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vlasiator.cpp
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vlasiator.cpp
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/*
* This file is part of Vlasiator.
* Copyright 2010-2016 Finnish Meteorological Institute
*
* For details of usage, see the COPYING file and read the "Rules of the Road"
* at http://www.physics.helsinki.fi/vlasiator/
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along
* with this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/
#include <cstdlib>
#include <iostream>
#include <cmath>
#include <vector>
#include <sstream>
#include <ctime>
#ifdef _OPENMP
#include <omp.h>
#endif
#include <fsgrid.hpp>
#include "vlasovmover.h"
#include "definitions.h"
#include "mpiconversion.h"
#include "logger.h"
#include "parameters.h"
#include "readparameters.h"
#include "spatial_cell_wrapper.hpp"
#include "datareduction/datareducer.h"
#include "sysboundary/sysboundary.h"
#include "fieldtracing/fieldtracing.h"
#include "fieldsolver/fs_common.h"
#include "projects/project.h"
#include "grid.h"
#include "iowrite.h"
#include "ioread.h"
#include "object_wrapper.h"
#include "fieldsolver/gridGlue.hpp"
#include "fieldsolver/derivatives.hpp"
#ifdef CATCH_FPE
#include <fenv.h>
#include <signal.h>
/*! Function used to abort the program upon detecting a floating point exception. Which exceptions are caught is defined using the function feenableexcept.
*/
void fpehandler(int sig_num)
{
signal(SIGFPE, fpehandler);
printf("SIGFPE: floating point exception occured, exiting.\n");
abort();
}
#endif
#include "phiprof.hpp"
Logger logFile, diagnostic;
static dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry> mpiGrid;
using namespace std;
int globalflags::bailingOut = 0;
bool globalflags::writeRestart = 0;
bool globalflags::balanceLoad = 0;
bool globalflags::doRefine=0;
bool globalflags::ionosphereJustSolved = false;
ObjectWrapper objectWrapper;
void addTimedBarrier(string name){
#ifdef NDEBUG
//let's not do a barrier
return;
#endif
phiprof::Timer btimer {name, {"Barriers", "MPI"}};
MPI_Barrier(MPI_COMM_WORLD);
}
/*! Report spatial cell counts per refinement level as well as velocity cell counts per population into logfile
*/
void report_cell_and_block_counts(dccrg::Dccrg<spatial_cell::SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid){
cint maxRefLevel = mpiGrid.get_maximum_refinement_level();
const vector<CellID> localCells = getLocalCells();
cint popCount = getObjectWrapper().particleSpecies.size();
// popCount+1 as we store the spatial cell counts and then the populations' v_cell counts.
// maxRefLevel+1 as e.g. there's 2 levels at maxRefLevel == 1
std::vector<int64_t> localCounts((popCount+1)*(maxRefLevel+1), 0), globalCounts((popCount+1)*(maxRefLevel+1), 0);
for (const auto cellid : localCells) {
cint level = mpiGrid.get_refinement_level(cellid);
localCounts[level]++;
for(int pop=0; pop<popCount; pop++) {
localCounts[maxRefLevel+1 + level*popCount + pop] += mpiGrid[cellid]->get_number_of_velocity_blocks(pop);
}
}
MPI_Reduce(localCounts.data(), globalCounts.data(), (popCount+1)*(maxRefLevel+1), MPI_INT64_T, MPI_SUM, MASTER_RANK, MPI_COMM_WORLD);
logFile << "(CELLS) tstep = " << P::tstep << " time = " << P::t << " spatial cells [ ";
for(int level = 0; level <= maxRefLevel; level++) {
logFile << globalCounts[level] << " ";
}
logFile << "] blocks ";
for(int pop=0; pop<popCount; pop++) {
logFile << getObjectWrapper().particleSpecies[pop].name << " [ ";
for(int level = 0; level <= maxRefLevel; level++) {
logFile << globalCounts[maxRefLevel+1 + level*popCount + pop] << " ";
}
logFile << "] ";
}
logFile << endl << flush;
}
void computeNewTimeStep(dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
FsGrid< fsgrids::technical, FS_STENCIL_WIDTH> & technicalGrid, Real &newDt, bool &isChanged) {
phiprof::Timer computeTimestepTimer {"compute-timestep"};
// Compute maximum time step. This cannot be done at the first step as the solvers compute the limits for each cell.
