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lammps/src/USER-REAXC/fix_reaxc_species.cpp
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fix_reaxc_species.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Ray Shan (Sandia, tnshan@sandia.gov)
Oleg Sergeev (VNIIA, sergeev@vniia.ru)
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <math.h>
#include "atom.h"
#include <string.h>
#include "fix_ave_atom.h"
#include "fix_reaxc_species.h"
#include "domain.h"
#include "update.h"
#include "pair_reax_c.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "comm.h"
#include "force.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
#include "reaxc_list.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 7) error->all(FLERR,"Illegal fix reax/c/species command");
force_reneighbor = 0;
vector_flag = 1;
size_vector = 2;
extvector = 0;
peratom_flag = 1;
size_peratom_cols = 0;
peratom_freq = 1;
nvalid = -1;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
ntypes = atom->ntypes;
nevery = atoi(arg[3]);
nrepeat = atoi(arg[4]);
global_freq = nfreq = atoi(arg[5]);
comm_forward = 5;
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all(FLERR,"Illegal fix reax/c/species command");
if (nfreq % nevery || nrepeat*nevery > nfreq)
error->all(FLERR,"Illegal fix reax/c/species command");
// Neighbor lists must stay unchanged during averaging of bonds,
// but may be updated when no averaging is performed.
int rene_flag = 0;
if (nevery * nrepeat != 1 && (nfreq % neighbor->every != 0 || neighbor->every < nevery * nrepeat)) {
int newneighborevery = nevery * nrepeat;
while (nfreq % newneighborevery != 0 && newneighborevery <= nfreq / 2)
newneighborevery++;
if (nfreq % newneighborevery != 0)
newneighborevery = nfreq;
neighbor->every = newneighborevery;
rene_flag = 1;
}
if (nevery * nrepeat != 1 && (neighbor->delay != 0 || neighbor->dist_check != 0)) {
neighbor->delay = 0;
neighbor->dist_check = 0;
rene_flag = 1;
}
if (me == 0 && rene_flag) {
char str[128];
sprintf(str,"Resetting reneighboring criteria for fix reax/c/species");
error->warning(FLERR,str);
}
tmparg = NULL;
memory->create(tmparg,4,4,"reax/c/species:tmparg");
strcpy(tmparg[0],arg[3]);
strcpy(tmparg[1],arg[4]);
strcpy(tmparg[2],arg[5]);
if (me == 0) {
fp = fopen(arg[6],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix reax/c/species file %s",arg[6]);
error->one(FLERR,str);
}
}
x0 = NULL;
PBCconnected = NULL;
clusterID = NULL;
int ntmp = 1;
memory->create(x0,ntmp,"reax/c/species:x0");
memory->create(PBCconnected,ntmp,"reax/c/species:PBCconnected");
memory->create(clusterID,ntmp,"reax/c/species:clusterID");
vector_atom = clusterID;
BOCut = NULL;
Name = NULL;
MolName = NULL;
MolType = NULL;
NMol = NULL;
nd = NULL;
molmap = NULL;
nmax = 0;
setupflag = 0;
// set default bond order cutoff
int n, i, j, itype, jtype;
double bo_cut;
bg_cut = 0.30;
n = ntypes+1;
memory->create(BOCut,n,n,"reax/c/species:BOCut");
for (i = 1; i < n; i ++)
for (j = 1; j < n; j ++)
BOCut[i][j] = bg_cut;
// optional args
eletype = NULL;
ele = filepos = NULL;
eleflag = posflag = padflag = 0;
singlepos_opened = multipos_opened = 0;
multipos = 0;
posfreq = 0;
int iarg = 7;
while (iarg < narg) {
// set BO cutoff
