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tim |
1695 |
#define _LARGEFILE_SOURCE64
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#define _FILE_OFFSET_BITS 64
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#include <string.h>
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#include <iostream>
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#include <fstream>
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#include <algorithm>
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#include <utility>
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#ifdef IS_MPI
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#include <mpi.h>
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#include "brains/mpiSimulation.hpp"
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namespace dWrite{
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void DieDieDie( void );
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}
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using namespace dWrite;
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#endif //is_mpi
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#include "io/ReadWrite.hpp"
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#include "utils/simError.h"
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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
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entry_plug = the_entry_plug;
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#ifdef IS_MPI
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if(worldRank == 0 ){
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#endif // is_mpi
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dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
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if( !dumpFile ){
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sprintf( painCave.errMsg,
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"Could not open \"%s\" for dump output.\n",
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entry_plug->sampleName.c_str());
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painCave.isFatal = 1;
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simError();
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}
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#ifdef IS_MPI
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}
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//sort the local atoms by global index
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sortByGlobalIndex();
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sprintf( checkPointMsg,
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"Sucessfully opened output file for dumping.\n");
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MPIcheckPoint();
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#endif // is_mpi
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}
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DumpWriter::~DumpWriter( ){
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#ifdef IS_MPI
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if(worldRank == 0 ){
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#endif // is_mpi
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dumpFile.close();
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#ifdef IS_MPI
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}
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#endif // is_mpi
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}
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#ifdef IS_MPI
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/**
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* A hook function to load balancing
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*/
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void DumpWriter::update(){
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sortByGlobalIndex();
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}
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/**
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* Auxiliary sorting function
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*/
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bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
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return p1.second < p2.second;
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}
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/**
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* Sorting the local index by global index
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*/
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void DumpWriter::sortByGlobalIndex(){
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Molecule* mols = entry_plug->molecules;
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indexArray.clear();
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for(int i = 0; i < entry_plug->n_mol;i++)
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indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
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sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
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}
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#endif
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void DumpWriter::writeDump(double currentTime){
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ofstream finalOut;
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vector<ofstream*> fileStreams;
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#ifdef IS_MPI
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if(worldRank == 0 ){
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#endif
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finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
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if( !finalOut ){
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sprintf( painCave.errMsg,
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"Could not open \"%s\" for final dump output.\n",
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entry_plug->finalName.c_str() );
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painCave.isFatal = 1;
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simError();
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}
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#ifdef IS_MPI
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}
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#endif // is_mpi
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fileStreams.push_back(&finalOut);
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fileStreams.push_back(&dumpFile);
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writeFrame(fileStreams, currentTime);
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#ifdef IS_MPI
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finalOut.close();
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#endif
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}
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void DumpWriter::writeFinal(double currentTime){
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ofstream finalOut;
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vector<ofstream*> fileStreams;
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#ifdef IS_MPI
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if(worldRank == 0 ){
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#endif // is_mpi
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finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
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if( !finalOut ){
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sprintf( painCave.errMsg,
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"Could not open \"%s\" for final dump output.\n",
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entry_plug->finalName.c_str() );
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painCave.isFatal = 1;
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simError();
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}
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#ifdef IS_MPI
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}
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#endif // is_mpi
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fileStreams.push_back(&finalOut);
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writeFrame(fileStreams, currentTime);
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#ifdef IS_MPI
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finalOut.close();
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#endif
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}
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void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
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const int BUFFERSIZE = 2000;
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const int MINIBUFFERSIZE = 100;
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char tempBuffer[BUFFERSIZE];
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char writeLine[BUFFERSIZE];
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int i;
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unsigned int k;
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#ifdef IS_MPI
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/*********************************************************************
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* Documentation? You want DOCUMENTATION?
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*
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* Why all the potatoes below?
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*
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* To make a long story short, the original version of DumpWriter
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* worked in the most inefficient way possible. Node 0 would
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* poke each of the node for an individual atom's formatted data
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* as node 0 worked its way down the global index. This was particularly
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* inefficient since the method blocked all processors at every atom
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* (and did it twice!).
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*
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* An intermediate version of DumpWriter could be described from Node
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* zero's perspective as follows:
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*
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* 1) Have 100 of your friends stand in a circle.
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* 2) When you say go, have all of them start tossing potatoes at
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* you (one at a time).
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* 3) Catch the potatoes.
