1 |
mmeineke |
723 |
#define _FILE_OFFSET_BITS 64 |
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3 |
gezelter |
829 |
#include <string.h> |
4 |
mmeineke |
377 |
#include <iostream> |
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#include <fstream> |
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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 |
|
11 |
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namespace dWrite{ |
12 |
gezelter |
907 |
void DieDieDie( void ); |
13 |
mmeineke |
440 |
} |
14 |
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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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mmeineke |
377 |
strcpy( outName, entry_plug->sampleName ); |
30 |
tim |
837 |
|
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mmeineke |
377 |
outFile.open(outName, ios::out | ios::trunc ); |
32 |
tim |
837 |
|
33 |
mmeineke |
377 |
if( !outFile ){ |
34 |
tim |
837 |
|
35 |
mmeineke |
377 |
sprintf( painCave.errMsg, |
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"Could not open \"%s\" for dump output.\n", |
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outName); |
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painCave.isFatal = 1; |
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simError(); |
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} |
41 |
mmeineke |
469 |
|
42 |
mmeineke |
377 |
//outFile.setf( ios::scientific ); |
43 |
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#ifdef IS_MPI |
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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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#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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outFile.close(); |
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
64 |
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} |
65 |
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66 |
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void DumpWriter::writeDump( double currentTime ){ |
67 |
tim |
837 |
|
68 |
mmeineke |
377 |
const int BUFFERSIZE = 2000; |
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gezelter |
907 |
const int MINIBUFFERSIZE = 10; |
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mmeineke |
377 |
char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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mmeineke |
787 |
int i; |
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#ifdef IS_MPI |
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int j, which_node, done, which_atom, local_index; |
77 |
gezelter |
907 |
double atomTransData[6]; |
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double atomOrientData[7]; |
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int isDirectional; |
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char* atomTypeString; |
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int me; |
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int atomTypeTag; |
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int atomIsDirectionalTag; |
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int atomTransDataTag; |
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int atomOrientDataTag; |
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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; |
93 |
mmeineke |
670 |
double pos[3], vel[3]; |
94 |
tim |
837 |
|
95 |
mmeineke |
804 |
// write current frame to the eor file |
96 |
mmeineke |
377 |
|
97 |
mmeineke |
804 |
this->writeFinal( currentTime ); |
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mmeineke |
377 |
#ifndef IS_MPI |
100 |
tim |
837 |
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101 |
mmeineke |
377 |
outFile << nAtoms << "\n"; |
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tim |
837 |
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outFile << currentTime << ";\t" |
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mmeineke |
590 |
<< 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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mmeineke |
572 |
|
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mmeineke |
590 |
<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
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mmeineke |
572 |
|
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mmeineke |
