# | Line 1 | Line 1 | |
---|---|---|
1 | < | #include <cstring> |
1 | > | #define _FILE_OFFSET_BITS 64 |
2 | > | |
3 | > | #include <string.h> |
4 | #include <iostream> | |
5 | #include <fstream> | |
6 | ||
7 | #ifdef IS_MPI | |
8 | #include <mpi.h> | |
7 | – | #include <mpi++.h> |
9 | #include "mpiSimulation.hpp" | |
10 | < | #define TAKE_THIS_TAG 1 |
10 | > | |
11 | > | namespace dWrite{ |
12 | > | void DieDieDie( void ); |
13 | > | } |
14 | > | |
15 | > | using namespace dWrite; |
16 | #endif //is_mpi | |
17 | ||
18 | #include "ReadWrite.hpp" | |
# | Line 19 | Line 25 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ | |
25 | #ifdef IS_MPI | |
26 | if(worldRank == 0 ){ | |
27 | #endif // is_mpi | |
28 | < | |
23 | < | |
24 | < | |
28 | > | |
29 | strcpy( outName, entry_plug->sampleName ); | |
30 | < | |
30 | > | |
31 | outFile.open(outName, ios::out | ios::trunc ); | |
32 | < | |
32 | > | |
33 | if( !outFile ){ | |
34 | < | |
34 | > | |
35 | sprintf( painCave.errMsg, | |
36 | "Could not open \"%s\" for dump output.\n", | |
37 | outName); | |
38 | painCave.isFatal = 1; | |
39 | simError(); | |
40 | } | |
41 | < | |
41 | > | |
42 | //outFile.setf( ios::scientific ); | |
43 | ||
44 | #ifdef IS_MPI | |
# | Line 60 | Line 64 | void DumpWriter::writeDump( double currentTime ){ | |
64 | } | |
65 | ||
66 | void DumpWriter::writeDump( double currentTime ){ | |
67 | < | |
67 | > | |
68 | const int BUFFERSIZE = 2000; | |
69 | + | const int MINIBUFFERSIZE = 100; |
70 | + | |
71 | char tempBuffer[BUFFERSIZE]; | |
72 | char writeLine[BUFFERSIZE]; | |
73 | ||
74 | < | int i, j, which_node, done, game_over, which_atom, local_index; |
74 | > | int i; |
75 | > | #ifdef IS_MPI |
76 | > | int j, which_node, done, which_atom, local_index; |
77 | > | double atomTransData[6]; |
78 | > | double atomOrientData[7]; |
79 | > | int isDirectional; |
80 | > | char* atomTypeString; |
81 | > | char MPIatomTypeString[MINIBUFFERSIZE]; |
82 | > | int me; |
83 | > | int atomTypeTag; |
84 | > | int atomIsDirectionalTag; |
85 | > | int atomTransDataTag; |
86 | > | int atomOrientDataTag; |
87 | > | #else //is_mpi |
88 | > | int nAtoms = entry_plug->n_atoms; |
89 | > | #endif //is_mpi |
90 | > | |
91 | double q[4]; | |
92 | DirectionalAtom* dAtom; | |
71 | – | int nAtoms = entry_plug->n_atoms; |
93 | Atom** atoms = entry_plug->atoms; | |
94 | < | |
94 | > | double pos[3], vel[3]; |
95 | ||
96 | + | // write current frame to the eor file |
97 | + | |
98 | + | this->writeFinal( currentTime ); |
99 | + | |
100 | #ifndef IS_MPI | |
101 | < | |
101 | > | |
102 | outFile << nAtoms << "\n"; | |
103 | < | |
104 | < | outFile << currentTime << "\t" |
105 | < | << entry_plug->box_x << "\t" |
106 | < | << entry_plug->box_y << "\t" |
107 | < | << entry_plug->box_z << "\n"; |
108 | < | |
103 | > | |
104 | > | outFile << currentTime << ";\t" |
105 | > | << entry_plug->Hmat[0][0] << "\t" |
106 | > | << entry_plug->Hmat[1][0] << "\t" |
107 | > | << entry_plug->Hmat[2][0] << ";\t" |
108 | > | |
109 | > | << entry_plug->Hmat[0][1] << "\t" |
110 | > | << entry_plug->Hmat[1][1] << "\t" |
111 | > | << entry_plug->Hmat[2][1] << ";\t" |
112 | > | |
113 | > | << entry_plug->Hmat[0][2] << "\t" |
114 | > | << entry_plug->Hmat[1][2] << "\t" |
115 | > | << entry_plug->Hmat[2][2] << ";"; |
116 | > | //write out additional parameters, such as chi and eta |
117 | > | outFile << entry_plug->the_integrator->getAdditionalParameters(); |
118 | > | outFile << endl; |
119 | > | |
120 | for( i=0; i<nAtoms; i++ ){ | |
85 | – | |
121 | ||
122 | + | atoms[i]->getPos(pos); |
123 | + | atoms[i]->getVel(vel); |
124 | + | |
125 | sprintf( tempBuffer, | |
126 | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", | |
127 | atoms[i]->getType(), | |
128 | < | atoms[i]->getX(), |
129 | < | atoms[i]->getY(), |
130 | < | atoms[i]->getZ(), |
131 | < | atoms[i]->get_vx(), |
132 | < | atoms[i]->get_vy(), |
133 | < | atoms[i]->get_vz()); |
128 | > | pos[0], |
129 | > | pos[1], |
130 | > | pos[2], |
131 | > | vel[0], |
132 | > | vel[1], |
133 | > | vel[2]); |
