ASEInterface: removed unnecessary type-mapping

Author: reinaual

src/python/espressomd/plugins/ase.py

@@ -32,36 +32,24 @@ class ASEInterface:
     ASE interface for ESPResSo.
     """
 
-    type_mapping: dict
-    """
-    Mapping of ESPResSo particle types to ASE symbols. E.g. ``{0: "H", 1: "O"}``.
-    """
     _system: typing.Union["System", None] = None
 
     def register_system(self, system):
         """Register the system."""
         self._system = system
 
-    def __getstate__(self):
-        return {"type_mapping": self.type_mapping}
-
     def get(self, folded=False) -> ase.Atoms:
         """Export the ESPResSo system particle data to an ASE atoms object."""
         particles = self._system.part.all()
         positions = np.copy(particles.pos_folded if folded else particles.pos)
         types = np.copy(particles.type)
         forces = np.copy(particles.f)
-        unknown_types = set(types) - set(self.type_mapping)
-        if unknown_types:
-            raise RuntimeError(
-                f"Particle types '{unknown_types}' haven't been registered in the ASE type map"  # nopep8
-            )
         if any(p.is_virtual() for p in particles):
             raise RuntimeError("ASE doesn't support virtual sites")
 
         atoms = ase.Atoms(
             positions=positions,
-            symbols=[self.type_mapping[t] for t in types],
+            numbers=types,
             pbc=np.copy(self._system.periodicity),
             cell=np.copy(self._system.box_l),
         )

src/python/espressomd/system.py

@@ -175,15 +175,10 @@ def __getstate__(self):
         odict = collections.OrderedDict()
         for property_name in checkpointable_properties:
             odict[property_name] = System.__getattribute__(self, property_name)
-        if self._ase_interface is not None:
-            odict["_ase_interface"] = self._ase_interface.__getstate__()
         return odict
 
     def __setstate__(self, params):
         # initialize Python-only members
-        if "_ase_interface" in params:
-            from espressomd.plugins.ase import ASEInterface
-            self.ase = ASEInterface(**params.pop("_ase_interface"))
         for property_name in params.keys():
             System.__setattr__(self, property_name, params[property_name])
         # note: several members can only be instantiated once

src/python/espressomd/zn.py

@@ -320,8 +320,7 @@ def update(self):
         particles = self.system.part.all()
         all_types = particles.type
         self.system.visualizer_params = self.params
-        Asedata = ase.ASEInterface(
-            {x: "X" for x in set(all_types)})
+        Asedata = ase.ASEInterface()
         Asedata.register_system(self.system)
         data = Asedata.get(folded=self.params["folded"])
         if self.params["colors"] is not None:

testsuite/python/CMakeLists.txt

@@ -217,7 +217,6 @@ checkpoint_test(MODES dp3m_cpu__therm_langevin__int_nvt)
 checkpoint_test(MODES therm_dpd__int_nvt)
 checkpoint_test(MODES scafacos__therm_bd__int_bd)
 checkpoint_test(MODES therm_sdm__int_sdm)
-checkpoint_test(MODES lj__ase SUFFIX 1_core MAX_NUM_PROC 1)
 
 python_test(FILE bond_breakage.py MAX_NUM_PROC 4)
 python_test(FILE cell_system.py MAX_NUM_PROC 4)

testsuite/python/ase_interface.py

@@ -34,9 +34,7 @@ def setUp(self):
         self.system.part.add(pos=[0., 0., 0.], f=[1., -1., 0.], type=0)
         self.system.part.add(pos=[0., 0., 1.], f=[0., 12., 0.], type=1)
         self.system.part.add(pos=[11., 13., 12.], f=[0., 0., -8.], type=1)
-        self.system.ase = espressomd.plugins.ase.ASEInterface(
-            type_mapping={0: "H", 1: "O"},
-        )
+        self.system.ase = espressomd.plugins.ase.ASEInterface()
 
     def tearDown(self):
         self.system.part.clear()

testsuite/python/save_checkpoint.py

@@ -20,10 +20,8 @@
 import unittest as ut
 import unittest_generator as utg
 import numpy as np
-import contextlib
 import pathlib
 import tempfile
-import sys
 
 import espressomd
 import espressomd.checkpointing
@@ -43,8 +41,6 @@
 import espressomd.bond_breakage
 import espressomd.reaction_methods
 
-with contextlib.suppress(ImportError):
-    import espressomd.plugins.ase
 
 config = utg.TestGenerator()
 modes = config.get_modes()
@@ -74,8 +70,6 @@
     system.lees_edwards.set_boundary_conditions(
         shear_direction="z", shear_plane_normal="y", protocol=protocol)
 
-has_ase = "ASE" in modes
-
 lbf_class = None
 lb_lattice = None
 if espressomd.has_features('WALBERLA') and 'LB.WALBERLA' in modes:
@@ -170,11 +164,6 @@
         system.electrostatics.solver = p3m
         p3m.charge_neutrality_tolerance = 5e-12
 
