Merge pull request #37 from FrederikLizakJohansen/pymatgen

Allow pymatgen objects, minor revisions, new tests, merging

Demo.ipynb

@@ -67,8 +67,6 @@
    "source": [
     "# Helper functions for generating different particle models\n",
     "from debyecalculator.utility.generate import (\n",
-    "    generate_core_shell_models, \n",
-    "    generate_core_shell_models_fixed_size, \n",
     "    generate_substitutional_alloy_models,\n",
     "    generate_periodic_plane_substitution,\n",
     "    generate_spherical_particle,\n",
@@ -617,7 +615,7 @@
    "source": [
     "# Particle Playground\n",
     "\n",
-    "In the following sections, we will dive into how the `DebyeCalculator` can be utilized to model and analyze the scattering properties of simulated nanoparticles. We’ve prepared several examples that demonstrate how to simulate particles with core-shell structures, substitutional alloy particles, and toy-model intermetallic alloys. Feel free to experiment and create your own models to explore the full capabilities of `DebyeCalculator`."
+    "In the following sections, we will dive into how the `DebyeCalculator` can be utilized to model and analyze the scattering properties of simulated nanoparticles. We’ve prepared several examples that demonstrate how to simulate substitutional alloy particles, and toy-model intermetallic alloys. Feel free to experiment and create your own models to explore the full capabilities of `DebyeCalculator`."
    ]
   },
   {

debyecalculator/debye_calculator.py

@@ -49,6 +49,12 @@
 from functools import partial
 from tqdm.auto import tqdm
 
+try:
+    from pymatgen.core import Structure
+    pymatgen_available = True
+except ImportError:
+    pymatgen_available = False
+
 # NamedTuple definitions
 StructureTuple = namedtuple('StructureTuple', 'elements size occupancy xyz triu_indices unique_inverse unique_form_factors form_avg_sq structure_inverse')
 IqTuple = namedtuple('IqTuple', 'q i')
@@ -59,16 +65,31 @@
 
 ArrayLike = Union[np.ndarray, torch.Tensor]
 IntArrayLike = Union[List[int], np.ndarray, torch.Tensor]
-StructureSourceType = Union[
-    Tuple[List[str], ArrayLike],
-    Tuple[IntArrayLike, ArrayLike],
-    List[Tuple[List[str], ArrayLike]],
-    List[Tuple[IntArrayLike, ArrayLike]],
-    str,
-    List[str],
-    Atoms,
-    List[Atoms],
-]
+
+if pymatgen_available:
+    StructureSourceType = Union[
+        Tuple[List[str], ArrayLike],
+        Tuple[IntArrayLike, ArrayLike],
+        List[Tuple[List[str], ArrayLike]],
+        List[Tuple[IntArrayLike, ArrayLike]],
+        str,
+        List[str],
+        Atoms,
+        List[Atoms],
+        Structure,
+        List[Structure],
+    ]
+else:
+    StructureSourceType = Union[
+        Tuple[List[str], ArrayLike],
+        Tuple[IntArrayLike, ArrayLike],
+        List[Tuple[List[str], ArrayLike]],
+        List[Tuple[IntArrayLike, ArrayLike]],
+        str,
+        List[str],
+        Atoms,
+        List[Atoms],
+    ]
 
 class DebyeCalculator:
     """
@@ -462,6 +483,18 @@ def parse_elements(elements, size):
 
             triu_indices, unique_inverse, unique_form_factors, form_avg_sq, structure_inverse = parse_elements(elements, size)
 
+            return StructureTuple(elements, size, occupancy, xyz, triu_indices, unique_inverse, unique_form_factors, form_avg_sq, structure_inverse)
+        elif isinstance(structure_source, Structure):
+            try:
+                elements = [site.species_string for site in structure_source.sites]
+                size = len(elements)
+                occupancy = torch.ones((size), dtype=torch.float32).to(device=self.device)
+                xyz = torch.from_numpy(np.array([[site.a, site.b, site.c] for site in structure_source.sites])).to(device=self.device, dtype=torch.float32)
+            except:
+                raise ValueError(f'Encountered invalid Structure object')
+
+            triu_indices, unique_inverse, unique_form_factors, form_avg_sq, structure_inverse = parse_elements(elements, size)
+
             return StructureTuple(elements, size, occupancy, xyz, triu_indices, unique_inverse, unique_form_factors, form_avg_sq, structure_inverse)
         else:
             raise TypeError('Encountered unknown structure source')

debyecalculator/unittests_files/AntiFluorite_Co2O.cif

@@ -0,0 +1,37 @@
+data_image0
+_chemical_formula_structural       Co8O4
+_chemical_formula_sum              "Co8 O4"
+_cell_length_a       4.86543
+_cell_length_b       4.86543
+_cell_length_c       4.86543
+_cell_angle_alpha    90
+_cell_angle_beta     90
+_cell_angle_gamma    90
+
+_space_group_name_H-M_alt    "P 1"
+_space_group_IT_number       1
+
+loop_
+  _space_group_symop_operation_xyz
+  '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
+  Co  Co1       1.0  0.25000  0.25000  0.25000  1.0000
+  Co  Co2       1.0  0.75000  0.75000  0.25000  1.0000
+  Co  Co3       1.0  0.75000  0.25000  0.75000  1.0000
+  Co  Co4       1.0  0.25000  0.75000  0.75000  1.0000
+  Co  Co5       1.0  0.25000  0.25000  0.75000  1.0000
+  Co  Co6       1.0  0.75000  0.75000  0.75000  1.0000
+  Co  Co7       1.0  0.25000  0.75000  0.25000  1.0000
+  Co  Co8       1.0  0.75000  0.25000  0.25000  1.0000
+  O   O1        1.0  0.00000  0.00000  0.00000  1.0000
+  O   O2        1.0  0.00000  0.50000  0.50000  1.0000
+  O   O3        1.0  0.50000  0.00000  0.50000  1.0000
+  O   O4        1.0  0.50000  0.50000  0.00000  1.0000

debyecalculator/unittests_files/fq_AntiFluorite_Co2O_radius10.0.dat

@@ -1,17 +1,3 @@
-qmin:1.0
-qmax:30.0
-qdamp:0.04
-qstep:0.05
-rmin:0.0
-rmax:20.0
-rstep:0.01
-rthres:0.0
-biso:0.3
-device:cuda
-batch_size:10000
-lorch_mod:False
-radiation_type:xray
-
 q,F(Q)
 1.0,-0.4698953
 1.05,-0.5819457

debyecalculator/unittests_files/gr_AntiFluorite_Co2O_radius10.0.dat

@@ -1,17 +1,3 @@
-qmin:1.0
-qmax:30.0
-qdamp:0.04
-qstep:0.05
-rmin:0.0
-rmax:20.0
-rstep:0.01
-rthres:0.0
-biso:0.3
-device:cuda
-batch_size:10000
-lorch_mod:False
-radiation_type:xray
-
 r,G(r)
 0.0,0.0
 0.01,-0.001527964