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#define _FILE_OFFSET_BITS 64 |
2 |
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|
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#include <cstring> |
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#include <iostream> |
5 |
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#include <fstream> |
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|
7 |
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#ifdef IS_MPI |
8 |
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#include <mpi.h> |
7 |
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#include <mpi++.h> |
9 |
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#include "mpiSimulation.hpp" |
10 |
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#define TAKE_THIS_TAG_CHAR 1 |
11 |
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#define TAKE_THIS_TAG_INT 2 |
29 |
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if(worldRank == 0 ){ |
30 |
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#endif // is_mpi |
31 |
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|
31 |
– |
|
32 |
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|
32 |
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strcpy( outName, entry_plug->sampleName ); |
33 |
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|
34 |
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outFile.open(outName, ios::out | ios::trunc ); |
41 |
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painCave.isFatal = 1; |
42 |
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simError(); |
43 |
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} |
44 |
< |
|
44 |
> |
|
45 |
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//outFile.setf( ios::scientific ); |
46 |
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|
47 |
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#ifdef IS_MPI |
72 |
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char tempBuffer[BUFFERSIZE]; |
73 |
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char writeLine[BUFFERSIZE]; |
74 |
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|
75 |
< |
int i, j, which_node, done, game_over, which_atom, local_index; |
75 |
> |
int i, j, which_node, done, which_atom, local_index; |
76 |
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double q[4]; |
77 |
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DirectionalAtom* dAtom; |
78 |
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int nAtoms = entry_plug->n_atoms; |
79 |
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Atom** atoms = entry_plug->atoms; |
80 |
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|
81 |
+ |
double pos[3], vel[3]; |
82 |
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|
83 |
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|
84 |
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#ifndef IS_MPI |
85 |
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|
86 |
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outFile << nAtoms << "\n"; |
87 |
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|
88 |
< |
outFile << currentTime << "\t" |
89 |
< |
<< entry_plug->box_x << "\t" |
90 |
< |
<< entry_plug->box_y << "\t" |
91 |
< |
<< entry_plug->box_z << "\n"; |
88 |
> |
outFile << currentTime << ";\t" |
89 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
90 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
91 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
92 |
> |
|
93 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
94 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
95 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
96 |
> |
|
97 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
98 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
99 |
> |
<< entry_plug->Hmat[2][2] << ";\n"; |
100 |
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|
101 |
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for( i=0; i<nAtoms; i++ ){ |
102 |
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|
103 |
+ |
atoms[i]->getPos(pos); |
104 |
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atoms[i]->getVel(vel); |
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|
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sprintf( tempBuffer, |
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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(), |
109 |
< |
atoms[i]->getX(), |
110 |
< |
atoms[i]->getY(), |
111 |
< |
atoms[i]->getZ(), |
112 |
< |
atoms[i]->get_vx(), |
113 |
< |
atoms[i]->get_vy(), |
114 |
< |
atoms[i]->get_vz()); |
109 |
> |
pos[0], |
110 |
> |
pos[1], |
111 |
> |
pos[2], |
112 |
> |
vel[0], |
113 |
> |
vel[1], |
114 |
> |
vel[2]); |
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strcpy( writeLine, tempBuffer ); |
116 |
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|
117 |
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if( atoms[i]->isDirectional() ){ |
145 |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
146 |
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int haveError; |
