git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
150
src/dump.cpp
150
src/dump.cpp
@ -5,7 +5,7 @@
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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@ -191,32 +191,32 @@ void Dump::init()
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int min = IBIG;
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int max = 0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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min = MIN(min,tag[i]);
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max = MAX(max,tag[i]);
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}
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if (mask[i] & groupbit) {
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min = MIN(min,tag[i]);
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max = MAX(max,tag[i]);
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}
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int minall,maxall;
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MPI_Allreduce(&min,&minall,1,MPI_INT,MPI_MIN,world);
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MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
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int isize = static_cast<int> (size);
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if (maxall-minall+1 == isize) {
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reorderflag = 1;
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double range = maxall-minall + EPSILON;
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idlo = static_cast<int> (range*me/nprocs + minall);
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int idhi = static_cast<int> (range*(me+1)/nprocs + minall);
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reorderflag = 1;
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double range = maxall-minall + EPSILON;
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idlo = static_cast<int> (range*me/nprocs + minall);
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int idhi = static_cast<int> (range*(me+1)/nprocs + minall);
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int lom1 = static_cast<int> ((idlo-1-minall)/range * nprocs);
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int lo = static_cast<int> ((idlo-minall)/range * nprocs);
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int him1 = static_cast<int> ((idhi-1-minall)/range * nprocs);
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int hi = static_cast<int> ((idhi-minall)/range * nprocs);
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if (me && me == lom1) idlo--;
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else if (me && me != lo) idlo++;
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if (me+1 == him1) idhi--;
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else if (me+1 != hi) idhi++;
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int lom1 = static_cast<int> ((idlo-1-minall)/range * nprocs);
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int lo = static_cast<int> ((idlo-minall)/range * nprocs);
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int him1 = static_cast<int> ((idhi-1-minall)/range * nprocs);
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int hi = static_cast<int> ((idhi-minall)/range * nprocs);
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if (me && me == lom1) idlo--;
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else if (me && me != lo) idlo++;
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if (me+1 == him1) idhi--;
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else if (me+1 != hi) idhi++;
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nme_reorder = idhi-idlo;
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ntotal_reorder = isize;
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nme_reorder = idhi-idlo;
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ntotal_reorder = isize;
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}
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}
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}
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@ -309,7 +309,7 @@ void Dump::write()
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else pack(NULL);
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if (sort_flag) sort();
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// multiproc = 1 = each proc writes own data to own file
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// multiproc = 1 = each proc writes own data to own file
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// multiproc = 0 = all procs write to one file thru proc 0
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// proc 0 pings each proc, receives it's data, writes to file
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// all other procs wait for ping, send their data to proc 0
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@ -322,18 +322,18 @@ void Dump::write()
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if (me == 0) {
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for (int iproc = 0; iproc < nprocs; iproc++) {
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if (iproc) {
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MPI_Irecv(buf,maxbuf*size_one,MPI_DOUBLE,iproc,0,world,&request);
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MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
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MPI_Wait(&request,&status);
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MPI_Get_count(&status,MPI_DOUBLE,&nlines);
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nlines /= size_one;
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} else nlines = nme;
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if (iproc) {
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MPI_Irecv(buf,maxbuf*size_one,MPI_DOUBLE,iproc,0,world,&request);
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MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
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MPI_Wait(&request,&status);
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MPI_Get_count(&status,MPI_DOUBLE,&nlines);
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nlines /= size_one;
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} else nlines = nme;
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write_data(nlines,buf);
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write_data(nlines,buf);
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}
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if (flush_flag) fflush(fp);
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} else {
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MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
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MPI_Rsend(buf,nme*size_one,MPI_DOUBLE,0,0,world);
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@ -374,9 +374,9 @@ void Dump::openfile()
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filecurrent = new char[strlen(filename) + 16];
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char *ptr = strchr(filename,'*');
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*ptr = '\0';
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if (padflag == 0)
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if (padflag == 0)
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sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
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filename,update->ntimestep,ptr+1);
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filename,update->ntimestep,ptr+1);
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else {
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char bif[8],pad[16];
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strcpy(bif,BIGINT_FORMAT);
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@ -433,8 +433,8 @@ void Dump::sort()
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memory->destroy(index);
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memory->create(index,maxsort,"dump:index");
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if (sortcol == 0) {
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memory->destroy(idsort);
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memory->create(idsort,maxsort,"dump:idsort");
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memory->destroy(idsort);
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memory->create(idsort,maxsort,"dump:idsort");
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}
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}
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@ -449,7 +449,7 @@ void Dump::sort()
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}
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// if multiple procs, exchange datums between procs via irregular
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} else {
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// grow proclist if necessary
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@ -459,32 +459,32 @@ void Dump::sort()
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memory->destroy(proclist);
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memory->create(proclist,maxproc,"dump:proclist");
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}
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// proclist[i] = which proc Ith datum will be sent to
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if (sortcol == 0) {
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int min = IBIG;
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int max = 0;
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for (i = 0; i < nme; i++) {
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min = MIN(min,ids[i]);
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max = MAX(max,ids[i]);
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min = MIN(min,ids[i]);
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max = MAX(max,ids[i]);
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}
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int minall,maxall;
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MPI_Allreduce(&min,&minall,1,MPI_INT,MPI_MIN,world);
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MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
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double range = maxall-minall + EPSILON;
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for (i = 0; i < nme; i++) {
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iproc = static_cast<int> ((ids[i]-minall)/range * nprocs);
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proclist[i] = iproc;
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iproc = static_cast<int> ((ids[i]-minall)/range * nprocs);
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proclist[i] = iproc;
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}
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} else {
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double min = BIG;
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double max = -BIG;
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for (i = 0; i < nme; i++) {
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value = buf[i*size_one + sortcolm1];
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min = MIN(min,value);
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max = MAX(max,value);
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value = buf[i*size_one + sortcolm1];
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min = MIN(min,value);
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max = MAX(max,value);
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}
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double minall,maxall;
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MPI_Allreduce(&min,&minall,1,MPI_DOUBLE,MPI_MIN,world);
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@ -492,9 +492,9 @@ void Dump::sort()
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double range = maxall-minall + EPSILON*(maxall-minall);
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if (range == 0.0) range = EPSILON;
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for (i = 0; i < nme; i++) {
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value = buf[i*size_one + sortcolm1];
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iproc = static_cast<int> ((value-minall)/range * nprocs);
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proclist[i] = iproc;
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value = buf[i*size_one + sortcolm1];
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iproc = static_cast<int> ((value-minall)/range * nprocs);
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proclist[i] = iproc;
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}
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}
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@ -511,14 +511,14 @@ void Dump::sort()
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memory->destroy(index);
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memory->create(index,maxsort,"dump:index");
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if (sortcol == 0) {
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memory->destroy(idsort);
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memory->create(idsort,maxsort,"dump:idsort");
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memory->destroy(idsort);
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memory->create(idsort,maxsort,"dump:idsort");
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}
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}
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irregular->exchange_data((char *) buf,size_one*sizeof(double),
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(char *) bufsort);
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if (sortcol == 0)
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(char *) bufsort);
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if (sortcol == 0)
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irregular->exchange_data((char *) ids,sizeof(int),(char *) idsort);
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irregular->destroy_data();
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}
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@ -537,7 +537,7 @@ void Dump::sort()
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if (reorderflag)
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for (i = 0; i < nme; i++)
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index[idsort[i]-idlo] = i;
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index[idsort[i]-idlo] = i;
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}
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if (!reorderflag) {
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@ -562,7 +562,7 @@ void Dump::sort()
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}
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// copy data from bufsort to buf using index
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int nbytes = size_one*sizeof(double);
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for (i = 0; i < nme; i++)
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memcpy(&buf[i*size_one],&bufsort[index[i]*size_one],nbytes);
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@ -649,17 +649,17 @@ void Dump::modify_params(int narg, char **arg)
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if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
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int idump;
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for (idump = 0; idump < output->ndump; idump++)
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if (strcmp(id,output->dump[idump]->id) == 0) break;
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if (strcmp(id,output->dump[idump]->id) == 0) break;
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int n;
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if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
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delete [] output->var_dump[idump];
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n = strlen(&arg[iarg+1][2]) + 1;
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output->var_dump[idump] = new char[n];
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strcpy(output->var_dump[idump],&arg[iarg+1][2]);
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n = 0;
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delete [] output->var_dump[idump];
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n = strlen(&arg[iarg+1][2]) + 1;
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output->var_dump[idump] = new char[n];
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strcpy(output->var_dump[idump],&arg[iarg+1][2]);
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n = 0;
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} else {
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n = atoi(arg[iarg+1]);
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if (n <= 0) error->all(FLERR,"Illegal dump_modify command");
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n = atoi(arg[iarg+1]);
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if (n <= 0) error->all(FLERR,"Illegal dump_modify command");
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}
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output->every_dump[idump] = n;
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iarg += 2;
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@ -680,9 +680,9 @@ void Dump::modify_params(int narg, char **arg)
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delete [] format_user;
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format_user = NULL;
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if (strcmp(arg[iarg+1],"none")) {
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int n = strlen(arg[iarg+1]) + 1;
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format_user = new char[n];
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strcpy(format_user,arg[iarg+1]);
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int n = strlen(arg[iarg+1]) + 1;
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format_user = new char[n];
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strcpy(format_user,arg[iarg+1]);
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}
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iarg += 2;
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} else if (strcmp(arg[iarg],"pad") == 0) {
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@ -694,19 +694,19 @@ void Dump::modify_params(int narg, char **arg)
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if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
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if (strcmp(arg[iarg+1],"off") == 0) sort_flag = 0;
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else if (strcmp(arg[iarg+1],"id") == 0) {
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sort_flag = 1;
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sortcol = 0;
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sortorder = ASCEND;
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sort_flag = 1;
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sortcol = 0;
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sortorder = ASCEND;
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} else {
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sort_flag = 1;
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sortcol = atoi(arg[iarg+1]);
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sortorder = ASCEND;
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if (sortcol == 0) error->all(FLERR,"Illegal dump_modify command");
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if (sortcol < 0) {
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sortorder = DESCEND;
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sortcol = -sortcol;
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}
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sortcolm1 = sortcol - 1;
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sort_flag = 1;
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sortcol = atoi(arg[iarg+1]);
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sortorder = ASCEND;
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if (sortcol == 0) error->all(FLERR,"Illegal dump_modify command");
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if (sortcol < 0) {
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sortorder = DESCEND;
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sortcol = -sortcol;
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}
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sortcolm1 = sortcol - 1;
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}
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iarg += 2;
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} else {
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