9 |
|
#include "SRI.hpp" |
10 |
|
#include "simError.h" |
11 |
|
|
12 |
– |
|
12 |
|
#ifdef IS_MPI |
14 |
– |
|
13 |
|
#include "mpiForceField.h" |
14 |
+ |
#endif // is_mpi |
15 |
|
|
16 |
+ |
namespace TPE { // restrict the access of the folowing to this file only. |
17 |
|
|
18 |
– |
// Declare the structures that will be passed by MPI |
18 |
|
|
19 |
< |
typedef struct{ |
20 |
< |
char name[15]; |
21 |
< |
double mass; |
22 |
< |
double epslon; |
23 |
< |
double sigma; |
24 |
< |
double dipole; |
25 |
< |
int isDipole; |
26 |
< |
int last; // 0 -> default |
27 |
< |
// 1 -> tells nodes to stop listening |
28 |
< |
} atomStruct; |
29 |
< |
MPI_Datatype mpiAtomStructType; |
19 |
> |
// Declare the structures that will be passed by MPI |
20 |
> |
|
21 |
> |
typedef struct{ |
22 |
> |
char name[15]; |
23 |
> |
double mass; |
24 |
> |
double epslon; |
25 |
> |
double sigma; |
26 |
> |
double dipole; |
27 |
> |
double w0; |
28 |
> |
double v0; |
29 |
> |
int isSSD; |
30 |
> |
int isDipole; |
31 |
> |
int ident; |
32 |
> |
int last; // 0 -> default |
33 |
> |
// 1 -> tells nodes to stop listening |
34 |
> |
} atomStruct; |
35 |
> |
|
36 |
> |
|
37 |
> |
typedef struct{ |
38 |
> |
char nameA[15]; |
39 |
> |
char nameB[15]; |
40 |
> |
char type[30]; |
41 |
> |
double d0; |
42 |
> |
int last; // 0 -> default |
43 |
> |
// 1 -> tells nodes to stop listening |
44 |
> |
} bondStruct; |
45 |
> |
|
46 |
> |
|
47 |
> |
typedef struct{ |
48 |
> |
char nameA[15]; |
49 |
> |
char nameB[15]; |
50 |
> |
char nameC[15]; |
51 |
> |
char type[30]; |
52 |
> |
double k1, k2, k3, t0; |
53 |
> |
int last; // 0 -> default |
54 |
> |
// 1 -> tells nodes to stop listening |
55 |
> |
} bendStruct; |
56 |
> |
|
57 |
|
|
58 |
< |
typedef struct{ |
59 |
< |
char nameA[15]; |
60 |
< |
char nameB[15]; |
61 |
< |
char type[30]; |
62 |
< |
double d0; |
63 |
< |
int last; // 0 -> default |
64 |
< |
// 1 -> tells nodes to stop listening |
65 |
< |
} bondStruct; |
66 |
< |
MPI_Datatype mpiBondStructType; |
67 |
< |
|
68 |
< |
typedef struct{ |
69 |
< |
char nameA[15]; |
70 |
< |
char nameB[15]; |
71 |
< |
char nameC[15]; |
72 |
< |
char type[30]; |
73 |
< |
double k1, k2, k3, t0; |
74 |
< |
int last; // 0 -> default |
75 |
< |
// 1 -> tells nodes to stop listening |
76 |
< |
} bendStruct; |
51 |
< |
MPI_Datatype mpiBendStructType; |
58 |
> |
typedef struct{ |
59 |
> |
char nameA[15]; |
60 |
> |
char nameB[15]; |
61 |
> |
char nameC[15]; |
62 |
> |
char nameD[15]; |
63 |
> |
char type[30]; |
64 |
> |
double k1, k2, k3, k4; |
65 |
> |
int last; // 0 -> default |
66 |
> |
// 1 -> tells nodes to stop listening |
67 |
> |
} torsionStruct; |
68 |
> |
|
69 |
> |
|
70 |
> |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
71 |
> |
int parseBond( char *lineBuffer, int lineNum, bondStruct &info ); |
72 |
> |
int parseBend( char *lineBuffer, int lineNum, bendStruct &info ); |
73 |
> |
int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ); |
74 |
> |
|
75 |
> |
|
76 |
> |
#ifdef IS_MPI |
77 |
|
|
78 |
< |
typedef struct{ |
79 |
< |
char nameA[15]; |
80 |
< |
char nameB[15]; |
81 |
< |
char nameC[15]; |
57 |
< |
char nameD[15]; |
58 |
< |
char type[30]; |
59 |
< |
double k1, k2, k3, k4; |
60 |
< |
int last; // 0 -> default |
61 |
< |
// 1 -> tells nodes to stop listening |
62 |
< |
} torsionStruct; |
63 |
< |
MPI_Datatype mpiTorsionStructType; |
78 |
> |
MPI_Datatype mpiAtomStructType; |
79 |
> |
MPI_Datatype mpiBondStructType; |
80 |
> |
MPI_Datatype mpiBendStructType; |
81 |
> |
MPI_Datatype mpiTorsionStructType; |
82 |
|
|
83 |
|
#endif |
84 |
|
|
85 |
+ |
} // namespace |
86 |
|
|
87 |
|
|
88 |
+ |
// declaration of functions needed to wrap the fortran module |
89 |
+ |
|
90 |
+ |
|
91 |
+ |
|
92 |
+ |
TraPPE_ExFF* currentTPEwrap; |
93 |
+ |
|
94 |
+ |
using namespace TPE; |
95 |
+ |
|
96 |
+ |
|
97 |
+ |
//**************************************************************** |
98 |
+ |
// begins the actual forcefield stuff. |
99 |
+ |
//**************************************************************** |
100 |
+ |
|
101 |
+ |
|
102 |
|
TraPPE_ExFF::TraPPE_ExFF(){ |
103 |
|
|
104 |
|
char fileName[200]; |
107 |
|
char temp[200]; |
108 |
|
char errMsg[1000]; |
109 |
|
|
110 |
+ |
// do the funtion wrapping |
111 |
+ |
currentTPEwrap = this; |
112 |
+ |
wrapMe(); |
113 |
+ |
|
114 |
+ |
|
115 |
|
#ifdef IS_MPI |
116 |
|
int i; |
117 |
|
|
118 |
< |
// ********************************************************************** |
118 |
> |
// ********************************************************************** |
119 |
|
// Init the atomStruct mpi type |
120 |
|
|
121 |
|
atomStruct atomProto; // mpiPrototype |
122 |
< |
int atomBC[3] = {15,4,2}; // block counts |
122 |
> |
int atomBC[3] = {15,6,4}; // block counts |
123 |
|
MPI_Aint atomDspls[3]; // displacements |
124 |
|
MPI_Datatype atomMbrTypes[3]; // member mpi types |
125 |
|
|
126 |
|
MPI_Address(&atomProto.name, &atomDspls[0]); |
127 |
|
MPI_Address(&atomProto.mass, &atomDspls[1]); |
128 |
< |
MPI_Address(&atomProto.isDipole, &atomDspls[2]); |
128 |
> |
MPI_Address(&atomProto.isSSD, &atomDspls[2]); |
129 |
|
|
130 |
|
atomMbrTypes[0] = MPI_CHAR; |
131 |
|
atomMbrTypes[1] = MPI_DOUBLE; |
275 |
|
#endif // is_mpi |
276 |
|
} |
277 |
|
|
278 |
+ |
|
279 |
+ |
void TraPPE_ExFF::wrapMe( void ){ |
280 |
+ |
|
281 |
+ |
char* currentFF = "TraPPE_Ex"; |
282 |
+ |
int isError = 0; |
283 |
+ |
|
284 |
+ |
forcefactory_( currentFF, &isError, TPEfunctionWrapper, strlen(currentFF) ); |
285 |
+ |
|
286 |
+ |
if( isError ){ |
287 |
+ |
|
288 |
+ |
sprintf( painCave.errMsg, |
289 |
+ |
"TraPPE_ExFF error: an error was returned from fortran when the " |
290 |
+ |
