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main_molecule = Molecule("main_molecule")
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main_molecule.add_atom(example_atom)
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secondary_molecule = Molecule("secondary_molecule")
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secondary_molecule.add_atom(example_atom)
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system = System()
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system.add_type(main_molecule)
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system.add_type(secondary_molecule)
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dice = DiceInterface()
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dice.configure(self.config, system)
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last_xyz_file = io.StringIO()
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last_xyz_file.writelines(
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[
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" TEST\n",
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" Configuration number : TEST = 1 1 1\n",
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" H 1.00000 1.00000 1.00000\n",
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" H 1.00000 1.00000 1.00000\n",
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]
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)
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last_xyz_file.seek(0)
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density = dice._new_density(last_xyz_file)
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self.assertEqual(density, 85.35451545000001)
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@mock.patch("builtins.open", new_callable=mock.mock_open)
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@mock.patch("diceplayer.shared.interface.dice_interface.random")
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def test_make_nvt_ter(self, mock_random, mock_open):
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mock_random.random.return_value = 1
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice._make_nvt_ter(1, "test")
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mock_handler = mock_open()
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calls = mock_handler.write.call_args_list
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lines = list(map(lambda x: x[0][0], calls))
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expected_lines = [
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"title = Diceplayer run - NVT Thermalization\n",
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"ncores = 4\n",
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"ljname = phb.ljc\n",
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"outname = phb\n",
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"nmol = 1 50\n",
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"dens = 0.75\n",
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"temp = 300.0\n",
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"init = yes\n",
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"nstep = 2000\n",
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"vstep = 0\n",
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"mstop = 1\n",
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"accum = no\n",
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"iprint = 1\n",
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"isave = 0\n",
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"irdf = 0\n",
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"seed = 1000000\n",
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"upbuf = 360",
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]
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self.assertEqual(lines, expected_lines)
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@mock.patch("builtins.open", new_callable=mock.mock_open)
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@mock.patch("diceplayer.shared.interface.dice_interface.random")
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def test_make_nvt_eq(self, mock_random, mock_open):
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mock_random.random.return_value = 1
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice._make_nvt_eq(1, "test")
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mock_handler = mock_open()
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calls = mock_handler.write.call_args_list
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lines = list(map(lambda x: x[0][0], calls))
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expected_lines = [
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"title = Diceplayer run - NVT Production\n",
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"ncores = 4\n",
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"ljname = phb.ljc\n",
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"outname = phb\n",
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"nmol = 1 50\n",
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"dens = 0.75\n",
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"temp = 300.0\n",
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"init = no\n",