134 | strcpy( writeLine, tempBuffer ); | |
135 | ||
136 | if( atoms[i]->isDirectional() ){ | |
137 | < | |
137 | > | |
138 | dAtom = (DirectionalAtom *)atoms[i]; | |
139 | dAtom->getQ( q ); | |
140 | < | |
140 | > | |
141 | sprintf( tempBuffer, | |
142 | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", | |
143 | q[0], | |
# | Line 113 | Line 151 | void DumpWriter::writeDump( double currentTime ){ | |
151 | } | |
152 | else | |
153 | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); | |
154 | < | |
154 | > | |
155 | outFile << writeLine; | |
156 | } | |
157 | outFile.flush(); | |
158 | ||
159 | #else // is_mpi | |
160 | ||
161 | < | MPI::Status istatus; |
161 | > | /* code to find maximum tag value */ |
162 | > | int *tagub, flag, MAXTAG; |
163 | > | MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
164 | > | if (flag) { |
165 | > | MAXTAG = *tagub; |
166 | > | } else { |
167 | > | MAXTAG = 32767; |
168 | > | } |
169 | > | |
170 | > | int haveError; |
171 | > | |
172 | > | MPI_Status istatus; |
173 | int *AtomToProcMap = mpiSim->getAtomToProcMap(); | |
174 | < | |
174 | > | |
175 | // write out header and node 0's coordinates | |
176 | < | |
176 | > | |
177 | if( worldRank == 0 ){ | |
178 | outFile << mpiSim->getTotAtoms() << "\n"; | |
179 | < | |
180 | < | outFile << currentTime << "\t" |
181 | < | << entry_plug->box_x << "\t" |
182 | < | << entry_plug->box_y << "\t" |
183 | < | << entry_plug->box_z << "\n"; |
179 | > | |
180 | > | outFile << currentTime << ";\t" |
181 | > | << entry_plug->Hmat[0][0] << "\t" |
182 | > | << entry_plug->Hmat[1][0] << "\t" |
183 | > | << entry_plug->Hmat[2][0] << ";\t" |
184 | > | |
185 | > | << entry_plug->Hmat[0][1] << "\t" |
186 | > | << entry_plug->Hmat[1][1] << "\t" |
187 | > | << entry_plug->Hmat[2][1] << ";\t" |
188 | > | |
189 | > | << entry_plug->Hmat[0][2] << "\t" |
190 | > | << entry_plug->Hmat[1][2] << "\t" |
191 | > | << entry_plug->Hmat[2][2] << ";"; |
192 | > | |
193 | > | outFile << entry_plug->the_integrator->getAdditionalParameters(); |
194 | > | outFile << endl; |
195 | outFile.flush(); | |
196 | + | |
197 | + | tag = 0; |
198 | + | |
199 | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { | |
200 | + | |
201 | + | if (tag + 2 >= MAXTAG) { |
202 | + | // The tag was going to exceed the maximum value, so wrap around to 0: |
203 | + | tag = 0; |
204 | + | // Send the newly zeroed tag on to the other nodes: |
205 | + | MPI_Bcast(&tag, 1, MPI_INT, 0, MPI_COMM_WORLD); |
206 | + | } |
207 | + | |
208 | // Get the Node number which has this atom; | |
209 | ||
210 | < | which_node = AtomToProcMap[i]; |
210 | > | which_node = AtomToProcMap[i]; |
211 | ||
212 | < | if (which_node == mpiSim->getMyNode()) { |
213 | < | sprintf( tempBuffer, |
214 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
215 | < | atoms[i]->getType(), |
216 | < | atoms[i]->getX(), |
217 | < | atoms[i]->getY(), |
218 | < | atoms[i]->getZ(), |
219 | < | atoms[i]->get_vx(), |
220 | < | atoms[i]->get_vy(), |
221 | < | atoms[i]->get_vz()); |
212 | > | if (which_node != 0) { |
213 | > | |
214 | > | MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
215 | > | atomTypeTag, MPI_COMM_WORLD, &istatus); |
216 | > | |
217 | > | strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
218 | > | |
219 | > | // Null terminate the atomTypeString just in case: |
220 | > | |
221 | > | atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
222 | > | |
223 | > | MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
224 | > | atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
225 | > | |
226 | > | MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
227 | > | atomTransDataTag, MPI_COMM_WORLD, &istatus); |
228 | > | |
229 | > | if (isDirectional) { |
230 | > | |
231 | > | MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
232 | > | atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
233 | > | |
234 | > | } |
235 | > | |
236 | > | } else { |
237 | > | |
238 | > | haveError = 0; |
239 | > | which_atom = i; |
240 | > | local_index=-1; |
241 | > | |