147 |
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|
148 |
< |
MPI::Status istatus; |
148 |
> |
MPI_Status istatus; |
149 |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
150 |
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|
151 |
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// write out header and node 0's coordinates |
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|
153 |
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if( worldRank == 0 ){ |
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outFile << mpiSim->getTotAtoms() << "\n"; |
155 |
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|
156 |
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outFile << currentTime << ";\t" |
157 |
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<< entry_plug->Hmat[0][0] << "\t" |
158 |
+ |
<< entry_plug->Hmat[1][0] << "\t" |
159 |
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<< entry_plug->Hmat[2][0] << ";\t" |
160 |
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|
161 |
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<< entry_plug->Hmat[0][1] << "\t" |
162 |
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<< entry_plug->Hmat[1][1] << "\t" |
163 |
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<< entry_plug->Hmat[2][1] << ";\t" |
164 |
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|
165 |
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<< entry_plug->Hmat[0][2] << "\t" |
166 |
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<< entry_plug->Hmat[1][2] << "\t" |
167 |
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<< entry_plug->Hmat[2][2] << ";\n"; |
168 |
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|
145 |
– |
outFile << currentTime << "\t" |
146 |
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<< entry_plug->box_x << "\t" |
147 |
– |
<< entry_plug->box_y << "\t" |
148 |
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<< entry_plug->box_z << "\n"; |
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outFile.flush(); |
170 |
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for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
171 |
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// Get the Node number which has this atom; |
182 |
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} |
183 |
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if (local_index != -1) { |
184 |
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//format the line |
185 |
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|
186 |
+ |
atoms[local_index]->getPos(pos); |
187 |
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atoms[local_index]->getVel(vel); |
188 |
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|
189 |
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sprintf( tempBuffer, |
190 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
191 |
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atoms[local_index]->getType(), |
192 |
< |
atoms[local_index]->getX(), |
193 |
< |
atoms[local_index]->getY(), |
194 |
< |
atoms[local_index]->getZ(), |
195 |
< |
atoms[local_index]->get_vx(), |
196 |
< |
atoms[local_index]->get_vy(), |
197 |
< |
atoms[local_index]->get_vz()); // check here. |
192 |
> |
pos[0], |
193 |
> |
pos[1], |
194 |
> |
pos[2], |
195 |
> |
vel[0], |
196 |
> |
vel[1], |
197 |
> |
vel[2]); // check here. |
198 |
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strcpy( writeLine, tempBuffer ); |
199 |
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|
200 |
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if( atoms[local_index]->isDirectional() ){ |
230 |
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} |
231 |
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else { |
232 |
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myStatus = 1; |
233 |
< |
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
234 |
< |
TAKE_THIS_TAG_INT); |
235 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
236 |
< |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
237 |
< |
TAKE_THIS_TAG_CHAR, istatus); |
238 |
< |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, |
239 |
< |
TAKE_THIS_TAG_INT, istatus); |
233 |
> |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
234 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
235 |
> |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
236 |
> |
MPI_COMM_WORLD); |
237 |
> |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
238 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
239 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
240 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
241 |
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|
242 |
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if(!myStatus) nodeZeroError(); |
243 |
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|
250 |
|
// kill everyone off: |
251 |
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myStatus = -1; |
252 |
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
253 |
< |
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, j, |