if (strcmp(arg[iarg],"cutoff") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix reax/c/species command");
itype = atoi(arg[iarg+1]);
jtype = atoi(arg[iarg+2]);
bo_cut = atof(arg[iarg+3]);
if (itype > ntypes || jtype > ntypes)
error->all(FLERR,"Illegal fix reax/c/species command");
if (itype <= 0 || jtype <= 0)
error->all(FLERR,"Illegal fix reax/c/species command");
if (bo_cut > 1.0 || bo_cut < 0.0)
error->all(FLERR,"Illegal fix reax/c/species command");
BOCut[itype][jtype] = bo_cut;
BOCut[jtype][itype] = bo_cut;
iarg += 4;
// modify element type names
} else if (strcmp(arg[iarg],"element") == 0) {
if (iarg+ntypes+1 > narg) error->all(FLERR,"Illegal fix reax/c/species command");
eletype = (char**) malloc(ntypes*sizeof(char*));
for (int i = 0; i < ntypes; i ++) {
eletype[i] = (char*) malloc(2*sizeof(char));
strcpy(eletype[i],arg[iarg+1+i]);
}
eleflag = 1;
iarg += ntypes + 1;
// position of molecules
} else if (strcmp(arg[iarg],"position") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix reax/c/species command");
posflag = 1;
posfreq = atoi(arg[iarg+1]);
if (posfreq < nfreq || (posfreq%nfreq != 0))
error->all(FLERR,"Illegal fix reax/c/species command");
filepos = new char[255];
strcpy(filepos,arg[iarg+2]);
if (strchr(filepos,'*')) {
multipos = 1;
} else {
if (me == 0) {
pos = fopen(filepos, "w");
if (pos == NULL) error->one(FLERR,"Cannot open fix reax/c/species position file");
}
singlepos_opened = 1;
multipos = 0;
}
iarg += 3;
} else error->all(FLERR,"Illegal fix reax/c/species command");
}
if (!eleflag) {
memory->create(ele,ntypes+1,"reax/c/species:ele");
ele[0]='C';
if (ntypes > 1)
ele[1]='H';
if (ntypes > 2)
ele[2]='O';
if (ntypes > 3)
ele[3]='N';
}
vector_nmole = 0;
vector_nspec = 0;
}
/* ---------------------------------------------------------------------- */
FixReaxCSpecies::~FixReaxCSpecies()
{
memory->destroy(ele);
memory->destroy(BOCut);
memory->destroy(clusterID);
memory->destroy(PBCconnected);
memory->destroy(x0);
memory->destroy(nd);
memory->destroy(Name);
memory->destroy(NMol);
memory->destroy(MolType);
memory->destroy(MolName);
memory->destroy(tmparg);
if (filepos)
delete [] filepos;
if (me == 0) fclose(fp);
if (me == 0 && posflag && multipos_opened) fclose(pos);
modify->delete_compute("SPECATOM");
modify->delete_fix("SPECBOND");
}
/* ---------------------------------------------------------------------- */
int FixReaxCSpecies::setmask()
{
int mask = 0;
mask |= POST_INTEGRATE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixReaxCSpecies::setup(int vflag)
{
ntotal = static_cast<int> (atom->natoms);
if (Name == NULL)
memory->create(Name,ntypes,"reax/c/species:Name");
post_integrate();
}
/* ---------------------------------------------------------------------- */
void FixReaxCSpecies::init()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use fix reax/c/species unless atoms have IDs");
Pair *pair_kk = force->pair_match("reax/c/kk",1);
if (pair_kk != NULL) error->all(FLERR,"Cannot (yet) use fix reax/c/species with "
"pair_style reax/c/kk");
reaxc = (PairReaxC *) force->pair_match("reax/c",1);
if (reaxc == NULL) error->all(FLERR,"Cannot use fix reax/c/species without "
"pair_style reax/c");
reaxc->fixspecies_flag = 1;
