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lammps/src/dump.cpp
Stan Moore f45663bfc2 Simplify loop structure to fix issues
2022-02-04 11:45:28 -08:00

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// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "dump.h"
#include "atom.h"
#include "compute.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "group.h"
#include "irregular.h"
#include "memory.h"
#include "modify.h"
#include "output.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
#if defined(LMP_QSORT)
// allocate space for static class variable
Dump *Dump::dumpptr;
#endif
#define BIG 1.0e20
#define EPSILON 1.0e-6
enum{ASCEND,DESCEND};
/* ---------------------------------------------------------------------- */
Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
id = utils::strdup(arg[0]);
igroup = group->find(arg[1]);
groupbit = group->bitmask[igroup];
style = utils::strdup(arg[2]);
filename = utils::strdup(arg[4]);
comm_forward = comm_reverse = 0;
first_flag = 0;
flush_flag = 1;
format = nullptr;
format_default = nullptr;
format_line_user = nullptr;
format_float_user = nullptr;
format_int_user = nullptr;
format_bigint_user = nullptr;
format_column_user = nullptr;
refreshflag = 0;
refresh = nullptr;
clearstep = 0;
sort_flag = 0;
balance_flag = 0;
append_flag = 0;
buffer_allow = 0;
buffer_flag = 0;
padflag = 0;
pbcflag = 0;
time_flag = 0;
unit_flag = 0;
unit_count = 0;
delay_flag = 0;
write_header_flag = 1;
maxfiles = -1;
numfiles = 0;
fileidx = 0;
nameslist = nullptr;
maxbuf = maxids = maxsort = maxproc = 0;
buf = bufsort = nullptr;
ids = idsort = nullptr;
index = proclist = nullptr;
irregular = nullptr;
maxsbuf = 0;
sbuf = nullptr;
maxpbc = -1;
xpbc = vpbc = nullptr;
imagepbc = nullptr;
// parse filename for special syntax
// if contains '%', write one file per proc and replace % with proc-ID
// if contains '*', write one file per timestep and replace * with timestep
// check file suffixes
// if ends in .bin -> binary file
// else if ends in .gz or other known extensions -> compressed text file
// else ASCII text file
fp = nullptr;
singlefile_opened = 0;
compressed = 0;
binary = 0;
multifile = 0;
multiproc = 0;
nclusterprocs = nprocs;
filewriter = 0;
if (me == 0) filewriter = 1;
fileproc = 0;
multiname = nullptr;
char *ptr;
if ((ptr = strchr(filename,'%'))) {
if (strstr(style,"mpiio"))
error->all(FLERR,"Dump file MPI-IO output not allowed with % in filename");
multiproc = 1;
nclusterprocs = 1;
filewriter = 1;
fileproc = me;
MPI_Comm_split(world,me,0,&clustercomm);
*ptr = '\0';
multiname = utils::strdup(fmt::format("{}{}{}", filename, me, ptr+1));
*ptr = '%';
}
if (strchr(filename,'*')) multifile = 1;
if (utils::strmatch(filename, "\\.bin$")) binary = 1;
if (platform::has_compress_extension(filename)) compressed = 1;
}
/* ---------------------------------------------------------------------- */
Dump::~Dump()
{
delete [] id;
delete [] style;
delete [] filename;
delete [] multiname;
delete [] format;
delete [] format_default;
delete [] format_line_user;
delete [] format_float_user;
delete [] format_int_user;
delete [] format_bigint_user;
delete [] refresh;
// format_column_user is deallocated by child classes that use it
memory->destroy(buf);
memory->destroy(bufsort);
memory->destroy(ids);
memory->destroy(idsort);
memory->destroy(index);
memory->destroy(proclist);
delete irregular;
memory->destroy(sbuf);
if (pbcflag) {
memory->destroy(xpbc);
memory->destroy(vpbc);
memory->destroy(imagepbc);
}
if (multiproc) MPI_Comm_free(&clustercomm);
// delete storage for caching file names
if (maxfiles > 0) {
for (int idx=0; idx < numfiles; ++idx)
delete[] nameslist[idx];
delete[] nameslist;
}
// XTC style sets fp to a null pointer since it closes file in its destructor
if (multifile == 0 && fp != nullptr) {
if (compressed) {
if (filewriter) platform::pclose(fp);
} else {
if (filewriter) fclose(fp);
}
fp = nullptr;
}
}
/* ---------------------------------------------------------------------- */
void Dump::init()
{
init_style();
if (!sort_flag) {
memory->destroy(bufsort);
memory->destroy(ids);
memory->destroy(idsort);
memory->destroy(index);
memory->destroy(proclist);
delete irregular;
