Interactive plotter

lobsterpy/cli.py

@@ -422,7 +422,7 @@ def run(args):
             filename=args.save_plot,
             title=args.title,
             sigma=sigma,
-            skip_show=args.hideplot,
+            hide=args.hideplot,
         )
 
     if args.action == "plot":

lobsterpy/cohp/analyze.py

@@ -36,11 +36,12 @@ class Analysis:
         path_to_icohplist: str that describes the path to ICOHPLIST.lobster
         path_to_poscar: str that describes path to POSCAR
         path_to_madelung: str that describes path to POSCAR
-        set_cohps: list of cohps
-        set_coordination_ions: list of coodination environment strings for each cation
+        seq_cohps: list of cohps
+        seq_coord_ions: list of coodination environment strings for each cation
         set_equivalent_sites: set of inequivalent sites
-        set_inequivalent_ions: set of inequivalent cations/sites in the structure
-        set_infos_bonds: information on cation anion bonds
+        seq_ineq_ions: set of inequivalent cations/sites in the structure
+        seq_infos_bonds (list): information on cation anion bonds (lists
+            of pymatgen.io.lobster.lobsterenv.ICOHPNeighborsInfo)
         spg: space group information
         structure: Structure object
         type_charge: which charges are considered here
@@ -141,7 +142,7 @@ def setup_env(self):
                 if (
                     str(err) == "min() arg is an empty sequence"
                     or str(err)
-                    == "All valences are equal to 0, additional_conditions 1 and 3 and 5 and 6 will not work"
+                    == "All valences are equal to 0, additional_conditions 1, 3, 5 and 6 will not work"
                 ):
                     raise ValueError(
                         "Consider switching to an analysis of all bonds and not only cation-anion bonds."
@@ -220,25 +221,24 @@ def get_information_all_bonds(self, summed_spins=True):
         """
         if self.whichbonds == "cation-anion":
             # this will only analyze cation anion bonds which simplifies the analysis
-            self.set_inequivalent_ions = []
-            self.set_coordination_ions = []
-            self.set_infos_bonds = []
-            self.set_labels_cohps = []
-            self.set_cohps = []
+            self.seq_ineq_ions = []
+            self.seq_coord_ions = []
+            self.seq_infos_bonds = []
+            self.seq_labels_cohps = []
+            self.seq_cohps = []
             # only_bonds_to
 
             self.anion_types = self.chemenv.get_anion_types()
             for ice, ce in enumerate(self.lse.coordination_environments):
                 # only look at inequivalent sites (use of symmetry to speed everything up!)!
                 # only look at those cations that have cation-anion bonds
                 if ice in self.set_equivalent_sites and ce[0]["ce_symbol"] is not None:
-                    self.set_inequivalent_ions.append(ice)
-                    ce = ce[0]["ce_symbol"]
-                    self.set_coordination_ions.append(ce)
-                    cation_anion_infos = self.chemenv.get_info_icohps_to_neighbors(
-                        [ice]
+                    self.seq_ineq_ions.append(ice)
+
+                    self.seq_coord_ions.append(ce[0]["ce_symbol"])
+                    self.seq_infos_bonds.append(
+                        self.chemenv.get_info_icohps_to_neighbors([ice])
                     )
-                    self.set_infos_bonds.append(cation_anion_infos)
 
                     aniontype_labels = []
                     aniontype_cohps = []
@@ -257,29 +257,29 @@ def get_information_all_bonds(self, summed_spins=True):
                         aniontype_labels.append(labels)
                         aniontype_cohps.append(summedcohps)
 
-                    self.set_labels_cohps.append(aniontype_labels)
-                    self.set_cohps.append(aniontype_cohps)
+                    self.seq_labels_cohps.append(aniontype_labels)
+                    self.seq_cohps.append(aniontype_cohps)
 
         elif self.whichbonds == "all":
             # this will only analyze all bonds
 
-            self.set_inequivalent_ions = []
-            self.set_coordination_ions = []
-            self.set_infos_bonds = []
-            self.set_labels_cohps = []
-            self.set_cohps = []
+            self.seq_ineq_ions = []
+            self.seq_coord_ions = []
+            self.seq_infos_bonds = []
+            self.seq_labels_cohps = []
+            self.seq_cohps = []
             # only_bonds_to
             self.elements = self.structure.composition.elements
             # self.anion_types = self.chemenv.get_anion_types()
             for ice, ce in enumerate(self.lse.coordination_environments):
                 # only look at inequivalent sites (use of symmetry to speed everything up!)!
                 # only look at those cations that have cation-anion bonds
                 if ice in self.set_equivalent_sites and ce[0]["ce_symbol"] is not None:
-                    self.set_inequivalent_ions.append(ice)
-                    ce = ce[0]["ce_symbol"]
-                    self.set_coordination_ions.append(ce)
-                    bonds_infos = self.chemenv.get_info_icohps_to_neighbors([ice])
-                    self.set_infos_bonds.append(bonds_infos)
+                    self.seq_ineq_ions.append(ice)
+                    self.seq_coord_ions.append(ce[0]["ce_symbol"])
+                    self.seq_infos_bonds.append(
+                        self.chemenv.get_info_icohps_to_neighbors([ice])
+                    )
 
