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#include <cstring> |
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#define _FILE_OFFSET_BITS 64 |
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|
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#include <string.h> |
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#include <iostream> |
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#include <fstream> |
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#include <algorithm> |
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#include <utility> |
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|
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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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#define TAKE_THIS_TAG 0 |
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|
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namespace dWrite{ |
14 |
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void DieDieDie( void ); |
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} |
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|
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using namespace dWrite; |
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#endif //is_mpi |
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|
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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|
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|
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|
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|
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|
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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
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|
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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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|
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|
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|
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strcpy( outName, entry_plug->sampleName ); |
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|
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outFile.open(outName, ios::out | ios::trunc ); |
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|
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if( !outFile ){ |
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|
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|
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|
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dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
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|
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if( !dumpFile ){ |
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|
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for dump output.\n", |
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outName); |
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entry_plug->sampleName); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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//outFile.setf( ios::scientific ); |
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|
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#ifdef IS_MPI |
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} |
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|
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//sort the local atoms by global index |
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sortByGlobalIndex(); |
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|
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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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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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outFile.close(); |
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dumpFile.close(); |
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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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} |
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|
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void DumpWriter::writeDump( double currentTime ){ |
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#ifdef IS_MPI |
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|
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/** |
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* A hook function to load balancing |
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*/ |
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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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const int BUFFERSIZE = 2000; |
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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/** |
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* Auxiliary sorting function |
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*/ |
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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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int i; |
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double q[4]; |
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DirectionalAtom* dAtom; |
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int nAtoms = entry_plug->n_atoms; |
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/** |
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* Sorting the local index by global index |
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*/ |
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|
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void DumpWriter::sortByGlobalIndex(){ |
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Atom** atoms = entry_plug->atoms; |
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|
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|
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indexArray.clear(); |
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|
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for(int i = 0; i < mpiSim->getMyNlocal();i++) |
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indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
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|
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sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
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} |
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#endif |
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|
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#ifndef IS_MPI |
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|
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outFile << nAtoms << "\n"; |
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|
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outFile << currentTime << "\t" |
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<< entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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|
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for( i=0; i<nAtoms; i++ ){ |
88 |
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|
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void DumpWriter::writeDump(double currentTime){ |
103 |
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|
104 |
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sprintf( tempBuffer, |
105 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
93 |
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atoms[i]->getX(), |
94 |
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atoms[i]->getY(), |
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atoms[i]->getZ(), |
96 |
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atoms[i]->get_vx(), |
97 |
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atoms[i]->get_vy(), |
98 |
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atoms[i]->get_vz()); |
99 |
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strcpy( writeLine, tempBuffer ); |
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ofstream finalOut; |
105 |
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vector<ofstream*> fileStreams; |
106 |
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|
107 |
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if( atoms[i]->isDirectional() ){ |
108 |
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|
109 |
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dAtom = (DirectionalAtom *)atoms[i]; |
110 |
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dAtom->getQ( q ); |
111 |
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|
112 |
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sprintf( tempBuffer, |
113 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
114 |
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q[0], |
