Merge pull request #199 from pyiron/extend_test

More tests

Author: jan-janssen

tests/test_ase_constraints.py

@@ -1,9 +1,18 @@
+import logging
 import unittest
 
 from ase.build import bulk
+from ase.constraints import FixAtoms, FixedPlane, FixCom
 import numpy as np
 
 from pylammpsmpi import LammpsASELibrary, LammpsLibrary
+from pylammpsmpi.wrapper.ase import (
+    cell_is_skewed,
+    get_species_symbols,
+    get_structure_indices,
+    get_lammps_indicies_from_ase_structure,
+    set_selective_dynamics,
+)
 
 
 class TestLammpsASELibrary(unittest.TestCase):
@@ -12,13 +21,13 @@ def test_static(self):
             working_directory=None,
             cores=1,
             comm=None,
-            logger=None,
+            logger=logging.getLogger("TestStaticLogger"),
             log_file=None,
             library=LammpsLibrary(cores=2, mode='local'),
             diable_log_file=True,
         )
         structure = bulk("Al", cubic=True).repeat([2, 2, 2])
-        lmp.interactive_lib_command(command="units	lj")
+        lmp.interactive_lib_command(command="units lj")
         lmp.interactive_lib_command(command="atom_style atomic")
         lmp.interactive_lib_command(command="atom_modify map array")
         lmp.interactive_structure_setter(
@@ -32,6 +41,8 @@ def test_static(self):
         )
         lmp.interactive_lib_command("pair_style lj/cut 6.0")
         lmp.interactive_lib_command("pair_coeff 1 1 1.0 1.0 4.04")
+        lmp.interactive_lib_command(command="thermo_style custom step temp pe etotal pxx pxy pxz pyy pyz pzz vol")
+        lmp.interactive_lib_command(command="thermo_modify format float %20.15g")
         lmp.interactive_lib_command("run 0")
         self.assertTrue(np.all(np.isclose(lmp.interactive_cells_getter(), structure.cell.array)))
         self.assertTrue(np.isclose(lmp.interactive_energy_pot_getter(), -0.04342932384411341))
@@ -41,20 +52,26 @@ def test_static(self):
         self.assertTrue(np.all(lmp.interactive_indices_getter() == [1] * len(structure)))
         self.assertEqual(lmp.interactive_steps_getter(), 0)
         self.assertEqual(lmp.interactive_temperatures_getter(), 0)
+        self.assertTrue(np.isclose(np.sum(lmp.interactive_pressures_getter()), -0.015661731917941832))
+        self.assertEqual(np.sum(lmp.interactive_velocities_getter()), 0.0)
+        self.assertTrue(np.isclose(np.sum(lmp.interactive_positions_getter()), 291.6))
+        lmp.interactive_cells_setter(cell=1.01 * structure.cell.array)
+        lmp.interactive_lib_command("run 0")
+        self.assertTrue(np.all(np.isclose(lmp.interactive_cells_getter(), 1.01 * structure.cell.array)))
         lmp.close()
 
