# | Line 1 | Line 1 | |
---|---|---|
1 | + | #define _FILE_OFFSET_BITS 64 |
2 | #include <iostream> | |
3 | < | #include <cmath> |
3 | > | #include <math.h> |
4 | ||
5 | #include <stdio.h> | |
6 | #include <stdlib.h> | |
# | Line 13 | Line 14 | |
14 | ||
15 | #ifdef IS_MPI | |
16 | #include <mpi.h> | |
16 | – | #include <mpi++.h> |
17 | #include "mpiSimulation.hpp" | |
18 | #define TAKE_THIS_TAG_CHAR 0 | |
19 | #define TAKE_THIS_TAG_INT 1 | |
# | Line 27 | Line 27 | using namespace initFile; | |
27 | ||
28 | #endif // is_mpi | |
29 | ||
30 | < | InitializeFromFile :: InitializeFromFile( char *in_name ){ |
30 | > | InitializeFromFile::InitializeFromFile( char *in_name ){ |
31 | > | |
32 | #ifdef IS_MPI | |
33 | if (worldRank == 0) { | |
34 | #endif | |
# | Line 49 | Line 50 | InitializeFromFile :: InitializeFromFile( char *in_nam | |
50 | return; | |
51 | } | |
52 | ||
53 | < | InitializeFromFile :: ~InitializeFromFile( ){ |
53 | > | InitializeFromFile::~InitializeFromFile( ){ |
54 | #ifdef IS_MPI | |
55 | if (worldRank == 0) { | |
56 | #endif | |
# | Line 70 | Line 71 | InitializeFromFile :: ~InitializeFromFile( ){ | |
71 | } | |
72 | ||
73 | ||
74 | < | void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
74 | > | void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ |
75 | ||
76 | < | int i, j, done, which_node, which_atom; // loop counter |
76 | > | int i, j; |
77 | > | |
78 | > | #ifdef IS_MPI |
79 | > | int done, which_node, which_atom; // loop counter |
80 | > | #endif //is_mpi |
81 | ||
82 | const int BUFFERSIZE = 2000; // size of the read buffer | |
83 | int n_atoms; // the number of atoms | |
84 | char read_buffer[BUFFERSIZE]; //the line buffer for reading | |
80 | – | #ifdef IS_MPI |
81 | – | char send_buffer[BUFFERSIZE]; |
82 | – | #endif |
85 | ||
86 | char *eof_test; // ptr to see when we reach the end of the file | |
87 | char *parseErr; | |
86 | – | int procIndex; |
88 | ||
89 | < | entry_plug = the_entry_plug; |
89 | > | double currTime; |
90 | > | double boxMat[9]; |
91 | > | double theBoxMat3[3][3]; |
92 | ||
93 | + | simnfo = the_simnfo; |
94 | ||
95 | + | |
96 | #ifndef IS_MPI | |
97 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
98 | if( eof_test == NULL ){ | |
# | Line 100 | Line 105 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
105 | ||
106 | n_atoms = atoi( read_buffer ); | |
107 | ||
108 | < | Atom **atoms = entry_plug->atoms; |
104 | < | DirectionalAtom* dAtom; |
105 | < | |
106 | < | 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 122 | 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 141 | 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 154 | 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 164 | Line 180 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
180 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
181 | if( eof_test == NULL ){ | |
182 | sprintf( painCave.errMsg, | |
183 | < | "Error reading 1st line of %d \n ",c_in_name); |
183 | > | "Error reading 1st line of %s \n ",c_in_name); |
184 | haveError = 1; | |
185 | simError(); | |
186 | } | |
187 | ||
188 | n_atoms = atoi( read_buffer ); | |
189 | ||
174 | – | Atom **atoms = entry_plug->atoms; |
175 | – | DirectionalAtom* dAtom; |
176 | – | |
190 | // Check to see that the number of atoms in the intial configuration file is the | |
191 | // same as declared in simBass. | |
192 | ||
# | Line 181 | Line 194 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
194 | sprintf( painCave.errMsg, | |
195 | "Initialize from File error. %s n_atoms, %d, " | |
196 | "does not match the BASS file's n_atoms, %d.\n", | |
197 | < | c_in_name, n_atoms, entry_plug->n_atoms ); |
197 | > | c_in_name, n_atoms, simnfo->n_atoms ); |
198 | haveError= 1; | |
199 | simError(); | |
200 | } | |
201 | ||
202 | < | //read and toss the comment line |
