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tim |
1078 |
#define _LARGEFILE_SOURCE64 |
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mmeineke |
723 |
#define _FILE_OFFSET_BITS 64 |
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gezelter |
829 |
#include <string.h> |
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mmeineke |
377 |
#include <iostream> |
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#include <fstream> |
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tim |
929 |
#include <algorithm> |
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#include <utility> |
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mmeineke |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#include "mpiSimulation.hpp" |
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mmeineke |
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namespace dWrite{ |
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gezelter |
907 |
void DieDieDie( void ); |
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mmeineke |
440 |
} |
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using namespace dWrite; |
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mmeineke |
377 |
#endif //is_mpi |
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#include "ReadWrite.hpp" |
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#include "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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tim |
837 |
|
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tim |
929 |
dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
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tim |
837 |
|
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tim |
929 |
if( !dumpFile ){ |
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tim |
837 |
|
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mmeineke |
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for dump output.\n", |
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tim |
929 |
entry_plug->sampleName); |
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mmeineke |
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painCave.isFatal = 1; |
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simError(); |
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} |
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mmeineke |
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mmeineke |
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#ifdef IS_MPI |
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} |
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tim |
929 |
//sort the local atoms by global index |
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sortByGlobalIndex(); |
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mmeineke |
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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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tim |
929 |
dumpFile.close(); |
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mmeineke |
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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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tim |
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#ifdef IS_MPI |
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tim |
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tim |
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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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tim |
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Molecule* mols = entry_plug->molecules; |
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tim |
929 |
indexArray.clear(); |
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tim |
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for(int i = 0; i < entry_plug->n_mol;i++) |
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tim |
1108 |
indexArray.push_back(make_pair(i, mols[i].getGlobalIndex())); |
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tim |
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|
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sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
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} |