// reset next output timestep if not yet set or timestep has been reset
if (nvalid != update->ntimestep)
nvalid = update->ntimestep+nfreq;
// check if this fix has been called twice
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"reax/c/species") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one fix reax/c/species");
if (!setupflag) {
// create a compute to store properties
create_compute();
// create a fix to point to fix_ave_atom for averaging stored properties
create_fix();
setupflag = 1;
}
}
/* ---------------------------------------------------------------------- */
void FixReaxCSpecies::create_compute()
{
int narg;
char **args;
narg = 34;
args = new char*[narg];
args[0] = (char *) "SPECATOM";
args[1] = (char *) "all";
args[2] = (char *) "SPEC/ATOM";
args[3] = (char *) "q";
args[4] = (char *) "x";
args[5] = (char *) "y";
args[6] = (char *) "z";
args[7] = (char *) "vx";
args[8] = (char *) "vy";
args[9] = (char *) "vz";
args[10] = (char *) "abo01";
args[11] = (char *) "abo02";
args[12] = (char *) "abo03";
args[13] = (char *) "abo04";
args[14] = (char *) "abo05";
args[15] = (char *) "abo06";
args[16] = (char *) "abo07";
args[17] = (char *) "abo08";
args[18] = (char *) "abo09";
args[19] = (char *) "abo10";
args[20] = (char *) "abo11";
args[21] = (char *) "abo12";
args[22] = (char *) "abo13";
args[23] = (char *) "abo14";
args[24] = (char *) "abo15";
args[25] = (char *) "abo16";
args[26] = (char *) "abo17";
args[27] = (char *) "abo18";
args[28] = (char *) "abo19";
args[29] = (char *) "abo20";
args[30] = (char *) "abo21";
args[31] = (char *) "abo22";
args[32] = (char *) "abo23";
args[33] = (char *) "abo24";
modify->add_compute(narg,args);
delete [] args;
}
/* ---------------------------------------------------------------------- */
void FixReaxCSpecies::create_fix()
{
int narg;
char **args;
narg = 37;
args = new char*[narg];
args[0] = (char *) "SPECBOND";
args[1] = (char *) "all";
args[2] = (char *) "ave/atom";
args[3] = tmparg[0];
args[4] = tmparg[1];
args[5] = tmparg[2];
args[6] = (char *) "c_SPECATOM[1]"; // q, array_atoms[i][0]
args[7] = (char *) "c_SPECATOM[2]"; // x, 1
args[8] = (char *) "c_SPECATOM[3]"; // y, 2
args[9] = (char *) "c_SPECATOM[4]"; // z, 3
args[10] = (char *) "c_SPECATOM[5]"; // vx, 4
args[11] = (char *) "c_SPECATOM[6]"; // vy, 5
args[12] = (char *) "c_SPECATOM[7]"; // vz, 6
args[13] = (char *) "c_SPECATOM[8]"; // abo01, 7
args[14] = (char *) "c_SPECATOM[9]";
args[15] = (char *) "c_SPECATOM[10]";
args[16] = (char *) "c_SPECATOM[11]";
args[17] = (char *) "c_SPECATOM[12]";
args[18] = (char *) "c_SPECATOM[13]";
args[19] = (char *) "c_SPECATOM[14]";
args[20] = (char *) "c_SPECATOM[15]";
args[21] = (char *) "c_SPECATOM[16]";
args[22] = (char *) "c_SPECATOM[17]";
args[23] = (char *) "c_SPECATOM[18]";
args[24] = (char *) "c_SPECATOM[19]"; // abo12, 18
args[25] = (char *) "c_SPECATOM[20]";
args[26] = (char *) "c_SPECATOM[21]";
args[27] = (char *) "c_SPECATOM[22]";
args[28] = (char *) "c_SPECATOM[23]";
args[29] = (char *) "c_SPECATOM[24]";
args[30] = (char *) "c_SPECATOM[25]";
args[31] = (char *) "c_SPECATOM[26]";
args[32] = (char *) "c_SPECATOM[27]";
args[33] = (char *) "c_SPECATOM[28]";
args[34] = (char *) "c_SPECATOM[29]";
