cleanup from aidan for fix reax/c/species and its KOKKOS version (8c54fcd1) · Commits · 郑智淋 / lammps

src/KOKKOS/fix_reaxc_species_kokkos.cpp

+15 −20

Original line number	Diff line number	Diff line
		@@ -124,10 +124,10 @@ void FixReaxCSpeciesKokkos::FindMolecule()
		for (jj = 0; jj < MAXSPECBOND; jj++) {
		j = reaxc->tmpid[i][jj];

		if (j < i) continue;
		if ((j == 0) && (j < i)) continue;
		if (!(mask[j] & groupbit)) continue;

		if (clusterID[i] == clusterID[j] && PBCconnected[i] == PBCconnected[j]
		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];
		@@ -136,12 +136,7 @@ void FixReaxCSpeciesKokkos::FindMolecule()

		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;
		}
		}

src/USER-REAXC/fix_reaxc_species.cpp

+22 −47

Original line number	Diff line number	Diff line
		@@ -68,7 +68,7 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS lmp, int narg, char *arg) :
		nrepeat = atoi(arg[4]);
		global_freq = nfreq = atoi(arg[5]);

		comm_forward = 5;
		comm_forward = 4;

		if (nevery <= 0 \|\| nrepeat <= 0 \|\| nfreq <= 0)
		error->all(FLERR,"Illegal fix reax/c/species command");
		@@ -133,12 +133,10 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS lmp, int narg, char *arg) :
		}

		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;

		@@ -251,7 +249,6 @@ FixReaxCSpecies::~FixReaxCSpecies()
		memory->destroy(ele);
		memory->destroy(BOCut);
		memory->destroy(clusterID);
		memory->destroy(PBCconnected);
		memory->destroy(x0);

		memory->destroy(nd);
		@@ -458,16 +455,13 @@ void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
		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;
		}

		@@ -559,7 +553,6 @@ void FixReaxCSpecies::FindMolecule ()
		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;
		@@ -570,21 +563,7 @@ void FixReaxCSpecies::FindMolecule ()

		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]);
		// spec_atom[][] contains filtered coordinates only for local atoms,
		// so we have to use unfiltered ones for ghost atoms.
		if (j < nlocal) {
		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;
		} else {
		if ((fabs(spec_atom[i][1] - x[j][1]) > reaxc->control->bond_cut)
		\|\| (fabs(spec_atom[i][2] - x[j][2]) > reaxc->control->bond_cut)
		\|\| (fabs(spec_atom[i][3] - x[j][3]) > reaxc->control->bond_cut))
		PBCconnected[i] = PBCconnected[j] = 1;
		}
		done = 0;
		}
		}
		@@ -878,7 +857,6 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
		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])
		@@ -891,7 +869,6 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
		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];
		}
		@@ -977,11 +954,10 @@ int FixReaxCSpecies::pack_forward_comm(int n, int list, double buf,
		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;
		buf[m+1] = x0[j].x;
		buf[m+2] = x0[j].y;
		buf[m+3] = x0[j].z;
		m += 4;
		}
		return m;
		}
		@@ -996,11 +972,10 @@ void FixReaxCSpecies::unpack_forward_comm(int n, int first, double *buf)
		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;
		x0[i].x = buf[m+1];
		x0[i].y = buf[m+2];
		x0[i].z = buf[m+3];
		m += 4;
		}
		}

		@@ -1010,7 +985,7 @@ double FixReaxCSpecies::memory_usage()
		{
		double bytes;

		bytes = 5nmaxsizeof(double); // clusterID + PBCconnected + x0
		bytes = 4nmaxsizeof(double); // clusterID + x0

		return bytes;
		}

src/USER-REAXC/fix_reaxc_species.h

+0 −1

Original line number	Diff line number	Diff line
		@@ -52,7 +52,6 @@ class FixReaxCSpecies : public Fix {
		int Nmoltype, vector_nmole, vector_nspec;
		int Name, MolName, NMol, nd, MolType, molmap;
		double *clusterID;
		int *PBCconnected;
		AtomCoord *x0;

		double bg_cut;

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