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chuckv |
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tim |
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#endif |
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void DumpWriter::writeDump(double currentTime){ |
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tim |
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ofstream finalOut; |
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tim |
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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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tim |
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#endif |
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tim |
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finalOut.open( entry_plug->finalName, 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 ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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tim |
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#ifdef IS_MPI |
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tim |
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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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tim |
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#ifdef IS_MPI |
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finalOut.close(); |
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#endif |
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tim |
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} |
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void DumpWriter::writeFinal(double currentTime){ |
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tim |
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ofstream finalOut; |
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tim |
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vector<ofstream*> fileStreams; |
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tim |
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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mmeineke |
951 |
#endif // is_mpi |
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tim |
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finalOut.open( entry_plug->finalName, 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 ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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152 |
mmeineke |
951 |
#ifdef IS_MPI |
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tim |
934 |
} |
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tim |
929 |
#endif // is_mpi |
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tim |
934 |
fileStreams.push_back(&finalOut); |
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writeFrame(fileStreams, currentTime); |
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tim |
936 |
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#ifdef IS_MPI |
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finalOut.close(); |
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#endif |
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tim |
929 |
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} |
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tim |
934 |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
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tim |
929 |
|
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mmeineke |
377 |
const int BUFFERSIZE = 2000; |
168 |
gezelter |
912 |
const int MINIBUFFERSIZE = 100; |
169 |
gezelter |
907 |
|
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tim |
936 |
char tempBuffer[BUFFERSIZE]; |
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mmeineke |
377 |
char writeLine[BUFFERSIZE]; |
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tim |
934 |
int i, k; |
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gezelter |
916 |
|
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mmeineke |
787 |
#ifdef IS_MPI |
176 |
gezelter |
916 |
|
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gezelter |
947 |
/********************************************************************* |
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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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gezelter |