590 |
<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
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tim |
837 |
<< entry_plug->Hmat[2][2] << ";"; |
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//write out additional parameters, such as chi and eta |
116 |
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outFile << entry_plug->the_integrator->getAdditionalParameters(); |
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outFile << endl; |
118 |
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mmeineke |
377 |
for( i=0; i<nAtoms; i++ ){ |
120 |
tim |
837 |
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121 |
mmeineke |
670 |
atoms[i]->getPos(pos); |
122 |
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atoms[i]->getVel(vel); |
123 |
mmeineke |
377 |
|
124 |
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sprintf( tempBuffer, |
125 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
126 |
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atoms[i]->getType(), |
127 |
mmeineke |
670 |
pos[0], |
128 |
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pos[1], |
129 |
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pos[2], |
130 |
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vel[0], |
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vel[1], |
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vel[2]); |
133 |
mmeineke |
377 |
strcpy( writeLine, tempBuffer ); |
134 |
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135 |
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if( atoms[i]->isDirectional() ){ |
136 |
tim |
837 |
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137 |
mmeineke |
377 |
dAtom = (DirectionalAtom *)atoms[i]; |
138 |
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dAtom->getQ( q ); |
139 |
tim |
837 |
|
140 |
mmeineke |
377 |
sprintf( tempBuffer, |
141 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
142 |
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q[0], |
143 |
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q[1], |
144 |
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q[2], |
145 |
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q[3], |
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dAtom->getJx(), |
147 |
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dAtom->getJy(), |
148 |
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dAtom->getJz()); |
149 |
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strcat( writeLine, tempBuffer ); |
150 |
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} |
151 |
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else |
152 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
153 |
tim |
837 |
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154 |
mmeineke |
377 |
outFile << writeLine; |
155 |
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} |
156 |
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outFile.flush(); |
157 |
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158 |
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#else // is_mpi |
159 |
gezelter |
416 |
|
160 |
mmeineke |
440 |
// first thing first, suspend fatalities. |
161 |
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painCave.isEventLoop = 1; |
162 |
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163 |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
164 |
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int haveError; |
165 |
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166 |
mmeineke |
447 |
MPI_Status istatus; |
167 |
gezelter |
416 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
168 |
tim |
837 |
|
169 |
mmeineke |
377 |
// write out header and node 0's coordinates |
170 |
tim |
837 |
|
171 |
mmeineke |
377 |
if( worldRank == 0 ){ |
172 |
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outFile << mpiSim->getTotAtoms() << "\n"; |
173 |
tim |
837 |
|
174 |
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outFile << currentTime << ";\t" |
175 |
gezelter |
591 |
<< entry_plug->Hmat[0][0] << "\t" |
176 |
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<< entry_plug->Hmat[1][0] << "\t" |
177 |
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<< entry_plug->Hmat[2][0] << ";\t" |
178 |
tim |
837 |
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179 |
gezelter |
591 |
<< entry_plug->Hmat[0][1] << "\t" |
