apply clangformat
This commit is contained in:
Axel Kohlmeyer
@ -41,10 +41,9 @@ using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
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{
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if (narg < 7) error->all(FLERR,"Illegal fix reaxff/species command");
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if (narg < 7) error->all(FLERR, "Illegal fix reaxff/species command");
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force_reneighbor = 0;
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@ -59,32 +58,31 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
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compressed = 0;
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nvalid = -1;
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MPI_Comm_rank(world,&me);
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MPI_Comm_size(world,&nprocs);
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MPI_Comm_rank(world, &me);
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MPI_Comm_size(world, &nprocs);
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ntypes = atom->ntypes;
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nevery = utils::inumeric(FLERR,arg[3],false,lmp);
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nrepeat = utils::inumeric(FLERR,arg[4],false,lmp);
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global_freq = nfreq = utils::inumeric(FLERR,arg[5],false,lmp);
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nevery = utils::inumeric(FLERR, arg[3], false, lmp);
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nrepeat = utils::inumeric(FLERR, arg[4], false, lmp);
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global_freq = nfreq = utils::inumeric(FLERR, arg[5], false, lmp);
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comm_forward = 4;
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if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
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error->all(FLERR,"Illegal fix reaxff/species command");
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if (nfreq % nevery || nrepeat*nevery > nfreq)
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error->all(FLERR,"Illegal fix reaxff/species command");
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error->all(FLERR, "Illegal fix reaxff/species command");
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if (nfreq % nevery || nrepeat * nevery > nfreq)
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error->all(FLERR, "Illegal fix reaxff/species command");
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// Neighbor lists must stay unchanged during averaging of bonds,
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// but may be updated when no averaging is performed.
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int rene_flag = 0;
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if (nevery * nrepeat != 1 && (nfreq % neighbor->every != 0 || neighbor->every < nevery * nrepeat)) {
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if (nevery * nrepeat != 1 &&
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(nfreq % neighbor->every != 0 || neighbor->every < nevery * nrepeat)) {
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int newneighborevery = nevery * nrepeat;
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while (nfreq % newneighborevery != 0 && newneighborevery <= nfreq / 2)
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newneighborevery++;
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while (nfreq % newneighborevery != 0 && newneighborevery <= nfreq / 2) newneighborevery++;
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if (nfreq % newneighborevery != 0)
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newneighborevery = nfreq;
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if (nfreq % newneighborevery != 0) newneighborevery = nfreq;
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neighbor->every = newneighborevery;
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rene_flag = 1;
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@ -97,26 +95,29 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
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}
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if (me == 0 && rene_flag)
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error->warning(FLERR,"Resetting reneighboring criteria to 'delay {} every {} check no' "
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"for fix reaxff/species",neighbor->delay, neighbor->every);
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error->warning(FLERR,
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"Resetting reneighboring criteria to 'delay {} every {} check no' "
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"for fix reaxff/species",
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neighbor->delay, neighbor->every);
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if (me == 0) {
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if (platform::has_compress_extension(arg[6])) {
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fp = platform::compressed_write(arg[6]);
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compressed = 1;
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if (!fp) error->one(FLERR,"Cannot open compressed file");
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} else fp = fopen(arg[6],"w");
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if (!fp) error->one(FLERR, "Cannot open compressed file");
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} else
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fp = fopen(arg[6], "w");
