Structure graphs

.github/workflows/python-package.yml

@@ -42,7 +42,7 @@ jobs:
       # run this locally to update tests durations
       # pytest --cov=lobsterpy --cov-append --splits 1 --group 1 --durations-path ./lobsterpy/TestData/.pytest-split-durations --store-durations
       run: |
-        pytest --cov=lobsterpy --cov-report term-missing --cov-append  --splits 5 --group ${{ matrix.split }} --durations-path ./lobsterpy/TestData/.pytest-split-durations
+        pytest --cov=lobsterpy --cov-report term-missing --cov-append --splits 5 --group ${{ matrix.split }} --durations-path ./lobsterpy/TestData/.pytest-split-durations
     - name: Upload coverage
       uses: actions/upload-artifact@v3
       with:

docs/source/conf.py

@@ -12,14 +12,15 @@
 #
 import os
 import sys
+
 sys.path.insert(0, os.path.abspath("../"))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'Lobsterpy'
-copyright = '2022, Janine George'
-author = 'Janine George'
+project = "Lobsterpy"
+copyright = "2022, Janine George"
+author = "Janine George"
 
 
 # -- General configuration ---------------------------------------------------
@@ -43,12 +44,20 @@
 source_suffix = [".rst", ".md"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ["../../lobsterpy/test","../../lobsterpy/cohp/test","../../lobsterpy/plotting/test","../../lobsterpy/TestData","Thumbs.db", ".DS_Store",]
+exclude_patterns = [
+    "../../lobsterpy/test",
+    "../../lobsterpy/cohp/test",
+    "../../lobsterpy/plotting/test",
+    "../../lobsterpy/TestData",
+    "Thumbs.db",
+    ".DS_Store",
+]
+
 
 def run_apidoc(_):
     import subprocess
@@ -60,7 +69,17 @@ def run_apidoc(_):
     excludes2 = glob.glob(os.path.join(output_path, "../../lobsterpy/plotting/test"))
     module = os.path.join(output_path, "../../lobsterpy")
     cmd_path = "sphinx-apidoc"
-    command = [cmd_path, "-e", "-o", output_path, module, " ".join(excludes)," ".join(excludes1)," ".join(excludes2), "--force"]
+    command = [
+        cmd_path,
+        "-e",
+        "-o",
+        output_path,
+        module,
+        " ".join(excludes),
+        " ".join(excludes1),
+        " ".join(excludes2),
+        "--force",
+    ]
     subprocess.check_call(command)
 
 
@@ -73,9 +92,9 @@ def setup(app):
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_book_theme'
+html_theme = "sphinx_book_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]