916 |
int *potatoes; |
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int myPotato; |
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int nProc; |
218 |
tim |
929 |
int j, which_node, done, which_atom, local_index, currentIndex; |
219 |
tim |
1152 |
double atomData[13]; |
220 |
gezelter |
907 |
int isDirectional; |
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char* atomTypeString; |
222 |
gezelter |
910 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
223 |
tim |
1108 |
int nObjects; |
224 |
tim |
1152 |
int msgLen; // the length of message actually recieved at master nodes |
225 |
mmeineke |
787 |
#endif //is_mpi |
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227 |
gezelter |
1097 |
double q[4], ji[3]; |
228 |
mmeineke |
377 |
DirectionalAtom* dAtom; |
229 |
mmeineke |
670 |
double pos[3], vel[3]; |
230 |
tim |
1108 |
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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mmeineke |
377 |
#ifndef IS_MPI |
237 |
tim |
934 |
|
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for(k = 0; k < outFile.size(); k++){ |
239 |
tim |
1108 |
*outFile[k] << nTotObjects << "\n"; |
240 |
tim |
837 |
|
241 |
tim |
934 |
*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" |
249 |
tim |
837 |
|
250 |
tim |
934 |
<< 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] << ";"; |
253 |
mmeineke |
572 |
|
254 |
tim |
934 |
//write out additional parameters, such as chi and eta |
255 |
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*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
256 |
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} |
257 |
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258 |
tim |
1108 |
for( i=0; i< entry_plug->n_mol; i++ ){ |
259 |
tim |
837 |
|
260 |
tim |
1108 |
integrableObjects = entry_plug->molecules[i].getIntegrableObjects(); |
261 |
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molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID(); |
262 |
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263 |
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for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){ |
264 |
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sd = *iter; |
265 |
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sd->getPos(pos); |
266 |
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sd->getVel(vel); |
267 |
mmeineke |
377 |
|
268 |
tim |
1108 |
sprintf( tempBuffer, |
269 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
270 |
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sd->getType(), |
271 |
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pos[0], |
272 |
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pos[1], |
273 |
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pos[2], |
274 |
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vel[0], |
275 |
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vel[1], |
276 |
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vel[2]); |
277 |
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strcpy( writeLine, tempBuffer ); |
278 |
mmeineke |
377 |
|
279 |
tim |
1108 |
if( sd->isDirectional() ){ |
280 |
tim |
837 |
|
281 |
tim |
1108 |
sd->getQ( q ); |
282 |
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sd->getJ( ji ); |
283 |
tim |
837 |
|
284 |
tim |
1108 |
sprintf( tempBuffer, |
285 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
286 |
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q[0], |
287 |
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q[1], |
288 |
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q[2], |
289 |
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q[3], |
290 |
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ji[0], |
291 |
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ji[1], |
292 |
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ji[2]); |
293 |
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strcat( writeLine, tempBuffer ); |
294 |
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} |
295 |
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else |
296 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
297 |
mmeineke |
377 |
} |
298 |
tim |
837 |
|
299 |
tim |
1108 |
|
300 |
tim |
934 |
for(k = 0; k < outFile.size(); k++) |
301 |