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if (!fp)
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error->one(FLERR,"Cannot open fix reaxff/species file {}: {}",arg[6],utils::getsyserror());
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error->one(FLERR, "Cannot open fix reaxff/species file {}: {}", arg[6], utils::getsyserror());
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}
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x0 = nullptr;
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clusterID = nullptr;
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int ntmp = 1;
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memory->create(x0,ntmp,"reaxff/species:x0");
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memory->create(clusterID,ntmp,"reaxff/species:clusterID");
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memory->create(x0, ntmp, "reaxff/species:x0");
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memory->create(clusterID, ntmp, "reaxff/species:clusterID");
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vector_atom = clusterID;
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BOCut = nullptr;
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@ -134,11 +135,10 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
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int n, i, j, itype, jtype;
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double bo_cut;
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bg_cut = 0.30;
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n = ntypes+1;
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memory->create(BOCut,n,n,"reaxff/species:BOCut");
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for (i = 1; i < n; i ++)
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for (j = 1; j < n; j ++)
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BOCut[i][j] = bg_cut;
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n = ntypes + 1;
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memory->create(BOCut, n, n, "reaxff/species:BOCut");
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for (i = 1; i < n; i++)
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for (j = 1; j < n; j++) BOCut[i][j] = bg_cut;
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// optional args
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eletype = nullptr;
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@ -153,74 +153,68 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
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while (iarg < narg) {
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// set BO cutoff
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if (strcmp(arg[iarg],"cutoff") == 0) {
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if (iarg+4 > narg) error->all(FLERR,"Illegal fix reaxff/species command");
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itype = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
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jtype = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
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bo_cut = utils::numeric(FLERR,arg[iarg+3],false,lmp);
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if (itype > ntypes || jtype > ntypes)
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error->all(FLERR,"Illegal fix reaxff/species command");
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if (itype <= 0 || jtype <= 0)
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error->all(FLERR,"Illegal fix reaxff/species command");
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if (bo_cut > 1.0 || bo_cut < 0.0)
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error->all(FLERR,"Illegal fix reaxff/species command");
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if (strcmp(arg[iarg], "cutoff") == 0) {
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if (iarg + 4 > narg) error->all(FLERR, "Illegal fix reaxff/species command");
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itype = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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jtype = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);
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bo_cut = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
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if (itype > ntypes || jtype > ntypes) error->all(FLERR, "Illegal fix reaxff/species command");
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if (itype <= 0 || jtype <= 0) error->all(FLERR, "Illegal fix reaxff/species command");
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if (bo_cut > 1.0 || bo_cut < 0.0) error->all(FLERR, "Illegal fix reaxff/species command");
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BOCut[itype][jtype] = bo_cut;
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BOCut[jtype][itype] = bo_cut;
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iarg += 4;
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// modify element type names
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} else if (strcmp(arg[iarg],"element") == 0) {
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if (iarg+ntypes+1 > narg) error->all(FLERR,"Illegal fix reaxff/species command");
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} else if (strcmp(arg[iarg], "element") == 0) {
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if (iarg + ntypes + 1 > narg) error->all(FLERR, "Illegal fix reaxff/species command");
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eletype = (char**) malloc(ntypes*sizeof(char*));
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eletype = (char **) malloc(ntypes * sizeof(char *));
