mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2573 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
7f019a4b37
commit
67b65ef552
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@ -32,6 +32,7 @@
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#include "pair_reax.h"
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#include "pair_reax_fortran.h"
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#include "atom.h"
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#include "update.h"
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#include "force.h"
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#include "comm.h"
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#include "neighbor.h"
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@ -61,12 +62,19 @@ PairREAX::PairREAX(LAMMPS *lmp) : Pair(lmp)
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chpot = 0;
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nmax = 0;
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arow_ptr = NULL;
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ch = NULL;
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elcvec = NULL;
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rcg = NULL;
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wcg = NULL;
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pcg = NULL;
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poldcg = NULL;
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qcg = NULL;
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matmax = 0;
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aval = NULL;
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acol_ind = NULL;
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comm_forward = 1;
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comm_reverse = 1;
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@ -87,13 +95,21 @@ PairREAX::~PairREAX()
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for (int i = 1; i <= atom->ntypes; i++)
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delete [] param_list[i].params;
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delete [] param_list;
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delete [] map;
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}
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memory->sfree(arow_ptr);
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memory->sfree(ch);
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memory->sfree(elcvec);
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memory->sfree(rcg);
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memory->sfree(wcg);
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memory->sfree(pcg);
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memory->sfree(poldcg);
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memory->sfree(qcg);
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memory->sfree(aval);
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memory->sfree(acol_ind);
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}
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/* ---------------------------------------------------------------------- */
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@ -114,7 +130,7 @@ void PairREAX::compute(int eflag, int vflag)
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if (vflag_atom) FORTRAN(cbkvirial, CBKVIRIAL).Latomvirial = 1;
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else FORTRAN(cbkvirial, CBKVIRIAL).Latomvirial = 0;
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// reallocate CG arrays if necessary
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// reallocate charge equilibration and CG arrays if necessary
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if (atom->nmax > nmax) {
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memory->sfree(rcg);
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@ -122,8 +138,13 @@ void PairREAX::compute(int eflag, int vflag)
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memory->sfree(pcg);
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memory->sfree(poldcg);
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memory->sfree(qcg);
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nmax = atom->nmax;
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int n = nmax+1;
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arow_ptr = (int *) memory->smalloc(n*sizeof(int),"reax:arow_ptr");
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ch = (double *) memory->smalloc(n*sizeof(double),"reax:ch");
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elcvec = (double *) memory->smalloc(n*sizeof(double),"reax:elcvec");
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rcg = (double *) memory->smalloc(n*sizeof(double),"reax:rcg");
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wcg = (double *) memory->smalloc(n*sizeof(double),"reax:wcg");
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pcg = (double *) memory->smalloc(n*sizeof(double),"reax:pcg");
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@ -162,6 +183,7 @@ void PairREAX::compute(int eflag, int vflag)
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read_reax_forces();
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// extract global and per-atom energy from ReaxFF Fortran
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// compute_charge already contributed to eatom
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if (eflag_global) {
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evdwl += FORTRAN(cbkenergies, CBKENERGIES).eb;
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@ -187,7 +209,7 @@ void PairREAX::compute(int eflag, int vflag)
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if (eflag_atom) {
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int ntotal = atom->nlocal + atom->nghost;
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for (i = 0; i < ntotal; i++)
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eatom[i] = FORTRAN(cbkd,CBKD).estrain[i];
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eatom[i] += FORTRAN(cbkd,CBKD).estrain[i];
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}
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// extract global and per-atom virial from ReaxFF Fortran
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@ -221,8 +243,6 @@ void PairREAX::compute(int eflag, int vflag)
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void PairREAX::write_reax_positions()
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{
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double xtmp, ytmp, ztmp;
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int itype;
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int itag;
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int j, jx, jy, jz, jia;
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double **x = atom->x;
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@ -235,25 +255,20 @@ void PairREAX::write_reax_positions()
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FORTRAN(rsmall, RSMALL).na = nlocal+nghost;
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FORTRAN(rsmall, RSMALL).na_local = nlocal;
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j = 0;
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jx = 0;
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jy = ReaxParams::nat;
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jz = 2*ReaxParams::nat;
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jia = 0;
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j = 0;
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for (int i = 0; i < nlocal+nghost; i++, j++) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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itag = tag[i];
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FORTRAN(cbkc, CBKC).c[j+jx] = xtmp;
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FORTRAN(cbkc, CBKC).c[j+jy] = ytmp;
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FORTRAN(cbkc, CBKC).c[j+jz] = ztmp;
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FORTRAN(cbkc, CBKC).c[j+jx] = x[i][0];
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FORTRAN(cbkc, CBKC).c[j+jy] = x[i][1];
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FORTRAN(cbkc, CBKC).c[j+jz] = x[i][2];
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FORTRAN(cbkch, CBKCH).ch[j] = q[i];
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FORTRAN(cbkia, CBKIA).ia[j+jia] = itype;
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FORTRAN(cbkia, CBKIA).iag[j+jia] = itype;
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FORTRAN(cbkc, CBKC).itag[j]= itag;
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FORTRAN(cbkia, CBKIA).ia[j+jia] = map[type[i]];
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FORTRAN(cbkia, CBKIA).iag[j+jia] = map[type[i]];
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FORTRAN(cbkc, CBKC).itag[j] = tag[i];
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}
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}
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@ -264,10 +279,10 @@ void PairREAX::write_reax_vlist()
