Merge pull request #323 from carlocamilloni/main

small fix for make_mat.py

tools/make_mat/make_mat.py

@@ -353,8 +353,8 @@ def c12_avg(values, weights, callback=allfunction):
     if np.sum(w) == 0:
         return 0
     r = np.where(w > 0.0)
-    v = v[r[0][0] : v.size]
-    w = w[r[0][0] : w.size]
+    v = v[r[0][0]:v.size]
+    w = w[r[0][0]:w.size]
 
     res = np.maximum(cutoff / 4.5, 0.1)
     exp_aver = (1.0 / res) / np.log(np.sum(w * np.exp(1.0 / v / res)) / norm)
@@ -505,8 +505,9 @@ def calculate_intra_probabilities(args):
         for ai, aj, c12 in user_pairs:
             ai = int(ai)
             aj = int(aj)
-            c12_cutoff[ai][aj] = CUTOFF_FACTOR * np.power(c12, 1.0 / 12.0)
-            c12_cutoff[aj][ai] = CUTOFF_FACTOR * np.power(c12, 1.0 / 12.0)
+            if c12 > 0.0:
+                c12_cutoff[ai][aj] = CUTOFF_FACTOR * np.power(c12, 1.0 / 12.0)
+                c12_cutoff[aj][ai] = CUTOFF_FACTOR * np.power(c12, 1.0 / 12.0)
 
         if np.any(c12_cutoff > args.cutoff):
             warning_cutoff_histo(args.cutoff, np.max(c12_cutoff))