# | 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 | ||
# | Line 27 | Line 29 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ | |
29 | if(worldRank == 0 ){ | |
30 | #endif // is_mpi | |
31 | ||
30 | – | |
31 | – | |
32 | strcpy( outName, entry_plug->sampleName ); | |
33 | ||
34 | outFile.open(outName, ios::out | ios::trunc ); | |
# | Line 41 | Line 41 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ | |
41 | painCave.isFatal = 1; | |
42 | simError(); | |
43 | } | |
44 | < | |
44 | > | |
45 | //outFile.setf( ios::scientific ); | |
46 | ||
47 | #ifdef IS_MPI | |
# | Line 72 | Line 72 | void DumpWriter::writeDump( double currentTime ){ | |
72 | char tempBuffer[BUFFERSIZE]; | |
73 | char writeLine[BUFFERSIZE]; | |
74 | ||
75 | < | int i, j, which_node, done, game_over, which_atom, local_index; |
75 | > | int i; |
76 | > | #ifdef IS_MPI |
77 | > | int j, which_node, done, which_atom, local_index; |
78 | > | #else //is_mpi |
79 | > | int nAtoms = entry_plug->n_atoms; |
80 | > | #endif //is_mpi |
81 | > | |
82 | double q[4]; | |
83 | DirectionalAtom* dAtom; | |
78 | – | int nAtoms = entry_plug->n_atoms; |
84 | Atom** atoms = entry_plug->atoms; | |
85 | + | double pos[3], vel[3]; |
86 | ||
87 | + | |
88 | + | // write current frame to the eor file |
89 | ||
90 | + | this->writeFinal( currentTime ); |
91 | + | |
92 | #ifndef IS_MPI | |
93 | ||
94 | outFile << nAtoms << "\n"; | |
95 | ||
96 | < | outFile << currentTime << "\t" |
97 | < | << entry_plug->box_x << "\t" |
98 | < | << entry_plug->box_y << "\t" |
99 | < | << entry_plug->box_z << "\n"; |
96 | > | outFile << currentTime << ";\t" |
97 | > | << entry_plug->Hmat[0][0] << "\t" |
98 | > | << entry_plug->Hmat[1][0] << "\t" |
99 | > | << entry_plug->Hmat[2][0] << ";\t" |
100 | > | |
101 | > | << entry_plug->Hmat[0][1] << "\t" |
102 | > | << entry_plug->Hmat[1][1] << "\t" |
103 | > | << entry_plug->Hmat[2][1] << ";\t" |
104 | > | |
105 | > | << entry_plug->Hmat[0][2] << "\t" |
106 | > | << entry_plug->Hmat[1][2] << "\t" |
107 | > | << entry_plug->Hmat[2][2] << ";\n"; |
108 | ||
109 | for( i=0; i<nAtoms; i++ ){ | |
110 | ||
111 | + | atoms[i]->getPos(pos); |
112 | + | atoms[i]->getVel(vel); |
113 | ||
114 | sprintf( tempBuffer, | |
115 | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", | |
116 | atoms[i]->getType(), | |
117 | < | atoms[i]->getX(), |
118 | < | atoms[i]->getY(), |
119 | < | atoms[i]->getZ(), |
120 | < | atoms[i]->get_vx(), |
121 | < | atoms[i]->get_vy(), |
122 | < | atoms[i]->get_vz()); |
117 | > | pos[0], |
118 | > | pos[1], |
119 | > | pos[2], |
120 | > | vel[0], |
121 | > | vel[1], |
122 | > | vel[2]); |
123 | strcpy( writeLine, tempBuffer ); | |
124 | ||
125 | if( atoms[i]->isDirectional() ){ | |
# | Line 140 | Line 160 | void DumpWriter::writeDump( double currentTime ){ | |
160 | ||
161 | if( worldRank == 0 ){ | |
162 | outFile << mpiSim->getTotAtoms() << "\n"; | |
163 | + | |
164 | + | outFile << currentTime << ";\t" |
165 | + | << entry_plug->Hmat[0][0] << "\t" |
166 | + | << entry_plug->Hmat[1][0] << "\t" |
167 | + | << entry_plug->Hmat[2][0] << ";\t" |
168 | + | |
169 | + | << entry_plug->Hmat[0][1] << "\t" |
170 | + | << entry_plug->Hmat[1][1] << "\t" |
171 | + | << entry_plug->Hmat[2][1] << ";\t" |
172 | + | |
173 | + | << entry_plug->Hmat[0][2] << "\t" |
174 | + | << entry_plug->Hmat[1][2] << "\t" |
175 | + | << entry_plug->Hmat[2][2] << ";\n"; |
176 | ||
144 | – | outFile << currentTime << "\t" |
145 | – | << entry_plug->box_x << "\t" |
146 | – | << entry_plug->box_y << "\t" |
147 | – | << entry_plug->box_z << "\n"; |
