1 |
mmeineke |
377 |
#include <cstring> |
2 |
|
|
#include <iostream> |
3 |
|
|
#include <fstream> |
4 |
|
|
|
5 |
|
|
#ifdef IS_MPI |
6 |
|
|
#include <mpi.h> |
7 |
gezelter |
416 |
#include <mpi++.h> |
8 |
mmeineke |
377 |
#include "mpiSimulation.hpp" |
9 |
|
|
#define TAKE_THIS_TAG 0 |
10 |
|
|
#endif //is_mpi |
11 |
|
|
|
12 |
|
|
#include "ReadWrite.hpp" |
13 |
|
|
#include "simError.h" |
14 |
|
|
|
15 |
|
|
DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
16 |
|
|
|
17 |
|
|
entry_plug = the_entry_plug; |
18 |
|
|
|
19 |
|
|
#ifdef IS_MPI |
20 |
|
|
if(worldRank == 0 ){ |
21 |
|
|
#endif // is_mpi |
22 |
|
|
|
23 |
|
|
|
24 |
|
|
|
25 |
|
|
strcpy( outName, entry_plug->sampleName ); |
26 |
|
|
|
27 |
|
|
outFile.open(outName, ios::out | ios::trunc ); |
28 |
|
|
|
29 |
|
|
if( !outFile ){ |
30 |
|
|
|
31 |
|
|
sprintf( painCave.errMsg, |
32 |
|
|
"Could not open \"%s\" for dump output.\n", |
33 |
|
|
outName); |
34 |
|
|
painCave.isFatal = 1; |
35 |
|
|
simError(); |
36 |
|
|
} |
37 |
|
|
|
38 |
|
|
//outFile.setf( ios::scientific ); |
39 |
|
|
|
40 |
|
|
#ifdef IS_MPI |
41 |
|
|
} |
42 |
|
|
|
43 |
|
|
sprintf( checkPointMsg, |
44 |
|
|
"Sucessfully opened output file for dumping.\n"); |
45 |
|
|
MPIcheckPoint(); |
46 |
|
|
#endif // is_mpi |
47 |
|
|
} |
48 |
|
|
|
49 |
|
|
DumpWriter::~DumpWriter( ){ |
50 |
|
|
|
51 |
|
|
#ifdef IS_MPI |
52 |
|
|
if(worldRank == 0 ){ |
53 |
|
|
#endif // is_mpi |
54 |
|
|
|
55 |
|
|
outFile.close(); |
56 |
|
|
|
57 |
|
|
#ifdef IS_MPI |
58 |
|
|
} |
59 |
|
|
#endif // is_mpi |
60 |
|
|
} |
61 |
|
|
|
62 |
|
|
void DumpWriter::writeDump( double currentTime ){ |
63 |
|
|
|
64 |
|
|
const int BUFFERSIZE = 2000; |
65 |
|
|
char tempBuffer[BUFFERSIZE]; |
66 |
|
|
char writeLine[BUFFERSIZE]; |
67 |
|
|
|
68 |
gezelter |
416 |
int i, j, which_node, done, game_over, which_atom; |
69 |
mmeineke |
377 |
double q[4]; |
70 |
|
|
DirectionalAtom* dAtom; |
71 |
|
|
int nAtoms = entry_plug->n_atoms; |
72 |
|
|
Atom** atoms = entry_plug->atoms; |
73 |
|
|
|
74 |
|
|
|
75 |
|
|
#ifndef IS_MPI |
76 |
|
|
|
77 |
|
|
outFile << nAtoms << "\n"; |
78 |
|
|
|
79 |
|
|
outFile << currentTime << "\t" |
80 |
|
|
<< entry_plug->box_x << "\t" |
81 |
|
|
<< entry_plug->box_y << "\t" |
82 |
|
|
<< entry_plug->box_z << "\n"; |
83 |
|
|
|
84 |
|
|
for( i=0; i<nAtoms; i++ ){ |
85 |
|
|
|
86 |
|
|
|
87 |
|
|
sprintf( tempBuffer, |
88 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
89 |
|
|
atoms[i]->getType(), |
90 |
|
|
atoms[i]->getX(), |
91 |
|
|
atoms[i]->getY(), |
92 |
|
|
atoms[i]->getZ(), |
93 |
|
|
atoms[i]->get_vx(), |
94 |
|
|
atoms[i]->get_vy(), |
95 |
|
|
atoms[i]->get_vz()); |
96 |
|
|
strcpy( writeLine, tempBuffer ); |
97 |
|
|
|
98 |
|
|
if( atoms[i]->isDirectional() ){ |
99 |
|
|
|
100 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
101 |
|
|
dAtom->getQ( q ); |
102 |
|
|
|
103 |
|
|
sprintf( tempBuffer, |
104 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
105 |
|
|
q[0], |
106 |
|
|
q[1], |
107 |
|
|
