Added fix reax/c/bonds

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8053 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/USER-REAXC/fix_reaxc_bonds.cpp

@@ -12,22 +12,29 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Contributing author: Ray Shan (Sandia)
+   Contributing author: Ray Shan (Sandia, tnshan@sandia.gov)
 ------------------------------------------------------------------------- */
 
+#include "lmptype.h"
 #include "stdlib.h"
 #include "string.h"
+#include "fix_ave_atom.h"
 #include "fix_reaxc_bonds.h"
 #include "atom.h"
-#include "pair_reax_c.h"
 #include "update.h"
-#include "force.h"
+#include "pair_reax_c.h"
 #include "modify.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "comm.h"
+#include "force.h"
 #include "compute.h"
 #include "input.h"
 #include "variable.h"
 #include "memory.h"
 #include "error.h"
+#include "reaxc_list.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -37,27 +44,54 @@ using namespace FixConst;
 FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg)
 {
-  if (narg < 5) error->all(FLERR,"Illegal fix reax/c/bonds command");
+  if (narg < 7) error->all(FLERR,"Illegal fix reax/c/bonds command");
 
   MPI_Comm_rank(world,&me);
+  MPI_Comm_size(world,&nprocs);
+  nmax = nint(atom->nlocal*1.05);
+  ntypes = atom->ntypes;
 
   nevery = atoi(arg[3]);
-  if (nevery < 1) error->all(FLERR,"Illegal fix reax/c/bonds command");
+  nrepeat = atoi(arg[4]);
+  global_freq = nfreq = atoi(arg[5]);
+  
+  if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
+    error->all(FLERR,"Illegal fix reax/c/bonds command");
+  if (nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
+    error->all(FLERR,"Illegal fix reax/c/bonds command");
 
   if (me == 0) {
-    fp = fopen(arg[4],"w");
+    fp = fopen(arg[6],"w");
     if (fp == NULL) {
       char str[128];
-      sprintf(str,"Cannot open fix reax/c/bonds file %s",arg[4]);
+      sprintf(str,"Cannot open fix reax/c/bonds file %s",arg[6]);
       error->one(FLERR,str);
     }
   }
+
+  if (atom->tag_consecutive() == 0)
+    error->all(FLERR,"Atom IDs must be consecutive for fix reax/c bonds");
+
+  allocate();
+
+  nvalid = nextvalid();
 }
 
 /* ---------------------------------------------------------------------- */
 
 FixReaxCBonds::~FixReaxCBonds()
 {
+  MPI_Comm_rank(world,&me);
+
+  memory->destroy(sbo);
+  memory->destroy(nlp);
+  memory->destroy(avq);
+  memory->destroy(numneigh);
+  memory->destroy(neighid);
+  memory->destroy(tmpid);
+  memory->destroy(abo);
+  memory->destroy(tmpabo);
+
   if (me == 0) fclose(fp);
 }
 
@@ -70,9 +104,7 @@ int FixReaxCBonds::setmask()
   return mask;
 }
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   perform initial write
-------------------------------------------------------------------------- */
 
 void FixReaxCBonds::setup(int vflag)
 {
@@ -83,155 +115,275 @@ void FixReaxCBonds::setup(int vflag)
 
 void FixReaxCBonds::init()
 {
-  // insure ReaxFF/C is defined
   reaxc = (PairReaxC *) force->pair_match("reax/c",1);
   if (reaxc == NULL) error->all(FLERR,"Cannot use fix reax/c/bonds without "
 		  "pair_style reax/c");
 
-  // Notify pair_reax_c to calculation bonding information
+  if (nvalid < update->ntimestep) {
-  reaxc->fixbond_flag = 1;
+    irepeat = 0;
-
+    nvalid = nextvalid();
+  }
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixReaxCBonds::end_of_step()
 {
-  OutputReaxCBonds(update->ntimestep,fp);
+  // skip if not step that requires calculating bonds
+  bigint ntimestep = update->ntimestep;
+
+  if (ntimestep != nvalid) return;
+
+  Output_ReaxC_Bonds(update->ntimestep,fp);
   if (me == 0) fflush(fp);
 }
 
 /* ---------------------------------------------------------------------- */
 
-void FixReaxCBonds::OutputReaxCBonds(bigint ntimestep, FILE *fp)
+void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
 
