# | Line 13 | Line 13 | |
---|---|---|
13 | ||
14 | #ifdef IS_MPI | |
15 | #include <mpi.h> | |
16 | – | #include <mpi++.h> |
16 | #include "mpiSimulation.hpp" | |
17 | #define TAKE_THIS_TAG_CHAR 0 | |
18 | #define TAKE_THIS_TAG_INT 1 | |
19 | ||
20 | < | void nodeZeroError( void ); |
21 | < | void anonymousNodeDie( void ); |
20 | > | namespace initFile{ |
21 | > | void nodeZeroError( void ); |
22 | > | void anonymousNodeDie( void ); |
23 | > | } |
24 | ||
25 | + | using namespace initFile; |
26 | + | |
27 | #endif // is_mpi | |
28 | ||
29 | InitializeFromFile :: InitializeFromFile( char *in_name ){ | |
# | Line 66 | Line 69 | InitializeFromFile :: ~InitializeFromFile( ){ | |
69 | } | |
70 | ||
71 | ||
72 | < | void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
72 | > | void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ |
73 | ||
74 | int i, j, done, which_node, which_atom; // loop counter | |
75 | ||
# | Line 80 | Line 83 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
83 | char *eof_test; // ptr to see when we reach the end of the file | |
84 | char *parseErr; | |
85 | int procIndex; | |
86 | + | double currTime; |
87 | + | double boxMat[9]; |
88 | + | double theBoxMat3[3][3]; |
89 | ||
90 | < | entry_plug = the_entry_plug; |
90 | > | simnfo = the_simnfo; |
91 | ||
92 | ||
93 | #ifndef IS_MPI | |
# | Line 96 | Line 102 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
102 | ||
103 | n_atoms = atoi( read_buffer ); | |
104 | ||
105 | < | Atom **atoms = entry_plug->atoms; |
105 | > | Atom **atoms = simnfo->atoms; |
106 | DirectionalAtom* dAtom; | |
107 | ||
108 | < | if( n_atoms != entry_plug->n_atoms ){ |
108 | > | if( n_atoms != simnfo->n_atoms ){ |
109 | sprintf( painCave.errMsg, | |
110 | "Initialize from File error. %s n_atoms, %d, " | |
111 | "does not match the BASS file's n_atoms, %d.\n", | |
112 | < | c_in_name, n_atoms, entry_plug->n_atoms ); |
112 | > | c_in_name, n_atoms, simnfo->n_atoms ); |
113 | painCave.isFatal = 1; | |
114 | simError(); | |
115 | } | |
116 | ||
117 | < | //read and toss the comment line |
117 | > | //read the box mat from the comment line |
118 | ||
119 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
120 | if(eof_test == NULL){ | |
# | Line 118 | Line 124 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
124 | simError(); | |
125 | } | |
126 | ||
127 | + | parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
128 | + | if( parseErr != NULL ){ |
129 | + | strcpy( painCave.errMsg, parseErr ); |
130 | + | painCave.isFatal = 1; |
131 | + | simError(); |
132 | + | } |
133 | + | |
134 | + | for(i=0;i<3;i++) |
135 | + | for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
136 | + | |
137 | + | simnfo->setBoxM( theBoxMat3 ); |
138 | + | simnfo->setTime( currTime ); |
139 | + | |
140 | + | |
141 | for( i=0; i < n_atoms; i++){ | |
142 | ||
143 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
# | Line 137 | Line 157 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
157 | strcpy( painCave.errMsg, parseErr ); | |
158 | painCave.isFatal = 1; | |
159 | simError(); | |
160 | < | } |
160 | > | } |
161 | } | |
162 | ||
163 | ||
# | Line 150 | Line 170 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
170 | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone | |
171 | int haveError; | |
172 | ||
173 | < | MPI::Status istatus; |
173 | > | MPI_Status istatus; |
174 | int *AtomToProcMap = mpiSim->getAtomToProcMap(); | |
175 | ||
176 | ||
# | Line 167 | Line 187 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
187 | ||
188 | n_atoms = atoi( read_buffer ); | |
189 | ||
190 | < | Atom **atoms = entry_plug->atoms; |
190 | > | Atom **atoms = simnfo->atoms; |
191 | DirectionalAtom* dAtom; | |
192 | ||
193 | // Check to see that the number of atoms in the intial configuration file is the | |
# | Line 177 | Line 197 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
197 | sprintf( painCave.errMsg, | |