q[2], |
108 |
|
|
q[3], |
109 |
|
|
dAtom->getJx(), |
110 |
|
|
dAtom->getJy(), |
111 |
|
|
dAtom->getJz()); |
112 |
|
|
strcat( writeLine, tempBuffer ); |
113 |
|
|
} |
114 |
|
|
else |
115 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
116 |
|
|
|
117 |
|
|
outFile << writeLine; |
118 |
|
|
} |
119 |
|
|
outFile.flush(); |
120 |
|
|
|
121 |
|
|
#else // is_mpi |
122 |
gezelter |
416 |
|
123 |
|
|
MPI::Status istatus; |
124 |
|
|
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
125 |
gezelter |
415 |
|
126 |
mmeineke |
377 |
// write out header and node 0's coordinates |
127 |
gezelter |
415 |
|
128 |
mmeineke |
377 |
if( worldRank == 0 ){ |
129 |
|
|
outFile << mpiSim->getTotAtoms() << "\n"; |
130 |
gezelter |
415 |
|
131 |
mmeineke |
377 |
outFile << currentTime << "\t" |
132 |
|
|
<< entry_plug->box_x << "\t" |
133 |
|
|
<< entry_plug->box_y << "\t" |
134 |
|
|
<< entry_plug->box_z << "\n"; |
135 |
gezelter |
415 |
|
136 |
gezelter |
416 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
137 |
gezelter |
415 |
// Get the Node number which has this molecule: |
138 |
mmeineke |
377 |
|
139 |
gezelter |
415 |
which_node = AtomToProcMap[i]; |
140 |
|
|
|
141 |
gezelter |
416 |
if (which_node == mpiSim->getMyNode()) { |
142 |
gezelter |
415 |
|
143 |
|
|
sprintf( tempBuffer, |
144 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
145 |
|
|
atoms[i]->getType(), |
146 |
|
|
atoms[i]->getX(), |
147 |
|
|
atoms[i]->getY(), |
148 |
|
|
atoms[i]->getZ(), |
149 |
|
|
atoms[i]->get_vx(), |
150 |
|
|
atoms[i]->get_vy(), |
151 |
|
|
atoms[i]->get_vz()); |
152 |
|
|
strcpy( writeLine, tempBuffer ); |
153 |
mmeineke |
377 |
|
154 |
gezelter |
415 |
if( atoms[i]->isDirectional() ){ |
155 |
mmeineke |
377 |
|
156 |
gezelter |
415 |
dAtom = (DirectionalAtom *)atoms[i]; |
157 |
|
|
dAtom->getQ( q ); |
158 |
mmeineke |
377 |
|
159 |
gezelter |
415 |
sprintf( tempBuffer, |
160 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
161 |
|
|
q[0], |
162 |
|
|
q[1], |
163 |
|
|
q[2], |
164 |
|
|
q[3], |
165 |
|
|
dAtom->getJx(), |
166 |
|
|
dAtom->getJy(), |
167 |
|
|
dAtom->getJz()); |
168 |
|
|
strcat( writeLine, tempBuffer ); |
169 |
|
|
} |
170 |
|
|
else |
171 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
172 |
|
|
|
173 |
|
|
} else { |
174 |
|
|
|
175 |
|
|
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
176 |
gezelter |
416 |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
177 |
gezelter |
415 |
TAKE_THIS_TAG, istatus); |
178 |
mmeineke |
377 |
} |
179 |
gezelter |
415 |
|
180 |
mmeineke |
377 |
outFile << writeLine; |
181 |
|
|
} |
182 |
|
|
|
183 |
gezelter |
415 |
// kill everyone off: |
184 |
gezelter |
416 |
game_over = -1; |
185 |
|
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
186 |
|
|
MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
187 |
mmeineke |
377 |
} |
188 |
|
|
|
189 |
gezelter |
415 |
} else { |
190 |
|
|
|
191 |
|
|
done = 0; |
192 |
|
|
while (!done) { |
193 |
gezelter |