177 | outFile.flush(); | |
178 | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { | |
179 | // Get the Node number which has this atom; | |
# | Line 161 | Line 190 | void DumpWriter::writeDump( double currentTime ){ | |
190 | } | |
191 | if (local_index != -1) { | |
192 | //format the line | |
193 | + | |
194 | + | atoms[local_index]->getPos(pos); |
195 | + | atoms[local_index]->getVel(vel); |
196 | + | |
197 | sprintf( tempBuffer, | |
198 | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", | |
199 | atoms[local_index]->getType(), | |
200 | < | atoms[local_index]->getX(), |
201 | < | atoms[local_index]->getY(), |
202 | < | atoms[local_index]->getZ(), |
203 | < | atoms[local_index]->get_vx(), |
204 | < | atoms[local_index]->get_vy(), |
205 | < | atoms[local_index]->get_vz()); // check here. |
200 | > | pos[0], |
201 | > | pos[1], |
202 | > | pos[2], |
203 | > | vel[0], |
204 | > | vel[1], |
205 | > | vel[2]); // check here. |
206 | strcpy( writeLine, tempBuffer ); | |
207 | ||
208 | if( atoms[local_index]->isDirectional() ){ | |
# | Line 251 | Line 284 | void DumpWriter::writeDump( double currentTime ){ | |
284 | } | |
285 | if (local_index != -1) { | |
286 | //format the line | |
287 | + | |
288 | + | atoms[local_index]->getPos(pos); |
289 | + | atoms[local_index]->getVel(vel); |
290 | + | |
291 | sprintf( tempBuffer, | |
292 | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", | |
293 | atoms[local_index]->getType(), | |
294 | < | atoms[local_index]->getX(), |
295 | < | atoms[local_index]->getY(), |
296 | < | atoms[local_index]->getZ(), |
297 | < | atoms[local_index]->get_vx(), |
298 | < | atoms[local_index]->get_vy(), |
299 | < | atoms[local_index]->get_vz()); // check here. |
294 | > | pos[0], |
295 | > | pos[1], |
296 | > | pos[2], |
297 | > | vel[0], |
298 | > | vel[1], |
299 | > | vel[2]); // check here. |
300 | strcpy( writeLine, tempBuffer ); | |
301 | ||
302 | if( atoms[local_index]->isDirectional() ){ | |
# | Line 309 | Line 346 | void DumpWriter::writeDump( double currentTime ){ | |
346 | #endif // is_mpi | |
347 | } | |
348 | ||
349 | < | void DumpWriter::writeFinal(){ |
349 | > | void DumpWriter::writeFinal(double finalTime){ |
350 | ||
351 | char finalName[500]; | |
352 | ofstream finalOut; | |
# | Line 320 | Line 357 | void DumpWriter::writeFinal(){ | |
357 | ||
358 | double q[4]; | |
359 | DirectionalAtom* dAtom; | |
323 | – | int nAtoms = entry_plug->n_atoms; |
360 | Atom** atoms = entry_plug->atoms; | |
361 | < | int i, j, which_node, done, game_over, which_atom, local_index; |
361 | > | int i; |
362 | > | #ifdef IS_MPI |
363 | > | int j, which_node, done, which_atom, local_index; |
364 | > | #else //is_mpi |
365 | > | int nAtoms = entry_plug->n_atoms; |
366 | > | #endif //is_mpi |
367 | ||
368 | + | double pos[3], vel[3]; |
369 | ||
370 | #ifdef IS_MPI | |
371 | if(worldRank == 0 ){ | |
# | Line 355 | Line 397 | void DumpWriter::writeFinal(){ | |
397 | ||
398 | finalOut << nAtoms << "\n"; | |
399 | ||
400 | < | finalOut << entry_plug->box_x << "\t" |
401 | < | << entry_plug->box_y << "\t" |
402 | < | << entry_plug->box_z << "\n"; |
400 | > | finalOut << finalTime << ";\t" |
401 | > | << entry_plug->Hmat[0][0] << "\t" |
402 | > | << entry_plug->Hmat[1][0] << "\t" |
403 | > | << entry_plug->Hmat[2][0] << ";\t" |
404 | > | |
405 | > | << entry_plug->Hmat[0][1] << "\t" |
406 | > | << entry_plug->Hmat[1][1] << "\t" |
407 | > | << entry_plug->Hmat[2][1] << ";\t" |
408 | > | |
409 | > | << entry_plug->Hmat[0][2] << "\t" |
410 | > | << entry_plug->Hmat[1][2] << "\t" |
411 | > | << entry_plug->Hmat[2][2] << ";\n"; |
412 | ||
413 | for( i=0; i<nAtoms; i++ ){ | |
414 | ||
415 | + | atoms[i]->getPos(pos); |
416 | + | atoms[i]->getVel(vel); |
417 | + | |
418 | sprintf( tempBuffer, | |
419 | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", | |
420 | atoms[i]->getType(), | |
421 | < | atoms[i]->getX(), |
422 | < | atoms[i]->getY(), |
423 | < | atoms[i]->getZ(), |
424 | < | atoms[i]->get_vx(), |
425 | < | atoms[i]->get_vy(), |
426 | < | atoms[i]->get_vz()); |
421 | > | pos[0], |
422 | > | pos[1], |
423 | > | pos[2], |
424 | > | vel[0], |
425 | > | vel[1], |
426 | > | vel[2]); |
427 | strcpy( writeLine, tempBuffer ); | |
428 | ||
429 | if( atoms[i]->isDirectional() ){ | |
# | Line 413 | Line 467 | void DumpWriter::writeFinal(){ | |
467 | if( worldRank == 0 ){ | |
468 | finalOut << mpiSim->getTotAtoms() << "\n"; | |
469 | ||
470 | < | finalOut << entry_plug->box_x << "\t" |
471 | < | << entry_plug->box_y << "\t" |
472 | < | << entry_plug->box_z << "\n"; |
470 | > | finalOut << finalTime << ";\t" |
471 | > | << entry_plug->Hmat[0][0] << "\t" |
472 | > | << entry_plug->Hmat[1][0] << "\t" |
473 | > | << entry_plug->Hmat[2][0] << ";\t" |
474 | > | |
475 | > | << entry_plug->Hmat[0][1] << "\t" |
476 | > | << entry_plug->Hmat[1][1] << "\t" |
477 | > | << entry_plug->Hmat[2][1] << ";\t" |
478 | > | |
479 | > | << entry_plug->Hmat[0][2] << "\t" |
480 | > | << entry_plug->Hmat[1][2] << "\t" |
481 | > | << entry_plug->Hmat[2][2] << ";\n"; |
482 | ||
483 | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { | |
484 | // Get the Node number which has this molecule: | |
# | Line 429 | Line 492 | void DumpWriter::writeFinal(){ | |
492 | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { | |
493 | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; | |
494 | } | |
495 | < | if (local_index != -1) { |
495 | > | if (local_index != -1) { |
496 | > | |
497 | > | atoms[local_index]->getPos(pos); |
498 | > | atoms[local_index]->getVel(vel); |
499 | > | |
500 | sprintf( tempBuffer, | |
501 | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", | |
502 | atoms[local_index]->getType(), | |
503 | < | atoms[local_index]->getX(), |
504 | < | atoms[local_index]->getY(), |
505 | < | atoms[local_index]->getZ(), |
506 | < | atoms[local_index]->get_vx(), |
507 | < | atoms[local_index]->get_vy(), |
508 | < | atoms[local_index]->get_vz()); |
503 | > | pos[0], |
504 | > | pos[1], |
505 | > | pos[2], |
506 | > | vel[0], |
507 | > | vel[1], |
508 | > | vel[2]); |
509 | strcpy( writeLine, tempBuffer ); | |
510 | ||
511 | if( atoms[local_index]->isDirectional() ){ | |
# | Line 518 | Line 585 | void DumpWriter::writeFinal(){ | |
585 | } | |
586 | if (local_index != -1) { | |
587 | ||
588 | + | atoms[local_index]->getPos(pos); |
589 | + | atoms[local_index]->getVel(vel); |
590 | + | |
591 | //format the line | |
592 | sprintf( tempBuffer, | |
593 | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", | |
594 | atoms[local_index]->getType(), | |
595 | < | atoms[local_index]->getX(), |
596 | < | atoms[local_index]->getY(), |
597 | < | atoms[local_index]->getZ(), |
598 | < | atoms[local_index]->get_vx(), |
599 | < | atoms[local_index]->get_vy(), |
600 | < | atoms[local_index]->get_vz()); // check here. |
595 | > | pos[0], |
596 | > | pos[1], |
597 | > | pos[2], |
598 | > | vel[0], |
599 | > | vel[1], |
600 | > | vel[2]); // check here. |
601 | strcpy( writeLine, tempBuffer ); | |
602 | ||
603 | if( atoms[local_index]->isDirectional() ){ |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |