mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7047 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
504227e2e6
commit
c8fa1bd5df
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@ -12,7 +12,7 @@
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Tzu-Ray Shan (U Florida, rayshan@ufl.edu)
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Contributing author: Tzu-Ray Shan (U Florida, present: tnshan@sandia.gov)
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LAMMPS implementation of the Charge-optimized many-body (COMB) potential
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based on the HELL MD program (Prof Simon Phillpot, UF, sphil@mse.ufl.edu)
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and Aidan Thompson's Tersoff code in LAMMPS
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@ -32,11 +32,13 @@
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#include "memory.h"
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#include "error.h"
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#include "group.h"
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#include "update.h"
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using namespace LAMMPS_NS;
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#define MAXLINE 1024
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#define DELTA 4
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#define PGDELTA 1
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/* ---------------------------------------------------------------------- */
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@ -52,6 +54,7 @@ PairComb::PairComb(LAMMPS *lmp) : Pair(lmp)
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nmax = 0;
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NCo = NULL;
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bbij = NULL;
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nelements = 0;
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elements = NULL;
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@ -68,6 +71,11 @@ PairComb::PairComb(LAMMPS *lmp) : Pair(lmp)
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dphin = NULL;
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erpaw = NULL;
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sht_num = NULL;
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sht_first = NULL;
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maxpage = 0;
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pages = NULL;
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// set comm size needed by this Pair
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comm_forward = 1;
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@ -84,6 +92,7 @@ PairComb::~PairComb()
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if (elements)
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for (int i = 0; i < nelements; i++) delete [] elements[i];
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delete [] elements;
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memory->sfree(params);
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memory->destroy(elem2param);
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@ -95,6 +104,9 @@ PairComb::~PairComb()
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memory->destroy(phin);
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memory->destroy(dphin);
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memory->destroy(erpaw);
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memory->destroy(bbij);
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memory->destroy(sht_num);
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memory->destroy(sht_first);
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if (allocated) {
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memory->destroy(setflag);
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@ -122,17 +134,25 @@ void PairComb::compute(int eflag, int vflag)
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double yaself;
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double potal,fac11,fac11e;
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double vionij,fvionij,sr1,sr2,sr3,Eov,Fov;
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int sht_jnum, *sht_jlist;
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evdwl = ecoul = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = vflag_fdotr = vflag_atom = 0;
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// grow coordination array if necessary
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// Build short range neighbor list
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// int every=neighbor->every;
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// int ntimestep=update->ntimestep;
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// if(ntimestep <= 1 || (ntimestep % every == 0))
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Short_neigh();
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// grow coordination array if necessary
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if (atom->nmax > nmax) {
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memory->destroy(NCo);
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memory->destroy(bbij);
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nmax = atom->nmax;
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memory->create(NCo,nmax,"pair:NCo");
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memory->create(bbij,nmax,nmax,"pair:bbij");
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}
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double **x = atom->x;
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@ -177,6 +197,8 @@ void PairComb::compute(int eflag, int vflag)
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jlist = firstneigh[i];
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jnum = numneigh[i];
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sht_jlist = sht_first[i];
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sht_jnum = sht_num[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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@ -258,8 +280,8 @@ void PairComb::compute(int eflag, int vflag)
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// accumulate coordination number information