416 |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
194 |
gezelter |
415 |
TAKE_THIS_TAG, istatus); |
195 |
mmeineke |
377 |
|
196 |
gezelter |
416 |
if (which_atom == -1) { |
197 |
gezelter |
415 |
done=1; |
198 |
|
|
continue; |
199 |
|
|
} else { |
200 |
mmeineke |
377 |
|
201 |
gezelter |
415 |
//format the line |
202 |
mmeineke |
377 |
sprintf( tempBuffer, |
203 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
204 |
gezelter |
415 |
atoms[which_atom]->getType(), |
205 |
|
|
atoms[which_atom]->getX(), |
206 |
|
|
atoms[which_atom]->getY(), |
207 |
|
|
atoms[which_atom]->getZ(), |
208 |
|
|
atoms[which_atom]->get_vx(), |
209 |
|
|
atoms[which_atom]->get_vy(), |
210 |
|
|
atoms[which_atom]->get_vz()); // check here. |
211 |
mmeineke |
377 |
strcpy( writeLine, tempBuffer ); |
212 |
|
|
|
213 |
gezelter |
415 |
if( atoms[which_atom]->isDirectional() ){ |
214 |
mmeineke |
377 |
|
215 |
gezelter |
415 |
dAtom = (DirectionalAtom *)atoms[which_atom]; |
216 |
mmeineke |
377 |
dAtom->getQ( q ); |
217 |
|
|
|
218 |
|
|
sprintf( tempBuffer, |
219 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
220 |
|
|
q[0], |
221 |
|
|
q[1], |
222 |
|
|
q[2], |
223 |
|
|
q[3], |
224 |
|
|
dAtom->getJx(), |
225 |
|
|
dAtom->getJy(), |
226 |
|
|
dAtom->getJz()); |
227 |
|
|
strcat( writeLine, tempBuffer ); |
228 |
|
|
} |
229 |
|
|
else |
230 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
231 |
gezelter |
415 |
|
232 |
|
|
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
233 |
|
|
TAKE_THIS_TAG); |
234 |
mmeineke |
377 |
} |
235 |
|
|
} |
236 |
gezelter |
415 |
} |
237 |
|
|
outFile.flush(); |
238 |
|
|
sprintf( checkPointMsg, |
239 |
|
|
"Sucessfully took a dump.\n"); |
240 |
|
|
MPIcheckPoint(); |
241 |
mmeineke |
377 |
#endif // is_mpi |
242 |
|
|
} |
243 |
|
|
|
244 |
|
|
void DumpWriter::writeFinal(){ |
245 |
gezelter |
416 |
|
246 |
mmeineke |
377 |
char finalName[500]; |
247 |
|
|
ofstream finalOut; |
248 |
gezelter |
416 |
|
249 |
|
|
const int BUFFERSIZE = 2000; |
250 |
|
|
char tempBuffer[BUFFERSIZE]; |
251 |
|
|
char writeLine[BUFFERSIZE]; |
252 |
|
|
|
253 |
|
|
double q[4]; |
254 |
|
|
DirectionalAtom* dAtom; |
255 |
|
|
int nAtoms = entry_plug->n_atoms; |
256 |
|
|
Atom** atoms = entry_plug->atoms; |
257 |
|
|
int i, j, which_node, done, game_over, which_atom; |
258 |
mmeineke |
377 |
|
259 |
gezelter |
416 |
|
260 |
mmeineke |
377 |
#ifdef IS_MPI |
261 |
|
|
if(worldRank == 0 ){ |
262 |
|
|
#endif // is_mpi |
263 |
|
|
|
264 |
|
|
strcpy( finalName, entry_plug->finalName ); |
265 |
|
|
|
266 |
|
|
finalOut.open( finalName, ios::out | ios::trunc ); |
267 |
|
|
if( !finalOut ){ |
268 |
|
|
sprintf( painCave.errMsg, |
269 |
|
|
"Could not open \"%s\" for final dump output.\n", |
270 |
|
|
finalName ); |
271 |
|
|
painCave.isFatal = 1; |
272 |
|
|
simError(); |
273 |
|
|
} |
274 |
|
|
|
275 |
|
|
// finalOut.setf( ios::scientific ); |
276 |
|
|
|
277 |
|
|
#ifdef IS_MPI |
278 |
|
|
} |
279 |
|
|
|
280 |
|
|
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
