Interactive plotter

docs/source/commandlineinterface.rst

@@ -227,6 +227,20 @@ command. Below is an example and sample output using this command.
 
 .. image:: Lobsterpy_tutorial_files/ICOHP.png
 
+-  ``lobsterpy automatic-plot-ia`` command can be used to obtain a interactive plot of analysis automatically. It will evaluate all COHPs with ICOHP values down to
+   10% of the strongest ICOHP. You can enforce an analysis of all bonds
+   by using ``lobsterpy automatic-plot-ia --allbonds``. Currently, the
+   computed Mulliken charges will be used to determine cations and
+   anions. If no CHARGE.lobster is available, the algorithm will fall
+   back to the BondValence analysis from pymatgen. Please be aware that
+   LobsterPy can only analyze bonds that have been included in the
+   initial Lobster computation. Below is an example and sample output
+   using this command. You can also obtain label resolved plot using
+   ``lobsterpy automatic-plot-ia --allbonds --label-resolved`` option
+
+.. raw:: html
+   :file: Lobsterpy_tutorial_files/CdF2.html
+
 2. Plotting of COHPs/COBIs/COOPs
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

docs/source/conf.py

@@ -48,7 +48,7 @@
 # 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/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
@@ -57,9 +57,10 @@ def run_apidoc(_):
     output_path = os.path.abspath(os.path.dirname(__file__))
     excludes = glob.glob(os.path.join(output_path, "../../lobsterpy/cohp/test"))
     excludes1 = glob.glob(os.path.join(output_path, "../../lobsterpy/test"))
+    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), "--force"]
+    command = [cmd_path, "-e", "-o", output_path, module, " ".join(excludes)," ".join(excludes1)," ".join(excludes2), "--force"]
     subprocess.check_call(command)
 
 

docs/source/pythoninterface.rst

@@ -41,9 +41,15 @@ Import the necessary modules
     # Automatic plots
     describe.plot_cohps(ylim=[-10, 2], xlim=[-4, 4])
 
+.. image:: Lobsterpy_tutorial_files/Lobsterpy_tutorial_38_0.png
+
+.. code:: ipython3
 
+    # Automatic interactive plots
+    describe.plot_interactive_cohps()
 
-.. image:: Lobsterpy_tutorial_files/Lobsterpy_tutorial_38_0.png
+.. raw:: html
+   :file: Lobsterpy_tutorial_files/CdF2.html
 
 
 .. code:: ipython3

lobsterpy/cli.py

@@ -16,7 +16,7 @@
 
 from lobsterpy.cohp.analyze import Analysis
 from lobsterpy.cohp.describe import Description
-from lobsterpy.plotting import PlainCohpPlotter, get_style_list
+from lobsterpy.plotting import PlainCohpPlotter, get_style_list, InteractiveCohpPlotter
 
 
 def main() -> None:
@@ -199,6 +199,14 @@ def get_parser() -> argparse.ArgumentParser:
     plotting_group.add_argument(
         "--fontsize", "--font-size", type=float, default=None, help="Base font size"
     )
+    plotting_group.add_argument(
+        "--labelresolved",
+        "--label-resolved",
+        action="store_true",
+        help="Will create automatic interactive plots with all relevant bond labels. "
+        "If not set, plots will consists of summed cohps. (This argument works only"
+        "for interactive plots) ",
+    )
 
     auto_parent = argparse.ArgumentParser(add_help=False)
     auto_group = auto_parent.add_argument_group("Automatic analysis")
@@ -244,6 +252,16 @@ def get_parser() -> argparse.ArgumentParser:
         ),
     )
 
+    subparsers.add_parser(
+        "automatic-plot-ia",
+        aliases=["automaticplotia", "autoplotia", "auto-plot-ia"],
+        parents=[input_parent, auto_parent, plotting_parent],
+        help=(
+            "Creates an interactive plot of most important COHPs automatically. Implementation "
+            "of COBIs and COOPs will follow."
+        ),
+    )
+
     subparsers.add_parser(
         "create-inputs",
         aliases=["createinputs"],
@@ -349,6 +367,11 @@ def run(args):
         "description",
         "automatic-plot",
         "plot",
+        "automatic-plot-ia",
+        "interactplot",
+        "automaticplotia",
+        "auto-plot-ia",
+        "autoplotia",
     ]:
         # Check for .gz files exist for default values and update accordingly
         default_files = {
@@ -373,7 +396,17 @@ def run(args):
     if args.action in ["automaticplot", "autoplot", "auto-plot"]:
         args.action = "automatic-plot"
 
-    if args.action in ["description", "automatic-plot"]:
+    if args.action in ["automaticplotia", "automatic-plot-ia", "auto-plot-ia"]:
+        args.action = "automaticplotia"
+
+    if args.action in [
+        "description",
+        "automatic-plot",
+        "automatic-plot-ia",
+        "automaticplotia",
+        "auto-plot-ia",
+        "autoplotia",
+    ]:
         if args.allbonds:
             whichbonds = "all"
         else:
@@ -395,7 +428,14 @@ def run(args):
             with open(args.json, "w") as fd:
                 json.dump(analysedict, fd)
 
-    if args.action in ["plot", "automatic-plot"]:
+    if args.action in [
+        "plot",
+        "automatic-plot",
+        "automaticplotia",
+        "automatic-plot-ia",
+        "auto-plot-ia",
+        "autoplotia",
+    ]:
         style_kwargs = {}
         style_kwargs.update(_user_figsize(args.width, args.height))
         if args.fontsize:
@@ -422,7 +462,25 @@ def run(args):
             filename=args.save_plot,
             title=args.title,
             sigma=sigma,
-            skip_show=args.hideplot,
+            hide=args.hideplot,
+        )
+
+    if args.action in [
+        "automatic-plot-ia",
+        "automaticplotia",
+        "auto-plot-ia",
+        "autoplotia",
+    ]:
+        describe.plot_interactive_cohps(
+            ylim=args.ylim,
+            xlim=args.xlim,
+            integrated=args.integrated,
+            save_as_html=args.save_plot,
+            filename=args.save_plot,
+            title=args.title,
+            sigma=sigma,
+            hide=args.hideplot,
+            label_resolved=args.labelresolved,
         )
 
     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 /