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*
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* It was an improvement, but MPI has buffers and caches that could
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* best be described in this analogy as "potato nets", so there's no
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* need to block the processors atom-by-atom.
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*
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* This new and improved DumpWriter works in an even more efficient
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* way:
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*
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* 1) Have 100 of your friend stand in a circle.
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* 2) When you say go, have them start tossing 5-pound bags of
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* potatoes at you.
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* 3) Once you've caught a friend's bag of potatoes,
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* toss them a spud to let them know they can toss another bag.
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*
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* How's THAT for documentation?
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*
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*********************************************************************/
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int *potatoes;
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int myPotato;
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int nProc;
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int j, which_node, done, which_atom, local_index, currentIndex;
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double atomData[13];
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int isDirectional;
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char* atomTypeString;
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char MPIatomTypeString[MINIBUFFERSIZE];
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int nObjects;
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int msgLen; // the length of message actually recieved at master nodes
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#endif //is_mpi
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Quat4d q;
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Vector3d ji;
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DirectionalAtom* dAtom;
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Vector3d pos;
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Vector3d vel;
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int nTotObjects;
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StuntDouble* sd;
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char* molName;
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vector<StuntDouble*> integrableObjects;
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vector<StuntDouble*>::iterator iter;
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nTotObjects = entry_plug->getTotIntegrableObjects();
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#ifndef IS_MPI
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for(k = 0; k < outFile.size(); k++){
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*outFile[k] << nTotObjects << "\n";
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*outFile[k] << currentTime << ";\t"
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<< entry_plug->Hmat[0][0] << "\t"
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<< entry_plug->Hmat[1][0] << "\t"
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<< entry_plug->Hmat[2][0] << ";\t"
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| 249 |
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| 250 |
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<< entry_plug->Hmat[0][1] << "\t"
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| 251 |
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<< entry_plug->Hmat[1][1] << "\t"
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<< entry_plug->Hmat[2][1] << ";\t"
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| 253 |
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| 254 |
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<< entry_plug->Hmat[0][2] << "\t"
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| 255 |
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<< entry_plug->Hmat[1][2] << "\t"
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<< entry_plug->Hmat[2][2] << ";";
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| 257 |
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| 258 |
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//write out additional parameters, such as chi and eta
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*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
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}
