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
|
|
@ -46,7 +46,7 @@ using namespace FixConst;
|
|||
FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg)
|
||||
{
|
||||
if (narg < 7) error->all(FLERR,"Illegal fix reax/c/bonds command");
|
||||
if (narg != 5) error->all(FLERR,"Illegal fix reax/c/bonds command");
|
||||
|
||||
MPI_Comm_rank(world,&me);
|
||||
MPI_Comm_size(world,&nprocs);
|
||||
|
|
@ -54,19 +54,15 @@ FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) :
|
|||
nmax = atom->nmax;
|
||||
|
||||
nevery = atoi(arg[3]);
|
||||
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)
|
||||
if (nevery <= 0 )
|
||||
error->all(FLERR,"Illegal fix reax/c/bonds command");
|
||||
|
||||
if (me == 0) {
|
||||
fp = fopen(arg[6],"w");
|
||||
fp = fopen(arg[4],"w");
|
||||
if (fp == NULL) {
|
||||
char str[128];
|
||||
sprintf(str,"Cannot open fix reax/c/bonds file %s",arg[6]);
|
||||
sprintf(str,"Cannot open fix reax/c/bonds file %s",arg[4]);
|
||||
error->one(FLERR,str);
|
||||
}
|
||||
}
|
||||
|
|
@ -74,19 +70,12 @@ FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) :
|
|||
if (atom->tag_consecutive() == 0)
|
||||
error->all(FLERR,"Atom IDs must be consecutive for fix reax/c bonds");
|
||||
|
||||
sbo = NULL;
|
||||
nlp = NULL;
|
||||
avq = NULL;
|
||||
numneigh = NULL;
|
||||
neighid = NULL;
|
||||
tmpid = NULL;
|
||||
abo = NULL;
|
||||
tmpabo = NULL;
|
||||
neighid = NULL;
|
||||
numneigh = NULL;
|
||||
|
||||
allocate();
|
||||
|
||||
irepeat = 0;
|
||||
nvalid = nextvalid();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
@ -124,21 +113,14 @@ void FixReaxCBonds::init()
|
|||
if (reaxc == NULL) error->all(FLERR,"Cannot use fix reax/c/bonds without "
|
||||
"pair_style reax/c");
|
||||
|
||||
if (nvalid < update->ntimestep) {
|
||||
irepeat = 0;
|
||||
nvalid = nextvalid();
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixReaxCBonds::end_of_step()
|
||||
{
|
||||
// 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);
|
||||
}
|
||||
|
|
@ -162,30 +144,14 @@ void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
|
|||
allocate();
|
||||
}
|
||||
|
||||
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 < MAXREAXBOND; j++) {
|
||||
tmpid[i][j] = 0;
|
||||
tmpabo[i][j] = 0.0;
|
||||
}
|
||||
for (i = 0; i < nmax; i++) {
|
||||
numneigh[i] = 0.0;
|
||||
for (j = 0; j < MAXREAXBOND; j++) {
|
||||
neighid[i][j] = 0;
|
||||
abo[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
|
||||
|
|
@ -207,7 +173,8 @@ void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixReaxCBonds::GatherBond( struct _reax_system *system, struct _reax_list *lists)
|
||||
void FixReaxCBonds::FindBond( struct _reax_system *system,
|
||||
struct _reax_list *lists, int &numbonds)
|
||||
{
|
||||
int *ilist, i, ii, inum;
|
||||
int j, pj, nj, jtag, jtype;
|
||||
|
|
@ -216,7 +183,7 @@ void FixReaxCBonds::GatherBond( struct _reax_system *system, struct _reax_list *
|
|||
inum = reaxc->list->inum;
|
||||
ilist = reaxc->list->ilist;
|
||||
bond_data *bo_ij;
|
||||
bo_cut = 0.10; //reaxc->control->bg_cut;
|
||||
bo_cut = reaxc->control->bg_cut;
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
|
|
@ -229,66 +196,16 @@ void FixReaxCBonds::GatherBond( struct _reax_system *system, struct _reax_list *