202 | > | //read the boxMat from the comment line |
203 | ||
204 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
205 | if(eof_test == NULL){ | |
206 | sprintf( painCave.errMsg, | |
207 | "error in reading commment in %s\n", c_in_name); | |
208 | < | haveError= 1; |
208 | > | haveError = 1; |
209 | simError(); | |
210 | } | |
211 | + | |
212 | + | parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
213 | + | if( parseErr != NULL ){ |
214 | + | strcpy( painCave.errMsg, parseErr ); |
215 | + | haveError = 1; |
216 | + | simError(); |
217 | + | } |
218 | + | |
219 | + | MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
220 | + | MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
221 | ||
222 | if(haveError) nodeZeroError(); | |
223 | ||
# | Line 228 | Line 251 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
251 | else { | |
252 | ||
253 | myStatus = 1; | |
254 | < | MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
255 | < | TAKE_THIS_TAG_INT); |
256 | < | MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
257 | < | TAKE_THIS_TAG_CHAR); |
258 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
259 | < | MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, istatus); |
254 | > | MPI_Send(&myStatus, 1, MPI_INT, which_node, |
255 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
256 | > | MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
257 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
258 | > | MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
259 | > | MPI_COMM_WORLD); |
260 | > | MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
261 | > | MPI_COMM_WORLD, &istatus); |
262 | ||
263 | if(!myStatus) nodeZeroError(); | |
264 | } | |
265 | } | |
266 | myStatus = -1; | |
267 | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { | |
268 | < | MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
269 | < | TAKE_THIS_TAG_INT); |
268 | > | MPI_Send( &myStatus, 1, MPI_INT, j, |
269 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
270 | } | |
271 | ||
272 | } else { | |
273 | ||
274 | + | MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
275 | + | MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
276 | + | |
277 | done = 0; | |
278 | while (!done) { | |
279 | ||
280 | < | MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
281 | < | TAKE_THIS_TAG_INT, istatus); |
280 | > | MPI_Recv(&myStatus, 1, MPI_INT, 0, |
281 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
282 | ||
283 | if(!myStatus) anonymousNodeDie(); | |
284 | ||
285 | if(myStatus < 0) break; | |
286 | ||
287 | < | MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
288 | < | TAKE_THIS_TAG_CHAR, istatus); |
289 | < | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
290 | < | TAKE_THIS_TAG_INT, istatus); |
287 | > | MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
288 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
289 | > | MPI_Recv(&which_atom, 1, MPI_INT, 0, |
290 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
291 | ||
292 | myStatus = 1; | |
293 | parseErr = parseDumpLine( read_buffer, which_atom ); | |
# | Line 269 | Line 297 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
297 | simError(); | |
298 | } | |
299 | ||
300 | < | MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
301 | < | TAKE_THIS_TAG_INT); |
300 | > | MPI_Send( &myStatus, 1, MPI_INT, 0, |
301 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
302 | ||
303 | } | |
304 | } | |
305 | ||
306 | // last thing last, enable fatalities. | |
307 | painCave.isEventLoop = 0; | |
308 | + | |
309 | + | for(i=0;i<3;i++) |
310 | + | for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
311 | + | |
312 | + | simnfo->setBoxM( theBoxMat3 ); |
313 | + | simnfo->setTime( currTime ); |
314 | + | |
315 | ||
316 | #endif | |
317 | } | |
