git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3598 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/XTC/dump_xtc.cpp

@@ -229,18 +229,18 @@ int DumpXTC::pack()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpXTC::write_data(int n, double *buf)
+void DumpXTC::write_data(int n, double *mybuf)
 {
   float *xyz;
   int j,tag;
 
   int m = 0;
   for (int i = 0; i < n; i++) {
-    tag = static_cast<int> (buf[m]) - 1;
+    tag = static_cast<int> (mybuf[m]) - 1;
     j = 3*tag;
-    coords[j++] = buf[m+1];
+    coords[j++] = mybuf[m+1];
-    coords[j++] = buf[m+2];
+    coords[j++] = mybuf[m+2];
-    coords[j] = buf[m+3];
+    coords[j] = mybuf[m+3];
     m += size_one;
   }
 

src/compute_com_molecule.cpp

@@ -150,7 +150,7 @@ void ComputeCOMMolecule::compute_array()
 double ComputeCOMMolecule::memory_usage()
 {
   double bytes = 2*nmolecules * sizeof(double);
-  if (molmap) bytes += nmolecules * sizeof(int);
+  if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
   bytes += 2*nmolecules*3 * sizeof(double);
   return bytes;
 }

src/compute_gyration_molecule.cpp

@@ -180,7 +180,7 @@ void ComputeGyrationMolecule::compute_vector()
 double ComputeGyrationMolecule::memory_usage()
 {
   double bytes = 4*nmolecules * sizeof(double);
-  if (molmap) bytes += nmolecules * sizeof(int);
+  if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
   bytes += 2*nmolecules*3 * sizeof(double);
   return bytes;
 }

src/compute_msd.cpp

@@ -118,6 +118,7 @@ void ComputeMSD::compute_vector()
 
   double cm[3];
   if (comflag) group->xcm(igroup,masstotal,cm);
+  else cm[0] = cm[1] = cm[2] = 0.0;
 
   // dx,dy,dz = displacement of atom from original position
   // original unwrapped position is stored by fix
@@ -148,15 +149,9 @@ void ComputeMSD::compute_vector()
 	xbox = (image[i] & 1023) - 512;
 	ybox = (image[i] >> 10 & 1023) - 512;
 	zbox = (image[i] >> 20) - 512;
-	if (comflag) {
 	dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0];
 	dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1];
 	dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2];
-	} else {
-	  dx = x[i][0] + xbox*xprd - xoriginal[i][0];
-	  dy = x[i][1] + ybox*yprd - xoriginal[i][1];
-	  dz = x[i][2] + zbox*zprd - xoriginal[i][2];
-	}
 	msd[0] += dx*dx;
 	msd[1] += dy*dy;
 	msd[2] += dz*dz;
@@ -169,16 +164,10 @@ void ComputeMSD::compute_vector()
 	xbox = (image[i] & 1023) - 512;
 	ybox = (image[i] >> 10 & 1023) - 512;
 	zbox = (image[i] >> 20) - 512;
-	if (comflag) {
 	dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - 
 	  cm[0] - xoriginal[i][0];
 	dy = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1] - xoriginal[i][1];
 	dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2];
-	} else {
-	  dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0];
-	  dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1];
-	  dz = x[i][2] + h[2]*zbox - xoriginal[i][2];
-	}
 	msd[0] += dx*dx;
 	msd[1] += dy*dy;
 	msd[2] += dz*dz;

src/compute_msd_molecule.cpp

@@ -183,7 +183,7 @@ void ComputeMSDMolecule::compute_array()
 double ComputeMSDMolecule::memory_usage()
 {
   double bytes = 2*nmolecules * sizeof(double);
-  if (molmap) bytes += nmolecules * sizeof(int);
+  if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
   bytes += 2*nmolecules*3 * sizeof(double);
   bytes += nmolecules*4 * sizeof(double);
   return bytes;

src/compute_property_atom.cpp

@@ -249,7 +249,7 @@ void ComputePropertyAtom::compute_peratom()
     buf = vector;
     (this->*pack_choice[0])(0);
   } else {
-    if (array) buf = array[0];
+    if (array) buf = &array[0][0];
     for (int n = 0; n < nvalues; n++)
       (this->*pack_choice[n])(n);
   }

src/compute_property_local.cpp

@@ -216,7 +216,7 @@ void ComputePropertyLocal::compute_local()
     buf = vector;
     (this->*pack_choice[0])(0);
   } else {
-    if (array) buf = array[0];
+    if (array) buf = &array[0][0];
     for (int n = 0; n < nvalues; n++)
       (this->*pack_choice[n])(n);
   }