|
|||
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 > MAXREAXBOND) error->all(FLERR,"Increase MAXREAXBOND 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( struct _reax_system *system, struct _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 < MAXREAXBOND; 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 < MAXREAXBOND; j++){
|
||||
if (tmpabo[i][j] > bo_cut) {
|
||||
neighid[i][nj] = tmpid[i][j];
|
||||
abo[i][nj] = tmpabo[i][j];
|
||||
neighid[i][nj] = jtag;
|
||||
abo[i][nj] = bo_tmp;
|
||||
nj ++;
|
||||
}
|
||||
}
|
||||
numneigh[i] = nj;
|
||||
if (nj > numbonds) numbonds = nj;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixReaxCBonds::PassBuffer( struct _reax_system *system, double *buf,
|
||||
|
|
@ -302,9 +219,9 @@ void FixReaxCBonds::PassBuffer( struct _reax_system *system, double *buf,
|
|||
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+1] = reaxc->workspace->total_bond_order[i];
|
||||
buf[j+2] = reaxc->workspace->nlp[i];
|
||||
buf[j+3] = atom->q[i];
|
||||
buf[j+4] = numneigh[i];
|
||||
numbonds = nint(buf[j+4]);
|
||||
|
||||
|
|
@ -407,49 +324,22 @@ int FixReaxCBonds::nint(const double &r)
|
|||
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::destroy()
|
||||
{
|
||||
memory->destroy(sbo);
|
||||
memory->destroy(nlp);
|
||||
memory->destroy(avq);
|
||||
memory->destroy(numneigh);
|
||||
memory->destroy(neighid);
|
||||
memory->destroy(tmpid);
|
||||
memory->destroy(abo);
|
||||
memory->destroy(tmpabo);
|
||||
memory->destroy(neighid);
|
||||
memory->destroy(numneigh);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixReaxCBonds::allocate()
|
||||
{
|
||||
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,MAXREAXBOND,"reax/c/bonds:abo");
|
||||
memory->create(neighid,nmax,MAXREAXBOND,"reax/c/bonds:neighid");
|
||||
memory->create(tmpabo,nmax,MAXREAXBOND,"reax/c/bonds:tmpabo");
|
||||
memory->create(tmpid,nmax,MAXREAXBOND,"reax/c/bonds:tmpid");
|
||||
memory->create(numneigh,nmax,"reax/c/bonds:numneigh");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
@ -460,8 +350,8 @@ double FixReaxCBonds::memory_usage()
|
|||
|
||||
bytes += 3.0*nmax*sizeof(double);
|
||||
bytes += nmax*sizeof(int);
|
||||
bytes += 2.0*nmax*MAXREAXBOND*sizeof(double);
|
||||
bytes += 2.0*nmax*MAXREAXBOND*sizeof(int);
|
||||
bytes += 1.0*nmax*MAXREAXBOND*sizeof(double);
|
||||
bytes += 1.0*nmax*MAXREAXBOND*sizeof(int);
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -37,15 +37,13 @@ class FixReaxCBonds : public Fix {
|
|||
|
||||
private:
|
||||
int me, nprocs, nmax, ntypes, maxsize;
|
||||
int nrepeat, irepeat, repeat, nfreq;
|
||||
int *numneigh, **neighid, **tmpid;
|
||||
double *sbo, *nlp, *avq, **abo, **tmpabo;
|
||||
int *numneigh, **neighid;
|
||||
double **abo;
|
||||
FILE *fp;
|
||||
|
||||
void allocate();
|
||||
void destroy();
|
||||
void Output_ReaxC_Bonds(bigint, FILE *);
|
||||
void GatherBond(struct _reax_system*, struct _reax_list*);
|
||||
void FindBond(struct _reax_system*, struct _reax_list*, int &);
|
||||
void PassBuffer(struct _reax_system*, double *, int &);
|
||||
void RecvBuffer(struct _reax_system*, double *, int, int, int, int);
|
||||
|
|
|
|||
Loading…
Reference in New Issue