isChanged = false;
const vector<CellID>& cells = getLocalCells();
/* Arrays for storing local (per process) and global max dt
0th position stores ordinary space propagation dt
1st position stores velocity space propagation dt
2nd position stores field propagation dt
*/
Real dtMaxLocal[3];
Real dtMaxGlobal[3];
dtMaxLocal[0] = numeric_limits<Real>::max();
dtMaxLocal[1] = numeric_limits<Real>::max();
dtMaxLocal[2] = numeric_limits<Real>::max();
for (vector<CellID>::const_iterator cell_id = cells.begin(); cell_id != cells.end(); ++cell_id) {
SpatialCell* cell = mpiGrid[*cell_id];
const Real dx = cell->parameters[CellParams::DX];
const Real dy = cell->parameters[CellParams::DY];
const Real dz = cell->parameters[CellParams::DZ];
cell->parameters[CellParams::MAXRDT] = numeric_limits<Real>::max();
for (uint popID = 0; popID < getObjectWrapper().particleSpecies.size(); ++popID) {
cell->set_max_r_dt(popID, numeric_limits<Real>::max());
vmesh::VelocityBlockContainer<vmesh::LocalID>& blockContainer = cell->get_velocity_blocks(popID);
const Real* blockParams = blockContainer.getParameters();
const Real EPS = numeric_limits<Real>::min() * 1000;
for (vmesh::LocalID blockLID = 0; blockLID < blockContainer.size(); ++blockLID) {
for (unsigned int i = 0; i < WID; i += WID - 1) {
const Real Vx =
blockParams[blockLID * BlockParams::N_VELOCITY_BLOCK_PARAMS + BlockParams::VXCRD] +
(i + HALF) * blockParams[blockLID * BlockParams::N_VELOCITY_BLOCK_PARAMS + BlockParams::DVX] + EPS;
const Real Vy =
blockParams[blockLID * BlockParams::N_VELOCITY_BLOCK_PARAMS + BlockParams::VYCRD] +
(i + HALF) * blockParams[blockLID * BlockParams::N_VELOCITY_BLOCK_PARAMS + BlockParams::DVY] + EPS;
const Real Vz =
blockParams[blockLID * BlockParams::N_VELOCITY_BLOCK_PARAMS + BlockParams::VZCRD] +
(i + HALF) * blockParams[blockLID * BlockParams::N_VELOCITY_BLOCK_PARAMS + BlockParams::DVZ] + EPS;
const Real dt_max_cell = min({dx / fabs(Vx), dy / fabs(Vy), dz / fabs(Vz)});
cell->set_max_r_dt(popID, min(dt_max_cell, cell->get_max_r_dt(popID)));
}
}
cell->parameters[CellParams::MAXRDT] = min(cell->get_max_r_dt(popID), cell->parameters[CellParams::MAXRDT]);
}
if (cell->sysBoundaryFlag == sysboundarytype::NOT_SYSBOUNDARY ||
(cell->sysBoundaryLayer == 1 && cell->sysBoundaryFlag != sysboundarytype::NOT_SYSBOUNDARY)) {
// spatial fluxes computed also for boundary cells
dtMaxLocal[0] = min(dtMaxLocal[0], cell->parameters[CellParams::MAXRDT]);
}
if (cell->parameters[CellParams::MAXVDT] != 0 &&
(cell->sysBoundaryFlag == sysboundarytype::NOT_SYSBOUNDARY ||
(P::vlasovAccelerateMaxwellianBoundaries && cell->sysBoundaryFlag == sysboundarytype::MAXWELLIAN))) {
// acceleration only done on non-boundary cells
dtMaxLocal[1] = min(dtMaxLocal[1], cell->parameters[CellParams::MAXVDT]);
}
}
// compute max dt for fieldsolver
const std::array<FsGridTools::FsIndex_t, 3> gridDims(technicalGrid.getLocalSize());
for (FsGridTools::FsIndex_t k = 0; k < gridDims[2]; k++) {
for (FsGridTools::FsIndex_t j = 0; j < gridDims[1]; j++) {
for (FsGridTools::FsIndex_t i = 0; i < gridDims[0]; i++) {
fsgrids::technical* cell = technicalGrid.get(i, j, k);
if (cell->sysBoundaryFlag == sysboundarytype::NOT_SYSBOUNDARY ||
(cell->sysBoundaryLayer == 1 && cell->sysBoundaryFlag != sysboundarytype::NOT_SYSBOUNDARY)) {
dtMaxLocal[2] = min(dtMaxLocal[2], cell->maxFsDt);
}
}
}
}
MPI_Allreduce(&(dtMaxLocal[0]), &(dtMaxGlobal[0]), 3, MPI_Type<Real>(), MPI_MIN, MPI_COMM_WORLD);
// If any of the solvers are disabled there should be no limits in timespace from it
if (!P::propagateVlasovTranslation)
dtMaxGlobal[0] = numeric_limits<Real>::max();
if (!P::propagateVlasovAcceleration)
dtMaxGlobal[1] = numeric_limits<Real>::max();
if (!P::propagateField)
dtMaxGlobal[2] = numeric_limits<Real>::max();
creal meanVlasovCFL = 0.5 * (P::vlasovSolverMaxCFL + P::vlasovSolverMinCFL);
creal meanFieldsCFL = 0.5 * (P::fieldSolverMaxCFL + P::fieldSolverMinCFL);
Real subcycleDt;
// reduce/increase dt if it is too high for any of the three propagators or too low for all propagators
if ((P::dt > dtMaxGlobal[0] * P::vlasovSolverMaxCFL ||
P::dt > dtMaxGlobal[1] * P::vlasovSolverMaxCFL * P::maxSlAccelerationSubcycles ||
P::dt > dtMaxGlobal[2] * P::fieldSolverMaxCFL * P::maxFieldSolverSubcycles) ||
(P::dt < dtMaxGlobal[0] * P::vlasovSolverMinCFL &&
P::dt < dtMaxGlobal[1] * P::vlasovSolverMinCFL * P::maxSlAccelerationSubcycles &&
P::dt < dtMaxGlobal[2] * P::fieldSolverMinCFL * P::maxFieldSolverSubcycles)) {
// new dt computed
isChanged = true;
// set new timestep to the lowest one of all interval-midpoints
newDt = meanVlasovCFL * dtMaxGlobal[0];
newDt = min(newDt, meanVlasovCFL * dtMaxGlobal[1] * P::maxSlAccelerationSubcycles);
newDt = min(newDt, meanFieldsCFL * dtMaxGlobal[2] * P::maxFieldSolverSubcycles);
logFile << "(TIMESTEP) New dt = " << newDt << " computed on step " << P::tstep << " at " << P::t
<< "s Maximum possible dt (not including vlasovsolver CFL " << P::vlasovSolverMinCFL << "-"
<< P::vlasovSolverMaxCFL << " or fieldsolver CFL " << P::fieldSolverMinCFL << "-" << P::fieldSolverMaxCFL
<< ") in {r, v, BE} was " << dtMaxGlobal[0] << " " << dtMaxGlobal[1] << " " << dtMaxGlobal[2] << " "
<< " Including subcycling { v, BE} was " << dtMaxGlobal[1] * P::maxSlAccelerationSubcycles << " "
<< dtMaxGlobal[2] * P::maxFieldSolverSubcycles << " " << endl
<< writeVerbose;
if (P::dynamicTimestep) {
subcycleDt = newDt;
} else {
logFile << "(TIMESTEP) However, fixed timestep in config overrides dt = " << P::dt << endl << writeVerbose;
subcycleDt = P::dt;
}
} else {
subcycleDt = P::dt;
}
// Subcycle if field solver dt < global dt (including CFL) (new or old dt hence the hassle with subcycleDt
if (meanFieldsCFL * dtMaxGlobal[2] < subcycleDt && P::propagateField) {
P::fieldSolverSubcycles =
min(convert<uint>(ceil(subcycleDt / (meanFieldsCFL * dtMaxGlobal[2]))), P::maxFieldSolverSubcycles);
} else {
P::fieldSolverSubcycles = 1;
}
}
ObjectWrapper& getObjectWrapper() {
return objectWrapper;
}
/** Get local cell IDs. This function creates a cached copy of the
* cell ID lists to significantly improve performance. The cell ID
* cache is recalculated every time the mesh partitioning changes.
