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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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44
src/irregular.cpp
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@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -121,16 +121,16 @@ void Irregular::migrate_atoms()
int i = 0;
while (i < nlocal) {
if (x[i][0] < sublo[0] || x[i][0] >= subhi[0] ||
x[i][1] < sublo[1] || x[i][1] >= subhi[1] ||
x[i][2] < sublo[2] || x[i][2] >= subhi[2]) {
x[i][1] < sublo[1] || x[i][1] >= subhi[1] ||
x[i][2] < sublo[2] || x[i][2] >= subhi[2]) {
proclist[nsendatom] = coord2proc(x[i]);
if (proclist[nsendatom] != me) {
if (nsend > maxsend) grow_send(nsend,1);
sizes[nsendatom] = avec->pack_exchange(i,&buf_send[nsend]);
nsend += sizes[nsendatom];
nsendatom++;
avec->copy(nlocal-1,i,1);
nlocal--;
if (nsend > maxsend) grow_send(nsend,1);
sizes[nsendatom] = avec->pack_exchange(i,&buf_send[nsend]);
nsend += sizes[nsendatom];
nsendatom++;
avec->copy(nlocal-1,i,1);
nlocal--;
} else i++;
} else i++;
}
@ -285,7 +285,7 @@ int Irregular::create_atom(int n, int *sizes, int *proclist)
delete [] count;
delete [] list;
// initialize plan
aplan->nsend = nsend;
@ -322,7 +322,7 @@ void Irregular::exchange_atom(double *sendbuf, int *sizes, double *recvbuf)
offset = 0;
for (int irecv = 0; irecv < aplan->nrecv; irecv++) {
MPI_Irecv(&recvbuf[offset],aplan->length_recv[irecv],MPI_DOUBLE,
aplan->proc_recv[irecv],0,world,&aplan->request[irecv]);
aplan->proc_recv[irecv],0,world,&aplan->request[irecv]);
offset += aplan->length_recv[irecv];
}
@ -345,12 +345,12 @@ void Irregular::exchange_atom(double *sendbuf, int *sizes, double *recvbuf)
for (i = 0; i < num_send; i++) {
m = index_send[n++];
memcpy(&buf[offset],&sendbuf[aplan->offset_send[m]],
sizes[m]*sizeof(double));
sizes[m]*sizeof(double));
offset += sizes[m];
}
MPI_Send(buf,aplan->length_send[isend],MPI_DOUBLE,
aplan->proc_send[isend],0,world);
}
aplan->proc_send[isend],0,world);
}
// free temporary send buffer
@ -507,7 +507,7 @@ int Irregular::create_data(int n, int *proclist)
delete [] count;
delete [] list;
// initialize plan and return it
dplan->nsend = nsend;
@ -544,7 +544,7 @@ void Irregular::exchange_data(char *sendbuf, int nbytes, char *recvbuf)
offset = dplan->num_self*nbytes;
for (int irecv = 0; irecv < dplan->nrecv; irecv++) {
MPI_Irecv(&recvbuf[offset],dplan->num_recv[irecv]*nbytes,MPI_CHAR,
dplan->proc_recv[irecv],0,world,&dplan->request[irecv]);
dplan->proc_recv[irecv],0,world,&dplan->request[irecv]);
offset += dplan->num_recv[irecv]*nbytes;
}
@ -568,8 +568,8 @@ void Irregular::exchange_data(char *sendbuf, int nbytes, char *recvbuf)
memcpy(&buf[i*nbytes],&sendbuf[m*nbytes],nbytes);
}
MPI_Send(buf,dplan->num_send[isend]*nbytes,MPI_CHAR,
dplan->proc_send[isend],0,world);
}
dplan->proc_send[isend],0,world);
}
// free temporary send buffer
@ -622,8 +622,8 @@ int Irregular::coord2proc(double *x)
if (uniform) {
if (triclinic == 0) {
loc[0] = static_cast<int> (procgrid[0] * (x[0]-boxlo[0]) / prd[0]);
loc[1] = static_cast<int> (procgrid[1] * (x[1]-boxlo[1]) / prd[1]);
loc[2] = static_cast<int> (procgrid[2] * (x[2]-boxlo[2]) / prd[2]);
loc[1] = static_cast<int> (procgrid[1] * (x[1]-boxlo[1]) / prd[1]);
loc[2] = static_cast<int> (procgrid[2] * (x[2]-boxlo[2]) / prd[2]);
} else {
loc[0] = static_cast<int> (procgrid[0] * x[0]);
loc[1] = static_cast<int> (procgrid[1] * x[1]);
@ -683,7 +683,7 @@ int Irregular::binary(double value, int n, double *vec)
}
/* ----------------------------------------------------------------------
realloc the size of the send buffer as needed with BUFFACTOR & BUFEXTRA
realloc the size of the send buffer as needed with BUFFACTOR & BUFEXTRA
if flag = 1, realloc
if flag = 0, don't need to realloc with copy, just free/malloc
------------------------------------------------------------------------- */
@ -700,7 +700,7 @@ void Irregular::grow_send(int n, int flag)
}
/* ----------------------------------------------------------------------
free/malloc the size of the recv buffer as needed with BUFFACTOR
free/malloc the size of the recv buffer as needed with BUFFACTOR
------------------------------------------------------------------------- */
void Irregular::grow_recv(int n)