git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15324 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/MISC/fix_deposit.cpp

@@ -38,6 +38,7 @@ using namespace MathConst;
 
 enum{ATOM,MOLECULE};
 enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED};    // several files
+enum{DIST_UNIFORM,DIST_GAUSSIAN};
 
 #define EPSILON 1.0e6
 
@@ -169,6 +170,10 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
   vyhi *= yscale;
   vzlo *= zscale;
   vzhi *= zscale;
+  xmid *= xscale;
+  ymid *= yscale;
+  zmid *= zscale;
+  sigma *= xscale; // same as in region sphere
   tx *= xscale;
   ty *= yscale;
   tz *= zscale;
@@ -336,15 +341,19 @@ void FixDeposit::pre_exchange()
     attempt++;
 
     // choose random position for new particle within region
-
+    if (distflag == DIST_UNIFORM) {
-    coord[0] = xlo + random->uniform() * (xhi-xlo);
+      do {
-    coord[1] = ylo + random->uniform() * (yhi-ylo);
+        coord[0] = xlo + random->uniform() * (xhi-xlo);
-    coord[2] = zlo + random->uniform() * (zhi-zlo);
+        coord[1] = ylo + random->uniform() * (yhi-ylo);
-    while (domain->regions[iregion]->match(coord[0],coord[1],coord[2]) == 0) {
+        coord[2] = zlo + random->uniform() * (zhi-zlo);
-      coord[0] = xlo + random->uniform() * (xhi-xlo);
+      } while (domain->regions[iregion]->match(coord[0],coord[1],coord[2]) == 0);
-      coord[1] = ylo + random->uniform() * (yhi-ylo);
+    } else if (distflag == DIST_GAUSSIAN) {
-      coord[2] = zlo + random->uniform() * (zhi-zlo);
+      do {
-    }
+        coord[0] = xmid + random->gaussian() * sigma;
+        coord[1] = ymid + random->gaussian() * sigma;
+        coord[2] = zmid + random->gaussian() * sigma;
+      } while (domain->regions[iregion]->match(coord[0],coord[1],coord[2]) == 0);
+    } else error->all(FLERR,"Unknown particle distribution in fix deposit");
 
     // adjust vertical coord by offset
 
@@ -644,6 +653,9 @@ void FixDeposit::options(int narg, char **arg)
   maxattempt = 10;
   rateflag = 0;
   vxlo = vxhi = vylo = vyhi = vzlo = vzhi = 0.0;
+  distflag = DIST_UNIFORM;
+  sigma = 1.0;
+  xmid = ymid = zmid = 0.0;
   scaleflag = 1;
   targetflag = 0;
 
@@ -759,6 +771,14 @@ void FixDeposit::options(int narg, char **arg)
       else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
       else error->all(FLERR,"Illegal fix deposit command");
       iarg += 2;
+    } else if (strcmp(arg[iarg],"gaussian") == 0) {
+      if (iarg+5 > narg) error->all(FLERR,"Illegal fix deposit command");
+      xmid = force->numeric(FLERR,arg[iarg+1]);
+      ymid = force->numeric(FLERR,arg[iarg+2]);
+      zmid = force->numeric(FLERR,arg[iarg+3]);
+      sigma = force->numeric(FLERR,arg[iarg+4]);
+      distflag = DIST_GAUSSIAN;
+      iarg += 5;
     } else if (strcmp(arg[iarg],"target") == 0) {
       if (iarg+4 > narg) error->all(FLERR,"Illegal fix deposit command");
       tx = force->numeric(FLERR,arg[iarg+1]);

src/MISC/fix_deposit.h

@@ -39,10 +39,10 @@ class FixDeposit : public Fix {
  private:
   int ninsert,ntype,nfreq,seed;
   int iregion,globalflag,localflag,maxattempt,rateflag,scaleflag,targetflag;
-  int mode,rigidflag,shakeflag,idnext;
+  int mode,rigidflag,shakeflag,idnext,distflag;
-  double lo,hi,deltasq,nearsq,rate;
+  double lo,hi,deltasq,nearsq,rate,sigma;
   double vxlo,vxhi,vylo,vyhi,vzlo,vzhi;
-  double xlo,xhi,ylo,yhi,zlo,zhi;
+  double xlo,xhi,ylo,yhi,zlo,zhi,xmid,ymid,zmid;
   double tx,ty,tz;
   char *idregion;
   char *idrigid,*idshake;

src/compute.cpp

@@ -133,7 +133,7 @@ void Compute::modify_params(int narg, char **arg)
   while (iarg < narg) {
     if (strcmp(arg[iarg],"extra") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal compute_modify command");
-      extra_dof = force->inumeric(FLERR,arg[iarg+1]);
+      extra_dof = force->numeric(FLERR,arg[iarg+1]);
       iarg += 2;
     } else if (strcmp(arg[iarg],"dynamic") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal compute_modify command");

src/compute.h

@@ -147,7 +147,7 @@ class Compute : protected Pointers {
   int instance_me;             // which Compute class instantiation I am
 
   double natoms_temp;          // # of atoms used for temperature calculation
-  int extra_dof;               // extra DOF for temperature computes
+  double extra_dof;            // extra DOF for temperature computes
   int fix_dof;                 // DOF due to fixes
   int dynamic;                 // recount atoms for temperature computes
   int dynamic_user;            // user request for temp compute to be dynamic

src/info.cpp

@@ -262,7 +262,7 @@ void Info::command(int narg, char **arg)
         fprintf(out,"Communication cutoff for type %d = %g\n", i, cut);
       }
     }
-    fprintf(out,"Nprocs = %d    Nthreads = %d\n",
+    fprintf(out,"Nprocs = %d,   Nthreads = %d\n",
             comm->nprocs, comm->nthreads);
     fprintf(out,"Processor grid = %d x %d x %d\n",comm->procgrid[0],
             comm->procgrid[1], comm->procgrid[2]);
@@ -411,7 +411,7 @@ void Info::command(int narg, char **arg)
     fprintf(out,"\nVariable information:\n");
     for (int i=0; i < nvar; ++i) {
       int ndata = 1;
-      fprintf(out,"Variable[%3d]: %-10s  style = %-10s  def =",
+      fprintf(out,"Variable[%3d]: %-10s,  style = %-10s,  def =",
               i,names[i],varstyles[style[i]]);
       if ((style[i] != LOOP) && (style[i] != ULOOP))
         ndata = input->variable->num[i];