                     type_labels = []
                     type_cohps = []
@@ -298,8 +298,8 @@ def get_information_all_bonds(self, summed_spins=True):
                         type_labels.append(labels)
                         type_cohps.append(summedcohps)
 
-                    self.set_labels_cohps.append(type_labels)
-                    self.set_cohps.append(type_cohps)
+                    self.seq_labels_cohps.append(type_labels)
+                    self.seq_cohps.append(type_cohps)
 
     @staticmethod
     def _get_strenghts_for_each_bond(pairs, strengths, nameion=None):
@@ -648,9 +648,9 @@ def set_condensed_bonding_analysis(self):
 
         # how many inequivalent cations are in the structure
         if self.whichbonds == "cation-anion":
-            number_considered_ions = len(self.set_inequivalent_ions)
+            number_considered_ions = len(self.seq_ineq_ions)
         elif self.whichbonds == "all":
-            number_considered_ions = len(self.set_inequivalent_ions)
+            number_considered_ions = len(self.seq_ineq_ions)
 
         # what was the maximum bond lengths that was considered
         max_bond_lengths = max(self.chemenv.Icohpcollection._list_length)
@@ -662,11 +662,11 @@ def set_condensed_bonding_analysis(self):
         site_dict = {}
         if self.whichbonds == "cation-anion":
             for ication, ce, cation_anion_infos, labels, cohps in zip(
-                self.set_inequivalent_ions,
-                self.set_coordination_ions,
-                self.set_infos_bonds,
-                self.set_labels_cohps,
-                self.set_cohps,
+                self.seq_ineq_ions,
+                self.seq_coord_ions,
+                self.seq_infos_bonds,
+                self.seq_labels_cohps,
+                self.seq_cohps,
             ):
                 namecation = str(self.structure[ication].specie)
 
@@ -702,11 +702,11 @@ def set_condensed_bonding_analysis(self):
                 }
         elif self.whichbonds == "all":
             for iion, ce, bond_infos, labels, cohps in zip(
-                self.set_inequivalent_ions,
-                self.set_coordination_ions,
-                self.set_infos_bonds,
-                self.set_labels_cohps,
-                self.set_cohps,
+                self.seq_ineq_ions,
+                self.seq_coord_ions,
+                self.seq_infos_bonds,
+                self.seq_labels_cohps,
+                self.seq_cohps,
             ):
                 nameion = str(self.structure[iion].specie)
 
@@ -810,9 +810,7 @@ def set_summary_dicts(self):
 
         """
         relevant_ion_ids = [
-            isite
-            for isite in self.list_equivalent_sites
-            if isite in self.set_inequivalent_ions
+            isite for isite in self.list_equivalent_sites if isite in self.seq_ineq_ions
         ]
 
         # formula_units = self.structure.composition.num_atoms /

lobsterpy/cohp/describe.py

@@ -9,6 +9,7 @@
 from pathlib import Path
 
 from lobsterpy.plotting import PlainCohpPlotter
+from lobsterpy.plotting import InteractiveCohpPlotter
 
 
 class Description:
@@ -45,7 +46,7 @@ def set_description(self):
                 [
                     str(site.specie) + str(isite + 1)
                     for isite, site in enumerate(self.analysis_object.structure)
-                    if isite in self.analysis_object.set_inequivalent_ions
+                    if isite in self.analysis_object.seq_ineq_ions
                 ]
             )
             self.text = []
@@ -119,7 +120,7 @@ def set_description(self):
                 [
                     str(site.specie) + str(isite + 1)
                     for isite, site in enumerate(self.analysis_object.structure)
-                    if isite in self.analysis_object.set_inequivalent_ions
+                    if isite in self.analysis_object.seq_ineq_ions
                 ]
             )
             self.text = []
@@ -210,7 +211,7 @@ def plot_cohps(
         integrated=False,
         title="",
         sigma=None,
-        skip_show=False,
+        hide=False,
     ):
         """
         Will automatically generate plots of the most relevant COHP
@@ -223,22 +224,23 @@ def plot_cohps(
             integrated (bool): if True, integrated COHPs will be shown
             sigma: Standard deviation of Gaussian broadening applied to
                 population data. If None, no broadening will be added.
-            skip_show (bool): if True, the plot will not be shown.
+            title: sets the title of figure generated
+            hide (bool): if True, the plot will not be shown.
 
