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#define _LARGEFILE_SOURCE64
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#define _FILE_OFFSET_BITS 64
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3 |
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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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9 |
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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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25 |
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entry_plug = the_entry_plug;
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27 |
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28 |
#ifdef IS_MPI
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29 |
if(worldRank == 0 ){
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30 |
#endif // is_mpi
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31 |
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dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
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33 |
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if( !dumpFile ){
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35 |
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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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40 |
simError();
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}
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42 |
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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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58 |
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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179 |
* 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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217 |
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218 |
int nProc;
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219 |
int j, which_node, done, which_atom, local_index, currentIndex;
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220 |
double atomData[13];
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int isDirectional;
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char* atomTypeString;
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223 |
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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227 |
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Quat4d q;
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229 |
Vector3d ji;
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DirectionalAtom* dAtom;
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Vector3d pos;
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Vector3d vel;
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233 |
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int nTotObjects;
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StuntDouble* sd;
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char* molName;
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237 |
vector<StuntDouble*> integrableObjects;
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vector<StuntDouble*>::iterator iter;
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239 |
nTotObjects = entry_plug->getTotIntegrableObjects();
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240 |
#ifndef IS_MPI
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241 |
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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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<< entry_plug->Hmat[0][1] << "\t"
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<< entry_plug->Hmat[1][1] << "\t"
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<< entry_plug->Hmat[2][1] << ";\t"
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<< entry_plug->Hmat[0][2] << "\t"
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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 |
//write out additional parameters, such as chi and eta
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259 |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
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260 |
}
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261 |
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262 |
for( i=0; i< entry_plug->n_mol; i++ ){
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263 |
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264 |
integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
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265 |
molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
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266 |
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267 |
for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){
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268 |
sd = *iter;
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pos = sd->getPos();
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vel = sd->getVel();
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271 |
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272 |
sprintf( tempBuffer,
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273 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
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sd->getType(),
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pos[0],
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pos[1],
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pos[2],
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vel[0],
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vel[1],
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vel[2]);
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281 |
strcpy( writeLine, tempBuffer );
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282 |
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283 |
if( sd->isDirectional() ){
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284 |
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285 |
q = sd->getQ();
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286 |
ji = sd->getJ();
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287 |
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288 |
sprintf( tempBuffer,
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289 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
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q[0],
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q[1],
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q[2],
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q[3],
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294 |
ji[0],
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ji[1],
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ji[2]);
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297 |
strcat( writeLine, tempBuffer );
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298 |
}
|
299 |
else
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300 |
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 |
for(k = 0; k < outFile.size(); k++)
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303 |
*outFile[k] << writeLine;
|
304 |
}
|
305 |
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306 |
}
|
307 |
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308 |
#else // is_mpi
|
309 |
|
310 |
/* code to find maximum tag value */
|
311 |
|
312 |
int *tagub, flag, MAXTAG;
|
313 |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
|
314 |
if (flag) {
|
315 |
MAXTAG = *tagub;
|
316 |
} else {
|
317 |
MAXTAG = 32767;
|
318 |
}
|
319 |
|
320 |
int haveError;
|
321 |
|
322 |
MPI_Status istatus;
|
323 |
int nCurObj;
|
324 |
int *MolToProcMap = mpiSim->getMolToProcMap();
|
325 |
|
326 |
// write out header and node 0's coordinates
|
327 |
|
328 |
if( worldRank == 0 ){
|
329 |
|
330 |
// Node 0 needs a list of the magic potatoes for each processor;
|
331 |
|
332 |
nProc = mpiSim->getNProcessors();
|
333 |
potatoes = new int[nProc];
|
334 |
|
335 |
//write out the comment lines
|
336 |
for (i = 0; i < nProc; i++)
|
337 |
potatoes[i] = 0;
|
338 |
|
339 |
for(k = 0; k < outFile.size(); k++){
|
340 |
*outFile[k] << nTotObjects << "\n";
|
341 |
|
342 |
*outFile[k] << currentTime << ";\t"
|
343 |
<< entry_plug->Hmat[0][0] << "\t"
|
344 |
<< entry_plug->Hmat[1][0] << "\t"
|
345 |
<< entry_plug->Hmat[2][0] << ";\t"
|
346 |
|
347 |
<< entry_plug->Hmat[0][1] << "\t"
|
348 |
<< entry_plug->Hmat[1][1] << "\t"
|
349 |
<< entry_plug->Hmat[2][1] << ";\t"
|
350 |
|
351 |
<< entry_plug->Hmat[0][2] << "\t"
|
352 |
<< entry_plug->Hmat[1][2] << "\t"
|
353 |
<< entry_plug->Hmat[2][2] << ";";
|
354 |
|
355 |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
|
356 |
}
|
357 |
|
358 |
currentIndex = 0;
|
359 |
|
360 |
for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
|
361 |
|
362 |
// Get the Node number which has this atom;
|
363 |
|
364 |
which_node = MolToProcMap[i];
|
365 |
|
366 |
if (which_node != 0) {
|
367 |
|
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
|