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iowrite.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.
*/
/*! \file vlsvdiff.cpp
\brief File containing write IO for vlasiator. More info at: https://agora.fmi.fi/display/CORSAIR/VLSV+File+Format
*/
#include <cstdlib>
#include <iostream>
#include <iomanip> // for setprecision()
#include <cmath>
#include <sstream>
#include <ctime>
#include <cstring>
#include <array>
#include <algorithm>
#include <limits>
#include "iowrite.h"
#include "grid.h"
#include "phiprof.hpp"
#include "parameters.h"
#include "logger.h"
#include "vlasovmover.h"
#include "object_wrapper.h"
using namespace std;
using namespace phiprof;
using namespace vlsv;
extern Logger logFile, diagnostic;
typedef Parameters P;
bool writeVelocityDistributionData(const uint popID,Writer& vlsvWriter,
dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
const std::vector<CellID>& cells,MPI_Comm comm);
/*! Updates local ids across MPI to let other processes know in which order this process saves the local cell ids
\param mpiGrid Vlasiator's MPI grid
\param local_cells local cells on in the current process (no ghost cells included)
\param comm The MPi comm
\return Returns true if operation was successful
*/
bool updateLocalIds( dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
const std::vector<CellID> & local_cells,
MPI_Comm comm ) {
int myRank;
MPI_Comm_rank(comm,&myRank);
//Declare an iterator for iterating though the cell ids
vector<CellID>::const_iterator it;
//Local ids for the process start from 0 (this is used in the iteration)
CellID thisProcessLocalId = 0;
//Iterate through local cells
for( it = local_cells.begin(); it != local_cells.end(); ++it ) {
//NOTE: (*it) = cellId
//Set the local id
mpiGrid[(*it)]->ioLocalCellId = thisProcessLocalId;
//Increment the local id
thisProcessLocalId++;
}
//Update the local ids (let the other processes know they've been updated)
SpatialCell::set_mpi_transfer_type(Transfer::CELL_IOLOCALCELLID);
mpiGrid.update_copies_of_remote_neighbors(FULL_NEIGHBORHOOD_ID);
return true;
}
/*! Checks the success of write IO
\param success Parameter for determining whether the IO has been successful
\param errorMessage The message to be shown if global success is false
\param comm The MPI comm
\return Returns true if all of the processes running this function had success value of true, false otherwise
*/
bool globalSuccess(bool success,string errorMessage,MPI_Comm comm){
int successInt;
int globalSuccessInt;
if(success)
successInt=1;
else
successInt=0;
MPI_Allreduce(&successInt,&globalSuccessInt,1,MPI_INT,MPI_MIN,comm);
if(globalSuccessInt==1) {
return true;
}
else{
logFile << errorMessage << endl<<write ;
return false;
}
}
/** Writes the velocity distribution into the file.
@param vlsvWriter Some vlsv writer with a file open.
@param mpiGrid Vlasiator's grid.
@param cells Vector of local cells within this process (no ghost cells).
@param comm The MPI communicator.
@return Returns true if operation was successful.*/
bool writeVelocityDistributionData(Writer& vlsvWriter,
dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
const vector<CellID>& cells,MPI_Comm comm) {
bool success = true;
for (size_t p=0; p<getObjectWrapper().particleSpecies.size(); ++p) {
if (writeVelocityDistributionData(p,vlsvWriter,mpiGrid,cells,comm) == false) success = false;
}
return success;
}
/** Writes the velocity distribution of specified population into the file.
@param vlsvWriter Some vlsv writer with a file open.
@param mpiGrid Vlasiator's grid.
@param cells Vector of local cells within this process (no ghost cells).
@param comm The MPI communicator.
@return Returns true if operation was successful.*/
bool writeVelocityDistributionData(const uint popID,Writer& vlsvWriter,
dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
const std::vector<CellID>& cells,MPI_Comm comm) {
// Write velocity blocks and related data.
// In restart we just write velocity grids for all cells.
// First write global Ids of those cells which write velocity blocks (here: all cells):
map<string,string> attribs;
const string popName = getObjectWrapper().particleSpecies[popID].name;
const string spatMeshName = "SpatialGrid";
attribs["name"] = popName;
bool success=true;
// Compute totalBlocks
uint64_t totalBlocks = 0;
vector<vmesh::LocalID> blocksPerCell;
for (size_t cell=0; cell<cells.size(); ++cell){
totalBlocks+=mpiGrid[cells[cell]]->get_number_of_velocity_blocks(popID);
blocksPerCell.push_back(mpiGrid[cells[cell]]->get_number_of_velocity_blocks(popID));
}
// The name of the mesh is "SpatialGrid"
attribs["mesh"] = spatMeshName;
const unsigned int vectorSize = 1;
// Write the array:
if (vlsvWriter.writeArray("CELLSWITHBLOCKS",attribs,cells.size(),vectorSize,cells.data()) == false) success = false;
if (success == false) logFile << "(MAIN) writeGrid: ERROR failed to write CELLSWITHBLOCKS to file!" << endl << writeVerbose;
// Write blocks per cell, this has to be in the same order as cellswitblocks so that extracting works
if(vlsvWriter.writeArray("BLOCKSPERCELL",attribs,blocksPerCell.size(),vectorSize,blocksPerCell.data()) == false) success = false;
if (success == false) logFile << "(MAIN) writeGrid: ERROR failed to write CELLSWITHBLOCKS to file!" << endl << writeVerbose;
// Write (partial) velocity mesh data
// The mesh bounding box gives the outer extent of the available velocity space
// in blocks and cells. Note that this is not the physical extent of that
// space, but a purely numerical bounding box.
