Updating all PythonModules to sync with PROJ_irox

dft_job_automat/job_analysis.py

@@ -224,9 +224,14 @@ def __load_dataframe__(self):
             fle_name = self.root_dir + "/jobs_bin/job_dataframe.pickle"
 
         with open(fle_name, "rb") as fle:
+
+
             if sys.version_info.major > 2:
-                df = pickle.load(fle, encoding="latin1")
+                #  print("IJDIFIDSj89yu892sdf")
+                #  print("fle_name:", fle_name)
+
                 # NOTE Added encoding="latin1" for p36 support (180415 - RF)
+                df = pickle.load(fle, encoding="latin1")
             else:
                 df = pickle.load(fle)
 

dft_job_automat/job_setup.py

@@ -364,8 +364,18 @@ def __Job_list__(self):
 
                 print(job_i_dir)
                 if rev_dirs:
+
+                    print("rev_dirs:", rev_dirs)
+
                     if self.parse_all_revisions is False:
-                        rev_dirs = [rev_dirs[-1]]
+
+                        last_rev_int = np.sort(
+                                    [int(i.split("_")[-1]) for i in rev_dirs])[-1]
+                        rev_dirs = ["_" + str(last_rev_int), ]
+                        # rev_dirs = [rev_dirs[-1]]
+
+                        print("rev_dirs:", rev_dirs)
+                        print("IOPSDFJOKIDSIJFIJDSF")
 
                     for rev_i in rev_dirs:
                         path_i = os.path.join(job_i_dir, rev_i)

oxr_reaction/oxr_methods.py

@@ -214,6 +214,7 @@ def df_calc_adsorption_e(
             oxy_ref_e=oxy_ref,
             hyd_ref_e=hyd_ref,
             )
+        #  print("ads_e_i:", ads_e_i)
         ads_e_list.append(ads_e_i)
 
     df["ads_e"] = np.array(ads_e_list)

oxr_reaction/oxr_plotting_classes/oxr_plot_2d_volcano.py

@@ -39,11 +39,20 @@ class Volcano_Plot_2D():
     def __init__(self,
         ORR_Free_E_Plot,
         plot_range=None,
+        smart_format_dict=None,
+        marker_color_key="color2",
+        marker_border_color_key="color1",
+        marker_shape_key="symbol",
+
         ):
         """
         """
         # | - __init__
         self.ORR_Free_E_Plot = ORR_Free_E_Plot
+        self.smart_format_dict = smart_format_dict
+        self.marker_color_key = marker_color_key
+        self.marker_border_color_key = marker_border_color_key
+        self.marker_shape_key = marker_shape_key
 
         if plot_range is None:
             self.plot_range = {
@@ -167,9 +176,54 @@ def __create_data_point_traces__(self):
         """
         """
         # | - __create_data_point_traces__
+
+
+        # | - Default Smart Format Dict
+        smart_format_dict = self.smart_format_dict
+
+        if smart_format_dict is None:
+            print("No smart format given!")
+            smart_format_dict = [
+                [{"bulk_system": "IrO3"}, {self.marker_color_key: "green"}],
+                [{"bulk_system": "IrO2"}, {self.marker_color_key: "yellow"}],
+
+                [{"coverage_type": "o_covered"}, {"symbol": "s"}],
+                [{"coverage_type": "h_covered"}, {"symbol": "^"}],
+
+                [{"facet": "110"}, {"color1": "red"}],
+                [{"facet": "211"}, {"color1": "green"}],
+                [{"facet": "100"}, {"color1": "black"}],
+                ]
+        # __|
+
+
         data_list = []
-        for sys_i in self.ORR_Free_E_Plot.series_list:
-            trace_i = self.__create_scatter_trace_i__(sys_i)
+        for series_i in self.ORR_Free_E_Plot.series_list:
+
+
+            smart_format_i = self.ORR_Free_E_Plot.__create_smart_format_dict__(
+                series_i.properties,
+                smart_format_dict,
+                )
+
+            name_i = series_i.series_name
+
+            if series_i.color is not None:
+                smart_format_i[self.marker_color_key] = series_i.color
+
+
+            format_i = smart_format_i
+
+            if series_i.format_dict:
+                format_i = series_i.format_dict
+
+
+            print("format_i:", format_i)
+
+            trace_i = self.__create_scatter_trace_i__(
+                series_i,
+                smart_format_i=format_i,
+                )
             data_list.append(trace_i)
 
