Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes

doc/src/dump_modify.txt

@@ -486,7 +486,7 @@ to respond to the call from the dump command, and update the
 appropriate reference positions.  This is done be defining an
 "atom-style variable"_variable.html, {check} in this example, which
 calculates a Boolean value (0 or 1) for each atom, based on the same
-criterion used by dump_modify thresh.  
+criterion used by dump_modify thresh.
 
 See the "compute displace/atom"_compute_displace_atom.html command for
 more details, including an example of how to produce output that
@@ -600,13 +600,13 @@ included.)
 
 region foo sphere 10 20 10 15
 variable inregion atom rmask(foo)
-dump_modify ... thresh v_inregion |^ LAST
+dump_modify ... thresh v_inregion |^ LAST :pre
 
 This will dump atoms which crossed the boundary of the spherical
 region since the last dump.
 
 variable charge atom "(q > 0.5) || (q < -0.5)"
-dump_modify ... thresh v_charge |^ LAST
+dump_modify ... thresh v_charge |^ LAST :pre
 
 This will dump atoms whose charge has changed from an absolute value
 less than 1/2 to greater than 1/2 (or vice versa) since the last dump.

src/LATTE/fix_latte.cpp

@@ -62,7 +62,7 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) :
   if (comm->nprocs != 1)
     error->all(FLERR,"Fix latte currently runs only in serial");
 
-  if (latte_abiversion() != ABIVERSION)
+  if (LATTE_ABIVERSION != latte_abiversion())
     error->all(FLERR,"LAMMPS is linked against incompatible LATTE library");
 
   if (narg != 4) error->all(FLERR,"Illegal fix latte command");

src/USER-MISC/compute_entropy_atom.cpp

@@ -59,11 +59,11 @@ ComputeEntropyAtom(LAMMPS *lmp, int narg, char **arg) :
   //     the g(r)
 
   sigma = force->numeric(FLERR,arg[3]);
-  if (sigma < 0.0) error->all(FLERR,"Illegal compute entropy/atom"
-                              " command; negative sigma");
+  if (sigma <= 0.0) error->all(FLERR,"Illegal compute entropy/atom"
+                              " command; sigma must be positive");
   cutoff = force->numeric(FLERR,arg[4]);
-  if (cutoff < 0.0) error->all(FLERR,"Illegal compute entropy/atom"
-                               " command; negative cutoff");
+  if (cutoff <= 0.0) error->all(FLERR,"Illegal compute entropy/atom"
+                               " command; cutoff must be positive");
 
   avg_flag = 0;
   local_flag = 0;
@@ -121,7 +121,7 @@ ComputeEntropyAtom::~ComputeEntropyAtom()
 void ComputeEntropyAtom::init()
 {
   if (force->pair == NULL)
-    error->all(FLERR,"Compute centro/atom requires a pair style be"
+    error->all(FLERR,"Compute entropy/atom requires a pair style be"
                " defined");
 
   if ( (cutoff+cutoff2) > (force->pair->cutforce  + neighbor->skin) )
@@ -163,7 +163,8 @@ void ComputeEntropyAtom::compute_peratom()
   int i,j,ii,jj,inum,jnum;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
   int *ilist,*jlist,*numneigh,**firstneigh;
-  double rbin[nbin], rbinsq[nbin];
+  double *rbin = new double[nbin];
+  double *rbinsq = new double[nbin];
 
   invoked_peratom = update->ntimestep;
 
@@ -207,6 +208,8 @@ void ComputeEntropyAtom::compute_peratom()
 
   double **x = atom->x;
   int *mask = atom->mask;
+  double *gofr = new double[nbin];
+  double *integrand = new double[nbin];
 
   for (ii = 0; ii < inum; ii++) {
     i = ilist[ii];
@@ -235,7 +238,6 @@ void ComputeEntropyAtom::compute_peratom()
       // loop over list of all neighbors within force cutoff
 
       // initialize gofr
-      double gofr[nbin];
       for(int k=0;k<nbin;++k) gofr[k]=0.;
 
       for (jj = 0; jj < jnum; jj++) {
@@ -265,7 +267,6 @@ void ComputeEntropyAtom::compute_peratom()
       }
 
       // Calculate integrand
-      double integrand[nbin];
       for(int k=0;k<nbin;++k){
         if (gofr[k]<1.e-10) {
           integrand[k] = rbinsq[k];
@@ -284,10 +285,10 @@ void ComputeEntropyAtom::compute_peratom()
       value *= deltar;
 
       pair_entropy[i] = -2*MY_PI*density*value;
-
     }
   }
-
+  delete [] gofr;
+  delete [] integrand;
 
   if (avg_flag) {
     for (ii = 0; ii < inum; ii++) {
@@ -320,7 +321,8 @@ void ComputeEntropyAtom::compute_peratom()
       }
     }
   }
-
+  delete [] rbin;
+  delete [] rbinsq;
 }
 
 

src/USER-MISC/compute_entropy_atom.h

@@ -41,7 +41,6 @@ class ComputeEntropyAtom : public Compute {
   double cutsq, cutsq2;
   double deltar;
   int deltabin;
-  double invNormConstantBase;
   int avg_flag;
   int local_flag;
 };