242 | > | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
243 | > | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
244 | > | } |
245 | > | |
246 | > | if (local_index != -1) { |
247 | > | |
248 | > | atomTypeString = atoms[local_index]->getType(); |
249 | > | |
250 | > | atoms[local_index]->getPos(pos); |
251 | > | atoms[local_index]->getVel(vel); |
252 | > | |
253 | > | atomTransData[0] = pos[0]; |
254 | > | atomTransData[1] = pos[1]; |
255 | > | atomTransData[2] = pos[2]; |
256 | > | |
257 | > | atomTransData[3] = vel[0]; |
258 | > | atomTransData[4] = vel[1]; |
259 | > | atomTransData[5] = vel[2]; |
260 | > | |
261 | > | isDirectional = 0; |
262 | > | |
263 | > | if( atoms[local_index]->isDirectional() ){ |
264 | > | |
265 | > | isDirectional = 1; |
266 | > | |
267 | > | dAtom = (DirectionalAtom *)atoms[local_index]; |
268 | > | dAtom->getQ( q ); |
269 | > | |
270 | > | atomOrientData[0] = q[0]; |
271 | > | atomOrientData[1] = q[1]; |
272 | > | atomOrientData[2] = q[2]; |
273 | > | atomOrientData[3] = q[3]; |
274 | > | |
275 | > | atomOrientData[4] = dAtom->getJx(); |
276 | > | atomOrientData[5] = dAtom->getJy(); |
277 | > | atomOrientData[6] = dAtom->getJz(); |
278 | > | } |
279 | > | |
280 | > | } else { |
281 | > | sprintf(painCave.errMsg, |
282 | > | "Atom %d not found on processor %d\n", |
283 | > | i, worldRank ); |
284 | > | haveError= 1; |
285 | > | simError(); |
286 | > | } |
287 | > | |
288 | > | if(haveError) DieDieDie(); |
289 | > | |
290 | > | // If we've survived to here, format the line: |
291 | > | |
292 | > | sprintf( tempBuffer, |
293 | > | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
294 | > | atomTypeString, |
295 | > | atomTransData[0], |
296 | > | atomTransData[1], |
297 | > | atomTransData[2], |
298 | > | atomTransData[3], |
299 | > | atomTransData[4], |
300 | > | atomTransData[5]); |
301 | > | |
302 | strcpy( writeLine, tempBuffer ); | |
303 | < | |
304 | < | if( atoms[i]->isDirectional() ){ |
305 | < | |
155 | < | dAtom = (DirectionalAtom *)atoms[i]; |
156 | < | dAtom->getQ( q ); |
157 | < | |
303 | > | |
304 | > | if (isDirectional) { |
305 | > | |
306 | sprintf( tempBuffer, | |
307 | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", | |
308 | < | q[0], |
309 | < | q[1], |
310 | < | q[2], |
311 | < | q[3], |
312 | < | dAtom->getJx(), |
313 | < | dAtom->getJy(), |
314 | < | dAtom->getJz()); |
308 | > | atomOrientData[0], |
309 | > | atomOrientData[1], |
310 | > | atomOrientData[2], |
311 | > | atomOrientData[3], |
312 | > | atomOrientData[4], |
313 | > | atomOrientData[5], |
314 | > | atomOrientData[6]); |
315 | strcat( writeLine, tempBuffer ); | |
316 | + | |
317 | + | } else { |
318 | + | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
319 | } | |
320 | < | else |
321 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
322 | < | |
172 | < | } else { |
173 | < | |
174 | < | std::cerr << "node 0: sending node " << which_node << " request for atom " << i << "\n"; |
175 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
176 | < | std::cerr << "node 0: sent!\n"; |
177 | < | MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
178 | < | TAKE_THIS_TAG, istatus); |
179 | < | std::cerr << "node 0: got this line: " << writeLine; |
320 | > | |
321 | > | outFile << writeLine; |
322 | > | outFile.flush(); |
323 | } | |
181 | – | |
182 | – | outFile << writeLine; |
183 | – | outFile.flush(); |
324 | } | |
185 | – | |
186 | – | // kill everyone off: |
187 | – | game_over = -1; |
188 | – | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
189 | – | MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
190 | – | } |
325 | ||
326 | + | outFile.flush(); |
327 | + | sprintf( checkPointMsg, |
328 | + | "Sucessfully took a dump.\n"); |
329 | + | MPIcheckPoint(); |
330 | + | |
331 | } else { | |
332 | + | |
333 | + | // worldRank != 0, so I'm a remote node. |
334 | ||
335 | < | done = 0; |
336 | < | while (!done) { |
337 | < | std::cerr << "node: " << mpiSim->getMyNode() << " Waiting for receive \n"; |
338 | < | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
