a few bug fixes for support for multi and triclinic in CommTiled (304d6876) · Commits · 郑智淋 / lammps

src/atom_vec.cpp

+4 −2

Original line number	Diff line number	Diff line
		@@ -1096,8 +1096,9 @@ void AtomVec::unpack_border(int n, int first, double *buf)

		m = 0;
		last = first + n;
		while (last > nmax) grow(0);

		for (i = first; i < last; i++) {
		if (i == nmax) grow(0);
		x[i][0] = buf[m++];
		x[i][1] = buf[m++];
		x[i][2] = buf[m++];
		@@ -1165,8 +1166,9 @@ void AtomVec::unpack_border_vel(int n, int first, double *buf)

		m = 0;
		last = first + n;
		while (last > nmax) grow(0);

		for (i = first; i < last; i++) {
		if (i == nmax) grow(0);
		x[i][0] = buf[m++];
		x[i][1] = buf[m++];
		x[i][2] = buf[m++];

src/comm_tiled.cpp

+37 −31

Original line number	Diff line number	Diff line
		@@ -12,7 +12,8 @@
		------------------------------------------------------------------------- */

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

		#include "comm_tiled.h"
		@@ -99,7 +100,6 @@ void CommTiled::init_buffers()
		sendbox_multi = NULL;

		maxswap = 6;
		nswap = 2*domain->dimension;
		allocate_swap(maxswap);
		}

		@@ -109,6 +109,11 @@ void CommTiled::init()
		{
		Comm::init();

		// cannot set nswap in init_buffers() b/c
		// dimension command can be after comm_style command

		nswap = 2*domain->dimension;

		memory->destroy(cutghostmulti);
		if (mode == Comm::MULTI)
		memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti");
		@@ -374,21 +379,23 @@ void CommTiled::setup()

		if (idir == 0) {
		sbox[idim] = sublo[idim];
		if (i < noverlap1) sbox[3+idim] = MIN(sbox[3+idim]+cut,subhi[idim]);
		else sbox[3+idim] = MIN(sbox[3+idim]-prd[idim]+cut,subhi[idim]);
		if (i < noverlap1)
		sbox[3+idim] = MIN(sbox[3+idim]+cutghost[idim],subhi[idim]);
		else
		sbox[3+idim] = MIN(sbox[3+idim]-prd[idim]+cutghost[idim],subhi[idim]);
		} else {
		if (i < noverlap1) sbox[idim] = MAX(sbox[idim]-cut,sublo[idim]);
		else sbox[idim] = MAX(sbox[idim]+prd[idim]-cut,sublo[idim]);
		if (i < noverlap1) sbox[idim] = MAX(sbox[idim]-cutghost[idim],sublo[idim]);
		else sbox[idim] = MAX(sbox[idim]+prd[idim]-cutghost[idim],sublo[idim]);
		sbox[3+idim] = subhi[idim];
		}

		if (idim >= 1) {
		if (sbox[0] == oboxlo[0]) sbox[0] -= cut;
		if (sbox[3] == oboxhi[0]) sbox[3] += cut;
		if (sbox[0] == oboxlo[0]) sbox[0] -= cutghost[0];
		if (sbox[3] == oboxhi[0]) sbox[3] += cutghost[0];
		}
		if (idim == 2) {
		if (sbox[1] == oboxlo[1]) sbox[1] -= cut;
		if (sbox[4] == oboxhi[1]) sbox[4] += cut;
		if (sbox[1] == oboxlo[1]) sbox[1] -= cutghost[1];
		if (sbox[4] == oboxhi[1]) sbox[4] += cutghost[1];
		}

		memcpy(sendbox[iswap][i],sbox,6*sizeof(double));
		@@ -1074,9 +1081,8 @@ void CommTiled::borders()
		if (rmaxallsize_border > maxrecv) grow_recv(rmaxallsize_border);

		// swap atoms with other procs using pack_border(), unpack_border()
		// use Waitall() instead of Waitany() because calls to unpack_border()
		// must increment per-atom arrays in ascending order
		// For the same reason, sendself unpacks must occur after recvother unpacks
		// can use Waitany() because calls to unpack_border()
		// increment per-atom arrays as much as needed

		if (ghost_velocity) {
		if (recvother[iswap]) {
		@@ -1092,13 +1098,6 @@ void CommTiled::borders()
		MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap][m],0,world);
		}
		}
		if (recvother[iswap]) {
		MPI_Waitall(nrecv,requests,MPI_STATUS_IGNORE);
		for (m = 0; m < nrecv; m++)
		avec->unpack_border_vel(recvnum[iswap][m],firstrecv[iswap][m],
		&buf_recv[size_border*
		forward_recv_offset[iswap][m]]);
		}
		if (sendself[iswap]) {
		avec->pack_border_vel(sendnum[iswap][nsend],sendlist[iswap][nsend],
		buf_send,pbc_flag[iswap][nsend],
		@@ -1106,6 +1105,14 @@ void CommTiled::borders()
		avec->unpack_border_vel(recvnum[iswap][nrecv],firstrecv[iswap][nrecv],
		buf_send);
		}
		if (recvother[iswap]) {
		for (i = 0; i < nrecv; i++) {
		MPI_Waitany(nrecv,requests,&m,MPI_STATUS_IGNORE);
		avec->unpack_border_vel(recvnum[iswap][m],firstrecv[iswap][m],
		&buf_recv[size_border*
		forward_recv_offset[iswap][m]]);
		}
		}

		} else {
		if (recvother[iswap]) {
		@@ -1121,19 +1128,20 @@ void CommTiled::borders()
		MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap][m],0,world);
		}
		}
		if (recvother[iswap]) {
		MPI_Waitall(nrecv,requests,MPI_STATUS_IGNORE);
		for (m = 0; m < nrecv; m++)
		avec->unpack_border(recvnum[iswap][m],firstrecv[iswap][m],
		&buf_recv[size_border*
		forward_recv_offset[iswap][m]]);
		}
		if (sendself[iswap]) {
		avec->pack_border(sendnum[iswap][nsend],sendlist[iswap][nsend],
		buf_send,pbc_flag[iswap][nsend],pbc[iswap][nsend]);
		avec->unpack_border(recvnum[iswap][nrecv],firstrecv[iswap][nrecv],
		buf_send);
		}
		if (recvother[iswap]) {
		for (i = 0; i < nrecv; i++) {
		MPI_Waitany(nrecv,requests,&m,MPI_STATUS_IGNORE);
		avec->unpack_border(recvnum[iswap][m],firstrecv[iswap][m],
		&buf_recv[size_border*
		forward_recv_offset[iswap][m]]);
		}
		}
		}

		// increment ghost atoms
		@@ -1636,11 +1644,9 @@ int CommTiled::exchange_variable(int n, double * /inbuf/, double & /outbuf*/

		void CommTiled::box_drop_brick(int idim, double lo, double hi, int &indexme)
		{
		// NOTE: this is not triclinic compatible
		// NOTE: these error messages are internal sanity checks
		// should not occur, can be removed at some point
		int dir;
		int index = -1;

		int index=-1,dir;
		if (hi[idim] == sublo[idim]) {
		index = myloc[idim] - 1;
		dir = -1;

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