updated comm tiled to have multi (9a3f9029) · Commits · 郑智淋 / lammps

src/comm_tiled.cpp

+179 −10

Original line number	Diff line number	Diff line
		@@ -11,6 +11,10 @@
		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		/* ----------------------------------------------------------------------
		Contributing author (multi) : Adrian Diaz (University of Florida)
		------------------------------------------------------------------------- */

		#include <cstring>
		#include "comm_tiled.h"
		#include "comm_brick.h"
		@@ -72,6 +76,9 @@ CommTiled::~CommTiled()
		memory->destroy(overlap);
		deallocate_swap(nswap);
		memory->sfree(rcbinfo);
		if (mode == Comm::MULTI) {
		memory->destroy(cutghostmulti);
		}
		}

		/* ----------------------------------------------------------------------
		@@ -80,6 +87,8 @@ CommTiled::~CommTiled()

		void CommTiled::init_buffers()
		{
		sendbox_multi = NULL;
		cutghostmulti = NULL;
		// bufextra = max size of one exchanged atom
		// = allowed overflow of sendbuf in exchange()
		// atomvec, fix reset these 2 maxexchange values if needed
		@@ -108,12 +117,20 @@ void CommTiled::init()
		{
		Comm::init();

		// memory for multi-style communication
		int maxswap = 6;
		if (mode == Comm::MULTI) {
		memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti");
		}
		if (mode == Comm::SINGLE && cutghostmulti) {
		memory->destroy(cutghostmulti);
		}

		// temporary restrictions

		if (triclinic)
		error->all(FLERR,"Cannot yet use comm_style tiled with triclinic box");
		if (mode == Comm::MULTI)
		error->all(FLERR,"Cannot yet use comm_style tiled with multi-mode comm");

		}

		/* ----------------------------------------------------------------------
		@@ -124,7 +141,7 @@ void CommTiled::init()
		void CommTiled::setup()
		{
		int i,j,n;

		int ntypes = atom->ntypes;
		// domain properties used in setup method and methods it calls

		dimension = domain->dimension;
		@@ -157,9 +174,22 @@ void CommTiled::setup()
		// set cutoff for comm forward and comm reverse
		// check that cutoff < any periodic box length

		double cut = MAX(neighbor->cutneighmax,cutghostuser);
		double cut;

		if (mode == Comm::MULTI) {
		double *cuttype = neighbor->cuttype;
		for (i = 1; i <= ntypes; i++) {
		cut = 0.0;
		if (cutusermulti) cut = cutusermulti[i];
		cutghostmulti[i][0] = MAX(cut,cuttype[i]);
		cutghostmulti[i][1] = MAX(cut,cuttype[i]);
		cutghostmulti[i][2] = MAX(cut,cuttype[i]);
		}
		}
		cut = MAX(neighbor->cutneighmax,cutghostuser);
		cutghost[0] = cutghost[1] = cutghost[2] = cut;


		if ((periodicity[0] && cut > prd[0]) \|\|
		(periodicity[1] && cut > prd[1]) \|\|
		(dimension == 3 && periodicity[2] && cut > prd[2]))
		@@ -261,6 +291,7 @@ void CommTiled::setup()
		grow_swap_send(iswap,nprocmax[iswap],oldmax);
		if (idir == 0) grow_swap_recv(iswap+1,nprocmax[iswap]);
		else grow_swap_recv(iswap-1,nprocmax[iswap]);

		}

		// overlap how has list of noverlap procs
		@@ -293,8 +324,8 @@ void CommTiled::setup()
		// if sbox touches other proc's sub-box boundaries in lower dims,
		// extend sbox in those lower dims to include ghost atoms

		double oboxlo[3],oboxhi[3],sbox[6];

		double oboxlo[3],oboxhi[3],sbox[6],sbox_multi[6];
		if (mode == Comm::SINGLE) {
		for (i = 0; i < noverlap; i++) {
		pbc_flag[iswap][i] = 0;
		pbc[iswap][i][0] = pbc[iswap][i][1] = pbc[iswap][i][2] =
		@@ -342,7 +373,65 @@ void CommTiled::setup()

		memcpy(sendbox[iswap][i],sbox,6*sizeof(double));
		}
		}
		else{
		for (i = 0; i < noverlap; i++) {


		pbc_flag[iswap][i] = 0;
		pbc[iswap][i][0] = pbc[iswap][i][1] = pbc[iswap][i][2] =
		pbc[iswap][i][3] = pbc[iswap][i][4] = pbc[iswap][i][5] = 0;