180 |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
182 |
tim |
837 |
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183 |
gezelter |
591 |
<< entry_plug->Hmat[0][2] << "\t" |
184 |
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<< entry_plug->Hmat[1][2] << "\t" |
185 |
tim |
837 |
<< entry_plug->Hmat[2][2] << ";"; |
186 |
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187 |
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outFile << entry_plug->the_integrator->getAdditionalParameters(); |
188 |
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outFile << endl; |
189 |
chuckv |
434 |
outFile.flush(); |
190 |
gezelter |
416 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
191 |
gezelter |
417 |
// Get the Node number which has this atom; |
192 |
tim |
837 |
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193 |
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which_node = AtomToProcMap[i]; |
194 |
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195 |
gezelter |
907 |
if (which_node != 0) { |
196 |
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atomTypeTag = 4*i; |
198 |
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atomIsDirectionalTag = 4*i + 1; |
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atomTransDataTag = 4*i + 2; |
200 |
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atomOrientDataTag = 4*i + 3; |
201 |
tim |
837 |
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202 |
gezelter |
907 |
MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
203 |
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atomTypeTag, MPI_COMM_WORLD, &istatus); |
204 |
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205 |
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MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
206 |
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atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
207 |
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208 |
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MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
209 |
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atomTransDataTag, MPI_COMM_WORLD, &istatus); |
210 |
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211 |
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if (isDirectional) { |
212 |
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213 |
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MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
214 |
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atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
215 |
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216 |
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} |
217 |
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218 |
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} else { |
219 |
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220 |
mmeineke |
440 |
haveError = 0; |
221 |
chuckv |
436 |
which_atom = i; |
222 |
tim |
837 |
local_index=-1; |
223 |
gezelter |
907 |
|
224 |
chuckv |
436 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
225 |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
226 |
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} |
227 |
gezelter |
907 |
|
228 |
chuckv |
436 |
if (local_index != -1) { |
229 |
tim |
837 |
|
230 |
gezelter |
907 |
atomTypeString = atoms[local_index]->getType(); |
231 |
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232 |
mmeineke |
670 |
atoms[local_index]->getPos(pos); |
233 |
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atoms[local_index]->getVel(vel); |
234 |
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235 |
gezelter |
907 |
atomTransData[0] = pos[0]; |
236 |
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atomTransData[1] = pos[1]; |
237 |
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atomTransData[2] = pos[2]; |
238 |
tim |
837 |
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239 |
gezelter |
907 |
atomTransData[3] = vel[0]; |
240 |
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atomTransData[4] = vel[1]; |
241 |
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atomTransData[5] = vel[2]; |
242 |
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243 |
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isDirectional = 0; |
244 |
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245 |