* @return Local cell IDs.*/
const std::vector<CellID>& getLocalCells() {
return Parameters::localCells;
}
void recalculateLocalCellsCache() {
{
vector<CellID> dummy;
dummy.swap(Parameters::localCells);
}
Parameters::localCells = mpiGrid.get_cells();
}
int main(int argn,char* args[]) {
int myRank, doBailout=0;
const creal DT_EPSILON=1e-12;
typedef Parameters P;
Real newDt;
bool dtIsChanged {false};
// Before MPI_Init we hardwire some settings, if we are in OpenMPI
int required=MPI_THREAD_FUNNELED;
int provided, resultlen;
char mpiversion[MPI_MAX_LIBRARY_VERSION_STRING];
bool overrideMCAompio = false;
MPI_Get_library_version(mpiversion, &resultlen);
string versionstr = string(mpiversion);
stringstream mpiioMessage;
if(versionstr.find("Open MPI") != std::string::npos) {
#ifdef VLASIATOR_ALLOW_MCA_OMPIO
mpiioMessage << "We detected OpenMPI but the compilation flag VLASIATOR_ALLOW_MCA_OMPIO was set so we do not override the default MCA io flag." << endl;
#else
overrideMCAompio = true;
int index, count;
char io_value[64];
MPI_T_cvar_handle io_handle;
MPI_T_init_thread(required, &provided);
MPI_T_cvar_get_index("io", &index);
MPI_T_cvar_handle_alloc(index, NULL, &io_handle, &count);
MPI_T_cvar_write(io_handle, "^ompio");
MPI_T_cvar_read(io_handle, io_value);
MPI_T_cvar_handle_free(&io_handle);
mpiioMessage << "We detected OpenMPI so we set the cvars value to disable ompio, MCA io: " << io_value << endl;
#endif
}
// After the MPI_T settings we can init MPI all right.
MPI_Init_thread(&argn,&args,required,&provided);
MPI_Comm_rank(MPI_COMM_WORLD,&myRank);
if (required > provided){
if(myRank==MASTER_RANK) {
cerr << "(MAIN): MPI_Init_thread failed! Got " << provided << ", need "<<required <<endl;
}
exit(1);
}
if (myRank == MASTER_RANK) {
const char* mpiioenv = std::getenv("OMPI_MCA_io");
if(mpiioenv != nullptr) {
std::string mpiioenvstr(mpiioenv);
if(mpiioenvstr.find("^ompio") == std::string::npos) {
cout << mpiioMessage.str();
}
}
}
phiprof::initialize();
double initialWtime = MPI_Wtime();
SysBoundary& sysBoundaryContainer = getObjectWrapper().sysBoundaryContainer;
#ifdef CATCH_FPE
// WARNING FE_INEXACT is too sensitive to be used. See man fenv.
//feenableexcept(FE_DIVBYZERO|FE_INVALID|FE_OVERFLOW|FE_UNDERFLOW);
feenableexcept(FE_DIVBYZERO|FE_INVALID|FE_OVERFLOW);
//feenableexcept(FE_DIVBYZERO|FE_INVALID);
signal(SIGFPE, fpehandler);
#endif
phiprof::Timer mainTimer {"main"};
phiprof::Timer initTimer {"Initialization"};
phiprof::Timer readParamsTimer {"Read parameters"};
//init parameter file reader
Readparameters readparameters(argn,args);
P::addParameters();
getObjectWrapper().addParameters();
readparameters.parse();
P::getParameters();
getObjectWrapper().addPopulationParameters();
sysBoundaryContainer.addParameters();
projects::Project::addParameters();
Project* project = projects::createProject();
getObjectWrapper().project = project;
readparameters.parse(true, false); // 2nd parsing for specific population parameters
readparameters.helpMessage(); // Call after last parse, exits after printing help if help requested
getObjectWrapper().getParameters();
sysBoundaryContainer.getParameters();
project->getParameters();
readParamsTimer.stop();
//Get version and config info here
std::string version;
std::string config;
//Only master needs the info
if (myRank==MASTER_RANK){
version=readparameters.versionInfo();
config=readparameters.configInfo();
}
// Init parallel logger:
phiprof::Timer openLoggerTimer {"open logFile & diagnostic"};
//if restarting we will append to logfiles
if(!P::writeFullBGB) {
if (logFile.open(MPI_COMM_WORLD,MASTER_RANK,"logfile.txt",P::isRestart) == false) {
if(myRank == MASTER_RANK) cerr << "(MAIN) ERROR: Logger failed to open logfile!" << endl;
exit(1);
}
} else {
// If we are out to write the full background field and derivatives, we don't want to overwrite the existing run's logfile.