lobsterpy/structuregraph/graph.py

@@ -0,0 +1,171 @@
+# Copyright (c) lobsterpy development team
+# Distributed under the terms of a BSD 3-Clause "New" or "Revised" License
+
+"""
+This package provides the modules for generating graph objects using lobsterpy data
+"""
+
+from typing import Optional
+from pymatgen.core.structure import Structure
+from pymatgen.io.lobster.lobsterenv import LobsterNeighbors
+from pymatgen.io.lobster.outputs import Charge
+from lobsterpy.cohp.analyze import Analysis
+
+
+class LobsterGraph:
+    """
+    LobsterGraph class for bonding data from Lobster
+
+    Attributes:
+        sg: return structure_graph object
+    """
+
+    def __init__(
+        self,
+        path_to_poscar: str,
+        path_to_charge: str,
+        path_to_cohpcar: str,
+        path_to_icohplist: str,
+        path_to_madelung: str,
+        add_additional_data_sg=True,
+        path_to_icooplist: Optional[str] = None,
+        path_to_icobilist: Optional[str] = None,
+        which_bonds: str = "all",
+        cutoff_icohp: float = 0.10,
+        start: str = None,
+    ):
+        """
+        This is a class to get structure graph object with bonding information from lobsterpy
+
+        Args:
+            path_to_poscar: path to POSCAR (e.g., "POSCAR")
+            path_to_charge: path to CHARGE.lobster (e.g., "CHARGE.lobster")
+            path_to_cohpcar: path to COHPCAR.lobster (e.g., "COHPCAR.lobster")
+            path_to_icohplist: path to ICOHPLIST.lobster (e.g., "ICOHPLIST.lobster")
+            path_to_icooplist: path to ICOOPLIST.lobster (e.g., "ICOOPLIST.lobster")
+            path_to_icobilist: path to ICOBILIST.lobster (e.g., "ICOBILIST.lobster")
+            path_to_madelung: path to MadelungEnergies.lobster (e.g., "MadelungEnergies.lobster")
+            cutoff_icohp : only bonds that are stronger than cutoff_icohp*strongest ICOHP will be considered
+            add_additional_data_sg: (bool) if True will add the information from ICOOPLIST.lobster
+            and ICOBILIST.lobster based on ICOHPLIST.lobster relevant bond
+            which_bonds: selects which kind of bonds are analyzed. "all" is the default
+            start: start energy for bonding antibonding percent integration
+        """
+        if add_additional_data_sg:
+            self.add_additional_data_sg = add_additional_data_sg
+            if path_to_icooplist is not None and path_to_icobilist is not None:
+                self.path_to_icooplist = path_to_icooplist
+                self.path_to_icobilist = path_to_icobilist
+            else:
+                raise ValueError(
+                    "add_additional_data_sg is set to True."
+                    "Please provide path_to_icooplist and path_to_icobilist"
+                )
+        else:
+            self.add_additional_data_sg = add_additional_data_sg
+
+        self.path_to_poscar = path_to_poscar
+        self.path_to_charge = path_to_charge
+        self.path_to_cohpcar = path_to_cohpcar
+        self.path_to_icohplist = path_to_icohplist
+        self.path_to_madelung = path_to_madelung
+        self.which_bonds = which_bonds
+        self.cutoff_icohp = cutoff_icohp
+
+        if self.which_bonds == "all":
+            self.additional_condition = 0
+        elif self.which_bonds == "cation-anion":
+            self.additional_condition = 1
+        else:
+            raise ValueError(
+                "Only accepted values are 'all' and 'cation-anion'."
+                "Please check the input parameters of which_bonds arg"
+            )
+        self.start = start
+
+        self.sg = self.get_decorated_sg()
+
+    def get_decorated_sg(self):
+        """
+        Method to generate graph object decorated with bonding data from lobsterpy
+        Returns:
+            structure graph object
+        """
+        if self.add_additional_data_sg:
+            chemenvlobster = LobsterNeighbors(
+                are_coops=False,
+                filename_ICOHP=self.path_to_icohplist,
+                perc_strength_ICOHP=self.cutoff_icohp,
+                structure=Structure.from_file(self.path_to_poscar),
+                additional_condition=self.additional_condition,
+                filename_CHARGE=self.path_to_charge,
+                add_additional_data_sg=self.add_additional_data_sg,
+                filename_blist_sg1=self.path_to_icobilist,
+                id_blist_sg1="ICOBI",
+                filename_blist_sg2=self.path_to_icooplist,
+                id_blist_sg2="ICOOP",
+                valences_from_charges=True,
+                adapt_extremum_to_add_cond=True,
+            )
+
+        else:
+            chemenvlobster = LobsterNeighbors(
+                are_coops=False,
+                filename_ICOHP=self.path_to_icohplist,
+                perc_strength_ICOHP=self.cutoff_icohp,
+                structure=Structure.from_file(self.path_to_poscar),
+                additional_condition=self.additional_condition,
+                filename_CHARGE=self.path_to_charge,
+                add_additional_data_sg=self.add_additional_data_sg,
+                valences_from_charges=True,
+                adapt_extremum_to_add_cond=True,
+            )
+
+        # Adds Mulliken and Löwdin charges as site properties to structure object (node properties)
+        decorated_structure = Charge(self.path_to_charge).get_structure_with_charges(
+            self.path_to_poscar
+        )
+
+        # Create the structure graph object decorated with site and edge properties based on ICOHP/ICOBI/ICOOP data
+        lobster_env = chemenvlobster.get_bonded_structure(
+            structure=decorated_structure, decorate=True, edge_properties=True
+        )
+
+        # Initialize automating bonding analysis from Lobsterpy based on ICOHP
+        analyze = Analysis(
+            path_to_charge=self.path_to_charge,
+            path_to_cohpcar=self.path_to_cohpcar,
+            path_to_poscar=self.path_to_poscar,
+            path_to_icohplist=self.path_to_icohplist,
+            path_to_madelung=self.path_to_madelung,
+            whichbonds=self.which_bonds,
+            cutoff_icohp=self.cutoff_icohp,
+        )
+
+        # Store the summarized dictionary object containing bonding information
+        cba = analyze.condensed_bonding_analysis
+
+        # Iterate over sites in the dictionary
+        for k, v in cba["sites"].items():
+            for k2, v2 in lobster_env.graph.nodes.data():
+                # Check if ions are same and add its corresponding environment in node properties
+                if v["ion"] == v2["specie"]:
+                    v2["properties"].update({"env": v["env"]})
+
+        for (
+            edge_prop
+        ) in lobster_env.graph.edges.data():  # Iterate over structure graph edges
+            _ab, ab_p, _b, b_p = analyze._integrate_antbdstates_below_efermi(
+                cohp=analyze.chemenv.completecohp.get_cohp_by_label(
+                    edge_prop[2]["bond_label"]
+                ),
+                start=self.start,
+            )  # Compute bonding- antibonding percentages for each bond in structure graph object
+            edge_prop[2][
+                "ICOHP_bonding_perc"
+            ] = b_p  # Store bonding percentage in edge of graph object
+            edge_prop[2][
+                "ICOHP_antibonding_perc"
+            ] = ab_p  # Store anti-bonding percentage in edge graph object
+
+        return lobster_env