chuckv |
436 |
if( atoms[local_index]->isDirectional() ){ |
246 |
tim |
837 |
|
247 |
gezelter |
907 |
isDirectional = 1; |
248 |
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|
249 |
chuckv |
436 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
250 |
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dAtom->getQ( q ); |
251 |
gezelter |
907 |
|
252 |
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atomOrientData[0] = q[0]; |
253 |
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atomOrientData[1] = q[1]; |
254 |
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atomOrientData[2] = q[2]; |
255 |
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atomOrientData[3] = q[3]; |
256 |
tim |
837 |
|
257 |
gezelter |
907 |
atomOrientData[4] = dAtom->getJx(); |
258 |
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atomOrientData[5] = dAtom->getJy(); |
259 |
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atomOrientData[6] = dAtom->getJz(); |
260 |
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} |
261 |
tim |
837 |
|
262 |
gezelter |
907 |
} else { |
263 |
mmeineke |
440 |
sprintf(painCave.errMsg, |
264 |
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"Atom %d not found on processor %d\n", |
265 |
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i, worldRank ); |
266 |
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haveError= 1; |
267 |
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simError(); |
268 |
tim |
837 |
} |
269 |
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270 |
gezelter |
907 |
if(haveError) DieDieDie(); |
271 |
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272 |
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// If we've survived to here, format the line: |
273 |
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274 |
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sprintf( tempBuffer, |
275 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
276 |
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atomTypeString, |
277 |
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atomTransData[0], |
278 |
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atomTransData[1], |
279 |
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atomTransData[2], |
280 |
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atomTransData[3], |
281 |
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atomTransData[4], |
282 |
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atomTransData[5]); |
283 |
mmeineke |
440 |
|
284 |
gezelter |
907 |
strcpy( writeLine, tempBuffer ); |
285 |
tim |
837 |
|
286 |
gezelter |
907 |
if (isDirectional) { |
287 |
mmeineke |
440 |
|
288 |
gezelter |
907 |
sprintf( tempBuffer, |
289 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
290 |
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atomOrientData[0], |
291 |
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atomOrientData[1], |
292 |
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atomOrientData[2], |
293 |
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atomOrientData[3], |
294 |
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atomOrientData[4], |
295 |
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atomOrientData[5], |
296 |
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atomOrientData[6]); |
297 |
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strcat( writeLine, tempBuffer ); |
298 |
tim |
837 |
|
299 |
gezelter |
907 |
} else { |
300 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
301 |
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} |
302 |
tim |
837 |
|
303 |
gezelter |
907 |
outFile << writeLine; |
304 |
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outFile.flush(); |
305 |
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} |
306 |
mmeineke |
377 |
} |
307 |
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|
308 |
gezelter |
907 |
outFile.flush(); |
309 |
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sprintf( checkPointMsg, |
310 |
|
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"Sucessfully took a dump.\n"); |
311 |
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MPIcheckPoint(); |
312 |
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|
313 |
gezelter |
415 |
} else { |
314 |
tim |
837 |
|
315 |
gezelter |
907 |
// worldRank != 0, so I'm a remote node. |
316 |
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|