		(this->*box_other)(idim,idir,overlap[i],oboxlo,oboxhi);

		if (i < noverlap1) {
		sbox[0] = MAX(oboxlo[0],lo1[0]);
		sbox[1] = MAX(oboxlo[1],lo1[1]);
		sbox[2] = MAX(oboxlo[2],lo1[2]);
		sbox[3] = MIN(oboxhi[0],hi1[0]);
		sbox[4] = MIN(oboxhi[1],hi1[1]);
		sbox[5] = MIN(oboxhi[2],hi1[2]);
		} else {
		pbc_flag[iswap][i] = 1;
		if (idir == 0) pbc[iswap][i][idim] = 1;
		else pbc[iswap][i][idim] = -1;
		sbox[0] = MAX(oboxlo[0],lo2[0]);
		sbox[1] = MAX(oboxlo[1],lo2[1]);
		sbox[2] = MAX(oboxlo[2],lo2[2]);
		sbox[3] = MIN(oboxhi[0],hi2[0]);
		sbox[4] = MIN(oboxhi[1],hi2[1]);
		sbox[5] = MIN(oboxhi[2],hi2[2]);
		}
		for (int itype = 1; itype <= atom->ntypes; itype++) {
		sbox_multi[0] = sbox[0];
		sbox_multi[1] = sbox[1];
		sbox_multi[2] = sbox[2];
		sbox_multi[3] = sbox[3];
		sbox_multi[4] = sbox[4];
		sbox_multi[5] = sbox[5];
		if (idir == 0) {
		sbox_multi[idim] = sublo[idim];
		if (i < noverlap1) sbox_multi[3+idim] = MIN(sbox_multi[3+idim]+cutghostmulti[itype][idim],subhi[idim]);
		else sbox_multi[3+idim] = MIN(sbox_multi[3+idim]-prd[idim]+cutghostmulti[itype][idim],subhi[idim]);
		} else {
		if (i < noverlap1) sbox_multi[idim] = MAX(sbox_multi[idim]-cutghostmulti[itype][idim],sublo[idim]);
		else sbox_multi[idim] = MAX(sbox_multi[idim]+prd[idim]-cutghostmulti[itype][idim],sublo[idim]);
		sbox_multi[3+idim] = subhi[idim];
		}

		if (idim >= 1) {
		if (sbox_multi[0] == oboxlo[0]) sbox_multi[0] -= cutghostmulti[itype][idim];
		if (sbox_multi[3] == oboxhi[0]) sbox_multi[3] += cutghostmulti[itype][idim];
		}
		if (idim == 2) {
		if (sbox_multi[1] == oboxlo[1]) sbox_multi[1] -= cutghostmulti[itype][idim];
		if (sbox_multi[4] == oboxhi[1]) sbox_multi[4] += cutghostmulti[itype][idim];
		}

		memcpy(sendbox_multi[iswap][i][itype],sbox_multi,6*sizeof(double));
		}
		}
		}
		iswap++;
		}
		}
		@@ -765,6 +854,7 @@ void CommTiled::borders()
		double xlo,xhi,ylo,yhi,zlo,zhi;
		double *bbox;
		double **x;

		AtomVec *avec = atom->avec;