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int ii, jj, i, j, iii, jjj;
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double xitmp, yitmp, zitmp;
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double xjtmp, yjtmp, zjtmp;
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int itype, jtype, itag, jtag;
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int itag,jtag;
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int nvpair, nvlself, nvpairmax;
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int nbond;
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int inum, jnum;
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int inum,jnum;
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int *ilist;
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int *jlist;
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int *numneigh,**firstneigh;
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@ -276,7 +291,6 @@ void PairREAX::write_reax_vlist()
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double rtmp[3];
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double **x = atom->x;
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int *type = atom->type;
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int *tag = atom->tag;
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int nlocal = atom->nlocal;
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int nghost = atom->nghost;
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@ -297,7 +311,6 @@ void PairREAX::write_reax_vlist()
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xitmp = x[i][0];
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yitmp = x[i][1];
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zitmp = x[i][2];
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itype = type[i];
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itag = tag[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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@ -307,7 +320,6 @@ void PairREAX::write_reax_vlist()
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xjtmp = x[j][0];
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yjtmp = x[j][1];
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zjtmp = x[j][2];
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jtype = type[j];
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jtag = tag[j];
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delx = xitmp - xjtmp;
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@ -362,14 +374,12 @@ void PairREAX::write_reax_vlist()
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xitmp = x[i][0];
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yitmp = x[i][1];
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zitmp = x[i][2];
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itype = type[i];
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itag = tag[i];
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for (int j = i+1; j < ntotal; j++) {
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xjtmp = x[j][0];
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yjtmp = x[j][1];
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zjtmp = x[j][2];
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jtype = type[j];
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jtag = tag[j];
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delx = xitmp - xjtmp;
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@ -415,14 +425,10 @@ void PairREAX::read_reax_forces()
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int ntotal = atom->nlocal + atom->nghost;
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int j = 0;
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int jx = 0;
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int jy = 1;
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int jz = 2;
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for (int i = 0; i < ntotal; i++) {
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ftmp[0] = -FORTRAN(cbkd, CBKD).d[j+jx];
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ftmp[1] = -FORTRAN(cbkd, CBKD).d[j+jy];
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ftmp[2] = -FORTRAN(cbkd, CBKD).d[j+jz];
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ftmp[0] = -FORTRAN(cbkd, CBKD).d[j];
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ftmp[1] = -FORTRAN(cbkd, CBKD).d[j+1];
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ftmp[2] = -FORTRAN(cbkd, CBKD).d[j+2];
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f[i][0] = ftmp[0];
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f[i][1] = ftmp[1];
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f[i][2] = ftmp[2];
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@ -443,6 +449,8 @@ void PairREAX::allocate()
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param_list = new ff_params[n+1];
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for (int i = 1; i <= n; i++)
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param_list[i].params = new double[5];
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map = new int[n+1];
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}
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/* ----------------------------------------------------------------------
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@ -470,13 +478,32 @@ void PairREAX::coeff(int narg, char **arg)
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{
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if (!allocated) allocate();
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if (narg != 3 + atom->ntypes)
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error->all("Incorrect args for pair coefficients");
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// insure I,J args are * *
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if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
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error->all("Incorrect args for pair coefficients");
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// insure filename is ffield.reax
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if (strcmp(arg[2],"ffield.reax") != 0)
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error->all("Incorrect args for pair coefficients");
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// read args that map atom types to elements in potential file
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// map[i] = which element the Ith atom type is, -1 if NULL
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for (int i = 3; i < narg; i++) {
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if (strcmp(arg[i],"NULL") == 0) {
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map[i-2] = -1;
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continue;
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}
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map[i-2] = atoi(arg[i]);
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if (map[i-2] < 1) error->all("Incorrect args for pair coefficients");
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}
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int n = atom->ntypes;
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for (int i = 1; i <= n; i++)
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for (int j = i; j <= n; j++)
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setflag[i][j] = 0;
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int count = 0;
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for (int i = 1; i <= n; i++)
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@ -494,14 +521,15 @@ void PairREAX::coeff(int narg, char **arg)
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void PairREAX::init_style()
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{
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// REAX requires pair newton off
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if (atom->tag_enable == 0)
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error->all("Pair style reax requires atom IDs");
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if (force->newton_pair)
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if (force->newton_pair == 0)
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error->all("Pair style reax requires newton pair on");
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if (strcmp(update->unit_style,"real") != 0 && comm->me == 0)
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error->warning("Not using real units with pair reax");
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int irequest = neighbor->request(this);
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neighbor->requests[irequest]->newton = 2;
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FORTRAN(readc, READC)();
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FORTRAN(init, INIT)();
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@ -529,9 +557,9 @@ void PairREAX::init_style()
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FORTRAN(getswa, GETSWA)(&swa);
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double chi, eta, gamma;
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for (int itype = 1; itype <= atom->ntypes; itype++) {