         Returns:
             A matplotlib object.
 
         """
-        set_cohps = self.analysis_object.set_cohps
+        seq_cohps = self.analysis_object.seq_cohps
         if self.analysis_object.whichbonds == "cation-anion":
-            set_inequivalent_cations = self.analysis_object.set_inequivalent_ions
+            seq_ineq_cations = self.analysis_object.seq_ineq_ions
         elif self.analysis_object.whichbonds == "all":
-            set_inequivalent_cations = self.analysis_object.set_inequivalent_ions
-        set_labels_cohps = self.analysis_object.set_labels_cohps
+            seq_ineq_cations = self.analysis_object.seq_ineq_ions
+        seq_labels = self.analysis_object.seq_labels_cohps
         structure = self.analysis_object.structure
 
         for iplot, (ication, labels, cohps) in enumerate(
-            zip(set_inequivalent_cations, set_labels_cohps, set_cohps)
+            zip(seq_ineq_cations, seq_labels, seq_cohps)
         ):
             namecation = str(structure[ication].specie)
 
@@ -253,7 +255,7 @@ def plot_cohps(
 
             plot.title(title)
             if save:
-                if len(set_inequivalent_cations) > 1:
+                if len(seq_ineq_cations) > 1:
                     if isinstance(filename, str):
                         filename = Path(filename)
                     filename_new = (
@@ -262,12 +264,68 @@ def plot_cohps(
                 else:
                     filename_new = filename
                 plot.savefig(filename_new)
-        if not skip_show:
+        if not hide:
             plot.show()
         else:
             if not save:
                 plot.close()
 
+    def plot_interactive_cohps(
+        self,
+        save_as_html=False,
+        filename=None,
+        ylim=None,
+        xlim=None,
+        integrated=False,
+        title="",
+        sigma=None,
+        skip_show=False,
+    ):
+        """
+        Will automatically generate interactive plots of the most relevant COHP
+
+        Args:
+            save_as_html (bool): will save the plot to a html file
+            filename (str/Path):
+            ylim (list of float): energy scale that is shown in plot (eV)
+            xlim (list of float): energy range for COHPs in eV
+            integrated (bool): if True, integrated COHPs will be shown
+            sigma: Standard deviation of Gaussian broadening applied to
+                population data. If None, no broadening will be added.
+            title : Title of the interactive plot
+            skip_show (bool): if True, the plot will not be shown.
+
+        Returns:
+            A plotly.graph_objects.Figure object.
+
+        """
+        cba_cohp_plot_data = {}  # Initialize dict to store plot data
+
+        set_cohps = self.analysis_object.seq_cohps
+        set_labels_cohps = self.analysis_object.seq_labels_cohps
+        set_inequivalent_cations = self.analysis_object.seq_ineq_ions
+        structure = self.analysis_object.structure
+
+        for _iplot, (ication, labels, cohps) in enumerate(
+            zip(set_inequivalent_cations, set_labels_cohps, set_cohps)
+        ):
+            label_str = f"{str(structure[ication].specie)}{str(ication + 1)}: "
+            for label, cohp in zip(labels, cohps):
+                if label is not None:
+                    cba_cohp_plot_data[label_str + label] = cohp
+
+        ia = InteractiveCohpPlotter()
+        ia.add_cohps_from_plot_data(plot_data_dict=cba_cohp_plot_data)
+        plot = ia.get_plot(integrated=integrated, xlim=xlim, ylim=ylim, sigma=sigma)
+
+        plot.update_layout(title_text=title)
+        if save_as_html:
+            plot.write_html(filename, include_mathjax="cdn")
+        if not skip_show:
+            return plot.show()
+
+        return plot
+
     @staticmethod
     def _coordination_environment_to_text(ce):
         """

lobsterpy/cohp/test/test_describe.py

@@ -356,7 +356,7 @@ def test_plot(self):
             self.assertFalse(Path(filename_test).exists())
             self.assertTrue(Path(filename_test_1).exists())
 
-    def test_write_descritoin(self):
+    def test_write_description(self):
         self.describe_NaCl.write_description()
         self.describe_NaSi_madelung_all.write_description()
         self.describe_NaSbF6.write_description()