115 |
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q[1], |
116 |
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q[2], |
111 |
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q[3], |
112 |
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dAtom->getJx(), |
113 |
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dAtom->getJy(), |
114 |
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dAtom->getJz()); |
115 |
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strcat( writeLine, tempBuffer ); |
107 |
> |
#ifdef IS_MPI |
108 |
> |
if(worldRank == 0 ){ |
109 |
> |
|
110 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
111 |
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if( !finalOut ){ |
112 |
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sprintf( painCave.errMsg, |
113 |
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"Could not open \"%s\" for final dump output.\n", |
114 |
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entry_plug->finalName ); |
115 |
> |
painCave.isFatal = 1; |
116 |
> |
simError(); |
117 |
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} |
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else |
118 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
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|
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outFile << writeLine; |
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} |
119 |
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outFile.flush(); |
119 |
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#endif // is_mpi |
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|
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#else // is_mpi |
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fileStreams.push_back(&finalOut); |
122 |
> |
fileStreams.push_back(&dumpFile); |
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|
124 |
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int masterIndex; |
127 |
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int nodeAtomsStart; |
128 |
< |
int nodeAtomsEnd; |
129 |
< |
int mpiErr; |
130 |
< |
int sendError; |
131 |
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int procIndex; |
132 |
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|
133 |
< |
MPI_Status istatus[MPI_STATUS_SIZE]; |
124 |
> |
writeFrame(fileStreams, currentTime); |
125 |
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|
126 |
< |
|
127 |
< |
// write out header and node 0's coordinates |
126 |
> |
#ifdef IS_MPI |
127 |
> |
finalOut.close(); |
128 |
> |
#endif |
129 |
> |
|
130 |
> |
} |
131 |
|
|
132 |
< |
if( worldRank == 0 ){ |
139 |
< |
outFile << mpiSim->getTotAtoms() << "\n"; |
140 |
< |
|
141 |
< |
outFile << currentTime << "\t" |
142 |
< |
<< entry_plug->box_x << "\t" |
143 |
< |
<< entry_plug->box_y << "\t" |
144 |
< |
<< entry_plug->box_z << "\n"; |
132 |
> |
void DumpWriter::writeFinal(double currentTime){ |
133 |
|
|
134 |
< |
masterIndex = 0; |
135 |
< |
for( i=0; i<nAtoms; i++ ){ |
148 |
< |
|
149 |
< |
sprintf( tempBuffer, |
150 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
151 |
< |
atoms[i]->getType(), |
152 |
< |
atoms[i]->getX(), |
153 |
< |
atoms[i]->getY(), |
154 |
< |
atoms[i]->getZ(), |
155 |
< |
atoms[i]->get_vx(), |
156 |
< |
atoms[i]->get_vy(), |
157 |
< |
atoms[i]->get_vz()); |
158 |
< |
strcpy( writeLine, tempBuffer ); |
159 |
< |
|
160 |
< |
if( atoms[i]->isDirectional() ){ |
161 |
< |
|
162 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
163 |
< |
dAtom->getQ( q ); |
164 |
< |
|
165 |
< |
sprintf( tempBuffer, |
166 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
167 |
< |
q[0], |
168 |
< |
q[1], |
169 |
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q[2], |
170 |
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q[3], |
171 |
< |
dAtom->getJx(), |
172 |
< |
dAtom->getJy(), |
173 |
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dAtom->getJz()); |
174 |
< |
strcat( writeLine, tempBuffer ); |
175 |
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} |
176 |
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else |
177 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
178 |
< |
|
179 |
< |
outFile << writeLine; |
180 |
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masterIndex++; |
181 |
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} |
182 |
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outFile.flush(); |
183 |
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} |
134 |
> |
ofstream finalOut; |
135 |
> |
vector<ofstream*> fileStreams; |
136 |
