diff --git a/.gitignore b/.gitignore index 284e278a..dd78d741 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,6 @@ __pycache__/ # auto-generated documentation docs_rst/_build +build +dist +*.egg-info diff --git a/crystal_toolkit/apps/examples/LiMnP2O7_mg.json b/crystal_toolkit/apps/examples/LiMnP2O7_mg.json new file mode 100644 index 00000000..e7d3d7a1 --- /dev/null +++ b/crystal_toolkit/apps/examples/LiMnP2O7_mg.json @@ -0,0 +1 @@ +{"@module": "pymatgen.analysis.diffusion.neb.full_path_mapper", "@class": "MigrationGraph", "@version": null, "structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0, "lattice": {"matrix": [[7.833467, 0.0, 0.0], [0.0, 4.761443, 0.0], [0.0, 1.910264, 6.629352]], "a": 7.833467, "b": 4.761443, "c": 6.899088091161034, "alpha": 73.92553422004923, "beta": 90.0, "gamma": 90.0, "volume": 247.26559234631586}, "sites": [{"species": [{"element": "Mn", "occu": 1}], "abc": [0.99139, 0.781175, 0.728269], "xyz": [7.766020849129999, 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-3.7588548525000034}}, {"species": [{"element": "Li", "occu": 1}], "abc": [0.323680325, 0.6476350000000002, 0.08915524999999994], "xyz": [2.535539144436775, 3.2539872017910008, 0.5910415348979996], "label": "Li", "properties": {"insertion_energy": -4.156210358750002}}, {"species": [{"element": "Li", "occu": 1}], "abc": [0.14589401666666674, 0.1843109999999999, 0.33993766666666664], "xyz": [1.142855965055784, 1.5269570076503327, 2.253566450392], "label": "Li", "properties": {"insertion_energy": -3.7588548525000034}}]}, "spacegroup": [{"@module": "pymatgen.core.operations", "@class": "SymmOp", "matrix": [[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]], "tolerance": 0.1, "@version": null}, {"@module": "pymatgen.core.operations", "@class": "SymmOp", "matrix": [[1.0, 0.0, 0.0, 0.5], [0.0, -1.0, 0.0, 0.0], [0.0, 0.0, -1.0, 0.0], [0.0, 0.0, 0.0, 1.0]], "tolerance": 0.1, "@version": null}], "equivalent_positions": {"@module": "numpy", "@class": "array", "dtype": "int32", "data": [0, 0, 2, 2, 4, 4, 6, 7, 7, 9, 10, 11, 12, 6, 10, 15, 15, 12, 11, 9, 20, 21, 20, 21]}, "wyckoff_letters": ["a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a"]}, "host_symm_struct": null, "symprec": 0.1}, "hop_label": 0, "id": 3, "key": 1}], []]}}, "symprec": 0.1, "vac_mode": false} diff --git a/crystal_toolkit/apps/examples/migrationgraph.py b/crystal_toolkit/apps/examples/migrationgraph.py new file mode 100644 index 00000000..61f47f9b --- /dev/null +++ b/crystal_toolkit/apps/examples/migrationgraph.py @@ -0,0 +1,37 @@ +import os + +import dash +from dash import html +from dash_mp_components import CrystalToolkitScene +from monty.serialization import loadfn + +import crystal_toolkit.components as ctc +from crystal_toolkit.settings import SETTINGS + +app = dash.Dash(assets_folder=SETTINGS.ASSETS_PATH) + +# create the MigrationGraph object +module_dir = os.path.dirname(os.path.abspath(__file__)) +mg = loadfn(f"{module_dir}/LiMnP2O7_mg.json") + +# create the Crystal Toolkit component +# no MigrationGraph component yet +component = ctc.StructureMoleculeComponent(mg.structure, id="my_structure") +test_scene = mg.get_scene() + +# example layout +my_layout = html.Div( + [html.Div([CrystalToolkitScene(data=test_scene.to_json())])], + style=dict( + margin="2em auto", display="grid", placeContent="center", placeItems="center" + ), +) + +# tell crystal toolkit about your app and layout +ctc.register_crystal_toolkit(app, layout=my_layout) + +# run this app with "python path/to/this/file.py" +# in production, deploy behind gunicorn or similar +# see Dash documentation for more information +if __name__ == "__main__": + app.run_server(debug=True, port=8050) diff --git a/crystal_toolkit/renderables/__init__.py b/crystal_toolkit/renderables/__init__.py index fd40b795..632558cb 100644 --- a/crystal_toolkit/renderables/__init__.py +++ b/crystal_toolkit/renderables/__init__.py @@ -1,4 +1,5 @@ from crystal_toolkit.renderables.lattice import Lattice as Lattice +from crystal_toolkit.renderables.migrationgraph import MigrationGraph as MigrationGraph from crystal_toolkit.renderables.molecule import Molecule as Molecule from crystal_toolkit.renderables.moleculegraph import MoleculeGraph as MoleculeGraph from crystal_toolkit.renderables.phasediagram import PhaseDiagram as PhaseDiagram diff --git a/crystal_toolkit/renderables/migrationgraph.py b/crystal_toolkit/renderables/migrationgraph.py new file mode 100644 index 00000000..597c9ab2 --- /dev/null +++ b/crystal_toolkit/renderables/migrationgraph.py @@ -0,0 +1,96 @@ +import numpy as np +from pymatgen.analysis.diffusion.neb.full_path_mapper import MigrationGraph + +from crystal_toolkit.core.scene import Cylinders, Scene + +color_scheme = [ + (32, 178, 170), + (0, 255, 127), + (47, 79, 79), + (30, 144, 255), + (138, 43, 226), + (186, 85, 211), + (199, 21, 133), + (255, 20, 147), + (250, 235, 215), + (160, 82, 45), + (244, 164, 96), + (176, 196, 222), +] + + +def _get_extras_cross_boundary(self, one_hop, only_wi_structure, color_code): + extras = [] + working_struct = only_wi_structure.copy() + wi = working_struct[0].specie.name + ori_epos = working_struct[one_hop["eindex"]] + + # extra atoms + working_struct.insert(0, wi, one_hop["epos"]) + shifted_ipos = one_hop["ipos"] - np.array(one_hop["to_jimage"]) + working_struct.insert(0, wi, shifted_ipos) + sites_contents = [working_struct[0].get_scene(), working_struct[1].get_scene()] + extras.extend(sites_contents) + + # extra cylinders + extra_ipos = list(working_struct[0].coords) + extra_epos = list(ori_epos.coords) + extras.append( + Cylinders( + positionPairs=[[extra_ipos, extra_epos]], + radius=0.3, + clickable=True, + color=color_code, + ) + ) + + return extras + + +def get_migrationgraph_scene( + self, +) -> Scene: + """ + Creates CTK object to display hops from a MigrationGraph object + Args: + mg: MigrationGraph object with hops to be visualized + + Returns: + CTK scene object to be rendered + """ + + result_scene = self.structure.get_scene() + hop_contents = [] + + for k, one_hop in self.unique_hops.items(): + one_hop_contents = [] + rgb_code = color_scheme[k % len(color_scheme)] + color_code = f"#{rgb_code[0]:02x}{rgb_code[1]:02x}{rgb_code[2]:02x}" + + hop_cyl = Cylinders( + positionPairs=[[list(one_hop["ipos_cart"]), list(one_hop["epos_cart"])]], + radius=0.3, + clickable=True, + color=color_code, + ) + one_hop_contents.append(hop_cyl) + + if one_hop["to_jimage"] != (0, 0, 0): + extras_cross_boundary = self._get_extras_cross_boundary( + one_hop, self.only_sites, color_code + ) + one_hop_contents.extend(extras_cross_boundary) + + one_hop_scene = Scene(name=f"hop_{k}", contents=one_hop_contents) + hop_contents.append(one_hop_scene) + + result_scene.contents.append( + Scene( + name="hops", origin=result_scene.contents[0].origin, contents=hop_contents + ) + ) + return result_scene + + +MigrationGraph._get_extras_cross_boundary = _get_extras_cross_boundary +MigrationGraph.get_scene = get_migrationgraph_scene