         return(data_list)
@@ -182,6 +236,7 @@ def __create_scatter_trace_i__(self,
         """
         """
         # | - __create_trace_i__
+        print("sys_i:", sys_i)
         trace_i = go.Scatter(
             x=[sys_i.energy_states_dict["o"] - sys_i.energy_states_dict["oh"]],
             y=[sys_i.energy_states_dict["oh"]],
@@ -193,15 +248,41 @@ def __create_scatter_trace_i__(self,
             # <br>
             hoverinfo="name",
 
+            # marker=dict(
+            #     size=20,
+            #     #  symbol=sys_i.format_dict["symbol_i"],
+            #     symbol=sys_i.format_dict.get("symbol_i", "circle"),
+            #     color=sys_i.format_dict.get("color_2", "blue"),
+            #     line=dict(
+            #         width=2,
+            #         smart_format_i
+            #         color=sys_i.format_dict.get("color_1", "black"),
+            #         ),
+            #     ),
+
             marker=dict(
-                size=20,
-                symbol=sys_i.format_dict["symbol_i"],
-                color=sys_i.format_dict["color_2"],
+                size=smart_format_i.get("marker_size", 9),
+                color=smart_format_i.get(self.marker_color_key, "red"),
+                symbol=smart_format_i.get(
+                    self.marker_shape_key, "circle"),
                 line=dict(
-                    width=2,
-                    color=sys_i.format_dict["color_1"],
+                    width=smart_format_i.get("marker_border_width", 1.),
+                    color=smart_format_i.get(
+                        self.marker_border_color_key, "black"),
                     ),
                 ),
+
+            # marker=dict(
+            #     size=20,
+            #     #  symbol=sys_i.format_dict["symbol_i"],
+            #     symbol=sys_i.format_dict.get("symbol_i", "circle"),
+            #     color=sys_i.format_dict.get("color_2", "blue"),
+            #     line=dict(
+            #         width=2,
+            #         color=sys_i.format_dict.get("color_1", "black"),
+            #         ),
+            #     ),
+
             )
 
         return(trace_i)
@@ -223,7 +304,7 @@ def ooh_oh_scaling(self, doh):
         """ooh_oh_scaling equation."""
         # | - ooh_oh_scaling
         #like ambars
-        #dooh=0.5*doh  + 3.0		 #O
+        #dooh=0.5*doh  + 3.0         #O
         #normal one
         # dooh = doh + 3.2
 

oxr_reaction/oxr_plotting_classes/oxr_plot_scaling.py

@@ -269,7 +269,9 @@ def __create_trace_i__(self,
                     # color=smart_format_i[marker_border_color_key],
                     color=smart_format_i.get(
                         self.marker_border_color_key, "black"),
-                    width=1.,
+                    #  width=1.,
+
+                    width=smart_format_i.get("marker_border_width", 1.),
                     )
                 )
             )
@@ -381,10 +383,11 @@ def fit_scaling_lines(self,
         # | - Equation Annotations
         if dependent_species == "ooh":
             eqn_str_i = ("" +
-                "ΔG<sub>OOH</sub>=" +
+                "ΔG<sub>OOH</sub> = " +
                 str(round(slope_i, num_round)) +
-                " ΔG<sub>OH</sub>+" +
+                " ΔG<sub>OH</sub> + " +
                 str(round(intercept_i, num_round)) +
+                " (eV)" +
                 ""
                 )
 
@@ -394,17 +397,19 @@ def fit_scaling_lines(self,
             eqn_str_i = ("" +
                 "ΔG<sub>O</sub> = " +
                 str(round(slope_i, num_round)) +
-                " ΔG<sub>OH</sub>+" +
+                " ΔG<sub>OH</sub> + " +
                 str(round(intercept_i, num_round)) +
+                " (eV)" +
                 ""
                 )
 
         elif dependent_species == "oh":
             eqn_str_i = ("" +
                 "ΔG<sub>OH</sub> = " +
                 str(round(slope_i, num_round)) +
-                " ΔG<sub>OH</sub>+" +
+                " ΔG<sub>OH</sub> + " +
                 str(round(intercept_i, num_round)) +
+                " (eV)" +
                 ""
                 )
 