|
|
137 |
< |
sprintf( checkPointMsg, |
138 |
< |
"Sucessfully wrote node 0's dump configuration.\n"); |
187 |
< |
MPIcheckPoint(); |
188 |
< |
|
189 |
< |
for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
190 |
< |
procIndex++){ |
137 |
> |
#ifdef IS_MPI |
138 |
> |
if(worldRank == 0 ){ |
139 |
|
|
140 |
< |
if( worldRank == 0 ){ |
193 |
< |
|
194 |
< |
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
195 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
196 |
< |
|
197 |
< |
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
198 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
199 |
< |
|
200 |
< |
// Make sure where node 0 is writing to, matches where the |
201 |
< |
// receiving node expects it to be. |
202 |
< |
|
203 |
< |
if (masterIndex != nodeAtomsStart){ |
204 |
< |
sendError = 1; |
205 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
206 |
< |
MPI_COMM_WORLD); |
207 |
< |
sprintf(painCave.errMsg, |
208 |
< |
"DumpWriter error: atoms start index (%d) for " |
209 |
< |
"node %d not equal to master index (%d)", |
210 |
< |
nodeAtomsStart,procIndex,masterIndex ); |
211 |
< |
painCave.isFatal = 1; |
212 |
< |
simError(); |
213 |
< |
} |
214 |
< |
|
215 |
< |
sendError = 0; |
216 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
217 |
< |
MPI_COMM_WORLD); |
218 |
< |
|
219 |
< |
// recieve the nodes writeLines |
220 |
< |
|
221 |
< |
for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
222 |
< |
|
223 |
< |
mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
224 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); |
225 |
< |
|
226 |
< |
outFile << writeLine; |
227 |
< |
masterIndex++; |
228 |
< |
} |
229 |
< |
} |
140 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
141 |
|
|
142 |
< |
else if( worldRank == procIndex ){ |
143 |
< |
|
144 |
< |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
145 |
< |
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
146 |
< |
|
147 |
< |
mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, |
237 |
< |
MPI_COMM_WORLD); |
238 |
< |
mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, |
239 |
< |
MPI_COMM_WORLD); |
240 |
< |
|
241 |
< |
sendError = -1; |
242 |
< |
mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, |
243 |
< |
MPI_COMM_WORLD, istatus); |
244 |
< |
|
245 |
< |
if (sendError) MPIcheckPoint(); |
246 |
< |
|
247 |
< |
// send current node's configuration line by line. |
248 |
< |
|
249 |
< |
for( i=0; i<nAtoms; i++ ){ |
250 |
< |
|
251 |
< |
sprintf( tempBuffer, |
252 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
253 |
< |
atoms[i]->getType(), |
254 |
< |
atoms[i]->getX(), |
255 |
< |
atoms[i]->getY(), |
256 |
< |
atoms[i]->getZ(), |
257 |
< |
atoms[i]->get_vx(), |
258 |
< |
atoms[i]->get_vy(), |
259 |
< |
atoms[i]->get_vz()); // check here. |
260 |
< |
strcpy( writeLine, tempBuffer ); |
261 |
< |
|
262 |
< |
if( atoms[i]->isDirectional() ){ |
263 |
< |
|
264 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
265 |
< |
dAtom->getQ( q ); |
266 |
< |
|
267 |
< |
sprintf( tempBuffer, |
268 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
269 |
< |
q[0], |
270 |
< |
q[1], |
271 |
< |
q[2], |
272 |
< |
q[3], |
273 |
< |
dAtom->getJx(), |
274 |
< |
dAtom->getJy(), |
275 |
< |
dAtom->getJz()); |
276 |
< |
strcat( writeLine, tempBuffer ); |
277 |
< |
} |
278 |
< |
else |
279 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
280 |
< |
|
281 |
< |
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
282 |
< |
MPI_COMM_WORLD); |
283 |
< |
} |
142 |
> |
if( !finalOut ){ |
143 |
> |
sprintf( painCave.errMsg, |
144 |
> |
"Could not open \"%s\" for final dump output.\n", |
145 |
> |
entry_plug->finalName ); |
146 |
> |
painCave.isFatal = 1; |
147 |
> |
simError(); |
148 |
|
} |
149 |
< |
|
286 |
< |
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
287 |
< |
procIndex); |
288 |
< |
MPIcheckPoint(); |
149 |
> |
|
150 |
|
} |
290 |
– |
|
151 |
|
#endif // is_mpi |
152 |
+ |
|
153 |
+ |
fileStreams.push_back(&finalOut); |
154 |
+ |
writeFrame(fileStreams, currentTime); |
155 |
+ |
|
156 |
+ |
#ifdef IS_MPI |
157 |
+ |
finalOut.close(); |
158 |
+ |
#endif |
159 |
+ |
|
160 |
|
} |
161 |
|
|
162 |
+ |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
163 |
|
|
164 |
+ |
const int BUFFERSIZE = 2000; |
165 |
+ |
const int MINIBUFFERSIZE = 100; |
166 |
|
|
167 |
< |
void DumpWriter::writeFinal(){ |
167 |
> |
char tempBuffer[BUFFERSIZE]; |
168 |
> |
char writeLine[BUFFERSIZE]; |
169 |
|
|
170 |
+ |
int i, k; |
171 |
|
|
172 |
< |
const int BUFFERSIZE = 2000; |
300 |
< |
char tempBuffer[500]; |
301 |
< |