src/dump_atom.cpp

@@ -153,9 +153,9 @@ int DumpAtom::pack()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpAtom::write_data(int n, double *buf)
+void DumpAtom::write_data(int n, double *mybuf)
 {
-  (this->*write_choice)(n,buf);
+  (this->*write_choice)(n,mybuf);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -397,36 +397,36 @@ int DumpAtom::pack_noscale_noimage()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpAtom::write_binary(int n, double *buf)
+void DumpAtom::write_binary(int n, double *mybuf)
 {
   n *= size_one;
   fwrite(&n,sizeof(int),1,fp);
-  fwrite(buf,sizeof(double),n,fp);
+  fwrite(mybuf,sizeof(double),n,fp);
 }
 
 /* ---------------------------------------------------------------------- */
 
-void DumpAtom::write_image(int n, double *buf)
+void DumpAtom::write_image(int n, double *mybuf)
 {
   int m = 0;
   for (int i = 0; i < n; i++) {
     fprintf(fp,format,
-	    static_cast<int> (buf[m]), static_cast<int> (buf[m+1]),
+	    static_cast<int> (mybuf[m]), static_cast<int> (mybuf[m+1]),
-	    buf[m+2],buf[m+3],buf[m+4], static_cast<int> (buf[m+5]),
+	    mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]),
-	    static_cast<int> (buf[m+6]), static_cast<int> (buf[m+7]));
+	    static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7]));
     m += size_one;
   }
 }
 
 /* ---------------------------------------------------------------------- */
 
-void DumpAtom::write_noimage(int n, double *buf)
+void DumpAtom::write_noimage(int n, double *mybuf)
 {
   int m = 0;
   for (int i = 0; i < n; i++) {
     fprintf(fp,format,
-	    static_cast<int> (buf[m]), static_cast<int> (buf[m+1]),
+	    static_cast<int> (mybuf[m]), static_cast<int> (mybuf[m+1]),
-	    buf[m+2],buf[m+3],buf[m+4]);
+	    mybuf[m+2],mybuf[m+3],mybuf[m+4]);
     m += size_one;
   }
 }

src/dump_cfg.cpp

@@ -229,7 +229,7 @@ void DumpCFG::write_header(int n)
    write head of block (mass & element name) only if has atoms of the type
 ------------------------------------------------------------------------- */
 
-void DumpCFG::write_data(int n, double *buf)
+void DumpCFG::write_data(int n, double *mybuf)
 {
   int i,j,m,itype;
   int tag_i,index;
@@ -241,7 +241,7 @@ void DumpCFG::write_data(int n, double *buf)
   if (sort_flag == 0) {
     for (i = 0, m = 0; i < n; i++) {
       for (j = 0; j < size_one; j++)
-	rbuf[nlines][j] = buf[m++];
+	rbuf[nlines][j] = mybuf[m++];
       nlines++;
     }
 
@@ -282,7 +282,7 @@ void DumpCFG::write_data(int n, double *buf)
     //   to this index
 
     for (i = 0, m = 0; i < n; i++) {
-      tag_i = static_cast<int>(buf[m]);
+      tag_i = static_cast<int>(mybuf[m]);
       for (j = 0; j < nchosen; j++) {
 	if (tag_i == tags[j]) {
 	  index = j;
@@ -290,7 +290,7 @@ void DumpCFG::write_data(int n, double *buf)
 	}
       }
       for (j = 0; j < size_one; j++)
-	rbuf[index][j] = buf[m++];
+	rbuf[index][j] = mybuf[m++];
     }
 
     //  write data lines in rbuf to file after transfer is done

src/dump_custom.cpp

@@ -751,31 +751,31 @@ int DumpCustom::pack()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpCustom::write_data(int n, double *buf)
+void DumpCustom::write_data(int n, double *mybuf)
 {
-  (this->*write_choice)(n,buf);
+  (this->*write_choice)(n,mybuf);
 }
 
 /* ---------------------------------------------------------------------- */
 
-void DumpCustom::write_binary(int n, double *buf)
+void DumpCustom::write_binary(int n, double *mybuf)
 {
   n *= size_one;
   fwrite(&n,sizeof(int),1,fp);
-  fwrite(buf,sizeof(double),n,fp);
+  fwrite(mybuf,sizeof(double),n,fp);
 }
 