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if (cor_flag) {
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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for (jj = 0; jj < sht_jnum; jj++) {
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j = sht_jlist[jj];
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j &= NEIGHMASK;
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jtype = map[type[j]];
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iparam_ij = elem2param[itype][jtype][jtype];
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@ -277,11 +299,12 @@ void PairComb::compute(int eflag, int vflag)
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}
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// three-body interactions
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// skip immediately if I-J is not within cutoff
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// half i-j loop
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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for (jj = 0; jj < sht_jnum; jj++) {
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j = sht_jlist[jj];
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j &= NEIGHMASK;
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jtype = map[type[j]];
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iparam_ij = elem2param[itype][jtype][jtype];
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@ -301,9 +324,9 @@ void PairComb::compute(int eflag, int vflag)
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zeta_ij = 0.0;
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cuo_flag1 = 0; cuo_flag2 = 0;
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for (kk = 0; kk < jnum; kk++) {
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if (jj == kk) continue;
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k = jlist[kk];
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for (kk = 0; kk < sht_jnum; kk++) {
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k = sht_jlist[kk];
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if (j == k) continue;
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k &= NEIGHMASK;
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ktype = map[type[k]];
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iparam_ijk = elem2param[itype][jtype][ktype];
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@ -324,9 +347,9 @@ void PairComb::compute(int eflag, int vflag)
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if (cuo_flag1 && cuo_flag2) cuo_flag = 1;
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else cuo_flag = 0;
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force_zeta(¶ms[iparam_ij],rsq1,zeta_ij,fpair,
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prefactor,eflag,evdwl,iq,jq);
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force_zeta(¶ms[iparam_ij],eflag,i,j,rsq1,zeta_ij,
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iq,jq,fpair,prefactor,evdwl);
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// over-coordination correction for HfO2
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if (cor_flag && NCo[i] != 0)
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@ -346,9 +369,9 @@ void PairComb::compute(int eflag, int vflag)
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// attractive term via loop over k (3-body forces)
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for (kk = 0; kk < jnum; kk++) {
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if (jj == kk) continue;
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k = jlist[kk];
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for (kk = 0; kk < sht_jnum; kk++) {
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k = sht_jlist[kk];
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if (j == k) continue;
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k &= NEIGHMASK;
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ktype = map[type[k]];
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iparam_ijk = elem2param[itype][jtype][ktype];
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@ -530,6 +553,11 @@ void PairComb::init_style()
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int irequest = neighbor->request(this);
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neighbor->requests[irequest]->half = 0;
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neighbor->requests[irequest]->full = 1;
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neighbor->requests[irequest]->ghost = 1;
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pgsize = neighbor->pgsize;
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oneatom = neighbor->oneatom;
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if (maxpage == 0) add_pages(0);
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}
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/* ----------------------------------------------------------------------
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@ -799,11 +827,12 @@ void PairComb::setup()
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// set cutmax to max of all params
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cutmax = 0.0;
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cutmax = cutmin = 0.0;
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cor_flag = 0;
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for (m = 0; m < nparams; m++) {
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if (params[m].cut > cutmax) cutmax = params[m].cut;
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if (params[m].lcut > cutmax) cutmax = params[m].lcut;
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if (params[m].cutsq > cutmin) cutmin = params[m].cutsq+1.0;
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if (params[m].hfocor > 0.0001) cor_flag = 1;
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}
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}
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@ -930,7 +959,7 @@ double PairComb::elp(Param *param, double rsqij, double rsqik,
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comtt += param->aconf *(4.0-(rmu-c123)*(rmu-c123));
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}
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return 0.5 * fck * comtt;