@@ -481,21 +486,21 @@ def add_ideal_lines(self):
             name="*OOH vs *OH Scaling",
             color="black",
             width=1,
-            dash="dash",
+            dash="dot",
             )
 
         self.add_line({"slope": 2, "intercept": 0.},
             name="*O vs *OH Scaling",
             color="black",
             width=1,
-            dash="dash",
+            dash="dot",
             )
 
         self.add_line({"slope": 1, "intercept": 0.},
             name="*OH vs *OH Scaling",
             color="black",
             width=1,
-            dash="dash",
+            dash="dot",
             )
         # __|
 

oxr_reaction/oxr_plotting_classes/oxr_plot_volcano.py

@@ -400,7 +400,7 @@ def __create_trace_i__(self,
 
             legendgroup=group,
 
-            hoverinfo="text",
+            # hoverinfo="text",
 
             # hoverinfo=None,
             # hoverinfosrc=None,

oxr_reaction/oxr_series.py

@@ -103,7 +103,10 @@ def __init__(
         self.hover_text_col = hover_text_col
         self.plot_mode = plot_mode
         self.smart_format = smart_format
+
         self.format_dict = format_dict
+        if format_dict is None:
+            self.format_dict = dict()
 
         # self.overpotential_type = overpotential_type
         self.rxn_type = rxn_type

plotting/my_plotly.py

@@ -80,6 +80,42 @@ def add_duplicate_axes(
     ):
     """
     Note: range must be set for this to work
+
+    Example usage:
+
+    from plotting.my_plotly import add_duplicate_axes
+
+    shared_axis_data = {
+	"tickcolor": "black",
+	"ticklen": 3,
+	}
+
+    shared_xaxis_data = {
+	"dtick": 50,
+	**shared_axis_data,
+	}
+
+    shared_yaxis_data = {
+	"dtick": 1,
+	**shared_axis_data,
+	}
+
+    shared_meth_props = dict(
+	tmp_define_both_axis_types=True,
+	)
+
+    add_duplicate_axes(
+	fig, axis_type='x',
+	axis_data=shared_xaxis_data,
+	axis_num_list=[1, ],
+	**shared_meth_props)
+    add_duplicate_axes(
+	fig, axis_type='y',
+	axis_data=shared_yaxis_data,
+	axis_num_list=[1, ],
+	**shared_meth_props)
+
+
     """
     # | - add_duplicate_axes
 
@@ -309,6 +345,12 @@ def my_plotly_plot(
             )
     # __|
 
+    if write_svg:
+        try:
+            fig.write_image(prepath + ".svg")
+        except:
+            print("Couldn't write svg")
+
     # | - Write pdf and svg (if ORCA is installed and working)
     # Getting the hostname of computer
     import socket
@@ -333,11 +375,6 @@ def my_plotly_plot(
                 fig.write_image(prepath + ".pdf")
             except:
                 print("Couldn't write pdf")
-        if write_svg:
-            try:
-                fig.write_image(prepath + ".svg")
-            except:
-                print("Couldn't write svg")
         if write_png:
             try:
                 fig.write_image(prepath + ".png", scale=png_scale)
@@ -393,11 +430,6 @@ def reapply_colors(data):
     # __|
 
 
-def plot_layout(
-    # xax_labels =
-    ):
-    """
-
 
 
 
@@ -408,6 +440,13 @@ def plot_layout(
 
 
 # | - OLD | add_duplicate_axes
+
+# def plot_layout(
+#     # xax_labels =
+#     ):
+#     """
+
+
 # def add_duplicate_axes(
 #     fig,
 #     axis_type="x",  # 'x' or 'y'
@@ -461,4 +500,3 @@ def plot_layout(
 #                 }).to_plotly_json())
 #     # __|
 # __|
-