317 |
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for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
318 |
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|
319 |
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// Am I the node which has this atom? |
320 |
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|
321 |
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if (AtomToProcMap[i] == worldRank) { |
322 |
tim |
837 |
|
323 |
gezelter |
907 |
local_index=-1; |
324 |
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for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
325 |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
326 |
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} |
327 |
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if (local_index != -1) { |
328 |
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|
329 |
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atomTypeString = atoms[local_index]->getType(); |
330 |
mmeineke |
440 |
|
331 |
gezelter |
907 |
atoms[local_index]->getPos(pos); |
332 |
|
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atoms[local_index]->getVel(vel); |
333 |
tim |
837 |
|
334 |
gezelter |
907 |
atomTransData[0] = pos[0]; |
335 |
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atomTransData[1] = pos[1]; |
336 |
|
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atomTransData[2] = pos[2]; |
337 |
mmeineke |
440 |
|
338 |
gezelter |
907 |
atomTransData[3] = vel[0]; |
339 |
|
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atomTransData[4] = vel[1]; |
340 |
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atomTransData[5] = vel[2]; |
341 |
|
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|
342 |
|
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isDirectional = 0; |
343 |
tim |
837 |
|
344 |
gezelter |
907 |
if( atoms[local_index]->isDirectional() ){ |
345 |
mmeineke |
670 |
|
346 |
gezelter |
907 |
isDirectional = 1; |
347 |
|
|
|
348 |
|
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
349 |
|
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dAtom->getQ( q ); |
350 |
|
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|
351 |
|
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atomOrientData[0] = q[0]; |
352 |
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atomOrientData[1] = q[1]; |
353 |
|
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atomOrientData[2] = q[2]; |
354 |
|
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atomOrientData[3] = q[3]; |
355 |
mmeineke |
670 |
|
356 |
gezelter |
907 |
atomOrientData[4] = dAtom->getJx(); |
357 |
|
|
atomOrientData[5] = dAtom->getJy(); |
358 |
|
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atomOrientData[6] = dAtom->getJz(); |
359 |
|
|
} |
360 |
tim |
837 |
|
361 |
gezelter |
907 |
} else { |
362 |
|
|
sprintf(painCave.errMsg, |
363 |
|
|
"Atom %d not found on processor %d\n", |
364 |
|
|
i, worldRank ); |
365 |
|
|
haveError= 1; |
366 |
|
|
simError(); |
367 |
|
|
} |
368 |
tim |
837 |
|
369 |
gezelter |
907 |
// I've survived this far, so send off the data! |
370 |
tim |
837 |
|
371 |
gezelter |
907 |
atomTypeTag = 4*i; |
372 |
|
|
atomIsDirectionalTag = 4*i + 1; |
373 |
|
|
atomTransDataTag = 4*i + 2; |
374 |
|
|
atomOrientDataTag = 4*i + 3; |
375 |
mmeineke |
440 |
|
376 |
gezelter |
907 |
MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
377 |
|
|
atomTypeTag, MPI_COMM_WORLD); |
378 |
|
|
|
379 |
|
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
380 |
|
|
atomIsDirectionalTag, MPI_COMM_WORLD); |
381 |
|
|
|
382 |
|
|
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
383 |
|
|
atomTransDataTag, MPI_COMM_WORLD); |
384 |
|
|
|
385 |
|
|
if (isDirectional) { |
386 |
|
|
|
387 |
|
|
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
388 |
|
|
atomOrientDataTag, MPI_COMM_WORLD); |
389 |
|
|
|
390 |
|
|
} |
391 |
|
|
|
392 |
mmeineke |
377 |
} |
393 |
gezelter |
907 |
} |
394 |
mmeineke |
440 |
|
395 |
gezelter |
907 |
sprintf( checkPointMsg, |
396 |
|
|
"Sucessfully took a dump.\n"); |
397 |
|
|
MPIcheckPoint(); |
398 |
|
|
|
399 |
tim |
837 |
} |
400 |
gezelter |
907 |
|
401 |
mmeineke |
440 |
painCave.isEventLoop = 0; |
402 |
|
|
|
403 |
mmeineke |
377 |
#endif // is_mpi |
404 |
|
|
} |
405 |
|
|
|
406 |
mmeineke |
572 |
void DumpWriter::writeFinal(double finalTime){ |
407 |
gezelter |
416 |
|
408 |
mmeineke |
377 |
char finalName[500]; |
409 |
|
|
ofstream finalOut; |
410 |
gezelter |
416 |
|
411 |
|
|
const int BUFFERSIZE = 2000; |
412 |
gezelter |
907 |
const int MINIBUFFERSIZE = 10; |
413 |
gezelter |
416 |
char tempBuffer[BUFFERSIZE]; |
414 |
tim |
837 |
char writeLine[BUFFERSIZE]; |
415 |
gezelter |
416 |
|
416 |
|
|
double q[4]; |
417 |
|
|
DirectionalAtom* dAtom; |
418 |
mmeineke |
787 |
Atom** atoms = entry_plug->atoms; |
419 |
|
|
int i; |
420 |
|
|
#ifdef IS_MPI |
421 |
|
|
int j, which_node, done, which_atom, local_index; |
422 |
gezelter |
907 |
double atomTransData[6]; |
423 |
|
|
double atomOrientData[7]; |
424 |
|
|
int isDirectional; |
425 |
|
|
char* atomTypeString; |
426 |
|
|
int atomTypeTag; |
427 |
|
|
int atomIsDirectionalTag; |
428 |
|
|
int atomTransDataTag; |
429 |
|
|
int atomOrientDataTag; |
430 |
mmeineke |
787 |
#else //is_mpi |
431 |
gezelter |
416 |
int nAtoms = entry_plug->n_atoms; |
432 |
mmeineke |
787 |
#endif //is_mpi |
433 |
tim |
837 |
|
434 |
mmeineke |
670 |
double pos[3], vel[3]; |
435 |
tim |
837 |
|
436 |
mmeineke |
377 |
#ifdef IS_MPI |
437 |
|
|
if(worldRank == 0 ){ |
438 |
|
|
#endif // is_mpi |
439 |
tim |
837 |
|
440 |
mmeineke |
377 |
strcpy( finalName, entry_plug->finalName ); |
441 |
tim |
837 |
|
442 |
mmeineke |
377 |
finalOut.open( finalName, ios::out | ios::trunc ); |
443 |
|
|
if( !finalOut ){ |
444 |
|
|
sprintf( painCave.errMsg, |
445 |
|
|
"Could not open \"%s\" for final dump output.\n", |
446 |
|
|
finalName ); |
447 |
|
|
painCave.isFatal = 1; |
448 |
|
|
simError(); |
449 |
|
|
} |
450 |
tim |
837 |
|
451 |
mmeineke |
377 |
// finalOut.setf( ios::scientific ); |
452 |
tim |
837 |
|
453 |
mmeineke |
377 |
#ifdef IS_MPI |
454 |
|
|
} |
455 |
tim |
837 |
|
456 |
mmeineke |
377 |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
457 |
tim |
837 |
MPIcheckPoint(); |
458 |
|
|
|
459 |
mmeineke |
377 |
#endif //is_mpi |
460 |
|
|
|
461 |
tim |
837 |
|
462 |
mmeineke |
377 |
#ifndef IS_MPI |
463 |
tim |
837 |
|
464 |
mmeineke |
377 |
finalOut << nAtoms << "\n"; |
465 |
tim |
837 |
|
466 |
gezelter |
591 |
finalOut << finalTime << ";\t" |
467 |
mmeineke |
590 |
<< entry_plug->Hmat[0][0] << "\t" |
468 |
|
|
<< entry_plug->Hmat[1][0] << "\t" |
469 |
gezelter |
591 |
<< entry_plug->Hmat[2][0] << ";\t" |
470 |
tim |
837 |
|
471 |
mmeineke |
590 |
<< entry_plug->Hmat[0][1] << "\t" |
472 |
|
|
<< entry_plug->Hmat[1][1] << "\t" |
473 |
gezelter |
591 |
<< entry_plug->Hmat[2][1] << ";\t" |
474 |
tim |
837 |
|
475 |
mmeineke |
590 |
<< entry_plug->Hmat[0][2] << "\t" |
476 |
|
|
<< entry_plug->Hmat[1][2] << "\t" |
477 |
tim |
837 |
<< entry_plug->Hmat[2][2] << ";"; |
478 |
|
|
|
479 |
|
|
//write out additional parameters, such as chi and eta |
480 |
|
|
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
481 |
|
|
finalOut << endl; |
482 |
|
|
|
483 |
mmeineke |
377 |
for( i=0; i<nAtoms; i++ ){ |
484 |
tim |
837 |
|
485 |
mmeineke |
670 |
atoms[i]->getPos(pos); |
486 |
|
|
atoms[i]->getVel(vel); |
487 |
tim |
837 |
|
488 |
mmeineke |
377 |
sprintf( tempBuffer, |
489 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
490 |
|
|
atoms[i]->getType(), |
491 |
mmeineke |
670 |
pos[0], |
492 |
|
|
pos[1], |
493 |
|
|
pos[2], |
494 |
|
|
vel[0], |
495 |
|
|
vel[1], |
496 |
|
|
vel[2]); |
497 |
mmeineke |
377 |
strcpy( writeLine, tempBuffer ); |
498 |
|
|
|
499 |
|
|
if( atoms[i]->isDirectional() ){ |
500 |
tim |
837 |
|
501 |
mmeineke |
377 |
dAtom = (DirectionalAtom *)atoms[i]; |
502 |
|
|
dAtom->getQ( q ); |
503 |
tim |
837 |
|
504 |
mmeineke |
377 |
sprintf( tempBuffer, |
505 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
506 |
|
|
q[0], |
507 |
|
|
q[1], |
508 |
|
|
q[2], |
509 |
|
|
q[3], |
510 |
|
|
dAtom->getJx(), |
511 |
|
|
dAtom->getJy(), |
512 |
|
|
dAtom->getJz()); |
513 |
|
|
strcat( writeLine, tempBuffer ); |
514 |
|
|
} |
515 |
|
|
else |
516 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
517 |
tim |
837 |
|
518 |
mmeineke |
377 |
finalOut << writeLine; |
519 |
|
|
} |
520 |
|
|
finalOut.flush(); |
521 |
gezelter |
415 |
finalOut.close(); |
522 |
mmeineke |
377 |
|
523 |
|
|
#else // is_mpi |
524 |
tim |
837 |
|
525 |
mmeineke |
440 |
// first thing first, suspend fatalities. |
526 |
|
|
painCave.isEventLoop = 1; |
527 |
|
|
|
528 |
|
|
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
529 |
|
|
int haveError; |
530 |
|
|
|
531 |
mmeineke |
447 |
MPI_Status istatus; |
532 |
gezelter |