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*outFile[k] << writeLine; |
302 |
tim |
1108 |
} |
303 |
mmeineke |
377 |
|
304 |
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#else // is_mpi |
305 |
gezelter |
416 |
|
306 |
chuckv |
913 |
/* code to find maximum tag value */ |
307 |
tim |
919 |
|
308 |
tim |
920 |
int *tagub, flag, MAXTAG; |
309 |
chuckv |
913 |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
310 |
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if (flag) { |
311 |
tim |
920 |
MAXTAG = *tagub; |
312 |
chuckv |
913 |
} else { |
313 |
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MAXTAG = 32767; |
314 |
gezelter |
916 |
} |
315 |
mmeineke |
440 |
|
316 |
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int haveError; |
317 |
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|
318 |
mmeineke |
447 |
MPI_Status istatus; |
319 |
tim |
1108 |
int nCurObj; |
320 |
|
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int *MolToProcMap = mpiSim->getMolToProcMap(); |
321 |
tim |
837 |
|
322 |
mmeineke |
377 |
// write out header and node 0's coordinates |
323 |
tim |
837 |
|
324 |
mmeineke |
377 |
if( worldRank == 0 ){ |
325 |
gezelter |
916 |
|
326 |
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// Node 0 needs a list of the magic potatoes for each processor; |
327 |
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|
328 |
gezelter |
1203 |
nProc = mpiSim->getNProcessors(); |
329 |
gezelter |
916 |
potatoes = new int[nProc]; |
330 |
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|
331 |
tim |
934 |
//write out the comment lines |
332 |
gezelter |
916 |
for (i = 0; i < nProc; i++) |
333 |
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potatoes[i] = 0; |
334 |
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|
335 |
tim |
934 |
for(k = 0; k < outFile.size(); k++){ |
336 |
tim |
1108 |
*outFile[k] << nTotObjects << "\n"; |
337 |
tim |
837 |
|
338 |
tim |
934 |
*outFile[k] << currentTime << ";\t" |
339 |
|
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<< entry_plug->Hmat[0][0] << "\t" |
340 |
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<< entry_plug->Hmat[1][0] << "\t" |
341 |
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<< entry_plug->Hmat[2][0] << ";\t" |
342 |
tim |
837 |
|
343 |
tim |
934 |
<< entry_plug->Hmat[0][1] << "\t" |
344 |
|
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<< entry_plug->Hmat[1][1] << "\t" |
345 |
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<< entry_plug->Hmat[2][1] << ";\t" |
346 |
tim |
837 |
|
347 |
tim |
934 |
<< entry_plug->Hmat[0][2] << "\t" |
348 |
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<< entry_plug->Hmat[1][2] << "\t" |
349 |
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<< entry_plug->Hmat[2][2] << ";"; |
350 |
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351 |
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*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
352 |
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} |
353 |
tim |
837 |
|
354 |
tim |
929 |
currentIndex = 0; |
355 |
tim |
934 |
|
356 |
gezelter |
1203 |
for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { |
357 |
chuckv |
913 |
|
358 |
gezelter |
417 |
// Get the Node number which has this atom; |
359 |
chuckv |
913 |
|
360 |
tim |
1108 |
which_node = MolToProcMap[i]; |
361 |
chuckv |
913 |
|
362 |
gezelter |
907 |
if (which_node != 0) { |
363 |
tim |
1108 |
|
364 |
|
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if (potatoes[which_node] + 1 >= MAXTAG) { |
365 |
gezelter |
916 |
// The potato was going to exceed the maximum value, |
366 |
|
|
// so wrap this processor potato back to 0: |
367 |
|
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|
368 |
|
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potatoes[which_node] = 0; |
369 |
tim |
1129 |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
370 |
gezelter |
916 |
|
371 |
|
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} |
372 |
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|
373 |
|
|
myPotato = potatoes[which_node]; |
374 |
tim |
1108 |
|
375 |
|
|
//recieve the number of integrableObject in current molecule |
376 |
|
|
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
377 |
gezelter |
916 |
myPotato, MPI_COMM_WORLD, &istatus); |
378 |
tim |
1129 |
myPotato++; |
379 |
gezelter |
907 |
|
380 |
tim |
1108 |
for(int l = 0; l < nCurObj; l++){ |
381 |
gezelter |
916 |
|
382 |
tim |
1152 |
if (potatoes[which_node] + 2 >= MAXTAG) { |
383 |
tim |
1108 |
// The potato was going to exceed the maximum value, |
384 |
|
|
// so wrap this processor potato back to 0: |
385 |
|
|
|
386 |
|
|
potatoes[which_node] = 0; |
387 |
tim |
1129 |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
388 |
tim |
1108 |
|
389 |
|
|
} |
390 |
|
|
|
391 |
|
|
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
392 |
|
|
myPotato, MPI_COMM_WORLD, &istatus); |
393 |
|
|
|
394 |
|
|
atomTypeString = MPIatomTypeString; |
395 |
|
|
|
396 |
|
|
myPotato++; |
397 |
|
|
|
398 |
tim |
1152 |
MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus); |
399 |
tim |
1108 |
myPotato++; |
400 |
gezelter |
907 |
|
401 |
tim |
1152 |
MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
402 |
tim |
1108 |
|
403 |
tim |
1152 |
if(msgLen == 13) |
404 |
|
|
isDirectional = 1; |
405 |
|
|
else |
406 |
|
|
isDirectional = 0; |
407 |
|
|
|
408 |
gezelter |
907 |
} |
409 |
gezelter |
916 |
potatoes[which_node] = myPotato; |
410 |
gezelter |
907 |
|
411 |
|
|
} else { |
412 |
|
|
|
413 |
tim |
934 |
haveError = 0; |
414 |
gezelter |
916 |
|
415 |
tim |
1108 |
local_index = indexArray[currentIndex].first; |
416 |
tim |
837 |
|
417 |
tim |
1108 |
integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects(); |
418 |
gezelter |
907 |
|
419 |
tim |
1108 |
for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){ |
420 |
|
|
sd = *iter; |
421 |
|
|
atomTypeString = sd->getType(); |
422 |
|
|
|
423 |
|
|
sd->getPos(pos); |
424 |
|
|
sd->getVel(vel); |
425 |
|
|
|
426 |
tim |
1152 |
atomData[0] = pos[0]; |
427 |
|
|
atomData[1] = pos[1]; |
428 |
|
|
atomData[2] = pos[2]; |
429 |
tim |
837 |
|
430 |
tim |
1152 |
atomData[3] = vel[0]; |
431 |
|
|
atomData[4] = vel[1]; |
432 |
|
|
atomData[5] = vel[2]; |
433 |
tim |
1108 |
|
434 |
|
|
isDirectional = 0; |
435 |
gezelter |
916 |
|
436 |
tim |
1108 |
if( sd->isDirectional() ){ |
437 |
|
|
|
438 |
|
|
isDirectional = 1; |
439 |
|
|
|
440 |
|
|
sd->getQ( q ); |
441 |
|
|
sd->getJ( ji ); |
442 |
|
|
|
443 |
|
|
for (int j = 0; j < 6 ; j++) |
444 |
tim |
1152 |
atomData[j] = atomData[j]; |
445 |
tim |
1108 |
|
446 |
tim |
1152 |
atomData[6] = q[0]; |
447 |
|
|
atomData[7] = q[1]; |
448 |
|
|
atomData[8] = q[2]; |
449 |
|
|
atomData[9] = q[3]; |
450 |
tim |
1108 |
|
451 |
tim |
1152 |
atomData[10] = ji[0]; |
452 |
|
|
atomData[11] = ji[1]; |
453 |
|
|
atomData[12] = ji[2]; |
454 |
tim |
1108 |
} |
455 |
gezelter |
907 |
|
456 |
tim |
1108 |
} |
457 |
gezelter |
916 |
|
458 |
tim |
1108 |
currentIndex++; |
459 |
tim |
926 |
} |
460 |
|
|
// If we've survived to here, format the line: |
461 |
|
|
|
462 |
|
|
if (!isDirectional) { |
463 |
|
|
|
464 |
tim |
934 |
sprintf( writeLine, |
465 |
chuckv |
949 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
466 |
|
|
atomTypeString, |
467 |
tim |
1152 |
atomData[0], |
468 |
|
|
atomData[1], |
469 |
|
|
atomData[2], |
470 |
|
|
atomData[3], |
471 |
|
|
atomData[4], |
472 |
|
|
atomData[5]); |
473 |
tim |
926 |
|
474 |
chuckv |
949 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
475 |
|
|
|
476 |
tim |
926 |
} else { |
477 |
|
|
|
478 |
chuckv |
949 |
sprintf( writeLine, |
479 |
|
|
"%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", |
480 |
|
|
atomTypeString, |
481 |
tim |
1152 |
atomData[0], |
482 |
|
|
atomData[1], |
483 |
|
|
atomData[2], |
484 |
|
|
atomData[3], |
485 |
|
|
atomData[4], |
486 |
|
|
atomData[5], |
487 |
|
|
atomData[6], |
488 |
|
|
atomData[7], |
489 |
|
|
atomData[8], |
490 |
|
|
atomData[9], |
491 |
|
|
atomData[10], |
492 |
|
|
atomData[11], |
493 |
|
|
atomData[12]); |
494 |
gezelter |
907 |
|
495 |
|
|
} |
496 |
tim |
926 |
|
497 |
tim |
934 |
for(k = 0; k < outFile.size(); k++) |
498 |
|
|
*outFile[k] << writeLine; |
499 |
mmeineke |
377 |
} |
500 |
tim |
926 |
|
501 |
tim |
934 |
for(k = 0; k < outFile.size(); k++) |
502 |
|
|
outFile[k]->flush(); |
503 |
|
|
|
504 |
gezelter |
907 |
sprintf( checkPointMsg, |
505 |
|
|
"Sucessfully took a dump.\n"); |
506 |
chuckv |
949 |
|
507 |
gezelter |
907 |
MPIcheckPoint(); |
508 |
chuckv |
949 |
|
509 |
tim |
919 |
delete[] potatoes; |
510 |
chuckv |
949 |
|
511 |
gezelter |
415 |
} else { |
512 |
tim |
837 |
|
513 |
gezelter |
907 |
// worldRank != 0, so I'm a remote node. |
