1 |
#include <cstdlib> |
2 |
#include <cstdio> |
3 |
#include <cstring> |
4 |
|
5 |
#include <iostream> |
6 |
using namespace std; |
7 |
|
8 |
#include "ForceFields.hpp" |
9 |
#include "SRI.hpp" |
10 |
#include "simError.h" |
11 |
|
12 |
#ifdef IS_MPI |
13 |
#include "mpiForceField.h" |
14 |
#endif // is_mpi |
15 |
|
16 |
namespace TPE { // restrict the access of the folowing to this file only. |
17 |
|
18 |
|
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 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 |
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]; |
105 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
106 |
char* ffPath; |
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 |
// ********************************************************************** |
119 |
// Init the atomStruct mpi type |
120 |
|
121 |
atomStruct atomProto; // mpiPrototype |
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.isSSD, &atomDspls[2]); |
129 |
|
130 |
atomMbrTypes[0] = MPI_CHAR; |
131 |
atomMbrTypes[1] = MPI_DOUBLE; |
132 |
atomMbrTypes[2] = MPI_INT; |
133 |
|
134 |
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
135 |
|
136 |
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
137 |
MPI_Type_commit(&mpiAtomStructType); |
138 |
|
139 |
|
140 |
// ********************************************************************** |
141 |
// Init the bondStruct mpi type |
142 |
|
143 |
bondStruct bondProto; // mpiPrototype |
144 |
int bondBC[3] = {60,1,1}; // block counts |
145 |
MPI_Aint bondDspls[3]; // displacements |
146 |
MPI_Datatype bondMbrTypes[3]; // member mpi types |
147 |
|
148 |
MPI_Address(&bondProto.nameA, &bondDspls[0]); |
149 |
MPI_Address(&bondProto.d0, &bondDspls[1]); |
150 |
MPI_Address(&bondProto.last, &bondDspls[2]); |
151 |
|
152 |
bondMbrTypes[0] = MPI_CHAR; |
153 |
bondMbrTypes[1] = MPI_DOUBLE; |
154 |
bondMbrTypes[2] = MPI_INT; |
155 |
|
156 |
for (i=2; i >= 0; i--) bondDspls[i] -= bondDspls[0]; |
157 |
|
158 |
MPI_Type_struct(3, bondBC, bondDspls, bondMbrTypes, &mpiBondStructType); |
159 |
MPI_Type_commit(&mpiBondStructType); |
160 |
|
161 |
|
162 |
// ********************************************************************** |
163 |
// Init the bendStruct mpi type |
164 |
|
165 |
bendStruct bendProto; // mpiPrototype |
166 |
int bendBC[3] = {75,4,1}; // block counts |
167 |
MPI_Aint bendDspls[3]; // displacements |
168 |
MPI_Datatype bendMbrTypes[3]; // member mpi types |
169 |
|
170 |
MPI_Address(&bendProto.nameA, &bendDspls[0]); |
171 |
MPI_Address(&bendProto.k1, &bendDspls[1]); |
172 |
MPI_Address(&bendProto.last, &bendDspls[2]); |
173 |
|
174 |
bendMbrTypes[0] = MPI_CHAR; |
175 |
bendMbrTypes[1] = MPI_DOUBLE; |
176 |
bendMbrTypes[2] = MPI_INT; |
177 |
|
178 |
for (i=2; i >= 0; i--) bendDspls[i] -= bendDspls[0]; |
179 |
|
180 |
MPI_Type_struct(3, bendBC, bendDspls, bendMbrTypes, &mpiBendStructType); |
181 |
MPI_Type_commit(&mpiBendStructType); |
182 |
|
183 |
|
184 |
// ********************************************************************** |
185 |
// Init the torsionStruct mpi type |
186 |
|
187 |
torsionStruct torsionProto; // mpiPrototype |
188 |
int torsionBC[3] = {90,4,1}; // block counts |
189 |
MPI_Aint torsionDspls[3]; // displacements |
190 |
MPI_Datatype torsionMbrTypes[3]; // member mpi types |
191 |
|
192 |
MPI_Address(&torsionProto.nameA, &torsionDspls[0]); |
193 |
MPI_Address(&torsionProto.k1, &torsionDspls[1]); |
194 |
MPI_Address(&torsionProto.last, &torsionDspls[2]); |
195 |
|
196 |
torsionMbrTypes[0] = MPI_CHAR; |
197 |
torsionMbrTypes[1] = MPI_DOUBLE; |
198 |
torsionMbrTypes[2] = MPI_INT; |
199 |
|
200 |
for (i=2; i >= 0; i--) torsionDspls[i] -= torsionDspls[0]; |
201 |
|
202 |
MPI_Type_struct(3, torsionBC, torsionDspls, torsionMbrTypes, |
203 |
&mpiTorsionStructType); |
204 |
MPI_Type_commit(&mpiTorsionStructType); |
205 |
|
206 |
