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tim |
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#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, "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, "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, |
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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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} |
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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; |
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int which_node; |
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int done; |
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int which_atom; |
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int local_index; |
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int 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" << entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" << entry_plug->Hmat[2][0] |
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<< ";\t" << entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" << entry_plug->Hmat[2][1] |
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<< ";\t" << entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" << entry_plug->Hmat[2][2] << ";"; |
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//write out additional parameters, such as chi and eta |
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//another circular reference nightmare |
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*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() |
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<< endl; |
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} |
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for(i = 0; i < entry_plug->n_mol; i++) { |
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integrableObjects = entry_plug->molecules[i].getIntegrableObjects(); |
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molName |
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= (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID(); |
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for(iter = integrableObjects.begin(); |
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iter != integrableObjects.end(); ++iter) { |
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sd = *iter; |
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pos = sd->getPos(); |
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vel = sd->getVel(); |
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sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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sd->getType(), pos[0], |
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pos[1], pos[2], |
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vel[0], vel[1], |
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vel[2]); |
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strcpy(writeLine, tempBuffer); |
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if (sd->isDirectional()) { |
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q = sd->getQ(); |
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ji = sd->getJ(); |
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sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", q[0], |
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q[1], q[2], q[3], |
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ji[0], ji[1], ji[2]); |
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strcat(writeLine, tempBuffer); |
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} else { |
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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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} |
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for(k = 0; k < outFile.size(); k++) { |
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*outFile[k] << writeLine; |
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} |
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} |
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} |
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#else // is_mpi |
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/* code to find maximum tag value */ |
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int * tagub, flag, MAXTAG; |
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MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
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if (flag) { |
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MAXTAG = *tagub; |
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} else { |
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MAXTAG = 32767; |
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} |
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int haveError; |
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MPI_Status istatus; |
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int nCurObj; |
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int * MolToProcMap = mpiSim->getMolToProcMap(); |
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// write out header and node 0's coordinates |
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if (worldRank == 0) { |
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// Node 0 needs a list of the magic potatoes for each processor; |
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nProc = mpiSim->getNProcessors(); |
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potatoes = new int[nProc]; |
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//write out the comment lines |
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for(i = 0; i < nProc; i++) { |