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"nstep = 3000\n",
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"vstep = 0\n",
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"mstop = 1\n",
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"accum = no\n",
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"iprint = 1\n",
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"isave = 1000\n",
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"irdf = 40\n",
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"seed = 1000000\n",
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]
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self.assertEqual(lines, expected_lines)
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@mock.patch("builtins.open", new_callable=mock.mock_open)
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@mock.patch("diceplayer.shared.interface.dice_interface.random")
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def test_make_npt_ter(self, mock_random, mock_open):
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mock_random.random.return_value = 1
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dice = DiceInterface()
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dice.configure(self.config, System())
|
|
|
|
dice._make_npt_ter(1, "test")
|
|
|
|
mock_handler = mock_open()
|
|
calls = mock_handler.write.call_args_list
|
|
|
|
lines = list(map(lambda x: x[0][0], calls))
|
|
|
|
expected_lines = [
|
|
"title = Diceplayer run - NPT Thermalization\n",
|
|
"ncores = 4\n",
|
|
"ljname = phb.ljc\n",
|
|
"outname = phb\n",
|
|
"nmol = 1 50\n",
|
|
"press = 1.0\n",
|
|
"temp = 300.0\n",
|
|
"init = no\n",
|
|
"vstep = 600\n",
|
|
"nstep = 5\n",
|
|
"mstop = 1\n",
|
|
"accum = no\n",
|
|
"iprint = 1\n",
|
|
"isave = 0\n",
|
|
"irdf = 0\n",
|
|
"seed = 1000000\n",
|
|
]
|
|
|
|
self.assertEqual(lines, expected_lines)
|
|
|
|
@mock.patch("builtins.open", new_callable=mock.mock_open)
|
|
@mock.patch("diceplayer.shared.interface.dice_interface.random")
|
|
def test_make_npt_eq(self, mock_random, mock_open):
|
|
mock_random.random.return_value = 1
|
|
|
|
dice = DiceInterface()
|
|
dice.configure(self.config, System())
|
|
|
|
dice._make_npt_eq("test")
|
|
|
|
mock_handler = mock_open()
|
|
calls = mock_handler.write.call_args_list
|
|
|
|
lines = list(map(lambda x: x[0][0], calls))
|
|
|
|
expected_lines = [
|
|
"title = Diceplayer run - NPT Production\n",
|
|
"ncores = 4\n",
|
|
"ljname = phb.ljc\n",
|
|
"outname = phb\n",
|
|
"nmol = 1 50\n",
|
|
"press = 1.0\n",
|
|
"temp = 300.0\n",
|
|
"nstep = 5\n",
|
|
"vstep = 800\n",
|
|
"init = no\n",
|
|
"mstop = 1\n",
|
|
"accum = no\n",
|
|
"iprint = 1\n",
|
|
"isave = 1000\n",
|
|
"irdf = 40\n",
|
|
"seed = 1000000\n",
|
|
]
|
|
|
|
self.assertEqual(lines, expected_lines)
|
|
|
|
@mock.patch("builtins.open", new_callable=mock.mock_open)
|
|
def test_make_potentials(self, mock_open):
|
|
example_atom = Atom(
|
|
lbl=1,
|
|
na=1,
|
|
rx=1.0,
|
|
ry=1.0,
|
|
rz=1.0,
|
|
chg=1.0,
|
|
eps=1.0,
|
|
sig=1.0,
|
|
)
|
|
|
|
main_molecule = Molecule("main_molecule")
|
|
main_molecule.add_atom(example_atom)
|
|
|
|
secondary_molecule = Molecule("secondary_molecule")
|
|
secondary_molecule.add_atom(example_atom)
|
|
|
|
system = System()
|
|
system.add_type(main_molecule)
|
|
system.add_type(secondary_molecule)
|
|
|
|
dice = DiceInterface()
|
|
dice.configure(self.config, system)
|
|
|
|
dice._make_potentials("test")
|
|
|
|
mock_handler = mock_open()
|
|
calls = mock_handler.write.call_args_list
|
|
|
|
lines = list(map(lambda x: x[0][0], calls))
|
|
|
|
expected_lines = [
|
|
"*\n",
|
|
"2\n",
|
|
"1 main_molecule\n",
|
|
"1 1 1.00000 1.00000 1.00000 1.000000 1.00000 1.0000\n",
|
|
"1 secondary_molecule\n",
|
|
"1 1 1.00000 1.00000 1.00000 1.000000 1.00000 1.0000\n",
|
|
]
|
|
|
|
self.assertEqual(lines, expected_lines)
|
|
|
|
@mock.patch("diceplayer.shared.interface.dice_interface.subprocess")
|
|
@mock.patch(
|
|
"builtins.open",
|
|
new_callable=mock.mock_open,
|
|
read_data="End of simulation\nBLABLA",
|
|
)
|
|
def test_run_dice_file(self, mock_open, mock_subprocess):
|
|
mock_subprocess.call.return_value = 0
|
|
dice = DiceInterface()
|
|
dice.configure(self.config, System())
|
|
|
|
dice.run_dice_file(1, 1, "test")
|
|
|
|
self.assertTrue(mock_subprocess.call.called)
|
|
self.assertTrue(mock_open.called)
|
|
|
|
@mock.patch("diceplayer.shared.interface.dice_interface.subprocess")
|
|
@mock.patch("builtins.open", new_callable=mock.mock_open, read_data="Error\nBLABLA")
|
|
def test_run_dice_file_raises_runtime_error_on_dice_file(
|
|
self, mock_open, mock_subprocess
|
|
):
|
|
mock_subprocess.call.return_value = 0
|
|
dice = DiceInterface()
|
|
dice.configure(self.config, System())
|
|
|
|
with self.assertRaises(RuntimeError):
|
|
dice.run_dice_file(1, 1, "test")
|
|
|
|
@mock.patch("diceplayer.shared.interface.dice_interface.subprocess")
|
|
@mock.patch(
|
|
"builtins.open",
|
|
new_callable=mock.mock_open,
|
|
read_data="End of simulation\nBLABLA",
|
|
)
|
|
def test_run_dice_file_raises_runtime_error_of_dice_exit_code(
|
|
self, mock_open, mock_subprocess
|
|
):
|
|
mock_subprocess.call.return_value = 1
|
|
dice = DiceInterface()
|
|
dice.configure(self.config, System())
|
|
|
|
with self.assertRaises(RuntimeError):
|
|
dice.run_dice_file(1, 1, "test")
|
|
|
|
|
|
if __name__ == "__main__":
|
|
unittest.main()
|