7 |
|
|
8 |
|
#include "ForceFields.hpp" |
9 |
|
#include "SRI.hpp" |
10 |
+ |
#include "simError.h" |
11 |
|
|
12 |
|
|
13 |
|
#ifdef IS_MPI |
14 |
|
|
15 |
|
#include "mpiForceField.h" |
16 |
|
|
16 |
– |
int myNode; |
17 |
|
|
18 |
|
// Declare the structures that will be passed by MPI |
19 |
|
|
26 |
|
int isDipole; |
27 |
|
int last; // 0 -> default |
28 |
|
// 1 -> tells nodes to stop listening |
29 |
– |
// -1 -> an error has occured. (handled in mpiForceField) |
29 |
|
} atomStruct; |
30 |
|
MPI_Datatype mpiAtomStructType; |
31 |
|
|
36 |
|
double d0; |
37 |
|
int last; // 0 -> default |
38 |
|
// 1 -> tells nodes to stop listening |
40 |
– |
// -1 -> an error has occured. (handled in mpiForceField) |
39 |
|
} bondStruct; |
40 |
|
MPI_Datatype mpiBondStructType; |
41 |
|
|
47 |
|
double k1, k2, k3, t0; |
48 |
|
int last; // 0 -> default |
49 |
|
// 1 -> tells nodes to stop listening |
52 |
– |
// -1 -> an error has occured. (handled in mpiForceField) |
50 |
|
} bendStruct; |
51 |
|
MPI_Datatype mpiBendStructType; |
52 |
|
|
59 |
|
double k1, k2, k3, k4; |
60 |
|
int last; // 0 -> default |
61 |
|
// 1 -> tells nodes to stop listening |
62 |
< |
// -1 -> an error has occured. (handled in mpiForceField) |
66 |
< |
} TorsionStruct; |
62 |
> |
} torsionStruct; |
63 |
|
MPI_Datatype mpiTorsionStructType; |
64 |
|
|
65 |
|
#endif |
76 |
|
|
77 |
|
#ifdef IS_MPI |
78 |
|
int i; |
83 |
– |
int mpiError; |
84 |
– |
int cleanOpen = 0; |
79 |
|
|
80 |
< |
mpiError = MPI_Comm_rank(MPI_COMM_WORLD,&myNode); |
87 |
< |
|
88 |
< |
// ********************************************************************** |
80 |
> |
// ********************************************************************** |
81 |
|
// Init the atomStruct mpi type |
82 |
|
|
83 |
|
atomStruct atomProto; // mpiPrototype |
85 |
|
MPI_Aint atomDspls[3]; // displacements |
86 |
|
MPI_Datatype atomMbrTypes[3]; // member mpi types |
87 |
|
|
96 |
– |
|
97 |
– |
|
88 |
|
MPI_Address(&atomProto.name, &atomDspls[0]); |
89 |
|
MPI_Address(&atomProto.mass, &atomDspls[1]); |
90 |
|
MPI_Address(&atomProto.isDipole, &atomDspls[2]); |
167 |
|
|
168 |
|
// *********************************************************************** |
169 |
|
|
170 |
< |
if( myNode == 0 ){ |
170 |
> |
if( worldRank == 0 ){ |
171 |
|
#endif |
172 |
|
|
173 |
|
// generate the force file name |
185 |
|
|
186 |
|
ffPath = getenv( ffPath_env ); |
187 |
|
if( ffPath == NULL ) { |
188 |
< |
sprintf( errMsg, |
188 |
> |
sprintf( painCave.errMsg, |
189 |
|
"Error opening the force field parameter file: %s\n" |
190 |
|
"Have you tried setting the FORCE_PARAM_PATH environment " |
191 |
|
"vairable?\n", |
192 |
|
fileName ); |
193 |
< |
#ifdef IS_MPI |
194 |
< |
cleanOpen = 0; |
205 |
< |
mpiError = MPI_Bcast(cleanOpen,1,MPI_INT,0,MPI_COMM_WORLD); |
206 |
< |
#endif |
207 |
< |
ffError( errMsg ); |
193 |
> |
painCave.isFatal = 1; |
194 |
> |
simError(); |
195 |
|
} |
196 |
|
|
197 |
|
|
204 |
|
|
205 |
|
if( frcFile == NULL ){ |
206 |
|
|
207 |
< |
sprintf( errMsg, |
207 |
> |
sprintf( painCave.errMsg, |
208 |
|
"Error opening the force field parameter file: %s\n" |
209 |
|
"Have you tried setting the FORCE_PARAM_PATH environment " |
210 |
|
"vairable?\n", |
211 |
|
fileName ); |
212 |
< |
#ifdef IS_MPI |
213 |
< |
cleanOpen = 0; |
227 |
< |
mpiError = MPI_Bcast(cleanOpen,1,MPI_INT,0,MPI_COMM_WORLD); |
228 |
< |
#endif |
229 |
< |
ffError( errMsg ); |
212 |
> |
painCave.isFatal = 1; |
213 |
> |
simError(); |
214 |
|
} |
215 |
|
} |
216 |
< |
cleanOpen = 1; |
216 |
> |
|
217 |
|
#ifdef IS_MPI |
218 |
|
} |
219 |
< |
|
220 |
< |
mpiError = MPI_Bcast(cleanOpen,1,MPI_INT,0,MPI_COMM_WORLD); |
221 |
< |
if( !cleanOpen ) fferror( NULL ); |
222 |
< |
#endif |
219 |
> |
|
220 |
> |
sprintf( checkPointMsg, "TraPPE_ExFF file opened sucessfully." ); |
221 |
> |
MPIcheckPoint(); |
222 |
> |
|
223 |
> |
#endif // is_mpi |
224 |
|
} |
225 |
|
|
226 |
|
|
227 |
|
TraPPE_ExFF::~TraPPE_ExFF(){ |
228 |
< |
|
229 |
< |
fclose( frcFile ); |
228 |
> |
|
229 |
> |
#ifdef IS_MPI |
230 |
> |
if( worldRank == 0 ){ |
231 |
> |
#endif // is_mpi |
232 |
> |
|
233 |
> |
fclose( frcFile ); |
234 |
> |
|
235 |
> |
#ifdef IS_MPI |
236 |
> |
} |
237 |
> |
#endif // is_mpi |
238 |
|
} |
239 |
|
|
240 |
|
void TraPPE_ExFF::initializeAtoms( void ){ |
295 |
|
|
296 |
|
#ifdef IS_MPI |
297 |
|
atomStruct info; |
298 |
< |
info.last = -1; // initialize last to have the error set. |
299 |
< |
// if things go well, last will be set to 0 |
298 |
> |
info.last = 1; // initialize last to have the last set. |
299 |
> |
// if things go well, last will be set to 0 |
300 |
|
#endif |
301 |
|
|
302 |
|
|
306 |
|
int foundAtom = 0; |
307 |
|
int lineNum = 0; |
308 |
|
int i; |
316 |
– |
char errMsg[1000]; |
309 |
|
|
310 |
|
|
311 |
|
////////////////////////////////////////////////// |
349 |
|
|
350 |
|
|
351 |
|
#ifdef IS_MPI |
352 |
< |
if( myNode == 0 ){ |
352 |
> |
if( worldRank == 0 ){ |
353 |
|
#endif |
354 |
|
|
355 |
|
// read in the atom types. |
361 |
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
362 |
|
lineNum++; |
363 |
|
if( eof_test == NULL ){ |
364 |
< |
sprintf( errMsg, "Error in reading Atoms from force file.\n" ); |
365 |
< |
#ifdef IS_MPI |
366 |
< |
sendFrcStruct( &info, mpiAtomStructType ); |
375 |
< |
#endif |
376 |
< |
ffError(errMsg); |
364 |
> |
sprintf( painCave.errMsg, "Error in reading Atoms from force file.\n" ); |
365 |
> |
painCave.isFatal = 1; |
366 |
> |
simError(); |
367 |
|
} |
368 |
|
|
369 |
|
|
373 |
|
lineNum++; |
374 |
|
} |
375 |
|
if( eof_test == NULL ){ |
376 |
< |
sprintf( errMsg, |
376 |
> |
sprintf( painCave.errMsg, |