args[35] = (char *) "c_SPECATOM[30]";
args[36] = (char *) "c_SPECATOM[31]";
modify->add_fix(narg,args);
f_SPECBOND = (FixAveAtom *) modify->fix[modify->nfix-1];
delete [] args;
}
/* ---------------------------------------------------------------------- */
void FixReaxCSpecies::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void FixReaxCSpecies::post_integrate()
{
Output_ReaxC_Bonds(update->ntimestep,fp);
if (me == 0) fflush(fp);
}
/* ---------------------------------------------------------------------- */
void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
{
int Nmole, Nspec;
// point to fix_ave_atom
f_SPECBOND->end_of_step();
if (ntimestep != nvalid) return;
nlocal = atom->nlocal;
if (atom->nmax > nmax) {
nmax = atom->nmax;
memory->destroy(x0);
memory->destroy(PBCconnected);
memory->destroy(clusterID);
memory->create(x0,nmax,"reax/c/species:x0");
memory->create(PBCconnected,nmax,"reax/c/species:PBCconnected");
memory->create(clusterID,nmax,"reax/c/species:clusterID");
vector_atom = clusterID;
}
for (int i = 0; i < nmax; i++) {
PBCconnected[i] = 0;
x0[i].x = x0[i].y = x0[i].z = 0.0;
}
Nmole = Nspec = 0;
FindMolecule();
SortMolecule (Nmole);
FindSpecies(Nmole, Nspec);
vector_nmole = Nmole;
vector_nspec = Nspec;
if (me == 0 && ntimestep >= 0)
WriteFormulas (Nmole, Nspec);
if (posflag && ((ntimestep)%posfreq==0)) {
WritePos(Nmole, Nspec);
if (me == 0) fflush(pos);
}
nvalid += nfreq;
}
/* ---------------------------------------------------------------------- */
AtomCoord chAnchor(AtomCoord in1, AtomCoord in2)
{
if (in1.x < in2.x)
return in1;
return in2;
}
/* ---------------------------------------------------------------------- */
void FixReaxCSpecies::FindMolecule ()
{
int i,j,ii,jj,inum,itype,jtype,loop,looptot;
int change,done,anychange;
int *mask = atom->mask;
int *ilist;
double bo_tmp,bo_cut;
double **spec_atom = f_SPECBOND->array_atom;
inum = reaxc->list->inum;
ilist = reaxc->list->ilist;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
clusterID[i] = atom->tag[i];
x0[i].x = spec_atom[i][1];
x0[i].y = spec_atom[i][2];
x0[i].z = spec_atom[i][3];
}
else clusterID[i] = 0.0;
}
loop = 0;
while (1) {
comm->forward_comm_fix(this);
loop ++;
change = 0;
while (1) {
done = 1;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (!(mask[i] & groupbit)) continue;
itype = atom->type[i];
for (jj = 0; jj < MAXSPECBOND; jj++) {
j = reaxc->tmpid[i][jj];
if (j < i) continue;
if (!(mask[j] & groupbit)) continue;
if (clusterID[i] == clusterID[j] && PBCconnected[i] == PBCconnected[j]
&& x0[i].x == x0[j].x && x0[i].y == x0[j].y && x0[i].z == x0[j].z) continue;
jtype = atom->type[j];
bo_cut = BOCut[itype][jtype];
bo_tmp = spec_atom[i][jj+7];
if (bo_tmp > bo_cut) {
clusterID[i] = clusterID[j] = MIN(clusterID[i], clusterID[j]);
PBCconnected[i] = PBCconnected[j] = MAX(PBCconnected[i], PBCconnected[j]);
x0[i] = x0[j] = chAnchor(x0[i], x0[j]);
if ((fabs(spec_atom[i][1] - spec_atom[j][1]) > reaxc->control->bond_cut)
|| (fabs(spec_atom[i][2] - spec_atom[j][2]) > reaxc->control->bond_cut)
|| (fabs(spec_atom[i][3] - spec_atom[j][3]) > reaxc->control->bond_cut))
PBCconnected[i] = PBCconnected[j] = 1;
done = 0;
}
}
}
if (!done) change = 1;
