| 1 |
#define _LARGEFILE_SOURCE64
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| 2 |
#define _FILE_OFFSET_BITS 64
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| 3 |
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| 4 |
#include <string.h>
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| 5 |
#include <iostream>
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#include <fstream>
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| 7 |
#include <algorithm>
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#include <utility>
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| 9 |
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| 10 |
#ifdef IS_MPI
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| 11 |
#include <mpi.h>
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#include "brains/mpiSimulation.hpp"
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| 14 |
namespace dWrite{
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| 15 |
void DieDieDie( void );
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| 16 |
}
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| 18 |
using namespace dWrite;
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#endif //is_mpi
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| 21 |
#include "io/ReadWrite.hpp"
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| 22 |
#include "utils/simError.h"
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| 23 |
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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
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| 26 |
entry_plug = the_entry_plug;
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| 28 |
#ifdef IS_MPI
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| 29 |
if(worldRank == 0 ){
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| 30 |
#endif // is_mpi
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| 31 |
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| 32 |
dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
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| 33 |
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| 34 |
if( !dumpFile ){
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| 36 |
sprintf( painCave.errMsg,
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| 37 |
"Could not open \"%s\" for dump output.\n",
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| 38 |
entry_plug->sampleName.c_str());
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| 39 |
painCave.isFatal = 1;
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| 40 |
simError();
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}
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| 42 |
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| 43 |
#ifdef IS_MPI
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| 44 |
}
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| 45 |
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| 46 |
//sort the local atoms by global index
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| 47 |
sortByGlobalIndex();
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| 48 |
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| 49 |
sprintf( checkPointMsg,
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| 50 |
"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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| 55 |
DumpWriter::~DumpWriter( ){
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| 57 |
#ifdef IS_MPI
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| 58 |
if(worldRank == 0 ){
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#endif // is_mpi
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dumpFile.close();
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| 63 |
#ifdef IS_MPI
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}
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#endif // is_mpi
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}
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#ifdef IS_MPI
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/**
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* A hook function to load balancing
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*/
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void DumpWriter::update(){
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sortByGlobalIndex();
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}
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/**
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* Auxiliary sorting function
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*/
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bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
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return p1.second < p2.second;
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}
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/**
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* Sorting the local index by global index
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*/
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void DumpWriter::sortByGlobalIndex(){
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Molecule* mols = entry_plug->molecules;
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indexArray.clear();
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for(int i = 0; i < entry_plug->n_mol;i++)
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indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
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sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
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}
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#endif
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void DumpWriter::writeDump(double currentTime){
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ofstream finalOut;
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| 105 |
vector<ofstream*> fileStreams;
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#ifdef IS_MPI
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if(worldRank == 0 ){
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| 109 |
#endif
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finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
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| 111 |
if( !finalOut ){
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sprintf( painCave.errMsg,
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| 113 |
"Could not open \"%s\" for final dump output.\n",
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entry_plug->finalName.c_str() );
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| 115 |
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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| 137 |
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| 138 |
#ifdef IS_MPI
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| 139 |
if(worldRank == 0 ){
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| 140 |
#endif // is_mpi
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| 142 |
finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
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| 144 |
if( !finalOut ){
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sprintf( painCave.errMsg,
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| 146 |
"Could not open \"%s\" for final dump output.\n",
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entry_plug->finalName.c_str() );
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| 148 |
painCave.isFatal = 1;
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| 149 |
simError();
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}
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| 151 |
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| 152 |
#ifdef IS_MPI
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| 153 |
}
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#endif // is_mpi
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| 155 |
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| 156 |
fileStreams.push_back(&finalOut);
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| 157 |
writeFrame(fileStreams, currentTime);
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| 158 |
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| 159 |
#ifdef IS_MPI
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| 160 |
finalOut.close();
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| 161 |
#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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| 169 |
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| 170 |
char tempBuffer[BUFFERSIZE];
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| 171 |
char writeLine[BUFFERSIZE];
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| 172 |
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| 173 |
int i;
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| 174 |
unsigned int k;
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| 175 |
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| 176 |
#ifdef IS_MPI
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| 177 |
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| 178 |
/*********************************************************************
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| 179 |
* Documentation? You want DOCUMENTATION?