377 |
|
"Error in reading Atoms from force file at line %d.\n", |
378 |
|
lineNum ); |
379 |
< |
#ifdef IS_MPI |
380 |
< |
sendFrcStruct( &info, mpiAtomStructType ); |
391 |
< |
#endif |
392 |
< |
ffError(errMsg); |
379 |
> |
painCave.isFatal = 1; |
380 |
> |
simError(); |
381 |
|
} |
382 |
|
|
383 |
|
the_token = strtok( readLine, " ,;\t#\n" ); |
388 |
|
lineNum++; |
389 |
|
|
390 |
|
if( eof_test == NULL ){ |
391 |
< |
sprintf( errMsg, |
391 |
> |
sprintf( painCave.errMsg, |
392 |
|
"Error in reading Atoms from force file at line %d.\n", |
393 |
|
lineNum ); |
394 |
< |
#ifdef IS_MPI |
395 |
< |
sendFrcStruct( &info, mpiAtomStructType ); |
408 |
< |
#endif |
409 |
< |
ffError(errMsg); |
394 |
> |
painCave.isFatal = 1; |
395 |
> |
simError(); |
396 |
|
} |
397 |
|
} |
398 |
|
} |
403 |
|
lineNum++; |
404 |
|
|
405 |
|
if( eof_test == NULL ){ |
406 |
< |
sprintf( errMsg, |
406 |
> |
sprintf( painCave.errMsg, |
407 |
|
"Error in reading Atoms from force file at line %d.\n", |
408 |
|
lineNum ); |
409 |
< |
#ifdef IS_MPI |
410 |
< |
sendFrcStruct( &info, mpiAtomStructType ); |
425 |
< |
#endif |
426 |
< |
ffError(errMsg); |
409 |
> |
painCave.isFatal = 1; |
410 |
> |
simError(); |
411 |
|
} |
412 |
|
|
413 |
|
while( readLine[0] != '#' && eof_test != NULL ){ |
420 |
|
strcpy( currentAtomType->name, the_token ); |
421 |
|
|
422 |
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
423 |
< |
sprintf( errMsg, "Error parseing AtomTypes: line %d\n", lineNum ); |
424 |
< |
#ifdef IS_MPI |
425 |
< |
sendFrcStruct( &info, mpiAtomStructType ); |
426 |
< |
#endif |
443 |
< |
ffError(errMsg); |
423 |
> |
sprintf( painCave.errMsg, |
424 |
> |
"Error parseing AtomTypes: line %d\n", lineNum ); |
425 |
> |
painCave.isFatal = 1; |
426 |
> |
simError(); |
427 |
|
} |
428 |
|
|
429 |
|
sscanf( the_token, "%d", ¤tAtomType->isDipole ); |
430 |
|
|
431 |
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
432 |
< |
sprintf( errMsg, "Error parseing AtomTypes: line %d\n", lineNum ); |
433 |
< |
#ifdef IS_MPI |
434 |
< |
sendFrcStruct( &info, mpiAtomStructType ); |
435 |
< |
#endif |
453 |
< |
ffError(errMsg); |
432 |
> |
sprintf( painCave.errMsg, |
433 |
> |
"Error parseing AtomTypes: line %d\n", lineNum ); |
434 |
> |
painCave.isFatal = 1; |
435 |
> |
simError(); |
436 |
|
} |
437 |
|
|
438 |
|
sscanf( the_token, "%lf", ¤tAtomType->mass ); |
439 |
|
|
440 |
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
441 |
< |
sprintf( errMsg, "Error parseing AtomTypes: line %d\n", lineNum ); |
442 |
< |
#ifdef IS_MPI |
443 |
< |
sendFrcStruct( &info, mpiAtomStructType ); |
444 |
< |
#endif |
463 |
< |
ffError(errMsg); |
441 |
> |
sprintf( painCave.errMsg, |
442 |
> |
"Error parseing AtomTypes: line %d\n", lineNum ); |
443 |
> |
painCave.isFatal = 1; |
444 |
> |
simError(); |
445 |
|
} |
446 |
|
|
447 |
|
sscanf( the_token, "%lf", ¤tAtomType->epslon ); |
448 |
|
|
449 |
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
450 |
< |
sprintf( errMsg, "Error parseing AtomTypes: line %d\n", lineNum ); |
451 |
< |
#ifdef IS_MPI |
452 |
< |
sendFrcStruct( &info, mpiAtomStructType ); |
453 |
< |
#endif |
473 |
< |
ffError(errMsg); |
450 |
> |
sprintf( painCave.errMsg, |
451 |
> |
"Error parseing AtomTypes: line %d\n", lineNum ); |
452 |
> |
painCave.isFatal = 1; |
453 |
> |
simError(); |
454 |
|
} |
455 |
|
|
456 |
|
sscanf( the_token, "%lf", ¤tAtomType->sigma ); |
457 |
|
|
458 |
|
if( currentAtomType->isDipole ){ |
459 |
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
460 |
< |
sprintf( errMsg, "Error parseing AtomTypes: line %d\n", |
460 |
> |
sprintf( painCave.errMsg, |
461 |
> |
"Error parseing AtomTypes: line %d\n", |
462 |
|
lineNum ); |
463 |
< |
#ifdef IS_MPI |
464 |
< |
sendFrcStruct( &info, mpiAtomStructType ); |
484 |
< |
#endif |
485 |
< |
ffError(errMsg); |
463 |
> |
painCave.isFatal = 1; |
464 |
> |
simError(); |
465 |
|
} |
466 |
|
|
467 |
|
sscanf( the_token, "%lf", ¤tAtomType->dipole ); |
480 |
|
#ifdef IS_MPI |
481 |
|
|
482 |
|
// send out the linked list to all the other processes |
483 |
< |
|
483 |
> |
|
484 |
> |
sprintf( checkPointMsg, |
485 |
> |
"TraPPE_Ex atom structures read successfully." ); |
486 |
> |
MPIcheckPoint(); |
487 |
> |
|
488 |
|
currentAtomType = headAtomType; |
489 |
|
while( currentAtomType != NULL ){ |
490 |
|
currentAtomType->duplicate( info ); |
499 |
|
else{ |
500 |
|
|
501 |
|
// listen for node 0 to send out the force params |
502 |
+ |
|
503 |
+ |
MPIcheckPoint(); |
504 |
|
|
505 |
|
headAtomType = new LinkedType; |
506 |
|
recieveFrcStruct( &info, mpiAtomStructType ); |
509 |
|
headAtomType->add( info ); |
510 |
|
recieveFrcStruct( &info, mpiAtomStructType ); |
511 |
|
} |
527 |
– |
|
528 |
– |
if( info.last < 0 ) ffError( NULL ); // an error has occured, exit quietly. |
529 |
– |
|
530 |
– |
|
512 |
|
} |
513 |
< |
#endif |
513 |
> |
#endif // is_mpi |
514 |
|
|
515 |
|
|
516 |
|
// initialize the atoms |
521 |
|
|
522 |
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
523 |
|
if( currentAtomType == NULL ){ |
524 |
< |
sprintf( errMsg, "AtomType error, %s not found in force file.\n", |
524 |
> |
sprintf( painCave.errMsg, |
525 |
> |
"AtomType error, %s not found in force file.\n", |
526 |
|
the_atoms[i]->getType() ); |
527 |
< |
ffError(errMsg); |
527 |
> |
painCave.isFatal = 1; |
528 |
> |
simError(); |
529 |
|
} |
530 |
|
|
531 |
|
the_atoms[i]->setMass( currentAtomType->mass ); |
552 |
|
dAtom->setSSD( 0 ); |
553 |
|
} |
554 |
|
else{ |
555 |
< |
sprintf(errMsg, |
555 |
> |
sprintf(painCave.errMsg, |
556 |
|
"AtmType error, %s does not have a moment of inertia set.\n", |
557 |
|
the_atoms[i]->getType() ); |
