git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@399 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
84
src/comm.cpp
84
src/comm.cpp
@ -171,11 +171,12 @@ void Comm::set_procs()
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void Comm::setup()
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{
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// cutcomm = distance at which ghost atoms need to be acquired
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// for orthogonal, cutcomm = box coords = cutneigh in all 3 dims
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// for triclinic, cutneigh = distance between tilted planes in box coords
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// cutcomm = lamda coords = distance between those same planes
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// can be different for each dim
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// cutghost = distance at which ghost atoms need to be acquired
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// for orthogonal:
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// cutghost is in box coords = neigh->cutghost in all 3 dims
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// for triclinic:
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// neigh->cutghost = distance between tilted planes in box coords
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// cutghost is in lamda coords = distance between those planes
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double *prd,*prd_border,*sublo,*subhi;
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@ -183,7 +184,7 @@ void Comm::setup()
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prd = prd_border = domain->prd;
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sublo = domain->sublo;
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subhi = domain->subhi;
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cutcomm[0] = cutcomm[1] = cutcomm[2] = neighbor->cutneigh;
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cutghost[0] = cutghost[1] = cutghost[2] = neighbor->cutghost;
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} else {
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prd = domain->prd;
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prd_border = domain->prd_lamda;
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@ -192,19 +193,19 @@ void Comm::setup()
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double *h_inv = domain->h_inv;
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double length;
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length = sqrt(h_inv[0]*h_inv[0] + h_inv[5]*h_inv[5] + h_inv[4]*h_inv[4]);
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cutcomm[0] = neighbor->cutneigh * length;
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cutghost[0] = neighbor->cutghost * length;
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length = sqrt(h_inv[1]*h_inv[1] + h_inv[3]*h_inv[3]);
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cutcomm[1] = neighbor->cutneigh * length;
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cutghost[1] = neighbor->cutghost * length;
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length = h_inv[2];
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cutcomm[2] = neighbor->cutneigh * length;
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cutghost[2] = neighbor->cutghost * length;
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}
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// need = # of procs I need atoms from in each dim
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// for 2d, don't communicate in z
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need[0] = static_cast<int> (cutcomm[0] * procgrid[0] / prd_border[0]) + 1;
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need[1] = static_cast<int> (cutcomm[1] * procgrid[1] / prd_border[1]) + 1;
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need[2] = static_cast<int> (cutcomm[2] * procgrid[2] / prd_border[2]) + 1;
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need[0] = static_cast<int> (cutghost[0] * procgrid[0] / prd_border[0]) + 1;
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need[1] = static_cast<int> (cutghost[1] * procgrid[1] / prd_border[1]) + 1;
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need[2] = static_cast<int> (cutghost[2] * procgrid[2] / prd_border[2]) + 1;
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if (force->dimension == 2) need[2] = 0;
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// if non-periodic, do not communicate further than procgrid-1 away
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@ -230,8 +231,8 @@ void Comm::setup()
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// set slablo > slabhi for swaps across non-periodic boundaries
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// this insures no atoms are swapped
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// only for procs owning sub-box at non-periodic end of global box
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// pbc_flag: 0 = not across a boundary, 1 = yes across a boundary
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// pbc_dist/border: factors to add to atom coords across PBC for comm/borders
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// pbc_flag: 0 = nothing across a boundary, 1 = somthing across a boundary
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// pbc = -1/0/1 for PBC factor in each of 3/6 orthog/triclinic dirs
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// for triclinic, slablo/hi and pbc_border will be used in lamda (0-1) coords
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// 1st part of if statement is sending to the west/south/down
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// 2nd part of if statement is sending to the east/north/up
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@ -240,36 +241,31 @@ void Comm::setup()
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for (int dim = 0; dim < 3; dim++) {
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for (int ineed = 0; ineed < 2*need[dim]; ineed++) {
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pbc_flag[iswap] = 0;
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pbc_dist[iswap][0] = pbc_dist[iswap][1] = pbc_dist[iswap][2] = 0.0;
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pbc_dist_border[iswap][0] = pbc_dist_border[iswap][1] =
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pbc_dist_border[iswap][2] = 0.0;
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pbc[iswap][0] = pbc[iswap][1] = pbc[iswap][2] =
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pbc[iswap][3] = pbc[iswap][4] = pbc[iswap][5] = 0;
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if (ineed % 2 == 0) {
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sendproc[iswap] = procneigh[dim][0];
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recvproc[iswap] = procneigh[dim][1];
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if (ineed < 2) slablo[iswap] = -BIG;
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else slablo[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
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slabhi[iswap] = sublo[dim] + cutcomm[dim];
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slabhi[iswap] = sublo[dim] + cutghost[dim];
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if (myloc[dim] == 0) {
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if (periodicity[dim] == 0)
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slabhi[iswap] = slablo[iswap] - 1.0;
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else {
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pbc_flag[iswap] = 1;
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pbc_dist[iswap][dim] = prd[dim];
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pbc_dist_border[iswap][dim] = prd_border[dim];
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pbc[iswap][dim] = 1;
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if (triclinic) {
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if (dim == 1) pbc_dist[iswap][0] += domain->xy;
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else if (dim == 2) {
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pbc_dist[iswap][0] += domain->xz;
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pbc_dist[iswap][1] += domain->yz;
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}
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if (dim == 1) pbc[iswap][5] = 1;
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else if (dim == 2) pbc[iswap][4] = pbc[iswap][3] = 1;
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}
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}
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}
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} else {
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sendproc[iswap] = procneigh[dim][1];
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recvproc[iswap] = procneigh[dim][0];
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slablo[iswap] = subhi[dim] - cutcomm[dim];
