Changed behavior for non-periodic systems (fa01d915) · Commits · 郑智淋 / lammps

src/VORONOI/compute_voronoi_atom.cpp

+51 −20

Original line number	Diff line number	Diff line
		@@ -233,22 +233,38 @@ void ComputeVoronoi::buildCells()

		// cutghost is in lamda coordinates for triclinic boxes, use subxx_lamda
		double *h = domain->h;
		sublo_bound[0] = h[0]sublo_lamda[0] + h[5]sublo_lamda[1] + h[4]*sublo_lamda[2] + boxlo[0];
		sublo_bound[1] = h[1]sublo_lamda[1] + h[3]sublo_lamda[2] + boxlo[1];
		sublo_bound[2] = h[2]*sublo_lamda[2] + boxlo[2];
		subhi_bound[0] = h[0]subhi_lamda[0] + h[5]subhi_lamda[1] + h[4]*subhi_lamda[2] + boxlo[0];
		subhi_bound[1] = h[1]subhi_lamda[1] + h[3]subhi_lamda[2] + boxlo[1];
		subhi_bound[2] = h[2]*subhi_lamda[2] + boxlo[2];
		cut_bound[0] = h[0]cut[0] + h[5]cut[1] + h[4]*cut[2];
		cut_bound[1] = h[1]cut[1] + h[3]cut[2];
		cut_bound[2] = h[2]*cut[2];
		for( i=0; i<3; ++i ) {
		sublo_bound[i] = sublo[i]-cut[i]-e;
		subhi_bound[i] = subhi[i]+cut[i]+e;
		if (domain->periodicity[i]==0) {
		sublo_bound[i] = MAX(sublo_bound[i],0.0);
		subhi_bound[i] = MIN(subhi_bound[i],1.0);
		}
		}
		if (dim == 2) {
		sublo_bound[2] = 0.0;
		subhi_bound[2] = 1.0;
		}
		sublo_bound[0] = h[0]sublo_bound[0] + h[5]sublo_bound[1] + h[4]*sublo_bound[2] + boxlo[0];
		sublo_bound[1] = h[1]sublo_bound[1] + h[3]sublo_bound[2] + boxlo[1];
		sublo_bound[2] = h[2]*sublo_bound[2] + boxlo[2];
		subhi_bound[0] = h[0]subhi_bound[0] + h[5]subhi_bound[1] + h[4]*subhi_bound[2] + boxlo[0];
		subhi_bound[1] = h[1]subhi_bound[1] + h[3]subhi_bound[2] + boxlo[1];
		subhi_bound[2] = h[2]*subhi_bound[2] + boxlo[2];

		} else {
		// orthogonal box
		for( i=0; i<3; ++i ) {
		sublo_bound[i] = sublo[i];
		subhi_bound[i] = subhi[i];
		cut_bound[i] = cut[i];
		sublo_bound[i] = sublo[i]-cut[i]-e;
		subhi_bound[i] = subhi[i]+cut[i]+e;
		if (domain->periodicity[i]==0) {
		sublo_bound[i] = MAX(sublo_bound[i],domain->boxlo[i]);
		subhi_bound[i] = MIN(subhi_bound[i],domain->boxhi[i]);
		}
		}
		if (dim == 2) {
		sublo_bound[2] = sublo[2];
		subhi_bound[2] = subhi[2];
		}
		}

		@@ -290,10 +306,14 @@ void ComputeVoronoi::buildCells()

		// polydisperse voro++ container
		delete con_poly;
		con_poly = new container_poly(sublo_bound[0]-cut_bound[0]-e,subhi_bound[0]+cut_bound[0]+e,
		sublo_bound[1]-cut_bound[1]-e,subhi_bound[1]+cut_bound[1]+e,
		sublo_bound[2]-(dim==3 ? cut_bound[2]-e : 0.0),subhi_bound[2]+(dim==3 ? cut_bound[2]+e : 0.0),
		int(n[0]),int(n[1]),int(n[2]),false,false,false,8);
		con_poly = new container_poly(sublo_bound[0],
		subhi_bound[0],
		sublo_bound[1],
		subhi_bound[1],
		sublo_bound[2],
		subhi_bound[2],
		int(n[0]),int(n[1]),int(n[2]),
		false,false,false,8);

		// pass coordinates for local and ghost atoms to voro++
		for (i = 0; i < nall; i++) {
		@@ -303,10 +323,15 @@ void ComputeVoronoi::buildCells()
		} else {
		// monodisperse voro++ container
		delete con_mono;
		con_mono = new container(sublo_bound[0]-cut_bound[0]-e,subhi_bound[0]+cut_bound[0]+e,
		sublo_bound[1]-cut_bound[1]-e,subhi_bound[1]+cut_bound[1]+e,
		sublo_bound[2]-(dim==3 ? cut_bound[2]-e : 0.0),subhi_bound[2]+(dim==3 ? cut_bound[2]+e : 0.0),
		int(n[0]),int(n[1]),int(n[2]),false,false,false,8);

		con_mono = new container(sublo_bound[0],
		subhi_bound[0],
		sublo_bound[1],
		subhi_bound[1],
		sublo_bound[2],
		subhi_bound[2],
		int(n[0]),int(n[1]),int(n[2]),
		false,false,false,8);

		// pass coordinates for local and ghost atoms to voro++
		for (i = 0; i < nall; i++)
		@@ -434,6 +459,12 @@ void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
		c.neighbors(neigh);
		int neighs = neigh.size();

		// // DEBUG CODE!!
		// // loop over all faces (neighbors)
		// for (j=0; j<neighs; ++j)
		// printf("neighbors %d %d %d\n",i,j,neigh[j]);
		// // END DEBUG CODE!!

		if (fthresh > 0) {
		// count only faces above area threshold
		c.face_areas(narea);

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