558 |
< |
ffError(errMsg); |
558 |
> |
painCave.isFatal = 1; |
559 |
> |
simError(); |
560 |
|
} |
561 |
|
entry_plug->n_dipoles++; |
562 |
|
} |
563 |
|
else{ |
564 |
|
|
565 |
< |
sprintf( errMsg, |
565 |
> |
sprintf( painCave.errMsg, |
566 |
|
"TraPPE_ExFF error: Atom \"%s\" is a dipole, yet no standard" |
567 |
|
" orientation was specifed in the BASS file.\n", |
568 |
|
currentAtomType->name ); |
569 |
< |
|
570 |
< |
ffError(errMsg); |
569 |
> |
painCave.isFatal = 1; |
570 |
> |
simError(); |
571 |
|
} |
572 |
|
} |
573 |
|
else{ |
574 |
|
if( the_atoms[i]->isDirectional() ){ |
575 |
< |
sprintf( errMsg, |
575 |
> |
sprintf( painCave.errMsg, |
576 |
|
"TraPPE_ExFF error: Atom \"%s\" was given a standard" |
577 |
|
"orientation in the BASS file, yet it is not a dipole.\n", |
578 |
|
currentAtomType->name); |
579 |
< |
ffError(errMsg); |
579 |
> |
painCave.isFatal = 1; |
580 |
> |
simError(); |
581 |
|
} |
582 |
|
} |
583 |
|
} |
586 |
|
// clean up the memory |
587 |
|
|
588 |
|
delete headAtomType; |
589 |
+ |
|
590 |
+ |
#ifdef IS_MPI |
591 |
+ |
sprintf( checkPointMsg, "TraPPE_Ex atoms initialized succesfully" ); |
592 |
+ |
MPIcheckPoint(); |
593 |
+ |
#endif // is_mpi |
594 |
+ |
|
595 |
|
} |
596 |
|
|
597 |
|
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
650 |
|
LinkedType* currentBondType; |
651 |
|
LinkedType* tempBondType; |
652 |
|
|
653 |
+ |
#ifdef IS_MPI |
654 |
+ |
bondStruct info; |
655 |
+ |
info.last = 1; // initialize last to have the last set. |
656 |
+ |
// if things go well, last will be set to 0 |
657 |
+ |
#endif |
658 |
+ |
|
659 |
|
char readLine[500]; |
660 |
|
char* the_token; |
661 |
|
char* eof_test; |
672 |
|
the_atoms = entry_plug->atoms; |
673 |
|
nBonds = entry_plug->n_bonds; |
674 |
|
|
678 |
– |
// read in the bond types. |
679 |
– |
|
680 |
– |
rewind( frcFile ); |
681 |
– |
headBondType = new LinkedType; |
682 |
– |
currentBondType = headBondType; |
675 |
|
|
676 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
677 |
< |
lineNum++; |
678 |
< |
if( eof_test == NULL ){ |
679 |
< |
fprintf( stderr, "Error in reading Bonds from force file.\n" ); |
680 |
< |
exit(8); |
681 |
< |
} |
682 |
< |
|
683 |
< |
|
684 |
< |
while( !foundBond ){ |
685 |
< |
while( eof_test != NULL && readLine[0] != '#' ){ |
686 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
687 |
< |
lineNum++; |
696 |
< |
} |
676 |
> |
#ifdef IS_MPI |
677 |
> |
if( worldRank == 0 ){ |
678 |
> |
#endif |
679 |
> |
|
680 |
> |
// read in the bond types. |
681 |
> |
|
682 |
> |
rewind( frcFile ); |
683 |
> |
headBondType = new LinkedType; |
684 |
> |
currentBondType = headBondType; |
685 |
> |
|
686 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
687 |
> |
lineNum++; |
688 |
|
if( eof_test == NULL ){ |
689 |
< |
fprintf( stderr, |
690 |
< |
"Error in reading Bonds from force file at line %d.\n", |
691 |
< |
lineNum ); |
701 |
< |
exit(8); |
689 |
> |
sprintf( painCave.errMsg, "Error in reading Bonds from force file.\n" ); |
690 |
> |
painCave.isFatal = 1; |
691 |
> |
simError(); |
692 |
|
} |
703 |
– |
|
704 |
– |
the_token = strtok( readLine, " ,;\t#\n" ); |
705 |
– |
foundBond = !strcmp( "BondTypes", the_token ); |
693 |
|
|
694 |
< |
if( !foundBond ){ |
695 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
696 |
< |
lineNum++; |
697 |
< |
|
694 |
> |
|
695 |
> |
while( !foundBond ){ |
696 |
> |
while( eof_test != NULL && readLine[0] != '#' ){ |
697 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
698 |
> |
lineNum++; |
699 |
> |
} |
700 |
|
if( eof_test == NULL ){ |
701 |
< |
fprintf( stderr, |
701 |
> |
sprintf( painCave.errMsg, |
702 |
|
"Error in reading Bonds from force file at line %d.\n", |
703 |
|
lineNum ); |
704 |
< |
exit(8); |
705 |
< |
} |
706 |
< |
} |
718 |
< |
} |
719 |
< |
|
720 |
< |
// we are now at the BondTypes section. |
721 |
< |
|
722 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
723 |
< |
lineNum++; |
724 |
< |
|
725 |
< |
if( eof_test == NULL ){ |
726 |
< |
fprintf( stderr, |
727 |
< |
"Error in reading Bonds from force file at line %d.\n", |
728 |
< |
lineNum ); |
729 |
< |
exit(8); |
730 |
< |
} |
731 |
< |
|
732 |
< |
while( readLine[0] != '#' && eof_test != NULL ){ |
733 |
< |
|
734 |
< |
if( readLine[0] != '!' ){ |
704 |
> |
painCave.isFatal = 1; |
705 |
> |
simError(); |
706 |
> |
} |
707 |
|
|
708 |
< |
the_token = strtok( readLine, " \n\t,;" ); |
709 |
< |
if( the_token != NULL ){ |
708 |
> |
the_token = strtok( readLine, " ,;\t#\n" ); |
709 |
> |
foundBond = !strcmp( "BondTypes", the_token ); |
710 |
> |
|
711 |
> |
if( !foundBond ){ |
712 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
713 |
> |
lineNum++; |
714 |
|
|
715 |
< |
strcpy( currentBondType->nameA, the_token ); |
715 |
> |
if( eof_test == NULL ){ |
716 |
> |
sprintf( painCave.errMsg, |
717 |
> |
"Error in reading Bonds from force file at line %d.\n", |
718 |
> |
lineNum ); |
719 |
> |
painCave.isFatal = 1; |
720 |
> |
simError(); |
721 |
> |
} |
722 |
> |
} |
723 |
> |
} |
724 |
> |
|
725 |
> |
// we are now at the BondTypes section. |
726 |
> |
|
727 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
728 |
> |
lineNum++; |
729 |
> |
|
730 |
> |
if( eof_test == NULL ){ |
731 |
> |
sprintf( painCave.errMsg, |
732 |
> |
"Error in reading Bonds from force file at line %d.\n", |
733 |
> |
lineNum ); |
734 |
> |
painCave.isFatal = 1; |
735 |
> |
simError(); |
736 |
> |
} |
737 |
> |
|
738 |
> |
while( readLine[0] != '#' && eof_test != NULL ){ |
739 |
> |
|
740 |
> |
if( readLine[0] != '!' ){ |
741 |
|
|
742 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
743 |
< |