if (logFile.open(MPI_COMM_WORLD,MASTER_RANK,"logfile_fullbgbio.txt",false) == false) {
if(myRank == MASTER_RANK) cerr << "(MAIN) ERROR: Logger failed to open logfile_fullbgbio!" << endl;
exit(1);
}
}
if (P::diagnosticInterval != 0) {
if (diagnostic.open(MPI_COMM_WORLD,MASTER_RANK,"diagnostic.txt",P::isRestart) == false) {
if(myRank == MASTER_RANK) cerr << "(MAIN) ERROR: Logger failed to open diagnostic file!" << endl;
exit(1);
}
}
{
int mpiProcs;
MPI_Comm_size(MPI_COMM_WORLD,&mpiProcs);
logFile << "(MAIN) Starting simulation with " << mpiProcs << " MPI processes ";
#ifdef _OPENMP
logFile << "and " << omp_get_max_threads();
#else
logFile << "and 0";
#endif
logFile << " OpenMP threads per process" << endl << writeVerbose;
}
openLoggerTimer.stop();
// Init project
phiprof::Timer initProjectimer {"Init project"};
if (project->initialize() == false) {
if(myRank == MASTER_RANK) cerr << "(MAIN): Project did not initialize correctly!" << endl;
exit(1);
}
if (project->initialized() == false) {
if (myRank == MASTER_RANK) {
cerr << "(MAIN): Project base class was not initialized!" << endl;
cerr << "\t Call Project::initialize() in your project's initialize()-function." << endl;
exit(1);
}
}
initProjectimer.stop();
// Add VAMR refinement criterias:
vamr_ref_criteria::addRefinementCriteria();
// Initialize simplified Fieldsolver grids.
// Needs to be done here already ad the background field will be set right away, before going to initializeGrid even
phiprof::Timer initFsTimer {"Init fieldsolver grids"};
std::array<FsGridTools::FsSize_t, 3> fsGridDimensions = {convert<FsGridTools::FsSize_t>(P::xcells_ini * pow(2,P::amrMaxSpatialRefLevel)),
convert<FsGridTools::FsSize_t>(P::ycells_ini * pow(2,P::amrMaxSpatialRefLevel)),
convert<FsGridTools::FsSize_t>(P::zcells_ini * pow(2,P::amrMaxSpatialRefLevel))};
std::array<bool,3> periodicity{sysBoundaryContainer.isPeriodic(0),
sysBoundaryContainer.isPeriodic(1),
sysBoundaryContainer.isPeriodic(2)};
FsGridCouplingInformation gridCoupling;
FsGrid< std::array<Real, fsgrids::bfield::N_BFIELD>, FS_STENCIL_WIDTH> perBGrid(fsGridDimensions, MPI_COMM_WORLD, periodicity,gridCoupling, P::manualFsGridDecomposition);
FsGrid< std::array<Real, fsgrids::bfield::N_BFIELD>, FS_STENCIL_WIDTH> perBDt2Grid(fsGridDimensions, MPI_COMM_WORLD, periodicity,gridCoupling, P::manualFsGridDecomposition);
FsGrid< std::array<Real, fsgrids::efield::N_EFIELD>, FS_STENCIL_WIDTH> EGrid(fsGridDimensions, MPI_COMM_WORLD, periodicity,gridCoupling, P::manualFsGridDecomposition);
FsGrid< std::array<Real, fsgrids::efield::N_EFIELD>, FS_STENCIL_WIDTH> EDt2Grid(fsGridDimensions, MPI_COMM_WORLD, periodicity,gridCoupling, P::manualFsGridDecomposition);
FsGrid< std::array<Real, fsgrids::ehall::N_EHALL>, FS_STENCIL_WIDTH> EHallGrid(fsGridDimensions, MPI_COMM_WORLD, periodicity,gridCoupling, P::manualFsGridDecomposition);
FsGrid< std::array<Real, fsgrids::egradpe::N_EGRADPE>, FS_STENCIL_WIDTH> EGradPeGrid(fsGridDimensions, MPI_COMM_WORLD, periodicity,gridCoupling, P::manualFsGridDecomposition);
FsGrid< std::array<Real, fsgrids::moments::N_MOMENTS>, FS_STENCIL_WIDTH> momentsGrid(fsGridDimensions, MPI_COMM_WORLD, periodicity,gridCoupling, P::manualFsGridDecomposition);
FsGrid< std::array<Real, fsgrids::moments::N_MOMENTS>, FS_STENCIL_WIDTH> momentsDt2Grid(fsGridDimensions, MPI_COMM_WORLD, periodicity,gridCoupling, P::manualFsGridDecomposition);
FsGrid< std::array<Real, fsgrids::dperb::N_DPERB>, FS_STENCIL_WIDTH> dPerBGrid(fsGridDimensions, MPI_COMM_WORLD, periodicity,gridCoupling, P::manualFsGridDecomposition);
FsGrid< std::array<Real, fsgrids::dmoments::N_DMOMENTS>, FS_STENCIL_WIDTH> dMomentsGrid(fsGridDimensions, MPI_COMM_WORLD, periodicity,gridCoupling, P::manualFsGridDecomposition);
FsGrid< std::array<Real, fsgrids::bgbfield::N_BGB>, FS_STENCIL_WIDTH> BgBGrid(fsGridDimensions, MPI_COMM_WORLD, periodicity,gridCoupling, P::manualFsGridDecomposition);
FsGrid< std::array<Real, fsgrids::volfields::N_VOL>, FS_STENCIL_WIDTH> volGrid(fsGridDimensions, MPI_COMM_WORLD, periodicity,gridCoupling, P::manualFsGridDecomposition);
FsGrid< fsgrids::technical, FS_STENCIL_WIDTH> technicalGrid(fsGridDimensions, MPI_COMM_WORLD, periodicity,gridCoupling, P::manualFsGridDecomposition);
// Set DX, DY and DZ
// TODO: This is currently just taking the values from cell 1, and assuming them to be
// constant throughout the simulation.
