1 |
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 |
377 |
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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 |
440 |
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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 |
377 |
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 |
469 |
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mmeineke |
377 |
#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 |
377 |
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 |
377 |
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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 |
929 |
#ifdef IS_MPI |
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tim |
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tim |
929 |
/** |
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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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Atom** atoms = entry_plug->atoms; |
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indexArray.clear(); |
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chuckv |
949 |
for(int i = 0; i < mpiSim->getMyNlocal();i++) |
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tim |
929 |
indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
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sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
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chuckv |
949 |
|
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//for (int i = 0; i < mpiSim->getMyNlocal(); i++) { |
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// printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first); |
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//} |
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tim |
929 |
} |
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chuckv |
949 |
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tim |
929 |
#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 |
934 |
vector<ofstream*> fileStreams; |
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#ifdef IS_MPI |
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chuckv |
949 |
printf("Hello from node %d\n", worldRank); |
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sortByGlobalIndex(); |
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tim |
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if(worldRank == 0 ){ |
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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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} |
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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 |
936 |
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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; |
142 |
tim |
934 |
vector<ofstream*> fileStreams; |
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tim |
929 |
#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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tim |
936 |
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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 |
934 |
} |
158 |
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; |
172 |
gezelter |
912 |
const int MINIBUFFERSIZE = 100; |
173 |
gezelter |
907 |
|
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tim |
936 |
char tempBuffer[BUFFERSIZE]; |
175 |
mmeineke |
377 |
char writeLine[BUFFERSIZE]; |
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tim |
934 |
int i, k; |
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gezelter |
916 |
|
179 |
mmeineke |
787 |
#ifdef IS_MPI |
180 |
gezelter |
916 |
|
181 |
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; |
222 |
tim |
929 |
int j, which_node, done, which_atom, local_index, currentIndex; |
223 |
gezelter |
916 |
double atomData6[6]; |
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double atomData13[13]; |
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gezelter |
907 |
int isDirectional; |
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char* atomTypeString; |
227 |
gezelter |
910 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
228 |
gezelter |
916 |
|
229 |
mmeineke |
787 |
#else //is_mpi |
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int nAtoms = entry_plug->n_atoms; |
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#endif //is_mpi |