uint64_t bbox[6];
const size_t meshID = getObjectWrapper().particleSpecies[popID].velocityMesh;
bbox[0] = getObjectWrapper().velocityMeshes[meshID].gridLength[0];
bbox[1] = getObjectWrapper().velocityMeshes[meshID].gridLength[1];
bbox[2] = getObjectWrapper().velocityMeshes[meshID].gridLength[2];
bbox[3] = getObjectWrapper().velocityMeshes[meshID].blockLength[0];
bbox[4] = getObjectWrapper().velocityMeshes[meshID].blockLength[1];
bbox[5] = getObjectWrapper().velocityMeshes[meshID].blockLength[2];
attribs.clear();
attribs["mesh"] = getObjectWrapper().particleSpecies[popID].name;
attribs["type"] = vlsv::mesh::STRING_UCD_AMR;
// stringstream is necessary here to correctly convert refLevelMaxAllowed into a string
stringstream ss;
ss << static_cast<unsigned int>(getObjectWrapper().velocityMeshes[meshID].refLevelMaxAllowed);
attribs["max_velocity_ref_level"] = ss.str();
if (mpiGrid.get_rank() == MASTER_RANK) {
if (vlsvWriter.writeArray("MESH_BBOX",attribs,6,1,bbox) == false) success = false;
for (int crd=0; crd<3; ++crd) {
const size_t N_nodes = bbox[crd]*bbox[crd+3]+1;
Real* crds = new Real[N_nodes];
const Real dV = getObjectWrapper().velocityMeshes[meshID].cellSize[crd];
for (size_t i=0; i<N_nodes; ++i) {
crds[i] = getObjectWrapper().velocityMeshes[meshID].meshMinLimits[crd] + i*dV;
}
if (crd == 0) {
if (vlsvWriter.writeArray("MESH_NODE_CRDS_X",attribs,N_nodes,1,crds) == false) success = false;
}
if (crd == 1) {
if (vlsvWriter.writeArray("MESH_NODE_CRDS_Y",attribs,N_nodes,1,crds) == false) success = false;
}
if (crd == 2) {
if (vlsvWriter.writeArray("MESH_NODE_CRDS_Z",attribs,N_nodes,1,crds) == false) success = false;
}
delete [] crds; crds = NULL;
}
} else {
if (vlsvWriter.writeArray("MESH_BBOX",attribs,0,1,bbox) == false) success = false;
Real* crds = NULL;
if (vlsvWriter.writeArray("MESH_NODE_CRDS_X",attribs,0,1,crds) == false) success = false;
if (vlsvWriter.writeArray("MESH_NODE_CRDS_Y",attribs,0,1,crds) == false) success = false;
if (vlsvWriter.writeArray("MESH_NODE_CRDS_Z",attribs,0,1,crds) == false) success = false;
}
// Write velocity block IDs
vector<vmesh::GlobalID> velocityBlockIds;
try {
velocityBlockIds.reserve( totalBlocks );
// gather data for writing
for (size_t cell=0; cell<cells.size(); ++cell) {
SpatialCell* SC = mpiGrid[cells[cell]];
for (vmesh::LocalID block_i=0; block_i<SC->get_number_of_velocity_blocks(popID); ++block_i) {
vmesh::GlobalID block = SC->get_velocity_block_global_id(block_i,popID);
velocityBlockIds.push_back( block );
}
}
} catch (...) {
cerr << "FAILED TO WRITE VELOCITY BLOCK IDS AT: " << __FILE__ << " " << __LINE__ << endl;
success=false;
}
if (globalSuccess(success,"(MAIN) writeGrid: ERROR: Failed to fill temporary array velocityBlockIds",MPI_COMM_WORLD) == false) {
vlsvWriter.close();
return false;
}
attribs.clear();
attribs["mesh"] = spatMeshName;
attribs["name"] = popName;
if (vlsvWriter.writeArray("BLOCKIDS", attribs, totalBlocks, vectorSize, velocityBlockIds.data()) == false) success = false;
if (success == false) logFile << "(MAIN) writeGrid: ERROR failed to write BLOCKIDS to file!" << endl << writeVerbose;
{
vector<vmesh::GlobalID>().swap(velocityBlockIds);
}
// Write the velocity space data
// set everything that is needed for writing in data such as the array name, size, datatype, etc..
attribs.clear();
attribs["mesh"] = spatMeshName; // Name of the spatial mesh
attribs["name"] = popName; // Name of the velocity space distribution is written avgs
const string datatype_avgs = "float";
const uint64_t arraySize_avgs = totalBlocks;
const uint64_t vectorSize_avgs = WID3; // There are 64 elements in every velocity block
// Get the data size needed for writing in data
uint64_t dataSize_avgs = sizeof(Realf);
// Start multi write
vlsvWriter.startMultiwrite(datatype_avgs,arraySize_avgs,vectorSize_avgs,dataSize_avgs);
// Loop over cells
for (size_t cell = 0; cell<cells.size(); ++cell) {
// Get the spatial cell
SpatialCell* SC = mpiGrid[cells[cell]];
// Get the number of blocks in this cell
const uint64_t arrayElements = SC->get_number_of_velocity_blocks(popID);
char* arrayToWrite = reinterpret_cast<char*>(SC->get_data(popID));
// Add a subarray to write
vlsvWriter.addMultiwriteUnit(arrayToWrite, arrayElements); // Note: We told beforehands that the vectorsize = WID3 = 64
}
if (cells.size() == 0) {
vlsvWriter.addMultiwriteUnit(NULL, 0); //Dummy write to avoid hang in end multiwrite
}
// Write the subarrays
vlsvWriter.endMultiwrite("BLOCKVARIABLE", attribs);
if (globalSuccess(success,"(MAIN) writeGrid: ERROR: Failed to fill temporary velocityBlockData array",MPI_COMM_WORLD) == false) {
vlsvWriter.close();
return false;
}
if (success ==false) {
logFile << "(MAIN) writeGrid: ERROR occurred when writing BLOCKVARIABLE f" << endl << writeVerbose;
}
return success;
}
/*! Writes info received from data reducer. This function writes out the variable arrays into the file
\param mpiGrid The Vlasiator's grid
\param cells List of local cells (no ghost cells included)
\param writeAsFloat If true, the data reducer writes variable arrays as float instead of double
\param dataReducer The data reducer which contains the necessary functions for calculating variables
\param dataReducerIndex Index in the data reducer (determines which variable to read) Note: size of the data reducer can be retrieved with dataReducer.size()
\param vlsvWriter Some vlsv writer with a file open
\return Returns true if operation was successful
*/
bool writeDataReducer(const dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
const std::vector<CellID>& cells,