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return 1.0 * fck * comtt;
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}
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return 0.0;
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@ -996,10 +1025,10 @@ void PairComb::flp(Param *param, double rsqij, double rsqik,
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com4k = fcj * fck_d * comtt;
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com5 = fcj * fck * comtt_d;
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ffj1 =-0.5*(com5/(rij*rik));
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ffj2 = 0.5*(com5*rmu/rsqij);
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ffj1 =-1.0*(com5/(rij*rik));
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ffj2 = 1.0*(com5*rmu/rsqij);
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ffk1 = ffj1;
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ffk2 = 0.5*(-com4k/rik+com5*rmu/rsqik);
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ffk2 = 1.0*(-com4k/rik+com5*rmu/rsqik);
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} else {
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ffj1 = 0.0; ffj2 = 0.0;
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@ -1024,9 +1053,9 @@ void PairComb::flp(Param *param, double rsqij, double rsqik,
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/* ---------------------------------------------------------------------- */
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void PairComb::force_zeta(Param *param, double rsq, double zeta_ij,
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double &fforce, double &prefactor,
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int eflag, double &eng, double iq, double jq)
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void PairComb::force_zeta(Param *param, int eflag, int i, int j, double rsq,
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double zeta_ij, double iq, double jq, double &fforce,
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double &prefactor, double &eng)
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{
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double r,fa,fa_d,bij;
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@ -1035,11 +1064,13 @@ void PairComb::force_zeta(Param *param, double rsq, double zeta_ij,
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fa = comb_fa(r,param,iq,jq);
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fa_d = comb_fa_d(r,param,iq,jq);
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bij = comb_bij(zeta_ij,param);
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bbij[i][j] = bij;
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// force
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fforce = 0.5*bij*fa_d / r;
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prefactor = -0.5*fa * comb_bij_d(zeta_ij,param);
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// eng = attractive energy
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if (eflag) eng = 0.5*bij*fa;
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}
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@ -1343,6 +1374,7 @@ void PairComb::sm_table()
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double exp2ear,exp2ebr,exp2earsh,exp2ebrsh,fafbsh,dfafbsh;
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int n = atom->ntypes;
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int nmax = atom->nmax;
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dra = 0.001; // lookup table step size
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drin = 0.1; // starting distance of 1/r
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@ -1351,7 +1383,7 @@ void PairComb::sm_table()
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nntypes = int((n+1)*n/2); // interaction types
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ncoul = int((rc-drin)/dra)+1;
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/*
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memory->destroy(intype);
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memory->destroy(fafb);
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memory->destroy(dfafb);
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@ -1359,7 +1391,7 @@ void PairComb::sm_table()
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memory->destroy(phin);
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memory->destroy(dphin);
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memory->destroy(erpaw);
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*/
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// allocate arrays
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memory->create(intype,n,n,"pair:intype");
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@ -1369,6 +1401,11 @@ void PairComb::sm_table()
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memory->create(phin,ncoul,nntypes,"pair:phin");
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memory->create(dphin,ncoul,nntypes,"pair:dphin");
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memory->create(erpaw,25000,2,"pair:erpaw");
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memory->create(NCo,nmax,"pair:NCo");
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memory->create(bbij,nmax,nmax,"pair:bbij");
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memory->create(sht_num,nmax,"pair:sht_num");
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sht_first = (int **) memory->smalloc(nmax*sizeof(int *),
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"pair:sht_first");
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// set interaction number: 0-0=0, 1-1=1, 0-1=1-0=2
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@ -1614,7 +1651,7 @@ void PairComb::field(Param *param, double rsq, double iq,double jq,
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double PairComb::yasu_char(double *qf_fix, int &igroup)
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{
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int i,j,k,ii,jj,kk,jnum;
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int i,j,k,ii,jj,kk,jnum,itag,jtag;
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int itype,jtype,ktype,iparam_i,iparam_ij,iparam_ijk;
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double xtmp,ytmp,ztmp;
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double rsq1,rsq2,delr1[3],delr2[3],zeta_ij;
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@ -1622,10 +1659,12 @@ double PairComb::yasu_char(double *qf_fix, int &igroup)
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double iq,jq,fqi,fqj,fqij,fqjj;
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double potal,fac11,fac11e,sr1,sr2,sr3;
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int mr1,mr2,mr3,inty;
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int sht_jnum, *sht_jlist;
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double **x = atom->x;
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double *q = atom->q;
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int *type = atom->type;
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int *tag = atom->tag;
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int inum = list->inum;
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ilist = list->ilist;
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@ -1656,6 +1695,7 @@ double PairComb::yasu_char(double *qf_fix, int &igroup)
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for (ii = 0; ii < inum; ii ++) {
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i = ilist[ii];
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itag = tag[i];
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if (mask[i] & groupbit) {
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itype = map[type[i]];
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xtmp = x[i][0];
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@ -1672,10 +1712,24 @@ double PairComb::yasu_char(double *qf_fix, int &igroup)
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jlist = firstneigh[i];
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jnum = numneigh[i];
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sht_jlist = sht_first[i];
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sht_jnum = sht_num[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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jtag = tag[j];
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if (itag > jtag) {
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if ((itag+jtag) % 2 == 0) continue;
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} else if (itag < jtag) {
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if ((itag+jtag) % 2 == 1) continue;
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} else {
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if (x[j][2] < x[i][2]) continue;
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if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
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if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
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}
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jtype = map[type[j]];
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jq = q[j];
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@ -1706,38 +1760,31 @@ double PairComb::yasu_char(double *qf_fix, int &igroup)
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qfo_field(¶ms[iparam_ij],rsq1,iq,jq,fqij,fqjj);
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fqi += fqij;
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qf[j] += fqjj;
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}
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// polarization field charge force
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// three-body interactions
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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jtype = map[type[j]];
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jq = q[j];
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delr1[0] = x[j][0] - xtmp;
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delr1[1] = x[j][1] - ytmp;
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delr1[2] = x[j][2] - ztmp;
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rsq1 = vec3_dot(delr1,delr1);
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iparam_ij = elem2param[itype][jtype][jtype];
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if (rsq1 > params[iparam_ij].cutsq) continue;
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zeta_ij = 0.0;
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for (kk = 0; kk < jnum; kk++) {
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if (jj == kk) continue;
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k = jlist[kk];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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iparam_ijk = elem2param[itype][jtype][ktype];
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delr2[0] = x[k][0] - xtmp;
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delr2[1] = x[k][1] - ytmp;
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delr2[2] = x[k][2] - ztmp;
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rsq2 = vec3_dot(delr2,delr2);
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if (rsq2 > params[iparam_ijk].cutsq) continue;
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zeta_ij += zeta(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
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}
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// charge force in Aij and Bij
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qfo_short(¶ms[iparam_ij],rsq1,zeta_ij,iq,jq,fqij,fqjj);
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qfo_short(¶ms[iparam_ij],i,j,rsq1,iq,jq,fqij,fqjj);
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fqi += fqij; qf[j] += fqjj;
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}
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qf[i] += fqi;
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}
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}
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@ -1809,7 +1856,7 @@ void PairComb::qfo_direct(int inty, int mr1, int mr2, int mr3,
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erfcc = sr1*erpaw[mr1][0] + sr2*erpaw[mr2][0] + sr3*erpaw[mr3][0];
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fafbn1= sr1*fafb[mr1][inty] + sr2*fafb[mr2][inty] + sr3*fafb[mr3][inty];
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vm = (erfcc/r * esucon - fac11e);
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fqij = 0.5 * (vm+esucon*fafbn1);
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fqij = 1.0 * (vm+esucon*fafbn1);
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}
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/* ---------------------------------------------------------------------- */
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@ -1835,13 +1882,13 @@ void PairComb::qfo_field(Param *param, double rsq,double iq,double jq,
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// field correction charge force
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fqij = 0.5 * rf5 * (cmj1 + 2.0 * iq * cmj2);
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fqjj = 0.5 * rf5 * (cmi1 + 2.0 * jq * cmi2);
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fqij = 1.0 * rf5 * (cmj1 + 2.0 * iq * cmj2);
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fqjj = 1.0 * rf5 * (cmi1 + 2.0 * jq * cmi2);
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}
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/* ---------------------------------------------------------------------- */
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void PairComb::qfo_short(Param *param, double rsq, double zeta_ij,
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void PairComb::qfo_short(Param *param, int i, int j, double rsq,
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double iq, double jq, double &fqij, double &fqjj)
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||||
{
|
||||
double r,tmp_fc,tmp_fc_d,tmp_exp1,tmp_exp2;
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||||
|
|
@ -1866,7 +1913,7 @@ void PairComb::qfo_short(Param *param, double rsq, double zeta_ij,
|
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tmp_fc_d = comb_fc_d(r,param);
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tmp_exp1 = exp(-param->rlm1 * r);
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tmp_exp2 = exp(-param->rlm2 * r);
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||||
bij = comb_bij(zeta_ij,param);
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||||
bij = bbij[i][j]; //comb_bij(zeta_ij,param);
|
||||
|
||||
arr1 = 2.22850; arr2 = 1.89350;
|
||||
fc2j = comb_fc2(r);
|
||||
|
|
@ -2025,5 +2072,86 @@ double PairComb::memory_usage()
|
|||
double bytes = maxeatom * sizeof(double);
|
||||
bytes += maxvatom*6 * sizeof(double);
|
||||
bytes += nmax * sizeof(int);
|
||||
bytes += nmax * nmax * sizeof(int);
|
||||
return bytes;
|
||||
}
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairComb::Short_neigh()
|
||||
{
|
||||
int nj,npntj,*neighptrj,itype,jtype;
|
||||
int iparam_ij,*ilist,*jlist,*numneigh,**firstneigh;
|
||||
int inum,jnum,i,j,ii,jj;
|
||||
double xtmp,ytmp,ztmp,rr,rsq,delrj[3];
|
||||
double **x = atom->x;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
int ntype = atom->ntypes;
|
||||
|
||||
if (atom->nmax > nmax) {
|
||||
nmax = int(1.0 * atom->nmax);
|
||||
memory->sfree(sht_num);
|
||||
memory->sfree(sht_first);
|
||||
memory->create(sht_num,nmax,"pair:sht_num");
|
||||
sht_first = (int **) memory->smalloc(nmax*sizeof(int *),
|
||||
"pair:sht_first");
|
||||
}
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
npage = npntj = 0;
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
itype = type[i];
|
||||
|
||||
if(pgsize - npntj < oneatom) {
|
||||
npntj = 0;
|
||||
npage++;
|
||||
if (npage == maxpage) add_pages(npage);
|
||||
}
|
||||
|
||||
nj = 0;
|
||||
neighptrj = &pages[npage][npntj];
|
||||
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
jtype = type[j];
|
||||
iparam_ij = elem2param[itype][jtype][jtype];
|
||||
|
||||
delrj[0] = xtmp - x[j][0];
|
||||
delrj[1] = ytmp - x[j][1];
|
||||
delrj[2] = ztmp - x[j][2];
|
||||
rsq = vec3_dot(delrj,delrj);
|
||||
|
||||
if (rsq > cutmin) continue;
|
||||
neighptrj[nj++] = j;
|
||||
}
|
||||
sht_first[i] = neighptrj;
|
||||
sht_num[i] = nj;
|
||||
npntj += nj;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairComb::add_pages(int npage)
|
||||
{
|
||||
maxpage += PGDELTA;
|
||||
pages = (int **)
|
||||
memory->srealloc(pages,maxpage*sizeof(int *),"pair:pages");
|
||||
for (int i = npage; i < maxpage; i++)
|
||||
memory->create(pages[i],pgsize,"pair:pages[i]");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
|
|||
|
|
@ -76,6 +76,7 @@ class PairComb : public Pair {
|
|||
double *charge;
|
||||
int **intype, *typeno;
|
||||
int *NCo, cor_flag, cuo_flag, cuo_flag1, cuo_flag2;
|
||||
double **bbij;
|
||||
|
||||
void allocate();
|
||||
virtual void read_file(char *);
|
||||
|
|
@ -83,8 +84,8 @@ class PairComb : public Pair {
|
|||
virtual void repulsive(Param *, double, double &, int,
|
||||
double &, double, double);
|
||||
double zeta(Param *, double, double, double *, double *);
|
||||
void force_zeta(Param *, double, double, double &, double &,
|
||||
int, double &, double,double);
|
||||
void force_zeta(Param *, int, int, int, double, double, double, double,
|
||||
double &, double &, double &);
|
||||
void attractive(Param *, double, double, double, double *, double *,
|
||||
double *, double *, double *);
|
||||
double elp(Param *, double, double, double *, double *);
|
||||
|
|
@ -115,7 +116,8 @@ class PairComb : public Pair {
|
|||
double,double,double,double &,double &);
|
||||
void field(Param *,double,double,double,double &,double &);
|
||||
double qfo_self(Param *, double, double);
|
||||
void qfo_short(Param *, double, double, double, double, double &, double &);
|
||||
void qfo_short(Param *, int, int, double, double, double,
|
||||
double &, double &);
|
||||
void qfo_direct (int, int, int, int, double, double, double, double,
|
||||
double, double &);
|
||||
void qfo_field(Param *, double,double ,double ,double &, double &);
|
||||
|
|
@ -126,6 +128,13 @@ class PairComb : public Pair {
|
|||
int pack_comm(int , int *, double *, int, int *);
|
||||
void unpack_comm(int , int , double *);
|
||||
|
||||
// Short range neighbor list
|
||||
void add_pages(int );
|
||||
void Short_neigh();
|
||||
int npage, maxpage, pgsize, oneatom, **pages;
|
||||
int *sht_num, **sht_first; // short-range neighbor list
|
||||
double cutmin;
|
||||
|
||||
// vector functions, inline for efficiency
|
||||
|
||||
inline double vec3_dot(double *x, double *y) {
|
||||
|
|
|
|||
Loading…
Reference in New Issue