maxids = maxsort = maxproc = 0;
bufsort = nullptr;
ids = idsort = nullptr;
index = proclist = nullptr;
irregular = nullptr;
}
if (sort_flag) {
if (multiproc > 1)
error->all(FLERR,
"Cannot dump sort when 'nfile' or 'fileper' keywords are set to non-default values");
if (sortcol == 0 && atom->tag_enable == 0)
error->all(FLERR,"Cannot dump sort on atom IDs with no atom IDs defined");
if (sortcol && sortcol > size_one)
error->all(FLERR,"Dump sort column is invalid");
if (nprocs > 1 && irregular == nullptr)
irregular = new Irregular(lmp);
bigint size = group->count(igroup);
// set reorderflag = 1 if can simply reorder local atoms rather than sort
// criteria: sorting by ID, atom IDs are consecutive from 1 to Natoms
// min/max IDs of group match size of group
// compute ntotal_reorder, nme_reorder, idlo/idhi to test against later
reorderflag = 0;
int gcmcflag = 0;
for (const auto &fix : modify->get_fix_list())
if (utils::strmatch(fix->style,"^gcmc"))
gcmcflag = 1;
if (sortcol == 0 && atom->tag_consecutive() && !gcmcflag) {
tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
tagint min = MAXTAGINT;
tagint max = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
min = MIN(min,tag[i]);
max = MAX(max,tag[i]);
}
tagint minall,maxall;
MPI_Allreduce(&min,&minall,1,MPI_LMP_TAGINT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (maxall-minall+1 == size) {
reorderflag = 1;
double range = maxall-minall + EPSILON;
idlo = static_cast<tagint> (range*me/nprocs + minall);
tagint idhi = static_cast<tagint> (range*(me+1)/nprocs + minall);
tagint lom1 = static_cast<tagint> ((idlo-1-minall)/range * nprocs);
tagint lo = static_cast<tagint> ((idlo-minall)/range * nprocs);
tagint him1 = static_cast<tagint> ((idhi-1-minall)/range * nprocs);
tagint hi = static_cast<tagint> ((idhi-minall)/range * nprocs);
if (me && me == lom1) idlo--;
else if (me && me != lo) idlo++;
if (me+1 == him1) idhi--;
else if (me+1 != hi) idhi++;
nme_reorder = idhi-idlo;
ntotal_reorder = size;
}
}
}
// search for refresh compute specified by dump_modify refresh
if (refreshflag) {
int icompute;
for (icompute = 0; icompute < modify->ncompute; icompute++)
if (strcmp(refresh,modify->compute[icompute]->id) == 0) break;
if (icompute < modify->ncompute) irefresh = icompute;
else error->all(FLERR,"Dump could not find refresh compute ID");
}
// preallocation for PBC copies if requested
if (pbcflag && atom->nlocal > maxpbc) pbc_allocate();
}
/* ---------------------------------------------------------------------- */
int Dump::count()
{
if (igroup == 0) return atom->nlocal;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int m = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) m++;
return m;
}
/* ---------------------------------------------------------------------- */
void Dump::write()
{
imageint *imagehold;
double **xhold,**vhold;
// if timestep < delaystep, just return
if (delay_flag && update->ntimestep < delaystep) return;
// if file per timestep, open new file
if (multifile) openfile();
// simulation box bounds
if (domain->triclinic == 0) {
boxxlo = domain->boxlo[0];
boxxhi = domain->boxhi[0];
boxylo = domain->boxlo[1];
boxyhi = domain->boxhi[1];
boxzlo = domain->boxlo[2];
boxzhi = domain->boxhi[2];
} else {
boxxlo = domain->boxlo_bound[0];
boxxhi = domain->boxhi_bound[0];
boxylo = domain->boxlo_bound[1];
boxyhi = domain->boxhi_bound[1];
boxzlo = domain->boxlo_bound[2];
boxzhi = domain->boxhi_bound[2];
boxxy = domain->xy;
boxxz = domain->xz;
boxyz = domain->yz;
}
// nme = # of dump lines this proc contributes to dump
nme = count();
// ntotal = total # of dump lines in snapshot
// nmax = max # of dump lines on any proc
bigint bnme = nme;
MPI_Allreduce(&bnme,&ntotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
int nmax;
if (multiproc != nprocs) MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
else nmax = nme;
// insure buf is sized for packing and communicating
// use nmax to insure filewriter proc can receive info from others
// limit nmax*size_one to int since used as arg in MPI calls
if (nmax > maxbuf) {
if ((bigint) nmax * size_one > MAXSMALLINT)
error->all(FLERR,"Too much per-proc info for dump");
maxbuf = nmax;
memory->destroy(buf);
memory->create(buf,maxbuf*size_one,"dump:buf");
}
// insure ids buffer is sized for sorting
if (sort_flag && sortcol == 0 && nmax > maxids) {
maxids = nmax;
memory->destroy(ids);
memory->create(ids,maxids,"dump:ids");
}
// apply PBC on copy of x,v,image if requested
if (pbcflag) {
int nlocal = atom->nlocal;
if (nlocal > maxpbc) pbc_allocate();
if (nlocal) {
memcpy(&xpbc[0][0],&atom->x[0][0],3*nlocal*sizeof(double));
memcpy(&vpbc[0][0],&atom->v[0][0],3*nlocal*sizeof(double));
memcpy(imagepbc,atom->image,nlocal*sizeof(imageint));
}
xhold = atom->x;
vhold = atom->v;
imagehold = atom->image;
atom->x = xpbc;
atom->v = vpbc;
atom->image = imagepbc;
// for triclinic, PBC is applied in lamda coordinates
if (domain->triclinic) domain->x2lamda(nlocal);
domain->pbc();
if (domain->triclinic) domain->lamda2x(nlocal);
}
// pack my data into buf
// if sorting on IDs also request ID list from pack()
// sort buf as needed
if (sort_flag && sortcol == 0) pack(ids);
else pack(nullptr);
if (sort_flag) sort();
if (balance_flag) balance();
// write timestep header
// for multiproc,
// nheader = # of lines in this file via Allreduce on clustercomm
// must come after sort, which can change nme
bigint nheader = ntotal;
if (multiproc) {
bnme = nme;
MPI_Allreduce(&bnme,&nheader,1,MPI_LMP_BIGINT,MPI_SUM,clustercomm);
}
if (filewriter && write_header_flag) write_header(nheader);
// if buffering, convert doubles into strings
// insure sbuf is sized for communicating
// cannot buffer if output is to binary file
if (buffer_flag && !binary) {
nsme = convert_string(nme,buf);
int nsmin,nsmax;
MPI_Allreduce(&nsme,&nsmin,1,MPI_INT,MPI_MIN,world);
if (nsmin < 0) error->all(FLERR,"Too much buffered per-proc info for dump");
if (multiproc != nprocs)
MPI_Allreduce(&nsme,&nsmax,1,MPI_INT,MPI_MAX,world);
else nsmax = nsme;
if (nsmax > maxsbuf) {
maxsbuf = nsmax;
memory->grow(sbuf,maxsbuf,"dump:sbuf");
}
}
// filewriter = 1 = this proc writes to file
// ping each proc in my cluster, receive its data, write data to file
// else wait for ping from fileproc, send my data to fileproc
int tmp,nlines,nchars;
MPI_Status status;
MPI_Request request;
// comm and output buf of doubles
if (buffer_flag == 0 || binary) {
if (filewriter) {
for (int iproc = 0; iproc < nclusterprocs; iproc++) {
if (iproc) {
MPI_Irecv(buf,maxbuf*size_one,MPI_DOUBLE,me+iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,me+iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&nlines);
nlines /= size_one;
} else nlines = nme;
write_data(nlines,buf);
}
if (flush_flag && fp) fflush(fp);
} else {
MPI_Recv(&tmp,0,MPI_INT,fileproc,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(buf,nme*size_one,MPI_DOUBLE,fileproc,0,world);
}
// comm and output sbuf = one big string of formatted values per proc
} else {
if (filewriter) {
for (int iproc = 0; iproc < nclusterprocs; iproc++) {
if (iproc) {
MPI_Irecv(sbuf,maxsbuf,MPI_CHAR,me+iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,me+iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_CHAR,&nchars);
} else nchars = nsme;
write_data(nchars,(double *) sbuf);
}
if (flush_flag && fp) fflush(fp);
} else {
MPI_Recv(&tmp,0,MPI_INT,fileproc,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(sbuf,nsme,MPI_CHAR,fileproc,0,world);
}
}
// restore original x,v,image unaltered by PBC
if (pbcflag) {
atom->x = xhold;
atom->v = vhold;
atom->image = imagehold;
}
// trigger post-dump refresh by specified compute
// currently used for incremental dump files
if (refreshflag) modify->compute[irefresh]->refresh();
// if file per timestep, close file if I am filewriter
if (multifile) {
if (compressed) {
if (filewriter && fp != nullptr) platform::pclose(fp);
} else {
if (filewriter && fp != nullptr) fclose(fp);
}
fp = nullptr;
}
}
/* ----------------------------------------------------------------------
generic opening of a dump file
ASCII or binary or compressed
some derived classes override this function
------------------------------------------------------------------------- */
void Dump::openfile()
{
// single file, already opened, so just return
if (singlefile_opened) return;
if (multifile == 0) singlefile_opened = 1;
unit_count = 0;
