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 |
|
|
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 |
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){ |
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); |
157 |
|
strcpy( painCave.errMsg, parseErr ); |
158 |
|
painCave.isFatal = 1; |
159 |
|
simError(); |
160 |
< |
} |
160 |
> |
} |
161 |
|
} |
162 |
|
|
163 |
|
|
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 |
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 |
|
|
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 |
|
|
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 |
|
} |
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; |
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 |
|
|
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){ |
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){ |
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 |
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){ |
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){ |
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 |
532 |
|
|
533 |
|
// add the positions and velocities to the atom |
534 |
|
|
535 |
< |
atoms[atomIndex]->setX( rx ); |
536 |
< |
atoms[atomIndex]->setY( ry ); |
537 |
< |
atoms[atomIndex]->setZ( rz ); |
538 |
< |
|
539 |
< |
atoms[atomIndex]->set_vx( vx ); |
540 |
< |
atoms[atomIndex]->set_vy( vy ); |
541 |
< |
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 |
|
|