514 |
gezelter |
916 |
|
515 |
|
|
// Set my magic potato to 0: |
516 |
|
|
|
517 |
|
|
myPotato = 0; |
518 |
tim |
929 |
currentIndex = 0; |
519 |
gezelter |
907 |
|
520 |
gezelter |
1203 |
for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { |
521 |
gezelter |
907 |
|
522 |
tim |
1108 |
// Am I the node which has this integrableObject? |
523 |
gezelter |
907 |
|
524 |
tim |
1108 |
if (MolToProcMap[i] == worldRank) { |
525 |
tim |
837 |
|
526 |
tim |
1108 |
|
527 |
|
|
if (myPotato + 1 >= MAXTAG) { |
528 |
chuckv |
949 |
|
529 |
gezelter |
916 |
// The potato was going to exceed the maximum value, |
530 |
|
|
// so wrap this processor potato back to 0 (and block until |
531 |
|
|
// node 0 says we can go: |
532 |
chuckv |
949 |
|
533 |
gezelter |
916 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
534 |
|
|
|
535 |
|
|
} |
536 |
chuckv |
949 |
|
537 |
tim |
1108 |
local_index = indexArray[currentIndex].first; |
538 |
|
|
integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects(); |
539 |
|
|
|
540 |
|
|
nCurObj = integrableObjects.size(); |
541 |
|
|
|
542 |
|
|
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
543 |
|
|
myPotato, MPI_COMM_WORLD); |
544 |
tim |
1129 |
myPotato++; |
545 |
tim |
1108 |
|
546 |
|
|
for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){ |
547 |
|
|
|
548 |
tim |
1152 |
if (myPotato + 2 >= MAXTAG) { |
549 |
tim |
1108 |
|
550 |
|
|
// The potato was going to exceed the maximum value, |
551 |
|
|
// so wrap this processor potato back to 0 (and block until |
552 |
|
|
// node 0 says we can go: |
553 |
|
|
|
554 |
|
|
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
555 |
|
|
|
556 |
|
|
} |
557 |
|
|
|
558 |
|
|
sd = *iter; |
559 |
|
|
|
560 |
|
|
atomTypeString = sd->getType(); |
561 |
|
|
|
562 |
|
|
sd->getPos(pos); |
563 |
|
|
sd->getVel(vel); |
564 |
|
|
|
565 |
tim |
1152 |
atomData[0] = pos[0]; |
566 |
|
|
atomData[1] = pos[1]; |
567 |
|
|
atomData[2] = pos[2]; |
568 |
tim |
1108 |
|
569 |
tim |
1152 |
atomData[3] = vel[0]; |
570 |
|
|
atomData[4] = vel[1]; |
571 |
|
|
atomData[5] = vel[2]; |
572 |
tim |
1108 |
|
573 |
|
|
isDirectional = 0; |
574 |
|
|
|
575 |
|
|
if( sd->isDirectional() ){ |
576 |
|
|
|
577 |
|
|
isDirectional = 1; |
578 |
tim |
920 |
|
579 |
tim |
1108 |
sd->getQ( q ); |
580 |
|
|
sd->getJ( ji ); |
581 |
|
|
|
582 |
|
|
|
583 |
tim |
1152 |
atomData[6] = q[0]; |
584 |
|
|
atomData[7] = q[1]; |
585 |
|
|
atomData[8] = q[2]; |
586 |
|
|
atomData[9] = q[3]; |
587 |
tim |
1108 |
|
588 |
tim |
1152 |
atomData[10] = ji[0]; |
589 |
|
|
atomData[11] = ji[1]; |
590 |
|
|
atomData[12] = ji[2]; |
591 |
tim |
1108 |
} |
592 |
tim |
837 |
|
593 |
tim |
1108 |
|
594 |
|
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
595 |
tim |
837 |
|
596 |
tim |
1108 |
// null terminate the string before sending (just in case): |
597 |
|
|
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
598 |
mmeineke |
377 |
|
599 |
tim |
1108 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
600 |
|
|
myPotato, MPI_COMM_WORLD); |
601 |
gezelter |
907 |
|
602 |
tim |
1108 |
myPotato++; |
603 |
gezelter |
907 |
|
604 |
tim |
1108 |
if (isDirectional) { |
605 |
tim |
837 |
|
606 |
tim |
1152 |
MPI_Send(atomData, 13, MPI_DOUBLE, 0, |
607 |
tim |
1108 |
myPotato, MPI_COMM_WORLD); |
608 |
|
|
|
609 |
|
|
} else { |
610 |
tim |
837 |
|
611 |
tim |
1152 |
MPI_Send(atomData, 6, MPI_DOUBLE, 0, |
612 |
tim |
1108 |
myPotato, MPI_COMM_WORLD); |
613 |
|
|
} |
614 |
tim |
837 |
|
615 |
tim |
1108 |
myPotato++; |
616 |
gezelter |
916 |
|
617 |
tim |
1108 |
} |
618 |
gezelter |
907 |
|
619 |
tim |
1108 |
currentIndex++; |
620 |
gezelter |
907 |
|
621 |
|
|
} |
622 |
tim |
1108 |
|
623 |
mmeineke |
377 |
} |
624 |
mmeineke |
440 |
|
625 |
gezelter |
907 |
sprintf( checkPointMsg, |
626 |
gezelter |
916 |
"Sucessfully took a dump.\n"); |
627 |
tim |
1129 |
MPIcheckPoint(); |
628 |
gezelter |
907 |
|
629 |
tim |
1129 |
} |
630 |
|
|
|
631 |
|
|
|
632 |
gezelter |
907 |
|
633 |
mmeineke |
377 |
#endif // is_mpi |
634 |
|
|
} |
635 |
mmeineke |
440 |
|
636 |
|
|
#ifdef IS_MPI |
637 |
|
|
|
638 |
|
|
// a couple of functions to let us escape the write loop |
639 |
|
|
|
640 |
gezelter |
907 |
void dWrite::DieDieDie( void ){ |
641 |
tim |
837 |
|
642 |
mmeineke |
440 |
MPI_Finalize(); |
643 |
|
|
exit (0); |
644 |
|
|
} |
645 |
|
|
|
646 |
|
|
#endif //is_mpi |