 {
-  int npart,npart_tot,nbuf,nbuf_local,most,j;
+  int i, j, k, itype, jtype, iatom, itag, jtag;
-  int ii,jn,mbond,numbonds,nsbmax,nsbmax_most;
+  int b, nbuf, nbuf_local, inode;
-  int nprocs,nlocal_tmp;
+  int nlocal_max, numbonds, numbonds_max;
-  double cutof3;
   double *buf;
+
+  int nlocal = atom->nlocal;
+  int nlocal_tot = static_cast<int> (atom->natoms);
+
+  repeat = nrepeat;
+  // zero out average BO for next Nfreq
+  if (irepeat == 0)
+    for (i = 0; i < nmax; i++) {
+      sbo[i] = nlp[i] = avq[i] = 0.0;
+      for (j = 0; j < MAXBOND; j++) {
+	tmpid[i][j] = 0;
+        tmpabo[i][j] = 0.0;
+      }
+    }
+
+  // Accumulate bonding information for each nvalid
+  GatherBond( system, lists);
+
+  // done if irepeat < nrepeat, else reset irepeat and nvalid
+  irepeat++;
+  if (irepeat < nrepeat) {
+    nvalid += nevery;
+    return;
+  }
+  irepeat = numbonds = 0;
+  nvalid = ntimestep + nfreq - (nrepeat-1)*nevery;
+
+  // Determine actual bonding based on averaged bond order
+  FindBond( system, lists, numbonds);
+
+  // allocate a temporary buffer for the snapshot info
+  MPI_Allreduce(&numbonds,&numbonds_max,1,MPI_INT,MPI_MAX,world);
+  MPI_Allreduce(&nlocal,&nlocal_max,1,MPI_INT,MPI_MAX,world);
+  nbuf = 1+(numbonds_max*2+10)*nlocal_max;
+  memory->create(buf,nbuf,"reax/c/bonds:buf");
+  for (i = 0; i < nbuf; i ++) buf[i] = 0.0;
+
+  // Pass information to buffer
+  PassBuffer( system, buf, nbuf_local);
+
+  // Receive information from buffer for output
+  RecvBuffer( system, buf, nbuf, nbuf_local, nlocal_tot, numbonds_max);
+
+  memory->destroy(buf);
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixReaxCBonds::GatherBond( reax_system *system, reax_list *lists)
+{
+  int *ilist, i, ii, inum;
+  int j, pj, nj, jtag, jtype;
+  double bo_tmp,bo_cut;
+
+  inum = reaxc->list->inum;
+  ilist = reaxc->list->ilist;
+  bond_data *bo_ij;
+  bo_cut = 0.10; //reaxc->control->bg_cut;
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    nj = 0;
+
+    for( pj = Start_Index(i, reaxc->lists); pj < End_Index(i, reaxc->lists); ++pj ) {
+      bo_ij = &( reaxc->lists->select.bond_list[pj] );
+      j = bo_ij->nbr;
+      jtag = reaxc->system->my_atoms[j].orig_id;
+      bo_tmp = bo_ij->bo_data.BO;
+
+      if (bo_tmp > bo_cut) {
+	here:;
+	if (jtag != tmpid[i][nj] && tmpid[i][nj] != 0) {
+	  nj ++;
+	  if (nj > MAXBOND) error->all(FLERR,"Increase MAXBOND value");
+	  goto here;
+	}
+	tmpid[i][nj] = jtag;
+	tmpabo[i][nj] += bo_tmp;
+        nj ++;
+      }
+
+    }
+    sbo[i] += reaxc->workspace->total_bond_order[i];
+    nlp[i] += reaxc->workspace->nlp[i];
+    avq[i] += atom->q[i];
+  }
+
+}
+/* ---------------------------------------------------------------------- */
+
+void FixReaxCBonds::FindBond( reax_system *system, reax_list *lists,
+		int &numbonds)
+{
+  int *ilist, i, ii, inum;
+  int j, pj, nj, jtag, jtype;
+  double bo_tmp,bo_cut;
+
+  inum = reaxc->list->inum;
+  ilist = reaxc->list->ilist;
+  bo_cut = reaxc->control->bg_cut;
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    sbo[i] /= repeat;
+    nlp[i] /= repeat;
+    avq[i] /= repeat;
+    numneigh[i] = 0;
+    for (j = 0; j < MAXBOND; j++) {
+      tmpabo[i][j] /= repeat;
+      neighid[i][j] = 0;
+      abo[i][j] = 0.0;
+    }
+  }
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    nj = 0;
+
+    for (j = 0; j < MAXBOND; j++){
+      if (tmpabo[i][j] > bo_cut) {
+	neighid[i][nj] = tmpid[i][j];
+	abo[i][nj] = tmpabo[i][j];
+	nj ++;
+      }
+    }
+    numneigh[i] = nj;
+    if (nj > numbonds) numbonds = nj;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixReaxCBonds::PassBuffer( reax_system *system, double *buf, 
+		int &nbuf_local)
+{
+  int i, j, k, jtag, numbonds;
+  int nlocal = atom->nlocal;
+
+  j = 2;
+  buf[0] = nlocal;
+  for (i = 0; i < nlocal; i++) {
+    buf[j-1] = atom->tag[i];
+    buf[j+0] = atom->type[i];
+    buf[j+1] = sbo[i];
+    buf[j+2] = nlp[i];
+    buf[j+3] = avq[i];
+    buf[j+4] = numneigh[i];
+    numbonds = nint(buf[j+4]);
+
+    for (k = 5; k < 5+numbonds; k++) {  
+      buf[j+k] = neighid[i][k-5];
+    }
+    j += (5+numbonds);
+
+    if (atom->molecule == NULL ) buf[j] = 0.0;
+    else buf[j] = atom->molecule[i];
+    j ++;
+
+    for (k = 0; k < numbonds; k++) {	
+      buf[j+k] = abo[i][k];
+    }
+    j += (1+numbonds);
+  }
+  nbuf_local = j - 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixReaxCBonds::RecvBuffer( reax_system *system, double *buf, 
+		int nbuf, int nbuf_local, int natoms, int maxnum)
+{
+  int i, j, k, l, itype, jtype, itag, jtag;
+  int inode, nlocal_tmp, numbonds, molid;
+  int nlocal = atom->nlocal;
+  int ntimestep = update->ntimestep;
+  double sbotmp, nlptmp, avqtmp, abotmp;
+
+  double cutof3 = reaxc->control->bg_cut;
   MPI_Request irequest, irequest2;
   MPI_Status istatus;
-  MPI_Comm_size(world,&nprocs);
 