perBGrid.DX = perBDt2Grid.DX = EGrid.DX = EDt2Grid.DX = EHallGrid.DX = EGradPeGrid.DX = momentsGrid.DX
= momentsDt2Grid.DX = dPerBGrid.DX = dMomentsGrid.DX = BgBGrid.DX = volGrid.DX = technicalGrid.DX
= P::dx_ini / pow(2, P::amrMaxSpatialRefLevel);
perBGrid.DY = perBDt2Grid.DY = EGrid.DY = EDt2Grid.DY = EHallGrid.DY = EGradPeGrid.DY = momentsGrid.DY
= momentsDt2Grid.DY = dPerBGrid.DY = dMomentsGrid.DY = BgBGrid.DY = volGrid.DY = technicalGrid.DY
= P::dy_ini / pow(2, P::amrMaxSpatialRefLevel);
perBGrid.DZ = perBDt2Grid.DZ = EGrid.DZ = EDt2Grid.DZ = EHallGrid.DZ = EGradPeGrid.DZ = momentsGrid.DZ
= momentsDt2Grid.DZ = dPerBGrid.DZ = dMomentsGrid.DZ = BgBGrid.DZ = volGrid.DZ = technicalGrid.DZ
= P::dz_ini / pow(2, P::amrMaxSpatialRefLevel);
// Set the physical start (lower left corner) X, Y, Z
perBGrid.physicalGlobalStart = perBDt2Grid.physicalGlobalStart = EGrid.physicalGlobalStart = EDt2Grid.physicalGlobalStart
= EHallGrid.physicalGlobalStart = EGradPeGrid.physicalGlobalStart = momentsGrid.physicalGlobalStart
= momentsDt2Grid.physicalGlobalStart = dPerBGrid.physicalGlobalStart = dMomentsGrid.physicalGlobalStart
= BgBGrid.physicalGlobalStart = volGrid.physicalGlobalStart = technicalGrid.physicalGlobalStart
= {P::xmin, P::ymin, P::zmin};
// Checking that spatial cells are cubic, otherwise field solver is incorrect (cf. derivatives in E, Hall term)
constexpr Real uniformTolerance=1e-3;
if ((abs((technicalGrid.DX - technicalGrid.DY) / technicalGrid.DX) >uniformTolerance) ||
(abs((technicalGrid.DX - technicalGrid.DZ) / technicalGrid.DX) >uniformTolerance) ||
(abs((technicalGrid.DY - technicalGrid.DZ) / technicalGrid.DY) >uniformTolerance)) {
if (myRank == MASTER_RANK) {
std::cerr << "WARNING: Your spatial cells seem not to be cubic. The simulation will now abort!" << std::endl;
}
//just abort sending SIGTERM to all tasks
MPI_Abort(MPI_COMM_WORLD, -1);
}
initFsTimer.stop();
// Initialize grid. After initializeGrid local cells have dist
// functions, and B fields set. Cells have also been classified for
// the various sys boundary conditions. All remote cells have been
// created. All spatial date computed this far is up to date for
// FULL_NEIGHBORHOOD. Block lists up to date for
// VLASOV_SOLVER_NEIGHBORHOOD (but dist function has not been communicated)
phiprof::Timer initGridsTimer {"Init grids"};
initializeGrids(
argn,
args,
mpiGrid,
perBGrid,
BgBGrid,
momentsGrid,
momentsDt2Grid,
EGrid,
EGradPeGrid,
volGrid,
technicalGrid,
sysBoundaryContainer,
*project
);
// There are projects that have non-uniform and non-zero perturbed B, e.g. Magnetosphere with dipole type 4.
// For inflow cells (e.g. maxwellian), we cannot take a FSgrid perturbed B value from the templateCell,
// because we need a copy of the value from initialization in both perBGrid and perBDt2Grid and it isn't
// touched as we are in boundary cells for components that aren't solved. We do a straight full copy instead
// of looping and detecting boundary types here.
perBDt2Grid.copyData(perBGrid);
const std::vector<CellID>& cells = getLocalCells();
initGridsTimer.stop();
// Initialize data reduction operators. This should be done elsewhere in order to initialize
// user-defined operators:
phiprof::Timer initDROsTimer {"Init DROs"};
DataReducer outputReducer, diagnosticReducer;
if(P::writeFullBGB) {
// We need the following variables for this, let's just erase and replace the entries in the list
P::outputVariableList.clear();
P::outputVariableList= {"fg_b_background", "fg_b_background_vol", "fg_derivs_b_background"};
}
initializeDataReducers(&outputReducer, &diagnosticReducer);
initDROsTimer.stop();
// Free up memory:
readparameters.~Readparameters();
if(P::writeFullBGB) {
logFile << "Writing out full BGB components and derivatives and exiting." << endl << writeVerbose;
// initialize the communicators so we can write out ionosphere grid metadata.