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mmeineke |
377 |
double q[4]; |
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DirectionalAtom* dAtom; |
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Atom** atoms = entry_plug->atoms; |
236 |
mmeineke |
670 |
double pos[3], vel[3]; |
237 |
tim |
837 |
|
238 |
mmeineke |
377 |
#ifndef IS_MPI |
239 |
tim |
934 |
|
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for(k = 0; k < outFile.size(); k++){ |
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*outFile[k] << nAtoms << "\n"; |
242 |
tim |
837 |
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243 |
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" |
250 |
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<< entry_plug->Hmat[2][1] << ";\t" |
251 |
tim |
837 |
|
252 |
tim |
934 |
<< entry_plug->Hmat[0][2] << "\t" |
253 |
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<< entry_plug->Hmat[1][2] << "\t" |
254 |
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<< entry_plug->Hmat[2][2] << ";"; |
255 |
mmeineke |
572 |
|
256 |
tim |
934 |
//write out additional parameters, such as chi and eta |
257 |
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*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
258 |
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} |
259 |
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260 |
mmeineke |
377 |
for( i=0; i<nAtoms; i++ ){ |
261 |
tim |
837 |
|
262 |
mmeineke |
670 |
atoms[i]->getPos(pos); |
263 |
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atoms[i]->getVel(vel); |
264 |
mmeineke |
377 |
|
265 |
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sprintf( tempBuffer, |
266 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
267 |
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atoms[i]->getType(), |
268 |
mmeineke |
670 |
pos[0], |
269 |
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pos[1], |
270 |
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pos[2], |
271 |
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vel[0], |
272 |
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vel[1], |
273 |
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vel[2]); |
274 |
mmeineke |
377 |
strcpy( writeLine, tempBuffer ); |
275 |
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276 |
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if( atoms[i]->isDirectional() ){ |
277 |
tim |
837 |
|
278 |
mmeineke |
377 |
dAtom = (DirectionalAtom *)atoms[i]; |
279 |
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dAtom->getQ( q ); |
280 |
tim |
837 |
|
281 |
mmeineke |
377 |
sprintf( tempBuffer, |
282 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
283 |
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q[0], |
284 |
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q[1], |
285 |
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q[2], |
286 |
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q[3], |
287 |
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dAtom->getJx(), |
288 |
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dAtom->getJy(), |
289 |
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dAtom->getJz()); |
290 |
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strcat( writeLine, tempBuffer ); |
291 |
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} |
292 |
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else |
293 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
294 |
tim |
837 |
|
295 |
tim |
934 |
for(k = 0; k < outFile.size(); k++) |
296 |
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*outFile[k] << writeLine; |
297 |
mmeineke |
377 |
} |
298 |
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299 |
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#else // is_mpi |
300 |
gezelter |
416 |
|
301 |
chuckv |
913 |
/* code to find maximum tag value */ |
302 |
tim |
919 |
|
303 |
tim |
920 |
int *tagub, flag, MAXTAG; |
304 |
chuckv |
913 |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
305 |
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if (flag) { |
306 |
tim |
920 |
MAXTAG = *tagub; |
307 |
chuckv |
913 |
} else { |
308 |
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MAXTAG = 32767; |
309 |
gezelter |
916 |
} |
310 |
mmeineke |
440 |
|
311 |
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int haveError; |
312 |
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|