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| 261 |
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| 262 |
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for( i=0; i< entry_plug->n_mol; i++ ){
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| 263 |
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| 264 |
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integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
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| 265 |
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molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
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| 266 |
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| 267 |
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for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){
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| 268 |
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sd = *iter;
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| 269 |
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pos = sd->getPos();
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| 270 |
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vel = sd->getVel();
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| 271 |
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| 272 |
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sprintf( tempBuffer,
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
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| 274 |
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sd->getType(),
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| 275 |
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pos[0],
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pos[1],
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pos[2],
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| 278 |
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vel[0],
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| 279 |
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vel[1],
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| 280 |
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vel[2]);
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| 281 |
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strcpy( writeLine, tempBuffer );
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| 282 |
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| 283 |
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if( sd->isDirectional() ){
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| 284 |
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| 285 |
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q = sd->getQ();
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| 286 |
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ji = sd->getJ();
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| 287 |
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| 288 |
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sprintf( tempBuffer,
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| 289 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
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| 290 |
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q[0],
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q[1],
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| 292 |
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q[2],
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| 293 |
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q[3],
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| 294 |
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ji[0],
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| 295 |
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ji[1],
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| 296 |
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ji[2]);
|
| 297 |
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strcat( writeLine, tempBuffer );
|
| 298 |
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}
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| 299 |
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else
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| 300 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
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| 301 |
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| 302 |
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for(k = 0; k < outFile.size(); k++)
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| 303 |
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*outFile[k] << writeLine;
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| 304 |
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}
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| 305 |
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| 306 |
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}
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| 307 |
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| 308 |