FsGrid< std::array<Real, fsgrids::bfield::N_BFIELD>, FS_STENCIL_WIDTH> & perBGrid,
FsGrid< std::array<Real, fsgrids::efield::N_EFIELD>, FS_STENCIL_WIDTH> & EGrid,
FsGrid< std::array<Real, fsgrids::ehall::N_EHALL>, FS_STENCIL_WIDTH> & EHallGrid,
FsGrid< std::array<Real, fsgrids::egradpe::N_EGRADPE>, FS_STENCIL_WIDTH> & EGradPeGrid,
FsGrid< std::array<Real, fsgrids::moments::N_MOMENTS>, FS_STENCIL_WIDTH> & momentsGrid,
FsGrid< std::array<Real, fsgrids::dperb::N_DPERB>, FS_STENCIL_WIDTH> & dPerBGrid,
FsGrid< std::array<Real, fsgrids::dmoments::N_DMOMENTS>, FS_STENCIL_WIDTH> & dMomentsGrid,
FsGrid< std::array<Real, fsgrids::bgbfield::N_BGB>, FS_STENCIL_WIDTH> & BgBGrid,
FsGrid< std::array<Real, fsgrids::volfields::N_VOL>, FS_STENCIL_WIDTH> & volGrid,
FsGrid< fsgrids::technical, FS_STENCIL_WIDTH> & technicalGrid,
const bool writeAsFloat,
DataReducer& dataReducer,
int dataReducerIndex,
Writer& vlsvWriter){
map<string,string> attribs;
string variableName,dataType,unitString,unitStringLaTeX, variableStringLaTeX, unitConversionFactor;
bool success=true;
const string meshName = "SpatialGrid";
variableName = dataReducer.getName(dataReducerIndex);
phiprof::start("DRO_"+variableName);
// If the DataReducer can write its data directly to the output file, do it here.
// Otherwise the output data is buffered and written below.
if (dataReducer.handlesWriting(dataReducerIndex) == true) {
success = dataReducer.writeData(dataReducerIndex,mpiGrid,cells,meshName,vlsvWriter);
phiprof::stop("DRO_"+variableName);
return success;
}
//Get basic data on a variable:
uint dataSize,vectorSize;
attribs["mesh"] = meshName;
attribs["name"] = variableName;
if (dataReducer.getDataVectorInfo(dataReducerIndex,dataType,dataSize,vectorSize) == false) {
cerr << "ERROR when requesting info from DRO " << dataReducerIndex << endl;
phiprof::stop("DRO_"+variableName);
return false;
}
// Request variable unit metadata: unit, latex-formatted unit, and conversion factor to SI
if (dataReducer.getMetadata(dataReducerIndex,unitString,unitStringLaTeX,variableStringLaTeX,unitConversionFactor) == false) {
cerr << "ERROR when requesting unit metadata from DRO " << dataReducerIndex << endl;
phiprof::stop("DRO_"+variableName);
return false;
}
attribs["unit"]=unitString;
attribs["unitLaTeX"]=unitStringLaTeX;
attribs["unitConversion"]=unitConversionFactor;
attribs["variableLaTeX"]=variableStringLaTeX;
// If DRO has a vector size of 0 it means this DRO should not write out anything. This is used e.g. for DROs we want only for certain populations.
if (vectorSize == 0) {
phiprof::stop("DRO_"+variableName);
return true;
}
const uint64_t varBufferArraySize = cells.size()*vectorSize*dataSize;
//Request DataReductionOperator to calculate the reduced data for all local cells:
char* varBuffer = NULL;
try {
varBuffer = new char[varBufferArraySize];
} catch( bad_alloc& ) {
cerr << "ERROR, FAILED TO ALLOCATE MEMORY AT: " << __FILE__ << " " << __LINE__ << endl;
logFile << "(MAIN) writeGrid: ERROR FAILED TO ALLOCATE MEMORY AT: " << __FILE__ << " " << __LINE__ << endl << writeVerbose;
phiprof::stop("DRO_"+variableName);
return false;
}
for (size_t cell=0; cell<cells.size(); ++cell) {
//Reduce data ( return false if the operation fails )
if (dataReducer.reduceData(mpiGrid[cells[cell]],dataReducerIndex,varBuffer + cell*vectorSize*dataSize) == false){
success = false;
// Note that this is not an error (anymore), since fsgrid reducers will return false here.
}
}
if( success ) {
if( (writeAsFloat == true && dataType.compare("float") == 0) && dataSize == sizeof(double) ) {
double * varBuffer_double = reinterpret_cast<double*>(varBuffer);
//Declare smaller varbuffer:
const uint64_t arraySize_smaller = cells.size();
const uint32_t vectorSize_smaller = vectorSize;
const uint32_t dataSize_smaller = sizeof(float);
const string dataType_smaller = dataType;
float * varBuffer_smaller = NULL;
try {
varBuffer_smaller = new float[arraySize_smaller * vectorSize_smaller];
} catch( bad_alloc& ) {
cerr << "ERROR, FAILED TO ALLOCATE MEMORY AT: " << __FILE__ << " " << __LINE__ << endl;
logFile << "(MAIN) writeGrid: ERROR FAILED TO ALLOCATE MEMORY AT: " << __FILE__ << " " << __LINE__ << endl << writeVerbose;
delete[] varBuffer;
varBuffer = NULL;
phiprof::stop("DRO_"+variableName);
return false;
}
//Input varBuffer_double into varBuffer_smaller:
for( uint64_t i = 0; i < arraySize_smaller * vectorSize_smaller; ++i ) {
const double value = varBuffer_double[i];
varBuffer_smaller[i] = (float)(value);
}
//Cast the varBuffer to char:
char * varBuffer_smaller_char = reinterpret_cast<char*>(varBuffer_smaller);
//Write the array:
phiprof::start("writeArray");
if (vlsvWriter.writeArray("VARIABLE", attribs, dataType_smaller, arraySize_smaller, vectorSize_smaller, dataSize_smaller, varBuffer_smaller_char) == false) {
success = false;
logFile << "(MAIN) writeGrid: ERROR failed to write datareductionoperator data to file!" << endl << writeVerbose;
}
phiprof::stop("writeArray");
delete[] varBuffer_smaller;
varBuffer_smaller = NULL;
} else {
// Write reduced data to file if DROP was successful:
phiprof::start("writeArray");
if (vlsvWriter.writeArray("VARIABLE",attribs, dataType, cells.size(), vectorSize, dataSize, varBuffer) == false) {
success = false;
logFile << "(MAIN) writeGrid: ERROR failed to write datareductionoperator data to file!" << endl << writeVerbose;
}
phiprof::stop("writeArray");
}
} else {
// If the data reducer didn't want to write dccrg data, maybe it will be happy
// dumping data straight from fsgrid into our file.