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chi = FORTRAN(cbkchb, CBKCHB).chi[itype-1];
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eta = FORTRAN(cbkchb, CBKCHB).eta[itype-1];
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gamma = FORTRAN(cbkchb, CBKCHB).gam[itype-1];
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chi = FORTRAN(cbkchb, CBKCHB).chi[map[itype]-1];
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eta = FORTRAN(cbkchb, CBKCHB).eta[map[itype]-1];
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gamma = FORTRAN(cbkchb, CBKCHB).gam[map[itype]-1];
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param_list[itype].np = 5;
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param_list[itype].rcutsq = cutmax;
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param_list[itype].params[0] = chi;
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@ -681,19 +709,14 @@ void PairREAX::compute_charge(double &energy_charge_equilibration)
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int ii, jj, i, j;
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double delr2, delr_norm, gamt, hulp1, hulp2;
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double delx, dely, delz;
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double qsum, qi;
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double *ch;
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double *elcvec;
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double *aval;
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int *arow_ptr;
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int *acol_ind;
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int maxmatentries, nmatentries;
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double qsum,qi;
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int nmatentries;
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double sw;
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double rtmp[3];
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int inum, jnum;
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int inum,jnum;
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int *ilist;
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int *jlist;
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int *numneigh, **firstneigh;
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int *numneigh,**firstneigh;
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double **x = atom->x;
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double *q = atom->q;
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@ -708,20 +731,24 @@ void PairREAX::compute_charge(double &energy_charge_equilibration)
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// realloc neighbor based arrays if necessary
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int numneigh_total = 0;
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for (ii = 0; ii < inum; ii++)
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numneigh_total += numneigh[ilist[ii]];
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arow_ptr = new int[nlocal+nghost+1];
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ch = new double[nlocal+nghost+1];
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elcvec = new double[nlocal+nghost+1];
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maxmatentries = numneigh_total+2*nlocal;
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aval = new double[maxmatentries];
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acol_ind = new int[maxmatentries];
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nmatentries = 0;
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if (numneigh_total + 2*nlocal > matmax) {
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memory->sfree(aval);
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memory->sfree(acol_ind);
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matmax = numneigh_total + 2*nlocal;
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aval = (double *) memory->smalloc(matmax*sizeof(double),"reax:aval");
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acol_ind = (int *) memory->smalloc(matmax*sizeof(int),"reax:acol_ind");
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}
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// build linear system
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nmatentries = 0;
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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xitmp = x[i][0];
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@ -816,7 +843,6 @@ void PairREAX::compute_charge(double &energy_charge_equilibration)
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for (i = nlocal; i < nlocal+nghost; i++) {
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qi = q[i];
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ch[i] = qi;
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if (i<nlocal) qsum += qi;
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}
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double qtot;
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@ -839,24 +865,21 @@ void PairREAX::compute_charge(double &energy_charge_equilibration)
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itype = type[i];
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// 23.02 is the ReaxFF conversion from eV to kcal/mol
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// Should really use constants.evfactor ~ 23.06, but
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// that would break consistency with serial ReaxFF code
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// should really use constants.evfactor ~23.06
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// but that would break consistency with serial ReaxFF code
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// NOTE: this hard-wired real units
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// if want other units would have to change params[] in file
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qi = 23.02 * (param_list[itype].params[0]*ch[i]+
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param_list[itype].params[1]*ch[i]*ch[i]);
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energy_charge_equilibration += qi;
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if (eflag_atom) eatom[i] += qi;
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}
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// copy charge vector back to particles from the calculated values
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for (i = 0; i < nlocal+nghost; i++) q[i] = ch[i];
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chpot = ch[nlocal+nghost];
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delete [] aval;
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delete [] arow_ptr;
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delete [] elcvec;
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delete [] ch;
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delete [] acol_ind;
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}
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/* ---------------------------------------------------------------------- */
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@ -1000,6 +1023,9 @@ void PairREAX::sparse_product(const int &n, const int &nlocal,
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double PairREAX::memory_usage()
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{
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double bytes = 5 * nmax * sizeof(double);
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double bytes = nmax * sizeof(int);
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bytes += 7 * nmax * sizeof(double);
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bytes += matmax * sizeof(int);
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bytes += matmax * sizeof(double);
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return bytes;
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}
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@ -52,11 +52,15 @@ class PairREAX : public Pair {
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double *params;
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};
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ff_params *param_list;
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int *map;
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int nentries;
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double chpot;
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int *arow_ptr,*acol_ind;
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double *ch,*elcvec;
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double *rcg,*wcg,*pcg,*poldcg,*qcg;
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int nmax;
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double *aval;
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int nmax,matmax;
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void allocate();
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void read_files(char *, char *);
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