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
744 |
< |
exit(8); |
745 |
< |
} |
746 |
< |
|
746 |
< |
strcpy( currentBondType->nameB, the_token ); |
747 |
< |
|
748 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
749 |
< |
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
750 |
< |
exit(8); |
751 |
< |
} |
752 |
< |
|
753 |
< |
strcpy( currentBondType->type, the_token ); |
754 |
< |
|
755 |
< |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
742 |
> |
the_token = strtok( readLine, " \n\t,;" ); |
743 |
> |
if( the_token != NULL ){ |
744 |
> |
|
745 |
> |
strcpy( currentBondType->nameA, the_token ); |
746 |
> |
|
747 |
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
748 |
< |
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
749 |
< |
exit(8); |
748 |
> |
sprintf( painCave.errMsg, |
749 |
> |
"Error parseing BondTypes: line %d\n", lineNum ); |
750 |
> |
painCave.isFatal = 1; |
751 |
> |
simError(); |
752 |
|
} |
753 |
|
|
754 |
< |
sscanf( the_token, "%lf", ¤tBondType->d0 ); |
754 |
> |
strcpy( currentBondType->nameB, the_token ); |
755 |
> |
|
756 |
> |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
757 |
> |
sprintf( painCave.errMsg, |
758 |
> |
"Error parseing BondTypes: line %d\n", lineNum ); |
759 |
> |
painCave.isFatal = 1; |
760 |
> |
simError(); |
761 |
> |
} |
762 |
> |
|
763 |
> |
strcpy( currentBondType->type, the_token ); |
764 |
> |
|
765 |
> |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
766 |
> |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
767 |
> |
sprintf( painCave.errMsg, |
768 |
> |
"Error parseing BondTypes: line %d\n", lineNum ); |
769 |
> |
painCave.isFatal = 1; |
770 |
> |
simError(); |
771 |
> |
} |
772 |
> |
|
773 |
> |
sscanf( the_token, "%lf", ¤tBondType->d0 ); |
774 |
> |
} |
775 |
> |
|
776 |
> |
else{ |
777 |
> |
sprintf( painCave.errMsg, |
778 |
> |
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
779 |
> |
currentBondType->type, |
780 |
> |
lineNum ); |
781 |
> |
painCave.isFatal = 1; |
782 |
> |
simError(); |
783 |
> |
} |
784 |
|
} |
763 |
– |
|
764 |
– |
else{ |
765 |
– |
fprintf(stderr, |
766 |
– |
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
767 |
– |
currentBondType->type, |
768 |
– |
lineNum ); |
769 |
– |
exit(8); |
770 |
– |
} |
785 |
|
} |
786 |
+ |
|
787 |
+ |
tempBondType = new LinkedType; |
788 |
+ |
currentBondType->next = tempBondType; |
789 |
+ |
currentBondType = tempBondType; |
790 |
+ |
|
791 |
+ |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
792 |
+ |
lineNum++; |
793 |
|
} |
794 |
|
|
795 |
< |
tempBondType = new LinkedType; |
775 |
< |
currentBondType->next = tempBondType; |
776 |
< |
currentBondType = tempBondType; |
795 |
> |
#ifdef IS_MPI |
796 |
|
|
797 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
798 |
< |
lineNum++; |
797 |
> |
// send out the linked list to all the other processes |
798 |
> |
|
799 |
> |
sprintf( checkPointMsg, |
800 |
> |
"TraPPE_Ex bond structures read successfully." ); |
801 |
> |
MPIcheckPoint(); |
802 |
> |
|
803 |
> |
currentBondType = headBondType; |
804 |
> |
while( currentBondType != NULL ){ |
805 |
> |
currentBondType->duplicate( info ); |
806 |
> |
sendFrcStruct( &info, mpiBondStructType ); |
807 |
> |
currentBondType = currentBondType->next; |
808 |
> |
} |
809 |
> |
info.last = 1; |
810 |
> |
sendFrcStruct( &info, mpiBondStructType ); |
811 |
> |
|
812 |
|
} |
813 |
|
|
814 |
+ |
else{ |
815 |
+ |
|
816 |
+ |
// listen for node 0 to send out the force params |
817 |
+ |
|
818 |
+ |
MPIcheckPoint(); |
819 |
+ |
|
820 |
+ |
headBondType = new LinkedType; |
821 |
+ |
recieveFrcStruct( &info, mpiBondStructType ); |
822 |
+ |
while( !info.last ){ |
823 |
+ |
|
824 |
+ |
headBondType->add( info ); |
825 |
+ |
recieveFrcStruct( &info, mpiBondStructType ); |
826 |
+ |
} |
827 |
+ |
} |
828 |
+ |
#endif // is_mpi |
829 |
|
|
830 |
+ |
|
831 |
|
// initialize the Bonds |
832 |
|
|
833 |
|
|
840 |
|
atomB = the_atoms[b]->getType(); |
841 |
|
currentBondType = headBondType->find( atomA, atomB ); |
842 |
|
if( currentBondType == NULL ){ |
843 |
< |
fprintf( stderr, "BondType error, %s - %s not found in force file.\n", |
843 |
> |
sprintf( painCave.errMsg, |
844 |
> |
"BondType error, %s - %s not found in force file.\n", |
845 |
|
atomA, atomB ); |
846 |
< |
exit(8); |
846 |
> |
painCave.isFatal = 1; |
847 |
> |
simError(); |
848 |
|
} |
849 |
|
|
850 |
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
861 |
|
|
862 |
|
delete headBondType; |
863 |
|
|
864 |
+ |
#ifdef IS_MPI |
865 |
+ |
sprintf( checkPointMsg, "TraPPE_Ex bonds initialized succesfully" ); |
866 |
+ |
MPIcheckPoint(); |
867 |
+ |
#endif // is_mpi |
868 |
+ |
|
869 |
|
} |
870 |
|
|
871 |
|
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
919 |
|
info.last = 0; |
920 |
|
} |
921 |
|
|
922 |
< |
#endif |
922 |
> |
#endif // is_mpi |
923 |
|
|
924 |
|
char nameA[15]; |
925 |
|
char nameB[15]; |
934 |
|
LinkedType* currentBendType; |
935 |
|
LinkedType* tempBendType; |
936 |
|
|
937 |
+ |
#ifdef IS_MPI |
938 |
+ |
bendStruct info; |
939 |
+ |
info.last = 1; // initialize last to have the last set. |
940 |
+ |
// if things go well, last will be set to 0 |
941 |
+ |
#endif |
942 |
+ |
|
943 |
|
char readLine[500]; |
944 |
|
char* the_token; |
945 |
|
char* eof_test; |
958 |
|
the_atoms = entry_plug->atoms; |
959 |
|
nBends = entry_plug->n_bends; |
960 |
|
|
900 |
– |
// read in the bend types. |
961 |
|
|
962 |
< |
rewind( frcFile ); |
963 |
< |
headBendType = new LinkedType; |
964 |
< |
currentBendType = headBendType; |
905 |
< |
|
906 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
907 |
< |
lineNum++; |