// *********************************************************************** |
207 |
|
208 |
if( worldRank == 0 ){ |
209 |
#endif |
210 |
|
211 |
// generate the force file name |
212 |
|
213 |
strcpy( fileName, "TraPPE_Ex.frc" ); |
214 |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
215 |
|
216 |
// attempt to open the file in the current directory first. |
217 |
|
218 |
frcFile = fopen( fileName, "r" ); |
219 |
|
220 |
if( frcFile == NULL ){ |
221 |
|
222 |
// next see if the force path enviorment variable is set |
223 |
|
224 |
ffPath = getenv( ffPath_env ); |
225 |
if( ffPath == NULL ) { |
226 |
sprintf( painCave.errMsg, |
227 |
"Error opening the force field parameter file: %s\n" |
228 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
229 |
"vairable?\n", |
230 |
fileName ); |
231 |
painCave.isFatal = 1; |
232 |
simError(); |
233 |
} |
234 |
|
235 |
|
236 |
strcpy( temp, ffPath ); |
237 |
strcat( temp, "/" ); |
238 |
strcat( temp, fileName ); |
239 |
strcpy( fileName, temp ); |
240 |
|
241 |
frcFile = fopen( fileName, "r" ); |
242 |
|
243 |
if( frcFile == NULL ){ |
244 |
|
245 |
sprintf( painCave.errMsg, |
246 |
"Error opening the force field parameter file: %s\n" |
247 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
248 |
"vairable?\n", |
249 |
fileName ); |
250 |
painCave.isFatal = 1; |
251 |
simError(); |
252 |
} |
253 |
} |
254 |
|
255 |
#ifdef IS_MPI |
256 |
} |
257 |
|
258 |
sprintf( checkPointMsg, "TraPPE_ExFF file opened sucessfully." ); |
259 |
MPIcheckPoint(); |
260 |
|
261 |
#endif // is_mpi |
262 |
} |
263 |
|
264 |
|
265 |
TraPPE_ExFF::~TraPPE_ExFF(){ |
266 |
|
267 |
#ifdef IS_MPI |
268 |
if( worldRank == 0 ){ |
269 |
#endif // is_mpi |
270 |
|
271 |
fclose( frcFile ); |
272 |
|
273 |
#ifdef IS_MPI |
274 |
} |
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 { |
321 |
public: |
322 |
LinkedType(){ |
323 |
next = NULL; |
324 |
name[0] = '\0'; |
325 |
} |
326 |
~LinkedType(){ if( next != NULL ) delete next; } |
327 |
|
328 |
LinkedType* find(char* key){ |
329 |
if( !strcmp(name, key) ) return this; |
330 |
if( next != NULL ) return next->find(key); |
331 |
return NULL; |
332 |
} |
333 |
|
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.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 = 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 |
|
378 |
|
379 |
#endif |
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; |
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 |
|
400 |
|
401 |
|
402 |
int i; |
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 |
|
414 |
double waterI[3][3]; |
415 |
waterI[0][0] = 1.76958347772500; |
416 |
waterI[0][1] = 0.0; |
417 |
waterI[0][2] = 0.0; |
418 |
|
419 |
waterI[1][0] = 0.0; |
420 |
waterI[1][1] = 0.614537057924513; |
421 |
waterI[1][2] = 0.0; |
422 |
|
423 |
waterI[2][0] = 0.0; |
424 |
waterI[2][1] = 0.0; |
425 |
waterI[2][2] = 1.15504641980049; |
426 |
|
427 |
|
428 |
double headI[3][3]; |
429 |
headI[0][0] = 1125; |
430 |
headI[0][1] = 0.0; |
431 |
headI[0][2] = 0.0; |
432 |
|
433 |
headI[1][0] = 0.0; |
434 |
headI[1][1] = 1125; |
435 |
headI[1][2] = 0.0; |
436 |
|
437 |
headI[2][0] = 0.0; |
438 |
headI[2][1] = 0.0; |
439 |
headI[2][2] = 250; |
440 |
|
441 |
|
442 |
|
443 |
////////////////////////////////////////////////// |
444 |
|
445 |
|
446 |
#ifdef IS_MPI |
447 |
if( worldRank == 0 ){ |
448 |
#endif |
449 |
|
450 |
// read in the atom types. |
451 |
|
452 |
headAtomType = new LinkedType; |
453 |
|
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", |
467 |
lineNum ); |
468 |
painCave.isFatal = 1; |
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 |
|
476 |
// toss comment lines |
477 |
if( readLine[0] != '!' ){ |
478 |
|
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 |
} |
486 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
487 |
lineNum++; |
488 |
} |
489 |
|
490 |
#ifdef IS_MPI |
491 |
|
492 |