# | Line 285 | Line 320 | char* InitializeFromFile::parseDumpLine(char* readLine | |
320 | ||
321 | char *foo; // the pointer to the current string token | |
322 | ||
323 | < | double rx, ry, rz; // position place holders |
324 | < | double vx, vy, vz; // velocity placeholders |
323 | > | double pos[3]; // position place holders |
324 | > | double vel[3]; // velocity placeholders |
325 | double q[4]; // the quaternions | |
326 | double jx, jy, jz; // angular velocity placeholders; | |
327 | double qSqr, qLength; // needed to normalize the quaternion vector. | |
328 | ||
329 | < | Atom **atoms = entry_plug->atoms; |
329 | > | Atom **atoms = simnfo->atoms; |
330 | DirectionalAtom* dAtom; | |
331 | ||
332 | < | int j, n_atoms, atomIndex; |
332 | > | int n_atoms, atomIndex; |
333 | ||
334 | #ifdef IS_MPI | |
335 | + | int j; |
336 | + | |
337 | n_atoms = mpiSim->getTotAtoms(); | |
338 | atomIndex=-1; | |
339 | for (j=0; j < mpiSim->getMyNlocal(); j++) { | |
# | Line 310 | Line 347 | char* InitializeFromFile::parseDumpLine(char* readLine | |
347 | return strdup( painCave.errMsg ); | |
348 | } | |
349 | #else | |
350 | < | n_atoms = entry_plug->n_atoms; |
350 | > | n_atoms = simnfo->n_atoms; |
351 | atomIndex = globalIndex; | |
352 | #endif // is_mpi | |
353 | ||
# | Line 339 | Line 376 | char* InitializeFromFile::parseDumpLine(char* readLine | |
376 | c_in_name, n_atoms, atomIndex ); | |
377 | return strdup( painCave.errMsg ); | |
378 | } | |
379 | < | rx = atof( foo ); |
379 | > | pos[0] = atof( foo ); |
380 | ||
381 | foo = strtok(NULL, " ,;\t"); | |
382 | if(foo == NULL){ | |
# | Line 349 | Line 386 | char* InitializeFromFile::parseDumpLine(char* readLine | |
386 | c_in_name, n_atoms, atomIndex ); | |
387 | return strdup( painCave.errMsg ); | |
388 | } | |
389 | < | ry = atof( foo ); |
389 | > | pos[1] = atof( foo ); |
390 | ||
391 | foo = strtok(NULL, " ,;\t"); | |
392 | if(foo == NULL){ | |
# | Line 359 | Line 396 | char* InitializeFromFile::parseDumpLine(char* readLine | |
396 | c_in_name, n_atoms, atomIndex ); | |
397 | return strdup( painCave.errMsg ); | |
398 | } | |
399 | < | rz = atof( foo ); |
399 | > | pos[2] = atof( foo ); |
400 | ||
401 | ||
402 | // get the velocities | |
# | Line 372 | Line 409 | char* InitializeFromFile::parseDumpLine(char* readLine | |
409 | c_in_name, n_atoms, atomIndex ); | |
410 | return strdup( painCave.errMsg ); | |
411 | } | |
412 | < | vx = atof( foo ); |
412 | > | vel[0] = atof( foo ); |
413 | ||
414 | foo = strtok(NULL, " ,;\t"); | |
415 | if(foo == NULL){ | |
# | Line 382 | Line 419 | char* InitializeFromFile::parseDumpLine(char* readLine | |
419 | c_in_name, n_atoms, atomIndex ); | |
420 | return strdup( painCave.errMsg ); | |
421 | } | |
422 | < | vy = atof( foo ); |
422 | > | vel[1] = atof( foo ); |
423 | ||
424 | foo = strtok(NULL, " ,;\t"); | |
425 | if(foo == NULL){ | |
# | Line 392 | Line 429 | char* InitializeFromFile::parseDumpLine(char* readLine | |
429 | c_in_name, n_atoms, atomIndex ); | |
430 | return strdup( painCave.errMsg ); | |
431 | } | |
432 | < | vz = atof( foo ); |
432 | > | vel[2] = atof( foo ); |
433 | ||
434 | ||
435 | // get the quaternions | |
# | Line 494 | Line 531 | char* InitializeFromFile::parseDumpLine(char* readLine | |
531 | ||
532 | // add the positions and velocities to the atom | |
533 | ||
534 | < | atoms[atomIndex]->setX( rx ); |
535 | < | atoms[atomIndex]->setY( ry ); |
499 | < | atoms[atomIndex]->setZ( rz ); |
500 | < | |
501 | < | atoms[atomIndex]->set_vx( vx ); |
502 | < | atoms[atomIndex]->set_vy( vy ); |
503 | < | atoms[atomIndex]->set_vz( vz ); |
534 | > | atoms[atomIndex]->setPos( pos ); |
535 | > | atoms[atomIndex]->setVel( vel ); |
536 | ||
537 | return NULL; | |
538 | } | |
539 | ||
540 | ||
541 | + | char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9], |
542 | + | double &time ){ |
543 | + | |
544 | + | char *foo; // the pointer to the current string token |
545 | + | |
546 | + | // set the string tokenizer |
547 | + | |
548 | + | foo = strtok(readLine, " ,;\t"); |
549 | + | // set the timeToken. |
550 | + | |
551 | + | if(foo == NULL){ |
552 | + | sprintf( painCave.errMsg, |
553 | + | "error in reading Time from %s\n", |
554 | + | c_in_name ); |
555 | + | return strdup( painCave.errMsg ); |
556 | + | } |
557 | + | time = atof( foo ); |
558 | + | |
559 | + | // get the Hx vector |
560 | + | |
561 | + | foo = strtok(NULL, " ,;\t"); |
562 | + | if(foo == NULL){ |
563 | + | sprintf( painCave.errMsg, |
564 | + | "error in reading Hx[0] from %s\n", |
565 | + | c_in_name ); |
566 | + | return strdup( painCave.errMsg ); |
567 | + | } |
568 | + | boxMat[0] = atof( foo ); |
569 | + | |
570 | + | foo = strtok(NULL, " ,;\t"); |
571 | + | if(foo == NULL){ |
572 | + | sprintf( painCave.errMsg, |
573 | + | "error in reading Hx[1] from %s\n", |
574 | + | c_in_name ); |
575 | + | return strdup( painCave.errMsg ); |
576 | + | } |
577 | + | boxMat[1] = atof( foo ); |
578 | + | |
579 | + | foo = strtok(NULL, " ,;\t"); |
580 | + | if(foo == NULL){ |
581 | + | sprintf( painCave.errMsg, |
582 | + | "error in reading Hx[2] from %s\n", |
583 | + | c_in_name ); |
584 | + | return strdup( painCave.errMsg ); |
585 | + | } |
586 | + | boxMat[2] = atof( foo ); |
587 | + | |
588 | + | // get the Hy vector |
589 | + | |
590 | + | foo = strtok(NULL, " ,;\t"); |
591 | + | if(foo == NULL){ |
592 | + | sprintf( painCave.errMsg, |
593 | + | "error in reading Hy[0] from %s\n", |
594 | + | c_in_name ); |
595 | + | return strdup( painCave.errMsg ); |
596 | + | } |
597 | + | boxMat[3] = atof( foo ); |
598 | + | |
599 | + | foo = strtok(NULL, " ,;\t"); |
600 | + | if(foo == NULL){ |
601 | + | sprintf( painCave.errMsg, |
602 | + | "error in reading Hy[1] from %s\n", |
603 | + | c_in_name ); |
604 | + | return strdup( painCave.errMsg ); |
605 | + | } |
606 | + | boxMat[4] = atof( foo ); |
607 | + | |
608 | + | foo = strtok(NULL, " ,;\t"); |
609 | + | if(foo == NULL){ |
610 | + | sprintf( painCave.errMsg, |
611 | + | "error in reading Hy[2] from %s\n", |
612 | + | c_in_name ); |
613 | + | return strdup( painCave.errMsg ); |
614 | + | } |
615 | + | boxMat[5] = atof( foo ); |
616 | + | |
617 | + | // get the Hz vector |
618 | + | |
619 | + | foo = strtok(NULL, " ,;\t"); |
620 | + | if(foo == NULL){ |
621 | + | sprintf( painCave.errMsg, |
622 | + | "error in reading Hz[0] from %s\n", |
623 | + | c_in_name ); |
624 | + | return strdup( painCave.errMsg ); |
625 | + | } |
626 | + | boxMat[6] = atof( foo ); |
627 | + | |
628 | + | foo = strtok(NULL, " ,;\t"); |
629 | + | if(foo == NULL){ |
630 | + | sprintf( painCave.errMsg, |
631 | + | "error in reading Hz[1] from %s\n", |
632 | + | c_in_name ); |
633 | + | return strdup( painCave.errMsg ); |
634 | + | } |
635 | + | boxMat[7] = atof( foo ); |
636 | + | |
637 | + | foo = strtok(NULL, " ,;\t"); |
638 | + | if(foo == NULL){ |
639 | + | sprintf( painCave.errMsg, |
640 | + | "error in reading Hz[2] from %s\n", |
641 | + | c_in_name ); |
642 | + | return strdup( painCave.errMsg ); |
643 | + | } |
644 | + | boxMat[8] = atof( foo ); |
645 | + | |
646 | + | return NULL; |
647 | + | } |
648 | + | |
649 | + | |
650 | #ifdef IS_MPI | |
651 | ||
652 | // a couple of functions to let us escape the read loop | |
# | Line 515 | Line 656 | void initFile::nodeZeroError( void ){ | |
656 | ||
657 | myStatus = 0; | |
658 | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { | |
659 | < | MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
660 | < | TAKE_THIS_TAG_INT); |
659 | > | MPI_Send( &myStatus, 1, MPI_INT, j, |
660 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
661 | } | |
662 | ||
663 |
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+ | Added lines |
< | Changed lines |
> | Changed lines |