339 | < | TAKE_THIS_TAG, istatus); |
340 | < | std::cerr << "node: " << mpiSim->getMyNode() << " got request for atom " << which_atom << "\n"; |
341 | < | if (which_atom == -1) { |
342 | < | done=1; |
202 | < | continue; |
203 | < | } else { |
204 | < | local_index=-1; |
205 | < | for (j=0; j < mpiSim->getMyNlocal(); j++) { |
335 | > | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
336 | > | |
337 | > | // Am I the node which has this atom? |
338 | > | |
339 | > | if (AtomToProcMap[i] == worldRank) { |
340 | > | |
341 | > | local_index=-1; |
342 | > | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
343 | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; | |
344 | } | |
345 | if (local_index != -1) { | |
346 | < | //format the line |
347 | < | sprintf( tempBuffer, |
348 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
349 | < | atoms[local_index]->getType(), |
350 | < | atoms[local_index]->getX(), |
351 | < | atoms[local_index]->getY(), |
352 | < | atoms[local_index]->getZ(), |
353 | < | atoms[local_index]->get_vx(), |
354 | < | atoms[local_index]->get_vy(), |
355 | < | atoms[local_index]->get_vz()); // check here. |
356 | < | strcpy( writeLine, tempBuffer ); |
357 | < | |
346 | > | |
347 | > | atomTypeString = atoms[local_index]->getType(); |
348 | > | |
349 | > | atoms[local_index]->getPos(pos); |
350 | > | atoms[local_index]->getVel(vel); |
351 | > | |
352 | > | atomTransData[0] = pos[0]; |
353 | > | atomTransData[1] = pos[1]; |
354 | > | atomTransData[2] = pos[2]; |
355 | > | |
356 | > | atomTransData[3] = vel[0]; |
357 | > | atomTransData[4] = vel[1]; |
358 | > | atomTransData[5] = vel[2]; |
359 | > | |
360 | > | isDirectional = 0; |
361 | > | |
362 | if( atoms[local_index]->isDirectional() ){ | |
363 | + | |
364 | + | isDirectional = 1; |
365 | ||
366 | dAtom = (DirectionalAtom *)atoms[local_index]; | |
367 | dAtom->getQ( q ); | |
368 | ||
369 | < | sprintf( tempBuffer, |
370 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
371 | < | q[0], |
372 | < | q[1], |
373 | < | q[2], |
374 | < | q[3], |
375 | < | dAtom->getJx(), |
376 | < | dAtom->getJy(), |
234 | < | dAtom->getJz()); |
235 | < | strcat( writeLine, tempBuffer ); |
369 | > | atomOrientData[0] = q[0]; |
370 | > | atomOrientData[1] = q[1]; |
371 | > | atomOrientData[2] = q[2]; |
372 | > | atomOrientData[3] = q[3]; |
373 | > | |
374 | > | atomOrientData[4] = dAtom->getJx(); |
375 | > | atomOrientData[5] = dAtom->getJy(); |
376 | > | atomOrientData[6] = dAtom->getJz(); |
377 | } | |
378 | < | else |
238 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
239 | < | std::cerr << "node: " << mpiSim->getMyNode() << " sending this line" << writeLine; |
240 | < | MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
241 | < | TAKE_THIS_TAG); |
378 | > | |
379 | } else { | |
380 | < | strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
381 | < | MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
382 | < | TAKE_THIS_TAG); |
380 | > | sprintf(painCave.errMsg, |
381 | > | "Atom %d not found on processor %d\n", |
382 | > | i, worldRank ); |
383 | > | haveError= 1; |
384 | > | simError(); |
385 | > | } |
386 | > | |
387 | > | // I've survived this far, so send off the data! |
388 | > | |
389 | > | atomTypeTag = 4*i; |
390 | > | atomIsDirectionalTag = 4*i + 1; |
391 | > | atomTransDataTag = 4*i + 2; |
392 | > | atomOrientDataTag = 4*i + 3; |
393 | > | |
394 | > | |
395 | > | strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
396 | > | |
397 | > | // null terminate the string before sending (just in case): |
398 | > | MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
399 | > | |
400 | > | MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
401 | > | atomTypeTag, MPI_COMM_WORLD); |
402 | > | |
403 | > | MPI_Send(&isDirectional, 1, MPI_INT, 0, |
404 | > | atomIsDirectionalTag, MPI_COMM_WORLD); |
405 | > | |
406 | > | MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
407 | > | atomTransDataTag, MPI_COMM_WORLD); |
408 | > | |
409 | > | if (isDirectional) { |