phiprof::start("writeFsGrid");
success = dataReducer.writeFsGridData(perBGrid,EGrid,EHallGrid,EGradPeGrid,momentsGrid,dPerBGrid,dMomentsGrid,BgBGrid,volGrid, technicalGrid, "fsgrid", dataReducerIndex, vlsvWriter, writeAsFloat);
phiprof::stop("writeFsGrid");
}
// Check if the DataReducer wants to write paramters to the output file
if (dataReducer.hasParameters(dataReducerIndex) == true) {
success = dataReducer.writeParameters(dataReducerIndex,vlsvWriter);
}
delete[] varBuffer;
varBuffer = NULL;
phiprof::stop("DRO_"+variableName);
return success;
}
/*! Writes common grid data such as parameters (time steps, x_min, ..) as well as local cell ids as variables
\param vlsvWriter Some vlsv writer with a file open
\param mpiGrid Vlasiator's grid
\param local_cells The local cell ids in this process
\param fileIndex File index, file will be called "name.index.vlsv"
\param comm The MPI comm
\return Returns true if operation was successful
*/
bool writeCommonGridData(
Writer& vlsvWriter,
dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
const vector<uint64_t>& local_cells,
const uint& fileIndex,
MPI_Comm comm
) {
// Writes parameters and cell ids into the VLSV file
int myRank;
MPI_Comm_rank(comm, &myRank);
const int masterProcessId = 0;
//Write local cells into array as a variable:
//Note: This needs to be done separately from the array MESH
const short unsigned int vectorSize = 1;
const uint32_t arraySize = local_cells.size();
map<string, string> xmlAttributes;
xmlAttributes["name"] = "CellID";
xmlAttributes["mesh"] = "SpatialGrid";
if( vlsvWriter.writeArray( "VARIABLE", xmlAttributes, arraySize, vectorSize, local_cells.data() ) == false ) {
return false;
}
//Write parameters:
if( vlsvWriter.writeParameter("time", &P::t) == false ) { return false; }
if( vlsvWriter.writeParameter("dt", &P::dt) == false ) { return false; }
if( vlsvWriter.writeParameter("timestep", &P::tstep) == false ) { return false; }
if( vlsvWriter.writeParameter("fieldSolverSubcycles", &P::fieldSolverSubcycles) == false ) { return false; }
if( vlsvWriter.writeParameter("fileIndex", &fileIndex) == false ) { return false; }
if( vlsvWriter.writeParameter("xmin", &P::xmin) == false ) { return false; }
if( vlsvWriter.writeParameter("xmax", &P::xmax) == false ) { return false; }
if( vlsvWriter.writeParameter("ymin", &P::ymin) == false ) { return false; }
if( vlsvWriter.writeParameter("ymax", &P::ymax) == false ) { return false; }
if( vlsvWriter.writeParameter("zmin", &P::zmin) == false ) { return false; }
if( vlsvWriter.writeParameter("zmax", &P::zmax) == false ) { return false; }
if( vlsvWriter.writeParameter("xcells_ini", &P::xcells_ini) == false ) { return false; }
if( vlsvWriter.writeParameter("ycells_ini", &P::ycells_ini) == false ) { return false; }
if( vlsvWriter.writeParameter("zcells_ini", &P::zcells_ini) == false ) { return false; }
//Mark the new version:
float version = 3.00;
if( vlsvWriter.writeParameter( "version", &version ) == false ) { return false; }
return true;
}
/*! Writes ghost cell ids into the file
\param mpiGrid Vlasiator's grid
\param vlsvWriter Some vlsv writer with a file open
\param meshName Name of the mesh (If unsure, put SpatialGrid)
\param ghost_cells List of cell ids on the process boundary (Ghost cells)
\return Returns true if operation was successful
\sa updateLocalIds
*/
bool writeGhostZoneDomainAndLocalIdNumbers( dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
Writer & vlsvWriter,
const string & meshName,
const vector<uint64_t> & ghost_cells ) {
//Declare vectors for storing data
vector<uint64_t> ghostDomainIds;
ghostDomainIds.reserve( ghost_cells.size() );
vector<uint64_t> ghostLocalIds;
ghostLocalIds.reserve( ghost_cells.size() );
//Iterate through all ghost zones:
vector<uint64_t>::const_iterator it;
for( it = ghost_cells.begin(); it != ghost_cells.end(); ++it ) {
//Domain id is the MPI process rank owning the ghost zone
//get the local id of the zone in the process where THIS ghost zone is a local zone:
//In order to do this we need MPI (Done in createZone)
//Example:
//Marking zones with a letter A, B, C, D etc and local ids are numbers above the zones
//local id: 0 1 2 3 4 5
//Process 1. has: local zones ( A, B, C ), ghost zones ( D E F )
//local id: 0 1 2
//Process 2. has: local zones ( D, G ), ghost zones ( H )
//Now if we're in process 1. and our ghost zone is D, its domainId would be 2. because process 2. has D as local zone
//In process 2, the local id of D is 0, so that's the local id we want now
//The local id is being saved in createZone function
//Append to the vectors Note: Check updateLocalIds function
ghostDomainIds.push_back( mpiGrid.get_process( *it ) );
ghostLocalIds.push_back( mpiGrid[(*it)]->ioLocalCellId );
}
//We need the number of ghost zones for vlsvWriter:
uint64_t numberOfGhosts = ghost_cells.size();
//Write:
map<string, string> xmlAttributes; //Used for writing in info
//Note: should be "SpatialGrid"
xmlAttributes["mesh"] = meshName;
const unsigned int vectorSize = 1;
//Write the in the number of ghost domains: (Returns false if writing fails)
