Merge branch 'develop' into BPM
This commit is contained in:
Axel Kohlmeyer
99
src/dump.cpp
99
src/dump.cpp
@ -150,19 +150,19 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
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Dump::~Dump()
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{
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delete [] id;
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delete [] style;
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delete [] filename;
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delete [] multiname;
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delete[] id;
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delete[] style;
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delete[] filename;
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delete[] multiname;
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delete [] format;
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delete [] format_default;
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delete [] format_line_user;
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delete [] format_float_user;
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delete [] format_int_user;
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delete [] format_bigint_user;
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delete[] format;
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delete[] format_default;
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delete[] format_line_user;
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delete[] format_float_user;
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delete[] format_int_user;
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delete[] format_bigint_user;
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delete [] refresh;
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delete[] refresh;
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// format_column_user is deallocated by child classes that use it
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@ -270,12 +270,12 @@ void Dump::init()
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reorderflag = 1;
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double range = maxall-minall + EPSILON;
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idlo = static_cast<tagint> (range*me/nprocs + minall);
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tagint idhi = static_cast<tagint> (range*(me+1)/nprocs + minall);
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auto idhi = static_cast<tagint> (range*(me+1)/nprocs + minall);
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tagint lom1 = static_cast<tagint> ((idlo-1-minall)/range * nprocs);
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tagint lo = static_cast<tagint> ((idlo-minall)/range * nprocs);
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tagint him1 = static_cast<tagint> ((idhi-1-minall)/range * nprocs);
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tagint hi = static_cast<tagint> ((idhi-minall)/range * nprocs);
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auto lom1 = static_cast<tagint> ((idlo-1-minall)/range * nprocs);
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auto lo = static_cast<tagint> ((idlo-minall)/range * nprocs);
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auto him1 = static_cast<tagint> ((idhi-1-minall)/range * nprocs);
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auto hi = static_cast<tagint> ((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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@ -549,20 +549,7 @@ void Dump::openfile()
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if (multiproc) filecurrent = multiname;
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if (multifile) {
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char *filestar = filecurrent;
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filecurrent = new char[strlen(filestar) + 16];
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char *ptr = strchr(filestar,'*');
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*ptr = '\0';
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if (padflag == 0)
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sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
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filestar,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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sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
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sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
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}
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*ptr = '*';
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filecurrent = utils::strdup(utils::star_subst(filecurrent, update->ntimestep, padflag));
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if (maxfiles > 0) {
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if (numfiles < maxfiles) {
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nameslist[numfiles] = utils::strdup(filecurrent);
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@ -594,7 +581,7 @@ void Dump::openfile()
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// delete string with timestep replaced
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if (multifile) delete [] filecurrent;
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if (multifile) delete[] filecurrent;
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}
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/* ----------------------------------------------------------------------
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@ -854,7 +841,7 @@ int Dump::idcompare(const int i, const int j, void *ptr)
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int Dump::bufcompare(const int i, const int j, void *ptr)
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{
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Dump *dptr = (Dump *) ptr;
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auto dptr = (Dump *) ptr;
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double *bufsort = dptr->bufsort;
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const int size_one = dptr->size_one;
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const int sortcolm1 = dptr->sortcolm1;
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@ -875,7 +862,7 @@ int Dump::bufcompare(const int i, const int j, void *ptr)
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int Dump::bufcompare_reverse(const int i, const int j, void *ptr)
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{
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Dump *dptr = (Dump *) ptr;
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auto dptr = (Dump *) ptr;
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double *bufsort = dptr->bufsort;
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const int size_one = dptr->size_one;
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const int sortcolm1 = dptr->sortcolm1;
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@ -951,7 +938,7 @@ void Dump::balance()
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// post recvs first
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int nswap = 0;
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MPI_Request *request = new MPI_Request[nprocs];
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auto request = new MPI_Request[nprocs];
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// find which proc starting atom belongs to
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@ -1032,7 +1019,7 @@ void Dump::balance()
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memory->destroy(tmp);
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memory->destroy(proc_offsets);
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memory->destroy(proc_new_offsets);
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delete [] request;
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delete[] request;
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}
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/* ----------------------------------------------------------------------
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@ -1072,7 +1059,7 @@ void Dump::modify_params(int narg, char **arg)
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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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delete[] output->var_dump[idump];
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output->var_dump[idump] = utils::strdup(&arg[iarg+1][2]);
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n = 0;
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} else {
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@ -1090,7 +1077,7 @@ void Dump::modify_params(int narg, char **arg)
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if (strcmp(id,output->dump[idump]->id) == 0) break;
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double delta;
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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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delete[] output->var_dump[idump];
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output->var_dump[idump] = utils::strdup(&arg[iarg+1][2]);
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delta = 0.0;
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} else {
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@ -1120,7 +1107,7 @@ void Dump::modify_params(int narg, char **arg)
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MPI_Comm_free(&clustercomm);
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MPI_Comm_split(world,icluster,0,&clustercomm);
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delete [] multiname;
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delete[] multiname;
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char *ptr = strchr(filename,'%');
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*ptr = '\0';
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multiname = utils::strdup(fmt::format("{}{}{}", filename, icluster, ptr+1));
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@ -1137,14 +1124,38 @@ void Dump::modify_params(int narg, char **arg)
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flush_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg],"colname") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
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if (strcmp(arg[iarg+1],"default") == 0) {
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for (auto item : keyword_user) item.clear();
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iarg += 2;
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} else {
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if (iarg+3 > narg) error->all(FLERR,"Illegal dump_modify command");
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int icol = -1;
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if (utils::is_integer(arg[iarg + 1])) {
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icol = utils::inumeric(FLERR,arg[iarg + 1],false,lmp);
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if (icol < 0) icol = keyword_user.size() + icol + 1;
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icol--;
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} else {
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try {
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icol = key2col.at(arg[iarg + 1]);
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} catch (std::out_of_range &) {
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icol = -1;
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}
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}
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if ((icol < 0) || (icol >= (int)keyword_user.size()))
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error->all(FLERR, "Illegal thermo_modify command");
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keyword_user[icol] = arg[iarg+2];
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iarg += 3;
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}
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} else if (strcmp(arg[iarg],"format") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
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if (strcmp(arg[iarg+1],"none") == 0) {
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delete [] format_line_user;
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delete [] format_int_user;
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delete [] format_bigint_user;
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delete [] format_float_user;
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delete[] format_line_user;
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delete[] format_int_user;
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delete[] format_bigint_user;
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delete[] format_float_user;
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format_line_user = nullptr;
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format_int_user = nullptr;
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format_bigint_user = nullptr;
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@ -1159,7 +1170,7 @@ void Dump::modify_params(int narg, char **arg)
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if (iarg+3 > narg) error->all(FLERR,"Illegal dump_modify command");
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if (strcmp(arg[iarg+1],"line") == 0) {
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delete [] format_line_user;
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delete[] format_line_user;
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format_line_user = utils::strdup(arg[iarg+2]);
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iarg += 3;
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} else { // pass other format options to child classes
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@ -1217,7 +1228,7 @@ void Dump::modify_params(int narg, char **arg)
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MPI_Comm_free(&clustercomm);
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MPI_Comm_split(world,icluster,0,&clustercomm);
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delete [] multiname;
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delete[] multiname;
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char *ptr = strchr(filename,'%');
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*ptr = '\0';
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multiname = utils::strdup(fmt::format("{}{}{}", filename, icluster, ptr+1));
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