908 |
< |
if( eof_test == NULL ){ |
909 |
< |
fprintf( stderr, "Error in reading Bends from force file.\n" ); |
910 |
< |
exit(8); |
911 |
< |
} |
962 |
> |
#ifdef IS_MPI |
963 |
> |
if( worldRank == 0 ){ |
964 |
> |
#endif |
965 |
|
|
966 |
+ |
// read in the bend types. |
967 |
+ |
|
968 |
+ |
rewind( frcFile ); |
969 |
+ |
headBendType = new LinkedType; |
970 |
+ |
currentBendType = headBendType; |
971 |
|
|
972 |
< |
while( !foundBend ){ |
973 |
< |
while( eof_test != NULL && readLine[0] != '#' ){ |
916 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
917 |
< |
lineNum++; |
918 |
< |
} |
972 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
973 |
> |
lineNum++; |
974 |
|
if( eof_test == NULL ){ |
975 |
< |
fprintf( stderr, |
976 |
< |
"Error in reading Bends from force file at line %d.\n", |
977 |
< |
lineNum ); |
923 |
< |
exit(8); |
975 |
> |
sprintf( painCave.errMsg, "Error in reading Bends from force file.\n" ); |
976 |
> |
painCave.isFatal = 1; |
977 |
> |
simError(); |
978 |
|
} |
979 |
|
|
980 |
< |
the_token = strtok( readLine, " ,;\t#\n" ); |
981 |
< |
foundBend = !strcmp( "BendTypes", the_token ); |
982 |
< |
|
983 |
< |
if( !foundBend ){ |
984 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
985 |
< |
lineNum++; |
932 |
< |
|
980 |
> |
|
981 |
> |
while( !foundBend ){ |
982 |
> |
while( eof_test != NULL && readLine[0] != '#' ){ |
983 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
984 |
> |
lineNum++; |
985 |
> |
} |
986 |
|
if( eof_test == NULL ){ |
987 |
< |
fprintf( stderr, |
987 |
> |
sprintf( painCave.errMsg, |
988 |
|
"Error in reading Bends from force file at line %d.\n", |
989 |
|
lineNum ); |
990 |
< |
exit(8); |
991 |
< |
} |
990 |
> |
painCave.isFatal = 1; |
991 |
> |
simError(); |
992 |
> |
} |
993 |
> |
|
994 |
> |
the_token = strtok( readLine, " ,;\t#\n" ); |
995 |
> |
foundBend = !strcmp( "BendTypes", the_token ); |
996 |
> |
|
997 |
> |
if( !foundBend ){ |
998 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
999 |
> |
lineNum++; |
1000 |
> |
|
1001 |
> |
if( eof_test == NULL ){ |
1002 |
> |
sprintf( painCave.errMsg, |
1003 |
> |
"Error in reading Bends from force file at line %d.\n", |
1004 |
> |
lineNum ); |
1005 |
> |
painCave.isFatal = 1; |
1006 |
> |
simError(); |
1007 |
> |
} |
1008 |
> |
} |
1009 |
|
} |
940 |
– |
} |
1010 |
|
|
1011 |
< |
// we are now at the BendTypes section. |
1011 |
> |
// we are now at the BendTypes section. |
1012 |
|
|
1013 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1014 |
< |
lineNum++; |
1013 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1014 |
> |
lineNum++; |
1015 |
|
|
1016 |
< |
if( eof_test == NULL ){ |
1017 |
< |
fprintf( stderr, |
1018 |
< |
"Error in reading Bends from force file at line %d.\n", |
1019 |
< |
lineNum ); |
1020 |
< |
exit(8); |
1021 |
< |
} |
1016 |
> |
if( eof_test == NULL ){ |
1017 |
> |
sprintf( painCave.errMsg, |
1018 |
> |
"Error in reading Bends from force file at line %d.\n", |
1019 |
> |
lineNum ); |
1020 |
> |
painCave.isFatal = 1; |
1021 |
> |
simError(); |
1022 |
> |
} |
1023 |
|
|
1024 |
< |
while( readLine[0] != '#' && eof_test != NULL ){ |
1024 |
> |
while( readLine[0] != '#' && eof_test != NULL ){ |
1025 |
|
|
1026 |
< |
if( readLine[0] != '!' ){ |
1026 |
> |
if( readLine[0] != '!' ){ |
1027 |
|
|
1028 |
< |
the_token = strtok( readLine, " \n\t,;" ); |
1029 |
< |
if( the_token != NULL ){ |
1028 |
> |
the_token = strtok( readLine, " \n\t,;" ); |
1029 |
> |
if( the_token != NULL ){ |
1030 |
|
|
1031 |
< |
strcpy( currentBendType->nameA, the_token ); |
1031 |
> |
strcpy( currentBendType->nameA, the_token ); |
1032 |
|
|
1033 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1034 |
< |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
1035 |
< |
exit(8); |
1036 |
< |
} |
1033 |
> |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1034 |
> |
sprintf( painCave.errMsg, |
1035 |
> |
"Error parseing BendTypes: line %d\n", lineNum ); |
1036 |
> |
painCave.isFatal = 1; |
1037 |
> |
simError(); |
1038 |
> |
} |
1039 |
|
|
1040 |
< |
strcpy( currentBendType->nameB, the_token ); |
1040 |
> |
strcpy( currentBendType->nameB, the_token ); |
1041 |
|
|
1042 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1043 |
< |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
1044 |
< |
exit(8); |
1045 |
< |
} |
1042 |
> |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1043 |
> |
sprintf( painCave.errMsg, |
1044 |
> |
"Error parseing BendTypes: line %d\n", lineNum ); |
1045 |
> |
painCave.isFatal = 1; |
1046 |
> |
simError(); |
1047 |
> |
} |
1048 |
|
|
1049 |
< |
strcpy( currentBendType->nameC, the_token ); |
1049 |
> |
strcpy( currentBendType->nameC, the_token ); |
1050 |
|
|
977 |
– |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
978 |
– |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
979 |
– |
exit(8); |
980 |
– |
} |
981 |
– |
|
982 |
– |
strcpy( currentBendType->type, the_token ); |
983 |
– |
|
984 |
– |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1051 |
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1052 |
< |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
1053 |
< |
exit(8); |
1052 |
> |
sprintf( painCave.errMsg, |
1053 |
> |
"Error parseing BendTypes: line %d\n", lineNum ); |
1054 |
> |
painCave.isFatal = 1; |
1055 |
> |
simError(); |
1056 |
|
} |
1057 |
+ |
|
1058 |
+ |
strcpy( currentBendType->type, the_token ); |
1059 |
+ |
|
1060 |
+ |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1061 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1062 |
+ |
sprintf( painCave.errMsg, |
1063 |
+ |
"Error parseing BendTypes: line %d\n", lineNum ); |