if( vlsvWriter.writeArray( "MESH_GHOST_DOMAINS", xmlAttributes, numberOfGhosts, vectorSize, ghostDomainIds.data() ) == false ) {
cerr << "Error, failed to write MEST_GHOST_DOMAINS at: " << __FILE__ << " " << __LINE__ << endl;
logFile << "(MAIN) writeGrid: ERROR failed to write MEST_GHOST_DOMAINS at: " << __FILE__ << " " << __LINE__ << endl << writeVerbose;
return false;
}
//Write the in the number of ghost local ids: (Returns false if writing fails)
if( vlsvWriter.writeArray( "MESH_GHOST_LOCALIDS", xmlAttributes, numberOfGhosts, vectorSize, ghostLocalIds.data()) == false ) {
cerr << "Error, failed to write MEST_GHOST_LOCALIDS at: " << __FILE__ << " " << __LINE__ << endl;
logFile << "(MAIN) writeGrid: ERROR failed to write MEST_GHOST_LOCALIDS at: " << __FILE__ << " " << __LINE__ << endl << writeVerbose;
return false;
}
//Everything good
return true;
}
/*! Writes domain sizes into the vlsv file, so the number of ghost and local cell ids in this process
\param vlsvWriter Some vlsv writer with a file open
\param meshName Name of the mesh (SpatialGrid used in the writeGrid function)
\param numberOfLocalZones Number of local cells in this process
\param numberOfGhostZones Number of ghost cells in this process ( Cells on the process boundary )
\return Returns true if operation was successful
*/
bool writeDomainSizes( Writer & vlsvWriter,
const string & meshName,
const unsigned int & numberOfLocalZones,
const unsigned int & numberOfGhostZones ) {
//Declare domainSize. There are two types of domain sizes -- ghost and local
const unsigned int numberOfDomainTypes = 2;
uint32_t domainSize[numberOfDomainTypes];
domainSize[0] = numberOfLocalZones + numberOfGhostZones;
domainSize[1] = numberOfGhostZones;
//Write the array:
map<string, string> xmlAttributes;
//Put the meshName
xmlAttributes["mesh"] = meshName;
const unsigned int arraySize = 1;
const unsigned int vectorSize = 2;
//Write (writeArray does the writing) Note: Here the important part is "MESH_DOMAIN_SIZES" -- visit plugin needs this
if( vlsvWriter.writeArray( "MESH_DOMAIN_SIZES", xmlAttributes, arraySize, vectorSize, domainSize ) == false ) {
cerr << "Error at: " << __FILE__ << " " << __LINE__ << ", FAILED TO WRITE MESH_DOMAIN_SIZES" << endl;
logFile << "(MAIN) writeGrid: ERROR FAILED TO WRITE MESH_DOMAIN_SIZES AT: " << __FILE__ << " " << __LINE__ << endl << writeVerbose;
return false;
}
return true;
}
/*! Writes the zone global id numbers into the file. The vlsv file needs to know in which order the local cells + ghost cells are written. Local cells are first appended to a vector called global ids, after which the ghost cells are appended. The global ids vector will then be saved into a vlsv file
\param mpiGrid Vlasiator's MPI grid
\param vlsvWriter Some vlsv writer with a file open
\param meshName Name of the mesh ("SpatialGrid" used in the writeGrid function and it should be the default)
\param local_cells Vector containing the local cells of this process
\param ghost_cells Vector containing the ghost cells of this process ( The cells on process boundary )
\return Returns true if the operation was successful
*/
bool writeZoneGlobalIdNumbers( const dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
Writer & vlsvWriter,
const string & meshName,
const vector<uint64_t> & local_cells,
const vector<uint64_t> & ghost_cells ) {
if( local_cells.empty() ) {
if( !ghost_cells.empty() ) {
//Something very wrong -- local zones should always have members when ghost zones has members
cerr << "ERROR, LOCAL ZONES EMPTY BUT GHOST ZONES NOT AT " << __FILE__ << __LINE__ << endl;
return false;
}
}
//Get the cells in x, y, z direction right off the bat (for the sake of clarity):
const unsigned int xCells = P::xcells_ini;
const unsigned int yCells = P::ycells_ini;
const unsigned int zCells = P::zcells_ini;
vector<uint64_t> globalIds;
globalIds.reserve( local_cells.size() + ghost_cells.size() );
//Iterate through local_cells and store the values into globalIDs
//Note: globalID is defined as follows: global ID = z*yCells*xCells + y*xCells + x
vector<uint64_t>::const_iterator it;
for( it = local_cells.begin(); it != local_cells.end(); ++it ) {
if( (*it) == 0 ) {
cerr << "ERROR, Invalid cell id at " << __FILE__ << " " << __LINE__ << endl;
return false;
}
//Add the global id:
//Note: Unlike cell ids, global ids start from 0
globalIds.push_back( (*it) - 1 );
}
//Do the same for ghost zones: (Append to the end of the list of global ids)
for( it = ghost_cells.begin(); it != ghost_cells.end(); ++it ) {
if( (*it) == 0 ) {
cerr << "ERROR, Invalid cell id at " << __FILE__ << " " << __LINE__ << endl;
return false;
}
//Add the global id:
globalIds.push_back( (*it) - 1 );
}
//Get the total number of zones:
const uint64_t numberOfZones = globalIds.size();
//Write the array:
map<string, string> xmlAttributes;
//The name of the mesh (user input -- should be "SpatialGrid")
xmlAttributes["name"] = meshName;
//A mandatory 'type' -- just something visit hopefully understands, because I dont (some of us do!) :)
xmlAttributes["type"] = vlsv::mesh::STRING_UCD_AMR;
char refLevelString[] = "0";
// Ultra-dirty number-to-string
refLevelString[0] += P::amrMaxSpatialRefLevel;