// if one file per timestep, replace '*' with current timestep
char *filecurrent = filename;
if (multiproc) filecurrent = multiname;
if (multifile) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
if (maxfiles > 0) {
if (numfiles < maxfiles) {
nameslist[numfiles] = utils::strdup(filecurrent);
++numfiles;
} else {
remove(nameslist[fileidx]);
delete[] nameslist[fileidx];
nameslist[fileidx] = utils::strdup(filecurrent);
fileidx = (fileidx + 1) % maxfiles;
}
}
}
// each proc with filewriter = 1 opens a file
if (filewriter) {
if (compressed) {
fp = platform::compressed_write(filecurrent);
} else if (binary) {
fp = fopen(filecurrent,"wb");
} else if (append_flag) {
fp = fopen(filecurrent,"a");
} else {
fp = fopen(filecurrent,"w");
}
if (fp == nullptr) error->one(FLERR,"Cannot open dump file");
} else fp = nullptr;
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
}
/* ----------------------------------------------------------------------
parallel sort of buf across all procs
changes nme, reorders datums in buf, grows buf if necessary
------------------------------------------------------------------------- */
void Dump::sort()
{
int i,iproc;
double value;
// if single proc, swap ptrs to buf,ids <-> bufsort,idsort
if (nprocs == 1) {
if (nme > maxsort) {
maxsort = nme;
memory->destroy(bufsort);
memory->create(bufsort,maxsort*size_one,"dump:bufsort");
memory->destroy(index);
memory->create(index,maxsort,"dump:index");
if (sortcol == 0) {
memory->destroy(idsort);
memory->create(idsort,maxsort,"dump:idsort");
}
}
double *dptr = buf;
buf = bufsort;
bufsort = dptr;
if (sortcol == 0) {
tagint *iptr = ids;
ids = idsort;
idsort = iptr;
}
// if multiple procs, exchange datums between procs via irregular
} else {
// grow proclist if necessary
if (nme > maxproc) {
maxproc = nme;
memory->destroy(proclist);
memory->create(proclist,maxproc,"dump:proclist");
}
// proclist[i] = which proc Ith datum will be sent to
if (sortcol == 0) {
tagint min = MAXTAGINT;
tagint max = 0;
for (i = 0; i < nme; i++) {
min = MIN(min,ids[i]);
max = MAX(max,ids[i]);
}
tagint minall,maxall;
MPI_Allreduce(&min,&minall,1,MPI_LMP_TAGINT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
// use 0.5 instead of EPSILON since atom IDs are integers
// if use EPSILON, it can be lost if 64-bit maxall-minall is too big
// then iproc == nprocs for largest ID, causing irregular to crash
double range = maxall-minall + 0.5;
for (i = 0; i < nme; i++) {
iproc = static_cast<int> ((ids[i]-minall)/range * nprocs);
proclist[i] = iproc;
}
} else {
double min = BIG;
double max = -BIG;
for (i = 0; i < nme; i++) {
value = buf[i*size_one + sortcolm1];
min = MIN(min,value);
max = MAX(max,value);
}
double minall,maxall;
MPI_Allreduce(&min,&minall,1,MPI_DOUBLE,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_DOUBLE,MPI_MAX,world);
double range = maxall-minall + EPSILON*(maxall-minall);
if (range == 0.0) range = EPSILON;
// proc assignment is inverted if sortorder = DESCEND
for (i = 0; i < nme; i++) {
value = buf[i*size_one + sortcolm1];
iproc = static_cast<int> ((value-minall)/range * nprocs);
if (sortorder == DESCEND) iproc = nprocs-1 - iproc;
proclist[i] = iproc;
}
}
// create comm plan, grow recv bufs if necessary,
// exchange datums, destroy plan
// if sorting on atom IDs, exchange IDs also
nme = irregular->create_data(nme,proclist);
if (nme > maxsort) {
maxsort = nme;
memory->destroy(bufsort);
memory->create(bufsort,maxsort*size_one,"dump:bufsort");
memory->destroy(index);
memory->create(index,maxsort,"dump:index");
if (sortcol == 0) {
memory->destroy(idsort);
memory->create(idsort,maxsort,"dump:idsort");
}
}
irregular->exchange_data((char *) buf,size_one*sizeof(double),
(char *) bufsort);
if (sortcol == 0)
irregular->exchange_data((char *) ids,sizeof(tagint),(char *) idsort);
irregular->destroy_data();
}
// if reorder flag is set & total/per-proc counts match pre-computed values,
// then create index directly from idsort
// else quicksort of index using IDs or buf column as comparator
if (reorderflag) {
if (ntotal != ntotal_reorder) reorderflag = 0;
int flag = 0;
if (nme != nme_reorder) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) reorderflag = 0;