313 |
mmeineke |
447 |
MPI_Status istatus; |
314 |
gezelter |
416 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
315 |
tim |
837 |
|
316 |
mmeineke |
377 |
// write out header and node 0's coordinates |
317 |
tim |
837 |
|
318 |
mmeineke |
377 |
if( worldRank == 0 ){ |
319 |
gezelter |
916 |
|
320 |
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// Node 0 needs a list of the magic potatoes for each processor; |
321 |
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322 |
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nProc = mpiSim->getNumberProcessors(); |
323 |
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potatoes = new int[nProc]; |
324 |
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325 |
tim |
934 |
//write out the comment lines |
326 |
gezelter |
916 |
for (i = 0; i < nProc; i++) |
327 |
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potatoes[i] = 0; |
328 |
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|
329 |
tim |
934 |
for(k = 0; k < outFile.size(); k++){ |
330 |
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*outFile[k] << mpiSim->getTotAtoms() << "\n"; |
331 |
tim |
837 |
|
332 |
tim |
934 |
*outFile[k] << currentTime << ";\t" |
333 |
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<< entry_plug->Hmat[0][0] << "\t" |
334 |
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<< entry_plug->Hmat[1][0] << "\t" |
335 |
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<< entry_plug->Hmat[2][0] << ";\t" |
336 |
tim |
837 |
|
337 |
tim |
934 |
<< entry_plug->Hmat[0][1] << "\t" |
338 |
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<< entry_plug->Hmat[1][1] << "\t" |
339 |
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<< entry_plug->Hmat[2][1] << ";\t" |
340 |
tim |
837 |
|
341 |
tim |
934 |
<< entry_plug->Hmat[0][2] << "\t" |
342 |
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<< entry_plug->Hmat[1][2] << "\t" |
343 |
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<< entry_plug->Hmat[2][2] << ";"; |
344 |
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|
345 |
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*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
346 |
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} |
347 |
tim |
837 |
|
348 |
tim |
929 |
currentIndex = 0; |
349 |
tim |
934 |
|
350 |
gezelter |
416 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
351 |
chuckv |
913 |
|
352 |
gezelter |
417 |
// Get the Node number which has this atom; |
353 |
chuckv |
913 |
|
354 |
tim |
837 |
which_node = AtomToProcMap[i]; |
355 |
chuckv |
913 |
|
356 |
gezelter |
907 |
if (which_node != 0) { |
357 |
gezelter |
916 |
|
358 |
|
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if (potatoes[which_node] + 3 >= MAXTAG) { |
359 |
|
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// The potato was going to exceed the maximum value, |
360 |
|
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// so wrap this processor potato back to 0: |
361 |
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362 |
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potatoes[which_node] = 0; |
363 |
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MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
364 |
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|
365 |
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} |
366 |
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|
367 |
|
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myPotato = potatoes[which_node]; |
368 |
gezelter |
907 |
|
369 |
gezelter |
910 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
370 |
gezelter |
916 |
myPotato, MPI_COMM_WORLD, &istatus); |
371 |
gezelter |
907 |
|
372 |
tim |
920 |
atomTypeString = MPIatomTypeString; |
373 |
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|
374 |
gezelter |
916 |
myPotato++; |
375 |
|
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|
376 |
gezelter |
907 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
377 |
gezelter |
916 |
myPotato, MPI_COMM_WORLD, &istatus); |
378 |
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|
379 |
|
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myPotato++; |
380 |
gezelter |
907 |
|
381 |
gezelter |
916 |
if (isDirectional) { |
382 |
|
|
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
383 |
|
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myPotato, MPI_COMM_WORLD, &istatus); |