410 | > | |
411 | > | MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
412 | > | atomOrientDataTag, MPI_COMM_WORLD); |
413 | > | |
414 | } | |
415 | + | |
416 | } | |
417 | } | |
418 | < | } |
419 | < | outFile.flush(); |
420 | < | sprintf( checkPointMsg, |
421 | < | "Sucessfully took a dump.\n"); |
422 | < | MPIcheckPoint(); |
418 | > | |
419 | > | sprintf( checkPointMsg, |
420 | > | "Sucessfully took a dump.\n"); |
421 | > | MPIcheckPoint(); |
422 | > | |
423 | > | } |
424 | > | |
425 | > | painCave.isEventLoop = 0; |
426 | > | |
427 | #endif // is_mpi | |
428 | } | |
429 | ||
430 | < | void DumpWriter::writeFinal(){ |
430 | > | void DumpWriter::writeFinal(double finalTime){ |
431 | ||
432 | char finalName[500]; | |
433 | ofstream finalOut; | |
434 | ||
435 | const int BUFFERSIZE = 2000; | |
436 | + | const int MINIBUFFERSIZE = 100; |
437 | char tempBuffer[BUFFERSIZE]; | |
438 | < | char writeLine[BUFFERSIZE]; |
438 | > | char writeLine[BUFFERSIZE]; |
439 | ||
440 | double q[4]; | |
441 | DirectionalAtom* dAtom; | |
268 | – | int nAtoms = entry_plug->n_atoms; |
442 | Atom** atoms = entry_plug->atoms; | |
443 | < | int i, j, which_node, done, game_over, which_atom, local_index; |
271 | < | |
272 | < | |
443 | > | int i; |
444 | #ifdef IS_MPI | |
445 | + | int j, which_node, done, which_atom, local_index; |
446 | + | double atomTransData[6]; |
447 | + | double atomOrientData[7]; |
448 | + | int isDirectional; |
449 | + | char* atomTypeString; |
450 | + | char MPIatomTypeString[MINIBUFFERSIZE]; |
451 | + | int atomTypeTag; |
452 | + | int atomIsDirectionalTag; |
453 | + | int atomTransDataTag; |
454 | + | int atomOrientDataTag; |
455 | + | #else //is_mpi |
456 | + | int nAtoms = entry_plug->n_atoms; |
457 | + | #endif //is_mpi |
458 | + | |
459 | + | double pos[3], vel[3]; |
460 | + | |
461 | + | #ifdef IS_MPI |
462 | if(worldRank == 0 ){ | |
463 | #endif // is_mpi | |
464 | < | |
464 | > | |
465 | strcpy( finalName, entry_plug->finalName ); | |
466 | < | |
466 | > | |
467 | finalOut.open( finalName, ios::out | ios::trunc ); | |
468 | if( !finalOut ){ | |
469 | sprintf( painCave.errMsg, | |
# | Line 284 | Line 472 | void DumpWriter::writeFinal(){ | |
472 | painCave.isFatal = 1; | |
473 | simError(); | |
474 | } | |
475 | < | |
475 | > | |
476 | // finalOut.setf( ios::scientific ); | |
477 | < | |
477 | > | |
478 | #ifdef IS_MPI | |
479 | } | |
480 | < | |
480 | > | |
481 | sprintf(checkPointMsg,"Opened file for final configuration\n"); | |
482 | < | MPIcheckPoint(); |
483 | < | |
482 | > | MPIcheckPoint(); |
483 | > | |
484 | #endif //is_mpi | |
485 | ||
486 | < | |
486 | > | |
487 | #ifndef IS_MPI | |
488 | < | |
488 | > | |
489 | finalOut << nAtoms << "\n"; | |
490 | < | |
491 | < | finalOut << entry_plug->box_x << "\t" |
492 | < | << entry_plug->box_y << "\t" |
493 | < | << entry_plug->box_z << "\n"; |
494 | < | |
490 | > | |
491 | > | finalOut << finalTime << ";\t" |
492 | > | << entry_plug->Hmat[0][0] << "\t" |
493 | > | << entry_plug->Hmat[1][0] << "\t" |
494 | > | << entry_plug->Hmat[2][0] << ";\t" |
495 | > | |
496 | > | << entry_plug->Hmat[0][1] << "\t" |
497 | > | << entry_plug->Hmat[1][1] << "\t" |
498 | > | << entry_plug->Hmat[2][1] << ";\t" |
499 | > | |
500 | > | << entry_plug->Hmat[0][2] << "\t" |
501 | > | << entry_plug->Hmat[1][2] << "\t" |
502 | > | << entry_plug->Hmat[2][2] << ";"; |
503 | > | |
504 | > | //write out additional parameters, such as chi and eta |
505 | > | finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
506 | > | finalOut << endl; |
507 | > | |
508 | for( i=0; i<nAtoms; i++ ){ | |
509 | < | |
509 | > | |
510 | > | atoms[i]->getPos(pos); |
511 | > | atoms[i]->getVel(vel); |
512 | > | |
513 | sprintf( tempBuffer, | |
514 | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", | |
515 | atoms[i]->getType(), | |
516 | < | atoms[i]->getX(), |
517 | < | atoms[i]->getY(), |
518 | < | atoms[i]->getZ(), |
519 | < | atoms[i]->get_vx(), |
520 | < | atoms[i]->get_vy(), |
521 | < | atoms[i]->get_vz()); |
516 | > | pos[0], |
517 | > | pos[1], |
