USER-DPD: move centroid bin of stencil_ssa to the first slot. (37810bdc) · Commits · 郑智淋 / lammps

src/USER-DPD/npair_half_bin_newton_ssa.cpp

+5 −27

Original line number	Diff line number	Diff line
		@@ -180,35 +180,13 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
		iatom = molatom[i];
		tagprev = tag[i] - iatom - 1;
		}
		// loop over rest of local atoms in i's bin if this is subphase 0
		// just store them, since j is beyond i in linked list
		if (subphase == 0) for (j = bins[i]; j >= 0; j = bins[j]) {
		jtype = type[j];
		if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
		delx = xtmp - x[j][0];
		dely = ytmp - x[j][1];
		delz = ztmp - x[j][2];
		rsq = delxdelx + delydely + delz*delz;
		if (rsq <= cutneighsq[itype][jtype]) {
		if (molecular) {
		if (!moltemplate)
		which = find_special(special[i],nspecial[i],tag[j]);
		else if (imol >= 0)
		which = find_special(onemols[imol]->special[iatom],
		onemols[imol]->nspecial[iatom],
		tag[j]-tagprev);
		else which = 0;
		if (which == 0) neighptr[n++] = j;
		else if (domain->minimum_image_check(delx,dely,delz))
		neighptr[n++] = j;
		else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
		} else neighptr[n++] = j;
		}
		}

		// loop over all local atoms in other bins in "subphase" of stencil
		// loop over all local atoms in the current stencil "subphase"
		for (k = nstencil_ssa[subphase]; k < nstencil_ssa[subphase+1]; k++) {
		for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
		const int jbin = ibin+stencil[k];
		if (jbin != ibin) j = binhead[jbin];
		else j = bins[i]; // same bin as i, so start just past i in the bin
		for (; j >= 0; j = bins[j]) {
		jtype = type[j];
		if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
		delx = xtmp - x[j][0];

src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp

+8 −6

Original line number	Diff line number	Diff line
		@@ -43,6 +43,14 @@ void NStencilHalfBin2dNewtonSSA::create()
		{
		int i,j,pos = 0;
		nstencil_ssa[0] = 0; // redundant info, but saves a conditional

		// Include the centroid at the start.
		// It will be handled as part of Subphase 0.
		stencilxyz[pos][0] = 0;
		stencilxyz[pos][1] = 0;
		stencilxyz[pos][2] = 0;
		stencil[pos++] = 0;

		// Subphase 0: upper right front bins (red)
		for (j = 0; j <= sy; j++)
		for (i = 0; i <= sx; i++)
		@@ -101,11 +109,5 @@ void NStencilHalfBin2dNewtonSSA::create()
		}
		// nstencil_ssa[8] = pos;

		// Also, include the centroid for the AIR ghosts.
		stencilxyz[pos][0] = 0;
		stencilxyz[pos][1] = 0;
		stencilxyz[pos][2] = 0;
		stencil[pos++] = 0;

		nstencil = pos; // record where full stencil ends
		}

src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp

+8 −6

Original line number	Diff line number	Diff line
		@@ -43,6 +43,14 @@ void NStencilHalfBin3dNewtonSSA::create()
		{
		int i,j,k,pos = 0;
		nstencil_ssa[0] = 0; // redundant info, but saves a conditional

		// Include the centroid at the start.
		// It will be handled as part of Subphase 0.
		stencilxyz[pos][0] = 0;
		stencilxyz[pos][1] = 0;
		stencilxyz[pos][2] = 0;
		stencil[pos++] = 0;

		// Subphase 0: upper right front bins (red)
		for (k = 0; k <= sz; k++)
		for (j = 0; j <= sy; j++)
		@@ -141,11 +149,5 @@ void NStencilHalfBin3dNewtonSSA::create()
		}
		//nstencil_ssa[8] = pos;

		// Also, include the centroid for the AIR ghosts.
		stencilxyz[pos][0] = 0;
		stencilxyz[pos][1] = 0;
		stencilxyz[pos][2] = 0;
		stencil[pos++] = 0;

		nstencil = pos; // record where full stencil ends
		}

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