1064 |
+ |
painCave.isFatal = 1; |
1065 |
+ |
simError(); |
1066 |
+ |
} |
1067 |
|
|
1068 |
< |
sscanf( the_token, "%lf", ¤tBendType->k1 ); |
1068 |
> |
sscanf( the_token, "%lf", ¤tBendType->k1 ); |
1069 |
|
|
1070 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1071 |
< |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
1072 |
< |
exit(8); |
1073 |
< |
} |
1070 |
> |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1071 |
> |
sprintf( painCave.errMsg, |
1072 |
> |
"Error parseing BendTypes: line %d\n", lineNum ); |
1073 |
> |
painCave.isFatal = 1; |
1074 |
> |
simError(); |
1075 |
> |
} |
1076 |
|
|
1077 |
< |
sscanf( the_token, "%lf", ¤tBendType->k2 ); |
1077 |
> |
sscanf( the_token, "%lf", ¤tBendType->k2 ); |
1078 |
|
|
1079 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1080 |
< |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
1081 |
< |
exit(8); |
1082 |
< |
} |
1079 |
> |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1080 |
> |
sprintf( painCave.errMsg, |
1081 |
> |
"Error parseing BendTypes: line %d\n", lineNum ); |
1082 |
> |
painCave.isFatal = 1; |
1083 |
> |
simError(); |
1084 |
> |
} |
1085 |
|
|
1086 |
< |
sscanf( the_token, "%lf", ¤tBendType->k3 ); |
1086 |
> |
sscanf( the_token, "%lf", ¤tBendType->k3 ); |
1087 |
|
|
1088 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1089 |
< |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
1090 |
< |
exit(8); |
1091 |
< |
} |
1088 |
> |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1089 |
> |
sprintf( painCave.errMsg, |
1090 |
> |
"Error parseing BendTypes: line %d\n", lineNum ); |
1091 |
> |
painCave.isFatal = 1; |
1092 |
> |
simError(); |
1093 |
> |
} |
1094 |
|
|
1095 |
< |
sscanf( the_token, "%lf", ¤tBendType->t0 ); |
1096 |
< |
} |
1095 |
> |
sscanf( the_token, "%lf", ¤tBendType->t0 ); |
1096 |
> |
} |
1097 |
|
|
1098 |
< |
else{ |
1099 |
< |
fprintf(stderr, |
1100 |
< |
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
1101 |
< |
currentBendType->type, |
1102 |
< |
lineNum ); |
1103 |
< |
exit(8); |
1104 |
< |
} |
1098 |
> |
else{ |
1099 |
> |
sprintf( painCave.errMsg, |
1100 |
> |
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
1101 |
> |
currentBendType->type, |
1102 |
> |
lineNum ); |
1103 |
> |
painCave.isFatal = 1; |
1104 |
> |
simError(); |
1105 |
> |
} |
1106 |
> |
} |
1107 |
|
} |
1022 |
– |
} |
1108 |
|
|
1109 |
< |
tempBendType = new LinkedType; |
1110 |
< |
currentBendType->next = tempBendType; |
1111 |
< |
currentBendType = tempBendType; |
1109 |
> |
tempBendType = new LinkedType; |
1110 |
> |
currentBendType->next = tempBendType; |
1111 |
> |
currentBendType = tempBendType; |
1112 |
|
|
1113 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1114 |
< |
lineNum++; |
1113 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1114 |
> |
lineNum++; |
1115 |
> |
} |
1116 |
> |
|
1117 |
> |
#ifdef IS_MPI |
1118 |
> |
|
1119 |
> |
// send out the linked list to all the other processes |
1120 |
> |
|
1121 |
> |
sprintf( checkPointMsg, |
1122 |
> |
"TraPPE_Ex bend structures read successfully." ); |
1123 |
> |
MPIcheckPoint(); |
1124 |
> |
|
1125 |
> |
currentBendType = headBendType; |
1126 |
> |
while( currentBendType != NULL ){ |
1127 |
> |
currentBendType->duplicate( info ); |
1128 |
> |
sendFrcStruct( &info, mpiBendStructType ); |
1129 |
> |
currentBendType = currentBendType->next; |
1130 |
> |
} |
1131 |
> |
info.last = 1; |
1132 |
> |
sendFrcStruct( &info, mpiBendStructType ); |
1133 |
> |
|
1134 |
|
} |
1135 |
|
|
1136 |
+ |
else{ |
1137 |
+ |
|
1138 |
+ |
// listen for node 0 to send out the force params |
1139 |
+ |
|
1140 |
+ |
MPIcheckPoint(); |
1141 |
+ |
|
1142 |
+ |
headBendType = new LinkedType; |
1143 |
+ |
recieveFrcStruct( &info, mpiBendStructType ); |
1144 |
+ |
while( !info.last ){ |
1145 |
+ |
|
1146 |
+ |
headBendType->add( info ); |
1147 |
+ |
recieveFrcStruct( &info, mpiBendStructType ); |
1148 |
+ |
} |
1149 |
+ |
} |
1150 |
+ |
#endif // is_mpi |
1151 |
|
|
1152 |
|
// initialize the Bends |
1153 |
|
|
1162 |
|
atomC = the_atoms[c]->getType(); |
1163 |
|
currentBendType = headBendType->find( atomA, atomB, atomC ); |
1164 |
|
if( currentBendType == NULL ){ |
1165 |
< |
fprintf( stderr, "BendType error, %s - %s - %s not found" |
1165 |
> |
sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found" |
1166 |
|
" in force file.\n", |
1167 |
|
atomA, atomB, atomC ); |
1168 |
< |
exit(8); |
1168 |
> |
painCave.isFatal = 1; |
1169 |
> |
simError(); |
1170 |
|
} |
1171 |
|
|
1172 |
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1188 |
|
|
1189 |
|
delete headBendType; |
1190 |
|
|
1191 |
+ |
#ifdef IS_MPI |
1192 |
+ |
sprintf( checkPointMsg, "TraPPE_Ex bends initialized succesfully" ); |
1193 |
+ |
MPIcheckPoint(); |
1194 |
+ |
#endif // is_mpi |
1195 |
+ |
|
1196 |
|
} |
1197 |
|
|
1198 |
|
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
1265 |
|
LinkedType* currentTorsionType; |
1266 |
|
LinkedType* tempTorsionType; |
1267 |
|
|
1268 |
+ |
#ifdef IS_MPI |
1269 |
+ |
torsionStruct info; |
1270 |
+ |
info.last = 1; // initialize last to have the last set. |
1271 |
+ |
// if things go well, last will be set to 0 |
1272 |
+ |
#endif |
1273 |
+ |
|
1274 |
|
char readLine[500]; |
1275 |
|
char* the_token; |
1276 |
|
char* eof_test; |
1290 |
|
the_atoms = entry_plug->atoms; |
1291 |
|
nTorsions = entry_plug->n_torsions; |
1292 |
|
|
1293 |
< |
// read in the torsion types. |
1293 |
> |
#ifdef IS_MPI |
1294 |
> |
if( worldRank == 0 ){ |
1295 |
> |
#endif |
1296 |
|
|
1297 |
< |
rewind( frcFile ); |
1165 |
< |
headTorsionType = new LinkedType; |
1166 |
< |
currentTorsionType = headTorsionType; |