// send out the linked list to all the other processes |
493 |
|
494 |
sprintf( checkPointMsg, |
495 |
"TraPPE_ExFF atom structures read successfully." ); |
496 |
MPIcheckPoint(); |
497 |
|
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; |
514 |
sendFrcStruct( &info, mpiAtomStructType ); |
515 |
|
516 |
} |
517 |
|
518 |
else{ |
519 |
|
520 |
// listen for node 0 to send out the force params |
521 |
|
522 |
MPIcheckPoint(); |
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++ ){ |
582 |
|
583 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
584 |
if( currentAtomType == NULL ){ |
585 |
sprintf( painCave.errMsg, |
586 |
"AtomType error, %s not found in force file.\n", |
587 |
the_atoms[i]->getType() ); |
588 |
painCave.isFatal = 1; |
589 |
simError(); |
590 |
} |
591 |
|
592 |
the_atoms[i]->setMass( currentAtomType->mass ); |
593 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
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 |
|
602 |
dAtom = (DirectionalAtom *) the_atoms[i]; |
603 |
dAtom->setMu( currentAtomType->dipole ); |
604 |
dAtom->setHasDipole( 1 ); |
605 |
dAtom->setJx( 0.0 ); |
606 |
dAtom->setJy( 0.0 ); |
607 |
dAtom->setJz( 0.0 ); |
608 |
|
609 |
if(!strcmp("SSD",the_atoms[i]->getType())){ |
610 |
dAtom->setI( waterI ); |
611 |
dAtom->setSSD( 1 ); |
612 |
} |
613 |
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
614 |
dAtom->setI( headI ); |
615 |
dAtom->setSSD( 0 ); |
616 |
} |
617 |
else{ |
618 |
sprintf(painCave.errMsg, |
619 |
"AtmType error, %s does not have a moment of inertia set.\n", |
620 |
the_atoms[i]->getType() ); |
621 |
painCave.isFatal = 1; |
622 |
simError(); |
623 |
} |
624 |
entry_plug->n_dipoles++; |
625 |
} |
626 |
else{ |
627 |
|
628 |
sprintf( painCave.errMsg, |
629 |
"TraPPE_ExFF error: Atom \"%s\" is a dipole, yet no standard" |
630 |
" orientation was specifed in the BASS file.\n", |
631 |
currentAtomType->name ); |
632 |
painCave.isFatal = 1; |
633 |
simError(); |
634 |
} |
635 |
} |
636 |
else{ |
637 |
if( the_atoms[i]->isDirectional() ){ |
638 |
sprintf( painCave.errMsg, |
639 |
"TraPPE_ExFF error: Atom \"%s\" was given a standard" |
640 |
"orientation in the BASS file, yet it is not a dipole.\n", |
641 |
currentAtomType->name); |
642 |
painCave.isFatal = 1; |
643 |
simError(); |
644 |
} |
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; |
672 |
|
673 |
#ifdef IS_MPI |
674 |
sprintf( checkPointMsg, "TraPPE_Ex atoms initialized succesfully" ); |
675 |
MPIcheckPoint(); |
676 |
#endif // is_mpi |
677 |
|
678 |
} |
679 |
|
680 |
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
681 |
|
682 |
class LinkedType { |
683 |
public: |
684 |
LinkedType(){ |
685 |
next = NULL; |
686 |
nameA[0] = '\0'; |
687 |
nameB[0] = '\0'; |
688 |
type[0] = '\0'; |
689 |
} |
690 |
~LinkedType(){ if( next != NULL ) delete next; } |
691 |
|
692 |
LinkedType* find(char* key1, char* key2){ |
693 |
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
694 |
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
695 |
if( next != NULL ) return next->find(key1, key2); |
696 |
return NULL; |
697 |
} |
698 |
|
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(); |
721 |
strcpy(next->nameA, info.nameA); |
722 |
strcpy(next->nameB, info.nameB); |
723 |
strcpy(next->type, info.type); |
724 |
next->d0 = info.d0; |
725 |
} |
726 |
} |
727 |
|
728 |
#ifdef IS_MPI |
729 |
void duplicate( bondStruct &info ){ |
730 |
strcpy(info.nameA, nameA); |
731 |
strcpy(info.nameB, nameB); |
732 |
strcpy(info.type, type); |
733 |
info.d0 = d0; |
734 |
info.last = 0; |
735 |
} |
736 |
|
737 |
|
738 |
#endif |
739 |
|
740 |
char nameA[15]; |
741 |
char nameB[15]; |
742 |
char type[30]; |
743 |
double d0; |
744 |
|
745 |
LinkedType* next; |
746 |
}; |
747 |
|
748 |
|
749 |
|
750 |
LinkedType* headBondType; |
751 |
LinkedType* currentBondType; |
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 |