518 | > | pos[2], |
519 | > | vel[0], |
520 | > | vel[1], |
521 | > | vel[2]); |
522 | strcpy( writeLine, tempBuffer ); | |
523 | ||
524 | if( atoms[i]->isDirectional() ){ | |
525 | < | |
525 | > | |
526 | dAtom = (DirectionalAtom *)atoms[i]; | |
527 | dAtom->getQ( q ); | |
528 | < | |
528 | > | |
529 | sprintf( tempBuffer, | |
530 | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", | |
531 | q[0], | |
# | Line 335 | Line 539 | void DumpWriter::writeFinal(){ | |
539 | } | |
540 | else | |
541 | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); | |
542 | < | |
542 | > | |
543 | finalOut << writeLine; | |
544 | } | |
545 | finalOut.flush(); | |
546 | finalOut.close(); | |
547 | ||
548 | #else // is_mpi | |
549 | < | |
550 | < | MPI::Status istatus; |
549 | > | |
550 | > | // first thing first, suspend fatalities. |
551 | > | painCave.isEventLoop = 1; |
552 | > | |
553 | > | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
554 | > | int haveError; |
555 | > | |
556 | > | MPI_Status istatus; |
557 | int *AtomToProcMap = mpiSim->getAtomToProcMap(); | |
558 | ||
559 | // write out header and node 0's coordinates | |
560 | < | |
560 | > | |
561 | if( worldRank == 0 ){ | |
562 | finalOut << mpiSim->getTotAtoms() << "\n"; | |
563 | < | |
564 | < | finalOut << entry_plug->box_x << "\t" |
565 | < | << entry_plug->box_y << "\t" |
566 | < | << entry_plug->box_z << "\n"; |
567 | < | |
563 | > | |
564 | > | finalOut << finalTime << ";\t" |
565 | > | << entry_plug->Hmat[0][0] << "\t" |
566 | > | << entry_plug->Hmat[1][0] << "\t" |
567 | > | << entry_plug->Hmat[2][0] << ";\t" |
568 | > | |
569 | > | << entry_plug->Hmat[0][1] << "\t" |
570 | > | << entry_plug->Hmat[1][1] << "\t" |
571 | > | << entry_plug->Hmat[2][1] << ";\t" |
572 | > | |
573 | > | << entry_plug->Hmat[0][2] << "\t" |
574 | > | << entry_plug->Hmat[1][2] << "\t" |
575 | > | << entry_plug->Hmat[2][2] << ";"; |
576 | > | |
577 | > | finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
578 | > | finalOut << endl; |
579 | > | finalOut.flush(); |
580 | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { | |
581 | < | // Get the Node number which has this molecule: |
582 | < | |
583 | < | which_node = AtomToProcMap[i]; |
584 | < | |
585 | < | if (which_node == mpiSim->getMyNode()) { |
581 | > | // Get the Node number which has this atom; |
582 | > | |
583 | > | which_node = AtomToProcMap[i]; |
584 | > | |
585 | > | if (which_node != 0) { |
586 | ||
587 | + | atomTypeTag = 4*i; |
588 | + | atomIsDirectionalTag = 4*i + 1; |
589 | + | atomTransDataTag = 4*i + 2; |
590 | + | atomOrientDataTag = 4*i + 3; |
591 | + | |
592 | + | MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
593 | + | atomTypeTag, MPI_COMM_WORLD, &istatus); |
594 | + | |
595 | + | strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
596 | + | |
597 | + | MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
598 | + | atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
599 | + | |
600 | + | MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
601 | + | atomTransDataTag, MPI_COMM_WORLD, &istatus); |
602 | + | |
603 | + | if (isDirectional) { |
604 | + | |
605 | + | MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
606 | + | atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
607 | + | |
608 | + | } |
609 | + | |
610 | + | } else { |
611 | + | |
612 | + | haveError = 0; |
613 | + | which_atom = i; |
614 | + | local_index=-1; |
615 | + | |
616 | + | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
617 | + | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
618 | + | } |
619 | + | |
620 | + | if (local_index != -1) { |
621 | + | |
622 | + | atomTypeString = atoms[local_index]->getType(); |
623 | + | |
624 | + | atoms[local_index]->getPos(pos); |
625 | + | atoms[local_index]->getVel(vel); |
626 | + | |
627 | + | atomTransData[0] = pos[0]; |
628 | + | atomTransData[1] = pos[1]; |
629 | + | atomTransData[2] = pos[2]; |
630 | + | |
631 | + | atomTransData[3] = vel[0]; |
632 | + | atomTransData[4] = vel[1]; |
633 | + | atomTransData[5] = vel[2]; |
