Integrate LOBSTER apps into crystal toolkit

.github/workflows/pull-request.yml

@@ -39,6 +39,7 @@ jobs:
           python${{ matrix.python-version }} -m pip install -r requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
           python${{ matrix.python-version }} -m pip install --upgrade pip
           python${{ matrix.python-version }} -m pip install --no-deps .[server,test]
+          python${{ matrix.python-version }} -m pip install lobsterpy
       - name: Test modules
         run: python${{ matrix.python-version }} -m pytest --cov=crystal_toolkit --cov-report=xml tests
       - name: Test example apps

crystal_toolkit/_version.py

@@ -0,0 +1 @@
+__version__ = "2020.8.15.dev2217"

crystal_toolkit/apps/examples/cohp.py

@@ -0,0 +1,114 @@
+import os
+import warnings
+
+import dash
+import numpy as np
+from pymatgen.core import Structure
+from pymatgen.electronic_structure.cohp import CompleteCohp
+from pymatgen.io.lobster.inputs import Lobsterin
+from pymatgen.io.lobster.outputs import (
+    Bandoverlaps,
+    Charge,
+    Doscar,
+    Icohplist,
+    Lobsterout,
+    MadelungEnergies,
+)
+from pymatgen.io.vasp.outputs import Vasprun
+
+import crystal_toolkit.components as ctc
+from crystal_toolkit.helpers.layouts import H3, Container
+from crystal_toolkit.settings import SETTINGS
+
+
+class CustomVasprun(Vasprun):
+    """Override final_energy property without unitized decorator"""
+
+    def __init__(self, filename, **kwargs):
+        super().__init__(filename, **kwargs)
+
+    @property
+    def final_energy(self) -> float:
+        """Final energy from the VASP run."""
+
+        try:
+            final_istep = self.ionic_steps[-1]
+            total_energy = final_istep["e_0_energy"]
+
+            # Fix a bug in vasprun.xml.
+            # See https://www.vasp.at/forum/viewtopic.php?f=3&t=16942
+            final_estep = final_istep["electronic_steps"][-1]
+            electronic_energy_diff = (
+                final_estep["e_0_energy"] - final_estep["e_fr_energy"]
+            )
+            total_energy_bugfix = np.round(
+                electronic_energy_diff + final_istep["e_fr_energy"], 8
+            )
+            if np.abs(total_energy - total_energy_bugfix) > 1e-7:
+                return total_energy_bugfix
+
+            return total_energy
+
+        except (IndexError, KeyError):
+            warnings.warn(
+                "Calculation does not have a total energy. Possibly a GW or similar kind of run. Infinity is returned.",
+                stacklevel=2,
+            )
+            return float("inf")
+
+
+calc_dir = "path/to/your/lobster/output"  # Replace with your actual path
+
+icohplist_obj = Icohplist(
+    filename=f"{calc_dir}/ICOHPLIST.lobster.gz", are_cobis=False, are_coops=False
+)
+
+completecohp_obj = CompleteCohp.from_file(
+    filename=f"{calc_dir}/COHPCAR.lobster.gz",
+    structure_file=f"{calc_dir}/CONTCAR.gz",
+    fmt="LOBSTER",
+    are_cobis=False,
+    are_coops=False,
+)
+
+charge_obj = Charge(filename=f"{calc_dir}/CHARGE.lobster.gz")
+madelung_obj = MadelungEnergies(filename=f"{calc_dir}/MadelungEnergies.lobster.gz")
+lob_dos = Doscar(
+    doscar=f"{calc_dir}/DOSCAR.LSO.lobster.gz", structure_file=f"{calc_dir}/CONTCAR.gz"
+)
+
+vasprun_obj = CustomVasprun(filename=f"{calc_dir}/vasprun.xml.gz")
+structure_obj = Structure.from_file(f"{calc_dir}/CONTCAR.gz")
+lobsterin_obj = Lobsterin.from_file(f"{calc_dir}/lobsterin.gz")
+lobsterout_obj = Lobsterout(filename=f"{calc_dir}/lobsterout.gz")
+# Include band overlaps file if it exists available
+bandoverlaps_obj = (
+    Bandoverlaps(filename=f"{calc_dir}/bandOverlaps.lobster.gz")
+    if os.path.exists(f"{calc_dir}/bandOverlaps.lobster.gz")
+    else None
+)
+
+cohp_component = ctc.CohpAndDosComponent(
+    density_of_states=lob_dos.completedos,
+    charge_obj=charge_obj,
+    icohplist_obj=icohplist_obj,
+    completecohp_obj=completecohp_obj,
+    madelung_obj=madelung_obj,
+    vasprun_obj=vasprun_obj,
+    structure_obj=structure_obj,
+    lobsterin_obj=lobsterin_obj,
+    lobsterout_obj=lobsterout_obj,
+    bandoverlaps_obj=bandoverlaps_obj,
+    mpid="mp-xxx",
+    disable_callbacks=False,
+)
+
+# example layout to demonstrate capabilities of component
+layout = Container([H3("COHP and Density of States Example"), cohp_component.layout()])
+
+app = dash.Dash(assets_folder=SETTINGS.ASSETS_PATH, prevent_initial_callbacks=True)  #
+
+ctc.register_crystal_toolkit(app, layout=layout)
+
+if __name__ == "__main__":
+    app.run(debug=True, port=8051)

crystal_toolkit/components/__init__.py

@@ -4,6 +4,11 @@
     BandstructureAndDosComponent,
     BandstructureAndDosPanelComponent,
 )
+
+# from crystal_toolkit.components.transformations.rattle import (
+#     MonteCarloRattleTransformationComponent,
+# )
+from crystal_toolkit.components.cohp import CohpAndDosComponent
 from crystal_toolkit.components.diffraction import XRayDiffractionComponent
 from crystal_toolkit.components.diffraction_tem import TEMDiffractionComponent
 from crystal_toolkit.components.fermi_surface import FermiSurfaceComponent
@@ -33,10 +38,6 @@
 from crystal_toolkit.components.transformations.grainboundary import (
     GrainBoundaryTransformationComponent,
 )
-
-# from crystal_toolkit.components.transformations.rattle import (
-#     MonteCarloRattleTransformationComponent,
-# )
 from crystal_toolkit.components.transformations.slab import SlabTransformationComponent
 from crystal_toolkit.components.transformations.substitution import (
     SubstitutionTransformationComponent,