if (reorderflag)
for (i = 0; i < nme; i++)
index[idsort[i]-idlo] = i;
}
#if defined(LMP_QSORT)
if (!reorderflag) {
dumpptr = this;
for (i = 0; i < nme; i++) index[i] = i;
if (sortcol == 0) qsort(index,nme,sizeof(int),idcompare);
else if (sortorder == ASCEND) qsort(index,nme,sizeof(int),bufcompare);
else qsort(index,nme,sizeof(int),bufcompare_reverse);
}
#else
if (!reorderflag) {
for (i = 0; i < nme; i++) index[i] = i;
if (sortcol == 0) utils::merge_sort(index,nme,(void *)this,idcompare);
else if (sortorder == ASCEND) utils::merge_sort(index,nme,(void *)this,bufcompare);
else utils::merge_sort(index,nme,(void *)this,bufcompare_reverse);
}
#endif
// reset buf size and maxbuf to largest of any post-sort nme values
// this insures proc 0 can receive everyone's info
int nmax;
MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
if (nmax > maxbuf) {
maxbuf = nmax;
memory->destroy(buf);
memory->create(buf,maxbuf*size_one,"dump:buf");
}
// copy data from bufsort to buf using index
int nbytes = size_one*sizeof(double);
for (i = 0; i < nme; i++)
memcpy(&buf[i*size_one],&bufsort[index[i]*size_one],nbytes);
}
#if defined(LMP_QSORT)
/* ----------------------------------------------------------------------
compare two atom IDs
called via qsort() in sort() method
is a static method so access data via dumpptr
------------------------------------------------------------------------- */
int Dump::idcompare(const void *pi, const void *pj)
{
tagint *idsort = dumpptr->idsort;
int i = *((int *) pi);
int j = *((int *) pj);
if (idsort[i] < idsort[j]) return -1;
if (idsort[i] > idsort[j]) return 1;
return 0;
}
/* ----------------------------------------------------------------------
compare two buffer values with size_one stride
called via qsort() in sort() method
is a static method so access data via dumpptr
sort in ASCENDing order
------------------------------------------------------------------------- */
int Dump::bufcompare(const void *pi, const void *pj)
{
double *bufsort = dumpptr->bufsort;
int size_one = dumpptr->size_one;
int sortcolm1 = dumpptr->sortcolm1;
int i = *((int *) pi)*size_one + sortcolm1;
int j = *((int *) pj)*size_one + sortcolm1;
if (bufsort[i] < bufsort[j]) return -1;
if (bufsort[i] > bufsort[j]) return 1;
return 0;
}
/* ----------------------------------------------------------------------
compare two buffer values with size_one stride
called via qsort() in sort() method
is a static method so access data via dumpptr
sort in DESCENDing order
------------------------------------------------------------------------- */
int Dump::bufcompare_reverse(const void *pi, const void *pj)
{
double *bufsort = dumpptr->bufsort;
int size_one = dumpptr->size_one;
int sortcolm1 = dumpptr->sortcolm1;
int i = *((int *) pi)*size_one + sortcolm1;
int j = *((int *) pj)*size_one + sortcolm1;
if (bufsort[i] > bufsort[j]) return -1;
if (bufsort[i] < bufsort[j]) return 1;
return 0;
}
#else
/* ----------------------------------------------------------------------
compare two atom IDs
called via merge_sort() in sort() method
------------------------------------------------------------------------- */
int Dump::idcompare(const int i, const int j, void *ptr)
{
tagint *idsort = ((Dump *)ptr)->idsort;
if (idsort[i] < idsort[j]) return -1;
else if (idsort[i] > idsort[j]) return 1;
else return 0;
}
/* ----------------------------------------------------------------------
compare two buffer values with size_one stride
called via merge_sort() in sort() method
sort in ASCENDing order
------------------------------------------------------------------------- */
int Dump::bufcompare(const int i, const int j, void *ptr)
{
Dump *dptr = (Dump *) ptr;
double *bufsort = dptr->bufsort;
const int size_one = dptr->size_one;
const int sortcolm1 = dptr->sortcolm1;
const int ii=i*size_one + sortcolm1;
const int jj=j*size_one + sortcolm1;
if (bufsort[ii] < bufsort[jj]) return -1;
else if (bufsort[ii] > bufsort[jj]) return 1;
else return 0;
}
/* ----------------------------------------------------------------------
compare two buffer values with size_one stride
called via merge_sort() in sort() method
sort in DESCENDing order