if (done) break;
}
MPI_Allreduce(&change,&anychange,1,MPI_INT,MPI_MAX,world);
if (!anychange) break;
MPI_Allreduce(&loop,&looptot,1,MPI_INT,MPI_SUM,world);
if (looptot >= 400*nprocs) break;
}
}
/* ---------------------------------------------------------------------- */
void FixReaxCSpecies::SortMolecule(int &Nmole)
{
memory->destroy(molmap);
molmap = NULL;
int n, idlo, idhi;
int *mask =atom->mask;
int lo = ntotal;
int hi = -ntotal;
int flag = 0;
for (n = 0; n < nlocal; n++) {
if (!(mask[n] & groupbit)) continue;
if (clusterID[n] == 0.0) flag = 1;
lo = MIN(lo,nint(clusterID[n]));
hi = MAX(hi,nint(clusterID[n]));
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && me == 0)
error->warning(FLERR,"Atom with cluster ID = 0 included in "
"fix reax/c/species group");
MPI_Allreduce(&lo,&idlo,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&hi,&idhi,1,MPI_INT,MPI_MAX,world);
if (idlo == ntotal)
if (me == 0)
error->warning(FLERR,"Atom with cluster ID = maxmol "
"included in fix reax/c/species group");
int nlen = idhi - idlo + 1;
memory->create(molmap,nlen,"reax/c/species:molmap");
for (n = 0; n < nlen; n++) molmap[n] = 0;
for (n = 0; n < nlocal; n++) {
if (!(mask[n] & groupbit)) continue;
molmap[nint(clusterID[n])-idlo] = 1;
}
int *molmapall;
memory->create(molmapall,nlen,"reax/c/species:molmapall");
MPI_Allreduce(molmap,molmapall,nlen,MPI_INT,MPI_MAX,world);
Nmole = 0;
for (n = 0; n < nlen; n++) {
if (molmapall[n]) molmap[n] = Nmole++;
else molmap[n] = -1;
}
memory->destroy(molmapall);
flag = 0;
for (n = 0; n < nlocal; n++) {
if (mask[n] & groupbit) continue;
if (nint(clusterID[n]) < idlo || nint(clusterID[n]) > idhi) continue;
if (molmap[nint(clusterID[n])-idlo] >= 0) flag = 1;
}
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->warning(FLERR,"One or more cluster has atoms not in group");
for (n = 0; n < nlocal; n++) {
if (!(mask[n] & groupbit)) continue;
clusterID[n] = molmap[nint(clusterID[n])-idlo] + 1;
}
memory->destroy(molmap);
molmap = NULL;
}
/* ---------------------------------------------------------------------- */
void FixReaxCSpecies::FindSpecies(int Nmole, int &Nspec)
{
int k, l, m, n, itype, cid;
int flag_identity, flag_mol, flag_spec;
int flag_tmp;
int *mask =atom->mask;
int *Nameall, *NMolall;
memory->destroy(MolName);
MolName = NULL;
memory->create(MolName,Nmole*(ntypes+1),"reax/c/species:MolName");
memory->destroy(NMol);
NMol = NULL;
memory->create(NMol,Nmole,"reax/c/species:NMol");
for (m = 0; m < Nmole; m ++)
NMol[m] = 1;
memory->create(Nameall,ntypes,"reax/c/species:Nameall");
memory->create(NMolall,Nmole,"reax/c/species:NMolall");
for (m = 1, Nspec = 0; m <= Nmole; m ++) {
for (n = 0; n < ntypes; n ++) Name[n] = 0;
for (n = 0, flag_mol = 0; n < nlocal; n ++) {
if (!(mask[n] & groupbit)) continue;
cid = nint(clusterID[n]);
if (cid == m) {
itype = atom->type[n]-1;
Name[itype] ++;
flag_mol = 1;
}
}
MPI_Allreduce(&flag_mol,&flag_tmp,1,MPI_INT,MPI_MAX,world);
flag_mol = flag_tmp;
MPI_Allreduce(Name,Nameall,ntypes,MPI_INT,MPI_SUM,world);
for (n = 0; n < ntypes; n++) Name[n] = Nameall[n];
if (flag_mol == 1) {
flag_identity = 1;
for (k = 0; k < Nspec; k ++) {
flag_spec=0;
for (l = 0; l < ntypes; l ++)