"the functions were being wrapped.\n" ); |
291 |
+ |
painCave.isFatal = 1; |
292 |
+ |
simError(); |
293 |
+ |
} |
294 |
+ |
|
295 |
+ |
#ifdef IS_MPI |
296 |
+ |
sprintf( checkPointMsg, "TraPPE_ExFF functions succesfully wrapped." ); |
297 |
+ |
MPIcheckPoint(); |
298 |
+ |
#endif // is_mpi |
299 |
+ |
} |
300 |
+ |
|
301 |
+ |
|
302 |
+ |
void TPEfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, |
303 |
+ |
double* sigma, int* isDipole, |
304 |
+ |
int* isSSD, double* dipole, double* w0, |
305 |
+ |
double* v0, int* isError ), |
306 |
+ |
void (*p2)( int*, int*, int* ), |
307 |
+ |
void (*p3)( double*,double*,double*,double*, |
308 |
+ |
short int*, int* ) ){ |
309 |
+ |
|
310 |
+ |
|
311 |
+ |
newTPEtype = p1; |
312 |
+ |
initTPEfortran = p2; |
313 |
+ |
currentTPEwrap->setTPEfortran( p3 ); |
314 |
+ |
} |
315 |
+ |
|
316 |
+ |
|
317 |
+ |
|
318 |
|
void TraPPE_ExFF::initializeAtoms( void ){ |
319 |
|
|
320 |
|
class LinkedType { |
331 |
|
return NULL; |
332 |
|
} |
333 |
|
|
256 |
– |
#ifdef IS_MPI |
334 |
|
void add( atomStruct &info ){ |
335 |
+ |
|
336 |
+ |
// check for duplicates |
337 |
+ |
|
338 |
+ |
if( !strcmp( info.name, name ) ){ |
339 |
+ |
sprintf( painCave.errMsg, |
340 |
+ |
"Duplicate TraPPE_Ex atom type \"%s\" found in " |
341 |
+ |
"the TraPPE_ExFF param file./n", |
342 |
+ |
name ); |
343 |
+ |
painCave.isFatal = 1; |
344 |
+ |
simError(); |
345 |
+ |
} |
346 |
+ |
|
347 |
|
if( next != NULL ) next->add(info); |
348 |
|
else{ |
349 |
|
next = new LinkedType(); |
350 |
|
strcpy(next->name, info.name); |
351 |
< |
next->isDipole = info.dipole; |
351 |
> |
next->isDipole = info.isDipole; |
352 |
> |
next->isSSD = info.isSSD; |
353 |
|
next->mass = info.mass; |
354 |
|
next->epslon = info.epslon; |
355 |
|
next->sigma = info.sigma; |
356 |
|
next->dipole = info.dipole; |
357 |
+ |
next->w0 = info.w0; |
358 |
+ |
next->v0 = info.v0; |
359 |
+ |
next->ident = info.ident; |
360 |
|
} |
361 |
|
} |
362 |
+ |
|
363 |
+ |
#ifdef IS_MPI |
364 |
|
|
365 |
|
void duplicate( atomStruct &info ){ |
366 |
|
strcpy(info.name, name); |
367 |
< |
info.isDipole = dipole; |
367 |
> |
info.isDipole = isDipole; |
368 |
> |
info.isSSD = isSSD; |
369 |
|
info.mass = mass; |
370 |
|
info.epslon = epslon; |
371 |
|
info.sigma = sigma; |
372 |
|
info.dipole = dipole; |
373 |
+ |
info.w0 = w0; |
374 |
+ |
info.v0 = v0; |
375 |
|
info.last = 0; |
376 |
|
} |
377 |
|
|
380 |
|
|
381 |
|
char name[15]; |
382 |
|
int isDipole; |
383 |
+ |
int isSSD; |
384 |
|
double mass; |
385 |
|
double epslon; |
386 |
|
double sigma; |
387 |
|
double dipole; |
388 |
+ |
double w0; |
389 |
+ |
double v0; |
390 |
+ |
int ident; |
391 |
|
LinkedType* next; |
392 |
|
}; |
393 |
|
|
394 |
|
LinkedType* headAtomType; |
395 |
|
LinkedType* currentAtomType; |
294 |
– |
LinkedType* tempAtomType; |
295 |
– |
|
296 |
– |
#ifdef IS_MPI |
396 |
|
atomStruct info; |
397 |
|
info.last = 1; // initialize last to have the last set. |
398 |
|
// if things go well, last will be set to 0 |
399 |
< |
#endif |
399 |
> |
|
400 |
|
|
401 |
|
|
303 |
– |
char readLine[500]; |
304 |
– |
char* the_token; |
305 |
– |
char* eof_test; |
306 |
– |
int foundAtom = 0; |
307 |
– |
int lineNum = 0; |
402 |
|
int i; |
403 |
< |
|
403 |
> |
int identNum; |
404 |
|
|
405 |
+ |
Atom** the_atoms; |
406 |
+ |
int nAtoms; |
407 |
+ |
the_atoms = entry_plug->atoms; |
408 |
+ |
nAtoms = entry_plug->n_atoms; |
409 |
+ |
|
410 |
+ |
|
411 |
|
////////////////////////////////////////////////// |
412 |
|
// a quick water fix |
413 |
|
|
442 |
|
|
443 |
|
////////////////////////////////////////////////// |
444 |
|
|
445 |
< |
Atom** the_atoms; |
346 |
< |
int nAtoms; |
347 |
< |
the_atoms = entry_plug->atoms; |
348 |
< |
nAtoms = entry_plug->n_atoms; |
349 |
< |
|
350 |
< |
|
445 |
> |
|
446 |
|
#ifdef IS_MPI |
447 |
|
if( worldRank == 0 ){ |
448 |
|
#endif |
449 |
|
|
450 |
|
// read in the atom types. |
451 |
< |
|
357 |
< |
rewind( frcFile ); |
451 |
> |
|
452 |
|
headAtomType = new LinkedType; |
359 |
– |
currentAtomType = headAtomType; |
453 |
|
|
454 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
455 |
< |
lineNum++; |
363 |
< |
if( eof_test == NULL ){ |
364 |
< |
sprintf( painCave.errMsg, "Error in reading Atoms from force file.\n" ); |
365 |
< |
painCave.isFatal = 1; |
366 |
< |
simError(); |
367 |
< |
} |
368 |
< |
|
369 |
< |
|
370 |
< |
while( !foundAtom ){ |
371 |
< |
while( eof_test != NULL && readLine[0] != '#' ){ |
372 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
373 |
< |
lineNum++; |
374 |
< |
} |
375 |
< |
if( eof_test == NULL ){ |
376 |
< |
sprintf( painCave.errMsg, |
377 |
< |
"Error in reading Atoms from force file at line %d.\n", |
378 |
< |
lineNum ); |
379 |
< |
painCave.isFatal = 1; |
380 |
< |
simError(); |
381 |
< |
} |
382 |
< |
|
383 |
< |
the_token = strtok( readLine, " ,;\t#\n" ); |
384 |
< |
foundAtom = !strcmp( "AtomTypes", the_token ); |
385 |
< |
|
386 |
< |
if( !foundAtom ){ |
387 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
388 |
< |
lineNum++; |
389 |
< |
|
390 |
< |
if( eof_test == NULL ){ |
391 |
< |
sprintf( painCave.errMsg, |
392 |
< |
"Error in reading Atoms from force file at line %d.\n", |
393 |
< |
lineNum ); |
394 |
< |
painCave.isFatal = 1; |
395 |
< |
simError(); |
396 |
< |
} |
397 |
< |
} |
398 |
< |
} |
399 |
< |
|
454 |
> |
fastForward( "AtomTypes", "initializeAtoms" ); |
455 |
> |
|
456 |
|
// we are now at the AtomTypes section. |
457 |
|
|
458 |
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
459 |
|
lineNum++; |
460 |
|
|
461 |
+ |
|
462 |
+ |
// read a line, and start parseing out the atom types |
463 |
+ |
|
464 |
|
if( eof_test == NULL ){ |
465 |
|
sprintf( painCave.errMsg, |
466 |
|
"Error in reading Atoms from force file at line %d.\n", |
469 |
|
simError(); |
470 |
|
} |
471 |
|
|
472 |
+ |
identNum = 1; |
473 |
+ |
// stop reading at end of file, or at next section |
474 |
|
while( readLine[0] != '#' && eof_test != NULL ){ |
475 |
< |
|
475 |
> |
|
476 |
> |
// toss comment lines |
477 |
|
if( readLine[0] != '!' ){ |
478 |
|
|
479 |
< |
the_token = strtok( readLine, " \n\t,;" ); |
480 |
< |
if( the_token != NULL ){ |
481 |
< |
|
482 |
< |
strcpy( currentAtomType->name, the_token ); |
483 |
< |
|
422 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
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( 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( 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( 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( painCave.errMsg, |
461 |
< |
"Error parseing AtomTypes: line %d\n", |
462 |
< |
lineNum ); |
463 |
< |
painCave.isFatal = 1; |
464 |
< |
simError(); |
465 |
< |
} |
466 |
< |
|
467 |
< |
sscanf( the_token, "%lf", ¤tAtomType->dipole ); |
468 |
< |
} |
479 |
> |
// the parser returns 0 if the line was blank |
480 |
> |
if( parseAtom( readLine, lineNum, info ) ){ |
481 |
> |
info.ident = identNum; |
482 |
> |
headAtomType->add( info );; |
483 |
> |
identNum++; |
484 |
|
} |
485 |
|
} |
471 |
– |
|
472 |
– |
tempAtomType = new LinkedType; |
473 |
– |
currentAtomType->next = tempAtomType; |
474 |
– |
currentAtomType = tempAtomType; |
475 |
– |
|
486 |
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
487 |
|
lineNum++; |
488 |
|
} |
492 |
|
// send out the linked list to all the other processes |
493 |
|
|
494 |
|
sprintf( checkPointMsg, |
495 |
< |
"TraPPE_Ex atom structures read successfully." ); |
495 |
> |
"TraPPE_ExFF atom structures read successfully." ); |
496 |
|
MPIcheckPoint(); |
497 |
|
|
498 |
< |
currentAtomType = headAtomType; |
498 |
> |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
499 |
|
while( currentAtomType != NULL ){ |
500 |
|
currentAtomType->duplicate( info ); |
501 |
+ |
|
502 |
+ |
|
503 |
+ |
|
504 |
|
sendFrcStruct( &info, mpiAtomStructType ); |
505 |
+ |
|
506 |
+ |
sprintf( checkPointMsg, |
507 |
+ |
"successfully sent TraPPE_Ex force type: \"%s\"\n", |
508 |
+ |
info.name ); |
509 |
+ |
MPIcheckPoint(); |
510 |
+ |
|
511 |
|
currentAtomType = currentAtomType->next; |
512 |
|
} |
513 |
|
info.last = 1; |
523 |
|
|
524 |
|
headAtomType = new LinkedType; |
525 |
|
recieveFrcStruct( &info, mpiAtomStructType ); |
526 |
+ |
|
527 |
|
while( !info.last ){ |
528 |
|
|
529 |
+ |
|
530 |
+ |
|
531 |
|
headAtomType->add( info ); |
532 |
+ |
|
533 |
+ |
MPIcheckPoint(); |
534 |
+ |
|
535 |
|
recieveFrcStruct( &info, mpiAtomStructType ); |
536 |
|
} |
537 |
|
} |
538 |
|
#endif // is_mpi |
539 |
|
|
540 |
+ |
// call new A_types in fortran |
541 |
|
|
542 |
+ |
int isError; |
543 |
+ |
currentAtomType = headAtomType; |
544 |
+ |
while( currentAtomType != NULL ){ |
545 |
+ |
|
546 |
+ |
if( currentAtomType->name[0] != '\0' ){ |
547 |
+ |
isError = 0; |
548 |
+ |
newTPEtype( &(currentAtomType->ident), |
549 |
+ |
&(currentAtomType->mass), |
550 |
+ |
&(currentAtomType->epslon), |
551 |
+ |
&(currentAtomType->sigma), |
552 |
+ |
&(currentAtomType->isDipole), |
553 |
+ |
&(currentAtomType->isSSD), |
554 |
+ |
&(currentAtomType->dipole), |
555 |
+ |
&(currentAtomType->w0), |
556 |
+ |
&(currentAtomType->v0), |
557 |
+ |
&isError ); |
558 |
+ |
if( isError ){ |
559 |
+ |
sprintf( painCave.errMsg, |
560 |
+ |
"Error initializing the \"%s\" atom type in fortran\n", |
561 |
+ |
currentAtomType->name ); |
562 |
+ |
painCave.isFatal = 1; |
563 |
+ |
simError(); |
564 |
+ |
} |
565 |
+ |
} |
566 |
+ |
currentAtomType = currentAtomType->next; |
567 |
+ |
} |
568 |
+ |
|
569 |
+ |
#ifdef IS_MPI |
570 |
+ |
sprintf( checkPointMsg, |
571 |
+ |
"TraPPE_ExFF atom structures successfully sent to fortran\n" ); |
572 |
+ |
MPIcheckPoint(); |
573 |
+ |
#endif // is_mpi |
574 |
+ |
|
575 |
+ |
|
576 |
|
// initialize the atoms |
577 |
|
|
578 |
+ |
double bigSigma = 0.0; |
579 |
|
DirectionalAtom* dAtom; |
580 |
|
|
581 |
|
for( i=0; i<nAtoms; i++ ){ |
594 |
|
the_atoms[i]->setSigma( currentAtomType->sigma ); |
595 |
|
the_atoms[i]->setLJ(); |
596 |
|
|
597 |
+ |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
598 |
+ |
|
599 |
|
if( currentAtomType->isDipole ){ |
600 |
|
if( the_atoms[i]->isDirectional() ){ |
601 |
|
|
645 |
|
} |
646 |
|
} |
647 |
|
|
648 |
+ |
#ifdef IS_MPI |
649 |
+ |
double tempBig = bigSigma; |
650 |
+ |
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
651 |
+ |
#endif //is_mpi |
652 |
|
|
653 |
+ |
//calc rCut and rList |
654 |
+ |
|
655 |
+ |
entry_plug->rCut = 2.5 * bigSigma; |
656 |
+ |
|
657 |
+ |
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) |
658 |
+ |
entry_plug->rCut = entry_plug->box_x / 2.0; |
659 |
+ |
|
660 |
+ |
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) |
661 |
+ |
entry_plug->rCut = entry_plug->box_y / 2.0; |
662 |
+ |
|
663 |
+ |
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) |
664 |
+ |
entry_plug->rCut = entry_plug->box_z / 2.0; |
665 |
+ |
|
666 |
+ |
entry_plug->rList = entry_plug->rCut + 1.0; |
667 |
+ |
|
668 |
+ |
|
669 |
|
// clean up the memory |
670 |
|
|
671 |
|
delete headAtomType; |
696 |
|
return NULL; |
697 |
|
} |
698 |
|
|
699 |
< |
#ifdef IS_MPI |
699 |
> |
|
700 |
|
void add( bondStruct &info ){ |
701 |
+ |
|
702 |
+ |
// check for duplicates |
703 |
+ |
int dup = 0; |
704 |
+ |
|
705 |
+ |
if( !strcmp(nameA, info.nameA ) && !strcmp( nameB, info.nameB ) ) dup = 1; |
706 |
+ |