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slablo[iswap] = subhi[dim] - cutghost[dim];
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if (ineed < 2) slabhi[iswap] = BIG;
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else slabhi[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
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if (myloc[dim] == procgrid[dim]-1) {
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@ -277,14 +273,10 @@ void Comm::setup()
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slabhi[iswap] = slablo[iswap] - 1.0;
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else {
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pbc_flag[iswap] = 1;
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pbc_dist[iswap][dim] = -prd[dim];
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pbc_dist_border[iswap][dim] = -prd_border[dim];
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pbc[iswap][dim] = -1;
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if (triclinic) {
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if (dim == 1) pbc_dist[iswap][0] -= domain->xy;
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else if (dim == 2) {
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pbc_dist[iswap][0] -= domain->xz;
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pbc_dist[iswap][1] -= domain->yz;
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}
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if (dim == 1) pbc[iswap][5] = -1;
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else if (dim == 2) pbc[iswap][4] = pbc[iswap][3] = -1;
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}
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}
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}
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@ -321,14 +313,14 @@ void Comm::communicate()
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MPI_Irecv(buf,size_comm_recv[iswap],MPI_DOUBLE,
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recvproc[iswap],0,world,&request);
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n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
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buf_send,pbc_flag[iswap],pbc_dist[iswap]);
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buf_send,pbc_flag[iswap],pbc[iswap]);
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MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
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MPI_Wait(&request,&status);
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} else {
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MPI_Irecv(buf_recv,size_comm_recv[iswap],MPI_DOUBLE,
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recvproc[iswap],0,world,&request);
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n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
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buf_send,pbc_flag[iswap],pbc_dist[iswap]);
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buf_send,pbc_flag[iswap],pbc[iswap]);
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MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
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MPI_Wait(&request,&status);
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avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv);
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@ -338,11 +330,10 @@ void Comm::communicate()
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if (comm_x_only) {
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if (sendnum[iswap])
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n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
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x[firstrecv[iswap]],
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pbc_flag[iswap],pbc_dist[iswap]);
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x[firstrecv[iswap]],pbc_flag[iswap],pbc[iswap]);
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} else {
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n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
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buf_send,pbc_flag[iswap],pbc_dist[iswap]);
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buf_send,pbc_flag[iswap],pbc[iswap]);
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avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_send);
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}
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}
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@ -567,8 +558,8 @@ void Comm::borders()
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if (nsend*size_border > maxsend)
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grow_send(nsend*size_border,0);
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n = avec->pack_border(nsend,sendlist[iswap],buf_send,
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pbc_flag[iswap],pbc_dist_border[iswap]);
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pbc_flag[iswap],pbc[iswap]);
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// swap atoms with other proc
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// put incoming ghosts at end of my atom arrays
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// if swapping with self, simply copy, no messages
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@ -635,7 +626,7 @@ void Comm::comm_pair(Pair *pair)
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// pack buffer
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n = pair->pack_comm(sendnum[iswap],sendlist[iswap],
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buf_send,pbc_flag[iswap],pbc_dist[iswap]);
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buf_send,pbc_flag[iswap],pbc[iswap]);
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// exchange with another proc
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// if self, set recv buffer to send buffer
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@ -704,7 +695,7 @@ void Comm::comm_fix(Fix *fix)
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// pack buffer
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n = fix->pack_comm(sendnum[iswap],sendlist[iswap],
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buf_send,pbc_flag[iswap],pbc_dist[iswap]);
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buf_send,pbc_flag[iswap],pbc[iswap]);
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// exchange with another proc
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// if self, set recv buffer to send buffer
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@ -773,7 +764,7 @@ void Comm::comm_compute(Compute *compute)
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// pack buffer
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n = compute->pack_comm(sendnum[iswap],sendlist[iswap],
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buf_send,pbc_flag[iswap],pbc_dist[iswap]);
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buf_send,pbc_flag[iswap],pbc[iswap]);
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// exchange with another proc
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// if self, set recv buffer to send buffer
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@ -980,9 +971,7 @@ void Comm::allocate_swap(int n)
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slabhi = (double *) memory->smalloc(n*sizeof(double),"comm:slabhi");
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firstrecv = (int *) memory->smalloc(n*sizeof(int),"comm:firstrecv");
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pbc_flag = (int *) memory->smalloc(n*sizeof(int),"comm:pbc_flag");
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pbc_dist = (double **) memory->create_2d_double_array(n,3,"comm:pbc_dist");
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pbc_dist_border = (double **)
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memory->create_2d_double_array(n,3,"comm:pbc_dist_border");
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pbc = (int **) memory->create_2d_int_array(n,6,"comm:pbc");
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}
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/* ----------------------------------------------------------------------
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@ -1002,8 +991,7 @@ void Comm::free_swap()
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memory->sfree(slabhi);
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memory->sfree(firstrecv);
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memory->sfree(pbc_flag);
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memory->destroy_2d_double_array(pbc_dist);
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memory->destroy_2d_double_array(pbc_dist_border);
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memory->destroy_2d_int_array(pbc);
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}
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/* ----------------------------------------------------------------------
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