------------------------------------------------------------------------- */
int Dump::bufcompare_reverse(const int i, const int j, void *ptr)
{
Dump *dptr = (Dump *) ptr;
double *bufsort = dptr->bufsort;
const int size_one = dptr->size_one;
const int sortcolm1 = dptr->sortcolm1;
const int ii=i*size_one + sortcolm1;
const int jj=j*size_one + sortcolm1;
if (bufsort[ii] < bufsort[jj]) return 1;
else if (bufsort[ii] > bufsort[jj]) return -1;
else return 0;
}
#endif
/* ----------------------------------------------------------------------
parallel load balance of buf across all procs
must come after sort
------------------------------------------------------------------------- */
void Dump::balance()
{
bigint *proc_offsets,*proc_new_offsets;
memory->create(proc_offsets,nprocs+1,"dump:proc_offsets");
memory->create(proc_new_offsets,nprocs+1,"dump:proc_new_offsets");
// compute atom offset for this proc
bigint offset;
bigint bnme = nme;
MPI_Scan(&bnme,&offset,1,MPI_LMP_BIGINT,MPI_SUM,world);
// gather atom offsets for all procs
MPI_Allgather(&offset,1,MPI_LMP_BIGINT,&proc_offsets[1],1,MPI_LMP_BIGINT,world);
proc_offsets[0] = 0;
// how many atoms should I own after balance
int nme_balance = static_cast<int>(ntotal/nprocs);
// include remainder atoms on first procs
int remainder = ntotal % nprocs;
if (me < remainder) nme_balance += 1;
// compute new atom offset for this proc
bigint offset_balance;
bigint bnme_balance = nme_balance;
MPI_Scan(&bnme_balance,&offset_balance,1,MPI_LMP_BIGINT,MPI_SUM,world);
// gather new atom offsets for all procs
MPI_Allgather(&offset_balance,1,MPI_LMP_BIGINT,&proc_new_offsets[1],1,MPI_LMP_BIGINT,world);
proc_new_offsets[0] = 0;
// reset buf size to largest of any post-balance nme values
// this insures proc 0 can receive everyone's info
// cannot shrink buf to nme_balance, must use previous maxbuf value
int nmax;
MPI_Allreduce(&nme_balance,&nmax,1,MPI_INT,MPI_MAX,world);
if (nmax > maxbuf) maxbuf = nmax;
// allocate a second buffer for balanced data
double* buf_balance;
memory->create(buf_balance,maxbuf*size_one,"dump:buf_balance");
// compute from which procs I am receiving atoms
// post recvs first
int nswap = 0;
MPI_Request *request = new MPI_Request[nprocs];
// find which proc starting atom belongs to
int startproc = me;
while (proc_new_offsets[me] < proc_offsets[startproc]) startproc--;
while (proc_new_offsets[me] > proc_offsets[startproc+1]-1) startproc++;
// find which proc ending atom belongs to
int endproc = me;
while (proc_new_offsets[me] + nme_balance-1 < proc_offsets[endproc]) endproc--;
while (proc_new_offsets[me] + nme_balance-1 > proc_offsets[endproc+1]-1) endproc++;
// loop over procs
for (int iproc = startproc; iproc <= endproc; iproc++) {
int istart = MAX(0, proc_offsets[iproc] - proc_new_offsets[me]);
int iend = MIN(nme_balance-1, proc_offsets[iproc+1]-1 - proc_new_offsets[me]);
int nrecv = iend - istart + 1;
if (nrecv == 0) continue;
// post receive for this proc
if (iproc != me)
MPI_Irecv(&buf_balance[istart*size_one],nrecv*size_one,MPI_DOUBLE,
iproc,0,world,&request[nswap++]);
}
// compute which atoms I am sending and to which procs
// find which proc starting atom belongs to
startproc = me;
while (proc_offsets[me] < proc_new_offsets[startproc]) startproc--;
while (proc_offsets[me] > proc_new_offsets[startproc+1]-1) startproc++;
// find which proc ending atom belongs to
endproc = me;
while (proc_offsets[me] + nme-1 < proc_new_offsets[endproc]) endproc--;
while (proc_offsets[me] + nme-1 > proc_new_offsets[endproc+1]-1) endproc++;
// loop over procs
for (int iproc = startproc; iproc <= endproc; iproc++) {
int istart = MAX(0,proc_new_offsets[iproc] - proc_offsets[me]);
int iend = MIN(nme-1,proc_new_offsets[iproc+1]-1 - proc_offsets[me]);
int nsend = iend - istart + 1;
if (nsend == 0) continue;
// send for this proc
if (iproc != me) {
MPI_Send(&buf[istart*size_one],nsend*size_one,MPI_DOUBLE,iproc,0,world);
} else {
// sending to self, copy buffers
int offset_me = proc_offsets[me] - proc_new_offsets[me];
memcpy(&buf_balance[(offset_me + istart)*size_one],&buf[istart*size_one],sizeof(double)*nsend*size_one);
}
}
// wait for all recvs
for (int n = 0; n < nswap; n++)
MPI_Wait(&request[n],MPI_STATUS_IGNORE);