SBC::ionosphereGrid.updateIonosphereCommunicator(mpiGrid, technicalGrid);
P::systemWriteDistributionWriteStride.push_back(0);
P::systemWriteName.push_back("bgb");
P::systemWriteDistributionWriteXlineStride.push_back(0);
P::systemWriteDistributionWriteYlineStride.push_back(0);
P::systemWriteDistributionWriteZlineStride.push_back(0);
P::systemWritePath.push_back("./");
P::systemWriteFsGrid.push_back(true);
for(uint si=0; si<P::systemWriteName.size(); si++) {
P::systemWrites.push_back(0);
}
const bool writeGhosts = true;
if( writeGrid(mpiGrid,
perBGrid,
EGrid,
EHallGrid,
EGradPeGrid,
momentsGrid,
dPerBGrid,
dMomentsGrid,
BgBGrid,
volGrid,
technicalGrid,
version,
config,
&outputReducer,
P::systemWriteName.size()-1,
P::restartStripeFactor,
writeGhosts
) == false
) {
cerr << "FAILED TO WRITE GRID AT " << __FILE__ << " " << __LINE__ << endl;
}
initTimer.stop();
mainTimer.stop();
phiprof::print(MPI_COMM_WORLD,"phiprof");
if (myRank == MASTER_RANK) logFile << "(MAIN): Exiting." << endl << writeVerbose;
logFile.close();
if (P::diagnosticInterval != 0) diagnostic.close();
perBGrid.finalize();
perBDt2Grid.finalize();
EGrid.finalize();
EDt2Grid.finalize();
EHallGrid.finalize();
EGradPeGrid.finalize();
momentsGrid.finalize();
momentsDt2Grid.finalize();
dPerBGrid.finalize();
dMomentsGrid.finalize();
BgBGrid.finalize();
volGrid.finalize();
technicalGrid.finalize();
MPI_Finalize();
return 0;
}
// Run the field solver once with zero dt. This will initialize
// Fieldsolver dt limits, and also calculate volumetric B-fields.
// At restart, all we need at this stage has been read from the restart, the rest will be recomputed in due time.
if(P::isRestart == false) {
propagateFields(
perBGrid,
perBDt2Grid,
EGrid,
EDt2Grid,
EHallGrid,
EGradPeGrid,
momentsGrid,
momentsDt2Grid,
dPerBGrid,
dMomentsGrid,
BgBGrid,
volGrid,
technicalGrid,
sysBoundaryContainer, 0.0, 1.0
);
}
phiprof::Timer getFieldsTimer {"getFieldsFromFsGrid"};
volGrid.updateGhostCells();
getFieldsFromFsGrid(volGrid, BgBGrid, EGradPeGrid, technicalGrid, mpiGrid, cells);
getFieldsTimer.stop();
// Build communicator for ionosphere solving
SBC::ionosphereGrid.updateIonosphereCommunicator(mpiGrid, technicalGrid);
// If not a restart, perBGrid and dPerBGrid are up to date after propagateFields just above. Otherwise, we should compute them.
if(P::isRestart) {
calculateDerivativesSimple(
perBGrid,
perBDt2Grid,
momentsGrid,
momentsDt2Grid,
dPerBGrid,
dMomentsGrid,
technicalGrid,
sysBoundaryContainer,
RK_ORDER1, // Update and compute on non-dt2 grids.
false // Don't communicate moments, they are not needed here.
);
dPerBGrid.updateGhostCells();
}
FieldTracing::calculateIonosphereFsgridCoupling(technicalGrid, perBGrid, dPerBGrid, SBC::ionosphereGrid.nodes, SBC::Ionosphere::radius);
SBC::ionosphereGrid.initSolver(!P::isRestart); // If it is a restart we do not want to zero out everything
if(SBC::Ionosphere::couplingInterval > 0 && P::isRestart) {
SBC::Ionosphere::solveCount = floor(P::t / SBC::Ionosphere::couplingInterval)+1;
} else {
SBC::Ionosphere::solveCount = 1;
}
if(P::isRestart) {
// If it is a restart, we want to regenerate proper ig_inplanecurrent as well in case there's IO before the next solver step.
SBC::ionosphereGrid.calculateConductivityTensor(SBC::Ionosphere::F10_7, SBC::Ionosphere::recombAlpha, SBC::Ionosphere::backgroundIonisation, true);
}
if (P::isRestart == false) {
phiprof::Timer timer {"compute-dt"};
// Run Vlasov solver once with zero dt to initialize
// per-cell dt limits. In restarts, we read the dt from file.