xmlAttributes["max_refinement_level"] = refLevelString;
//Set periodicity:
if( mpiGrid.topology.is_periodic( 0 ) ) { xmlAttributes["xperiodic"] = "yes"; } else { xmlAttributes["xperiodic"] = "no"; }
if( mpiGrid.topology.is_periodic( 1 ) ) { xmlAttributes["yperiodic"] = "yes"; } else { xmlAttributes["yperiodic"] = "no"; }
if( mpiGrid.topology.is_periodic( 2 ) ) { xmlAttributes["zperiodic"] = "yes"; } else { xmlAttributes["zperiodic"] = "no"; }
//Write:
if( numberOfZones == 0 ) {
const uint64_t dummy_data = 0;
const unsigned int dummy_array = 0;
if( vlsvWriter.writeArray( "MESH", xmlAttributes, dummy_array, 1, &dummy_data ) == false ) {
cerr << "Unsuccessful writing of MESH at: " << __FILE__ << " " << __LINE__ << endl;
return false;
}
} else {
if( vlsvWriter.writeArray( "MESH", xmlAttributes, numberOfZones, 1, globalIds.data() ) == false ) {
cerr << "Unsuccessful writing of MESH at: " << __FILE__ << " " << __LINE__ << endl;
return false;
}
}
//Successfully wrote the array
return true;
}
/*! Writes the node coordinates. This means basically every cell's node (Corner of each cell). Note: The grid is a structured one, so writing the nodes means starting from the corner of the grid and writing coordinates per every cell length until reaching the other corner of the grid
\param vlsvWriter Some vlsv writer with a file open
\param meshName Name of the mesh (SpatialGrid used in writeGrid and should be the default)
\param masterRank The master rank (Vlasiator uses 0)
\param comm The MPI comm
\return Returns true if the operation was successful
*/
bool writeBoundingBoxNodeCoordinates ( Writer & vlsvWriter,
const string & meshName,
const int masterRank,
MPI_Comm comm ) {
//Create variables xCells, yCells, zCells which tell the number of zones in the given direction
//Note: This is for the sake of clarity.
const uint64_t & xCells = P::xcells_ini;
const uint64_t & yCells = P::ycells_ini;
const uint64_t & zCells = P::zcells_ini;
//Create variables xmin, ymin, zmin for calculations
const Real & xmin = (Real)P::xmin;
const Real & ymin = (Real)P::ymin;
const Real & zmin = (Real)P::zmin;
//Create variables for cell lengths in x, y, z directions for calculations
const Real & xCellLength = (Real)P::dx_ini;
const Real & yCellLength = (Real)P::dy_ini;
const Real & zCellLength = (Real)P::dz_ini;
//Create node coordinates:
//These are the coordinates for any given node in x y or z direction
//Note: Nodes are basically the box coordinates
vector<Real> xNodeCoordinates;
xNodeCoordinates.reserve(xCells + 1);
vector<Real> yNodeCoordinates;
yNodeCoordinates.reserve(yCells + 1);
vector<Real> zNodeCoordinates;
zNodeCoordinates.reserve(zCells + 1);
//Input the coordinates for the nodes:
for( unsigned int i = 0; i < xCells + 1; ++i ) {
//The x coordinate of the first node should be xmin, the second xmin + xCellLength and so on
xNodeCoordinates.push_back(xmin + xCellLength * i);
}
for( unsigned int i = 0; i < yCells + 1; ++i ) {
yNodeCoordinates.push_back(ymin + yCellLength * i);
}
for( unsigned int i = 0; i < zCells + 1; ++i ) {
zNodeCoordinates.push_back(zmin + zCellLength * i);
}
//Write the arrays:
map<string, string> xmlAttributes;
//Note: meshName should be "SpatialGrid", probably
xmlAttributes["mesh"] = meshName;
//"success"'s value will be returned. By default it's true but if some of the vlsvWriter operations fail it will be false:
bool success = true;
//Depending on whether our rank is master rank or not the operation is slightly different, so let's get out rank from the MPI_Comm comm:
int myRank;
//Input myRank:
MPI_Comm_rank(comm, &myRank);
//Check the rank and write the arrays:
const unsigned int vectorSize = 1;
uint64_t arraySize;
if( myRank == masterRank ) {
//Save with the correct name "MESH_NODE_CRDS_X" -- writeArray returns false if something goes wrong
arraySize = xCells + 1;
if( vlsvWriter.writeArray("MESH_NODE_CRDS_X", xmlAttributes, arraySize, vectorSize, xNodeCoordinates.data()) == false ) success = false;
arraySize = yCells + 1;
if( vlsvWriter.writeArray("MESH_NODE_CRDS_Y", xmlAttributes, arraySize, vectorSize, yNodeCoordinates.data()) == false ) success = false;
arraySize = zCells + 1;
if( vlsvWriter.writeArray("MESH_NODE_CRDS_Z", xmlAttributes, arraySize, vectorSize, zNodeCoordinates.data()) == false ) success = false;
} else {
//Not a master process, so write empty:
arraySize = 0;
if( vlsvWriter.writeArray("MESH_NODE_CRDS_X", xmlAttributes, arraySize, vectorSize, xNodeCoordinates.data()) == false ) success = false;
if( vlsvWriter.writeArray("MESH_NODE_CRDS_Y", xmlAttributes, arraySize, vectorSize, yNodeCoordinates.data()) == false ) success = false;
if( vlsvWriter.writeArray("MESH_NODE_CRDS_Z", xmlAttributes, arraySize, vectorSize, zNodeCoordinates.data()) == false ) success = false;
}
//Free the memory
xNodeCoordinates.clear();
yNodeCoordinates.clear();
zNodeCoordinates.clear();
return success;
}
/*! Function for writing the bounding box. This writes only if the process running it is the master rank. This array contains info on the boundaries of the grid so for example the number of cells in x, y, z direction.