nme = nme_balance;
// swap buffers
double *tmp = buf;
buf = buf_balance;
// cleanup
memory->destroy(tmp);
memory->destroy(proc_offsets);
memory->destroy(proc_new_offsets);
delete [] request;
}
/* ----------------------------------------------------------------------
process params common to all dumps here
if unknown param, call modify_param specific to the dump
------------------------------------------------------------------------- */
void Dump::modify_params(int narg, char **arg)
{
if (narg == 0) error->all(FLERR,"Illegal dump_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"append") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
append_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"buffer") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
buffer_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
if (buffer_flag && buffer_allow == 0)
error->all(FLERR,"Dump_modify buffer yes not allowed for this style");
iarg += 2;
} else if (strcmp(arg[iarg],"delay") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
delaystep = utils::bnumeric(FLERR,arg[iarg+1],false,lmp);
if (delaystep >= 0) delay_flag = 1;
else delay_flag = 0;
iarg += 2;
} else if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
int idump;
for (idump = 0; idump < output->ndump; idump++)
if (strcmp(id,output->dump[idump]->id) == 0) break;
int n;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
delete [] output->var_dump[idump];
output->var_dump[idump] = utils::strdup(&arg[iarg+1][2]);
n = 0;
} else {
n = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (n <= 0) error->all(FLERR,"Illegal dump_modify command");
}
output->mode_dump[idump] = 0;
output->every_dump[idump] = n;
iarg += 2;
} else if (strcmp(arg[iarg],"every/time") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
int idump;
for (idump = 0; idump < output->ndump; idump++)
if (strcmp(id,output->dump[idump]->id) == 0) break;
double delta;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
delete [] output->var_dump[idump];
output->var_dump[idump] = utils::strdup(&arg[iarg+1][2]);
delta = 0.0;
} else {
delta = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (delta <= 0.0) error->all(FLERR,"Illegal dump_modify command");
}
output->mode_dump[idump] = 1;
output->every_time_dump[idump] = delta;
iarg += 2;
} else if (strcmp(arg[iarg],"fileper") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (!multiproc)
error->all(FLERR,"Cannot use dump_modify fileper without % in dump file name");
int nper = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (nper <= 0) error->all(FLERR,"Illegal dump_modify command");
multiproc = nprocs/nper;
if (nprocs % nper) multiproc++;
fileproc = me/nper * nper;
int fileprocnext = MIN(fileproc+nper,nprocs);
nclusterprocs = fileprocnext - fileproc;
if (me == fileproc) filewriter = 1;
else filewriter = 0;
int icluster = fileproc/nper;
MPI_Comm_free(&clustercomm);
MPI_Comm_split(world,icluster,0,&clustercomm);
delete [] multiname;
char *ptr = strchr(filename,'%');
*ptr = '\0';
multiname = utils::strdup(fmt::format("{}{}{}", filename, icluster, ptr+1));
*ptr = '%';
iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
first_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"flush") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
flush_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"none") == 0) {
delete [] format_line_user;
delete [] format_int_user;
delete [] format_bigint_user;
delete [] format_float_user;
format_line_user = nullptr;
format_int_user = nullptr;
format_bigint_user = nullptr;
format_float_user = nullptr;
// pass format none to child classes which may use it
// not an error if they don't
modify_param(narg-iarg,&arg[iarg]);
iarg += 2;
continue;
}
if (iarg+3 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"line") == 0) {
delete [] format_line_user;
format_line_user = utils::strdup(arg[iarg+2]);
iarg += 3;
} else { // pass other format options to child classes
int n = modify_param(narg-iarg,&arg[iarg]);
if (n == 0) error->all(FLERR,"Illegal dump_modify command");
iarg += n;
}
} else if (strcmp(arg[iarg],"header") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