if (MolName[ntypes*k+l] != Name[l]) flag_spec = 1;
if (flag_spec == 0) NMol[k] ++;
flag_identity *= flag_spec;
}
if (Nspec == 0 || flag_identity == 1) {
for (l = 0; l < ntypes; l ++)
MolName[ntypes*Nspec+l] = Name[l];
Nspec ++;
}
}
}
memory->destroy(NMolall);
memory->destroy(Nameall);
memory->destroy(nd);
nd = NULL;
memory->create(nd,Nspec,"reax/c/species:nd");
memory->destroy(MolType);
MolType = NULL;
memory->create(MolType,Nspec*(ntypes+2),"reax/c/species:MolType");
}
/* ---------------------------------------------------------------------- */
int FixReaxCSpecies::CheckExistence(int id, int ntypes)
{
int i, j, molid, flag;
for (i = 0; i < Nmoltype; i ++) {
flag = 0;
for (j = 0; j < ntypes; j ++) {
molid = MolType[ntypes * i + j];
if (molid != MolName[ntypes * id + j]) flag = 1;
}
if (flag == 0) return i;
}
for (i = 0; i < ntypes; i ++)
MolType[ntypes * Nmoltype + i] = MolName[ntypes *id + i];
Nmoltype ++;
return Nmoltype - 1;
}
/* ---------------------------------------------------------------------- */
void FixReaxCSpecies::WriteFormulas(int Nmole, int Nspec)
{
int i, j, itemp;
bigint ntimestep = update->ntimestep;
fprintf(fp,"# Timestep No_Moles No_Specs ");
Nmoltype = 0;
for (i = 0; i < Nspec; i ++)
nd[i] = CheckExistence(i, ntypes);
for (i = 0; i < Nmoltype; i ++) {
for (j = 0;j < ntypes; j ++) {
itemp = MolType[ntypes * i + j];
if (itemp != 0) {
if (eletype) fprintf(fp,"%s",eletype[j]);
else fprintf(fp,"%c",ele[j]);
if (itemp != 1) fprintf(fp,"%d",itemp);
}
}
fprintf(fp,"\t");
}
fprintf(fp,"\n");
fprintf(fp,BIGINT_FORMAT,ntimestep);
fprintf(fp,"%11d%11d\t",Nmole,Nspec);
for (i = 0; i < Nmoltype; i ++)
fprintf(fp," %d\t",NMol[i]);
fprintf(fp,"\n");
}
/* ---------------------------------------------------------------------- */
void FixReaxCSpecies::OpenPos()
{
char *filecurrent;
bigint ntimestep = update->ntimestep;
filecurrent = (char*) malloc((strlen(filepos)+16)*sizeof(char));
char *ptr = strchr(filepos,'*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filepos,ntimestep,ptr+1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filepos,ntimestep,ptr+1);
}
*ptr = '*';
if (me == 0) {
pos = fopen(filecurrent, "w");
if (pos == NULL) error->one(FLERR,"Cannot open fix reax/c/species position file");
} else pos = NULL;
multipos_opened = 1;
free(filecurrent);
}
/* ---------------------------------------------------------------------- */
void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
{
int i, itype, cid;
int count, count_tmp, m, n, k;
int *Nameall;
int *mask =atom->mask;
double avq, avq_tmp, avx[3], avx_tmp, box[3], halfbox[3];
double **spec_atom = f_SPECBOND->array_atom;
if (multipos) OpenPos();
box[0] = domain->boxhi[0] - domain->boxlo[0];
box[1] = domain->boxhi[1] - domain->boxlo[1];
box[2] = domain->boxhi[2] - domain->boxlo[2];
for (int j = 0; j < 3; j++)
halfbox[j] = box[j] / 2;
if (me == 0) {
fprintf(pos,"Timestep " BIGINT_FORMAT " NMole %d NSpec %d xlo %f "
"xhi %f ylo %f yhi %f zlo %f zhi %f\n",
update->ntimestep,Nmole, Nspec,
domain->boxlo[0],domain->boxhi[0],
domain->boxlo[1],domain->boxhi[1],
domain->boxlo[2],domain->boxhi[2]);
fprintf(pos,"ID\tAtom_Count\tType\tAve_q\t\tCoM_x\t\tCoM_y\t\tCoM_z\n");
}
Nameall = NULL;