* Note that this is *not* the physical coordinate bounding box, but the computational domain bounding box, measured in blocks and cells.
\param vlsvWriter Some vlsv writer with a file open
\param meshName Name of the mesh to write ("SpatialGrid" is used in writeGrid and it should be the default)
\param masterRank The master process' id. Vlasiator uses 0 as the master process id, so by default should be 0
\param comm MPI comm
\return Returns true if operation was successful
*/
bool writeMeshBoundingBox( Writer & vlsvWriter,
const string & meshName,
const int masterRank,
MPI_Comm comm ) {
//Get my rank from the MPI_Comm
int myRank;
MPI_Comm_rank(comm, &myRank);
//Declare boundaryBox (writeArray expects it to tell the size of
const unsigned int box_size = 6;
const unsigned int notBlockBasedMesh = 1; // 1 because we are not interested in block based mesh
//Note: If we were, the 3 last values in boundaryBox(below) would tell the
//number of cells in blocks in x, y, z direction
//Set the boundary box
const uint64_t & numberOfXCells = P::xcells_ini;
const uint64_t & numberOfYCells = P::ycells_ini;
const uint64_t & numberOfZCells = P::zcells_ini;
uint64_t boundaryBox[box_size] = { numberOfXCells, numberOfYCells, numberOfZCells,
notBlockBasedMesh, notBlockBasedMesh, notBlockBasedMesh };
//Write:
//Declare attributes
map<string, string> xmlAttributes;
//We received mesh name as a parameter: MOST LIKELY THIS IS SpatialGrid!
xmlAttributes["mesh"] = meshName;
//Write an array (NOTE: success will be returned and writeArray will return true or false depending on whether or not the write is successful)
bool success;
if( myRank == masterRank ) {
//The visit plugin expects MESH_BBOX as a keyword
//NOTE: writeArray writes boundaryBox
const unsigned int arraySize = 6;
const unsigned int vectorSize = 1;
success = vlsvWriter.writeArray("MESH_BBOX", xmlAttributes, arraySize, vectorSize, boundaryBox);
} else {
const unsigned int arraySize = 0;
const unsigned int vectorSize = 1;
success = vlsvWriter.writeArray("MESH_BBOX", xmlAttributes, arraySize, vectorSize, boundaryBox);
}
return success;
}
/** Writes the mesh metadata for Visit to read FSGrid variable data.
* @param technicalGrid An fsgrid instance used to extract metadata info.
* @param vlsvWriter file object to write into.
*/
bool writeFsGridMetadata(FsGrid< fsgrids::technical, FS_STENCIL_WIDTH> & technicalGrid, vlsv::Writer& vlsvWriter) {
std::map<std::string, std::string> xmlAttributes;
const std::string meshName="fsgrid";
xmlAttributes["mesh"] = meshName;
//The visit plugin expects MESH_BBOX as a keyword. We only write one
//from the first rank.
std::array<int32_t, 3>& globalSize = technicalGrid.getGlobalSize();
std::array<int64_t, 6> boundaryBox({globalSize[0], globalSize[1], globalSize[2],
1,1,1});
if(technicalGrid.getRank() == 0) {
const unsigned int arraySize = 6;
const unsigned int vectorSize = 1;
vlsvWriter.writeArray("MESH_BBOX", xmlAttributes, arraySize, vectorSize, &boundaryBox[0]);
} else {
const unsigned int arraySize = 0;
const unsigned int vectorSize = 1;
vlsvWriter.writeArray("MESH_BBOX", xmlAttributes, arraySize, vectorSize, &boundaryBox);
}
// Write three 1-dimensional arrays of node coordinates (x,y,z) for
// visit to create a cartesian grid out of.
std::vector<double> xNodeCoordinates(globalSize[0]+1);
for(int64_t i=0; i<globalSize[0]+1; i++) {
xNodeCoordinates[i] = technicalGrid.getPhysicalCoords(i,0,0)[0];
}
std::vector<double> yNodeCoordinates(globalSize[1]+1);
for(int64_t i=0; i<globalSize[1]+1; i++) {
yNodeCoordinates[i] = technicalGrid.getPhysicalCoords(0,i,0)[1];
}
std::vector<double> zNodeCoordinates(globalSize[2]+1);
for(int64_t i=0; i<globalSize[2]+1; i++) {
zNodeCoordinates[i] = technicalGrid.getPhysicalCoords(0,0,i)[2];
}
if(technicalGrid.getRank() == 0) {
// Write this data only on rank 0
vlsvWriter.writeArray("MESH_NODE_CRDS_X", xmlAttributes, globalSize[0]+1, 1, xNodeCoordinates.data());
vlsvWriter.writeArray("MESH_NODE_CRDS_Y", xmlAttributes, globalSize[1]+1, 1, yNodeCoordinates.data());
vlsvWriter.writeArray("MESH_NODE_CRDS_Z", xmlAttributes, globalSize[2]+1, 1, zNodeCoordinates.data());
} else {
// The others just write an empty dummy
vlsvWriter.writeArray("MESH_NODE_CRDS_X", xmlAttributes, 0, 1, xNodeCoordinates.data());
vlsvWriter.writeArray("MESH_NODE_CRDS_Y", xmlAttributes, 0, 1, yNodeCoordinates.data());
vlsvWriter.writeArray("MESH_NODE_CRDS_Z", xmlAttributes, 0, 1, zNodeCoordinates.data());
}
// Dummy ghost info
int dummyghost=0;
vlsvWriter.writeArray("MESH_GHOST_DOMAINS", xmlAttributes, 0, 1, &dummyghost);
vlsvWriter.writeArray("MESH_GHOST_LOCALIDS", xmlAttributes, 0, 1, &dummyghost);
// Write cell "globalID" numbers, which are just the global array indices.