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int len;
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for (int i = 0; i < ntypes; i ++) {
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len = strlen(arg[iarg+1+i])+1;
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eletype[i] = (char*) malloc(len*sizeof(char));
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strcpy(eletype[i],arg[iarg+1+i]);
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for (int i = 0; i < ntypes; i++) {
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len = strlen(arg[iarg + 1 + i]) + 1;
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eletype[i] = (char *) malloc(len * sizeof(char));
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strcpy(eletype[i], arg[iarg + 1 + i]);
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}
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eleflag = 1;
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iarg += ntypes + 1;
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// position of molecules
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} else if (strcmp(arg[iarg],"position") == 0) {
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if (iarg+3 > narg) error->all(FLERR,"Illegal fix reaxff/species command");
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} else if (strcmp(arg[iarg], "position") == 0) {
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if (iarg + 3 > narg) error->all(FLERR, "Illegal fix reaxff/species command");
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posflag = 1;
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posfreq = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
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if (posfreq < nfreq || (posfreq%nfreq != 0))
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error->all(FLERR,"Illegal fix reaxff/species command");
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posfreq = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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if (posfreq < nfreq || (posfreq % nfreq != 0))
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error->all(FLERR, "Illegal fix reaxff/species command");
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filepos = new char[255];
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strcpy(filepos,arg[iarg+2]);
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if (strchr(filepos,'*')) {
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strcpy(filepos, arg[iarg + 2]);
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if (strchr(filepos, '*')) {
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multipos = 1;
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} else {
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if (me == 0) {
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pos = fopen(filepos, "w");
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if (pos == nullptr) error->one(FLERR,"Cannot open fix reaxff/species position file");
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if (pos == nullptr) error->one(FLERR, "Cannot open fix reaxff/species position file");
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}
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singlepos_opened = 1;
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multipos = 0;
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}
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iarg += 3;
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} else error->all(FLERR,"Illegal fix reaxff/species command");
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} else
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error->all(FLERR, "Illegal fix reaxff/species command");
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}
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if (!eleflag) {
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memory->create(ele,ntypes+1,"reaxff/species:ele");
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ele[0]='C';
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if (ntypes > 1)
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ele[1]='H';
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if (ntypes > 2)
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ele[2]='O';
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if (ntypes > 3)
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ele[3]='N';
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memory->create(ele, ntypes + 1, "reaxff/species:ele");
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ele[0] = 'C';
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if (ntypes > 1) ele[1] = 'H';
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if (ntypes > 2) ele[2] = 'O';
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if (ntypes > 3) ele[3] = 'N';
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}
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vector_nmole = 0;
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vector_nspec = 0;
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}
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/* ---------------------------------------------------------------------- */
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@ -238,19 +232,21 @@ FixReaxFFSpecies::~FixReaxFFSpecies()
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memory->destroy(MolType);
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memory->destroy(MolName);
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if (filepos)
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delete [] filepos;
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if (filepos) delete[] filepos;
