Merge branch 'main' of github.com:rinikerlab/reeds into main

rinikerlab · Sep 4, 2023 · 5e79089 · 5e79089
2 parents 99d600f + 208749a
commit 5e79089
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Showing 2 changed files with 42 additions and 28 deletions.
diff --git a/reeds/function_libs/input_prep/hybrid_topology_maker.py b/reeds/function_libs/input_prep/hybrid_topology_maker.py
@@ -912,10 +912,14 @@ def find_14_neighbours(atomID, bonds, neigh12, neigh13):
 
     # Now we need to remove any potential "false" 3rd neighbour
     # which occur for cyclic systems.
-
+    to_remove = []
     for neigh in neigh14:
-        if neigh in neigh13 or neigh in neigh12: neigh14.remove(neigh)
+        if neigh in neigh13 or neigh in neigh12: 
+            to_remove.append(neigh)
 
+    for atom in to_remove:
+        neigh14.remove(atom)
+
     return sorted(list(set(neigh14)))
 
 

diff --git a/reeds/function_libs/visualization/sampling_plots.py b/reeds/function_libs/visualization/sampling_plots.py
@@ -284,9 +284,9 @@ def plot_stateOccurence_matrix(data: dict,
         [np.array([data[replica]["max_contributing_state"][key] for key in sorted(data[replica]["max_contributing_state"])])
          for replica in sorted(data)]).T
 
-    # Plot occurence:
+    # Plot occurrence:
     ##Title setting
-    title = "occurence sampling"
+    title = "occurrence sampling"
     if title_suffix is not None:
         title += title_suffix
 
@@ -295,14 +295,24 @@ def plot_stateOccurence_matrix(data: dict,
 
     mappable = ax.matshow(occurrence_sampling_matrix, cmap="Blues")
 
-    ## set ticks
+    ## add title for axes
+    ax.set_title(title)
+
+    ## set y-ticks, tick labels, label axis
     ax.set_yticks(range(0, states_num))
     ax.set_yticklabels(range(1, states_num + 1))
-
-    # nice s-value x-axis
+    ax.set_ylabel("states")
+
+    ## set x-ticks, tick labels, label axis
+    ax.xaxis.set_ticks_position("bottom")
     if (not s_values is None):
         ax.set_xticks(np.arange(0, len(s_values) - 0.25))
-        ax.set_xticklabels(nice_s_vals(s_values), rotation=45)
+        if len(set(s_values)) == 1: # change labels to number of states if in step a
+            ax.set_xticklabels(range(1, states_num + 1))
+            ax.set_xlabel("simulation biased to")
+        else: 
+            ax.set_xticklabels(nice_s_vals(s_values), rotation=45) # else add s-values as labels
+            ax.set_xlabel("s-values")
 
     ##set colorbar
     cax = fig.add_axes([ax.get_position().x1 + 0.1, ax.get_position().y0, 0.02, ax.get_position().height])
@@ -314,36 +324,42 @@ def plot_stateOccurence_matrix(data: dict,
             if (data[undersampling_ind]["undersampling"]):
                 break
         ax.vlines(x=undersampling_ind - 1.5, ymin=-0.5, ymax=states_num - 0.5, color="red", lw=3, label="undersampling")
-
-    ##labelling
-    ax.set_title(title)
-    ax.set_xlabel("s-values")
-    ax.set_ylabel("states")
-    ax.xaxis.set_ticks_position("bottom")
-
+
     #fig.tight_layout()
 
     if (not out_dir is None):
         fig.savefig(out_dir + '/sampling_undersample_matrix.png', bbox_inches='tight')
         plt.close()
-
+
+    # Plot MaxContrib:
     ##Title setting
     title = "maxContrib Sampling"
     if title_suffix is not None:
         title += title_suffix
 
     fig = plt.figure(figsize=ps.figsize_doubleColumn)
     ax = fig.add_subplot(111)
-
+    
     mappable = ax.matshow(maxcontrib_sampling_matrix, cmap="Reds")
-
-    ## set ticks
+
+    ## add title for axes
+    ax.set_title(title)
+
+    ## set y-ticks, tick labels, label axis
     ax.set_yticks(range(0, states_num))
     ax.set_yticklabels(range(1, states_num + 1))
-
+    ax.set_ylabel("states")
+
+    ## set x-ticks, tick labels, label axis
+    ax.xaxis.set_ticks_position("bottom")
     if (not s_values is None):
         ax.set_xticks(range(0, len(s_values)))
-        ax.set_xticklabels(nice_s_vals(s_values), rotation=45)
+        if len(set(s_values)) == 1: # change labels to number of states if in step a
+            ax.set_xticklabels(range(1, states_num + 1))
+            ax.set_xlabel("simulation biased to")
+        else:
+            ax.set_xticklabels(nice_s_vals(s_values), rotation=45)
+            ax.set_xlabel("s-values")
 
     ##set colorbar
     cax = fig.add_axes([ax.get_position().x1 + 0.1, ax.get_position().y0, 0.02, ax.get_position().height])
@@ -356,14 +372,8 @@ def plot_stateOccurence_matrix(data: dict,
                 break
         ax.vlines(x=undersampling_ind - 1.5, ymin=-0.5, ymax=states_num - 0.5, color="k", lw=3, label="undersampling")
 
-    ##labelling
-    ax.set_title(title)
-    ax.set_xlabel("s-values")
-    ax.set_ylabel("states")
-    ax.xaxis.set_ticks_position("bottom")
-
     #fig.tight_layout()
 
     if (not out_dir is None):
-        fig.savefig(out_dir + '/sampling_minstate_matrix.png', bbox_inches='tight')
+        fig.savefig(out_dir + '/sampling_maxContrib_matrix.png', bbox_inches='tight')
         plt.close()