 /* ---------------------------------------------------------------------- */
 
-void DumpCustom::write_text(int n, double *buf)
+void DumpCustom::write_text(int n, double *mybuf)
 {
   int i,j;
 
   int m = 0;
   for (i = 0; i < n; i++) {
     for (j = 0; j < size_one; j++) {
-      if (vtype[j] == INT) fprintf(fp,vformat[j],static_cast<int> (buf[m]));
+      if (vtype[j] == INT) fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
-      else fprintf(fp,vformat[j],buf[m]);
+      else fprintf(fp,vformat[j],mybuf[m]);
       m++;
     }
     fprintf(fp,"\n");

src/dump_dcd.cpp

@@ -233,17 +233,17 @@ int DumpDCD::pack()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpDCD::write_data(int n, double *buf)
+void DumpDCD::write_data(int n, double *mybuf)
 {
   // spread buf atom coords into global arrays
 
   int tag;
   int m = 0;
   for (int i = 0; i < n; i++) {
-    tag = static_cast<int> (buf[m]) - 1;
+    tag = static_cast<int> (mybuf[m]) - 1;
-    xf[tag] = buf[m+1];
+    xf[tag] = mybuf[m+1];
-    yf[tag] = buf[m+2];
+    yf[tag] = mybuf[m+2];
-    zf[tag] = buf[m+3];
+    zf[tag] = mybuf[m+3];
     m += size_one;
   }
 

src/dump_local.cpp

@@ -245,15 +245,15 @@ int DumpLocal::pack()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpLocal::write_data(int n, double *buf)
+void DumpLocal::write_data(int n, double *mybuf)
 {
   int i,j;
 
   int m = 0;
   for (i = 0; i < n; i++) {
     for (j = 0; j < size_one; j++) {
-      if (vtype[j] == INT) fprintf(fp,vformat[j],static_cast<int> (buf[m]));
+      if (vtype[j] == INT) fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
-      else fprintf(fp,vformat[j],buf[m]);
+      else fprintf(fp,vformat[j],mybuf[m]);
       m++;
     }
     fprintf(fp,"\n");

src/dump_xyz.cpp

@@ -155,7 +155,7 @@ int DumpXYZ::pack()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpXYZ::write_data(int n, double *buf)
+void DumpXYZ::write_data(int n, double *mybuf)
 {
   // for group = all, spread buf atom coords into global arrays
   // if last chunk of atoms in this snapshot, write global arrays to file
@@ -165,12 +165,12 @@ void DumpXYZ::write_data(int n, double *buf)
 
     int m = 0;
     for (int i = 0; i < n; i++) {
-      tag = static_cast<int> (buf[m]) - 1;
+      tag = static_cast<int> (mybuf[m]) - 1;
-      types[tag] = static_cast<int> (buf[m+1]);
+      types[tag] = static_cast<int> (mybuf[m+1]);
       j = 3*tag;
-      coords[j++] = buf[m+2];
+      coords[j++] = mybuf[m+2];
-      coords[j++] = buf[m+3];
+      coords[j++] = mybuf[m+3];
-      coords[j] = buf[m+4];
+      coords[j] = mybuf[m+4];
       m += size_one;
     }
 
@@ -186,7 +186,7 @@ void DumpXYZ::write_data(int n, double *buf)
     int m = 0;
     for (int i = 0; i < n; i++) {
       fprintf(fp,format,
-	      static_cast<int> (buf[m+1]),buf[m+2],buf[m+3],buf[m+4]);
+	      static_cast<int> (mybuf[m+1]),mybuf[m+2],mybuf[m+3],mybuf[m+4]);
       m += size_one;
     }
   }

src/style.h

@@ -103,6 +103,7 @@ CommandStyle(write_restart,WriteRestart)
 #include "compute_erotate_sphere.h"
 #include "compute_property_atom.h"
 #include "compute_property_local.h"
+#include "compute_property_molecule.h"
 #include "compute_stress_atom.h"
 #include "compute_temp.h"
 #include "compute_temp_com.h"
@@ -142,6 +143,7 @@ ComputeStyle(reduce/region,ComputeReduceRegion)
 ComputeStyle(erotate/sphere,ComputeERotateSphere)
 ComputeStyle(property/atom,ComputePropertyAtom)
 ComputeStyle(property/local,ComputePropertyLocal)
+ComputeStyle(property/molecule,ComputePropertyMolecule)
 ComputeStyle(stress/atom,ComputeStressAtom)
 ComputeStyle(temp,ComputeTemp)
 ComputeStyle(temp/com,ComputeTempCOM)