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if (me == 0) {
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if (compressed) platform::pclose(fp);
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else fclose(fp);
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if (compressed)
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platform::pclose(fp);
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else
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fclose(fp);
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if (posflag && multipos_opened) fclose(pos);
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}
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try {
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modify->delete_compute(fmt::format("SPECATOM_{}",id));
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modify->delete_fix(fmt::format("SPECBOND_{}",id));
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} catch (std::exception &) {}
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modify->delete_compute(fmt::format("SPECATOM_{}", id));
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modify->delete_fix(fmt::format("SPECBOND_{}", id));
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} catch (std::exception &) {
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}
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}
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/* ---------------------------------------------------------------------- */
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@ -266,9 +262,8 @@ int FixReaxFFSpecies::setmask()
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void FixReaxFFSpecies::setup(int /*vflag*/)
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{
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ntotal = static_cast<int> (atom->natoms);
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if (Name == nullptr)
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memory->create(Name,ntypes,"reaxff/species:Name");
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ntotal = static_cast<int>(atom->natoms);
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if (Name == nullptr) memory->create(Name, ntypes, "reaxff/species:Name");
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post_integrate();
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}
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@ -278,28 +273,30 @@ void FixReaxFFSpecies::setup(int /*vflag*/)
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void FixReaxFFSpecies::init()
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{
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if (atom->tag_enable == 0)
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error->all(FLERR,"Cannot use fix reaxff/species unless atoms have IDs");
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error->all(FLERR, "Cannot use fix reaxff/species unless atoms have IDs");
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reaxff = (PairReaxFF *) force->pair_match("^reax..",0);
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if (reaxff == nullptr) error->all(FLERR,"Cannot use fix reaxff/species without "
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"pair_style reaxff, reaxff/kk, or reaxff/omp");
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reaxff = (PairReaxFF *) force->pair_match("^reax..", 0);
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if (reaxff == nullptr)
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error->all(FLERR,
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"Cannot use fix reaxff/species without "
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"pair_style reaxff, reaxff/kk, or reaxff/omp");
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reaxff->fixspecies_flag = 1;
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// reset next output timestep if not yet set or timestep has been reset
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if (nvalid != update->ntimestep)
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nvalid = update->ntimestep+nfreq;
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if (nvalid != update->ntimestep) nvalid = update->ntimestep + nfreq;
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if (!setupflag) {
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// create a compute to store properties
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modify->add_compute(fmt::format("SPECATOM_{} all SPEC/ATOM q x y z vx vy vz abo01 abo02 "
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"abo03 abo04 abo05 abo06 abo07 abo08 abo09 abo10 abo11 "
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"abo12 abo13 abo14 abo15 abo16 abo17 abo18 abo19 abo20 "
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"abo21 abo22 abo23 abo24",id));
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"abo21 abo22 abo23 abo24",
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id));
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// create a fix to point to fix_ave_atom for averaging stored properties
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auto fixcmd = fmt::format("SPECBOND_{} all ave/atom {} {} {}",id,nevery,nrepeat,nfreq);
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for (int i = 1; i < 32; ++i) fixcmd += fmt::format(" c_SPECATOM_{}[{}]",id,i);
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auto fixcmd = fmt::format("SPECBOND_{} all ave/atom {} {} {}", id, nevery, nrepeat, nfreq);
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for (int i = 1; i < 32; ++i) fixcmd += fmt::format(" c_SPECATOM_{}[{}]", id, i);
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f_SPECBOND = (FixAveAtom *) modify->add_fix(fixcmd);