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| 180 |
*
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| 181 |
* Why all the potatoes below?
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| 182 |
*
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| 183 |
* To make a long story short, the original version of DumpWriter
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| 184 |
* 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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| 186 |
* as node 0 worked its way down the global index. This was particularly
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| 187 |
* inefficient since the method blocked all processors at every atom
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| 188 |
* (and did it twice!).
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*
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| 190 |
* An intermediate version of DumpWriter could be described from Node
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* zero's perspective as follows:
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| 192 |
*
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| 193 |
* 1) Have 100 of your friends stand in a circle.
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| 194 |
* 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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| 196 |
* 3) Catch the potatoes.
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| 197 |
*
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| 198 |
* It was an improvement, but MPI has buffers and caches that could
|
| 199 |
* best be described in this analogy as "potato nets", so there's no
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| 200 |
* need to block the processors atom-by-atom.
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| 201 |
*
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| 202 |
* This new and improved DumpWriter works in an even more efficient
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| 203 |
* way:
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| 204 |
*
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| 205 |
* 1) Have 100 of your friend stand in a circle.
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| 206 |
* 2) When you say go, have them start tossing 5-pound bags of
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| 207 |
* potatoes at you.
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* 3) Once you've caught a friend's bag of potatoes,
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| 209 |
* toss them a spud to let them know they can toss another bag.
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| 210 |
*
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| 211 |
* How's THAT for documentation?
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| 212 |
*
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| 213 |
*********************************************************************/
|
| 214 |
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| 215 |
int *potatoes;
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| 216 |
int myPotato;
|
| 217 |
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| 218 |
int nProc;
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| 219 |
int j, which_node, done, which_atom, local_index, currentIndex;
|
| 220 |
double atomData[13];
|
| 221 |
int isDirectional;
|
| 222 |
char* atomTypeString;
|
| 223 |
char MPIatomTypeString[MINIBUFFERSIZE];
|
| 224 |
int nObjects;
|
| 225 |
int msgLen; // the length of message actually recieved at master nodes
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| 226 |
#endif //is_mpi
|
| 227 |
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| 228 |
Quat4d q;
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| 229 |
Vector3d ji;
|
| 230 |
DirectionalAtom* dAtom;
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| 231 |
Vector3d pos;
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| 232 |
Vector3d vel;
|
| 233 |
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| 234 |
int nTotObjects;
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| 235 |
StuntDouble* sd;
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| 236 |
char* molName;
|
| 237 |
vector<StuntDouble*> integrableObjects;
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| 238 |
vector<StuntDouble*>::iterator iter;
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| 239 |
nTotObjects = entry_plug->getTotIntegrableObjects();
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| 240 |
#ifndef IS_MPI
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| 241 |
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| 242 |
for(k = 0; k < outFile.size(); k++){
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| 243 |
*outFile[k] << nTotObjects << "\n";
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| 244 |
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| 245 |
*outFile[k] << currentTime << ";\t"
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| 246 |
<< entry_plug->Hmat[0][0] << "\t"
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| 247 |
<< entry_plug->Hmat[1][0] << "\t"
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| 248 |
<< entry_plug->Hmat[2][0] << ";\t"
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| 249 |
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| 250 |
<< entry_plug->Hmat[0][1] << "\t"
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| 251 |
<< entry_plug->Hmat[1][1] << "\t"
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<< entry_plug->Hmat[2][1] << ";\t"
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| 254 |
<< entry_plug->Hmat[0][2] << "\t"
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| 255 |
<< entry_plug->Hmat[1][2] << "\t"
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| 256 |
<< entry_plug->Hmat[2][2] << ";";
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| 258 |
//write out additional parameters, such as chi and eta
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| 259 |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
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| 260 |
}
|
| 261 |
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| 262 |
for( i=0; i< entry_plug->n_mol; i++ ){
|
| 263 |
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| 264 |
integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
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| 265 |
molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
|
| 266 |
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| 267 |
for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){
|
| 268 |
sd = *iter;
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| 269 |
pos = sd->getPos();
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| 270 |
vel = sd->getVel();
|
| 271 |
|
| 272 |
sprintf( tempBuffer,
|
| 273 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
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| 274 |
sd->getType(),
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| 275 |
pos[0],
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| 276 |
pos[1],
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| 277 |
pos[2],
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| 278 |
vel[0],
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| 279 |
vel[1],
|
| 280 |
vel[2]);
|
| 281 |
strcpy( writeLine, tempBuffer );
|
| 282 |
|
| 283 |
if( sd->isDirectional() ){
|
| 284 |
|
| 285 |
q = sd->getQ();
|
| 286 |
ji = sd->getJ();
|
| 287 |
|
| 288 |
sprintf( tempBuffer,
|
| 289 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
|
| 290 |
q[0],
|
| 291 |
q[1],
|
| 292 |
q[2],
|
| 293 |
q[3],
|
| 294 |
ji[0],
|
| 295 |
ji[1],
|
| 296 |
ji[2]);
|
| 297 |
strcat( writeLine, tempBuffer );
|
| 298 |
}
|
| 299 |
else
|
| 300 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
|
| 301 |
|
| 302 |
for(k = 0; k < outFile.size(); k++)
|
| 303 |
*outFile[k] << writeLine;
|
| 304 |
}
|
| 305 |
|
| 306 |
}
|
| 307 |
|
| 308 |
#else // is_mpi
|
| 309 |
|
| 310 |
/* code to find maximum tag value */
|
| 311 |
|
| 312 |
int *tagub, flag, MAXTAG;
|
| 313 |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
|
| 314 |
if (flag) {
|
| 315 |
MAXTAG = *tagub;
|
| 316 |
} else {
|
| 317 |
MAXTAG = 32767;
|
| 318 |
}
|
| 319 |
|
| 320 |
int haveError;
|
| 321 |
|
| 322 |
MPI_Status istatus;
|
| 323 |
int nCurObj;
|
| 324 |
int *MolToProcMap = mpiSim->getMolToProcMap();
|
| 325 |
|
| 326 |
// write out header and node 0's coordinates
|
| 327 |
|
| 328 |
if( worldRank == 0 ){
|
| 329 |
|
| 330 |
// Node 0 needs a list of the magic potatoes for each processor;
|
| 331 |
|
| 332 |
nProc = mpiSim->getNProcessors();
|
| 333 |
potatoes = new int[nProc];
|
| 334 |
|
| 335 |
//write out the comment lines
|
| 336 |
for (i = 0; i < nProc; i++)
|
| 337 |
potatoes[i] = 0;
|
| 338 |
|
| 339 |
for(k = 0; k < outFile.size(); k++){
|
| 340 |
*outFile[k] << nTotObjects << "\n";
|
| 341 |
|
| 342 |
*outFile[k] << currentTime << ";\t"
|
| 343 |
<< entry_plug->Hmat[0][0] << "\t"
|
| 344 |
<< entry_plug->Hmat[1][0] << "\t"
|
| 345 |
<< entry_plug->Hmat[2][0] << ";\t"
|
| 346 |
|
| 347 |
<< entry_plug->Hmat[0][1] << "\t"
|
| 348 |
<< entry_plug->Hmat[1][1] << "\t"
|
| 349 |
<< entry_plug->Hmat[2][1] << ";\t"
|
| 350 |
|
| 351 |
<< entry_plug->Hmat[0][2] << "\t"
|
| 352 |
<< entry_plug->Hmat[1][2] << "\t"
|
| 353 |
<< entry_plug->Hmat[2][2] << ";";
|
| 354 |
|
| 355 |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
|
| 356 |
}
|
| 357 |
|
| 358 |
currentIndex = 0;
|
| 359 |
|
| 360 |
for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
|
| 361 |
|
| 362 |
// Get the Node number which has this atom;
|
| 363 |
|
| 364 |
which_node = MolToProcMap[i];
|
| 365 |
|
| 366 |
if (which_node != 0) {
|
| 367 |
|
| 368 |
if (potatoes[which_node] + 1 >= MAXTAG) {
|
| 369 |
// The potato was going to exceed the maximum value,
|
| 370 |
// so wrap this processor potato back to 0:
|
| 371 |
|
| 372 |
potatoes[which_node] = 0;
|
| 373 |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
|
| 374 |
|
| 375 |
}
|
| 376 |
|
| 377 |
myPotato = potatoes[which_node];
|
| 378 |
|
| 379 |
//recieve the number of integrableObject in current molecule
|
| 380 |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
|
| 381 |
myPotato, MPI_COMM_WORLD, &istatus);
|
| 382 |
myPotato++;
|
| 383 |
|
| 384 |
for(int l = 0; l < nCurObj; l++){
|
| 385 |
|
| 386 |
if (potatoes[which_node] + 2 >= MAXTAG) {
|
| 387 |
// The potato was going to exceed the maximum value,
|
| 388 |
// so wrap this processor potato back to 0:
|
| 389 |
|
| 390 |
potatoes[which_node] = 0;
|
| 391 |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
|
| 392 |
|
| 393 |
}
|
| 394 |
|
| 395 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
|
| 396 |
myPotato, MPI_COMM_WORLD, &istatus);
|
| 397 |
|
| 398 |
atomTypeString = MPIatomTypeString;
|
| 399 |
|
| 400 |
myPotato++;
|
| 401 |
|
| 402 |
MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
|
| 403 |
myPotato++;
|
| 404 |
|
| 405 |
MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
|
| 406 |
|
| 407 |
if(msgLen == 13)
|
| 408 |
isDirectional = 1;
|
| 409 |
else
|
| 410 |
isDirectional = 0;
|
| 411 |
|
| 412 |
// If we've survived to here, format the line:
|
| 413 |
|
| 414 |
if (!isDirectional) {
|
| 415 |
|
| 416 |
sprintf( writeLine,
|
| 417 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
|
| 418 |
atomTypeString,
|
| 419 |
atomData[0],
|
| 420 |
atomData[1],
|
| 421 |
atomData[2],
|
| 422 |
atomData[3],
|
| 423 |
atomData[4],
|
| 424 |
atomData[5]);
|
| 425 |
|
| 426 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
|
| 427 |
|
| 428 |
}
|
| 429 |
else {
|
| 430 |
|
| 431 |
sprintf( writeLine,
|
| 432 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
|
| 433 |
atomTypeString,
|
| 434 |
atomData[0],
|
| 435 |
atomData[1],
|
| 436 |
atomData[2],
|
| 437 |
atomData[3],
|
| 438 |
atomData[4],
|
| 439 |
atomData[5],
|
| 440 |
atomData[6],
|
| 441 |
atomData[7],
|
| 442 |
atomData[8],
|
| 443 |
atomData[9],
|
| 444 |
atomData[10],
|
| 445 |
atomData[11],
|
| 446 |
atomData[12]);
|
| 447 |
|
| 448 |
}
|
| 449 |
|
| 450 |
for(k = 0; k < outFile.size(); k++)
|
| 451 |
*outFile[k] << writeLine;
|
| 452 |
|
| 453 |
}// end for(int l =0)
|
| 454 |
potatoes[which_node] = myPotato;
|
| 455 |
|
| 456 |
}
|
| 457 |
else {
|
| 458 |
|
| 459 |
haveError = 0;
|
| 460 |
|
| 461 |
local_index = indexArray[currentIndex].first;
|
| 462 |
|
| 463 |
integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
|
| 464 |
|
| 465 |
for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){
|
| 466 |
sd = *iter;
|
| 467 |
atomTypeString = sd->getType();
|
| 468 |
|
| 469 |
pos = sd->getPos();
|
| 470 |
vel = sd->getVel();
|
| 471 |
|
| 472 |
atomData[0] = pos[0];
|
| 473 |
atomData[1] = pos[1];
|
| 474 |
atomData[2] = pos[2];
|
| 475 |
|
| 476 |
atomData[3] = vel[0];
|
| 477 |
atomData[4] = vel[1];
|
| 478 |
atomData[5] = vel[2];
|
| 479 |
|
| 480 |
isDirectional = 0;
|
| 481 |
|
| 482 |
if( sd->isDirectional() ){
|
| 483 |
|
| 484 |
isDirectional = 1;
|
| 485 |
|
| 486 |
q = sd->getQ();
|
| 487 |
ji = sd->getJ();
|
| 488 |
|
| 489 |
for (int j = 0; j < 6 ; j++)
|
| 490 |
atomData[j] = atomData[j];
|
| 491 |
|
| 492 |
atomData[6] = q[0];
|
| 493 |
atomData[7] = q[1];
|
| 494 |
atomData[8] = q[2];
|
| 495 |
atomData[9] = q[3];
|
| 496 |
|
| 497 |
atomData[10] = ji[0];
|
| 498 |
atomData[11] = ji[1];
|
| 499 |
atomData[12] = ji[2];
|
| 500 |
}
|
| 501 |
|
| 502 |
// If we've survived to here, format the line:
|
| 503 |
|
| 504 |
if (!isDirectional) {
|
| 505 |
|
| 506 |
sprintf( writeLine,
|
| 507 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
|
| 508 |
atomTypeString,
|
| 509 |
atomData[0],
|
| 510 |
atomData[1],
|
| 511 |
atomData[2],
|
| 512 |
atomData[3],
|
| 513 |
atomData[4],
|
| 514 |
atomData[5]);
|
| 515 |
|
| 516 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
|
| 517 |
|
| 518 |
}
|
| 519 |
else {
|
| 520 |
|
| 521 |
sprintf( writeLine,
|
| 522 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
|
| 523 |
atomTypeString,
|
| 524 |
atomData[0],
|
| 525 |
atomData[1],
|
| 526 |
atomData[2],
|
| 527 |
atomData[3],
|
| 528 |
atomData[4],
|
| 529 |
atomData[5],
|
| 530 |
atomData[6],
|
| 531 |
atomData[7],
|
| 532 |
atomData[8],
|
| 533 |
atomData[9],
|
| 534 |
atomData[10],
|
| 535 |
atomData[11],
|
| 536 |
atomData[12]);
|
| 537 |
|
| 538 |
}
|
| 539 |
|
| 540 |
for(k = 0; k < outFile.size(); k++)
|
| 541 |
*outFile[k] << writeLine;
|
| 542 |
|
| 543 |
|
| 544 |
}//end for(iter = integrableObject.begin())
|
| 545 |
|
| 546 |
currentIndex++;
|
| 547 |
}
|
| 548 |
|
| 549 |
}//end for(i = 0; i < mpiSim->getNmol())
|
| 550 |
|
| 551 |
for(k = 0; k < outFile.size(); k++)
|
| 552 |
outFile[k]->flush();
|
| 553 |
|
| 554 |
sprintf( checkPointMsg,
|
| 555 |
"Sucessfully took a dump.\n");
|
| 556 |
|
| 557 |
MPIcheckPoint();
|
| 558 |
|
| 559 |
delete[] potatoes;
|
| 560 |
|
| 561 |
} else {
|
| 562 |
|
| 563 |
// worldRank != 0, so I'm a remote node.
|
| 564 |
|
| 565 |
// Set my magic potato to 0:
|
| 566 |
|
| 567 |
myPotato = 0;
|
| 568 |
currentIndex = 0;
|
| 569 |
|
| 570 |
for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
|
| 571 |
|
| 572 |
// Am I the node which has this integrableObject?
|
| 573 |
|
| 574 |
if (MolToProcMap[i] == worldRank) {
|
| 575 |
|
| 576 |
|
| 577 |
if (myPotato + 1 >= MAXTAG) {
|
| 578 |
|
| 579 |
// The potato was going to exceed the maximum value,
|
| 580 |
// so wrap this processor potato back to 0 (and block until
|
| 581 |
// node 0 says we can go:
|
| 582 |
|
| 583 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
|
| 584 |
|
| 585 |
}
|
| 586 |
|
| 587 |
local_index = indexArray[currentIndex].first;
|
| 588 |
integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
|
| 589 |
|
| 590 |
nCurObj = integrableObjects.size();
|
| 591 |
|
| 592 |
MPI_Send(&nCurObj, 1, MPI_INT, 0,
|
| 593 |
myPotato, MPI_COMM_WORLD);
|
| 594 |
myPotato++;
|
| 595 |
|
| 596 |
for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){
|
| 597 |
|
| 598 |
if (myPotato + 2 >= MAXTAG) {
|
| 599 |
|
| 600 |
// The potato was going to exceed the maximum value,
|
| 601 |
// so wrap this processor potato back to 0 (and block until
|
| 602 |
// node 0 says we can go:
|
| 603 |
|
| 604 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
|
| 605 |
|
| 606 |
}
|
| 607 |
|
| 608 |
sd = *iter;
|
| 609 |
|
| 610 |
atomTypeString = sd->getType();
|
| 611 |
|
| 612 |
pos = sd->getPos();
|
| 613 |
vel = sd->getVel();
|
| 614 |
|
| 615 |
atomData[0] = pos[0];
|
| 616 |
atomData[1] = pos[1];
|
| 617 |
atomData[2] = pos[2];
|
| 618 |
|
| 619 |
atomData[3] = vel[0];
|
| 620 |
atomData[4] = vel[1];
|
| 621 |
atomData[5] = vel[2];
|
| 622 |
|
| 623 |
isDirectional = 0;
|
| 624 |
|
| 625 |
if( sd->isDirectional() ){
|
| 626 |
|
| 627 |
isDirectional = 1;
|
| 628 |
|
| 629 |
q = sd->getQ();
|
| 630 |
ji = sd->getJ();
|
| 631 |
|
| 632 |
|
| 633 |
atomData[6] = q[0];
|
| 634 |
atomData[7] = q[1];
|
| 635 |
atomData[8] = q[2];
|
| 636 |
atomData[9] = q[3];
|
| 637 |
|
| 638 |
atomData[10] = ji[0];
|
| 639 |
atomData[11] = ji[1];
|
| 640 |
atomData[12] = ji[2];
|
| 641 |
}
|
| 642 |
|
| 643 |
|
| 644 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
|
| 645 |
|
| 646 |
// null terminate the string before sending (just in case):
|
| 647 |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
|
| 648 |
|
| 649 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
|
| 650 |
myPotato, MPI_COMM_WORLD);
|
| 651 |
|
| 652 |
myPotato++;
|
| 653 |
|
| 654 |
if (isDirectional) {
|
| 655 |
|
| 656 |
MPI_Send(atomData, 13, MPI_DOUBLE, 0,
|
| 657 |
myPotato, MPI_COMM_WORLD);
|
| 658 |
|
| 659 |
} else {
|
| 660 |
|
| 661 |
MPI_Send(atomData, 6, MPI_DOUBLE, 0,
|
| 662 |
myPotato, MPI_COMM_WORLD);
|
| 663 |
}
|
| 664 |
|
| 665 |
myPotato++;
|
| 666 |
|
| 667 |
}
|
| 668 |
|
| 669 |
currentIndex++;
|
| 670 |
|
| 671 |
}
|
| 672 |
|
| 673 |
}
|
| 674 |
|
| 675 |
sprintf( checkPointMsg,
|
| 676 |
"Sucessfully took a dump.\n");
|
| 677 |
MPIcheckPoint();
|
| 678 |
|
| 679 |
}
|
| 680 |
|
| 681 |
|
| 682 |
|
| 683 |
#endif // is_mpi
|
| 684 |
}
|
| 685 |
|
| 686 |
#ifdef IS_MPI
|
| 687 |
|
| 688 |
// a couple of functions to let us escape the write loop
|
| 689 |
|
| 690 |
void dWrite::DieDieDie( void ){
|
| 691 |
|
| 692 |
MPI_Finalize();
|
| 693 |
exit (0);
|
| 694 |
}
|
| 695 |
|
| 696 |
#endif //is_mpi
|
