forked from lijiext/lammps
Removed reax/c time-averaging. Replaced integers with chemical symbols in pair_coeff command for reax/c (this actually happended on 2/25/2013, but should have happened now).
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9559 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
parent
dd0d1ab850
commit
cc237b52a6
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@ -46,7 +46,7 @@ using namespace FixConst;
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FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 7) error->all(FLERR,"Illegal fix reax/c/bonds command");
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if (narg != 5) error->all(FLERR,"Illegal fix reax/c/bonds command");
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MPI_Comm_rank(world,&me);
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MPI_Comm_size(world,&nprocs);
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@ -54,19 +54,15 @@ FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) :
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nmax = atom->nmax;
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nevery = atoi(arg[3]);
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nrepeat = atoi(arg[4]);
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global_freq = nfreq = atoi(arg[5]);
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if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
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error->all(FLERR,"Illegal fix reax/c/bonds command");
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if (nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
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if (nevery <= 0 )
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error->all(FLERR,"Illegal fix reax/c/bonds command");
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if (me == 0) {
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fp = fopen(arg[6],"w");
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fp = fopen(arg[4],"w");
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if (fp == NULL) {
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char str[128];
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sprintf(str,"Cannot open fix reax/c/bonds file %s",arg[6]);
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sprintf(str,"Cannot open fix reax/c/bonds file %s",arg[4]);
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error->one(FLERR,str);
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}
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}
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@ -74,19 +70,12 @@ FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) :
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if (atom->tag_consecutive() == 0)
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error->all(FLERR,"Atom IDs must be consecutive for fix reax/c bonds");
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sbo = NULL;
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nlp = NULL;
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avq = NULL;
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numneigh = NULL;
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neighid = NULL;
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tmpid = NULL;
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abo = NULL;
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tmpabo = NULL;
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neighid = NULL;
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numneigh = NULL;
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allocate();
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irepeat = 0;
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nvalid = nextvalid();
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}
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/* ---------------------------------------------------------------------- */
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@ -124,21 +113,14 @@ void FixReaxCBonds::init()
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if (reaxc == NULL) error->all(FLERR,"Cannot use fix reax/c/bonds without "
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"pair_style reax/c");
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if (nvalid < update->ntimestep) {
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irepeat = 0;
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nvalid = nextvalid();
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixReaxCBonds::end_of_step()
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{
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// skip if not step that requires calculating bonds
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bigint ntimestep = update->ntimestep;
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if (ntimestep != nvalid) return;
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Output_ReaxC_Bonds(update->ntimestep,fp);
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if (me == 0) fflush(fp);
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}
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@ -162,30 +144,14 @@ void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
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allocate();
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}
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repeat = nrepeat;
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// zero out average BO for next Nfreq
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if (irepeat == 0)
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for (i = 0; i < nmax; i++) {
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sbo[i] = nlp[i] = avq[i] = 0.0;
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numneigh[i] = 0.0;
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for (j = 0; j < MAXREAXBOND; j++) {
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tmpid[i][j] = 0;
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tmpabo[i][j] = 0.0;
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neighid[i][j] = 0;
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abo[i][j] = 0.0;
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}
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}
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// Accumulate bonding information for each nvalid
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GatherBond( system, lists);
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// done if irepeat < nrepeat, else reset irepeat and nvalid
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irepeat++;
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if (irepeat < nrepeat) {
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nvalid += nevery;
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return;
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}
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irepeat = numbonds = 0;
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nvalid = ntimestep + nfreq - (nrepeat-1)*nevery;
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// Determine actual bonding based on averaged bond order
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FindBond( system, lists, numbonds);
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// allocate a temporary buffer for the snapshot info
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@ -207,7 +173,8 @@ void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
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/* ---------------------------------------------------------------------- */
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void FixReaxCBonds::GatherBond( struct _reax_system *system, struct _reax_list *lists)
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void FixReaxCBonds::FindBond( struct _reax_system *system,
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struct _reax_list *lists, int &numbonds)
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{
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int *ilist, i, ii, inum;
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int j, pj, nj, jtag, jtype;
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@ -216,7 +183,7 @@ void FixReaxCBonds::GatherBond( struct _reax_system *system, struct _reax_list *
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inum = reaxc->list->inum;
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ilist = reaxc->list->ilist;
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bond_data *bo_ij;
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bo_cut = 0.10; //reaxc->control->bg_cut;
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bo_cut = reaxc->control->bg_cut;
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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@ -229,66 +196,16 @@ void FixReaxCBonds::GatherBond( struct _reax_system *system, struct _reax_list *
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bo_tmp = bo_ij->bo_data.BO;
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if (bo_tmp > bo_cut) {
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here:;
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if (jtag != tmpid[i][nj] && tmpid[i][nj] != 0) {
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nj ++;
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if (nj > MAXREAXBOND) error->all(FLERR,"Increase MAXREAXBOND value");
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goto here;
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}
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tmpid[i][nj] = jtag;
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tmpabo[i][nj] += bo_tmp;
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nj ++;
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}
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}
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sbo[i] += reaxc->workspace->total_bond_order[i];