254 |
< |
TAKE_THIS_TAG_INT); |
253 |
> |
MPI_Send(&myStatus, 1, MPI_INT, j, |
254 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
255 |
|
} |
256 |
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|
257 |
|
} else { |
259 |
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done = 0; |
260 |
|
while (!done) { |
261 |
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|
262 |
< |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
263 |
< |
TAKE_THIS_TAG_INT, istatus); |
262 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
263 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
264 |
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|
265 |
|
if(!myStatus) anonymousNodeDie(); |
266 |
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|
267 |
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if(myStatus < 0) break; |
268 |
|
|
269 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
270 |
< |
TAKE_THIS_TAG_INT, istatus); |
269 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
270 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
271 |
|
|
272 |
|
myStatus = 1; |
273 |
|
local_index=-1; |
276 |
|
} |
277 |
|
if (local_index != -1) { |
278 |
|
//format the line |
279 |
+ |
|
280 |
+ |
atoms[local_index]->getPos(pos); |
281 |
+ |
atoms[local_index]->getVel(vel); |
282 |
+ |
|
283 |
|
sprintf( tempBuffer, |
284 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
285 |
|
atoms[local_index]->getType(), |
286 |
< |
atoms[local_index]->getX(), |
287 |
< |
atoms[local_index]->getY(), |
288 |
< |
atoms[local_index]->getZ(), |
289 |
< |
atoms[local_index]->get_vx(), |
290 |
< |
atoms[local_index]->get_vy(), |
291 |
< |
atoms[local_index]->get_vz()); // check here. |
286 |
> |
pos[0], |
287 |
> |
pos[1], |
288 |
> |
pos[2], |
289 |
> |
vel[0], |
290 |
> |
vel[1], |
291 |
> |
vel[2]); // check here. |
292 |
|
strcpy( writeLine, tempBuffer ); |
293 |
|
|
294 |
|
if( atoms[local_index]->isDirectional() ){ |
321 |
|
strcpy( writeLine, "Hello, I'm an error.\n"); |
322 |
|
} |
323 |
|
|
324 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
325 |
< |
TAKE_THIS_TAG_CHAR); |
326 |
< |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
327 |
< |
TAKE_THIS_TAG_INT); |
324 |
> |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
325 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
326 |
> |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
327 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
328 |
|
} |
329 |
|
} |
330 |
|
outFile.flush(); |
338 |
|
#endif // is_mpi |
339 |
|
} |
340 |
|
|
341 |
< |
void DumpWriter::writeFinal(){ |
341 |
> |
void DumpWriter::writeFinal(double finalTime){ |
342 |
|
|
343 |
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char finalName[500]; |
344 |
|
ofstream finalOut; |
353 |
|
Atom** atoms = entry_plug->atoms; |
354 |
|
int i, j, which_node, done, game_over, which_atom, local_index; |
355 |
|
|
356 |
+ |
double pos[3], vel[3]; |
357 |
|
|
358 |
|
#ifdef IS_MPI |
359 |
|
if(worldRank == 0 ){ |
385 |
|
|
386 |
|
finalOut << nAtoms << "\n"; |
387 |
|
|
388 |
< |
finalOut << entry_plug->box_x << "\t" |
389 |
< |
<< entry_plug->box_y << "\t" |
390 |
< |
<< entry_plug->box_z << "\n"; |
388 |
> |
finalOut << finalTime << ";\t" |
389 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
390 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
391 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
392 |
> |
|
393 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
394 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
395 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
396 |
> |
|
397 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
398 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
399 |
> |
<< entry_plug->Hmat[2][2] << ";\n"; |
400 |
|
|
401 |
|
for( i=0; i<nAtoms; i++ ){ |
402 |
|
|
403 |
+ |
atoms[i]->getPos(pos); |
404 |
+ |
atoms[i]->getVel(vel); |
405 |
+ |
|
406 |
|
sprintf( tempBuffer, |
407 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
408 |
|
atoms[i]->getType(), |
409 |
< |
atoms[i]->getX(), |
410 |
< |
atoms[i]->getY(), |
411 |
< |
atoms[i]->getZ(), |
412 |
< |
atoms[i]->get_vx(), |
413 |
< |
atoms[i]->get_vy(), |
414 |
< |
atoms[i]->get_vz()); |
409 |
> |
pos[0], |
410 |
> |
pos[1], |
411 |
> |
pos[2], |
412 |
> |
vel[0], |
413 |
> |
vel[1], |
414 |
> |
vel[2]); |
415 |
|
strcpy( writeLine, tempBuffer ); |
416 |
|
|
417 |
|
if( atoms[i]->isDirectional() ){ |
446 |
|
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
447 |
|
int haveError; |
448 |
|
|
449 |
< |
MPI::Status istatus; |
449 |
> |
MPI_Status istatus; |
450 |
|
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
451 |
|
|
452 |
|
// write out header and node 0's coordinates |
455 |
|
if( worldRank == 0 ){ |
456 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
457 |
|
|
458 |
< |
finalOut << entry_plug->box_x << "\t" |
459 |
< |
<< entry_plug->box_y << "\t" |
460 |
< |
<< entry_plug->box_z << "\n"; |
458 |
> |
finalOut << finalTime << ";\t" |
459 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
460 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
461 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
462 |
> |
|
463 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
464 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
465 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
466 |
> |
|
467 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
468 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
469 |
> |
<< entry_plug->Hmat[2][2] << ";\n"; |
470 |
|
|
471 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
472 |
|
// Get the Node number which has this molecule: |
480 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
481 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
482 |
|
} |
483 |
< |
if (local_index != -1) { |
483 |
> |
if (local_index != -1) { |
484 |
> |
|
485 |
> |
atoms[local_index]->getPos(pos); |
486 |
> |
atoms[local_index]->getVel(vel); |
487 |
> |
|
488 |
|
sprintf( tempBuffer, |
489 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
490 |
|
atoms[local_index]->getType(), |
491 |
< |
atoms[local_index]->getX(), |
492 |
< |
atoms[local_index]->getY(), |
493 |
< |
atoms[local_index]->getZ(), |
494 |
< |
atoms[local_index]->get_vx(), |
495 |
< |
atoms[local_index]->get_vy(), |
496 |
< |
atoms[local_index]->get_vz()); |
491 |
> |
pos[0], |
492 |
> |
pos[1], |
493 |
> |
pos[2], |
494 |
> |
vel[0], |
495 |
> |
vel[1], |
496 |
> |
vel[2]); |
497 |
|
strcpy( writeLine, tempBuffer ); |
498 |
|
|
499 |
|
if( atoms[local_index]->isDirectional() ){ |
529 |
|
else { |
530 |
|
|
531 |
|
myStatus = 1; |
532 |
< |
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
533 |
< |
TAKE_THIS_TAG_INT); |
534 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
535 |
< |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
536 |
< |
TAKE_THIS_TAG_CHAR, istatus); |
537 |
< |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, |
538 |
< |
TAKE_THIS_TAG_INT, istatus); |
532 |
> |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
533 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
534 |
> |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
535 |
> |
MPI_COMM_WORLD); |
536 |
> |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
537 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
538 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
539 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
540 |
|
|
541 |
|
if(!myStatus) nodeZeroError(); |
542 |
|
} |
547 |
|
// kill everyone off: |
548 |
|
myStatus = -1; |
549 |
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
550 |
< |
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, j, |
551 |
< |
TAKE_THIS_TAG_INT); |
550 |
> |
MPI_Send(&myStatus, 1, MPI_INT, j, |
551 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
552 |
|
} |
553 |
|
|
554 |
|
} else { |
556 |
|
done = 0; |
557 |
|
while (!done) { |
558 |
|
|
559 |
< |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
560 |
< |
TAKE_THIS_TAG_INT, istatus); |
559 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
560 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
561 |
|
|
562 |
|
if(!myStatus) anonymousNodeDie(); |
563 |
|
|
564 |
|
if(myStatus < 0) break; |
565 |
|
|
566 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
567 |
< |
TAKE_THIS_TAG_INT, istatus); |
566 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
567 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
568 |
|
|
569 |
|
myStatus = 1; |
570 |
|
local_index=-1; |
573 |
|
} |
574 |
|
if (local_index != -1) { |
575 |
|
|
576 |
+ |
atoms[local_index]->getPos(pos); |
577 |
+ |
atoms[local_index]->getVel(vel); |
578 |
+ |
|
579 |
|
//format the line |
580 |
|
sprintf( tempBuffer, |
581 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
582 |
|
atoms[local_index]->getType(), |
583 |
< |
atoms[local_index]->getX(), |
584 |
< |
atoms[local_index]->getY(), |
585 |
< |
atoms[local_index]->getZ(), |
586 |
< |
atoms[local_index]->get_vx(), |
587 |
< |
atoms[local_index]->get_vy(), |
588 |
< |
atoms[local_index]->get_vz()); // check here. |
583 |
> |
pos[0], |
584 |
> |
pos[1], |
585 |
> |
pos[2], |
586 |
> |
vel[0], |
587 |
> |
vel[1], |
588 |
> |
vel[2]); // check here. |
589 |
|
strcpy( writeLine, tempBuffer ); |
590 |
|
|
591 |
|
if( atoms[local_index]->isDirectional() ){ |
618 |
|
strcpy( writeLine, "Hello, I'm an error.\n"); |
619 |
|
} |
620 |
|
|
621 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
622 |
< |
TAKE_THIS_TAG_CHAR); |
623 |
< |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
624 |
< |
TAKE_THIS_TAG_INT); |
621 |
> |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
622 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
623 |
> |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
624 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
625 |
|
} |
626 |
|
} |
627 |
|
finalOut.flush(); |
644 |
|
|
645 |
|
myStatus = 0; |
646 |
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
647 |
< |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
648 |
< |
TAKE_THIS_TAG_INT); |
647 |
> |
MPI_Send( &myStatus, 1, MPI_INT, j, |
648 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
649 |
|
} |
650 |
|
|
651 |
|
|