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#else // is_mpi
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| 309 |
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| 310 |
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/* code to find maximum tag value */
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| 311 |
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|
| 312 |
|
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int *tagub, flag, MAXTAG;
|
| 313 |
|
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MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
|
| 314 |
|
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if (flag) {
|
| 315 |
|
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MAXTAG = *tagub;
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| 316 |
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} else {
|
| 317 |
|
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MAXTAG = 32767;
|
| 318 |
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}
|
| 319 |
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| 320 |
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int haveError;
|
| 321 |
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|
| 322 |
|
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MPI_Status istatus;
|
| 323 |
|
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int nCurObj;
|
| 324 |
|
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int *MolToProcMap = mpiSim->getMolToProcMap();
|
| 325 |
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|
| 326 |
|
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// write out header and node 0's coordinates
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| 327 |
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| 328 |
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if( worldRank == 0 ){
|
| 329 |
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|
| 330 |
|
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// Node 0 needs a list of the magic potatoes for each processor;
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| 331 |
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| 332 |
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nProc = mpiSim->getNProcessors();
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| 333 |
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potatoes = new int[nProc];
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| 334 |
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| 335 |
|
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//write out the comment lines
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| 336 |
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for (i = 0; i < nProc; i++)
|
| 337 |
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potatoes[i] = 0;
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| 338 |
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|
| 339 |
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for(k = 0; k < outFile.size(); k++){
|
| 340 |
|
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*outFile[k] << nTotObjects << "\n";
|
| 341 |
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| 342 |
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*outFile[k] << currentTime << ";\t"
|
| 343 |
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<< entry_plug->Hmat[0][0] << "\t"
|
| 344 |
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<< entry_plug->Hmat[1][0] << "\t"
|
| 345 |
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<< entry_plug->Hmat[2][0] << ";\t"
|
| 346 |
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| 347 |
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<< entry_plug->Hmat[0][1] << "\t"
|
| 348 |
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<< entry_plug->Hmat[1][1] << "\t"
|
| 349 |
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<< entry_plug->Hmat[2][1] << ";\t"
|
| 350 |
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| 351 |
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<< entry_plug->Hmat[0][2] << "\t"
|
| 352 |
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<< entry_plug->Hmat[1][2] << "\t"
|
| 353 |
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<< entry_plug->Hmat[2][2] << ";";
|
| 354 |
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| 355 |
|
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*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
|
| 356 |
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}
|
| 357 |
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|
| 358 |
|
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currentIndex = 0;
|
| 359 |
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|
| 360 |
|
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for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
|
| 361 |
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|
| 362 |
|
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// Get the Node number which has this atom;
|
| 363 |
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|