memory->create(Nameall,ntypes,"reax/c/species:Nameall");
for (m = 1; m <= Nmole; m ++) {
count = 0;
avq = 0.0;
for (n = 0; n < 3; n++)
avx[n] = 0.0;
for (n = 0; n < ntypes; n ++)
Name[n] = 0;
for (i = 0; i < nlocal; i ++) {
if (!(mask[i] & groupbit)) continue;
cid = nint(clusterID[i]);
if (cid == m) {
itype = atom->type[i]-1;
Name[itype] ++;
count ++;
avq += spec_atom[i][0];
if (PBCconnected[i]) {
if ((x0[i].x - spec_atom[i][1]) > halfbox[0])
spec_atom[i][1] += box[0];
if ((spec_atom[i][1] - x0[i].x) > halfbox[0])
spec_atom[i][1] -= box[0];
if ((x0[i].y - spec_atom[i][2]) > halfbox[1])
spec_atom[i][2] += box[1];
if ((spec_atom[i][2] - x0[i].y) > halfbox[1])
spec_atom[i][2] -= box[1];
if ((x0[i].z - spec_atom[i][3]) > halfbox[2])
spec_atom[i][3] += box[2];
if ((spec_atom[i][3] - x0[i].z) > halfbox[2])
spec_atom[i][3] -= box[2];
}
for (n = 0; n < 3; n++)
avx[n] += spec_atom[i][n+1];
}
}
avq_tmp = 0.0;
MPI_Allreduce(&avq,&avq_tmp,1,MPI_DOUBLE,MPI_SUM,world);
avq = avq_tmp;
for (n = 0; n < 3; n++) {
avx_tmp = 0.0;
MPI_Reduce(&avx[n],&avx_tmp,1,MPI_DOUBLE,MPI_SUM,0,world);
avx[n] = avx_tmp;
}
MPI_Reduce(&count,&count_tmp,1,MPI_INT,MPI_SUM,0,world);
count = count_tmp;
MPI_Reduce(Name,Nameall,ntypes,MPI_INT,MPI_SUM,0,world);
for (n = 0; n < ntypes; n++) Name[n] = Nameall[n];
if (me == 0) {
fprintf(pos,"%d\t%d\t",m,count);
for (n = 0; n < ntypes; n++) {
if (Name[n] != 0) {
if (eletype) fprintf(pos,"%s",eletype[n]);
else fprintf(pos,"%c",ele[n]);
if (Name[n] != 1) fprintf(pos,"%d",Name[n]);
}
}
if (count > 0) {
avq /= count;
for (k = 0; k < 3; k++) {
avx[k] /= count;
if (avx[k] >= domain->boxhi[k])
avx[k] -= box[k];
if (avx[k] < domain->boxlo[k])
avx[k] += box[k];
avx[k] -= domain->boxlo[k];
avx[k] /= box[k];
}
fprintf(pos,"\t%.8f \t%.8f \t%.8f \t%.8f",
avq,avx[0],avx[1],avx[2]);
}
fprintf(pos,"\n");
}
}
if (me == 0 && !multipos) fprintf(pos,"#\n");
memory->destroy(Nameall);
}
/* ---------------------------------------------------------------------- */
double FixReaxCSpecies::compute_vector(int n)
{
if (n == 0)
return vector_nmole;
if (n == 1)
return vector_nspec;
return 0.0;
}
/* ---------------------------------------------------------------------- */
int FixReaxCSpecies::nint(const double &r)
{
int i = 0;
if (r>0.0) i = static_cast<int>(r+0.5);
else if (r<0.0) i = static_cast<int>(r-0.5);
return i;
}
/* ---------------------------------------------------------------------- */
int FixReaxCSpecies::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m] = clusterID[j];
buf[m+1] = (double)PBCconnected[j];
buf[m+2] = x0[j].x;
buf[m+3] = x0[j].y;
buf[m+4] = x0[j].z;
m += 5;
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixReaxCSpecies::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
clusterID[i] = buf[m];
PBCconnected[i] = (int)buf[m+1];
x0[i].x = buf[m+2];
x0[i].y = buf[m+3];
x0[i].z = buf[m+4];
m += 5;
}
}
/* ---------------------------------------------------------------------- */
double FixReaxCSpecies::memory_usage()
{
double bytes;
bytes = 5*nmax*sizeof(double); // clusterID + PBCconnected + x0
return bytes;
}
/* ---------------------------------------------------------------------- */
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