Merge branch 'small-bugfixes' into integration

doc/src/Section_start.txt

@@ -1785,7 +1785,7 @@ Pair    | 0.5127     | 0.5147     | 0.5167     |   0.3 | 75.18
 Bond    | 0.0043139  | 0.0046779  | 0.0050418  |   0.5 |  0.68
 Kspace  | 0.070572   | 0.074541   | 0.07851    |   1.5 | 10.89
 Neigh   | 0.084778   | 0.086969   | 0.089161   |   0.7 | 12.70
-Reduce  | 0.0036485  | 0.003737   | 0.0038254  |   0.1 |  0.55
+Reduce  | 0.0036485  | 0.003737   | 0.0038254  |   0.1 |  0.55 :pre
 
 The third section lists the number of owned atoms (Nlocal), ghost atoms
 (Nghost), and pair-wise neighbors stored per processor.  The max and min

examples/USER/tally/in.force

@@ -25,6 +25,9 @@ neighbor        2.0 bin
 fix		1 all shake 0.0001 20 0 b 1 a 1
 fix		2 all nvt temp 300.0 300.0 100.0
 
+# make certain that shake constraints are satisfied
+run 0 post no
+
 group		one molecule 1 2
 
 # the following section shows equivalences between using the force/tally compute and other computes and thermo keywords

examples/USER/tally/in.pe

@@ -25,6 +25,9 @@ neighbor        2.0 bin
 fix		1 all shake 0.0001 20 0 b 1 a 1
 fix		2 all nvt temp 300.0 300.0 100.0
 
+# make certain that shake constraints are satisfied
+run 0 post no
+
 group		oxy type 1
 group		hyd type 2
 

examples/USER/tally/in.stress

@@ -25,6 +25,9 @@ neighbor        2.0 bin
 fix		1 all shake 0.0001 20 0 b 1 a 1
 fix		2 all nvt temp 300.0 300.0 100.0
 
+# make certain that shake constraints are satisfied
+run 0 post no
+
 group		one molecule 1 2
 
 # the following section shows equivalences between using the stress/tally compute and other computes and thermo keywords

src/KOKKOS/comm_kokkos.cpp

@@ -364,8 +364,8 @@ void CommKokkos::exchange()
       if(print && comm->me==0) {
         error->warning(FLERR,"Fixes cannot send data in Kokkos communication, "
 		       "switching to classic communication");
-        print = 0;
       }
+      print = 0;
       exchange_comm_classic = true;
     }
   }

src/QEQ/fix_qeq_slater.cpp

@@ -90,14 +90,6 @@ void FixQEqSlater::init()
 
 void FixQEqSlater::extract_streitz()
 {
-  int ntypes = atom->ntypes;
-
-  memory->create(chi,ntypes+1,"qeq:chi");
-  memory->create(eta,ntypes+1,"qeq:eta");
-  memory->create(gamma,ntypes+1,"qeq:gamma");
-  memory->create(zeta,ntypes+1,"qeq:zeta");
-  memory->create(zcore,ntypes+1,"qeq:zcore");
-
   Pair *pair = force->pair_match("coul/streitz",1);
   if (pair == NULL) error->all(FLERR,"No pair coul/streitz for fix qeq/slater");
   int tmp;

src/dump.h

@@ -118,7 +118,7 @@ class Dump : protected Pointers {
   int *index,*proclist;
 
   double **xpbc,**vpbc;
-  int *imagepbc;
+  imageint *imagepbc;
   int maxpbc;
 
   class Irregular *irregular;

src/fix_ave_histo.cpp

@@ -203,14 +203,14 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
   for (int i = 0; i < nvalues; i++) {
     if (which[i] == X || which[i] == V || which[i] == F) kindflag = PERATOM;
     else if (which[i] == COMPUTE) {
-      Compute *compute = modify->compute[modify->find_compute(ids[0])];
+      Compute *compute = modify->compute[modify->find_compute(ids[i])];
       if (compute->scalar_flag || compute->vector_flag || compute->array_flag)
         kindflag = GLOBAL;
       else if (compute->peratom_flag) kindflag = PERATOM;
       else if (compute->local_flag) kindflag = LOCAL;
       else error->all(FLERR,"Fix ave/histo input is invalid compute");
     } else if (which[i] == FIX) {
-      Fix *fix = modify->fix[modify->find_fix(ids[0])];
+      Fix *fix = modify->fix[modify->find_fix(ids[i])];
       if (fix->scalar_flag || fix->vector_flag || fix->array_flag)
         kindflag = GLOBAL;
       else if (fix->peratom_flag) kindflag = PERATOM;

src/fix_controller.cpp

@@ -197,7 +197,7 @@ void FixController::end_of_step()
 
   // invoke compute if not previously invoked
 
-  double current;
+  double current = 0.0;
 
   if (pvwhich == COMPUTE) {
     if (pvindex == 0) {

src/variable.cpp

@@ -898,7 +898,7 @@ double Variable::compute_equal(int ivar)
     error->all(FLERR,"Variable has circular dependency");
   eval_in_progress[ivar] = 1;
 
-  double value;
+  double value = 0.0;
   if (style[ivar] == EQUAL) value = evaluate(data[ivar][0],NULL);
   else if (style[ivar] == INTERNAL) value = dvalue[ivar];
   else if (style[ivar] == PYTHON) {

src/velocity.cpp

@@ -151,6 +151,7 @@ void Velocity::init_external(const char *extgroup)
   rotation_flag = 0;
   loop_flag = ALL;
   scale_flag = 1;
+  bias_flag = 0;
 }
 
 /* ---------------------------------------------------------------------- */