Fixed more PBC and indexing stuff.

diff --git a/src/tools/gmx_densorder.c b/src/tools/gmx_densorder.c
index e058699cca56e13a821ca8472ebfc59ba63230ca..d45d2b07e3f2a60056f1f0d5b669bcf631080f1e 100644 (file)
--- a/src/tools/gmx_densorder.c
+++ b/src/tools/gmx_densorder.c
@@ -118,6 +118,7 @@ static void density_in_time (const char *fn, atom_id **index ,int gnx[], int grp
        real dscale; //physical scaling factor
        real t,x,y,z; // time and coordinates
        *tblock=0;/* blocknr in block average - initialise to 0*/
+       rvec bbww;
        
        /* Axis: X=0, Y=1,Z=2 */
        switch(axis)    
@@ -154,6 +155,9 @@ static void density_in_time (const char *fn, atom_id **index ,int gnx[], int grp
        *Densdevel=NULL;                
        
        do      {
+         bbww[XX] = box[ax1][ax1]/ *xslices;
+         bbww[YY] = box[ax2][ax2]/ *yslices;
+         bbww[ZZ] = box[axis][axis]/ *zslices;
          gmx_rmpbc(gpbc,top->atoms.nr,box,x0);
          //Reset Densslice every nsttblock steps
                if   ( framenr % nsttblock==0  ){ 
@@ -196,9 +200,9 @@ static void density_in_time (const char *fn, atom_id **index ,int gnx[], int grp
                        while(z>box[axis][axis])
                                z-=box[axis][axis];
                        
-                       slicex=(int) (x/bw);
-                       slicey=(int) (y/bw);
-                       slicez=(int) (z/bwz);
+                       slicex=((int) (x/bbww[XX])) % *xslices;
+                       slicey=((int) (y/bbww[YY])) % *yslices;
+                       slicez=((int) (z/bbww[ZZ])) % *zslices;
                        Densslice[slicex][slicey][slicez]+=(top->atoms.atom[index[0][j]].m*dscale);
                
                        
@@ -219,6 +223,21 @@ static void density_in_time (const char *fn, atom_id **index ,int gnx[], int grp
        //Free memory we no longer need and exit.
        gmx_rmpbc_done(gpbc);
        close_trj(status);
+       
+       if (0)
+       {
+         FILE *fp;
+         fp = fopen("koko.xvg","w");
+         for(j=0; (j<*zslices); j++) {
+           fprintf(fp,"%5d",j);
+           for(i=0; (i<*tblock); i++) {
+             fprintf(fp,"  %10g",(*Densdevel)[i][9][1][j]);
+           }
+           fprintf(fp,"\n");
+         }
+         fclose(fp); 
+       }
+       
 }
 
 
@@ -536,7 +555,7 @@ static void writeraw(t_interf ***int1, t_interf ***int2, int tblocks,int xbins,
 int gmx_densorder(int argc,char *argv[])
 {
   static const char *desc[] = {
-    "A small program to reduce a two-phase densitydistribution", 
+    "A small program to reduce a two-phase density distribution", 
     "along an axis, computed over a MD trajectory",
     "to 2D surfaces fluctuating in time, by a fit to",
     "a functional profile for interfacial densities",