| 364 |
|
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which_node = MolToProcMap[i];
|
| 365 |
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|
| 366 |
|
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if (which_node != 0) {
|
| 367 |
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|
| 368 |
|
|
if (potatoes[which_node] + 1 >= MAXTAG) {
|
| 369 |
|
|
// The potato was going to exceed the maximum value,
|
| 370 |
|
|
// so wrap this processor potato back to 0:
|
| 371 |
|
|
|
| 372 |
|
|
potatoes[which_node] = 0;
|
| 373 |
|
|
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
|
| 374 |
|
|
|
| 375 |
|
|
}
|
| 376 |
|
|
|
| 377 |
|
|
myPotato = potatoes[which_node];
|
| 378 |
|
|
|
| 379 |
|
|
//recieve the number of integrableObject in current molecule
|
| 380 |
|
|
MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
|
| 381 |
|
|
myPotato, MPI_COMM_WORLD, &istatus);
|
| 382 |
|
|
myPotato++;
|
| 383 |
|
|
|
| 384 |
|
|
for(int l = 0; l < nCurObj; l++){
|
| 385 |
|
|
|
| 386 |
|
|
if (potatoes[which_node] + 2 >= MAXTAG) {
|
| 387 |
|
|
// The potato was going to exceed the maximum value,
|
| 388 |
|
|
// so wrap this processor potato back to 0:
|
| 389 |
|
|
|
| 390 |
|
|
potatoes[which_node] = 0;
|
| 391 |
|
|
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
|
| 392 |
|
|
|
| 393 |
|
|
}
|
| 394 |
|
|
|
| 395 |
|
|
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
|
| 396 |
|
|
myPotato, MPI_COMM_WORLD, &istatus);
|
| 397 |
|
|
|
| 398 |
|
|
atomTypeString = MPIatomTypeString;
|
| 399 |
|
|
|
| 400 |
|
|
myPotato++;
|
| 401 |
|
|
|
| 402 |
|
|
MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
|
| 403 |
|
|
myPotato++;
|
| 404 |
|
|
|
| 405 |
|
|
MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
|
| 406 |
|
|
|
| 407 |
|
|
if(msgLen == 13)
|
| 408 |
|
|
isDirectional = 1;
|
| 409 |
|
|
else
|
| 410 |
|
|
isDirectional = 0;
|
| 411 |
|
|
|
| 412 |
|
|
// If we've survived to here, format the line:
|
| 413 |
|
|
|
| 414 |
|
|
if (!isDirectional) {
|
| 415 |
|
|
|
| 416 |
|
|
sprintf( writeLine,
|
| 417 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
|
| 418 |
|
|
atomTypeString,
|
| 419 |
|
|
atomData[0],
|
| 420 |
|
|
atomData[1],
|
| 421 |
|
|
atomData[2],
|
| 422 |
|
|
atomData[3],
|
| 423 |
|
|
atomData[4],
|
| 424 |
|
|
atomData[5]);
|
| 425 |
|
|
|
| 426 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
|
| 427 |
|
|
|
| 428 |
|
|
}
|
| 429 |
|
|
else {
|
| 430 |
|
|
|
| 431 |
|
|
sprintf( writeLine,
|
| 432 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
|
| 433 |
|
|
atomTypeString,
|
| 434 |
|
|
atomData[0],
|
| 435 |
|
|
atomData[1],
|
| 436 |
|
|
atomData[2],
|
| 437 |
|
|
atomData[3],
|
| 438 |
|
|
atomData[4],
|
| 439 |
|
|
atomData[5],
|
| 440 |
|
|
atomData[6],
|
| 441 |
|
|
atomData[7],
|
| 442 |
|
|
atomData[8],
|
| 443 |
|
|
atomData[9],
|
| 444 |
|
|
atomData[10],
|
| 445 |
|
|
atomData[11],
|
| 446 |
|
|
atomData[12]);
|
| 447 |
|
|
|
| 448 |
|
|
}
|
| 449 |
|
|
|
| 450 |
|
|
for(k = 0; k < outFile.size(); k++)
|
| 451 |
|
|
*outFile[k] << writeLine;
|
| 452 |
|
|
|
| 453 |
|
|
}// end for(int l =0)
|
| 454 |
|
|
potatoes[which_node] = myPotato;
|
| 455 |
|
|
|
| 456 |
|
|
}
|
| 457 |
|
|
else {
|
| 458 |
|
|
|
| 459 |
|
|
haveError = 0;
|
| 460 |
|
|
|
| 461 |
|
|
local_index = indexArray[currentIndex].first;
|
| 462 |
|
|
|
| 463 |
|
|
integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
|
| 464 |
|
|
|
| 465 |
|
|
for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){
|
| 466 |
|
|
sd = *iter;
|
| 467 |
|
|
atomTypeString = sd->getType();
|
| 468 |
|
|
|
| 469 |
|
|
pos = sd->getPos();
|
| 470 |
|
|
vel = sd->getVel();
|
| 471 |
|
|
|
| 472 |
|
|
atomData[0] = pos[0];
|
| 473 |
|
|
atomData[1] = pos[1];
|
| 474 |
|
|
atomData[2] = pos[2];
|
| 475 |
|
|
|
| 476 |
|
|
atomData[3] = vel[0];
|
| 477 |
|
|
atomData[4] = vel[1];
|
| 478 |
|
|
atomData[5] = vel[2];
|
| 479 |
|
|
|
| 480 |
|
|
isDirectional = 0;
|
| 481 |
|
|
|
| 482 |
|
|
if( sd->isDirectional() ){
|
| 483 |
|
|
|
| 484 |
|
|
isDirectional = 1;
|
| 485 |
|
|
|
| 486 |
|
|
q = sd->getQ();
|
| 487 |
|
|
ji = sd->getJ();
|
| 488 |
|
|
|
| 489 |
|
|
for (int j = 0; j < 6 ; j++)
|
| 490 |
|
|
atomData[j] = atomData[j];
|
| 491 |
|
|
|
| 492 |
|
|
atomData[6] = q[0];
|
| 493 |
|
|
atomData[7] = q[1];
|
| 494 |
|
|
atomData[8] = q[2];
|
| 495 |
|
|
atomData[9] = q[3];
|
| 496 |
|
|
|
| 497 |
|
|
atomData[10] = ji[0];
|
| 498 |
|
|
atomData[11] = ji[1];
|
| 499 |
|
|
atomData[12] = ji[2];
|
| 500 |
|
|
}
|
| 501 |
|
|
|
| 502 |
|
|
// If we've survived to here, format the line:
|
| 503 |
|
|
|
| 504 |
|
|
if (!isDirectional) {
|
| 505 |
|
|
|
| 506 |
|
|
sprintf( writeLine,
|
| 507 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
|
| 508 |
|
|
atomTypeString,
|
| 509 |
|
|
atomData[0],
|
| 510 |
|
|
atomData[1],
|
| 511 |
|
|
atomData[2],
|
| 512 |
|
|
atomData[3],
|
| 513 |
|
|
atomData[4],
|
| 514 |
|
|
atomData[5]);
|
| 515 |
|
|
|
| 516 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
|
| 517 |
|
|
|
| 518 |
|
|
}
|
| 519 |
|
|
else {
|
| 520 |
|
|
|
| 521 |
|
|
sprintf( writeLine,
|
| 522 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
|
| 523 |
|
|
atomTypeString,
|
| 524 |
|
|
atomData[0],
|
| 525 |
|
|
atomData[1],
|
| 526 |
|
|
atomData[2],
|
| 527 |
|
|
atomData[3],
|
| 528 |
|
|
atomData[4],
|
| 529 |
|
|
atomData[5],
|
| 530 |
|
|
atomData[6],
|
| 531 |
|
|
atomData[7],
|
| 532 |
|
|
atomData[8],
|
| 533 |
|
|
atomData[9],
|
| 534 |
|
|
atomData[10],
|
| 535 |
|
|
atomData[11],
|
| 536 |
|
|
atomData[12]);
|
| 537 |
|
|
|
| 538 |
|
|
}
|
| 539 |
|
|
|
| 540 |
|
|
for(k = 0; k < outFile.size(); k++)
|
| 541 |
|
|
*outFile[k] << writeLine;
|
| 542 |
|
|
|
| 543 |
|
|
|
| 544 |
|
|
}//end for(iter = integrableObject.begin())
|
| 545 |
|
|
|
| 546 |
|
|
currentIndex++;
|
| 547 |
|
|
}
|
| 548 |
|
|
|
| 549 |
|
|
}//end for(i = 0; i < mpiSim->getNmol())
|
| 550 |
|
|
|
| 551 |
|
|
for(k = 0; k < outFile.size(); k++)
|
| 552 |
|
|
outFile[k]->flush();
|
| 553 |
|
|
|
| 554 |
|
|
sprintf( checkPointMsg,
|
| 555 |
|
|
"Sucessfully took a dump.\n");
|
| 556 |
|
|
|
| 557 |
|
|
MPIcheckPoint();
|
| 558 |
|
|
|
| 559 |
|
|
delete[] potatoes;
|
| 560 |
|
|
|
| 561 |
|
|
} else {
|
| 562 |
|
|
|
| 563 |
|
|
// worldRank != 0, so I'm a remote node.
|
| 564 |
|
|
|
| 565 |
|
|
// Set my magic potato to 0:
|
| 566 |
|
|
|
| 567 |
|
|
myPotato = 0;
|
| 568 |
|
|
currentIndex = 0;
|
| 569 |
|
|
|
| 570 |
|
|
for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
|
| 571 |
|
|
|
| 572 |
|
|
// Am I the node which has this integrableObject?
|
| 573 |
|
|
|
| 574 |
|
|
if (MolToProcMap[i] == worldRank) {
|
| 575 |
|
|
|
| 576 |
|
|
|
| 577 |
|
|
if (myPotato + 1 >= MAXTAG) {
|
| 578 |
|
|
|
| 579 |
|
|
// The potato was going to exceed the maximum value,
|
| 580 |
|
|
// so wrap this processor potato back to 0 (and block until
|
| 581 |
|
|
// node 0 says we can go:
|
| 582 |
|
|
|
| 583 |
|
|
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
|
| 584 |
|
|
|
| 585 |
|
|
}
|
| 586 |
|
|
|
| 587 |
|
|
local_index = indexArray[currentIndex].first;
|
| 588 |
|
|
integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
|
| 589 |
|
|
|
| 590 |
|
|
nCurObj = integrableObjects.size();
|
| 591 |
|
|
|
| 592 |
|
|
MPI_Send(&nCurObj, 1, MPI_INT, 0,
|
| 593 |
|
|
myPotato, MPI_COMM_WORLD);
|
| 594 |
|
|
myPotato++;
|
| 595 |
|
|
|
| 596 |
|
|
for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){
|
| 597 |
|
|
|
| 598 |
|
|
if (myPotato + 2 >= MAXTAG) {
|
| 599 |
|
|
|
| 600 |
|
|
// The potato was going to exceed the maximum value,
|
| 601 |
|
|
// so wrap this processor potato back to 0 (and block until
|
| 602 |
|
|
// node 0 says we can go:
|
| 603 |
|
|
|
| 604 |
|
|
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
|
| 605 |
|
|
|
| 606 |
|
|
}
|
| 607 |
|
|
|
| 608 |
|
|
sd = *iter;
|
| 609 |
|
|
|
| 610 |
|
|
atomTypeString = sd->getType();
|
| 611 |
|
|
|
| 612 |
|
|
pos = sd->getPos();
|
| 613 |
|
|
vel = sd->getVel();
|
| 614 |
|
|
|
| 615 |
|
|
atomData[0] = pos[0];
|
| 616 |
|
|
atomData[1] = pos[1];
|
| 617 |
|
|
atomData[2] = pos[2];
|
| 618 |
|
|
|
| 619 |
|
|
atomData[3] = vel[0];
|
| 620 |
|
|
atomData[4] = vel[1];
|
| 621 |
|
|
atomData[5] = vel[2];
|
| 622 |
|
|
|
| 623 |
|
|
isDirectional = 0;
|
| 624 |
|
|
|
| 625 |
|
|
if( sd->isDirectional() ){
|
| 626 |
|
|
|
| 627 |
|
|
isDirectional = 1;
|
| 628 |
|
|
|
| 629 |
|
|
q = sd->getQ();
|
| 630 |
|
|
ji = sd->getJ();
|
| 631 |
|
|
|
| 632 |
|
|
|
| 633 |
|
|
atomData[6] = q[0];
|
| 634 |
|
|
atomData[7] = q[1];
|
| 635 |
|
|
atomData[8] = q[2];
|
| 636 |
|
|
atomData[9] = q[3];
|
| 637 |
|
|
|
| 638 |
|
|
atomData[10] = ji[0];
|
| 639 |
|
|
atomData[11] = ji[1];
|
| 640 |
|
|
atomData[12] = ji[2];
|
| 641 |
|
|
}
|
| 642 |
|
|
|
| 643 |
|
|
|
| 644 |
|
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
|
| 645 |
|
|
|
| 646 |
|
|
// null terminate the string before sending (just in case):
|
| 647 |
|
|
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
|
| 648 |
|
|
|
| 649 |
|
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
|
| 650 |
|
|
myPotato, MPI_COMM_WORLD);
|
| 651 |
|
|
|
| 652 |
|
|
myPotato++;
|
| 653 |
|
|
|
| 654 |
|
|
if (isDirectional) {
|
| 655 |
|
|
|
| 656 |
|
|
MPI_Send(atomData, 13, MPI_DOUBLE, 0,
|
| 657 |
|
|
myPotato, MPI_COMM_WORLD);
|
| 658 |
|
|
|
| 659 |
|
|
} else {
|
| 660 |
|
|
|
| 661 |
|
|
MPI_Send(atomData, 6, MPI_DOUBLE, 0,
|
| 662 |
|
|
myPotato, MPI_COMM_WORLD);
|
| 663 |
|
|
}
|
| 664 |
|
|
|
| 665 |
|
|
myPotato++;
|
| 666 |
|
|
|
| 667 |
|
|
}
|
| 668 |
|
|
|
| 669 |
|
|
currentIndex++;
|
| 670 |
|
|
|
| 671 |
|
|
}
|
| 672 |
|
|
|
| 673 |
|
|
}
|
| 674 |
|
|
|
| 675 |
|
|
sprintf( checkPointMsg,
|
| 676 |
|
|
"Sucessfully took a dump.\n");
|
| 677 |
|
|
MPIcheckPoint();
|
| 678 |
|
|
|
| 679 |
|
|
}
|
| 680 |
|
|
|
| 681 |
|
|
|
| 682 |
|
|
|
| 683 |
|
|
#endif // is_mpi
|
| 684 |
|
|
}
|
| 685 |
|
|
|
| 686 |
|
|
#ifdef IS_MPI
|
| 687 |
|
|
|
| 688 |
|
|
// a couple of functions to let us escape the write loop
|
| 689 |
|
|
|
| 690 |
|
|
void dWrite::DieDieDie( void ){
|
| 691 |
|
|
|
| 692 |
|
|
MPI_Finalize();
|
| 693 |
|
|
exit (0);
|
| 694 |
|
|
}
|
| 695 |
|
|
|
| 696 |
|
|
#endif //is_mpi
|