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setupflag = 1;
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}
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@ -316,7 +313,7 @@ void FixReaxFFSpecies::init_list(int /*id*/, NeighList *ptr)
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void FixReaxFFSpecies::post_integrate()
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{
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Output_ReaxFF_Bonds(update->ntimestep,fp);
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Output_ReaxFF_Bonds(update->ntimestep, fp);
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if (me == 0) fflush(fp);
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}
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@ -338,30 +335,27 @@ void FixReaxFFSpecies::Output_ReaxFF_Bonds(bigint ntimestep, FILE * /*fp*/)
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nmax = atom->nmax;
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memory->destroy(x0);
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memory->destroy(clusterID);
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memory->create(x0,nmax,"reaxff/species:x0");
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memory->create(clusterID,nmax,"reaxff/species:clusterID");
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memory->create(x0, nmax, "reaxff/species:x0");
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memory->create(clusterID, nmax, "reaxff/species:clusterID");
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vector_atom = clusterID;
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}
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for (int i = 0; i < nmax; i++) {
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x0[i].x = x0[i].y = x0[i].z = 0.0;
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}
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for (int i = 0; i < nmax; i++) { x0[i].x = x0[i].y = x0[i].z = 0.0; }
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Nmole = Nspec = 0;
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FindMolecule();
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SortMolecule (Nmole);
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SortMolecule(Nmole);
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FindSpecies(Nmole, Nspec);
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vector_nmole = Nmole;
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vector_nspec = Nspec;
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if (me == 0 && ntimestep >= 0)
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WriteFormulas (Nmole, Nspec);
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if (me == 0 && ntimestep >= 0) WriteFormulas(Nmole, Nspec);
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if (posflag && ((ntimestep)%posfreq==0)) {
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if (posflag && ((ntimestep) % posfreq == 0)) {
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WritePos(Nmole, Nspec);
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if (me == 0) fflush(pos);
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}
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@ -379,8 +373,7 @@ AtomCoord FixReaxFFSpecies::chAnchor(AtomCoord in1, AtomCoord in2)
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if (in1.y < in2.y)
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return in1;
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else if (in1.y == in2.y) {
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if (in1.z < in2.z)
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return in1;
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if (in1.z < in2.z) return in1;
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}
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}
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return in2;
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@ -388,13 +381,13 @@ AtomCoord FixReaxFFSpecies::chAnchor(AtomCoord in1, AtomCoord in2)
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/* ---------------------------------------------------------------------- */
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void FixReaxFFSpecies::FindMolecule ()
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void FixReaxFFSpecies::FindMolecule()
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{
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int i,j,ii,jj,inum,itype,jtype,loop,looptot;
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int change,done,anychange;
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int i, j, ii, jj, inum, itype, jtype, loop, looptot;
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int change, done, anychange;
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int *mask = atom->mask;
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int *ilist;
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double bo_tmp,bo_cut;
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double bo_tmp, bo_cut;
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double **spec_atom = f_SPECBOND->array_atom;
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inum = reaxff->list->inum;
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@ -407,14 +400,14 @@ void FixReaxFFSpecies::FindMolecule ()
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x0[i].x = spec_atom[i][1];
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x0[i].y = spec_atom[i][2];
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x0[i].z = spec_atom[i][3];
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}
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else clusterID[i] = 0.0;
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} else