calculateSpatialTranslation(mpiGrid,0.0);
calculateAcceleration(mpiGrid,0.0);
}
// Save restart data
if (P::writeInitialState) {
// Calculate these so refinement parameters can be tuned based on the vlsv
calculateScaledDeltasSimple(mpiGrid);
FieldTracing::reduceData(technicalGrid, perBGrid, dPerBGrid, mpiGrid, SBC::ionosphereGrid.nodes); /*!< Call the reductions (e.g. field tracing) */
phiprof::Timer timer {"write-initial-state"};
if (myRank == MASTER_RANK)
logFile << "(IO): Writing initial state to disk, tstep = " << endl << writeVerbose;
P::systemWriteDistributionWriteStride.push_back(1);
P::systemWriteName.push_back("initial-grid");
P::systemWriteDistributionWriteXlineStride.push_back(0);
P::systemWriteDistributionWriteYlineStride.push_back(0);
P::systemWriteDistributionWriteZlineStride.push_back(0);
P::systemWritePath.push_back("./");
P::systemWriteFsGrid.push_back(true);
for(uint si=0; si<P::systemWriteName.size(); si++) {
P::systemWrites.push_back(0);
}
const bool writeGhosts = true;
if( writeGrid(mpiGrid,
perBGrid, // TODO: Merge all the fsgrids passed here into one meta-object
EGrid,
EHallGrid,
EGradPeGrid,
momentsGrid,
dPerBGrid,
dMomentsGrid,
BgBGrid,
volGrid,
technicalGrid,
version,
config,
&outputReducer,
P::systemWriteName.size()-1,
P::restartStripeFactor,
writeGhosts
) == false
) {
cerr << "FAILED TO WRITE GRID AT " << __FILE__ << " " << __LINE__ << endl;
}
P::systemWriteDistributionWriteStride.pop_back();
P::systemWriteName.pop_back();
P::systemWriteDistributionWriteXlineStride.pop_back();
P::systemWriteDistributionWriteYlineStride.pop_back();
P::systemWriteDistributionWriteZlineStride.pop_back();
P::systemWritePath.pop_back();
P::systemWriteFsGrid.pop_back();
}
if (P::isRestart == false) {
//compute new dt
phiprof::Timer computeDtimer {"compute-dt"};
computeNewTimeStep(mpiGrid, technicalGrid, newDt, dtIsChanged);
if (P::dynamicTimestep == true && dtIsChanged == true) {
// Only actually update the timestep if dynamicTimestep is on
P::dt=newDt;
} else {
dtIsChanged = false;
}
computeDtimer.stop();
//go forward by dt/2 in V, initializes leapfrog split. In restarts the
//the distribution function is already propagated forward in time by dt/2
phiprof::Timer propagateHalfTimer {"propagate-velocity-space-dt/2"};
if (P::propagateVlasovAcceleration) {
calculateAcceleration(mpiGrid, 0.5*P::dt);
} else {
//zero step to set up moments _v
calculateAcceleration(mpiGrid, 0.0);
}
propagateHalfTimer.stop();
// Apply boundary conditions
if (P::propagateVlasovTranslation || P::propagateVlasovAcceleration ) {
phiprof::Timer updateBoundariesTimer {("update system boundaries (Vlasov post-acceleration)")};
sysBoundaryContainer.applySysBoundaryVlasovConditions(mpiGrid, 0.5*P::dt, true);
updateBoundariesTimer.stop();
addTimedBarrier("barrier-boundary-conditions");
}
// Also update all moments. They won't be transmitted to FSgrid until the field solver is called, though.
phiprof::Timer computeMomentsTimer {"Compute interp moments"};
calculateInterpolatedVelocityMoments(
mpiGrid,
CellParams::RHOM,
CellParams::VX,
CellParams::VY,
CellParams::VZ,
CellParams::RHOQ,
CellParams::P_11,
CellParams::P_22,
CellParams::P_33
);
computeMomentsTimer.stop();
}
initTimer.stop();
// ***********************************
// ***** INITIALIZATION COMPLETE *****
// ***********************************
// Main simulation loop:
if (myRank == MASTER_RANK){
logFile << "(MAIN): Starting main simulation loop." << endl << writeVerbose;
//report filtering if we are in an AMR run
if (P::amrMaxSpatialRefLevel>0){
logFile<<"Filtering Report: "<<endl;
for (int refLevel=0 ; refLevel<= P::amrMaxSpatialRefLevel; refLevel++){
logFile<<"\tRefinement Level " <<refLevel<<"==> Passes "<<P::numPasses.at(refLevel)<<endl;
}
logFile<<endl;
}
}
phiprof::Timer reportMemTimer {"report-memory-consumption"};
report_process_memory_consumption();
reportMemTimer.stop();
unsigned int computedCells=0;
unsigned int computedTotalCells=0;
//Compute here based on time what the file intervals are
P::systemWrites.clear();
for(uint i=0;i< P::systemWriteTimeInterval.size();i++){
int index=(int)(P::t_min/P::systemWriteTimeInterval[i]);
//if we are already over 1% further than the time interval time that
//is requested for writing, then jump to next writing index. This is to
//make sure that at restart we do not write in the middle of
//the interval.
if(P::t_min>(index+0.01)*P::systemWriteTimeInterval[i]) {
index++;
// Special case for large timesteps
int index2=(int)((P::t_min+P::dt)/P::systemWriteTimeInterval[i]);
if (index2>index) index=index2;
}
P::systemWrites.push_back(index);
}
// Invalidate cached cell lists just to be sure (might not be needed)
P::meshRepartitioned = true;
unsigned int wallTimeRestartCounter=1;
int doNow[3] = {0}; // 0: writeRestartNow, 1: balanceLoadNow, 2: refineNow ; declared outside main loop
int writeRestartNow; // declared outside main loop
bool overrideRebalanceNow = false; // declared outside main loop
bool refineNow = false; // declared outside main loop
addTimedBarrier("barrier-end-initialization");
phiprof::Timer simulationTimer {"Simulation"};
double startTime= MPI_Wtime();
double beforeTime = MPI_Wtime();
double beforeSimulationTime=P::t_min;
double beforeStep=P::tstep_min;
while(P::tstep <= P::tstep_max &&
P::t-P::dt <= P::t_max+DT_EPSILON &&
wallTimeRestartCounter <= P::exitAfterRestarts) {
addTimedBarrier("barrier-loop-start");
phiprof::Timer ioTimer {"IO"};
phiprof::Timer externalsTimer {"checkExternalCommands"};
if(myRank == MASTER_RANK) {
// check whether STOP or KILL or SAVE has been passed, should be done by MASTER_RANK only as it can reset P::bailout_write_restart
checkExternalCommands();
}
externalsTimer.stop();
//write out phiprof profiles and logs with a lower interval than normal
//diagnostic (every 10 diagnostic intervals).
