Merge branch 'develop' into plumed-plugin

examples/COUPLE/plugin/liblammpsplugin.c

@@ -41,7 +41,6 @@
 
 #include <stdlib.h>
 
-
 liblammpsplugin_t *liblammpsplugin_load(const char *lib)
 {
   liblammpsplugin_t *lmp;
@@ -191,6 +190,9 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
   ADDSYM(is_running);
   ADDSYM(force_timeout);
 
+  // symbol not present
+  if (!lmp->config_has_exceptions) return NULL;
+
   lmp->has_exceptions = lmp->config_has_exceptions();
   if (lmp->has_exceptions) {
     ADDSYM(has_error);

examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized

@@ -44,6 +44,7 @@ thermo 50
 fix myrxns all bond/react stabilization yes statted_grp .03 &
   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
 
 fix 1 statted_grp_REACT nvt temp 300 300 100
 

examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability

@@ -47,7 +47,7 @@ thermo 50
 
 fix myrxns all bond/react stabilization yes statted_grp .03 &
   react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 &
-  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
+  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 rescale_charges yes
 
 fix 1 statted_grp_REACT nvt temp 300 300 100
 

examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized

@@ -44,7 +44,7 @@ thermo 50
 
 fix myrxns all bond/react stabilization no &
   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
-  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
 
 fix 1 all nve/limit .03
 

examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.molecule_template

@@ -48,27 +48,6 @@ Types
      17 hc
      18 hc
 
-Charges
-
-      1 -0.300000
-      2  0.000000
-      3  0.000000
-      4  0.000000
-      5  0.000000
-      6  0.000000
-      7  0.000000
-      8  0.000000
-      9  0.000000
-     10  0.300000
-     11  0.000000
-     12  0.000000
-     13  0.000000
-     14  0.000000
-     15  0.000000
-     16  0.000000
-     17  0.000000
-     18  0.000000
-
 Molecules
 
       1      1

examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.molecule_template

@@ -44,21 +44,21 @@ Types
 
 Charges
 
-      1 -0.300000
-      2  0.000000
-      3  0.000000
-      4  0.410000
-      5  0.000000
-      6  0.000000
-      7  0.000000
-      8  0.000000
-      9  0.000000
-     10  0.300000
-     11  0.000000
-     12 -0.820000
-     13  0.000000
-     14  0.000000
-     15  0.410000
+      1 -0.60533
+      2 -0.01149
+      3 -0.76306
+      4 0.38
+      5 0.29346
+      6 0.18360
+      7 0.15396
+      8 -0.72636
+      9 -0.27437
+     10 0.40603
+     11 -0.65530
+     12 -0.76
+     13 0.21423
+     14 0.18949
+     15 0.38
 
 Molecules