std::array<int32_t,3>& localSize = technicalGrid.getLocalSize();
std::vector<uint64_t> globalIds(localSize[0]*localSize[1]*localSize[2]);
int i=0;
for(int z=0; z<localSize[2]; z++) {
for(int y=0; y<localSize[1]; y++) {
for(int x=0; x<localSize[0]; x++) {
std::array<int32_t,3> globalIndex = technicalGrid.getGlobalIndices(x,y,z);
globalIds[i++] = globalIndex[2]*globalSize[0]*globalSize[1]+
globalIndex[1]*globalSize[0] +
globalIndex[0];
}
}
}
// writeDomainSizes
std::array<uint64_t,2> meshDomainSize({globalIds.size(), 0});
vlsvWriter.writeArray("MESH_DOMAIN_SIZES", xmlAttributes, 1, 2, &meshDomainSize[0]);
// how many MPI ranks we wrote from
int size;
MPI_Comm_size(MPI_COMM_WORLD, &size);
vlsvWriter.writeParameter("numWritingRanks", &size);
// Finally, write mesh object itself.
xmlAttributes.clear();
xmlAttributes["name"] = meshName;
xmlAttributes["type"] = vlsv::mesh::STRING_UCD_MULTI;
xmlAttributes["xperiodic"]=technicalGrid.getPeriodic()[0]?"yes":"no";
xmlAttributes["yperiodic"]=technicalGrid.getPeriodic()[1]?"yes":"no";
xmlAttributes["zperiodic"]=technicalGrid.getPeriodic()[2]?"yes":"no";
vlsvWriter.writeArray("MESH", xmlAttributes, globalIds.size(), 1, globalIds.data());
return true;
}
/** This function writes the velocity space.
* @param mpiGrid Vlasiator's grid.
* @param vlsvWriter some vlsv writer with a file open.
* @param index Index to call the correct member of the various parameter vectors.
* @param cells Vector containing local cells of this process.
* @return Returns true if the operation was successful.
* @sa writeVelocityDistributionData. */
bool writeVelocitySpace(dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
Writer& vlsvWriter,int index,const vector<uint64_t>& cells) {
//Compute which cells will write out their velocity space
vector<uint64_t> velSpaceCells;
int lineX, lineY, lineZ;
Real shellRadiusSquare;
Real cellX, cellY, cellZ, DX, DY, DZ;
Real dx_rm, dx_rp, dy_rm, dy_rp, dz_rm, dz_rp;
Real rsquare_minus,rsquare_plus;
for (uint i = 0; i < cells.size(); i++) {
mpiGrid[cells[i]]->parameters[CellParams::ISCELLSAVINGF] = 0.0;
// CellID stride selection
if (P::systemWriteDistributionWriteStride[index] > 0 &&
cells[i] % P::systemWriteDistributionWriteStride[index] == 0) {
velSpaceCells.push_back(cells[i]);
mpiGrid[cells[i]]->parameters[CellParams::ISCELLSAVINGF] = 1.0;
continue; // Avoid double entries in case the cell also matches following conditions.
}
// Cell lines selection
// Determine cellID's 3D indices
// Loop over AMR levels
uint startindex=1;
uint endindex=1;
for (uint AMR = 0; AMR <= P::amrMaxSpatialRefLevel; AMR++) {
uint AMRm = std::floor(std::pow(2,AMR));
uint cellsthislevel = (AMRm*P::xcells_ini)*(AMRm*P::ycells_ini)*(AMRm*P::zcells_ini);
startindex = endindex;
endindex = endindex + cellsthislevel;
// If cell belongs to this AMR level, find indices
if ((cells[i]>=startindex)&&(cells[i]<endindex)) {
lineX = (cells[i]-startindex) % (AMRm*P::xcells_ini);
lineY = ((cells[i]-startindex) / (AMRm*P::xcells_ini)) % (AMRm*P::ycells_ini);
lineZ = ((cells[i]-startindex) /((AMRm*P::xcells_ini) * (AMRm*P::ycells_ini))) % (AMRm*P::zcells_ini);
// Check that indices are in correct intersection at least in one plane
if ((P::systemWriteDistributionWriteXlineStride[index] > 0 &&
P::systemWriteDistributionWriteYlineStride[index] > 0 &&
lineX % P::systemWriteDistributionWriteXlineStride[index] == 0 &&
lineY % P::systemWriteDistributionWriteYlineStride[index] == 0)
&&
(P::systemWriteDistributionWriteYlineStride[index] > 0 &&
P::systemWriteDistributionWriteZlineStride[index] > 0 &&
lineY % P::systemWriteDistributionWriteYlineStride[index] == 0 &&
lineZ % P::systemWriteDistributionWriteZlineStride[index] == 0)
&&
(P::systemWriteDistributionWriteZlineStride[index] > 0 &&
P::systemWriteDistributionWriteXlineStride[index] > 0 &&
lineZ % P::systemWriteDistributionWriteZlineStride[index] == 0 &&
lineX % P::systemWriteDistributionWriteXlineStride[index] == 0)
) {
velSpaceCells.push_back(cells[i]);
mpiGrid[cells[i]]->parameters[CellParams::ISCELLSAVINGF] = 1.0;
continue; // Avoid double entries in case the cell also matches following conditions.
}
}
}
// Loop over spherical shells at defined distances
for (uint ishell = 0; ishell < P::systemWriteDistributionWriteShellRadius.size(); ishell++) {
shellRadiusSquare = P::systemWriteDistributionWriteShellRadius[ishell] * P::systemWriteDistributionWriteShellRadius[ishell];
cellX = mpiGrid[cells[i]]->parameters[CellParams::XCRD];
cellY = mpiGrid[cells[i]]->parameters[CellParams::YCRD];
cellZ = mpiGrid[cells[i]]->parameters[CellParams::ZCRD];
DX = mpiGrid[cells[i]]->parameters[CellParams::DX];
DY = mpiGrid[cells[i]]->parameters[CellParams::DY];
DZ = mpiGrid[cells[i]]->parameters[CellParams::DZ];
dx_rm = cellX < 0 ? DX : 0;