if( !strcmp(nameA, info.nameB ) && !strcmp( nameB, info.nameA ) ) dup = 1; |
707 |
+ |
|
708 |
+ |
if(dup){ |
709 |
+ |
sprintf( painCave.errMsg, |
710 |
+ |
"Duplicate TraPPE_Ex bond type \"%s - %s\" found in " |
711 |
+ |
"the TraPPE_ExFF param file./n", |
712 |
+ |
nameA, nameB ); |
713 |
+ |
painCave.isFatal = 1; |
714 |
+ |
simError(); |
715 |
+ |
} |
716 |
+ |
|
717 |
+ |
|
718 |
|
if( next != NULL ) next->add(info); |
719 |
|
else{ |
720 |
|
next = new LinkedType(); |
725 |
|
} |
726 |
|
} |
727 |
|
|
728 |
+ |
#ifdef IS_MPI |
729 |
|
void duplicate( bondStruct &info ){ |
730 |
|
strcpy(info.nameA, nameA); |
731 |
|
strcpy(info.nameB, nameB); |
749 |
|
|
750 |
|
LinkedType* headBondType; |
751 |
|
LinkedType* currentBondType; |
651 |
– |
LinkedType* tempBondType; |
652 |
– |
|
653 |
– |
#ifdef IS_MPI |
752 |
|
bondStruct info; |
753 |
|
info.last = 1; // initialize last to have the last set. |
754 |
|
// if things go well, last will be set to 0 |
657 |
– |
#endif |
755 |
|
|
659 |
– |
char readLine[500]; |
660 |
– |
char* the_token; |
661 |
– |
char* eof_test; |
662 |
– |
int foundBond = 0; |
663 |
– |
int lineNum = 0; |
664 |
– |
int i, a, b; |
665 |
– |
char* atomA; |
666 |
– |
char* atomB; |
667 |
– |
|
756 |
|
SRI **the_sris; |
757 |
|
Atom** the_atoms; |
758 |
|
int nBonds; |
760 |
|
the_atoms = entry_plug->atoms; |
761 |
|
nBonds = entry_plug->n_bonds; |
762 |
|
|
763 |
+ |
int i, a, b; |
764 |
+ |
char* atomA; |
765 |
+ |
char* atomB; |
766 |
|
|
767 |
|
#ifdef IS_MPI |
768 |
|
if( worldRank == 0 ){ |
770 |
|
|
771 |
|
// read in the bond types. |
772 |
|
|
682 |
– |
rewind( frcFile ); |
773 |
|
headBondType = new LinkedType; |
684 |
– |
currentBondType = headBondType; |
774 |
|
|
775 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
775 |
> |
fastForward( "BondTypes", "initializeBonds" ); |
776 |
> |
|
777 |
> |
// we are now at the bondTypes section |
778 |
> |
|
779 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
780 |
|
lineNum++; |
688 |
– |
if( eof_test == NULL ){ |
689 |
– |
sprintf( painCave.errMsg, "Error in reading Bonds from force file.\n" ); |
690 |
– |
painCave.isFatal = 1; |
691 |
– |
simError(); |
692 |
– |
} |
781 |
|
|
782 |
|
|
783 |
< |
while( !foundBond ){ |
784 |
< |
while( eof_test != NULL && readLine[0] != '#' ){ |
697 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
698 |
< |
lineNum++; |
699 |
< |
} |
700 |
< |
if( eof_test == NULL ){ |
701 |
< |
sprintf( painCave.errMsg, |
702 |
< |
"Error in reading Bonds from force file at line %d.\n", |
703 |
< |
lineNum ); |
704 |
< |
painCave.isFatal = 1; |
705 |
< |
simError(); |
706 |
< |
} |
707 |
< |
|
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 |
< |
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 |
< |
|
783 |
> |
// read a line, and start parseing out the atom types |
784 |
> |
|
785 |
|
if( eof_test == NULL ){ |
786 |
|
sprintf( painCave.errMsg, |
787 |
< |
"Error in reading Bonds from force file at line %d.\n", |
787 |
> |
"Error in reading bonds from force file at line %d.\n", |
788 |
|
lineNum ); |
789 |
|
painCave.isFatal = 1; |
790 |
|
simError(); |
791 |
|
} |
792 |
|
|
793 |
+ |
// stop reading at end of file, or at next section |
794 |
|
while( readLine[0] != '#' && eof_test != NULL ){ |
795 |
< |
|
795 |
> |
|
796 |
> |
// toss comment lines |
797 |
|
if( readLine[0] != '!' ){ |
798 |
|
|
799 |
< |
the_token = strtok( readLine, " \n\t,;" ); |
800 |
< |
if( the_token != NULL ){ |
801 |
< |
|
745 |
< |
strcpy( currentBondType->nameA, the_token ); |
746 |
< |
|
747 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
748 |
< |
sprintf( painCave.errMsg, |
749 |
< |
"Error parseing BondTypes: line %d\n", lineNum ); |
750 |
< |
painCave.isFatal = 1; |
751 |
< |
simError(); |
752 |
< |
} |
753 |
< |
|
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 |
< |
} |
799 |
> |
// the parser returns 0 if the line was blank |
800 |
> |
if( parseBond( readLine, lineNum, info ) ){ |
801 |
> |
headBondType->add( info ); |
802 |
|
} |
803 |
|
} |
786 |
– |
|
787 |
– |
tempBondType = new LinkedType; |
788 |
– |
currentBondType->next = tempBondType; |
789 |
– |
currentBondType = tempBondType; |
790 |
– |
|
804 |
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
805 |
|
lineNum++; |
806 |
|
} |
807 |
< |
|
807 |
> |
|
808 |
|
#ifdef IS_MPI |
809 |
|
|
810 |
|
// send out the linked list to all the other processes |
903 |
|
return NULL; |
904 |
|
} |
905 |
|
|
893 |
– |
#ifdef IS_MPI |
894 |
– |
|
906 |
|
void add( bendStruct &info ){ |
907 |
+ |
|
908 |
+ |
// check for duplicates |
909 |
+ |
int dup = 0; |
910 |
+ |
|
911 |
+ |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) |
912 |
+ |
&& !strcmp( nameC, info.nameC ) ) dup = 1; |
913 |
+ |
if( !strcmp( nameA, info.nameC ) && !strcmp( nameB, info.nameB ) |
914 |
+ |
&& !strcmp( nameC, info.nameA ) ) dup = 1; |
915 |
+ |
|
916 |
+ |
if(dup){ |
917 |
+ |
sprintf( painCave.errMsg, |
918 |
+ |
"Duplicate TraPPE_Ex bend type \"%s - %s - %s\" found in " |
919 |
+ |
"the TraPPE_ExFF param file./n", |
920 |
+ |
nameA, nameB, nameC ); |
921 |
+ |
painCave.isFatal = 1; |
922 |
+ |
simError(); |
923 |
+ |
} |
924 |
+ |
|
925 |
|
if( next != NULL ) next->add(info); |
926 |
|
else{ |
927 |
|
next = new LinkedType(); |
935 |
|
next->t0 = info.t0; |
936 |
|
} |
937 |
|
} |
938 |
< |
|
938 |
> |
|
939 |
> |
#ifdef IS_MPI |
940 |
> |
|
941 |
|
void duplicate( bendStruct &info ){ |
942 |
|
strcpy(info.nameA, nameA); |
943 |
|
strcpy(info.nameB, nameB); |
963 |
|
|
964 |
|
LinkedType* headBendType; |
965 |
|
LinkedType* currentBendType; |
935 |
– |
LinkedType* tempBendType; |
936 |
– |
|
937 |
– |
#ifdef IS_MPI |
966 |
|
bendStruct info; |