-  npart = atom->nlocal;
+  if (me == 0 ){ 
-  npart_tot = static_cast<int> (atom->natoms);
-
-  mbond = MAX_BOND; 		 	// max bond per atom allowed
-  nsbmax = reaxc->system->my_bonds;	// max bond for each atom
-  cutof3 = reaxc->control->bg_cut;  	// bond order cutoff for determining bonds
-
-  // get maxval from all nodes
-  MPI_Allreduce(&npart,&most,1,MPI_INT,MPI_MAX,world);
-  MPI_Allreduce(&nsbmax,&nsbmax_most,1,MPI_INT,MPI_MAX,world);
- 
-  if (me == 0) {
     fprintf(fp,"# Timestep " BIGINT_FORMAT " \n",ntimestep);
     fprintf(fp,"# \n");
-    fprintf(fp,"# Number of particles %d \n",npart_tot);
+    fprintf(fp,"# Number of particles %d \n",natoms);
     fprintf(fp,"# \n");
     fprintf(fp,"# Max number of bonds per atom %d with "
-	    "coarse bond order cutoff %5.3f \n",
+	    "coarse bond order cutoff %5.3f \n",maxnum,cutof3);
-	    nsbmax_most,cutof3);
     fprintf(fp,"# Particle connection table and bond orders \n");
     fprintf(fp,"# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q \n");
   }
 
-  // allocate a temporary buffer for the snapshot info
-  // big enough for largest number of atoms on any one proc
-  // nbuf_local = size of local buffer for table of atom bonds
- 
-  nbuf = 1+(2*nsbmax_most+7)*most;
-  memory->create(buf,nbuf,"reax/c/bonds:buf");
- 
-  // put bonding information in buffers
   j = 2;
-  buf[0] = npart;
-  for (int ipart = 0; ipart < npart; ipart++) {
-    buf[j-1] = atom->tag[ipart];  		//atom tag
-    buf[j+0] = atom->type[ipart];  		//atom type
-    buf[j+1] = reaxc->system->my_atoms[ipart].numbonds;  	// no of bonds around i
-    numbonds = nint(buf[j+1]);
-
-    int k;
-    // connection table based on coarse bond order cutoff (> cutof3)
-    for (k=2;k<2+numbonds;k++) 
-      buf[j+k] = reaxc->system->my_atoms[ipart].nbr_id[k-1];	// calculated in reaxc_traj
-
-    // molecule id
-    if (atom->molecule == NULL )
-      buf[j+k] = 0;
-    else
-      buf[j+k] = atom->molecule[ipart];  	
-
-    j+=(3+numbonds);
-
-    // get bond order values for the connection table
-    for (k=0;k<numbonds;k++) 
-      buf[j+k] = reaxc->system->my_atoms[ipart].nbr_bo[k+1];
-
-    // sum of bond orders (abo), no. of lone pairs (vlp), charge (ch)
-    buf[j+k] = reaxc->workspace->total_bond_order[ipart];
-    buf[j+k+1] = reaxc->workspace->nlp[ipart]; 
-    buf[j+k+2] = atom->q[ipart];
-    j+=(4+numbonds);
-  }
-  nbuf_local = j-1;
- 
-  // node 0 pings each node, receives their buffer, writes to file
-  // all other nodes wait for ping, send buffer to node 0
- 
   if (me == 0) {
-    for (int inode = 0; inode<nprocs; inode++) {
+    for (inode = 0; inode < nprocs; inode ++) {
       if (inode == 0) {
-	nlocal_tmp = npart;
+	nlocal_tmp = nlocal;
       } else {
 	MPI_Irecv(&buf[0],nbuf,MPI_DOUBLE,inode,0,world,&irequest);
         MPI_Wait(&irequest,&istatus);
 	nlocal_tmp = nint(buf[0]);
       }
- 
       j = 2;
-      for (int ipart=0;ipart<nlocal_tmp;ipart++) {
+      for (i = 0; i < nlocal_tmp; i ++) {
-	// print atom tag, atom type, no.bonds
+	itag = nint(buf[j-1]);
+	itype = nint(buf[j+0]);
+	sbotmp = buf[j+1];
+	nlptmp = buf[j+2];
+	avqtmp = buf[j+3];
+	numbonds = nint(buf[j+4]);
 
-	fprintf(fp," %d %d %d",nint(buf[j-1]),nint(buf[j+0]),nint(buf[j+1]));
+	fprintf(fp," %d %d %d",itag,itype,numbonds);
-	int k;
+
-	numbonds = nint(buf[j+1]);
+	for (k = 5; k < 5+numbonds; k++) {
-	if (numbonds > nsbmax_most) {
+          jtag = nint(buf[j+k]);
-	  char str[128];
+	  fprintf(fp," %d",jtag);
-	  sprintf(str,"Fix reax/c/bonds numbonds > nsbmax_most");
-	  error->one(FLERR,str);
 	}
+	j += (5+numbonds);
 
-	// print connection table
+	fprintf(fp," %d",nint(buf[j]));
+	j ++;
 
-	for (k=2;k<2+numbonds;k++)
+	for (k = 0; k < numbonds; k++) {
-	  fprintf(fp," %d",nint(buf[j+k]));
+	  abotmp = buf[j+k];
-	fprintf(fp," %d",nint(buf[j+k]));
+	  fprintf(fp,"%14.3f",abotmp);
-	j+=(3+numbonds);
+	}
-
+	j += (1+numbonds);
-	// print bond orders
+	fprintf(fp,"%14.3f%14.3f%14.3f\n",sbotmp,nlptmp,avqtmp);
-
-	for (k=0;k<numbonds;k++)
-	  fprintf(fp,"%14.3f",buf[j+k]);
-
-	// print sum of bond orders, no. of lone pairs, charge
-
-	fprintf(fp,"%14.3f%14.3f%14.3f\n",buf[j+k],buf[j+k+1],buf[j+k+2]);
-	j+=(4+numbonds);
       }
     }
-
   } else {
     MPI_Isend(&buf[0],nbuf_local,MPI_DOUBLE,0,0,world,&irequest2);
     MPI_Wait(&irequest2,&istatus);
   }
+  if(me ==0) fprintf(fp,"# \n");
 