1167 |
< |
|
1168 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1169 |
< |
lineNum++; |
1170 |
< |
if( eof_test == NULL ){ |
1171 |
< |
fprintf( stderr, "Error in reading Torsions from force file.\n" ); |
1172 |
< |
exit(8); |
1173 |
< |
} |
1297 |
> |
// read in the torsion types. |
1298 |
|
|
1299 |
+ |
rewind( frcFile ); |
1300 |
+ |
headTorsionType = new LinkedType; |
1301 |
+ |
currentTorsionType = headTorsionType; |
1302 |
|
|
1303 |
< |
while( !foundTorsion ){ |
1304 |
< |
while( eof_test != NULL && readLine[0] != '#' ){ |
1178 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1179 |
< |
lineNum++; |
1180 |
< |
} |
1303 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1304 |
> |
lineNum++; |
1305 |
|
if( eof_test == NULL ){ |
1306 |
< |
fprintf( stderr, |
1307 |
< |
"Error in reading Torsions from force file at line %d.\n", |
1308 |
< |
lineNum ); |
1309 |
< |
exit(8); |
1306 |
> |
sprintf( painCave.errMsg, |
1307 |
> |
"Error in reading Torsions from force file.\n" ); |
1308 |
> |
painCave.isFatal = 1; |
1309 |
> |
simError(); |
1310 |
|
} |
1311 |
|
|
1312 |
< |
the_token = strtok( readLine, " ,;\t#\n" ); |
1313 |
< |
foundTorsion = !strcmp( "TorsionTypes", the_token ); |
1314 |
< |
|
1315 |
< |
if( !foundTorsion ){ |
1316 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1317 |
< |
lineNum++; |
1194 |
< |
|
1312 |
> |
|
1313 |
> |
while( !foundTorsion ){ |
1314 |
> |
while( eof_test != NULL && readLine[0] != '#' ){ |
1315 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1316 |
> |
lineNum++; |
1317 |
> |
} |
1318 |
|
if( eof_test == NULL ){ |
1319 |
< |
fprintf( stderr, |
1319 |
> |
sprintf( painCave.errMsg, |
1320 |
|
"Error in reading Torsions from force file at line %d.\n", |
1321 |
|
lineNum ); |
1322 |
< |
exit(8); |
1323 |
< |
} |
1322 |
> |
painCave.isFatal = 1; |
1323 |
> |
simError(); |
1324 |
> |
} |
1325 |
> |
|
1326 |
> |
the_token = strtok( readLine, " ,;\t#\n" ); |
1327 |
> |
foundTorsion = !strcmp( "TorsionTypes", the_token ); |
1328 |
> |
|
1329 |
> |
if( !foundTorsion ){ |
1330 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1331 |
> |
lineNum++; |
1332 |
> |
|
1333 |
> |
if( eof_test == NULL ){ |
1334 |
> |
sprintf( painCave.errMsg, |
1335 |
> |
"Error in reading Torsions from force file at line %d.\n", |
1336 |
> |
lineNum ); |
1337 |
> |
painCave.isFatal = 1; |
1338 |
> |
simError(); |
1339 |
> |
} |
1340 |
> |
} |
1341 |
|
} |
1202 |
– |
} |
1342 |
|
|
1343 |
< |
// we are now at the TorsionTypes section. |
1343 |
> |
// we are now at the TorsionTypes section. |
1344 |
|
|
1345 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1346 |
< |
lineNum++; |
1345 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1346 |
> |
lineNum++; |
1347 |
|
|
1348 |
< |
if( eof_test == NULL ){ |
1349 |
< |
fprintf( stderr, |
1350 |
< |
"Error in reading Torsions from force file at line %d.\n", |
1351 |
< |
lineNum ); |
1352 |
< |
exit(8); |
1353 |
< |
} |
1348 |
> |
if( eof_test == NULL ){ |
1349 |
> |
sprintf( painCave.errMsg, |
1350 |
> |
"Error in reading Torsions from force file at line %d.\n", |
1351 |
> |
lineNum ); |
1352 |
> |
painCave.isFatal = 1; |
1353 |
> |
simError(); |
1354 |
> |
} |
1355 |
|
|
1356 |
< |
while( readLine[0] != '#' && eof_test != NULL ){ |
1356 |
> |
while( readLine[0] != '#' && eof_test != NULL ){ |
1357 |
|
|
1358 |
< |
if( readLine[0] != '!' ){ |
1358 |
> |
if( readLine[0] != '!' ){ |
1359 |
|
|
1360 |
< |
the_token = strtok( readLine, " \n\t,;" ); |
1361 |
< |
if( the_token != NULL ){ |
1360 |
> |
the_token = strtok( readLine, " \n\t,;" ); |
1361 |
> |
if( the_token != NULL ){ |
1362 |
|
|
1363 |
< |
strcpy( currentTorsionType->nameA, the_token ); |
1363 |
> |
strcpy( currentTorsionType->nameA, the_token ); |
1364 |
|
|
1365 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1366 |
< |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1367 |
< |
exit(8); |
1368 |
< |
} |
1365 |
> |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1366 |
> |
sprintf( painCave.errMsg, |
1367 |
> |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1368 |
> |
painCave.isFatal = 1; |
1369 |
> |
simError(); |
1370 |
> |
} |
1371 |
|
|
1372 |
< |
strcpy( currentTorsionType->nameB, the_token ); |
1372 |
> |
strcpy( currentTorsionType->nameB, the_token ); |
1373 |
|
|
1374 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1375 |
< |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1376 |
< |
exit(8); |
1377 |
< |
} |
1374 |
> |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1375 |
> |
sprintf( painCave.errMsg, |
1376 |
> |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1377 |
> |
painCave.isFatal = 1; |
1378 |
> |
simError(); |
1379 |
> |
} |
1380 |
|
|
1381 |
< |
strcpy( currentTorsionType->nameC, the_token ); |
1381 |
> |
strcpy( currentTorsionType->nameC, the_token ); |
1382 |
|
|
1383 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1384 |
< |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1385 |
< |
exit(8); |
1386 |
< |
} |
1383 |
> |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1384 |
> |
sprintf( painCave.errMsg, |
1385 |
> |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1386 |
> |
painCave.isFatal = 1; |
1387 |
> |
simError(); |
1388 |
> |
} |
1389 |
|
|
1390 |
< |
strcpy( currentTorsionType->nameD, the_token ); |
1390 |
> |
strcpy( currentTorsionType->nameD, the_token ); |
1391 |
|
|
1246 |
– |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1247 |
– |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1248 |
– |
exit(8); |
1249 |
– |
} |
1250 |
– |
|
1251 |
– |
strcpy( currentTorsionType->type, the_token ); |