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clusterID[i] = 0.0;
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}
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loop = 0;
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while (true) {
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comm->forward_comm(this);
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loop ++;
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loop++;
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change = 0;
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while (true) {
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@ -432,14 +425,13 @@ void FixReaxFFSpecies::FindMolecule ()
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if ((j == 0) || (j < i)) continue;
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if (!(mask[j] & groupbit)) continue;
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if (clusterID[i] == clusterID[j]
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&& x0[i].x == x0[j].x
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||||
&& x0[i].y == x0[j].y
|
||||
&& x0[i].z == x0[j].z) continue;
|
||||
if (clusterID[i] == clusterID[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];
|
||||
bo_tmp = spec_atom[i][jj + 7];
|
||||
|
||||
if (bo_tmp > bo_cut) {
|
||||
clusterID[i] = clusterID[j] = MIN(clusterID[i], clusterID[j]);
|
||||
@ -451,12 +443,11 @@ void FixReaxFFSpecies::FindMolecule ()
|
||||
if (!done) change = 1;
|
||||
if (done) break;
|
||||
}
|
||||
MPI_Allreduce(&change,&anychange,1,MPI_INT,MPI_MAX,world);
|
||||
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;
|
||||
|
||||
MPI_Allreduce(&loop, &looptot, 1, MPI_INT, MPI_SUM, world);
|
||||
if (looptot >= 400 * nprocs) break;
|
||||
}
|
||||
}
|
||||
|
||||
@ -468,45 +459,45 @@ void FixReaxFFSpecies::SortMolecule(int &Nmole)
|
||||
molmap = nullptr;
|
||||
|
||||
int n, idlo, idhi;
|
||||
int *mask =atom->mask;
|
||||
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]));
|
||||
lo = MIN(lo, nint(clusterID[n]));
|
||||
hi = MAX(hi, nint(clusterID[n]));
|
||||
}
|
||||
int flagall;
|
||||
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
|
||||
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 reaxff/species group");
|
||||
MPI_Allreduce(&lo,&idlo,1,MPI_INT,MPI_MIN,world);
|
||||
MPI_Allreduce(&hi,&idhi,1,MPI_INT,MPI_MAX,world);
|
||||
error->warning(FLERR, "Atom with cluster ID = 0 included in fix reaxff/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 reaxff/species group");
|
||||
error->warning(FLERR, "Atom with cluster ID = maxmol included in fix reaxff/species group");
|
||||
|
||||
int nlen = idhi - idlo + 1;
|
||||
memory->create(molmap,nlen,"reaxff/species:molmap");
|
||||
memory->create(molmap, nlen, "reaxff/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;
|
||||
molmap[nint(clusterID[n]) - idlo] = 1;
|
||||
}
|
||||
|
||||
int *molmapall;
|
||||
memory->create(molmapall,nlen,"reaxff/species:molmapall");
|
||||
MPI_Allreduce(molmap,molmapall,nlen,MPI_INT,MPI_MAX,world);
|
||||
memory->create(molmapall, nlen, "reaxff/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;
|
||||
if (molmapall[n])
|
||||
molmap[n] = Nmole++;
|
||||
else
|
||||
molmap[n] = -1;
|
||||
}
|
||||
memory->destroy(molmapall);
|
||||
|
||||
@ -514,21 +505,19 @@ void FixReaxFFSpecies::SortMolecule(int &Nmole)
|
||||
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;
|
||||
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");
|
||||
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;
|
||||
clusterID[n] = molmap[nint(clusterID[n]) - idlo] + 1;
|
||||
}
|
||||
|
||||
memory->destroy(molmap);
|
||||
molmap = nullptr;
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -538,52 +527,50 @@ void FixReaxFFSpecies::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 *mask = atom->mask;
|
||||
int *Nameall, *NMolall;
|
||||
|
||||
memory->destroy(MolName);
|
||||
MolName = nullptr;
|
||||
memory->create(MolName,Nmole*(ntypes+1),"reaxff/species:MolName");
|
||||
memory->create(MolName, Nmole * (ntypes + 1), "reaxff/species:MolName");
|
||||
|
||||
memory->destroy(NMol);
|
||||
NMol = nullptr;
|
||||
memory->create(NMol,Nmole,"reaxff/species:NMol");
|
||||
for (m = 0; m < Nmole; m ++)
|
||||
NMol[m] = 1;
|
||||
memory->create(NMol, Nmole, "reaxff/species:NMol");
|
||||
for (m = 0; m < Nmole; m++) NMol[m] = 1;
|
||||
|
||||
memory->create(Nameall,ntypes,"reaxff/species:Nameall");
|
||||
memory->create(NMolall,Nmole,"reaxff/species:NMolall");
|
||||
memory->create(Nameall, ntypes, "reaxff/species:Nameall");
|
||||
memory->create(NMolall, Nmole, "reaxff/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 ++) {
|
||||
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] ++;
|
||||
itype = atom->type[n] - 1;
|
||||
Name[itype]++;
|
||||
flag_mol = 1;
|
||||
}
|
||||
}
|
||||
MPI_Allreduce(&flag_mol,&flag_tmp,1,MPI_INT,MPI_MAX,world);
|
||||
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);
|
||||
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] ++;
|
||||
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 ++;
|
||||
for (l = 0; l < ntypes; l++) MolName[ntypes * Nspec + l] = Name[l];
|
||||
Nspec++;
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -592,11 +579,11 @@ void FixReaxFFSpecies::FindSpecies(int Nmole, int &Nspec)
|
||||
|
||||
memory->destroy(nd);
|
||||
nd = nullptr;
|
||||
memory->create(nd,Nspec,"reaxff/species:nd");
|
||||
memory->create(nd, Nspec, "reaxff/species:nd");
|
||||
|
||||
memory->destroy(MolType);
|
||||
MolType = nullptr;
|
||||
memory->create(MolType,Nspec*(ntypes+2),"reaxff/species:MolType");
|
||||
memory->create(MolType, Nspec * (ntypes + 2), "reaxff/species:MolType");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -605,18 +592,17 @@ int FixReaxFFSpecies::CheckExistence(int id, int ntypes)