384 |
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|
} else { |
385 |
|
|
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
386 |
|
|
myPotato, MPI_COMM_WORLD, &istatus); |
387 |
gezelter |
907 |
} |
388 |
gezelter |
916 |
|
389 |
|
|
myPotato++; |
390 |
|
|
potatoes[which_node] = myPotato; |
391 |
gezelter |
907 |
|
392 |
|
|
} else { |
393 |
|
|
|
394 |
tim |
934 |
haveError = 0; |
395 |
chuckv |
949 |
which_atom = i; |
396 |
gezelter |
916 |
|
397 |
chuckv |
949 |
//local_index = -1; |
398 |
|
|
|
399 |
|
|
//for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
400 |
|
|
// if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
401 |
|
|
//} |
402 |
|
|
|
403 |
|
|
//if (local_index != -1) { |
404 |
|
|
|
405 |
|
|
local_index = indexArray[currentIndex].first; |
406 |
gezelter |
916 |
|
407 |
chuckv |
949 |
if (which_atom == indexArray[currentIndex].second) { |
408 |
|
|
|
409 |
|
|
atomTypeString = atoms[local_index]->getType(); |
410 |
|
|
|
411 |
|
|
atoms[local_index]->getPos(pos); |
412 |
|
|
atoms[local_index]->getVel(vel); |
413 |
|
|
|
414 |
gezelter |
916 |
atomData6[0] = pos[0]; |
415 |
|
|
atomData6[1] = pos[1]; |
416 |
|
|
atomData6[2] = pos[2]; |
417 |
tim |
837 |
|
418 |
gezelter |
916 |
atomData6[3] = vel[0]; |
419 |
|
|
atomData6[4] = vel[1]; |
420 |
|
|
atomData6[5] = vel[2]; |
421 |
gezelter |
907 |
|
422 |
|
|
isDirectional = 0; |
423 |
|
|
|
424 |
chuckv |
436 |
if( atoms[local_index]->isDirectional() ){ |
425 |
tim |
837 |
|
426 |
gezelter |
907 |
isDirectional = 1; |
427 |
|
|
|
428 |
chuckv |
436 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
429 |
|
|
dAtom->getQ( q ); |
430 |
gezelter |
916 |
|
431 |
|
|
for (int j = 0; j < 6 ; j++) |
432 |
|
|
atomData13[j] = atomData6[j]; |
433 |
gezelter |
907 |
|
434 |
gezelter |
916 |
atomData13[6] = q[0]; |
435 |
|
|
atomData13[7] = q[1]; |
436 |
|
|
atomData13[8] = q[2]; |
437 |
|
|
atomData13[9] = q[3]; |
438 |
|
|
|
439 |
|
|
atomData13[10] = dAtom->getJx(); |
440 |
|
|
atomData13[11] = dAtom->getJy(); |
441 |
|
|
atomData13[12] = dAtom->getJz(); |
442 |
gezelter |
907 |
} |
443 |
gezelter |
916 |
|
444 |
gezelter |
907 |
} else { |
445 |
chuckv |
949 |
sprintf(painCave.errMsg, |
446 |
|
|
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
447 |
|
|
which_atom, worldRank, currentIndex, local_index ); |
448 |
|
|
haveError= 1; |
449 |
|
|
simError(); |
450 |
|
|
} |
451 |
gezelter |
916 |
|
452 |
tim |
934 |
if(haveError) DieDieDie(); |
453 |
gezelter |
916 |
|
454 |
chuckv |
949 |
currentIndex++; |
455 |
tim |
926 |
} |
456 |
|
|
// If we've survived to here, format the line: |
457 |
|
|
|
458 |
|
|
if (!isDirectional) { |
459 |
|
|
|
460 |
tim |
934 |
sprintf( writeLine, |
461 |
chuckv |
949 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
462 |
|
|
atomTypeString, |
463 |
|
|
atomData6[0], |
464 |
|
|
atomData6[1], |
465 |
|
|
atomData6[2], |
466 |
|
|
atomData6[3], |
467 |
|
|
atomData6[4], |
468 |
|
|
atomData6[5]); |
469 |
tim |
926 |
|
470 |
chuckv |
949 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
471 |
|
|
|
472 |
tim |
926 |
} else { |
473 |
|
|
|
474 |
chuckv |
949 |
sprintf( writeLine, |
475 |
|
|
"%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", |
476 |
|
|
atomTypeString, |
477 |
|
|
atomData13[0], |
478 |
|
|
atomData13[1], |
479 |
|
|
atomData13[2], |
480 |
|
|
atomData13[3], |
481 |
|
|
atomData13[4], |
482 |
|
|
atomData13[5], |
483 |
|
|
atomData13[6], |
484 |
|
|
atomData13[7], |
485 |
|
|
atomData13[8], |
486 |
|
|
atomData13[9], |
487 |
|
|
atomData13[10], |
488 |
|
|
atomData13[11], |
489 |
|
|
atomData13[12]); |
490 |
gezelter |
907 |
|
491 |
|
|
} |
492 |
tim |
926 |
|
493 |
tim |
934 |
for(k = 0; k < outFile.size(); k++) |
494 |
|
|
*outFile[k] << writeLine; |
495 |
mmeineke |
377 |
} |
496 |
tim |
926 |
|
497 |
tim |
934 |
for(k = 0; k < outFile.size(); k++) |
498 |
|
|
outFile[k]->flush(); |
499 |
|
|
|
500 |
gezelter |
907 |
sprintf( checkPointMsg, |
501 |
|
|
"Sucessfully took a dump.\n"); |
502 |
chuckv |
949 |
|
503 |
gezelter |
907 |
MPIcheckPoint(); |
504 |
chuckv |
949 |
|
505 |
tim |
919 |
delete[] potatoes; |
506 |
chuckv |
949 |
|
507 |
gezelter |
415 |
} else { |
508 |
tim |
837 |
|
509 |
gezelter |
907 |
// worldRank != 0, so I'm a remote node. |
510 |
gezelter |
916 |
|
511 |
|
|
// Set my magic potato to 0: |
512 |
|
|
|
513 |
|
|
myPotato = 0; |
514 |
tim |
929 |