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potatoes[i] = 0; |
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} |
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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" << entry_plug->Hmat[0][0] |
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<< "\t" << entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" << entry_plug->Hmat[0][1] |
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<< "\t" << entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" << entry_plug->Hmat[0][2] |
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<< "\t" << entry_plug->Hmat[1][2] << "\t" |
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<< entry_plug->Hmat[2][2] << ";"; |
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*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() |
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<< endl; |
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} |
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currentIndex = 0; |
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for(i = 0; i < mpiSim->getNMolGlobal(); i++) { |
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// Get the Node number which has this atom; |
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which_node = MolToProcMap[i]; |
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if (which_node != 0) { |
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if (potatoes[which_node] + 1 >= MAXTAG) { |
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// The potato was going to exceed the maximum value, |
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// so wrap this processor potato back to 0: |
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potatoes[which_node] = 0; |
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MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, |
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MPI_COMM_WORLD); |
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} |
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myPotato = potatoes[which_node]; |
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//recieve the number of integrableObject in current molecule |
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MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato, |
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MPI_COMM_WORLD, &istatus); |
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myPotato++; |
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for(int l = 0; l < nCurObj; l++) { |
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if (potatoes[which_node] + 2 >= MAXTAG) { |
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// The potato was going to exceed the maximum value, |
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// so wrap this processor potato back to 0: |
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potatoes[which_node] = 0; |
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MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, |
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0, MPI_COMM_WORLD); |
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} |
403 |
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MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, |
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which_node, myPotato, MPI_COMM_WORLD, |
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&istatus); |
407 |
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408 |
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atomTypeString = MPIatomTypeString; |
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410 |
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myPotato++; |
411 |
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MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, |
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MPI_COMM_WORLD, &istatus); |
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|
|
myPotato++; |
415 |
|
|
|
416 |
|
|
MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
417 |
|
|
|
418 |
|
|
if (msgLen == 13) |
419 |
|
|
isDirectional = 1; |
420 |
|
|
else |
421 |
|
|
isDirectional = 0; |
422 |
|
|
|
423 |
|
|
// If we've survived to here, format the line: |
424 |
|
|
|
425 |
|
|
if (!isDirectional) { |
426 |
|
|
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
427 |
|
|
atomTypeString, atomData[0], |
428 |
|
|
atomData[1], atomData[2], |
429 |
|
|
atomData[3], atomData[4], |
430 |
|
|
atomData[5]); |
431 |
|
|
|
432 |
|
|
strcat(writeLine, |
433 |
|
|
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
434 |
|
|
} else { |
435 |
|
|
sprintf(writeLine, |
436 |
|
|
"%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", |
437 |
|
|
atomTypeString, |
438 |
|
|
atomData[0], |
439 |
|
|
atomData[1], |
440 |
|
|
atomData[2], |
441 |
|
|
atomData[3], |
442 |
|
|
atomData[4], |
443 |
|
|
atomData[5], |
444 |
|
|
atomData[6], |
445 |
|
|
atomData[7], |
446 |
|
|
atomData[8], |
447 |
|
|
atomData[9], |
448 |
|
|
atomData[10], |
449 |
|
|
atomData[11], |
450 |
|
|
atomData[12]); |
451 |
|
|
} |
452 |
|
|
|
453 |
|
|
for(k = 0; k < outFile.size(); k++) { |
454 |
|
|
*outFile[k] << writeLine; |
455 |
|
|
} |
456 |
|
|
} // end for(int l =0) |
457 |
|
|
|
458 |
|
|
potatoes[which_node] = myPotato; |
459 |
|
|
} else { |
460 |
|
|
haveError = 0; |
461 |
|
|
|
462 |
|
|
local_index = indexArray[currentIndex].first; |
463 |
|
|
|
464 |
|
|
integrableObjects |
465 |
|
|
= (entry_plug->molecules[local_index]).getIntegrableObjects(); |
466 |
|
|
|
467 |
|
|
for(iter = integrableObjects.begin(); |
468 |
|
|
iter != integrableObjects.end(); ++iter) { |
469 |
|
|
sd = *iter; |
470 |
|
|
atomTypeString = sd->getType(); |
471 |
|
|
|
472 |
|
|
pos = sd->getPos(); |
473 |
|
|
vel = sd->getVel(); |
474 |
|
|
|
475 |
|
|
atomData[0] = pos[0]; |
476 |
|
|
atomData[1] = pos[1]; |
477 |
|
|
atomData[2] = pos[2]; |
478 |
|
|
|
479 |
|
|
atomData[3] = vel[0]; |
480 |
|
|
atomData[4] = vel[1]; |
481 |
|
|
atomData[5] = vel[2]; |
482 |
|
|
|
483 |
|
|
isDirectional = 0; |
484 |
|
|
|
485 |
|
|
if (sd->isDirectional()) { |
486 |
|
|
isDirectional = 1; |
487 |
|
|
|
488 |
|
|
q = sd->getQ(); |
489 |
|
|
ji = sd->getJ(); |
490 |
|
|
|
491 |
|
|
for(int j = 0; j < 6; j++) { |
492 |
|
|
atomData[j] = atomData[j]; |
493 |
|
|
} |
494 |
|
|
|
495 |
|
|
atomData[6] = q[0]; |
496 |
|
|
atomData[7] = q[1]; |
497 |
|
|
atomData[8] = q[2]; |
498 |
|
|
atomData[9] = q[3]; |
499 |
|
|
|
500 |
|
|
atomData[10] = ji[0]; |
501 |
|
|
atomData[11] = ji[1]; |
502 |
|
|
atomData[12] = ji[2]; |
503 |
|
|
} |
504 |
|
|
|
505 |
|
|
// If we've survived to here, format the line: |
506 |
|
|
|
507 |
|
|
if (!isDirectional) { |
508 |
|
|
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
509 |
|
|
atomTypeString, atomData[0], |
510 |
|
|
atomData[1], atomData[2], |
511 |
|
|
atomData[3], atomData[4], |
512 |
|
|
atomData[5]); |
513 |
|
|
|
514 |
|
|
strcat(writeLine, |
515 |
|
|
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
516 |
|
|
} else { |
517 |
|
|
sprintf(writeLine, |
518 |
|
|
"%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", |
519 |
|
|
atomTypeString, |
520 |
|
|
atomData[0], |
521 |
|
|
atomData[1], |
522 |
|
|
atomData[2], |
523 |
|
|
atomData[3], |
524 |
|
|
atomData[4], |
525 |
|
|
atomData[5], |
526 |
|
|
atomData[6], |
527 |
|
|
atomData[7], |
528 |
|
|
atomData[8], |
529 |
|
|
atomData[9], |
530 |
|
|
atomData[10], |
531 |
|
|
atomData[11], |
532 |
|
|
atomData[12]); |
533 |
|
|
} |
534 |
|
|
|
535 |
|
|
for(k = 0; k < outFile.size(); k++) { |
536 |
|
|
*outFile[k] << writeLine; |
537 |
|
|
} |
538 |
|
|
} //end for(iter = integrableObject.begin()) |
539 |
|
|
|
540 |
|
|
currentIndex++; |
541 |
|
|
} |
542 |
|
|
} //end for(i = 0; i < mpiSim->getNmol()) |
543 |
|
|
|
544 |
|
|
for(k = 0; k < outFile.size(); k++) { |
545 |
|
|
outFile[k]->flush(); |
546 |
|
|
} |
547 |
|
|
|
548 |
|
|
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
549 |
|
|
|
550 |
|
|
MPIcheckPoint(); |
551 |
|
|
|
552 |
|
|
delete [] potatoes; |
553 |
|
|
} else { |
554 |
|
|
|
555 |
|
|
// worldRank != 0, so I'm a remote node. |
556 |
|
|
|
557 |
|
|
// Set my magic potato to 0: |
558 |
|
|
|
559 |
|
|
myPotato = 0; |
560 |
|
|
currentIndex = 0; |
561 |
|
|
|
562 |
|
|
for(i = 0; i < mpiSim->getNMolGlobal(); i++) { |
563 |
|
|
|
564 |
|
|
// Am I the node which has this integrableObject? |
565 |
|
|
|
566 |
|
|
if (MolToProcMap[i] == worldRank) { |
567 |
|
|
if (myPotato + 1 >= MAXTAG) { |
568 |
|
|
|
569 |
|
|
// The potato was going to exceed the maximum value, |
570 |
|
|
// so wrap this processor potato back to 0 (and block until |
571 |
|
|
// node 0 says we can go: |
572 |
|
|
|
573 |
|
|
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
574 |
|
|
&istatus); |
575 |
|
|
} |
576 |
|
|
|
577 |
|
|
local_index = indexArray[currentIndex].first; |
578 |
|
|
integrableObjects = |
579 |
|
|
entry_plug->molecules[local_index].getIntegrableObjects(); |
580 |
|
|
|
581 |
|
|
nCurObj = integrableObjects.size(); |
582 |
|
|
|
583 |
|
|
MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD); |
584 |
|
|
myPotato++; |
585 |
|
|
|
586 |
|
|
for(iter = integrableObjects.begin(); |
587 |
|
|
iter != integrableObjects.end(); iter++) { |
588 |
|
|
if (myPotato + 2 >= MAXTAG) { |
589 |
|
|
|
590 |
|
|
// The potato was going to exceed the maximum value, |
591 |
|
|
// so wrap this processor potato back to 0 (and block until |
592 |
|
|
// node 0 says we can go: |
593 |
|
|
|
594 |
|
|
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
595 |
|
|
&istatus); |
596 |
|
|
} |
597 |
|
|
|
598 |
|
|
sd = *iter; |
599 |
|
|
|
600 |
|
|
atomTypeString = sd->getType(); |
601 |
|
|
|
602 |
|
|
pos = sd->getPos(); |
603 |
|
|
vel = sd->getVel(); |
604 |
|
|
|
605 |
|
|
atomData[0] = pos[0]; |
606 |
|
|
atomData[1] = pos[1]; |
607 |
|
|
atomData[2] = pos[2]; |
608 |
|
|
|
609 |
|
|
atomData[3] = vel[0]; |
610 |
|
|
atomData[4] = vel[1]; |
611 |
|
|
atomData[5] = vel[2]; |
612 |
|
|
|
613 |
|
|
isDirectional = 0; |
614 |
|
|
|
615 |
|
|
if (sd->isDirectional()) { |
616 |
|
|
isDirectional = 1; |
617 |
|
|
|
618 |
|
|
q = sd->getQ(); |
619 |
|
|
ji = sd->getJ(); |
620 |
|
|
|
621 |
|
|
atomData[6] = q[0]; |
622 |
|
|
atomData[7] = q[1]; |
623 |
|
|
atomData[8] = q[2]; |
624 |
|
|
atomData[9] = q[3]; |
625 |
|
|
|
626 |
|
|
atomData[10] = ji[0]; |
627 |
|
|
atomData[11] = ji[1]; |
628 |
|
|
atomData[12] = ji[2]; |
629 |
|
|
} |
630 |
|
|
|
631 |
|
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
632 |
|
|
|
633 |
|
|
// null terminate the string before sending (just in case): |
634 |
|
|
MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0'; |
635 |
|
|
|
636 |
|
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
637 |
|
|
myPotato, MPI_COMM_WORLD); |
638 |
|
|
|
639 |
|
|
myPotato++; |
640 |
|
|
|
641 |
|
|
if (isDirectional) { |
642 |
|
|
MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato, |
643 |
|
|
MPI_COMM_WORLD); |
644 |
|
|
} else { |
645 |
|
|
MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato, |
646 |
|
|
MPI_COMM_WORLD); |
647 |
|
|
} |
648 |
|
|
|
649 |
|
|
myPotato++; |
650 |
|
|
} |
651 |
|
|
|
652 |
|
|
currentIndex++; |
653 |
|
|
} |
654 |
|
|
} |
655 |
|
|
|
656 |
|
|
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
657 |
|
|
MPIcheckPoint(); |
658 |
|
|
} |
659 |
|
|
|
660 |
|
|
#endif // is_mpi |
661 |
|
|
|
662 |
|
|
} |
663 |
|
|
|
664 |
|
|
#ifdef IS_MPI |
665 |
|
|
|
666 |
|
|
// a couple of functions to let us escape the write loop |
667 |
|
|
|
668 |
|
|
void dWrite::DieDieDie(void) { |
669 |
|
|
MPI_Finalize(); |
670 |
|
|
exit(0); |
671 |
|
|
} |
672 |
|
|
|
673 |
|
|
#endif //is_mpi |