416 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
533 |
|
|
|
534 |
mmeineke |
377 |
// write out header and node 0's coordinates |
535 |
tim |
837 |
|
536 |
mmeineke |
377 |
if( worldRank == 0 ){ |
537 |
|
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
538 |
tim |
837 |
|
539 |
gezelter |
591 |
finalOut << finalTime << ";\t" |
540 |
gezelter |
907 |
<< entry_plug->Hmat[0][0] << "\t" |
541 |
|
|
<< entry_plug->Hmat[1][0] << "\t" |
542 |
|
|
<< entry_plug->Hmat[2][0] << ";\t" |
543 |
tim |
837 |
|
544 |
gezelter |
907 |
<< entry_plug->Hmat[0][1] << "\t" |
545 |
|
|
<< entry_plug->Hmat[1][1] << "\t" |
546 |
|
|
<< entry_plug->Hmat[2][1] << ";\t" |
547 |
tim |
837 |
|
548 |
gezelter |
907 |
<< entry_plug->Hmat[0][2] << "\t" |
549 |
|
|
<< entry_plug->Hmat[1][2] << "\t" |
550 |
|
|
<< entry_plug->Hmat[2][2] << ";"; |
551 |
tim |
837 |
|
552 |
|
|
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
553 |
|
|
finalOut << endl; |
554 |
gezelter |
907 |
finalOut.flush(); |
555 |
gezelter |
416 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
556 |
gezelter |
907 |
// Get the Node number which has this atom; |
557 |
tim |
837 |
|
558 |
|
|
which_node = AtomToProcMap[i]; |
559 |
|
|
|
560 |
gezelter |
907 |
if (which_node != 0) { |
561 |
|
|
|
562 |
|
|
atomTypeTag = 4*i; |
563 |
|
|
atomIsDirectionalTag = 4*i + 1; |
564 |
|
|
atomTransDataTag = 4*i + 2; |
565 |
|
|
atomOrientDataTag = 4*i + 3; |
566 |
chuckv |
437 |
|
567 |
gezelter |
907 |
MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
568 |
|
|
atomTypeTag, MPI_COMM_WORLD, &istatus); |
569 |
|
|
|
570 |
|
|
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
571 |
|
|
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
572 |
|
|
|
573 |
|
|
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
574 |
|
|
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
575 |
|
|
|
576 |
|
|
if (isDirectional) { |
577 |
|
|
|
578 |
|
|
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
579 |
|
|
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
580 |
|
|
|
581 |
|
|
} |
582 |
|
|
|
583 |
|
|
} else { |
584 |
|
|
|
585 |
|
|
haveError = 0; |
586 |
chuckv |
437 |
which_atom = i; |
587 |
tim |
837 |
local_index=-1; |
588 |
gezelter |
907 |
|
589 |
chuckv |
437 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
590 |
|
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
591 |
|
|
} |
592 |
gezelter |
907 |
|
593 |
tim |
837 |
if (local_index != -1) { |
594 |
mmeineke |
670 |
|
595 |
gezelter |
907 |
atomTypeString = atoms[local_index]->getType(); |
596 |
|
|
|
597 |
mmeineke |
670 |
atoms[local_index]->getPos(pos); |
598 |
|
|
atoms[local_index]->getVel(vel); |
599 |
tim |
837 |
|
600 |
gezelter |
907 |
atomTransData[0] = pos[0]; |
601 |
|
|
atomTransData[1] = pos[1]; |
602 |
|
|
atomTransData[2] = pos[2]; |
603 |
tim |
837 |
|
604 |
gezelter |
907 |
atomTransData[3] = vel[0]; |
605 |
|
|
atomTransData[4] = vel[1]; |
606 |
|
|
atomTransData[5] = vel[2]; |
607 |
|
|
|
608 |
|
|
isDirectional = 0; |
609 |
tim |
837 |
|
610 |
gezelter |
907 |
if( atoms[local_index]->isDirectional() ){ |
611 |
tim |
837 |
|
612 |
gezelter |
907 |
isDirectional = 1; |
613 |
|
|
|
614 |
|
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
615 |
|
|
dAtom->getQ( q ); |
616 |
|
|
|
617 |
|
|
atomOrientData[0] = q[0]; |
618 |
|
|
atomOrientData[1] = q[1]; |
619 |
|
|
atomOrientData[2] = q[2]; |
620 |
|
|
atomOrientData[3] = q[3]; |
621 |
|
|
|
622 |
|
|
atomOrientData[4] = dAtom->getJx(); |
623 |
|
|
atomOrientData[5] = dAtom->getJy(); |
624 |
|
|
atomOrientData[6] = dAtom->getJz(); |
625 |
|
|
} |
626 |
|
|
|
627 |
|
|
} else { |
628 |
mmeineke |
440 |
sprintf(painCave.errMsg, |
629 |
|
|
"Atom %d not found on processor %d\n", |
630 |
|
|
i, worldRank ); |
631 |
|
|
haveError= 1; |
632 |
|
|
simError(); |
633 |
tim |
837 |
} |
634 |
mmeineke |
440 |
|
635 |
gezelter |
907 |
if(haveError) DieDieDie(); |
636 |
|
|
|
637 |
|
|
// If we've survived to here, format the line: |
638 |
|
|
|
639 |
|
|
sprintf( tempBuffer, |
640 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
641 |
|
|
atomTypeString, |
642 |
|
|
atomTransData[0], |
643 |
|
|
atomTransData[1], |
644 |
|
|
atomTransData[2], |
645 |
|
|
atomTransData[3], |
646 |
|
|
atomTransData[4], |
647 |
|
|
atomTransData[5]); |
648 |
tim |
837 |
|
649 |
gezelter |
907 |
strcpy( writeLine, tempBuffer ); |
650 |
tim |
837 |
|
651 |
gezelter |
907 |
if (isDirectional) { |
652 |
tim |
837 |
|
653 |
gezelter |
907 |
sprintf( tempBuffer, |
654 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
655 |
|
|
atomOrientData[0], |
656 |
|
|
atomOrientData[1], |
657 |
|
|
atomOrientData[2], |
658 |
|
|
atomOrientData[3], |
659 |
|
|
atomOrientData[4], |
660 |
|
|
atomOrientData[5], |
661 |
|
|
atomOrientData[6]); |
662 |
|
|
strcat( writeLine, tempBuffer ); |
663 |
tim |
837 |
|
664 |
gezelter |
907 |
} else { |
665 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
666 |
|
|
} |
667 |
tim |
837 |
|
668 |
gezelter |
907 |
finalOut << writeLine; |
669 |
|
|
finalOut.flush(); |
670 |
|
|
} |
671 |
mmeineke |
377 |
} |
672 |
|
|
|
673 |
gezelter |
907 |
finalOut.flush(); |
674 |
|
|
sprintf( checkPointMsg, |
675 |
|
|
"Sucessfully took a dump.\n"); |
676 |
|
|
MPIcheckPoint(); |
677 |
|
|
|
678 |
gezelter |
415 |
} else { |
679 |
tim |
837 |
|
680 |
gezelter |
907 |
// worldRank != 0, so I'm a remote node. |
681 |
|
|
|
682 |
|
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
683 |
|
|
|
684 |
|
|
// Am I the node which has this atom? |
685 |
|
|
|
686 |
|
|
if (AtomToProcMap[i] == worldRank) { |
687 |
mmeineke |
440 |
|
688 |
gezelter |
907 |
local_index=-1; |
689 |
|
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
690 |
|
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
691 |
|
|
} |
692 |
|
|
if (local_index != -1) { |
693 |
|
|
|
694 |
|
|
atomTypeString = atoms[local_index]->getType(); |
695 |
tim |
837 |
|
696 |
gezelter |
907 |
atoms[local_index]->getPos(pos); |
697 |
|
|
atoms[local_index]->getVel(vel); |
698 |
tim |
837 |
|
699 |
gezelter |
907 |
atomTransData[0] = pos[0]; |
700 |
|
|
atomTransData[1] = pos[1]; |
701 |
|
|
atomTransData[2] = pos[2]; |
702 |
tim |
837 |
|
703 |
gezelter |
907 |
atomTransData[3] = vel[0]; |
704 |
|
|
atomTransData[4] = vel[1]; |
705 |
|
|
atomTransData[5] = vel[2]; |
706 |
|
|
|
707 |
|
|
isDirectional = 0; |
708 |
tim |
837 |
|
709 |
gezelter |
907 |
if( atoms[local_index]->isDirectional() ){ |
710 |
mmeineke |
377 |
|
711 |
gezelter |
907 |
isDirectional = 1; |
712 |
|
|
|
713 |
|
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
714 |
|
|
dAtom->getQ( q ); |
715 |
|
|
|
716 |
|
|
atomOrientData[0] = q[0]; |
717 |
|
|
atomOrientData[1] = q[1]; |
718 |
|
|
atomOrientData[2] = q[2]; |
719 |
|
|
atomOrientData[3] = q[3]; |
720 |
mmeineke |
670 |
|
721 |
gezelter |
907 |
atomOrientData[4] = dAtom->getJx(); |
722 |
|
|
atomOrientData[5] = dAtom->getJy(); |
723 |
|
|
atomOrientData[6] = dAtom->getJz(); |
724 |
|
|
} |
725 |
tim |
837 |
|
726 |
gezelter |
907 |
} else { |
727 |
|
|
sprintf(painCave.errMsg, |
728 |
|
|
"Atom %d not found on processor %d\n", |
729 |
|
|
i, worldRank ); |
730 |
|
|
haveError= 1; |
731 |
|
|
simError(); |
732 |
|
|
} |
733 |
tim |
837 |
|
734 |
gezelter |
907 |
// I've survived this far, so send off the data! |
735 |
tim |
837 |
|
736 |
gezelter |
907 |
atomTypeTag = 4*i; |
737 |
|
|
atomIsDirectionalTag = 4*i + 1; |
738 |
|
|
atomTransDataTag = 4*i + 2; |
739 |
|
|
atomOrientDataTag = 4*i + 3; |
740 |
tim |
837 |
|
741 |
gezelter |
907 |
MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
742 |
|
|
atomTypeTag, MPI_COMM_WORLD); |
743 |
|
|
|
744 |
|
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
745 |
|
|
atomIsDirectionalTag, MPI_COMM_WORLD); |
746 |
|
|
|
747 |
|
|
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
748 |
|
|
atomTransDataTag, MPI_COMM_WORLD); |
749 |
|
|
|
750 |
|
|
if (isDirectional) { |
751 |
|
|
|
752 |
|
|
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
753 |
|
|
atomOrientDataTag, MPI_COMM_WORLD); |
754 |
|
|
|
755 |
|
|
} |
756 |
|
|
|
757 |
mmeineke |
377 |
} |
758 |
gezelter |
907 |
} |
759 |
mmeineke |
440 |
|
760 |
gezelter |
907 |
sprintf( checkPointMsg, |
761 |
|
|
"Sucessfully wrote final file.\n"); |
762 |
|
|
MPIcheckPoint(); |
763 |
|
|
|
764 |
gezelter |
419 |
} |
765 |
gezelter |
907 |
|
766 |
|
|
painCave.isEventLoop = 0; |
767 |
tim |
837 |
|
768 |
|
|
if( worldRank == 0 ) finalOut.close(); |
769 |
mmeineke |
377 |
#endif // is_mpi |
770 |
|
|
} |
771 |
mmeineke |
440 |
|
772 |
|
|
|
773 |
|
|
|
774 |
|
|
#ifdef IS_MPI |
775 |
|
|
|
776 |
|
|
// a couple of functions to let us escape the write loop |
777 |
|
|
|
778 |
gezelter |
907 |
void dWrite::DieDieDie( void ){ |
779 |
tim |
837 |
|
780 |
mmeineke |
440 |
MPI_Finalize(); |
781 |
|
|
exit (0); |
782 |
|
|
} |
783 |
|
|
|
784 |
|
|
#endif //is_mpi |