-  if (me == 0) fprintf(fp,"# \n");
-
-  memory->destroy(buf);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -243,3 +395,64 @@ int FixReaxCBonds::nint(const double &r)
   else if (r<0.0) i = static_cast<int>(r-0.5);
   return i;
 }
+
+/* ----------------------------------------------------------------------
+   calculate nvalid = next step on which end_of_step does something
+   can be this timestep if multiple of nfreq and nrepeat = 1
+   else backup from next multiple of nfreq
+------------------------------------------------------------------------- */
+
+bigint FixReaxCBonds::nextvalid()
+{
+  bigint nvalid = (update->ntimestep/nfreq)*nfreq + nfreq;
+  if (nvalid-nfreq == update->ntimestep && nrepeat == 1)
+    nvalid = update->ntimestep;
+  else
+    nvalid -= (nrepeat-1)*nevery;
+  if (nvalid < update->ntimestep) nvalid += nfreq;
+  return nvalid;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixReaxCBonds::allocate()
+{
+
+  irepeat = 0;
+
+  sbo = NULL;
+  nlp = NULL;
+  avq = NULL;
+  numneigh = NULL;
+  neighid = NULL;
+  tmpid = NULL;
+  abo = NULL;
+  tmpabo = NULL;
+
+  memory->create(sbo,nmax,"reax/c/bonds:sbo");
+  memory->create(nlp,nmax,"reax/c/bonds:nlp");
+  memory->create(avq,nmax,"reax/c/bonds:avq");
+  memory->create(numneigh,nmax,"reax/c/bonds:numneigh");
+  memory->create(abo,nmax,MAXBOND,"reax/c/bonds:abo");
+  memory->create(neighid,nmax,MAXBOND,"reax/c/bonds:neighid");
+  memory->create(tmpabo,nmax,MAXBOND,"reax/c/bonds:tmpabo");
+  memory->create(tmpid,nmax,MAXBOND,"reax/c/bonds:tmpid");
+
+  irepeat = 0;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+double FixReaxCBonds::memory_usage()
+{
+  double bytes;
+
+  bytes += 3.0*nmax*sizeof(double);
+  bytes += nmax*sizeof(int);
+  bytes += 2.0*nmax*MAXBOND*sizeof(double);
+  bytes += 2.0*nmax*MAXBOND*sizeof(int);
+
+  return bytes;
+}
+

src/USER-REAXC/fix_reaxc_bonds.h

@@ -23,7 +23,11 @@ FixStyle(reax/c/bonds,FixReaxCBonds)
 #include "stdio.h"
 #include "fix.h"
 #include "pair_reax_c.h"
+#include "reaxc_types.h"
 #include "reaxc_defs.h"
+#include "pointers.h"
+
+#define MAXBOND 24
 
 namespace LAMMPS_NS {
 
@@ -37,16 +41,28 @@ class FixReaxCBonds : public Fix {
   void end_of_step();
 
  private:
-  int me;
+  int me, nprocs, nmax, ntypes, maxsize;
-  int nfreq;
+  int nrepeat, irepeat, repeat, nfreq;
+  int *numneigh, **neighid, **tmpid;
+  double *sbo, *nlp, *avq, **abo, **tmpabo;
   FILE *fp;
 
-  void OutputReaxCBonds(bigint, FILE*);
+  void allocate();
-  int nint(const double&);
+  void Output_ReaxC_Bonds(bigint, FILE *);
+  void GatherBond(reax_system*, reax_list*);
+  void FindBond(reax_system*, reax_list*, int &);
+  void PassBuffer(reax_system*, double *, int &);
+  void RecvBuffer(reax_system*, double *, int, int, int, int);
+  int nint(const double &);
+  double memory_usage();
 
+  bigint nvalid, nextvalid();
+  reax_system *system;
+  reax_list *lists;
   class PairReaxC *reaxc;
-};
+  class NeighList *list;
 
+};
 }
 
 #endif