header_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"maxfiles") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (!multifile)
error->all(FLERR,"Cannot use dump_modify maxfiles without * in dump file name");
// wipe out existing storage
if (maxfiles > 0) {
for (int idx=0; idx < numfiles; ++idx)
delete[] nameslist[idx];
delete[] nameslist;
}
maxfiles = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (maxfiles == 0) error->all(FLERR,"Illegal dump_modify command");
if (maxfiles > 0) {
nameslist = new char*[maxfiles];
numfiles = 0;
for (int idx=0; idx < maxfiles; ++idx)
nameslist[idx] = nullptr;
fileidx = 0;
}
iarg += 2;
} else if (strcmp(arg[iarg],"nfile") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (!multiproc)
error->all(FLERR,"Cannot use dump_modify nfile without % in dump file name");
int nfile = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (nfile <= 0) error->all(FLERR,"Illegal dump_modify command");
nfile = MIN(nfile,nprocs);
multiproc = nfile;
int icluster = static_cast<int> ((bigint) me * nfile/nprocs);
fileproc = static_cast<int> ((bigint) icluster * nprocs/nfile);
int fcluster = static_cast<int> ((bigint) fileproc * nfile/nprocs);
if (fcluster < icluster) fileproc++;
int fileprocnext =
static_cast<int> ((bigint) (icluster+1) * nprocs/nfile);
fcluster = static_cast<int> ((bigint) fileprocnext * nfile/nprocs);
if (fcluster < icluster+1) fileprocnext++;
nclusterprocs = fileprocnext - fileproc;
if (me == fileproc) filewriter = 1;
else filewriter = 0;
MPI_Comm_free(&clustercomm);
MPI_Comm_split(world,icluster,0,&clustercomm);
delete [] multiname;
char *ptr = strchr(filename,'%');
*ptr = '\0';
multiname = utils::strdup(fmt::format("{}{}{}", filename, icluster, ptr+1));
*ptr = '%';
iarg += 2;
} else if (strcmp(arg[iarg],"pad") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
padflag = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (padflag < 0) error->all(FLERR,"Illegal dump_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"pbc") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
pbcflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"sort") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"off") == 0) sort_flag = 0;
else if (strcmp(arg[iarg+1],"id") == 0) {
sort_flag = 1;
sortcol = 0;
sortorder = ASCEND;
} else {
sort_flag = 1;
sortcol = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
sortorder = ASCEND;
if (sortcol == 0) error->all(FLERR,"Illegal dump_modify command");
if (sortcol < 0) {
sortorder = DESCEND;
sortcol = -sortcol;
}
sortcolm1 = sortcol - 1;
}
iarg += 2;
} else if (strcmp(arg[iarg],"balance") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (nprocs > 1)
balance_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"time") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
time_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
unit_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else {
int n = modify_param(narg-iarg,&arg[iarg]);
if (n == 0) error->all(FLERR,"Illegal dump_modify command");
iarg += n;
}
}
}
/* ---------------------------------------------------------------------- */
double Dump::compute_time()
{
return update->atime + (update->ntimestep - update->atimestep)*update->dt;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
void Dump::pbc_allocate()
{
memory->destroy(xpbc);
memory->destroy(vpbc);
memory->destroy(imagepbc);
maxpbc = atom->nmax;
memory->create(xpbc,maxpbc,3,"dump:xbpc");
memory->create(vpbc,maxpbc,3,"dump:vbpc");
memory->create(imagepbc,maxpbc,"dump:imagebpc");
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double Dump::memory_usage()
{
double bytes = memory->usage(buf,size_one*maxbuf);
bytes += memory->usage(sbuf,maxsbuf);
if (sort_flag) {
if (sortcol == 0) bytes += memory->usage(ids,maxids);
bytes += memory->usage(bufsort,size_one*maxsort);
if (sortcol == 0) bytes += memory->usage(idsort,maxsort);
bytes += memory->usage(index,maxsort);
bytes += memory->usage(proclist,maxproc);
if (irregular) bytes += (double)irregular->memory_usage();
}
if (pbcflag) {
bytes += (double)6*maxpbc * sizeof(double);
bytes += (double)maxpbc * sizeof(imageint);
}
return bytes;
}
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