pymatgen interconnect

src/pylattica/atomic/pymatgen_struct_converter.py

@@ -0,0 +1,46 @@
+from pymatgen.core.structure import Structure as PmgStructure
+from pymatgen.core.lattice import Lattice as PmgLattice
+
+from ..core import Lattice as PylLattice, StructureBuilder, PeriodicStructure
+
+
+class PymatgenStructureConverter:
+    def to_pylattica_lattice(self, pmg_lat: PmgLattice):
+        pmg_lat = pmg_lat
+        pyl_lat = PylLattice(pmg_lat.matrix)
+        return pyl_lat
+
+    def to_pylattica_structure_builder(self, pmg_struct: PmgStructure):
+        lat = self.to_pylattica_lattice(pmg_struct.lattice)
+
+        struct_motif = {}
+
+        for site in pmg_struct.sites:
+            site_cls = site.species_string
+            frac_coords = site.frac_coords
+
+            if site_cls in struct_motif:
+                struct_motif.get(site_cls).append(frac_coords)
+            else:
+                struct_motif[site_cls] = [frac_coords]
+
+        struct_builder = StructureBuilder(lat, struct_motif)
+        struct_builder.frac_coords = True
+        return struct_builder
+
+    def to_pymatgen_lattice(self, pyl_lat: PylLattice):
+        return PmgLattice(pyl_lat.vecs)
+
+    def to_pymatgen_structure(self, pyl_struct: PeriodicStructure):
+        pmg_lat = self.to_pymatgen_lattice(pyl_struct.lattice)
+
+        species = []
+        coords = []
+
+        for sid in pyl_struct.site_ids:
+            species.append(pyl_struct.site_class(sid))
+            coords.append(
+                pyl_struct.lattice.get_fractional_coords(pyl_struct.site_location(sid))
+            )
+
+        return PmgStructure(pmg_lat, species, coords)

src/pylattica/core/__init__.py

@@ -8,6 +8,7 @@
 from .simulation import Simulation
 from .lattice import Lattice
 from .analyzer import StateAnalyzer
+from .structure_builder import StructureBuilder
 
 from .neighborhoods import Neighborhood, StochasticNeighborhood
 from .neighborhood_builders import (

src/pylattica/core/periodic_structure.py

@@ -177,6 +177,12 @@ def site_at(self, location: Tuple[float]) -> Dict:
         else:
             return None
 
+    def site_class(self, site_id: int) -> str:
+        return self.get_site(site_id)[SITE_CLASS]
+
+    def site_location(self, site_id: int) -> str:
+        return self.get_site(site_id)[LOCATION]
+
     def get_site(self, site_id: int) -> Dict:
         """Returns the site with the specified ID.
 

src/pylattica/core/runner/synchronous_runner.py

@@ -55,7 +55,7 @@ def _run(
             if self.workers is None:
                 PROCESSES = mp.cpu_count()
             else:
-                PROCESSES = self.workers # pragma: no cover
+                PROCESSES = self.workers  # pragma: no cover
 
             printif(verbose, f"Running in parallel using {PROCESSES} workers")
             num_sites = initial_state.size

tests/atomic/Zr.cif

@@ -0,0 +1,28 @@
+# generated using pymatgen
+data_Zr
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   3.23923141
+_cell_length_b   3.23923141
+_cell_length_c   5.17222000
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   120.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Zr
+_chemical_formula_sum   Zr2
+_cell_volume   46.99931972
+_cell_formula_units_Z   2
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Zr  Zr0  1  0.33333333  0.66666667  0.25000000  1
+  Zr  Zr1  1  0.66666667  0.33333333  0.75000000  1

tests/atomic/conftest.py

@@ -0,0 +1,26 @@
+import pytest
+
+from pathlib import Path
+from pymatgen.core.structure import Structure
+
+from pylattica.core import Lattice, StructureBuilder
+
+THIS_DIR = Path(__file__).parent
+
+@pytest.fixture()
+def zr_pmg_struct():
+    return Structure.from_file(THIS_DIR / "./Zr.cif")
+
+@pytest.fixture()
+def pyl_struct():
+
+    lat = Lattice([[1,0,0], [0,1,0], [0,0,1]])
+
+    motif = {
+        "Zr": [[
+            0.5, 0.5, 0.5
+        ]]
+    }
+
+    builder = StructureBuilder(lat, motif)
+    return builder.build((1, 2, 3))

tests/atomic/test_convert_pymatgen_structure.py

@@ -0,0 +1,65 @@
+import pytest
+
+from pylattica.atomic.pymatgen_struct_converter import PymatgenStructureConverter
+from pylattica.core.constants import SITE_CLASS, LOCATION
+from pymatgen.core.structure import Structure as PmgStructure
+from pylattica.core import PeriodicStructure
+
+import numpy as np
+
+def test_can_convert_lattice(zr_pmg_struct: PmgStructure):
+    converter = PymatgenStructureConverter()
+
+    lattice = converter.to_pylattica_lattice(zr_pmg_struct.lattice)
+
+    assert np.isclose(lattice.vec_lengths[0], zr_pmg_struct.lattice.a)
+    assert np.isclose(lattice.vec_lengths[1], zr_pmg_struct.lattice.b)
+    assert np.isclose(lattice.vec_lengths[2], zr_pmg_struct.lattice.c)
+
+    assert np.allclose(lattice.vecs[0], zr_pmg_struct.lattice.matrix[0])
+    assert np.allclose(lattice.vecs[1], zr_pmg_struct.lattice.matrix[1])
+    assert np.allclose(lattice.vecs[2], zr_pmg_struct.lattice.matrix[2])
+
+def test_can_convert_pmg_struct(zr_pmg_struct: PmgStructure):
+    converter = PymatgenStructureConverter()
+
+    struct_builder = converter.to_pylattica_structure_builder(zr_pmg_struct)
+
+    struct = struct_builder.build(1)
+
+    assert len(struct.site_ids) == zr_pmg_struct.num_sites
+
+    species_label = zr_pmg_struct.sites[0].species_string
+    assert struct.site_class(0) == species_label
+
+    # brittle - relies on the order in which sites are enumerated
+    assert np.allclose(struct.site_location(0),zr_pmg_struct.sites[0].coords)
+    assert np.allclose(struct.site_location(1),zr_pmg_struct.sites[1].coords)
+
+    assert np.allclose(struct.lattice.get_fractional_coords(struct.site_location(1)), zr_pmg_struct.sites[1].frac_coords)
+
+def test_can_convert_pyl_lat(pyl_struct: PeriodicStructure):
+    converter = PymatgenStructureConverter()
+
+    pmg_lat = converter.to_pymatgen_lattice(pyl_struct.lattice)
+    assert pmg_lat.a == pyl_struct.lattice.vec_lengths[0]
+    assert pmg_lat.b == pyl_struct.lattice.vec_lengths[1]
+    assert pmg_lat.c == pyl_struct.lattice.vec_lengths[2]
+
+    assert np.allclose(pyl_struct.lattice.vecs[0], pmg_lat.matrix[0])
+    assert np.allclose(pyl_struct.lattice.vecs[1], pmg_lat.matrix[1])
+    assert np.allclose(pyl_struct.lattice.vecs[2], pmg_lat.matrix[2])
+
+def test_can_convert_pyl_struct(pyl_struct: PeriodicStructure):
+    converter = PymatgenStructureConverter()
+
+    pmg_struct = converter.to_pymatgen_structure(pyl_struct)
+
+    assert pmg_struct.num_sites == len(pyl_struct.site_ids)
+
+    for site in pmg_struct.sites:
+        matching_site = pyl_struct.site_at(site.coords)
+        assert matching_site is not None
+        assert matching_site[SITE_CLASS] == site.species_string
+
+        assert np.all(pyl_struct.lattice.get_fractional_coords(matching_site[LOCATION]) == site.frac_coords)