1252 |
– |
|
1253 |
– |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1392 |
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1393 |
< |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1394 |
< |
exit(8); |
1393 |
> |
sprintf( painCave.errMsg, |
1394 |
> |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1395 |
> |
painCave.isFatal = 1; |
1396 |
> |
simError(); |
1397 |
|
} |
1398 |
+ |
|
1399 |
+ |
strcpy( currentTorsionType->type, the_token ); |
1400 |
+ |
|
1401 |
+ |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1402 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1403 |
+ |
sprintf( painCave.errMsg, |
1404 |
+ |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1405 |
+ |
painCave.isFatal = 1; |
1406 |
+ |
simError(); |
1407 |
+ |
} |
1408 |
|
|
1409 |
< |
sscanf( the_token, "%lf", ¤tTorsionType->k1 ); |
1409 |
> |
sscanf( the_token, "%lf", ¤tTorsionType->k1 ); |
1410 |
|
|
1411 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1412 |
< |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1413 |
< |
exit(8); |
1414 |
< |
} |
1411 |
> |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1412 |
> |
sprintf( painCave.errMsg, |
1413 |
> |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1414 |
> |
painCave.isFatal = 1; |
1415 |
> |
simError(); |
1416 |
> |
} |
1417 |
|
|
1418 |
< |
sscanf( the_token, "%lf", ¤tTorsionType->k2 ); |
1418 |
> |
sscanf( the_token, "%lf", ¤tTorsionType->k2 ); |
1419 |
|
|
1420 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1421 |
< |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1422 |
< |
exit(8); |
1423 |
< |
} |
1420 |
> |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1421 |
> |
sprintf( painCave.errMsg, |
1422 |
> |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1423 |
> |
painCave.isFatal = 1; |
1424 |
> |
simError(); |
1425 |
> |
} |
1426 |
|
|
1427 |
< |
sscanf( the_token, "%lf", ¤tTorsionType->k3 ); |
1427 |
> |
sscanf( the_token, "%lf", ¤tTorsionType->k3 ); |
1428 |
|
|
1429 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1430 |
< |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1431 |
< |
exit(8); |
1432 |
< |
} |
1429 |
> |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1430 |
> |
sprintf( painCave.errMsg, |
1431 |
> |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1432 |
> |
painCave.isFatal = 1; |
1433 |
> |
simError(); |
1434 |
> |
} |
1435 |
|
|
1436 |
< |
sscanf( the_token, "%lf", ¤tTorsionType->k4 ); |
1437 |
< |
} |
1436 |
> |
sscanf( the_token, "%lf", ¤tTorsionType->k4 ); |
1437 |
> |
} |
1438 |
|
|
1439 |
< |
else{ |
1440 |
< |
fprintf(stderr, |
1441 |
< |
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
1442 |
< |
currentTorsionType->type, |
1443 |
< |
lineNum ); |
1444 |
< |
exit(8); |
1445 |
< |
} |
1439 |
> |
else{ |
1440 |
> |
sprintf( painCave.errMsg, |
1441 |
> |
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
1442 |
> |
currentTorsionType->type, |
1443 |
> |
lineNum ); |
1444 |
> |
painCave.isFatal = 1; |
1445 |
> |
simError(); |
1446 |
> |
} |
1447 |
> |
} |
1448 |
|
} |
1449 |
+ |
|
1450 |
+ |
tempTorsionType = new LinkedType; |
1451 |
+ |
currentTorsionType->next = tempTorsionType; |
1452 |
+ |
currentTorsionType = tempTorsionType; |
1453 |
+ |
|
1454 |
+ |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1455 |
+ |
lineNum++; |
1456 |
|
} |
1457 |
+ |
|
1458 |
+ |
#ifdef IS_MPI |
1459 |
|
|
1460 |
< |
tempTorsionType = new LinkedType; |
1294 |
< |
currentTorsionType->next = tempTorsionType; |
1295 |
< |
currentTorsionType = tempTorsionType; |
1460 |
> |
// send out the linked list to all the other processes |
1461 |
|
|
1462 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1463 |
< |
lineNum++; |
1462 |
> |
sprintf( checkPointMsg, |
1463 |
> |
"TraPPE_Ex torsion structures read successfully." ); |
1464 |
> |
MPIcheckPoint(); |
1465 |
> |
|
1466 |
> |
currentTorsionType = headTorsionType; |
1467 |
> |
while( currentTorsionType != NULL ){ |
1468 |
> |
currentTorsionType->duplicate( info ); |
1469 |
> |
sendFrcStruct( &info, mpiTorsionStructType ); |
1470 |
> |
currentTorsionType = currentTorsionType->next; |
1471 |
> |
} |
1472 |
> |
info.last = 1; |
1473 |
> |
sendFrcStruct( &info, mpiTorsionStructType ); |
1474 |
> |
|
1475 |
|
} |
1476 |
|
|
1477 |
+ |
else{ |
1478 |
+ |
|
1479 |
+ |
// listen for node 0 to send out the force params |
1480 |
+ |
|
1481 |
+ |
MPIcheckPoint(); |
1482 |
+ |
|
1483 |
+ |
headTorsionType = new LinkedType; |
1484 |
+ |
recieveFrcStruct( &info, mpiTorsionStructType ); |
1485 |
+ |
while( !info.last ){ |
1486 |
+ |
|
1487 |
+ |
headTorsionType->add( info ); |
1488 |
+ |
recieveFrcStruct( &info, mpiTorsionStructType ); |
1489 |
+ |
} |
1490 |
+ |
} |
1491 |
+ |
#endif // is_mpi |
1492 |
|
|
1493 |
|
// initialize the Torsions |
1494 |
|
|
1505 |
|
atomD = the_atoms[d]->getType(); |
1506 |
|
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1507 |
|
if( currentTorsionType == NULL ){ |
1508 |
< |
fprintf( stderr, "TorsionType error, %s - %s - %s - %s not found" |
1508 |
> |
sprintf( painCave.errMsg, |
1509 |
> |
"TorsionType error, %s - %s - %s - %s not found" |
1510 |
|
" in force file.\n", |
1511 |
|
atomA, atomB, atomC, atomD ); |
1512 |
< |
exit(8); |
1512 |
> |
painCave.isFatal = 1; |
1513 |
> |
simError(); |
1514 |
|
} |
1515 |
|
|
1516 |
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1529 |
|
|
1530 |
|
delete headTorsionType; |
1531 |
|
|
1532 |
+ |
#ifdef IS_MPI |
1533 |
+ |
sprintf( checkPointMsg, "TraPPE_Ex torsions initialized succesfully" ); |
1534 |
+ |
MPIcheckPoint(); |
1535 |
+ |
#endif // is_mpi |
1536 |
+ |
|
1537 |
|
} |