198 | "Initialize from File error. %s n_atoms, %d, " | |
199 | "does not match the BASS file's n_atoms, %d.\n", | |
200 | < | c_in_name, n_atoms, entry_plug->n_atoms ); |
200 | > | c_in_name, n_atoms, simnfo->n_atoms ); |
201 | haveError= 1; | |
202 | simError(); | |
203 | } | |
204 | ||
205 | < | //read and toss the comment line |
205 | > | //read the boxMat from the comment line |
206 | ||
207 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
208 | if(eof_test == NULL){ | |
209 | sprintf( painCave.errMsg, | |
210 | "error in reading commment in %s\n", c_in_name); | |
211 | < | haveError= 1; |
211 | > | haveError = 1; |
212 | simError(); | |
213 | } | |
214 | + | |
215 | + | parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
216 | + | if( parseErr != NULL ){ |
217 | + | strcpy( painCave.errMsg, parseErr ); |
218 | + | haveError = 1; |
219 | + | simError(); |
220 | + | } |
221 | + | |
222 | + | MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
223 | + | MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
224 | ||
225 | if(haveError) nodeZeroError(); | |
226 | ||
# | Line 224 | Line 254 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
254 | else { | |
255 | ||
256 | myStatus = 1; | |
257 | < | MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
258 | < | TAKE_THIS_TAG_INT); |
259 | < | MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
260 | < | TAKE_THIS_TAG_CHAR); |
261 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
262 | < | MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, istatus); |
257 | > | MPI_Send(&myStatus, 1, MPI_INT, which_node, |
258 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
259 | > | MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
260 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
261 | > | MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
262 | > | MPI_COMM_WORLD); |
263 | > | MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
264 | > | MPI_COMM_WORLD, &istatus); |
265 | ||
266 | if(!myStatus) nodeZeroError(); | |
267 | } | |
268 | } | |
269 | myStatus = -1; | |
270 | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { | |
271 | < | MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
272 | < | TAKE_THIS_TAG_INT); |
271 | > | MPI_Send( &myStatus, 1, MPI_INT, j, |
272 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
273 | } | |
274 | ||
275 | } else { | |
276 | ||
277 | + | MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
278 | + | MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
279 | + | |
280 | done = 0; | |
281 | while (!done) { | |
282 | ||
283 | < | MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
284 | < | TAKE_THIS_TAG_INT, istatus); |
283 | > | MPI_Recv(&myStatus, 1, MPI_INT, 0, |
284 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
285 | ||
286 | if(!myStatus) anonymousNodeDie(); | |
287 | ||
288 | if(myStatus < 0) break; | |
289 | ||
290 | < | MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
291 | < | TAKE_THIS_TAG_CHAR, istatus); |
292 | < | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
293 | < | TAKE_THIS_TAG_INT, istatus); |
290 | > | MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
291 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
292 | > | MPI_Recv(&which_atom, 1, MPI_INT, 0, |
293 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
294 | ||
295 | myStatus = 1; | |
296 | parseErr = parseDumpLine( read_buffer, which_atom ); | |
# | Line 265 | Line 300 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
300 | simError(); | |
301 | } | |
302 | ||
303 | < | MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
304 | < | TAKE_THIS_TAG_INT); |
303 | > | MPI_Send( &myStatus, 1, MPI_INT, 0, |
304 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
305 | ||
306 | } | |
307 | } | |
308 | ||
309 | // last thing last, enable fatalities. | |
310 | painCave.isEventLoop = 0; | |
311 | + | |
312 | + | for(i=0;i<3;i++) |
313 | + | for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