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nlp[i] += reaxc->workspace->nlp[i];
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avq[i] += atom->q[i];
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixReaxCBonds::FindBond( struct _reax_system *system, struct _reax_list *lists,
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int &numbonds)
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{
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int *ilist, i, ii, inum;
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int j, pj, nj, jtag, jtype;
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double bo_tmp,bo_cut;
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inum = reaxc->list->inum;
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ilist = reaxc->list->ilist;
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bo_cut = reaxc->control->bg_cut;
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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sbo[i] /= repeat;
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nlp[i] /= repeat;
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avq[i] /= repeat;
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numneigh[i] = 0;
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for (j = 0; j < MAXREAXBOND; j++) {
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tmpabo[i][j] /= repeat;
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neighid[i][j] = 0;
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abo[i][j] = 0.0;
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}
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}
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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nj = 0;
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for (j = 0; j < MAXREAXBOND; j++){
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if (tmpabo[i][j] > bo_cut) {
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neighid[i][nj] = tmpid[i][j];
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abo[i][nj] = tmpabo[i][j];
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neighid[i][nj] = jtag;
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abo[i][nj] = bo_tmp;
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nj ++;
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}
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}
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numneigh[i] = nj;
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if (nj > numbonds) numbonds = nj;
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixReaxCBonds::PassBuffer( struct _reax_system *system, double *buf,
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@ -302,9 +219,9 @@ void FixReaxCBonds::PassBuffer( struct _reax_system *system, double *buf,
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for (i = 0; i < nlocal; i++) {
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buf[j-1] = atom->tag[i];
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buf[j+0] = atom->type[i];
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buf[j+1] = sbo[i];
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buf[j+2] = nlp[i];
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buf[j+3] = avq[i];
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buf[j+1] = reaxc->workspace->total_bond_order[i];
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buf[j+2] = reaxc->workspace->nlp[i];
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buf[j+3] = atom->q[i];
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buf[j+4] = numneigh[i];
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numbonds = nint(buf[j+4]);
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@ -407,49 +324,22 @@ int FixReaxCBonds::nint(const double &r)
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return i;
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}
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/* ----------------------------------------------------------------------
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calculate nvalid = next step on which end_of_step does something
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can be this timestep if multiple of nfreq and nrepeat = 1
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else backup from next multiple of nfreq
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------------------------------------------------------------------------- */
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bigint FixReaxCBonds::nextvalid()
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{
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bigint nvalid = (update->ntimestep/nfreq)*nfreq + nfreq;
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if (nvalid-nfreq == update->ntimestep && nrepeat == 1)
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nvalid = update->ntimestep;
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else
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nvalid -= (nrepeat-1)*nevery;
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if (nvalid < update->ntimestep) nvalid += nfreq;
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return nvalid;
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}
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/* ---------------------------------------------------------------------- */
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void FixReaxCBonds::destroy()
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{
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memory->destroy(sbo);
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memory->destroy(nlp);
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memory->destroy(avq);
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memory->destroy(numneigh);
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memory->destroy(neighid);
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memory->destroy(tmpid);
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memory->destroy(abo);
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memory->destroy(tmpabo);
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memory->destroy(neighid);
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memory->destroy(numneigh);
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}
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/* ---------------------------------------------------------------------- */
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void FixReaxCBonds::allocate()
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{
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memory->create(sbo,nmax,"reax/c/bonds:sbo");
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memory->create(nlp,nmax,"reax/c/bonds:nlp");
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memory->create(avq,nmax,"reax/c/bonds:avq");
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memory->create(numneigh,nmax,"reax/c/bonds:numneigh");
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memory->create(abo,nmax,MAXREAXBOND,"reax/c/bonds:abo");
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memory->create(neighid,nmax,MAXREAXBOND,"reax/c/bonds:neighid");
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memory->create(tmpabo,nmax,MAXREAXBOND,"reax/c/bonds:tmpabo");
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memory->create(tmpid,nmax,MAXREAXBOND,"reax/c/bonds:tmpid");
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memory->create(numneigh,nmax,"reax/c/bonds:numneigh");
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}
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/* ---------------------------------------------------------------------- */
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@ -460,8 +350,8 @@ double FixReaxCBonds::memory_usage()
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bytes += 3.0*nmax*sizeof(double);
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bytes += nmax*sizeof(int);
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bytes += 2.0*nmax*MAXREAXBOND*sizeof(double);
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bytes += 2.0*nmax*MAXREAXBOND*sizeof(int);
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bytes += 1.0*nmax*MAXREAXBOND*sizeof(double);
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bytes += 1.0*nmax*MAXREAXBOND*sizeof(int);
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return bytes;
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}
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@ -37,15 +37,13 @@ class FixReaxCBonds : public Fix {
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private:
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int me, nprocs, nmax, ntypes, maxsize;
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int nrepeat, irepeat, repeat, nfreq;
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int *numneigh, **neighid, **tmpid;
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double *sbo, *nlp, *avq, **abo, **tmpabo;
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int *numneigh, **neighid;
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double **abo;
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FILE *fp;
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void allocate();
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void destroy();
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void Output_ReaxC_Bonds(bigint, FILE *);
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void GatherBond(struct _reax_system*, struct _reax_list*);
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void FindBond(struct _reax_system*, struct _reax_list*, int &);
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void PassBuffer(struct _reax_system*, double *, int &);
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void RecvBuffer(struct _reax_system*, double *, int, int, int, int);
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