-if has_ase and "ase" in sys.modules:
-    system.ase = espressomd.plugins.ase.ASEInterface(
-        type_mapping={0: "H", 1: "O", 10: "Cl"},
-    )
-
 # accumulators
 obs = espressomd.observables.ParticlePositions(ids=[0, 1])
 obs_dist = espressomd.observables.PairwiseDistances(
@@ -259,7 +248,7 @@
             approximation_method='ft', viscosity=0.5, radii={0: 1.5},
             pair_mobility=False, self_mobility=True)
 
-if espressomd.has_features(['VIRTUAL_SITES_RELATIVE']) and not has_ase:
+if espressomd.has_features(['VIRTUAL_SITES_RELATIVE']):
     p2.vs_auto_relate_to(p1, couple_to_lb=lbf_class is not None)
 
 # non-bonded interactions
@@ -477,7 +466,6 @@
 if espressomd.has_features(["ENGINE"]):
     p3.swimming = {"f_swim": 0.03}
 if espressomd.has_features(["ENGINE", "VIRTUAL_SITES_RELATIVE"]) and lbf_class:
-    assert not has_ase
     p4.swimming = {"v_swim": 0.02, "is_engine_force_on_fluid": True}
 if espressomd.has_features('LB_ELECTROHYDRODYNAMICS') and lbf_class:
     p8.mu_E = [-0.1, 0.2, -0.3]

testsuite/python/test_checkpoint.py

@@ -41,10 +41,6 @@
 with contextlib.suppress(ImportError):
     import espressomd.io.vtk
 
-with contextlib.suppress(ImportError):
-    import ase
-    import espressomd.plugins.ase
-
 with contextlib.suppress(ImportError):
     import h5py  # h5py has to be imported *after* espressomd (MPI)
 
@@ -57,7 +53,6 @@
 has_thermalized_bonds = 'THERM.LB' in modes or 'THERM.LANGEVIN' in modes
 has_drude = (espressomd.has_features(['ELECTROSTATICS', 'MASS', 'ROTATION'])
              and has_thermalized_bonds)
-has_ase = 'ASE' in modes
 
 
 class CheckpointTest(ut.TestCase):
@@ -472,14 +467,13 @@ def test_particle_properties(self):
             self.assertEqual(
                 p3.swimming,
                 {"f_swim": 0.03, "is_engine_force_on_fluid": False})
-            if espressomd.has_features(
-                    'VIRTUAL_SITES_RELATIVE') and has_lb_mode and not has_ase:
+            if espressomd.has_features('VIRTUAL_SITES_RELATIVE') and has_lb_mode:
                 self.assertEqual(
                     p4.swimming,
                     {"f_swim": 0., "is_engine_force_on_fluid": True})
         if espressomd.has_features('LB_ELECTROHYDRODYNAMICS') and has_lb_mode:
             np.testing.assert_allclose(np.copy(p8.mu_E), [-0.1, 0.2, -0.3])
-        if espressomd.has_features('VIRTUAL_SITES_RELATIVE') and not has_ase:
+        if espressomd.has_features('VIRTUAL_SITES_RELATIVE'):
             from scipy.spatial.transform import Rotation as R
             q_ind = ([1, 2, 3, 0],)  # convert from scalar-first to scalar-last
             vs_id, vs_dist, vs_quat = p2.vs_relative
@@ -765,7 +759,6 @@ def test_drude_helpers(self):
         self.assertEqual(dh.drude_id_list, [5])
 
     @utx.skipIfMissingFeatures(['VIRTUAL_SITES', 'VIRTUAL_SITES_RELATIVE'])
-    @ut.skipIf("ASE" in modes, "virtual sites not allowed by ASE")
     def test_virtual_sites(self):
         Propagation = espressomd.propagation.Propagation
         p_real = system.part.by_id(0)
@@ -1068,22 +1061,6 @@ def test_union(self):
         p2.remove()
         system.non_bonded_inter[2, 6].reset()
 
-    @ut.skipIf("ase" not in sys.modules, "missing module 'ase'")
-    @ut.skipIf("ASE" not in modes, "missing combination")
-    def test_ase_plugin(self):
-        atoms = system.ase.get()
-        self.assertIsNotNone(atoms)
-        self.assertIsInstance(atoms, ase.Atoms)
-        self.assertEqual(set(atoms.get_chemical_symbols()), {"H", "O"})
-        np.testing.assert_equal(atoms.pbc, np.copy(system.periodicity))
-        np.testing.assert_allclose(atoms.cell, np.diag(system.box_l))
-        np.testing.assert_allclose(
-            atoms.get_positions(),
-            np.copy(system.part.select(lambda p: p.type in [0, 1]).pos))
-        np.testing.assert_allclose(
-            atoms.get_forces(),
-            np.copy(system.part.select(lambda p: p.type in [0, 1]).f))
-
 
 if __name__ == '__main__':
     config.bind_test_class(CheckpointTest)