char writeLine[BUFFERSIZE]; |
172 |
> |
#ifdef IS_MPI |
173 |
|
|
174 |
< |
char finalName[500]; |
174 |
> |
int *potatoes; |
175 |
> |
int myPotato; |
176 |
|
|
177 |
< |
int i; |
177 |
> |
int nProc; |
178 |
> |
int j, which_node, done, which_atom, local_index, currentIndex; |
179 |
> |
double atomData6[6]; |
180 |
> |
double atomData13[13]; |
181 |
> |
int isDirectional; |
182 |
> |
char* atomTypeString; |
183 |
> |
char MPIatomTypeString[MINIBUFFERSIZE]; |
184 |
> |
|
185 |
> |
#else //is_mpi |
186 |
> |
int nAtoms = entry_plug->n_atoms; |
187 |
> |
#endif //is_mpi |
188 |
> |
|
189 |
|
double q[4]; |
190 |
|
DirectionalAtom* dAtom; |
308 |
– |
int nAtoms = entry_plug->n_atoms; |
191 |
|
Atom** atoms = entry_plug->atoms; |
192 |
+ |
double pos[3], vel[3]; |
193 |
+ |
|
194 |
+ |
#ifndef IS_MPI |
195 |
|
|
196 |
< |
ofstream finalOut; |
197 |
< |
|
198 |
< |
#ifdef IS_MPI |
199 |
< |
if(worldRank == 0 ){ |
200 |
< |
#endif // is_mpi |
201 |
< |
|
202 |
< |
strcpy( finalName, entry_plug->finalName ); |
203 |
< |
|
204 |
< |
finalOut.open( finalName, ios::out | ios::trunc ); |
205 |
< |
if( !finalOut ){ |
206 |
< |
sprintf( painCave.errMsg, |
207 |
< |
"Could not open \"%s\" for final dump output.\n", |
208 |
< |
finalName ); |
209 |
< |
painCave.isFatal = 1; |
210 |
< |
simError(); |
211 |
< |
} |
212 |
< |
|
213 |
< |
// finalOut.setf( ios::scientific ); |
329 |
< |
|
330 |
< |
#ifdef IS_MPI |
196 |
> |
for(k = 0; k < outFile.size(); k++){ |
197 |
> |
*outFile[k] << nAtoms << "\n"; |
198 |
> |
|
199 |
> |
*outFile[k] << currentTime << ";\t" |
200 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
201 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
202 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
203 |
> |
|
204 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
205 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
206 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
207 |
> |
|
208 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
209 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
210 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
211 |
> |
|
212 |
> |
//write out additional parameters, such as chi and eta |
213 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
214 |
|
} |
215 |
|
|
216 |
< |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
334 |
< |
MPIcheckPoint(); |
335 |
< |
|
336 |
< |
#endif //is_mpi |
216 |
> |
for( i=0; i<nAtoms; i++ ){ |
217 |
|
|
218 |
< |
|
218 |
> |
atoms[i]->getPos(pos); |
219 |
> |
atoms[i]->getVel(vel); |
220 |
|
|
340 |
– |
#ifndef IS_MPI |
341 |
– |
|
342 |
– |
finalOut << nAtoms << "\n"; |
343 |
– |
|
344 |
– |
finalOut << entry_plug->box_x << "\t" |
345 |
– |
<< entry_plug->box_y << "\t" |
346 |
– |
<< entry_plug->box_z << "\n"; |
347 |
– |
|
348 |
– |
for( i=0; i<nAtoms; i++ ){ |
349 |
– |
|
221 |
|
sprintf( tempBuffer, |
222 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
223 |
|
atoms[i]->getType(), |
224 |
< |
atoms[i]->getX(), |
225 |
< |
atoms[i]->getY(), |
226 |
< |
atoms[i]->getZ(), |
227 |
< |
atoms[i]->get_vx(), |
228 |
< |
atoms[i]->get_vy(), |
229 |
< |
atoms[i]->get_vz()); |
224 |
> |
pos[0], |
225 |
> |
pos[1], |
226 |
> |
pos[2], |
227 |
> |
vel[0], |
228 |
> |
vel[1], |
229 |
> |
vel[2]); |
230 |
|
strcpy( writeLine, tempBuffer ); |
231 |
|
|
232 |
|
if( atoms[i]->isDirectional() ){ |
233 |
< |
|
233 |
> |
|
234 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
235 |
|
dAtom->getQ( q ); |
236 |
< |
|
236 |
> |
|
237 |
|
sprintf( tempBuffer, |
238 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
239 |
|
q[0], |
247 |
|
} |
248 |
|
else |
249 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
250 |
< |
|
251 |
< |
finalOut << writeLine; |
250 |
> |
|
251 |
> |
for(k = 0; k < outFile.size(); k++) |
252 |
> |
*outFile[k] << writeLine; |
253 |
|
} |
382 |
– |
finalOut.flush(); |
254 |
|
|
255 |
|
#else // is_mpi |
256 |
|
|
257 |
< |
int masterIndex; |
258 |
< |
int nodeAtomsStart; |
259 |
< |
int nodeAtomsEnd; |
260 |
< |
int mpiErr; |
261 |
< |
int sendError; |
262 |
< |
int procIndex; |
263 |
< |
|
264 |
< |
MPI_Status istatus[MPI_STATUS_SIZE]; |
257 |
> |
/* code to find maximum tag value */ |
258 |
> |
|
259 |
> |
int *tagub, flag, MAXTAG; |
260 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
261 |
> |
if (flag) { |
262 |
> |
MAXTAG = *tagub; |
263 |
> |
} else { |
264 |
> |
MAXTAG = 32767; |
265 |
> |
} |
266 |
|
|
267 |
< |
|
267 |
> |
int haveError; |
268 |
> |
|
269 |
> |
MPI_Status istatus; |
270 |
> |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
271 |
> |
|
272 |
|
// write out header and node 0's coordinates |
273 |
|
|
274 |
|
if( worldRank == 0 ){ |
275 |
< |
finalOut << mpiSim->getTotAtoms() << "\n"; |
276 |
< |
|
277 |
< |
finalOut << entry_plug->box_x << "\t" |
278 |
< |
<< entry_plug->box_y << "\t" |
279 |
< |
<< entry_plug->box_z << "\n"; |
275 |
> |
|
276 |
> |
// Node 0 needs a list of the magic potatoes for each processor; |
277 |
> |
|
278 |
> |
nProc = mpiSim->getNumberProcessors(); |
279 |
> |
potatoes = new int[nProc]; |
280 |
> |
|
281 |
> |
//write out the comment lines |
282 |
> |
for (i = 0; i < nProc; i++) |
283 |
> |
potatoes[i] = 0; |
284 |
|
|
285 |
< |
masterIndex = 0; |
286 |
< |
|
287 |
< |
for( i=0; i<nAtoms; i++ ){ |
285 |
> |
for(k = 0; k < outFile.size(); k++){ |
286 |
> |
*outFile[k] << mpiSim->getTotAtoms() << "\n"; |
287 |
> |
|
288 |
> |
*outFile[k] << currentTime << ";\t" |
289 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
290 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
291 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
292 |
> |
|
293 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
294 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
295 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
296 |
> |
|
297 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
298 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
299 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
300 |
> |
|
301 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
302 |
> |
} |
303 |
> |
|
304 |
> |
currentIndex = 0; |
305 |
> |
|
306 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
307 |
|
|
308 |
< |
sprintf( tempBuffer, |
309 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
310 |
< |
atoms[i]->getType(), |
311 |
< |
atoms[i]->getX(), |
312 |
< |
atoms[i]->getY(), |
313 |
< |
atoms[i]->getZ(), |
314 |
< |
atoms[i]->get_vx(), |
315 |
< |
atoms[i]->get_vy(), |
316 |
< |
atoms[i]->get_vz()); |
317 |
< |
strcpy( writeLine, tempBuffer ); |
308 |
> |
// Get the Node number which has this atom; |
309 |
> |
|
310 |
> |
which_node = AtomToProcMap[i]; |
311 |
> |
|
312 |
> |
if (which_node != 0) { |
313 |
> |
|
314 |
> |
if (potatoes[which_node] + 3 >= MAXTAG) { |
315 |
> |
// The potato was going to exceed the maximum value, |
316 |
> |
// so wrap this processor potato back to 0: |
317 |
> |
|
318 |
> |
potatoes[which_node] = 0; |
319 |
> |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
320 |
> |
|
321 |
> |
} |
322 |
> |
|
323 |
> |
myPotato = potatoes[which_node]; |
324 |
> |
|
325 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
326 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
327 |
> |
|
328 |
> |
atomTypeString = MPIatomTypeString; |
329 |
|
|
330 |
< |
if( atoms[i]->isDirectional() ){ |
331 |
< |
|
332 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
333 |
< |
dAtom->getQ( q ); |
334 |
< |
|
335 |
< |
sprintf( tempBuffer, |
336 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
337 |
< |
q[0], |
338 |
< |
q[1], |
339 |
< |
q[2], |
340 |
< |
q[3], |
341 |
< |
dAtom->getJx(), |
342 |
< |
dAtom->getJy(), |
343 |
< |
dAtom->getJz()); |
344 |
< |
strcat( writeLine, tempBuffer ); |
330 |
> |
myPotato++; |
331 |
> |
|
332 |
> |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
333 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
334 |
> |
|
335 |
> |
myPotato++; |
336 |
> |
|
337 |
> |
if (isDirectional) { |
338 |
> |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
339 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
340 |
> |
} else { |
341 |
> |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
342 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
343 |
> |
} |
344 |
> |
|
345 |
> |
myPotato++; |
346 |
> |
potatoes[which_node] = myPotato; |
347 |
> |
|
348 |
> |
} else { |
349 |
> |
|
350 |
> |
haveError = 0; |
351 |
> |
which_atom = i; |
352 |
> |
|
353 |
> |
local_index = indexArray[currentIndex].first; |
354 |
> |
|
355 |
> |
if (which_atom == indexArray[currentIndex].second) { |
356 |
> |
|
357 |
> |
atomTypeString = atoms[local_index]->getType(); |
358 |
> |
|
359 |
> |
atoms[local_index]->getPos(pos); |
360 |
> |
atoms[local_index]->getVel(vel); |
361 |
> |
|
362 |
> |
atomData6[0] = pos[0]; |
363 |
> |
atomData6[1] = pos[1]; |
364 |
> |
atomData6[2] = pos[2]; |
365 |
> |
|
366 |
> |
atomData6[3] = vel[0]; |
367 |
> |
atomData6[4] = vel[1]; |
368 |
> |
atomData6[5] = vel[2]; |
369 |
> |
|
370 |
> |
isDirectional = 0; |
371 |
> |
|
372 |
> |
if( atoms[local_index]->isDirectional() ){ |
373 |
> |
|
374 |
> |
isDirectional = 1; |
375 |
> |
|
376 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
377 |
> |
dAtom->getQ( q ); |
378 |
> |
|
379 |
> |
for (int j = 0; j < 6 ; j++) |
380 |
> |
atomData13[j] = atomData6[j]; |
381 |
> |
|
382 |
> |
atomData13[6] = q[0]; |
383 |
> |
atomData13[7] = q[1]; |
384 |
> |
atomData13[8] = q[2]; |
385 |
> |
atomData13[9] = q[3]; |
386 |
> |
|
387 |
> |
atomData13[10] = dAtom->getJx(); |
388 |
> |
atomData13[11] = dAtom->getJy(); |
389 |
> |
atomData13[12] = dAtom->getJz(); |
390 |
> |
} |
391 |
> |
|
392 |
> |
} else { |
393 |
> |
sprintf(painCave.errMsg, |
394 |
> |
"Atom %d not found on processor %d\n", |
395 |
> |
i, worldRank ); |
396 |
> |
haveError= 1; |
397 |
> |
simError(); |
398 |
> |
} |
399 |
> |
|
400 |
> |
if(haveError) DieDieDie(); |
401 |
> |
|
402 |
> |
currentIndex ++; |
403 |
|
} |
404 |
< |
else |
405 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
404 |
> |
// If we've survived to here, format the line: |
405 |
> |
|
406 |
> |
if (!isDirectional) { |
407 |
|
|
408 |
< |
finalOut << writeLine; |
409 |
< |
masterIndex++; |
410 |
< |
} |
411 |
< |
finalOut.flush(); |
412 |
< |
} |
413 |
< |
|
414 |
< |
for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
415 |
< |
procIndex++){ |
408 |
> |
sprintf( writeLine, |
409 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
410 |
> |
atomTypeString, |
411 |
> |
atomData6[0], |
412 |
> |
atomData6[1], |
413 |
> |
atomData6[2], |
414 |
> |
atomData6[3], |
415 |
> |
atomData6[4], |
416 |
> |
atomData6[5]); |
417 |
|
|
418 |
< |
if( worldRank == 0 ){ |
418 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
419 |
|
|
420 |
< |
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
451 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
452 |
< |
|
453 |
< |
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
454 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
420 |
> |
} else { |
421 |
|
|
422 |
< |
// Make sure where node 0 is writing to, matches where the |
423 |
< |
// receiving node expects it to be. |
424 |
< |
|
425 |
< |
if (masterIndex != nodeAtomsStart){ |
426 |
< |
sendError = 1; |
427 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
428 |
< |
MPI_COMM_WORLD); |
429 |
< |
sprintf(painCave.errMsg, |
430 |
< |
"DumpWriter error: atoms start index (%d) for " |
431 |
< |
"node %d not equal to master index (%d)", |
432 |
< |
nodeAtomsStart,procIndex,masterIndex ); |
433 |
< |
painCave.isFatal = 1; |
434 |
< |
simError(); |
422 |
> |
sprintf( writeLine, |
423 |
> |
"%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", |
424 |
> |
atomTypeString, |
425 |
> |
atomData13[0], |
426 |
> |
atomData13[1], |
427 |
> |
atomData13[2], |
428 |
> |
atomData13[3], |
429 |
> |
atomData13[4], |
430 |
> |
atomData13[5], |
431 |
> |
atomData13[6], |
432 |
> |
atomData13[7], |
433 |
> |
atomData13[8], |
434 |
> |
atomData13[9], |
435 |
> |
atomData13[10], |
436 |
> |
atomData13[11], |
437 |
> |
atomData13[12]); |
438 |
> |
|
439 |
|
} |
440 |
< |
|
441 |
< |
sendError = 0; |
442 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
443 |
< |
MPI_COMM_WORLD); |
440 |
> |
|
441 |
> |
for(k = 0; k < outFile.size(); k++) |
442 |
> |
*outFile[k] << writeLine; |
443 |
> |
} |
444 |
> |
|
445 |
> |
for(k = 0; k < outFile.size(); k++) |
446 |
> |
outFile[k]->flush(); |
447 |
> |
|
448 |
> |
sprintf( checkPointMsg, |
449 |
> |
"Sucessfully took a dump.\n"); |
450 |
|
|
451 |
< |
// recieve the nodes writeLines |
451 |
> |
MPIcheckPoint(); |
452 |
|
|
453 |
< |
for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
478 |
< |
|
479 |
< |
mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
480 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); |
453 |
> |
delete[] potatoes; |
454 |
|
|
455 |
< |
finalOut << writeLine; |
483 |
< |
masterIndex++; |
484 |
< |
} |
455 |
> |
} else { |
456 |
|
|
457 |
< |
finalOut.flush(); |
487 |
< |
} |
457 |
> |
// worldRank != 0, so I'm a remote node. |
458 |
|
|
459 |
< |
else if( worldRank == procIndex ){ |
459 |
> |
// Set my magic potato to 0: |
460 |
|
|
461 |
< |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
462 |
< |
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
463 |
< |
|
464 |
< |
mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, |
465 |
< |
MPI_COMM_WORLD); |
466 |
< |
mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, |
467 |
< |
MPI_COMM_WORLD); |
468 |
< |
|
499 |
< |
mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, |
500 |
< |
MPI_COMM_WORLD, istatus); |
501 |
< |
if (sendError) MPIcheckPoint(); |
461 |
> |
myPotato = 0; |
462 |
> |
currentIndex = 0; |
463 |
> |
|
464 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
465 |
> |
|
466 |
> |
// Am I the node which has this atom? |
467 |
> |
|
468 |
> |
if (AtomToProcMap[i] == worldRank) { |
469 |
|
|
470 |
< |
// send current node's configuration line by line. |
470 |
> |
if (myPotato + 3 >= MAXTAG) { |
471 |
|
|
472 |
< |
for( i=0; i<nAtoms; i++ ){ |
473 |
< |
|
474 |
< |
sprintf( tempBuffer, |
475 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
476 |
< |
atoms[i]->getType(), |
477 |
< |
atoms[i]->getX(), |
478 |
< |
atoms[i]->getY(), |
479 |
< |
atoms[i]->getZ(), |
480 |
< |
atoms[i]->get_vx(), |
481 |
< |
atoms[i]->get_vy(), |
482 |
< |
atoms[i]->get_vz()); |
483 |
< |
strcpy( writeLine, tempBuffer ); |
484 |
< |
|
485 |
< |
if( atoms[i]->isDirectional() ){ |
486 |
< |
|
487 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
488 |
< |
dAtom->getQ( q ); |
489 |
< |
|
490 |
< |
sprintf( tempBuffer, |
491 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
492 |
< |
q[0], |
493 |
< |
q[1], |
494 |
< |
q[2], |
495 |
< |
q[3], |
496 |
< |
dAtom->getJx(), |
497 |
< |
dAtom->getJy(), |
498 |
< |
dAtom->getJz()); |
499 |
< |
strcat( writeLine, tempBuffer ); |
500 |
< |
} |
501 |
< |
else |
502 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
503 |
< |
|
504 |
< |
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
505 |
< |
MPI_COMM_WORLD); |
472 |
> |
// The potato was going to exceed the maximum value, |
473 |
> |
// so wrap this processor potato back to 0 (and block until |
474 |
> |
// node 0 says we can go: |
475 |
> |
|
476 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
477 |
> |
|
478 |
> |
} |
479 |
> |
which_atom = i; |
480 |
> |
local_index = indexArray[currentIndex].first; |
481 |
> |
|
482 |
> |
if (which_atom == indexArray[currentIndex].second) { |
483 |
> |
|
484 |
> |
atomTypeString = atoms[local_index]->getType(); |
485 |
> |
|
486 |
> |
atoms[local_index]->getPos(pos); |
487 |
> |
atoms[local_index]->getVel(vel); |
488 |
> |
|
489 |
> |
atomData6[0] = pos[0]; |
490 |
> |
atomData6[1] = pos[1]; |
491 |
> |
atomData6[2] = pos[2]; |
492 |
> |
|
493 |
> |
atomData6[3] = vel[0]; |
494 |
> |
atomData6[4] = vel[1]; |
495 |
> |
atomData6[5] = vel[2]; |
496 |
> |
|
497 |
> |
isDirectional = 0; |
498 |
> |
|
499 |
> |
if( atoms[local_index]->isDirectional() ){ |
500 |
> |
|
501 |
> |
isDirectional = 1; |
502 |
> |
|
503 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
504 |
> |
dAtom->getQ( q ); |
505 |
> |
|
506 |
> |
for (int j = 0; j < 6 ; j++) |
507 |
> |
atomData13[j] = atomData6[j]; |
508 |
> |
|
509 |
> |
atomData13[6] = q[0]; |
510 |
> |
atomData13[7] = q[1]; |
511 |
> |
atomData13[8] = q[2]; |
512 |
> |
atomData13[9] = q[3]; |
513 |
> |
|
514 |
> |
atomData13[10] = dAtom->getJx(); |
515 |
> |
atomData13[11] = dAtom->getJy(); |
516 |
> |
atomData13[12] = dAtom->getJz(); |
517 |
> |
} |
518 |
> |
|
519 |
> |
} else { |
520 |
> |
sprintf(painCave.errMsg, |
521 |
> |
"Atom %d not found on processor %d\n", |
522 |
> |
i, worldRank ); |
523 |
> |
haveError= 1; |
524 |
> |
simError(); |
525 |
> |
} |
526 |
> |
|
527 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
528 |
> |
|
529 |
> |
// null terminate the string before sending (just in case): |
530 |
> |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
531 |
> |
|
532 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
533 |
> |
myPotato, MPI_COMM_WORLD); |
534 |
> |
|
535 |
> |
myPotato++; |
536 |
> |
|
537 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
538 |
> |
myPotato, MPI_COMM_WORLD); |
539 |
> |
|
540 |
> |
myPotato++; |
541 |
> |
|
542 |
> |
if (isDirectional) { |
543 |
> |
|
544 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
545 |
> |
myPotato, MPI_COMM_WORLD); |
546 |
> |
|
547 |
> |
} else { |
548 |
> |
|
549 |
> |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
550 |
> |
myPotato, MPI_COMM_WORLD); |
551 |
> |
} |
552 |
> |
|
553 |
> |
myPotato++; |
554 |
> |
currentIndex++; |
555 |
|
} |
556 |
|
} |
541 |
– |
|
542 |
– |
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
543 |
– |
procIndex); |
544 |
– |
MPIcheckPoint(); |
545 |
– |
} |
557 |
|
|
558 |
< |
if( worldRank == 0 ) finalOut.close(); |
559 |
< |
|
558 |
> |
sprintf( checkPointMsg, |
559 |
> |
"Sucessfully took a dump.\n"); |
560 |
> |
MPIcheckPoint(); |
561 |
|
|
562 |
+ |
} |
563 |
+ |
|
564 |
|
#endif // is_mpi |
565 |
|
} |
566 |
+ |
|
567 |
+ |
#ifdef IS_MPI |
568 |
+ |
|
569 |
+ |
// a couple of functions to let us escape the write loop |
570 |
+ |
|
571 |
+ |
void dWrite::DieDieDie( void ){ |
572 |
+ |
|
573 |
+ |
MPI_Finalize(); |
574 |
+ |
exit (0); |
575 |
+ |
} |
576 |
+ |
|
577 |
+ |
#endif //is_mpi |