281 |
|
|
MPIcheckPoint(); |
282 |
|
|
|
283 |
|
|
#endif //is_mpi |
284 |
|
|
|
285 |
gezelter |
415 |
|
286 |
mmeineke |
377 |
#ifndef IS_MPI |
287 |
|
|
|
288 |
|
|
finalOut << nAtoms << "\n"; |
289 |
|
|
|
290 |
|
|
finalOut << entry_plug->box_x << "\t" |
291 |
|
|
<< entry_plug->box_y << "\t" |
292 |
|
|
<< entry_plug->box_z << "\n"; |
293 |
gezelter |
416 |
|
294 |
mmeineke |
377 |
for( i=0; i<nAtoms; i++ ){ |
295 |
|
|
|
296 |
|
|
sprintf( tempBuffer, |
297 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
298 |
|
|
atoms[i]->getType(), |
299 |
|
|
atoms[i]->getX(), |
300 |
|
|
atoms[i]->getY(), |
301 |
|
|
atoms[i]->getZ(), |
302 |
|
|
atoms[i]->get_vx(), |
303 |
|
|
atoms[i]->get_vy(), |
304 |
|
|
atoms[i]->get_vz()); |
305 |
|
|
strcpy( writeLine, tempBuffer ); |
306 |
|
|
|
307 |
|
|
if( atoms[i]->isDirectional() ){ |
308 |
|
|
|
309 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
310 |
|
|
dAtom->getQ( q ); |
311 |
|
|
|
312 |
|
|
sprintf( tempBuffer, |
313 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
314 |
|
|
q[0], |
315 |
|
|
q[1], |
316 |
|
|
q[2], |
317 |
|
|
q[3], |
318 |
|
|
dAtom->getJx(), |
319 |
|
|
dAtom->getJy(), |
320 |
|
|
dAtom->getJz()); |
321 |
|
|
strcat( writeLine, tempBuffer ); |
322 |
|
|
} |
323 |
|
|
else |
324 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
325 |
|
|
|
326 |
|
|
finalOut << writeLine; |
327 |
|
|
} |
328 |
|
|
finalOut.flush(); |
329 |
gezelter |
415 |
finalOut.close(); |
330 |
mmeineke |
377 |
|
331 |
|
|
#else // is_mpi |
332 |
gezelter |
415 |
|
333 |
gezelter |
416 |
MPI::Status istatus; |
334 |
|
|
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
335 |
|
|
|
336 |
mmeineke |
377 |
// write out header and node 0's coordinates |
337 |
gezelter |
415 |
|
338 |
mmeineke |
377 |
if( worldRank == 0 ){ |
339 |
|
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
340 |
gezelter |
415 |
|
341 |
mmeineke |
377 |
finalOut << entry_plug->box_x << "\t" |
342 |
gezelter |
415 |
<< entry_plug->box_y << "\t" |
343 |
|
|
<< entry_plug->box_z << "\n"; |
344 |
mmeineke |
377 |
|
345 |
gezelter |
416 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
346 |
gezelter |
415 |
// Get the Node number which has this molecule: |
347 |
mmeineke |
377 |
|
348 |
gezelter |
415 |
which_node = AtomToProcMap[i]; |
349 |
|
|
|
350 |
gezelter |
416 |
if (which_node == mpiSim->getMyNode()) { |
351 |
gezelter |
415 |
|
352 |
|
|
sprintf( tempBuffer, |
353 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
354 |
|
|
atoms[i]->getType(), |
355 |
|
|
atoms[i]->getX(), |
356 |
|
|
atoms[i]->getY(), |
357 |
|
|
atoms[i]->getZ(), |
358 |
|
|
atoms[i]->get_vx(), |
359 |
|
|
atoms[i]->get_vy(), |
360 |
|
|
atoms[i]->get_vz()); |
361 |
|
|
strcpy( writeLine, tempBuffer ); |
362 |
mmeineke |
377 |
|
363 |
gezelter |
415 |
if( atoms[i]->isDirectional() ){ |
364 |
mmeineke |
377 |
|
365 |
gezelter |
415 |
dAtom = (DirectionalAtom *)atoms[i]; |
366 |
|
|
dAtom->getQ( q ); |
367 |
mmeineke |
377 |
|
368 |
gezelter |
415 |
sprintf( tempBuffer, |
369 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
370 |
|
|
q[0], |
371 |
|
|
q[1], |
372 |
|
|
q[2], |
373 |
|
|
q[3], |
374 |
|
|
dAtom->getJx(), |
375 |
|
|
dAtom->getJy(), |
376 |
|
|
dAtom->getJz()); |
377 |
|
|
strcat( writeLine, tempBuffer ); |
378 |
|
|
} |
379 |
|
|
else |
380 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
381 |
|
|
|
382 |
|
|
} else { |
383 |
|
|
|
384 |
|
|
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
385 |
gezelter |
416 |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
386 |
gezelter |
415 |
TAKE_THIS_TAG, istatus); |
387 |
mmeineke |
377 |
} |
388 |
gezelter |
415 |
|
389 |
mmeineke |
377 |
finalOut << writeLine; |
390 |
|
|
} |
391 |
|
|
|
392 |
gezelter |
415 |
// kill everyone off: |
393 |
gezelter |
416 |
game_over = -1; |
394 |
|
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
395 |
|
|
MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
396 |
mmeineke |
377 |
} |
397 |
|
|
|
398 |
gezelter |
415 |
} else { |
399 |
|
|
|
400 |
|
|
done = 0; |
401 |
|
|
while (!done) { |
402 |
gezelter |
416 |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
403 |
|
|
TAKE_THIS_TAG, istatus); |
404 |
mmeineke |
377 |
|
405 |
gezelter |
416 |
if (which_atom == -1) { |
406 |
gezelter |
415 |
done=1; |
407 |
|
|
continue; |
408 |
|
|
} else { |
409 |
mmeineke |
377 |
|
410 |
gezelter |
415 |
//format the line |
411 |
mmeineke |
377 |
sprintf( tempBuffer, |
412 |
|
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
413 |
gezelter |
415 |
atoms[which_atom]->getType(), |
414 |
|
|
atoms[which_atom]->getX(), |
415 |
|
|
atoms[which_atom]->getY(), |
416 |
|
|
atoms[which_atom]->getZ(), |
417 |
|
|
atoms[which_atom]->get_vx(), |
418 |
|
|
atoms[which_atom]->get_vy(), |
419 |
|
|
atoms[which_atom]->get_vz()); // check here. |
420 |
mmeineke |
377 |
strcpy( writeLine, tempBuffer ); |
421 |
|
|
|
422 |
gezelter |
415 |
if( atoms[which_atom]->isDirectional() ){ |
423 |
mmeineke |
377 |
|
424 |
gezelter |
415 |
dAtom = (DirectionalAtom *)atoms[which_atom]; |
425 |
mmeineke |
377 |
dAtom->getQ( q ); |
426 |
|
|
|
427 |
|
|
sprintf( tempBuffer, |
428 |
|
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
429 |
|
|
q[0], |
430 |
|
|
q[1], |
431 |
|
|
q[2], |
432 |
|
|
q[3], |
433 |
|
|
dAtom->getJx(), |
434 |
|
|
dAtom->getJy(), |
435 |
|
|
dAtom->getJz()); |
436 |
|
|
strcat( writeLine, tempBuffer ); |
437 |
|
|
} |
438 |
|
|
else |
439 |
|
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
440 |
gezelter |
415 |
|
441 |
|
|
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
442 |
|
|
TAKE_THIS_TAG); |
443 |
mmeineke |
377 |
} |
444 |
|
|
} |
445 |
gezelter |
415 |
} |
446 |
|
|
finalOut.flush(); |
447 |
|
|
sprintf( checkPointMsg, |
448 |
|
|
"Sucessfully took a dump.\n"); |
449 |
|
|
MPIcheckPoint(); |
450 |
mmeineke |
377 |
|
451 |
gezelter |
415 |
if( worldRank == 0 ) finalOut.close(); |
452 |
mmeineke |
377 |
#endif // is_mpi |
453 |
|
|
} |