		// send/recv max one = max # of atoms in single send/recv for any swap
		@@ -790,6 +880,7 @@ void CommTiled::borders()

		ncountall = 0;
		for (m = 0; m < nsendproc[iswap]; m++) {
		if (mode == Comm::SINGLE) {
		bbox = sendbox[iswap][m];
		xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
		xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
		@@ -829,6 +920,58 @@ void CommTiled::borders()
		smaxone = MAX(smaxone,ncount);
		ncountall += ncount;
		}
		else{
		int* type=atom->type;
		int itype;
		ncount = 0;

		if (!bordergroup) {
		for (i = 0; i < nlast; i++) {
		itype=type[i];
		bbox = sendbox_multi[iswap][m][itype];
		xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
		xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
		if (x[i][0] >= xlo && x[i][0] < xhi &&
		x[i][1] >= ylo && x[i][1] < yhi &&
		x[i][2] >= zlo && x[i][2] < zhi) {
		if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
		sendlist[iswap][m][ncount++] = i;
		}

		}
		} else {
		ngroup = atom->nfirst;
		for (i = 0; i < ngroup; i++) {
		itype=type[i];
		bbox = sendbox_multi[iswap][m][itype];
		xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
		xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
		if (x[i][0] >= xlo && x[i][0] < xhi &&
		x[i][1] >= ylo && x[i][1] < yhi &&
		x[i][2] >= zlo && x[i][2] < zhi) {
		if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
		sendlist[iswap][m][ncount++] = i;
		}
		}
		for (i = atom->nlocal; i < nlast; i++) {
		itype=type[i];
		bbox = sendbox_multi[iswap][m][itype];
		xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
		xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
		if (x[i][0] >= xlo && x[i][0] < xhi &&
		x[i][1] >= ylo && x[i][1] < yhi &&
		x[i][2] >= zlo && x[i][2] < zhi) {
		if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
		sendlist[iswap][m][ncount++] = i;
		}
		}
		}

		sendnum[iswap][m] = ncount;
		smaxone = MAX(smaxone,ncount);
		ncountall += ncount;
		}
		}
		smaxall = MAX(smaxall,ncountall);

		// send sendnum counts to procs who recv from me except self
		@@ -1873,7 +2016,12 @@ void CommTiled::allocate_swap(int n)

		pbc_flag = new int*[n];
		pbc = new int**[n];
		//if(mode == SINGLE){
		sendbox = new double**[n];
		//}
		//else{
		sendbox_multi = new double***[n];
		//}
		maxsendlist = new int*[n];
		sendlist = new int**[n];

		@@ -1886,7 +2034,12 @@ void CommTiled::allocate_swap(int n)

		pbc_flag[i] = NULL;
		pbc[i] = NULL;
		//if(mode == SINGLE){
		sendbox[i] = NULL;
		// }
		//else{
		sendbox_multi[i] = NULL;
		//}
		maxsendlist[i] = NULL;
		sendlist[i] = NULL;
		}
		@@ -1933,8 +2086,14 @@ void CommTiled::grow_swap_send(int i, int n, int nold)
		pbc_flag[i] = new int[n];
		memory->destroy(pbc[i]);
		memory->create(pbc[i],n,6,"comm:pbc_flag");
		//if(mode == SINGLE){
		memory->destroy(sendbox[i]);
		memory->create(sendbox[i],n,6,"comm:sendbox");
		//}
		//else {
		memory->destroy(sendbox_multi[i]);
		memory->create(sendbox_multi[i],n,atom->ntypes+1,6,"comm:sendbox_multi");
		//}

		delete [] maxsendlist[i];
		maxsendlist[i] = new int[n];
		@@ -1992,7 +2151,12 @@ void CommTiled::deallocate_swap(int n)

		delete [] pbc_flag[i];
		memory->destroy(pbc[i]);
		//if(mode == Comm::SINGLE){
		memory->destroy(sendbox[i]);
		// }
		//else{
		memory->destroy(sendbox_multi[i]);
		// }
		delete [] maxsendlist[i];

		for (int j = 0; j < nprocmax[i]; j++) memory->destroy(sendlist[i][j]);
		@@ -2012,7 +2176,12 @@ void CommTiled::deallocate_swap(int n)

		delete [] pbc_flag;
		delete [] pbc;
		//if(mode == SINGLE){
		delete [] sendbox;
		// }
		//else{
		delete [] sendbox_multi;
		//}
		delete [] maxsendlist;
		delete [] sendlist;

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