314 | + | |
315 | + | simnfo->setBoxM( theBoxMat3 ); |
316 | + | simnfo->setTime( currTime ); |
317 | + | |
318 | ||
319 | #endif | |
320 | } | |
# | Line 281 | Line 323 | char* InitializeFromFile::parseDumpLine(char* readLine | |
323 | ||
324 | char *foo; // the pointer to the current string token | |
325 | ||
326 | < | double rx, ry, rz; // position place holders |
327 | < | double vx, vy, vz; // velocity placeholders |
326 | > | double pos[3]; // position place holders |
327 | > | double vel[3]; // velocity placeholders |
328 | double q[4]; // the quaternions | |
329 | double jx, jy, jz; // angular velocity placeholders; | |
330 | double qSqr, qLength; // needed to normalize the quaternion vector. | |
331 | ||
332 | < | Atom **atoms = entry_plug->atoms; |
332 | > | Atom **atoms = simnfo->atoms; |
333 | DirectionalAtom* dAtom; | |
334 | ||
335 | int j, n_atoms, atomIndex; | |
# | Line 306 | Line 348 | char* InitializeFromFile::parseDumpLine(char* readLine | |
348 | return strdup( painCave.errMsg ); | |
349 | } | |
350 | #else | |
351 | < | n_atoms = entry_plug->n_atoms; |
351 | > | n_atoms = simnfo->n_atoms; |
352 | atomIndex = globalIndex; | |
353 | #endif // is_mpi | |
354 | ||
# | Line 335 | Line 377 | char* InitializeFromFile::parseDumpLine(char* readLine | |
377 | c_in_name, n_atoms, atomIndex ); | |
378 | return strdup( painCave.errMsg ); | |
379 | } | |
380 | < | rx = atof( foo ); |
380 | > | pos[0] = atof( foo ); |
381 | ||
382 | foo = strtok(NULL, " ,;\t"); | |
383 | if(foo == NULL){ | |
# | Line 345 | Line 387 | char* InitializeFromFile::parseDumpLine(char* readLine | |
387 | c_in_name, n_atoms, atomIndex ); | |
388 | return strdup( painCave.errMsg ); | |
389 | } | |
390 | < | ry = atof( foo ); |
390 | > | pos[1] = atof( foo ); |
391 | ||
392 | foo = strtok(NULL, " ,;\t"); | |
393 | if(foo == NULL){ | |
# | Line 355 | Line 397 | char* InitializeFromFile::parseDumpLine(char* readLine | |
397 | c_in_name, n_atoms, atomIndex ); | |
398 | return strdup( painCave.errMsg ); | |
399 | } | |
400 | < | rz = atof( foo ); |
400 | > | pos[2] = atof( foo ); |
401 | ||
402 | ||
403 | // get the velocities | |
# | Line 368 | Line 410 | char* InitializeFromFile::parseDumpLine(char* readLine | |
410 | c_in_name, n_atoms, atomIndex ); | |
411 | return strdup( painCave.errMsg ); | |
412 | } | |
413 | < | vx = atof( foo ); |
413 | > | vel[0] = atof( foo ); |
414 | ||
415 | foo = strtok(NULL, " ,;\t"); | |
416 | if(foo == NULL){ | |
# | Line 378 | Line 420 | char* InitializeFromFile::parseDumpLine(char* readLine | |
420 | c_in_name, n_atoms, atomIndex ); | |
421 | return strdup( painCave.errMsg ); | |
422 | } | |
423 | < | vy = atof( foo ); |
423 | > | vel[1] = atof( foo ); |
424 | ||
425 | foo = strtok(NULL, " ,;\t"); | |
426 | if(foo == NULL){ | |
# | Line 388 | Line 430 | char* InitializeFromFile::parseDumpLine(char* readLine | |
430 | c_in_name, n_atoms, atomIndex ); | |
431 | return strdup( painCave.errMsg ); | |
432 | } | |
433 | < | vz = atof( foo ); |
433 | > | vel[2] = atof( foo ); |
434 | ||
435 | ||
436 | // get the quaternions | |
# | Line 490 | Line 532 | char* InitializeFromFile::parseDumpLine(char* readLine | |
532 | ||
533 | // add the positions and velocities to the atom | |
534 | ||
535 | < | atoms[atomIndex]->setX( rx ); |
536 | < | atoms[atomIndex]->setY( ry ); |
495 | < | atoms[atomIndex]->setZ( rz ); |
496 | < | |
497 | < | atoms[atomIndex]->set_vx( vx ); |
498 | < | atoms[atomIndex]->set_vy( vy ); |
499 | < | atoms[atomIndex]->set_vz( vz ); |
535 | > | atoms[atomIndex]->setPos( pos ); |
536 | > | atoms[atomIndex]->setVel( vel ); |
537 | ||
538 | return NULL; | |
539 | } | |
540 | ||
541 | ||
542 | + | char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9], |
543 | + | double &time ){ |
544 | + | |
545 | + | char *foo; // the pointer to the current string token |
546 | + | int j; |
547 | + | |
548 | + | // set the string tokenizer |
549 | + | |