967 |
|
info.last = 1; // initialize last to have the last set. |
968 |
|
// if things go well, last will be set to 0 |
941 |
– |
#endif |
969 |
|
|
943 |
– |
char readLine[500]; |
944 |
– |
char* the_token; |
945 |
– |
char* eof_test; |
946 |
– |
int foundBend = 0; |
947 |
– |
int lineNum = 0; |
948 |
– |
int i, a, b, c, index; |
949 |
– |
char* atomA; |
950 |
– |
char* atomB; |
951 |
– |
char* atomC; |
970 |
|
QuadraticBend* qBend; |
953 |
– |
|
971 |
|
SRI **the_sris; |
972 |
|
Atom** the_atoms; |
973 |
|
int nBends; |
975 |
|
the_atoms = entry_plug->atoms; |
976 |
|
nBends = entry_plug->n_bends; |
977 |
|
|
978 |
+ |
int i, a, b, c; |
979 |
+ |
char* atomA; |
980 |
+ |
char* atomB; |
981 |
+ |
char* atomC; |
982 |
|
|
983 |
+ |
|
984 |
|
#ifdef IS_MPI |
985 |
|
if( worldRank == 0 ){ |
986 |
|
#endif |
987 |
|
|
988 |
|
// read in the bend types. |
989 |
|
|
968 |
– |
rewind( frcFile ); |
990 |
|
headBendType = new LinkedType; |
970 |
– |
currentBendType = headBendType; |
971 |
– |
|
972 |
– |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
973 |
– |
lineNum++; |
974 |
– |
if( eof_test == NULL ){ |
975 |
– |
sprintf( painCave.errMsg, "Error in reading Bends from force file.\n" ); |
976 |
– |
painCave.isFatal = 1; |
977 |
– |
simError(); |
978 |
– |
} |
979 |
– |
|
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 |
– |
sprintf( painCave.errMsg, |
988 |
– |
"Error in reading Bends from force file at line %d.\n", |
989 |
– |
lineNum ); |
990 |
– |
painCave.isFatal = 1; |
991 |
– |
simError(); |
992 |
– |
} |
993 |
– |
|
994 |
– |
the_token = strtok( readLine, " ,;\t#\n" ); |
995 |
– |
foundBend = !strcmp( "BendTypes", the_token ); |
991 |
|
|
992 |
< |
if( !foundBend ){ |
998 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
999 |
< |
lineNum++; |
992 |
> |
fastForward( "BendTypes", "initializeBends" ); |
993 |
|
|
994 |
< |
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 |
< |
} |
994 |
> |
// we are now at the bendTypes section |
995 |
|
|
996 |
< |
// we are now at the BendTypes section. |
1012 |
< |
|
1013 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
996 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
997 |
|
lineNum++; |
998 |
< |
|
998 |
> |
|
999 |
> |
// read a line, and start parseing out the bend types |
1000 |
> |
|
1001 |
|
if( eof_test == NULL ){ |
1002 |
|
sprintf( painCave.errMsg, |
1003 |
< |
"Error in reading Bends from force file at line %d.\n", |
1003 |
> |
"Error in reading bends from force file at line %d.\n", |
1004 |
|
lineNum ); |
1005 |
|
painCave.isFatal = 1; |
1006 |
|
simError(); |
1007 |
|
} |
1023 |
– |
|
1024 |
– |
while( readLine[0] != '#' && eof_test != NULL ){ |
1008 |
|
|
1009 |
< |
if( readLine[0] != '!' ){ |
1009 |
> |
// stop reading at end of file, or at next section |
1010 |
> |
while( readLine[0] != '#' && eof_test != NULL ){ |
1011 |
|
|
1012 |
< |
the_token = strtok( readLine, " \n\t,;" ); |
1013 |
< |
if( the_token != NULL ){ |
1012 |
> |
// toss comment lines |
1013 |
> |
if( readLine[0] != '!' ){ |
1014 |
|
|
1015 |
< |
strcpy( currentBendType->nameA, the_token ); |
1016 |
< |
|
1017 |
< |
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 ); |
1041 |
< |
|
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 ); |
1050 |
< |
|
1051 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
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 ); |
1069 |
< |
|
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 ); |
1078 |
< |
|
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 ); |
1087 |
< |
|
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 |
< |
} |
1097 |
< |
|
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 |
< |
} |
1015 |
> |
// the parser returns 0 if the line was blank |
1016 |
> |
if( parseBend( readLine, lineNum, info ) ){ |
1017 |
> |
headBendType->add( info ); |
1018 |
|
} |
1019 |
|
} |
1108 |
– |
|
1109 |
– |
tempBendType = new LinkedType; |
1110 |
– |
currentBendType->next = tempBendType; |
1111 |
– |
currentBendType = tempBendType; |
1112 |
– |
|
1020 |
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1021 |
|
lineNum++; |
1022 |
|
} |
1023 |
< |
|
1023 |
> |
|
1024 |
|
#ifdef IS_MPI |
1025 |
|
|
1026 |
|
// send out the linked list to all the other processes |
1057 |
|
#endif // is_mpi |
1058 |
|
|
1059 |
|
// initialize the Bends |
1060 |
+ |
|
1061 |
+ |
int index; |
1062 |
|
|
1063 |
|
for( i=0; i<nBends; i++ ){ |
1064 |
|
|
1122 |
|
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
1123 |
|
|
1124 |
|
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
1125 |
< |
!strcmp( nameC, key2 ) && !strcmp( nameD, key4 ) ) return this; |
1125 |
> |
!strcmp( nameC, key2 ) && !strcmp( nameD, key1 ) ) return this; |
1126 |
|
|
1127 |
|
if( next != NULL ) return next->find(key1, key2, key3, key4); |
1128 |
|
return NULL; |
1129 |
|
} |
1221 |
– |
|
1222 |
– |
#ifdef IS_MPI |
1130 |
|
|
1131 |
|
void add( torsionStruct &info ){ |
1132 |
+ |
|
1133 |
+ |
// check for duplicates |
1134 |
+ |
int dup = 0; |
1135 |
+ |
|
1136 |
+ |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) && |
1137 |
+ |
!strcmp( nameC, info.nameC ) && !strcmp( nameD, info.nameD ) ) dup = 1; |
1138 |
+ |
|
1139 |
+ |
if( !strcmp( nameA, info.nameD ) && !strcmp( nameB, info.nameC ) && |
1140 |
+ |
!strcmp( nameC, info.nameB ) && !strcmp( nameD, info.nameA ) ) dup = 1; |
1141 |
+ |
|
1142 |
+ |
if(dup){ |
1143 |
+ |
sprintf( painCave.errMsg, |
1144 |
+ |
"Duplicate TraPPE_Ex torsion type \"%s - %s - %s - %s\" found in " |
1145 |
+ |
"the TraPPE_ExFF param file./n", nameA, nameB, nameC, nameD ); |
1146 |
+ |
painCave.isFatal = 1; |
1147 |
+ |
simError(); |
1148 |
+ |
} |
1149 |
+ |
|
1150 |
|
if( next != NULL ) next->add(info); |
1151 |
|
else{ |
1152 |
|
next = new LinkedType(); |
1160 |
|
next->k4 = info.k4; |
1161 |
|
} |
1162 |
|
} |
1163 |
+ |
|
1164 |
+ |
#ifdef IS_MPI |
1165 |
|
|
1166 |
|
void duplicate( torsionStruct &info ){ |
1167 |
|
strcpy(info.nameA, nameA); |
1190 |
|
|
1191 |
|
LinkedType* headTorsionType; |
1192 |
|
LinkedType* currentTorsionType; |
1266 |
– |
LinkedType* tempTorsionType; |
1267 |
– |
|
1268 |
– |
#ifdef IS_MPI |
1193 |
|
torsionStruct info; |
1194 |
|
info.last = 1; // initialize last to have the last set. |
1195 |
|
// if things go well, last will be set to 0 |
1272 |
– |
#endif |
1196 |
|
|
1274 |
– |
char readLine[500]; |
1275 |
– |
char* the_token; |
1276 |
– |
char* eof_test; |
1277 |
– |
int foundTorsion = 0; |
1278 |
– |
int lineNum = 0; |
1197 |
|
int i, a, b, c, d, index; |
1198 |
|
char* atomA; |
1199 |
|
char* atomB; |
1214 |
|
|
1215 |
|
// read in the torsion types. |
1216 |
|
|
1299 |
– |
rewind( frcFile ); |
1217 |
|
headTorsionType = new LinkedType; |
1301 |
– |
currentTorsionType = headTorsionType; |
1302 |
– |
|
1303 |
– |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1304 |
– |
lineNum++; |
1305 |
– |
if( eof_test == NULL ){ |
1306 |
– |
sprintf( painCave.errMsg, |
1307 |
– |
"Error in reading Torsions from force file.\n" ); |
1308 |
– |
painCave.isFatal = 1; |
1309 |
– |
simError(); |
1310 |
– |
} |
1311 |
– |
|
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 |
– |
sprintf( painCave.errMsg, |
1320 |
– |
"Error in reading Torsions from force file at line %d.\n", |
1321 |
– |
lineNum ); |
1322 |
– |
painCave.isFatal = 1; |
1323 |
– |
simError(); |
1324 |
– |
} |
1325 |
– |
|
1326 |
– |
the_token = strtok( readLine, " ,;\t#\n" ); |
1327 |
– |
foundTorsion = !strcmp( "TorsionTypes", the_token ); |
1218 |
|
|
1219 |
< |
if( !foundTorsion ){ |
1330 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1331 |
< |
lineNum++; |
1219 |
> |
fastForward( "TorsionTypes", "initializeTorsions" ); |
1220 |
|
|
1221 |
< |
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 |
< |
} |
1221 |
> |
// we are now at the torsionTypes section |
1222 |
|
|
1223 |
< |
// we are now at the TorsionTypes section. |
1344 |
< |
|
1345 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1223 |
> |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1224 |
|
lineNum++; |
1225 |
< |
|
1225 |
> |
|
1226 |
> |
|
1227 |
> |
// read a line, and start parseing out the atom types |
1228 |
> |
|
1229 |
|
if( eof_test == NULL ){ |
1230 |
|
sprintf( painCave.errMsg, |
1231 |
< |
"Error in reading Torsions from force file at line %d.\n", |
1231 |
> |
"Error in reading torsions from force file at line %d.\n", |
1232 |
|
lineNum ); |
1233 |
|
painCave.isFatal = 1; |
1234 |
|
simError(); |
1235 |
|
} |
1355 |
– |
|
1356 |
– |
while( readLine[0] != '#' && eof_test != NULL ){ |
1236 |
|
|
1237 |
+ |
// stop reading at end of file, or at next section |
1238 |
+ |
while( readLine[0] != '#' && eof_test != NULL ){ |
1239 |
+ |
|
1240 |
+ |
// toss comment lines |
1241 |
|
if( readLine[0] != '!' ){ |
1359 |
– |
|
1360 |
– |
the_token = strtok( readLine, " \n\t,;" ); |
1361 |
– |
if( the_token != NULL ){ |
1242 |
|
|
1243 |
< |
strcpy( currentTorsionType->nameA, the_token ); |
1244 |
< |
|
1245 |
< |
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 ); |
1373 |
< |
|
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 ); |
1382 |
< |
|
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 ); |
1391 |
< |
|
1392 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
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 ); |
1410 |
< |
|
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 ); |
1419 |
< |
|
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 ); |
1428 |
< |
|
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 |
< |
} |
1438 |
< |
|
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 |
< |
} |
1243 |
> |
// the parser returns 0 if the line was blank |
1244 |
> |
if( parseTorsion( readLine, lineNum, info ) ){ |
1245 |
> |
headTorsionType->add( info ); |
1246 |
|
} |
1247 |
|
} |
1449 |
– |
|
1450 |
– |
tempTorsionType = new LinkedType; |
1451 |
– |
currentTorsionType->next = tempTorsionType; |
1452 |
– |
currentTorsionType = tempTorsionType; |
1453 |
– |
|
1248 |
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1249 |
|
lineNum++; |
1250 |
|
} |
1327 |
|
sprintf( checkPointMsg, "TraPPE_Ex torsions initialized succesfully" ); |
1328 |
|
MPIcheckPoint(); |
1329 |
|
#endif // is_mpi |
1330 |
+ |
|
1331 |
+ |
} |
1332 |
+ |
|
1333 |
+ |
void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){ |
1334 |
+ |
|
1335 |
+ |
int foundText = 0; |
1336 |
+ |
char* the_token; |
1337 |
+ |
|
1338 |
+ |
rewind( frcFile ); |
1339 |
+ |
lineNum = 0; |
1340 |
+ |
|
1341 |
+ |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1342 |
+ |
lineNum++; |
1343 |
+ |
if( eof_test == NULL ){ |
1344 |
+ |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
1345 |
+ |
" file is empty.\n", |
1346 |
+ |
searchOwner ); |
1347 |
+ |
painCave.isFatal = 1; |
1348 |
+ |
simError(); |
1349 |
+ |
} |
1350 |
+ |
|
1351 |
+ |
|
1352 |
+ |
while( !foundText ){ |
1353 |
+ |
while( eof_test != NULL && readLine[0] != '#' ){ |
1354 |
+ |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1355 |
+ |
lineNum++; |
1356 |
+ |
} |
1357 |
+ |
if( eof_test == NULL ){ |
1358 |
+ |
sprintf( painCave.errMsg, |
1359 |
+ |
"Error fast forwarding force file for %s at " |
1360 |
+ |
"line %d: file ended unexpectedly.\n", |
1361 |
+ |
searchOwner, |
1362 |
+ |
lineNum ); |
1363 |
+ |
painCave.isFatal = 1; |
1364 |
+ |
simError(); |
1365 |
+ |
} |
1366 |
+ |
|
1367 |
+ |
the_token = strtok( readLine, " ,;\t#\n" ); |
1368 |
+ |
foundText = !strcmp( stopText, the_token ); |
1369 |
+ |
|
1370 |
+ |
if( !foundText ){ |
1371 |
+ |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1372 |
+ |
lineNum++; |
1373 |
+ |
|
1374 |
+ |
if( eof_test == NULL ){ |
1375 |
+ |
sprintf( painCave.errMsg, |
1376 |
+ |
"Error fast forwarding force file for %s at " |
1377 |
+ |
"line %d: file ended unexpectedly.\n", |
1378 |
+ |
searchOwner, |
1379 |
+ |
lineNum ); |
1380 |
+ |
painCave.isFatal = 1; |
1381 |
+ |
simError(); |
1382 |
+ |
} |
1383 |
+ |
} |
1384 |
+ |
} |
1385 |
+ |
} |
1386 |
+ |
|
1387 |
+ |
|
1388 |
+ |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1389 |
+ |
|
1390 |
+ |
char* the_token; |
1391 |
+ |
|
1392 |
+ |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1393 |
+ |
if( the_token != NULL ){ |
1394 |
+ |
|
1395 |
+ |
strcpy( info.name, the_token ); |
1396 |
|
|
1397 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1398 |
+ |
sprintf( painCave.errMsg, |
1399 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1400 |
+ |
painCave.isFatal = 1; |
1401 |
+ |
simError(); |
1402 |
+ |
} |
1403 |
+ |
|
1404 |
+ |
info.isDipole = atoi( the_token ); |
1405 |
+ |
|
1406 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1407 |
+ |
sprintf( painCave.errMsg, |
1408 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1409 |
+ |
painCave.isFatal = 1; |
1410 |
+ |
simError(); |
1411 |
+ |
} |
1412 |
+ |
|
1413 |
+ |
info.isSSD = atoi( the_token ); |
1414 |
+ |
|
1415 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1416 |
+ |
sprintf( painCave.errMsg, |
1417 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1418 |
+ |
painCave.isFatal = 1; |
1419 |
+ |
simError(); |
1420 |
+ |
} |
1421 |
+ |
|
1422 |
+ |
info.mass = atof( the_token ); |
1423 |
+ |
|
1424 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1425 |
+ |
sprintf( painCave.errMsg, |
1426 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1427 |
+ |
painCave.isFatal = 1; |
1428 |
+ |
simError(); |
1429 |
+ |
} |
1430 |
+ |
|
1431 |
+ |
info.epslon = atof( the_token ); |
1432 |
+ |
|
1433 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1434 |
+ |
sprintf( painCave.errMsg, |
1435 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1436 |
+ |
painCave.isFatal = 1; |
1437 |
+ |
simError(); |
1438 |
+ |
} |
1439 |
+ |
|
1440 |
+ |
info.sigma = atof( the_token ); |
1441 |
+ |
|
1442 |
+ |
if( info.isDipole ){ |
1443 |
+ |
|
1444 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1445 |
+ |
sprintf( painCave.errMsg, |
1446 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1447 |
+ |
painCave.isFatal = 1; |
1448 |
+ |
simError(); |
1449 |
+ |
} |
1450 |
+ |
|
1451 |
+ |
info.dipole = atof( the_token ); |
1452 |
+ |
} |
1453 |
+ |
else info.dipole = 0.0; |
1454 |
+ |
|
1455 |
+ |
if( info.isSSD ){ |
1456 |
+ |
|
1457 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1458 |
+ |
sprintf( painCave.errMsg, |
1459 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1460 |
+ |
painCave.isFatal = 1; |
1461 |
+ |
simError(); |
1462 |
+ |
} |
1463 |
+ |
|
1464 |
+ |
info.w0 = atof( the_token ); |
1465 |
+ |
|
1466 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1467 |
+ |
sprintf( painCave.errMsg, |
1468 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1469 |
+ |
painCave.isFatal = 1; |
1470 |
+ |
simError(); |
1471 |
+ |
} |
1472 |
+ |
|
1473 |
+ |
info.v0 = atof( the_token ); |
1474 |
+ |
} |
1475 |
+ |
else info.v0 = info.w0 = 0.0; |
1476 |
+ |
|
1477 |
+ |
return 1; |
1478 |
+ |
} |
1479 |
+ |
else return 0; |
1480 |
|
} |
1481 |
+ |
|
1482 |
+ |
int parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1483 |
+ |
|
1484 |
+ |
char* the_token; |
1485 |
+ |
|
1486 |
+ |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1487 |
+ |
if( the_token != NULL ){ |
1488 |
+ |
|
1489 |
+ |
strcpy( info.nameA, the_token ); |
1490 |
+ |
|
1491 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1492 |
+ |
sprintf( painCave.errMsg, |
1493 |
+ |
"Error parseing BondTypes: line %d\n", lineNum ); |
1494 |
+ |
painCave.isFatal = 1; |
1495 |
+ |
simError(); |
1496 |
+ |
} |
1497 |
+ |
|
1498 |
+ |
strcpy( info.nameB, the_token ); |
1499 |
+ |
|
1500 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1501 |
+ |
sprintf( painCave.errMsg, |
1502 |
+ |
"Error parseing BondTypes: line %d\n", lineNum ); |
1503 |
+ |
painCave.isFatal = 1; |
1504 |
+ |
simError(); |
1505 |
+ |
} |
1506 |
+ |
|
1507 |
+ |
strcpy( info.type, the_token ); |
1508 |
+ |
|
1509 |
+ |
if( !strcmp( info.type, "fixed" ) ){ |
1510 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1511 |
+ |
sprintf( painCave.errMsg, |
1512 |
+ |
"Error parseing BondTypes: line %d\n", lineNum ); |
1513 |
+ |
painCave.isFatal = 1; |
1514 |
+ |
simError(); |
1515 |
+ |
} |
1516 |
+ |
|
1517 |
+ |
info.d0 = atof( the_token ); |
1518 |
+ |
} |
1519 |
+ |
else{ |
1520 |
+ |
sprintf( painCave.errMsg, |
1521 |
+ |
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
1522 |
+ |
info.type, |
1523 |
+ |
lineNum ); |
1524 |
+ |
painCave.isFatal = 1; |
1525 |
+ |
simError(); |
1526 |
+ |
} |
1527 |
+ |
|
1528 |
+ |
return 1; |
1529 |
+ |
} |
1530 |
+ |
else return 0; |
1531 |
+ |
} |
1532 |
+ |
|
1533 |
+ |
|
1534 |
+ |
int parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1535 |
+ |
|
1536 |
+ |
char* the_token; |
1537 |
+ |
|
1538 |
+ |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1539 |
+ |
if( the_token != NULL ){ |
1540 |
+ |
|
1541 |
+ |
strcpy( info.nameA, the_token ); |
1542 |
+ |
|
1543 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1544 |
+ |
sprintf( painCave.errMsg, |
1545 |
+ |
"Error parseing BondTypes: line %d\n", lineNum ); |
1546 |
+ |
painCave.isFatal = 1; |
1547 |
+ |
simError(); |
1548 |
+ |
} |
1549 |
+ |
|
1550 |
+ |
strcpy( info.nameB, the_token ); |
1551 |
+ |
|
1552 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1553 |
+ |
sprintf( painCave.errMsg, |
1554 |
+ |
"Error parseing BondTypes: line %d\n", lineNum ); |
1555 |
+ |
painCave.isFatal = 1; |
1556 |
+ |
simError(); |
1557 |
+ |
} |
1558 |
+ |
|
1559 |
+ |
strcpy( info.nameC, the_token ); |
1560 |
+ |
|
1561 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1562 |
+ |
sprintf( painCave.errMsg, |
1563 |
+ |
"Error parseing BondTypes: line %d\n", lineNum ); |
1564 |
+ |
painCave.isFatal = 1; |
1565 |
+ |
simError(); |
1566 |
+ |
} |
1567 |
+ |
|
1568 |
+ |
strcpy( info.type, the_token ); |
1569 |
+ |
|
1570 |
+ |
if( !strcmp( info.type, "quadratic" ) ){ |
1571 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1572 |
+ |
sprintf( painCave.errMsg, |
1573 |
+ |
"Error parseing BendTypes: line %d\n", lineNum ); |
1574 |
+ |
painCave.isFatal = 1; |
1575 |
+ |
simError(); |
1576 |
+ |
} |
1577 |
+ |
|
1578 |
+ |
info.k1 = atof( the_token ); |
1579 |
+ |
|
1580 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1581 |
+ |
sprintf( painCave.errMsg, |
1582 |
+ |
"Error parseing BendTypes: line %d\n", lineNum ); |
1583 |
+ |
painCave.isFatal = 1; |
1584 |
+ |
simError(); |
1585 |
+ |
} |
1586 |
+ |
|
1587 |
+ |
info.k2 = atof( the_token ); |
1588 |
+ |
|
1589 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1590 |
+ |
sprintf( painCave.errMsg, |
1591 |
+ |
"Error parseing BendTypes: line %d\n", lineNum ); |
1592 |
+ |
painCave.isFatal = 1; |
1593 |
+ |
simError(); |
1594 |
+ |
} |
1595 |
+ |
|
1596 |
+ |
info.k3 = atof( the_token ); |
1597 |
+ |
|
1598 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1599 |
+ |
sprintf( painCave.errMsg, |
1600 |
+ |
"Error parseing BendTypes: line %d\n", lineNum ); |
1601 |
+ |
painCave.isFatal = 1; |
1602 |
+ |
simError(); |
1603 |
+ |
} |
1604 |
+ |
|
1605 |
+ |
info.t0 = atof( the_token ); |
1606 |
+ |
} |
1607 |
+ |
|
1608 |
+ |
else{ |
1609 |
+ |
sprintf( painCave.errMsg, |
1610 |
+ |
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
1611 |
+ |
info.type, |
1612 |
+ |
lineNum ); |
1613 |
+ |
painCave.isFatal = 1; |
1614 |
+ |
simError(); |
1615 |
+ |
} |
1616 |
+ |
|
1617 |
+ |
return 1; |
1618 |
+ |
} |
1619 |
+ |
else return 0; |
1620 |
+ |
} |
1621 |
+ |
|
1622 |
+ |
int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1623 |
+ |
|
1624 |
+ |
char* the_token; |
1625 |
+ |
|
1626 |
+ |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1627 |
+ |
if( the_token != NULL ){ |
1628 |
+ |
|
1629 |
+ |
strcpy( info.nameA, the_token ); |
1630 |
+ |
|
1631 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1632 |
+ |
sprintf( painCave.errMsg, |
1633 |
+ |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1634 |
+ |
painCave.isFatal = 1; |
1635 |
+ |
simError(); |
1636 |
+ |
} |
1637 |
+ |
|
1638 |
+ |
strcpy( info.nameB, the_token ); |
1639 |
+ |
|
1640 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1641 |
+ |
sprintf( painCave.errMsg, |
1642 |
+ |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1643 |
+ |
painCave.isFatal = 1; |
1644 |
+ |
simError(); |
1645 |
+ |
} |
1646 |
+ |
|
1647 |
+ |
strcpy( info.nameC, the_token ); |
1648 |
+ |
|
1649 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1650 |
+ |
sprintf( painCave.errMsg, |
1651 |
+ |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1652 |
+ |
painCave.isFatal = 1; |
1653 |
+ |
simError(); |
1654 |
+ |
} |
1655 |
+ |
|
1656 |
+ |
strcpy( info.nameD, the_token ); |
1657 |
+ |
|
1658 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1659 |
+ |
sprintf( painCave.errMsg, |
1660 |
+ |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1661 |
+ |
painCave.isFatal = 1; |
1662 |
+ |
simError(); |
1663 |
+ |
} |
1664 |
+ |
|
1665 |
+ |
strcpy( info.type, the_token ); |
1666 |
+ |
|
1667 |
+ |
if( !strcmp( info.type, "cubic" ) ){ |
1668 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1669 |
+ |
sprintf( painCave.errMsg, |
1670 |
+ |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1671 |
+ |
painCave.isFatal = 1; |
1672 |
+ |
simError(); |
1673 |
+ |
} |
1674 |
+ |
|
1675 |
+ |
info.k1 = atof( the_token ); |
1676 |
+ |
|
1677 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1678 |
+ |
sprintf( painCave.errMsg, |
1679 |
+ |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1680 |
+ |
painCave.isFatal = 1; |
1681 |
+ |
simError(); |
1682 |
+ |
} |
1683 |
+ |
|
1684 |
+ |
info.k2 = atof( the_token ); |
1685 |
+ |
|
1686 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1687 |
+ |
sprintf( painCave.errMsg, |
1688 |
+ |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1689 |
+ |
painCave.isFatal = 1; |
1690 |
+ |
simError(); |
1691 |
+ |
} |
1692 |
+ |
|
1693 |
+ |
info.k3 = atof( the_token ); |
1694 |
+ |
|
1695 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1696 |
+ |
sprintf( painCave.errMsg, |
1697 |
+ |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1698 |
+ |
painCave.isFatal = 1; |
1699 |
+ |
simError(); |
1700 |
+ |
} |
1701 |
+ |
|
1702 |
+ |
info.k4 = atof( the_token ); |
1703 |
+ |
|
1704 |
+ |
} |
1705 |
+ |
|
1706 |
+ |
else{ |
1707 |
+ |
sprintf( painCave.errMsg, |
1708 |
+ |
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
1709 |
+ |
info.type, |
1710 |
+ |
lineNum ); |
1711 |
+ |
painCave.isFatal = 1; |
1712 |
+ |
simError(); |
1713 |
+ |
} |
1714 |
+ |
|
1715 |
+ |
return 1; |
1716 |
+ |
} |
1717 |
+ |
|
1718 |
+ |
else return 0; |
1719 |
+ |
} |