634 | + | |
635 | + | isDirectional = 0; |
636 | + | |
637 | + | if( atoms[local_index]->isDirectional() ){ |
638 | + | |
639 | + | isDirectional = 1; |
640 | + | |
641 | + | dAtom = (DirectionalAtom *)atoms[local_index]; |
642 | + | dAtom->getQ( q ); |
643 | + | |
644 | + | atomOrientData[0] = q[0]; |
645 | + | atomOrientData[1] = q[1]; |
646 | + | atomOrientData[2] = q[2]; |
647 | + | atomOrientData[3] = q[3]; |
648 | + | |
649 | + | atomOrientData[4] = dAtom->getJx(); |
650 | + | atomOrientData[5] = dAtom->getJy(); |
651 | + | atomOrientData[6] = dAtom->getJz(); |
652 | + | } |
653 | + | |
654 | + | } else { |
655 | + | sprintf(painCave.errMsg, |
656 | + | "Atom %d not found on processor %d\n", |
657 | + | i, worldRank ); |
658 | + | haveError= 1; |
659 | + | simError(); |
660 | + | } |
661 | + | |
662 | + | if(haveError) DieDieDie(); |
663 | + | |
664 | + | // If we've survived to here, format the line: |
665 | + | |
666 | sprintf( tempBuffer, | |
667 | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", | |
668 | < | atoms[i]->getType(), |
669 | < | atoms[i]->getX(), |
670 | < | atoms[i]->getY(), |
671 | < | atoms[i]->getZ(), |
672 | < | atoms[i]->get_vx(), |
673 | < | atoms[i]->get_vy(), |
674 | < | atoms[i]->get_vz()); |
668 | > | atomTypeString, |
669 | > | atomTransData[0], |
670 | > | atomTransData[1], |
671 | > | atomTransData[2], |
672 | > | atomTransData[3], |
673 | > | atomTransData[4], |
674 | > | atomTransData[5]); |
675 | > | |
676 | strcpy( writeLine, tempBuffer ); | |
677 | < | |
678 | < | if( atoms[i]->isDirectional() ){ |
679 | < | |
378 | < | dAtom = (DirectionalAtom *)atoms[i]; |
379 | < | dAtom->getQ( q ); |
380 | < | |
677 | > | |
678 | > | if (isDirectional) { |
679 | > | |
680 | sprintf( tempBuffer, | |
681 | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", | |
682 | < | q[0], |
683 | < | q[1], |
684 | < | q[2], |
685 | < | q[3], |
686 | < | dAtom->getJx(), |
687 | < | dAtom->getJy(), |
688 | < | dAtom->getJz()); |
682 | > | atomOrientData[0], |
683 | > | atomOrientData[1], |
684 | > | atomOrientData[2], |
685 | > | atomOrientData[3], |
686 | > | atomOrientData[4], |
687 | > | atomOrientData[5], |
688 | > | atomOrientData[6]); |
689 | strcat( writeLine, tempBuffer ); | |
690 | + | |
691 | + | } else { |
692 | + | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
693 | } | |
694 | < | else |
695 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
696 | < | |
395 | < | } else { |
396 | < | |
397 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
398 | < | MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
399 | < | TAKE_THIS_TAG, istatus); |
694 | > | |
695 | > | finalOut << writeLine; |
696 | > | finalOut.flush(); |
697 | } | |
401 | – | |
402 | – | finalOut << writeLine; |
698 | } | |
404 | – | |
405 | – | // kill everyone off: |
406 | – | game_over = -1; |
407 | – | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
408 | – | MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
409 | – | } |
699 | ||
700 | + | finalOut.flush(); |
701 | + | sprintf( checkPointMsg, |
702 | + | "Sucessfully took a dump.\n"); |
703 | + | MPIcheckPoint(); |
704 | + | |
705 | } else { | |
706 | + | |
707 | + | // worldRank != 0, so I'm a remote node. |
708 | ||
709 | < | done = 0; |
710 | < | while (!done) { |
711 | < | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
712 | < | TAKE_THIS_TAG, istatus); |
709 | > | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
710 | > | |
711 | > | // Am I the node which has this atom? |
712 | > | |
713 | > | if (AtomToProcMap[i] == worldRank) { |
714 | ||
715 | < | if (which_atom == -1) { |
716 | < | done=1; |
420 | < | continue; |
421 | < | } else { |
422 | < | |
423 | < | local_index=-1; |
424 | < | for (j=0; j < mpiSim->getMyNlocal(); j++) { |
715 | > | local_index=-1; |
716 | > | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
717 | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; | |
718 | } | |
719 | if (local_index != -1) { | |
720 | + | |
721 | + | atomTypeString = atoms[local_index]->getType(); |