     def test_static_with_statement(self):
         structure = bulk("Al").repeat([2, 2, 2])
         with LammpsASELibrary(
             working_directory=None,
-            cores=1,
+            cores=2,
             comm=None,
             logger=None,
             log_file=None,
-            library=LammpsLibrary(cores=2, mode='local'),
+            library=None,
             diable_log_file=True,
         ) as lmp:
-            lmp.interactive_lib_command(command="units	lj")
+            lmp.interactive_lib_command(command="units lj")
             lmp.interactive_lib_command(command="atom_style atomic")
             lmp.interactive_lib_command(command="atom_modify map array")
             lmp.interactive_structure_setter(
@@ -68,6 +85,8 @@ def test_static_with_statement(self):
             )
             lmp.interactive_lib_command("pair_style lj/cut 6.0")
             lmp.interactive_lib_command("pair_coeff 1 1 1.0 1.0 4.04")
+            lmp.interactive_lib_command(command="thermo_style custom step temp pe etotal pxx pxy pxz pyy pyz pzz vol")
+            lmp.interactive_lib_command(command="thermo_modify format float %20.15g")
             lmp.interactive_lib_command("run 0")
             self.assertTrue(np.isclose(lmp.interactive_energy_pot_getter(), -0.3083820387630098))
             self.assertTrue(np.isclose(lmp.interactive_energy_tot_getter(), -0.3083820387630098))
@@ -76,3 +95,98 @@ def test_static_with_statement(self):
             self.assertTrue(np.all(lmp.interactive_indices_getter() == [1] * len(structure)))
             self.assertEqual(lmp.interactive_steps_getter(), 0)
             self.assertEqual(lmp.interactive_temperatures_getter(), 0)
+            self.assertTrue(np.isclose(np.sum(lmp.interactive_pressures_getter()), -0.00937227406237915))
+            self.assertEqual(np.sum(lmp.interactive_velocities_getter()), 0.0)
+
+
+class TestASEHelperFunctions(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        cls.structure_skewed = bulk("Al").repeat([2, 2, 2])
+        cls.structure_cubic = bulk("Al", cubic=True).repeat([2, 2, 2])
+
+    def test_get_species_symbols(self):
+        self.assertEqual(get_species_symbols(structure=self.structure_cubic),['Al'])
+
+    def test_get_structure_indices(self):
+        indicies = get_structure_indices(structure=self.structure_cubic)
+        self.assertEqual(len(indicies), len(self.structure_cubic))
+        self.assertEqual(len(set(indicies)), 1)
+        self.assertEqual(set(indicies), {0})
+
+    def test_cell_is_skewed(self):
+        self.assertTrue(cell_is_skewed(cell=self.structure_skewed.cell))
+        self.assertFalse(cell_is_skewed(cell=self.structure_cubic.cell))
+
+    def test_get_lammps_indicies_from_ase_structure(self):
+        indicies = get_lammps_indicies_from_ase_structure(
+            structure=self.structure_cubic,
+            el_eam_lst=["Al", "H"]
+        )
+        self.assertEqual(len(indicies), len(self.structure_cubic))
+        self.assertEqual(len(set(indicies)), 1)
+        self.assertEqual(set(indicies), {1})
+
+
+class TestConstraints(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        structure = bulk("Cu", cubic=True)
+        structure.symbols[2:] = "Al"
+        cls.structure = structure
+
+    def test_selective_dynamics_mixed_calcmd(self):
+        atoms = self.structure.copy()
+        c1 = FixAtoms(indices=[atom.index for atom in atoms if atom.symbol == 'Cu'])
+        c2 = FixedPlane(
+            [atom.index for atom in atoms if atom.symbol == 'Al'],
+            [1, 0, 0],
+        )
+        atoms.set_constraint([c1, c2])
+        control_dict = set_selective_dynamics(structure=atoms, calc_md=True)
+        self.assertEqual(len(control_dict), 6)
+        self.assertTrue(control_dict['group constraintxyz'], 'id 1 2')
+        self.assertTrue(control_dict['fix constraintxyz'], 'constraintxyz setforce 0.0 0.0 0.0')
+        self.assertTrue(control_dict['velocity constraintxyz'], 'set 0.0 0.0 0.0')
+        self.assertTrue(control_dict['group constraintx'], 'id 3 4')
+        self.assertTrue(control_dict['fix constraintx'], 'constraintx setforce 0.0 NULL NULL')
+        self.assertTrue(control_dict['velocity constraintx'], 'set 0.0 NULL NULL')
+
+    def test_selective_dynamics_mixed(self):
+        atoms = self.structure.copy()
+        c1 = FixAtoms(indices=[atom.index for atom in atoms if atom.symbol == 'Cu'])
+        c2 = FixedPlane(
+            [atom.index for atom in atoms if atom.symbol == 'Al'],
+            [1, 0, 0],
+        )
+        atoms.set_constraint([c1, c2])
+        control_dict = set_selective_dynamics(structure=atoms, calc_md=False)
+        self.assertEqual(len(control_dict), 4)
+        self.assertTrue(control_dict['group constraintxyz'], 'id 1 2')
+        self.assertTrue(control_dict['fix constraintxyz'], 'constraintxyz setforce 0.0 0.0 0.0')
+        self.assertTrue(control_dict['group constraintx'], 'id 3 4')
+        self.assertTrue(control_dict['fix constraintx'], 'constraintx setforce 0.0 NULL NULL')
+
+    def test_selective_dynamics_single_fix(self):
+        atoms = self.structure.copy()
+        c1 = FixAtoms(indices=[atom.index for atom in atoms if atom.symbol == 'Cu'])
+        atoms.set_constraint(c1)
+        control_dict = set_selective_dynamics(structure=atoms, calc_md=False)
+        self.assertEqual(len(control_dict), 2)
+        self.assertTrue(control_dict['group constraintxyz'], 'id 1 2')
+        self.assertTrue(control_dict['fix constraintxyz'], 'constraintxyz setforce 0.0 0.0 0.0')
+
+    def test_selective_dynamics_errors(self):
+        atoms = self.structure.copy()
+        atoms.set_constraint(FixCom())
+        with self.assertRaises(ValueError):
+            set_selective_dynamics(structure=atoms, calc_md=False)
+
+    def test_selective_dynamics_wrong_plane(self):
+        atoms = self.structure.copy()
+        atoms.set_constraint(FixedPlane(
+            [atom.index for atom in atoms if atom.symbol == 'Al'],
+            [2, 1, 0],
+        ))
+        with self.assertRaises(ValueError):
+            set_selective_dynamics(structure=atoms, calc_md=False)