phiprof::Timer loggingTimer {"logfile-io"};
logFile << "---------- tstep = " << P::tstep << " t = " << P::t <<" dt = " << P::dt << " FS cycles = " << P::fieldSolverSubcycles << " ----------" << endl;
if (P::diagnosticInterval != 0 &&
P::tstep % (P::diagnosticInterval*10) == 0 &&
P::tstep-P::tstep_min >0) {
phiprof::print(MPI_COMM_WORLD,"phiprof");
double currentTime=MPI_Wtime();
double timePerStep=double(currentTime - beforeTime) / (P::tstep-beforeStep);
double timePerSecond=double(currentTime - beforeTime) / (P::t-beforeSimulationTime + DT_EPSILON);
double remainingTime=min(timePerStep*(P::tstep_max-P::tstep),timePerSecond*(P::t_max-P::t));
time_t finalWallTime=time(NULL)+(time_t)remainingTime; //assume time_t is in seconds, as it is almost always
struct tm *finalWallTimeInfo=localtime(&finalWallTime);
logFile << "(TIME) current walltime/step " << timePerStep<< " s" <<endl;
logFile << "(TIME) current walltime/simusecond " << timePerSecond<<" s" <<endl;
logFile << "(TIME) Estimated completion time is " <<asctime(finalWallTimeInfo)<<endl;
//reset before values, we want to report speed since last report of speed.
beforeTime = MPI_Wtime();
beforeSimulationTime=P::t;
beforeStep=P::tstep;
}
logFile << writeVerbose;
loggingTimer.stop();
// Check whether diagnostic output has to be produced
if (P::diagnosticInterval != 0 && P::tstep % P::diagnosticInterval == 0) {
phiprof::Timer memTimer {"memory-report"};
memTimer.start();
report_process_memory_consumption();
memTimer.stop();
phiprof::Timer cellTimer {"cell-count-report"};
cellTimer.start();
report_cell_and_block_counts(mpiGrid);
cellTimer.stop();
phiprof::Timer diagnosticTimer {"diagnostic-io"};
if (writeDiagnostic(mpiGrid, diagnosticReducer) == false) {
if(myRank == MASTER_RANK) cerr << "ERROR with diagnostic computation" << endl;
}
}
// write system, loop through write classes
for (uint i = 0; i < P::systemWriteTimeInterval.size(); i++) {
if (P::systemWriteTimeInterval[i] >= 0.0 &&
P::t >= P::systemWrites[i] * P::systemWriteTimeInterval[i] - DT_EPSILON) {
// If we have only just restarted, the bulk file should already exist from the previous slot.
if ((P::tstep == P::tstep_min) && (P::tstep>0)) {
P::systemWrites[i]++;
// Special case for large timesteps
int index2=(int)((P::t+P::dt)/P::systemWriteTimeInterval[i]);
if (index2>P::systemWrites[i]) P::systemWrites[i]=index2;
continue;
}
// Calculate these so refinement parameters can be tuned based on the vlsv
calculateScaledDeltasSimple(mpiGrid);
FieldTracing::reduceData(technicalGrid, perBGrid, dPerBGrid, mpiGrid, SBC::ionosphereGrid.nodes); /*!< Call the reductions (e.g. field tracing) */
phiprof::Timer writeSysTimer {"write-system"};
logFile << "(IO): Writing spatial cell and reduced system data to disk, tstep = " << P::tstep << " t = " << P::t << endl << writeVerbose;
const bool writeGhosts = true;
if(writeGrid(mpiGrid,
perBGrid, // TODO: Merge all the fsgrids passed here into one meta-object
EGrid,
EHallGrid,
EGradPeGrid,
momentsGrid,
dPerBGrid,
dMomentsGrid,
BgBGrid,
volGrid,
technicalGrid,
version,
config,
&outputReducer,
i,
P::systemStripeFactor,
writeGhosts
) == false
) {
cerr << "FAILED TO WRITE GRID AT" << __FILE__ << " " << __LINE__ << endl;
}
P::systemWrites[i]++;
// Special case for large timesteps
int index2=(int)((P::t+P::dt)/P::systemWriteTimeInterval[i]);
if (index2>P::systemWrites[i]) P::systemWrites[i]=index2;
logFile << "(IO): .... done!" << endl << writeVerbose;
}
}
// Reduce globalflags::bailingOut from all processes
phiprof::Timer bailoutReduceTimer {"Bailout-allreduce"};
MPI_Allreduce(&(globalflags::bailingOut), &(doBailout), 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
bailoutReduceTimer.stop();
// Write restart data if needed
// Combined with checking of additional load balancing to have only one collective call.
phiprof::Timer restartCheckTimer {"compute-is-restart-written-and-extra-LB"};
if (myRank == MASTER_RANK) {
if ( (P::saveRestartWalltimeInterval >= 0.0
&& (P::saveRestartWalltimeInterval*wallTimeRestartCounter <= MPI_Wtime()-initialWtime
|| P::tstep == P::tstep_max
|| P::t >= P::t_max))
|| (doBailout > 0 && P::bailout_write_restart)
|| globalflags::writeRestart
) {
doNow[0] = 1;
if (globalflags::writeRestart == true) {
doNow[0] = 2; // Setting to 2 so as to not increment the restart count below.
globalflags::writeRestart = false; // This flag is only used by MASTER_RANK here and it needs to be reset after a restart write has been issued.
}
}
else {
doNow[0] = 0;
}
if (globalflags::balanceLoad || globalflags::doRefine) {
doNow[1] = 1;
globalflags::balanceLoad = false;
if (globalflags::doRefine) {
doNow[2] = 1;
globalflags::doRefine = false;
}
}
}
MPI_Bcast( &doNow, 3 , MPI_INT , MASTER_RANK ,MPI_COMM_WORLD);