550 | + | foo = strtok(readLine, " ,;\t"); |
551 | + | // set the timeToken. |
552 | + | |
553 | + | if(foo == NULL){ |
554 | + | sprintf( painCave.errMsg, |
555 | + | "error in reading Time from %s\n", |
556 | + | c_in_name ); |
557 | + | return strdup( painCave.errMsg ); |
558 | + | } |
559 | + | time = atof( foo ); |
560 | + | |
561 | + | // get the Hx vector |
562 | + | |
563 | + | foo = strtok(NULL, " ,;\t"); |
564 | + | if(foo == NULL){ |
565 | + | sprintf( painCave.errMsg, |
566 | + | "error in reading Hx[0] from %s\n", |
567 | + | c_in_name ); |
568 | + | return strdup( painCave.errMsg ); |
569 | + | } |
570 | + | boxMat[0] = atof( foo ); |
571 | + | |
572 | + | foo = strtok(NULL, " ,;\t"); |
573 | + | if(foo == NULL){ |
574 | + | sprintf( painCave.errMsg, |
575 | + | "error in reading Hx[1] from %s\n", |
576 | + | c_in_name ); |
577 | + | return strdup( painCave.errMsg ); |
578 | + | } |
579 | + | boxMat[1] = atof( foo ); |
580 | + | |
581 | + | foo = strtok(NULL, " ,;\t"); |
582 | + | if(foo == NULL){ |
583 | + | sprintf( painCave.errMsg, |
584 | + | "error in reading Hx[2] from %s\n", |
585 | + | c_in_name ); |
586 | + | return strdup( painCave.errMsg ); |
587 | + | } |
588 | + | boxMat[2] = atof( foo ); |
589 | + | |
590 | + | // get the Hy vector |
591 | + | |
592 | + | foo = strtok(NULL, " ,;\t"); |
593 | + | if(foo == NULL){ |
594 | + | sprintf( painCave.errMsg, |
595 | + | "error in reading Hy[0] from %s\n", |
596 | + | c_in_name ); |
597 | + | return strdup( painCave.errMsg ); |
598 | + | } |
599 | + | boxMat[3] = atof( foo ); |
600 | + | |
601 | + | foo = strtok(NULL, " ,;\t"); |
602 | + | if(foo == NULL){ |
603 | + | sprintf( painCave.errMsg, |
604 | + | "error in reading Hy[1] from %s\n", |
605 | + | c_in_name ); |
606 | + | return strdup( painCave.errMsg ); |
607 | + | } |
608 | + | boxMat[4] = atof( foo ); |
609 | + | |
610 | + | foo = strtok(NULL, " ,;\t"); |
611 | + | if(foo == NULL){ |
612 | + | sprintf( painCave.errMsg, |
613 | + | "error in reading Hy[2] from %s\n", |
614 | + | c_in_name ); |
615 | + | return strdup( painCave.errMsg ); |
616 | + | } |
617 | + | boxMat[5] = atof( foo ); |
618 | + | |
619 | + | // get the Hz vector |
620 | + | |
621 | + | foo = strtok(NULL, " ,;\t"); |
622 | + | if(foo == NULL){ |
623 | + | sprintf( painCave.errMsg, |
624 | + | "error in reading Hz[0] from %s\n", |
625 | + | c_in_name ); |
626 | + | return strdup( painCave.errMsg ); |
627 | + | } |
628 | + | boxMat[6] = atof( foo ); |
629 | + | |
630 | + | foo = strtok(NULL, " ,;\t"); |
631 | + | if(foo == NULL){ |
632 | + | sprintf( painCave.errMsg, |
633 | + | "error in reading Hz[1] from %s\n", |
634 | + | c_in_name ); |
635 | + | return strdup( painCave.errMsg ); |
636 | + | } |
637 | + | boxMat[7] = atof( foo ); |
638 | + | |
639 | + | foo = strtok(NULL, " ,;\t"); |
640 | + | if(foo == NULL){ |
641 | + | sprintf( painCave.errMsg, |
642 | + | "error in reading Hz[2] from %s\n", |
643 | + | c_in_name ); |
644 | + | return strdup( painCave.errMsg ); |
645 | + | } |
646 | + | boxMat[8] = atof( foo ); |
647 | + | |
648 | + | return NULL; |
649 | + | } |
650 | + | |
651 | + | |
652 | #ifdef IS_MPI | |
653 | ||
654 | // a couple of functions to let us escape the read loop | |
655 | ||
656 | < | void nodeZeroError( void ){ |
656 | > | void initFile::nodeZeroError( void ){ |
657 | int j, myStatus; | |
658 | ||
659 | myStatus = 0; | |
660 | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { | |
661 | < | MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
662 | < | TAKE_THIS_TAG_INT); |
661 | > | MPI_Send( &myStatus, 1, MPI_INT, j, |
662 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
663 | } | |
664 | ||
665 | ||
# | Line 521 | Line 668 | void nodeZeroError( void ){ | |
668 | ||
669 | } | |
670 | ||
671 | < | void anonymousNodeDie( void ){ |
671 | > | void initFile::anonymousNodeDie( void ){ |
672 | ||
673 | MPI_Finalize(); | |
674 | exit (0); |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |