git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@711 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_epair_atom.cpp

@@ -72,10 +72,11 @@ void ComputeEpairAtom::init()
 
 void ComputeEpairAtom::compute_peratom()
 {
-  int i,j,k,n,itype,jtype,numneigh;
+  int i,j,k,n,itype,jtype,numneigh,iflag;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
-  double factor_coul,factor_lj,e;
+  double factor_coul,factor_lj,eng;
   int *neighs;
+  Pair::One one;
 
   // grow energy array if necessary
 
@@ -90,8 +91,11 @@ void ComputeEpairAtom::compute_peratom()
   // clear energy array
   // n includes ghosts only if newton_pair flag is set
 
-  if (force->newton_pair) n = atom->nlocal + atom->nghost;
+  int nlocal = atom->nlocal;
-  else n = atom->nlocal;
+  int newton_pair = force->newton_pair;
+
+  if (newton_pair) n = nlocal + atom->nghost;
+  else n = nlocal;
 
   for (i = 0; i < n; i++) energy[i] = 0.0;
 
@@ -99,30 +103,30 @@ void ComputeEpairAtom::compute_peratom()
 
   if (!neighbor->half_every) neighbor->build_half();
 
-  // compute pairwise energy for all atoms via pair->single()
+  // compute pairwise energy for atoms via pair->single()
-  // ignore compute group, since using half neighbor list
+  // if neither atom is in compute group, skip that pair
 
   double *special_coul = force->special_coul;
   double *special_lj = force->special_lj;
   double **cutsq = force->pair->cutsq;
 
   double **x = atom->x;
+  int *mask = atom->mask;
   int *type = atom->type;
-  int nlocal = atom->nlocal;
+  int nall = nlocal + atom->nghost;
-  int nall = atom->nlocal + atom->nghost;
-
-  Pair::One one;
 
   for (i = 0; i < nlocal; i++) {
     xtmp = x[i][0];
     ytmp = x[i][1];
     ztmp = x[i][2];
     itype = type[i];
+    iflag = mask[i] & groupbit;
     neighs = neighbor->firstneigh[i];
     numneigh = neighbor->numneigh[i];
     
     for (k = 0; k < numneigh; k++) {
       j = neighs[k];
+      if (iflag == 0 && (mask[j] & groupbit) == 0) continue;
 
       if (j < nall) factor_coul = factor_lj = 1.0;
       else {
@@ -139,30 +143,30 @@ void ComputeEpairAtom::compute_peratom()
 
       if (rsq < cutsq[itype][jtype]) {
 	force->pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,1,one);
-	e = one.eng_coul + one.eng_vdwl;
+	eng = one.eng_coul + one.eng_vdwl;
-	energy[i] += e;
+	energy[i] += eng;
-	energy[j] += e;
+	if (newton_pair || j < nlocal) energy[j] += eng;
       }
     }
   }
 
   // communicate energy between neigchbor procs
 
-  if (force->newton_pair) comm->reverse_comm_compute(this);
+  if (newton_pair) comm->reverse_comm_compute(this);
 
   // remove double counting of per-atom energy
 
   for (i = 0; i < nlocal; i++) energy[i] *= 0.5;
 
   // for EAM, include embedding function contribution to energy
+  // only for atoms in compute group
 
   if (eamstyle) {
-    int *type = atom->type;
-    double etmp = 0.0;
-
     for (i = 0; i < nlocal; i++) {
-      force->pair->single_embed(i,type[i],etmp);
+      if (mask[i] & groupbit) {
-      energy[i] += etmp;
+	force->pair->single_embed(i,type[i],eng);
+	energy[i] += eng;
+      }
     }
   }
 }

src/compute_stress_atom.cpp

@@ -19,7 +19,9 @@
 #include "comm.h"
 #include "update.h"
 #include "force.h"
+#include "bond.h"
 #include "pair.h"
+#include "domain.h"
 #include "memory.h"
 #include "error.h"
 
@@ -33,13 +35,37 @@ using namespace LAMMPS_NS;
 ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg)
 {
-  if (narg != 3) error->all("Illegal compute stress/atom command");
+  if (narg < 3) error->all("Illegal compute stress/atom command");
 
   peratom_flag = 1;
   size_peratom = 6;
   comm_reverse = 6;
   neigh_half_once = 1;
 
+  // process args
+
+  kerequest = pairrequest = bondrequest = 1;
+
+  int iarg = 3;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"ke") == 0) {
+      if (iarg+2 > narg) error->all("Illegal compute ebond/atom command");
+      if (strcmp(arg[iarg+1],"yes") == 0) kerequest = 1;
+      else if (strcmp(arg[iarg+1],"no") == 0) kerequest = 0;
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"pair") == 0) {
+      if (iarg+2 > narg) error->all("Illegal compute ebond/atom command");
+      if (strcmp(arg[iarg+1],"yes") == 0) pairrequest = 1;
+      else if (strcmp(arg[iarg+1],"no") == 0) pairrequest = 0;
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"bond") == 0) {
+      if (iarg+2 > narg) error->all("Illegal compute ebond/atom command");
+      if (strcmp(arg[iarg+1],"yes") == 0) bondrequest = 1;
+      else if (strcmp(arg[iarg+1],"no") == 0) bondrequest = 0;
+      iarg += 2;
+    } else error->all("Illegal compute ebond/atom command");
+  }
+
   nmax = 0;
   stress = NULL;
 }
@@ -55,8 +81,14 @@ ComputeStressAtom::~ComputeStressAtom()
 
 void ComputeStressAtom::init()
 {
-  if (force->pair == NULL || force->pair->single_enable == 0)
+  if (pairrequest) {
-    error->all("Pair style does not support computing per-atom stress");
+    if (force->pair == NULL || force->pair->single_enable == 0)
+      error->all("Pair style does not support computing per-atom stress");
+    pairflag = 1;
+  } else pairflag = 0;
+
+  if (bondrequest && force->bond) bondflag = 1;
+  else bondflag = 0;
 
   int count = 0;
   for (int i = 0; i < modify->ncompute; i++)
@@ -69,8 +101,8 @@ void ComputeStressAtom::init()
 
 void ComputeStressAtom::compute_peratom()
 {
-  int i,j,k,n,itype,jtype,numneigh;
+  int i,j,k,n,i1,i2,itype,jtype,numneigh,iflag;
-  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+  double xtmp,ytmp,ztmp,delx,dely,delz,rsq,eng;
   double factor_coul,factor_lj,fforce,rmass;
   int *neighs;
   Pair::One one;
@@ -86,10 +118,12 @@ void ComputeStressAtom::compute_peratom()
   }
 
   // clear stress array
-  // n includes ghosts only if newton_pair flag is set
+  // n includes ghosts only if newton flag is set
 
-  if (force->newton_pair) n = atom->nlocal + atom->nghost;
+  int nlocal = atom->nlocal;
-  else n = atom->nlocal;
+
+  if (force->newton) n = nlocal + atom->nghost;
+  else n = nlocal;
 
   for (i = 0; i < n; i++) {
     stress[i][0] = 0.0;
@@ -100,73 +134,123 @@ void ComputeStressAtom::compute_peratom()
     stress[i][5] = 0.0;
   }
 
-  // if needed, build a half neighbor list
+  // compute pairwise stress for atoms via pair->single()
+  // if neither atom is in compute group, skip that pair
 
-  if (!neighbor->half_every) neighbor->build_half();
+  if (pairflag) {
 
-  // compute pairwise stress for all atoms via pair->single()
+    // if needed, build a half neighbor list
-  // use half neighbor list
 
-  double *special_coul = force->special_coul;
+    if (!neighbor->half_every) neighbor->build_half();
-  double *special_lj = force->special_lj;
-  double **cutsq = force->pair->cutsq;
 
-  double **x = atom->x;
+    double *special_coul = force->special_coul;
-  int *type = atom->type;
+    double *special_lj = force->special_lj;
-  int nlocal = atom->nlocal;
+    double **cutsq = force->pair->cutsq;
-  int nall = atom->nlocal + atom->nghost;
+    int newton_pair = force->newton_pair;
 
-  for (i = 0; i < nlocal; i++) {
+    double **x = atom->x;
-    xtmp = x[i][0];
+    int *mask = atom->mask;
-    ytmp = x[i][1];
+    int *type = atom->type;
-    ztmp = x[i][2];
+    int nall = nlocal + atom->nghost;
-    itype = type[i];
-    neighs = neighbor->firstneigh[i];
-    numneigh = neighbor->numneigh[i];
-    
-    for (k = 0; k < numneigh; k++) {
-      j = neighs[k];
 
-      if (j < nall) factor_coul = factor_lj = 1.0;
+    for (i = 0; i < nlocal; i++) {
-      else {
+      xtmp = x[i][0];
-	factor_coul = special_coul[j/nall];
+      ytmp = x[i][1];
-	factor_lj = special_lj[j/nall];
+      ztmp = x[i][2];
-	j %= nall;
+      itype = type[i];
-      }
+      iflag = mask[i] & groupbit;
+      neighs = neighbor->firstneigh[i];
+      numneigh = neighbor->numneigh[i];
+      
+      for (k = 0; k < numneigh; k++) {
+	j = neighs[k];
+	if (iflag == 0 && (mask[j] & groupbit) == 0) continue;
 
-      delx = xtmp - x[j][0];
+	if (j < nall) factor_coul = factor_lj = 1.0;
-      dely = ytmp - x[j][1];
+	else {
-      delz = ztmp - x[j][2];
+	  factor_coul = special_coul[j/nall];
-      rsq = delx*delx + dely*dely + delz*delz;
+	  factor_lj = special_lj[j/nall];
-      jtype = type[j];
+	  j %= nall;
-
-      if (rsq < cutsq[itype][jtype]) {
-	force->pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,0,one);
-	fforce = one.fforce;
-
-	stress[i][0] -= delx*delx*fforce;
-	stress[i][1] -= dely*dely*fforce;
-	stress[i][2] -= delz*delz*fforce;
-	stress[i][3] -= delx*dely*fforce;
-	stress[i][4] -= delx*delz*fforce;
-	stress[i][5] -= dely*delz*fforce;
-	if (force->newton_pair || j < nlocal) {
-	  stress[j][0] -= delx*delx*fforce;
-	  stress[j][1] -= dely*dely*fforce;
-	  stress[j][2] -= delz*delz*fforce;
-	  stress[j][3] -= delx*dely*fforce;
-	  stress[j][4] -= delx*delz*fforce;
-	  stress[j][5] -= dely*delz*fforce;
 	}
+	
+	delx = xtmp - x[j][0];
+	dely = ytmp - x[j][1];
+	delz = ztmp - x[j][2];
+	rsq = delx*delx + dely*dely + delz*delz;
+	jtype = type[j];
+	
+	if (rsq < cutsq[itype][jtype]) {
+	  force->pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,0,one);
+	  fforce = one.fforce;
+	  
+	  stress[i][0] -= delx*delx*fforce;
+	  stress[i][1] -= dely*dely*fforce;
+	  stress[i][2] -= delz*delz*fforce;
+	  stress[i][3] -= delx*dely*fforce;
+	  stress[i][4] -= delx*delz*fforce;
+	  stress[i][5] -= dely*delz*fforce;
+	  if (newton_pair || j < nlocal) {
+	    stress[j][0] -= delx*delx*fforce;
+	    stress[j][1] -= dely*dely*fforce;
+	    stress[j][2] -= delz*delz*fforce;
+	    stress[j][3] -= delx*dely*fforce;
+	    stress[j][4] -= delx*delz*fforce;
+	    stress[j][5] -= dely*delz*fforce;
+	  }
+	}
+      }
+    }
+    
+  }
+
+  // compute bond stress for atoms via bond->single()
+  // if neither atom is in compute group, skip that bond
+
+  if (bondflag) {
+    double **x = atom->x;
+    int *mask = atom->mask;
+    int **bondlist = neighbor->bondlist;
+    int nbondlist = neighbor->nbondlist;
+    int newton_bond = force->newton_bond;
+    int type;
+
+    for (n = 0; n < nbondlist; n++) {
+      i1 = bondlist[n][0];
+      i2 = bondlist[n][1];
+      type = bondlist[n][2];
+      if ((mask[i1] & groupbit) == 0 && (mask[i2] & groupbit) == 0) continue;
+      
+      delx = x[i1][0] - x[i2][0];
+      dely = x[i1][1] - x[i2][1];
+      delz = x[i1][2] - x[i2][2];
+      domain->minimum_image(delx,dely,delz);
+      
+      rsq = delx*delx + dely*dely + delz*delz;
+      force->bond->single(type,rsq,i1,i2,0,fforce,eng);
+      
+      stress[i1][0] -= delx*delx*fforce;
+      stress[i1][1] -= dely*dely*fforce;
+      stress[i1][2] -= delz*delz*fforce;
+      stress[i1][3] -= delx*dely*fforce;
+      stress[i1][4] -= delx*delz*fforce;
+      stress[i1][5] -= dely*delz*fforce;
+      
+      if (newton_bond || i2 < nlocal) {
+	stress[i2][0] -= delx*delx*fforce;
+	stress[i2][1] -= dely*dely*fforce;
+	stress[i2][2] -= delz*delz*fforce;
+	stress[i2][3] -= delx*dely*fforce;
+	stress[i2][4] -= delx*delz*fforce;
+	stress[i2][5] -= dely*delz*fforce;
       }
     }
   }
 
   // communicate stress between neighbor procs
 
-  if (force->newton_pair) comm->reverse_comm_compute(this);
+  if (force->newton) comm->reverse_comm_compute(this);
 
-  // remove double counting of per-atom stress
+  // remove double counting
 
   for (i = 0; i < nlocal; i++) {
     stress[i][0] *= 0.5;
@@ -177,21 +261,27 @@ void ComputeStressAtom::compute_peratom()
     stress[i][5] *= 0.5;
   }
 
-  // include kinetic energy term for each atom
+  // include kinetic energy term for each atom in group
   // mvv2e converts mv^2 to energy
 
-  double **v = atom->v;
+  if (kerequest) {
-  double *mass = atom->mass;
+    double **v = atom->v;
-  double mvv2e = force->mvv2e;
+    double *mass = atom->mass;
-
+    int *mask = atom->mask;
-  for (i = 0; i < nlocal; i++) {
+    int *type = atom->type;
-    rmass = mvv2e * mass[type[i]];
+    double mvv2e = force->mvv2e;
-    stress[i][0] -= rmass*v[i][0]*v[i][0];
+    
-    stress[i][1] -= rmass*v[i][1]*v[i][1];
+    for (i = 0; i < nlocal; i++) {
-    stress[i][2] -= rmass*v[i][2]*v[i][2];
+      if (mask[i] & groupbit) {
-    stress[i][3] -= rmass*v[i][0]*v[i][1];
+	rmass = mvv2e * mass[type[i]];
-    stress[i][4] -= rmass*v[i][0]*v[i][2];
+	stress[i][0] -= rmass*v[i][0]*v[i][0];
-    stress[i][5] -= rmass*v[i][1]*v[i][2];
+	stress[i][1] -= rmass*v[i][1]*v[i][1];
+	stress[i][2] -= rmass*v[i][2]*v[i][2];
+	stress[i][3] -= rmass*v[i][0]*v[i][1];
+	stress[i][4] -= rmass*v[i][0]*v[i][2];
+	stress[i][5] -= rmass*v[i][1]*v[i][2];
+      }
+    }
   }
 
   // convert to pressure units (actually stress/volume = pressure)

src/compute_stress_atom.h

@@ -30,7 +30,10 @@ class ComputeStressAtom : public Compute {
   int memory_usage();
 
  private:
+  int pairrequest,bondrequest,kerequest;
+  int pairflag,bondflag;
   int nmax;
+
   double **stress;
 };
 

src/dump_custom.cpp

@@ -33,7 +33,7 @@ enum{TAG,MOL,TYPE,X,Y,Z,XS,YS,ZS,XU,YU,ZU,IX,IY,IZ,
      VX,VY,VZ,FX,FY,FZ,
      Q,MUX,MUY,MUZ,
      QUATW,QUATI,QUATJ,QUATK,TQX,TQY,TQZ,
-     EPAIR,KE,ETOTAL,CENTRO,SXX,SYY,SZZ,SXY,SXZ,SYZ,
+     EPAIR,EBOND,KE,ETOTAL,CENTRO,SXX,SYY,SZZ,SXY,SXZ,SYZ,
      COMPUTE};
 enum{LT,LE,GT,GE,EQ,NEQ};
 enum{INT,DOUBLE};
@@ -57,9 +57,11 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
 
   // flags, IDs, and memory for compute objects dump may create
 
-  index_epair = index_ke = index_etotal = index_centro = index_stress = -1;
+  index_epair = index_ebond = index_ke = 
+    index_etotal = index_centro = index_stress = -1;
 
   style_epair = "epair/atom";
+  style_ebond = "ebond/atom";
   style_ke = "ke/atom";
   style_etotal = "etotal/atom";
   style_centro = "centro/atom";
@@ -79,6 +81,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
   // create the requested Computes
 
   if (index_epair >= 0) create_compute(style_epair,NULL);
+  if (index_ebond >= 0) create_compute(style_ebond,NULL);
   if (index_ke >= 0) create_compute(style_ke,NULL);
   if (index_etotal >= 0) create_compute(style_etotal,style_epair);
   if (index_centro >= 0) create_compute(style_centro,NULL);
@@ -122,6 +125,7 @@ DumpCustom::~DumpCustom()
   // delete Compute classes if dump custom created them
 
   if (index_epair >= 0)  modify->delete_compute(id_compute[index_epair]);
+  if (index_ebond >= 0)  modify->delete_compute(id_compute[index_ebond]);
   if (index_ke >= 0)  modify->delete_compute(id_compute[index_ke]);
   if (index_etotal >= 0)  modify->delete_compute(id_compute[index_etotal]);
   if (index_centro >= 0)  modify->delete_compute(id_compute[index_centro]);
@@ -430,6 +434,9 @@ int DumpCustom::count()
       } else if (thresh_array[ithresh] == EPAIR) {
 	ptr = compute[index_epair]->scalar_atom;
 	nstride = 1;
+      } else if (thresh_array[ithresh] == EBOND) {
+	ptr = compute[index_ebond]->scalar_atom;
+	nstride = 1;
       } else if (thresh_array[ithresh] == KE) {
 	ptr = compute[index_ke]->scalar_atom;
 	nstride = 1;
@@ -701,6 +708,10 @@ void DumpCustom::parse_fields(int narg, char **arg)
       pack_choice[i] = &DumpCustom::pack_epair;
       vtype[i] = DOUBLE;
       index_epair = add_compute(style_epair,1);
+    } else if (strcmp(arg[iarg],"ebond") == 0) {
+      pack_choice[i] = &DumpCustom::pack_ebond;
+      vtype[i] = DOUBLE;
+      index_ebond = add_compute(style_ebond,1);
     } else if (strcmp(arg[iarg],"ke") == 0) {
       pack_choice[i] = &DumpCustom::pack_ke;
       vtype[i] = DOUBLE;
@@ -943,6 +954,12 @@ int DumpCustom::modify_param(int narg, char **arg)
 	index_epair = add_compute(style_epair,1);
 	create_compute(style_epair,NULL);
       }
+    } else if (strcmp(arg[1],"ebond") == 0) {
+      thresh_array[nthresh] = EBOND;
+      if (index_ebond < 0) {
+	index_ebond = add_compute(style_ebond,1);
+	create_compute(style_ebond,NULL);
+      }
     } else if (strcmp(arg[1],"ke") == 0) {
       thresh_array[nthresh] = KE;
       if (index_ke < 0) {
@@ -1591,6 +1608,20 @@ void DumpCustom::pack_epair(int n)
 
 /* ---------------------------------------------------------------------- */
 
+void DumpCustom::pack_ebond(int n)
+{
+  double *ebond = compute[index_ebond]->scalar_atom;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++)
+    if (choose[i]) {
+      buf[n] = ebond[i];
+      n += size_one;
+    }
+}
+
+/* ---------------------------------------------------------------------- */
+
 void DumpCustom::pack_ke(int n)
 {
   double *ke = compute[index_ke]->scalar_atom;

src/dump_custom.h

@@ -50,8 +50,9 @@ class DumpCustom : public Dump {
 
                              // index = where keyword's Compute is in list
                              // style = style of Compute object
-  int index_epair,index_ke,index_etotal,index_centro,index_stress;
+  int index_epair,index_ebond,index_ke,index_etotal,index_centro,index_stress;
-  char *style_epair,*style_ke,*style_etotal,*style_centro,*style_stress;
+  char *style_epair,*style_ebond,*style_ke,*style_etotal;
+  char *style_centro,*style_stress;
 
   // private methods
 
@@ -117,6 +118,7 @@ class DumpCustom : public Dump {
   void pack_etotal(int);
   void pack_ke(int);
   void pack_epair(int);
+  void pack_ebond(int);
   void pack_centro(int);
   void pack_sxx(int);
   void pack_syy(int);