currentIndex = 0; |
515 |
gezelter |
907 |
|
516 |
|
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
517 |
|
|
|
518 |
|
|
// Am I the node which has this atom? |
519 |
|
|
|
520 |
|
|
if (AtomToProcMap[i] == worldRank) { |
521 |
tim |
837 |
|
522 |
gezelter |
916 |
if (myPotato + 3 >= MAXTAG) { |
523 |
chuckv |
949 |
|
524 |
gezelter |
916 |
// The potato was going to exceed the maximum value, |
525 |
|
|
// so wrap this processor potato back to 0 (and block until |
526 |
|
|
// node 0 says we can go: |
527 |
chuckv |
949 |
|
528 |
gezelter |
916 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
529 |
|
|
|
530 |
|
|
} |
531 |
tim |
919 |
which_atom = i; |
532 |
chuckv |
949 |
|
533 |
|
|
//local_index = -1; |
534 |
|
|
|
535 |
|
|
//for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
536 |
|
|
// if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
537 |
|
|
//} |
538 |
|
|
|
539 |
|
|
//if (local_index != -1) { |
540 |
|
|
|
541 |
|
|
local_index = indexArray[currentIndex].first; |
542 |
tim |
920 |
|
543 |
chuckv |
949 |
if (which_atom == indexArray[currentIndex].second) { |
544 |
gezelter |
907 |
|
545 |
|
|
atomTypeString = atoms[local_index]->getType(); |
546 |
chuckv |
949 |
|
547 |
|
|
atoms[local_index]->getPos(pos); |
548 |
|
|
atoms[local_index]->getVel(vel); |
549 |
|
|
|
550 |
gezelter |
916 |
atomData6[0] = pos[0]; |
551 |
|
|
atomData6[1] = pos[1]; |
552 |
|
|
atomData6[2] = pos[2]; |
553 |
tim |
837 |
|
554 |
gezelter |
916 |
atomData6[3] = vel[0]; |
555 |
|
|
atomData6[4] = vel[1]; |
556 |
|
|
atomData6[5] = vel[2]; |
557 |
gezelter |
907 |
|
558 |
|
|
isDirectional = 0; |
559 |
tim |
837 |
|
560 |
gezelter |
907 |
if( atoms[local_index]->isDirectional() ){ |
561 |
mmeineke |
377 |
|
562 |
gezelter |
907 |
isDirectional = 1; |
563 |
|
|
|
564 |
|
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
565 |
|
|
dAtom->getQ( q ); |
566 |
|
|
|
567 |
gezelter |
916 |
for (int j = 0; j < 6 ; j++) |
568 |
|
|
atomData13[j] = atomData6[j]; |
569 |
|
|
|
570 |
|
|
atomData13[6] = q[0]; |
571 |
|
|
atomData13[7] = q[1]; |
572 |
|
|
atomData13[8] = q[2]; |
573 |
|
|
atomData13[9] = q[3]; |
574 |
tim |
934 |
|
575 |
gezelter |
916 |
atomData13[10] = dAtom->getJx(); |
576 |
|
|
atomData13[11] = dAtom->getJy(); |
577 |
|
|
atomData13[12] = dAtom->getJz(); |
578 |
gezelter |
907 |
} |
579 |
tim |
837 |
|
580 |
gezelter |
907 |
} else { |
581 |
chuckv |
949 |
sprintf(painCave.errMsg, |
582 |
|
|
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
583 |
|
|
which_atom, worldRank, currentIndex, local_index ); |
584 |
|
|
haveError= 1; |
585 |
|
|
simError(); |
586 |
|
|
} |
587 |
|
|
|
588 |
gezelter |
916 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
589 |
tim |
837 |
|
590 |
gezelter |
916 |
// null terminate the string before sending (just in case): |
591 |
|
|
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
592 |
tim |
837 |
|
593 |
gezelter |
910 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
594 |
tim |
934 |
myPotato, MPI_COMM_WORLD); |
595 |
gezelter |
907 |
|
596 |
gezelter |
916 |
myPotato++; |
597 |
|
|
|
598 |
gezelter |
907 |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
599 |
tim |
934 |
myPotato, MPI_COMM_WORLD); |
600 |
gezelter |
907 |
|
601 |
gezelter |
916 |
myPotato++; |
602 |
|
|
|
603 |
gezelter |
907 |
if (isDirectional) { |
604 |
|
|
|
605 |
gezelter |
916 |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
606 |
|
|
myPotato, MPI_COMM_WORLD); |
607 |
gezelter |
907 |
|
608 |
gezelter |
916 |
} else { |
609 |
|
|
|
610 |
|
|
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
611 |
|
|
myPotato, MPI_COMM_WORLD); |
612 |
gezelter |
907 |
} |
613 |
gezelter |
916 |
|
614 |
tim |
929 |
myPotato++; |
615 |
|
|
currentIndex++; |
616 |
mmeineke |
377 |
} |
617 |
gezelter |
907 |
} |
618 |
mmeineke |
440 |
|
619 |
gezelter |
907 |
sprintf( checkPointMsg, |
620 |
gezelter |
916 |
"Sucessfully took a dump.\n"); |
621 |
gezelter |
907 |
MPIcheckPoint(); |
622 |
|
|
|
623 |
gezelter |
916 |
} |
624 |
gezelter |
907 |
|
625 |
mmeineke |
377 |
#endif // is_mpi |
626 |
|
|
} |
627 |
mmeineke |
440 |
|
628 |
|
|
#ifdef IS_MPI |
629 |
|
|
|
630 |
|
|
// a couple of functions to let us escape the write loop |
631 |
|
|
|
632 |
gezelter |
907 |
void dWrite::DieDieDie( void ){ |
633 |
tim |
837 |
|
634 |
mmeineke |
440 |
MPI_Finalize(); |
635 |
|
|
exit (0); |
636 |
|
|
} |
637 |
|
|
|
638 |
|
|
#endif //is_mpi |