|
||||
{
|
||||
int i, j, molid, flag;
|
||||
|
||||
for (i = 0; i < Nmoltype; i ++) {
|
||||
for (i = 0; i < Nmoltype; i++) {
|
||||
flag = 0;
|
||||
for (j = 0; j < ntypes; j ++) {
|
||||
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];
|
||||
for (i = 0; i < ntypes; i++) MolType[ntypes * Nmoltype + i] = MolName[ntypes * id + i];
|
||||
|
||||
Nmoltype ++;
|
||||
Nmoltype++;
|
||||
return Nmoltype - 1;
|
||||
}
|
||||
|
||||
@ -627,33 +613,31 @@ void FixReaxFFSpecies::WriteFormulas(int Nmole, int Nspec)
|
||||
int i, j, itemp;
|
||||
bigint ntimestep = update->ntimestep;
|
||||
|
||||
fprintf(fp,"# Timestep No_Moles No_Specs ");
|
||||
fprintf(fp, "# Timestep No_Moles No_Specs ");
|
||||
|
||||
Nmoltype = 0;
|
||||
|
||||
for (i = 0; i < Nspec; i ++)
|
||||
nd[i] = CheckExistence(i, ntypes);
|
||||
for (i = 0; i < Nspec; i++) nd[i] = CheckExistence(i, ntypes);
|
||||
|
||||
for (i = 0; i < Nmoltype; i ++) {
|
||||
for (j = 0;j < ntypes; j ++) {
|
||||
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);
|
||||
if (eletype)
|
||||
fprintf(fp, "%s", eletype[j]);
|
||||
else
|
||||
fprintf(fp, "%c", ele[j]);
|
||||
if (itemp != 1) fprintf(fp, "%d", itemp);
|
||||
}
|
||||
}
|
||||
fprintf(fp,"\t");
|
||||
fputs("\t", fp);
|
||||
}
|
||||
fprintf(fp,"\n");
|
||||
fputs("\n", fp);
|
||||
|
||||
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");
|
||||
fmt::print(fp, "{} {:11} {11}\t", ntimestep, Nmole, Nspec);
|
||||
|
||||
for (i = 0; i < Nmoltype; i++) fprintf(fp, " %d\t", NMol[i]);
|
||||
fprintf(fp, "\n");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -692,7 +676,7 @@ void FixReaxFFSpecies::WritePos(int Nmole, int Nspec)
|
||||
int i, itype, cid;
|
||||
int count, count_tmp, m, n, k;
|
||||
int *Nameall;
|
||||
int *mask =atom->mask;
|
||||
int *mask = atom->mask;
|
||||
double avq, avq_tmp, avx[3], avx_tmp, box[3], halfbox[3];
|
||||
double **spec_atom = f_SPECBOND->array_atom;
|
||||
|
||||
@ -702,101 +686,89 @@ void FixReaxFFSpecies::WritePos(int Nmole, int Nspec)
|
||||
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;
|
||||
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]);
|
||||
fmt::print(pos,
|
||||
"Timestep {} NMole {} NSpec {} 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");
|
||||
fprintf(pos, "ID\tAtom_Count\tType\tAve_q\t\tCoM_x\t\tCoM_y\t\tCoM_z\n");
|
||||
}
|
||||
|
||||
Nameall = nullptr;
|
||||
memory->create(Nameall,ntypes,"reaxff/species:Nameall");
|
||||
memory->create(Nameall, ntypes, "reaxff/species:Nameall");
|
||||
|
||||
for (m = 1; m <= Nmole; m ++) {
|
||||
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 (n = 0; n < 3; n++) avx[n] = 0.0;
|
||||
for (n = 0; n < ntypes; n++) Name[n] = 0;
|
||||
|
||||
for (i = 0; i < nlocal; i ++) {
|
||||
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 ++;
|
||||
itype = atom->type[i] - 1;
|
||||
Name[itype]++;
|
||||
count++;
|
||||
avq += spec_atom[i][0];
|
||||
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];
|
||||
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);
|
||||
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);
|
||||
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);
|
||||
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);
|
||||
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);
|
||||
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 (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];
|
||||
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, "\t%.8f \t%.8f \t%.8f \t%.8f", avq, avx[0], avx[1], avx[2]);
|
||||
}
|
||||
fprintf(pos,"\n");
|
||||
fprintf(pos, "\n");
|
||||
}
|
||||
}
|
||||
if (me == 0 && !multipos) fprintf(pos,"#\n");
|
||||
if (me == 0 && !multipos) fprintf(pos, "#\n");
|
||||
memory->destroy(Nameall);
|
||||
}
|
||||
|
||||
@ -804,12 +776,9 @@ void FixReaxFFSpecies::WritePos(int Nmole, int Nspec)
|
||||
|
||||
double FixReaxFFSpecies::compute_vector(int n)
|
||||
{
|
||||
if (n == 0)
|
||||
return vector_nmole;
|
||||
if (n == 1)
|
||||
return vector_nspec;
|
||||
if (n == 0) return vector_nmole;
|
||||
if (n == 1) return vector_nspec;
|
||||
return 0.0;
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -817,25 +786,27 @@ double FixReaxFFSpecies::compute_vector(int n)
|
||||
int FixReaxFFSpecies::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);
|
||||
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 FixReaxFFSpecies::pack_forward_comm(int n, int *list, double *buf,
|
||||
int /*pbc_flag*/, int * /*pbc*/)
|
||||
int FixReaxFFSpecies::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/,
|
||||
int * /*pbc*/)
|
||||
{
|
||||
int i,j,m;
|
||||
int i, j, m;
|
||||
|
||||
m = 0;
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
buf[m] = clusterID[j];
|
||||
buf[m+1] = x0[j].x;
|
||||
buf[m+2] = x0[j].y;
|
||||
buf[m+3] = x0[j].z;
|
||||
buf[m + 1] = x0[j].x;
|
||||
buf[m + 2] = x0[j].y;
|
||||
buf[m + 3] = x0[j].z;
|
||||
m += 4;
|
||||
}
|
||||
return m;
|
||||
@ -845,15 +816,15 @@ int FixReaxFFSpecies::pack_forward_comm(int n, int *list, double *buf,
|
||||
|
||||
void FixReaxFFSpecies::unpack_forward_comm(int n, int first, double *buf)
|
||||
{
|
||||
int i,m,last;
|
||||
int i, m, last;
|
||||
|
||||
m = 0;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++) {
|
||||
clusterID[i] = buf[m];
|
||||
x0[i].x = buf[m+1];
|
||||
x0[i].y = buf[m+2];
|
||||
x0[i].z = buf[m+3];
|
||||
x0[i].x = buf[m + 1];
|
||||
x0[i].y = buf[m + 2];
|
||||
x0[i].z = buf[m + 3];
|
||||
m += 4;
|
||||
}
|
||||
}
|
||||
@ -864,7 +835,7 @@ double FixReaxFFSpecies::memory_usage()
|
||||
{
|
||||
double bytes;
|
||||
|
||||
bytes = 4*nmax*sizeof(double); // clusterID + x0
|
||||
bytes = 4 * nmax * sizeof(double); // clusterID + x0
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user