Merge pull request #442 from jmmshn/jmmshn/patch_vol

Automatic iso surface determination and example

crystal_toolkit/apps/examples/chgcar.py

@@ -0,0 +1,26 @@
+# %%
+from __future__ import annotations
+
+import dash
+from dash import html
+from dash_mp_components import CrystalToolkitScene
+from pymatgen.io.vasp import Chgcar
+
+import crystal_toolkit.components as ctc
+from crystal_toolkit.settings import SETTINGS
+
+app = dash.Dash(assets_folder=SETTINGS.ASSETS_PATH)
+
+chgcar = Chgcar.from_file("../../../tests/test_files/chgcar.vasp")
+scene = chgcar.get_scene(isolvl=0.0001)
+
+layout = html.Div(
+    [CrystalToolkitScene(data=scene.to_json())],
+    style={"width": "100px", "height": "100px"},
+)
+# %%
+# as explained in "preamble" section in documentation
+ctc.register_crystal_toolkit(app=app, layout=layout)
+
+if __name__ == "__main__":
+    app.run(debug=True, port=8050)

crystal_toolkit/renderables/volumetric.py

@@ -1,32 +1,33 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, Literal
 
 import numpy as np
 from pymatgen.io.vasp import VolumetricData
 
 from crystal_toolkit.core.scene import Scene, Surface
 
 if TYPE_CHECKING:
-    from numpy.typing import ArrayLike
+    from numpy.typing import ArrayLike, NDArray
+    from pymatgen.core.structure import Lattice
 
 _ANGS2_TO_BOHR3 = 1.88973**3
 
 
 def get_isosurface_scene(
-    self,
-    data_key: str = "total",
-    isolvl: float = 0.05,
+    data: NDArray,
+    lattice: Lattice,
+    isolvl: float | None = None,
     step_size: int = 4,
     origin: ArrayLike | None = None,
     **kwargs: Any,
 ) -> Scene:
     """Get the isosurface from a VolumetricData object.
 
     Args:
-        data_key (str, optional): Use the volumetric data from self.data[data_key]. Defaults to 'total'.
-        isolvl (float, optional): The cutoff for the isosurface to using the same units as VESTA so
-            e/bohr and kept grid size independent
+        data (NDArray): The volumetric data array.
+        lattice (Lattice): The lattice.
+        isolvl (float, optional): The cutoff to compute the isosurface
         step_size (int, optional): step_size parameter for marching_cubes_lewiner. Defaults to 3.
         origin (ArrayLike, optional): The origin of the isosurface. Defaults to None.
         **kwargs: Passed to the Surface object.
@@ -36,42 +37,65 @@ def get_isosurface_scene(
     """
     import skimage.measure
 
-    origin = origin or list(
-        -self.structure.lattice.get_cartesian_coords([0.5, 0.5, 0.5])
-    )
-    vol_data = np.copy(self.data[data_key])
-    vol = self.structure.volume
-    vol_data = vol_data / vol / _ANGS2_TO_BOHR3
-
-    padded_data = np.pad(vol_data, (0, 1), "wrap")
-    vertices, faces, normals, values = skimage.measure.marching_cubes(
-        padded_data, level=isolvl, step_size=step_size, method="lewiner"
-    )
+    origin = origin or list(-lattice.get_cartesian_coords([0.5, 0.5, 0.5]))
+    if isolvl is None:
+        # get the value such that 20% of the weight is enclosed
+        isolvl = np.percentile(data, 20)
+
+    padded_data = np.pad(data, (0, 1), "wrap")
+    try:
+        vertices, faces, normals, values = skimage.measure.marching_cubes(
+            padded_data, level=isolvl, step_size=step_size, method="lewiner"
+        )
+    except (ValueError, RuntimeError) as err:
+        if "Surface level" in str(err):
+            raise ValueError(
+                f"Isosurface level is not within data range. min: {data.min()}, max: {data.max()}"
+            ) from err
+        raise err
     # transform to fractional coordinates
-    vertices = vertices / (vol_data.shape[0], vol_data.shape[1], vol_data.shape[2])
-    vertices = np.dot(vertices, self.structure.lattice.matrix)  # transform to Cartesian
+    vertices = vertices / (data.shape[0], data.shape[1], data.shape[2])
+    vertices = np.dot(vertices, lattice.matrix)  # transform to Cartesian
     pos = [vert for triangle in vertices[faces].tolist() for vert in triangle]
     return Scene(
         "isosurface", origin=origin, contents=[Surface(pos, show_edges=False, **kwargs)]
     )
 
 
-def get_volumetric_scene(self, data_key="total", isolvl=0.02, step_size=3, **kwargs):
+def get_volumetric_scene(
+    self,
+    data_key: str = "total",
+    isolvl: float | None = None,
+    step_size: int = 3,
+    normalization: Literal["vol", "vesta"] | None = "vol",
+    **kwargs,
+):
     """Get the Scene object which contains a structure and a isosurface components.
 
     Args:
         data_key (str, optional): Use the volumetric data from self.data[data_key]. Defaults to 'total'.
-        isolvl (float, optional): The cutoff for the isosurface to using the same units as VESTA so e/bhor
-        and kept grid size independent
+        isolvl (float, optional): The cutoff for the isosurface if none is provided we default to
+            a surface that encloses 20% of the weight.
         step_size (int, optional): step_size parameter for marching_cubes_lewiner. Defaults to 3.
+        normalization (str, optional): Normalize the volumetric data by the volume of the unit cell.
+            Default is 'vol', which divides the data by the volume of the unit cell, this is required
+            for all VASP volumetric data formats.  If normalization is 'vesta' we also change
+            the units from Angstroms to Bohr.
         **kwargs: Passed to the Structure.get_scene() function.
 
     Returns:
         Scene: object containing the structure and isosurface components
     """
     struct_scene = self.structure.get_scene(**kwargs)
-    iso_scene = self.get_isosurface_scene(
-        data_key=data_key,
+    vol_data = self.data[data_key]
+    if normalization in ("vol", "vesta"):
+        vol_data = vol_data / self.structure.volume
+    if normalization == "vesta":
+        vol_data = vol_data / _ANGS2_TO_BOHR3
+
+    iso_scene = get_isosurface_scene(
+        data=vol_data,
+        lattice=self.structure.lattice,
         isolvl=isolvl,
         step_size=step_size,
         origin=struct_scene.origin,
@@ -81,5 +105,4 @@ def get_volumetric_scene(self, data_key="total", isolvl=0.02, step_size=3, **kwa
 
 
 # todo: re-think origin, shift globally at end (scene.origin)
-VolumetricData.get_isosurface_scene = get_isosurface_scene
 VolumetricData.get_scene = get_volumetric_scene

tests/test_volumetric.py

@@ -0,0 +1,21 @@
+import pytest
+from pymatgen.io.vasp import Chgcar
+
+
+def test_volumetric(test_files):
+    chgcar = Chgcar.from_file(test_files / "chgcar.vasp")
+    max_val = chgcar.data["total"].max()
+
+    scene = chgcar.get_scene(isolvl=10, normalization=None)
+    assert scene is not None
+
+    # out of range
+    with pytest.raises(ValueError, match="Isosurface level is not within data range"):
+        scene = chgcar.get_scene(isolvl=max_val * 2, normalization=None)
+
+    # cannot be computed
+    with pytest.raises(RuntimeError):
+        scene = chgcar.get_scene(isolvl=max_val / 2, normalization=None)
+
+    # vesta units
+    scene = chgcar.get_scene(isolvl=0.001, normalization="vesta")