722 | ||
723 | < | //format the line |
724 | < | sprintf( tempBuffer, |
725 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
726 | < | atoms[local_index]->getType(), |
727 | < | atoms[local_index]->getX(), |
728 | < | atoms[local_index]->getY(), |
729 | < | atoms[local_index]->getZ(), |
730 | < | atoms[local_index]->get_vx(), |
731 | < | atoms[local_index]->get_vy(), |
732 | < | atoms[local_index]->get_vz()); // check here. |
733 | < | strcpy( writeLine, tempBuffer ); |
734 | < | |
723 | > | atoms[local_index]->getPos(pos); |
724 | > | atoms[local_index]->getVel(vel); |
725 | > | |
726 | > | atomTransData[0] = pos[0]; |
727 | > | atomTransData[1] = pos[1]; |
728 | > | atomTransData[2] = pos[2]; |
729 | > | |
730 | > | atomTransData[3] = vel[0]; |
731 | > | atomTransData[4] = vel[1]; |
732 | > | atomTransData[5] = vel[2]; |
733 | > | |
734 | > | isDirectional = 0; |
735 | > | |
736 | if( atoms[local_index]->isDirectional() ){ | |
737 | + | |
738 | + | isDirectional = 1; |
739 | ||
740 | dAtom = (DirectionalAtom *)atoms[local_index]; | |
741 | dAtom->getQ( q ); | |
742 | < | |
743 | < | sprintf( tempBuffer, |
744 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
745 | < | q[0], |
746 | < | q[1], |
747 | < | q[2], |
748 | < | q[3], |
749 | < | dAtom->getJx(), |
750 | < | dAtom->getJy(), |
454 | < | dAtom->getJz()); |
455 | < | strcat( writeLine, tempBuffer ); |
742 | > | |
743 | > | atomOrientData[0] = q[0]; |
744 | > | atomOrientData[1] = q[1]; |
745 | > | atomOrientData[2] = q[2]; |
746 | > | atomOrientData[3] = q[3]; |
747 | > | |
748 | > | atomOrientData[4] = dAtom->getJx(); |
749 | > | atomOrientData[5] = dAtom->getJy(); |
750 | > | atomOrientData[6] = dAtom->getJz(); |
751 | } | |
752 | < | else |
458 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
459 | < | |
460 | < | MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
461 | < | TAKE_THIS_TAG); |
752 | > | |
753 | } else { | |
754 | < | strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
755 | < | MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
756 | < | TAKE_THIS_TAG); |
754 | > | sprintf(painCave.errMsg, |
755 | > | "Atom %d not found on processor %d\n", |
756 | > | i, worldRank ); |
757 | > | haveError= 1; |
758 | > | simError(); |
759 | > | } |
760 | > | |
761 | > | // I've survived this far, so send off the data! |
762 | > | |
763 | > | atomTypeTag = 4*i; |
764 | > | atomIsDirectionalTag = 4*i + 1; |
765 | > | atomTransDataTag = 4*i + 2; |
766 | > | atomOrientDataTag = 4*i + 3; |
767 | > | |
768 | > | strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
769 | > | |
770 | > | MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
771 | > | atomTypeTag, MPI_COMM_WORLD); |
772 | > | |
773 | > | MPI_Send(&isDirectional, 1, MPI_INT, 0, |
774 | > | atomIsDirectionalTag, MPI_COMM_WORLD); |
775 | > | |
776 | > | MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
777 | > | atomTransDataTag, MPI_COMM_WORLD); |
778 | > | |
779 | > | if (isDirectional) { |
780 | > | |
781 | > | MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
782 | > | atomOrientDataTag, MPI_COMM_WORLD); |
783 | > | |
784 | } | |
785 | + | |
786 | } | |
787 | } | |
788 | + | |
789 | + | sprintf( checkPointMsg, |
790 | + | "Sucessfully wrote final file.\n"); |
791 | + | MPIcheckPoint(); |
792 | + | |
793 | } | |
794 | < | finalOut.flush(); |
795 | < | sprintf( checkPointMsg, |
472 | < | "Sucessfully took a dump.\n"); |
473 | < | MPIcheckPoint(); |
794 | > | |
795 | > | painCave.isEventLoop = 0; |
796 | ||
797 | < | if( worldRank == 0 ) finalOut.close(); |
797 | > | if( worldRank == 0 ) finalOut.close(); |
798 | #endif // is_mpi | |
799 | } | |
800 | + | |
801 | + | |
802 | + | |
803 | + | #ifdef IS_MPI |
804 | + | |
805 | + | // a couple of functions to let us escape the write loop |
806 | + | |
807 | + | void dWrite::DieDieDie( void ){ |
808 | + | |
809 | + | MPI_Finalize(); |
810 | + | exit (0); |
811 | + | } |
812 | + | |
813 | + | #endif //is_mpi |
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