755 |
|
756 |
SRI **the_sris; |
757 |
Atom** the_atoms; |
758 |
int nBonds; |
759 |
the_sris = entry_plug->sr_interactions; |
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 ){ |
769 |
#endif |
770 |
|
771 |
// read in the bond types. |
772 |
|
773 |
headBondType = new LinkedType; |
774 |
|
775 |
fastForward( "BondTypes", "initializeBonds" ); |
776 |
|
777 |
// we are now at the bondTypes section |
778 |
|
779 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
780 |
lineNum++; |
781 |
|
782 |
|
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", |
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 |
|
796 |
// toss comment lines |
797 |
if( readLine[0] != '!' ){ |
798 |
|
799 |
// the parser returns 0 if the line was blank |
800 |
if( parseBond( readLine, lineNum, info ) ){ |
801 |
headBondType->add( info ); |
802 |
} |
803 |
} |
804 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
805 |
lineNum++; |
806 |
} |
807 |
|
808 |
#ifdef IS_MPI |
809 |
|
810 |
// send out the linked list to all the other processes |
811 |
|
812 |
sprintf( checkPointMsg, |
813 |
"TraPPE_Ex bond structures read successfully." ); |
814 |
MPIcheckPoint(); |
815 |
|
816 |
currentBondType = headBondType; |
817 |
while( currentBondType != NULL ){ |
818 |
currentBondType->duplicate( info ); |
819 |
sendFrcStruct( &info, mpiBondStructType ); |
820 |
currentBondType = currentBondType->next; |
821 |
} |
822 |
info.last = 1; |
823 |
sendFrcStruct( &info, mpiBondStructType ); |
824 |
|
825 |
} |
826 |
|
827 |
else{ |
828 |
|
829 |
// listen for node 0 to send out the force params |
830 |
|
831 |
MPIcheckPoint(); |
832 |
|
833 |
headBondType = new LinkedType; |
834 |
recieveFrcStruct( &info, mpiBondStructType ); |
835 |
while( !info.last ){ |
836 |
|
837 |
headBondType->add( info ); |
838 |
recieveFrcStruct( &info, mpiBondStructType ); |
839 |
} |
840 |
} |
841 |
#endif // is_mpi |
842 |
|
843 |
|
844 |
// initialize the Bonds |
845 |
|
846 |
|
847 |
for( i=0; i<nBonds; i++ ){ |
848 |
|
849 |
a = the_bonds[i].a; |
850 |
b = the_bonds[i].b; |
851 |
|
852 |
atomA = the_atoms[a]->getType(); |
853 |
atomB = the_atoms[b]->getType(); |
854 |
currentBondType = headBondType->find( atomA, atomB ); |
855 |
if( currentBondType == NULL ){ |
856 |
sprintf( painCave.errMsg, |
857 |
"BondType error, %s - %s not found in force file.\n", |
858 |
atomA, atomB ); |
859 |
painCave.isFatal = 1; |
860 |
simError(); |
861 |
} |
862 |
|
863 |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
864 |
|
865 |
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
866 |
*the_atoms[b], |
867 |
currentBondType->d0 ); |
868 |
entry_plug->n_constraints++; |
869 |
} |
870 |
} |
871 |
|
872 |
|
873 |
// clean up the memory |
874 |
|
875 |
delete headBondType; |
876 |
|
877 |
#ifdef IS_MPI |
878 |
sprintf( checkPointMsg, "TraPPE_Ex bonds initialized succesfully" ); |
879 |
MPIcheckPoint(); |
880 |
#endif // is_mpi |
881 |
|
882 |
} |
883 |
|
884 |
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
885 |
|
886 |
class LinkedType { |
887 |
public: |
888 |
LinkedType(){ |
889 |
next = NULL; |
890 |
nameA[0] = '\0'; |
891 |
nameB[0] = '\0'; |
892 |
nameC[0] = '\0'; |
893 |
type[0] = '\0'; |
894 |
} |
895 |
~LinkedType(){ if( next != NULL ) delete next; } |
896 |
|
897 |
LinkedType* find( char* key1, char* key2, char* key3 ){ |
898 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
899 |
&& !strcmp( nameC, key3 ) ) return this; |
900 |
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
901 |
&& !strcmp( nameC, key1 ) ) return this; |
902 |
if( next != NULL ) return next->find(key1, key2, key3); |
903 |
return NULL; |
904 |
} |
905 |
|
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(); |
928 |
strcpy(next->nameA, info.nameA); |
929 |
strcpy(next->nameB, info.nameB); |
930 |
strcpy(next->nameC, info.nameC); |
931 |
strcpy(next->type, info.type); |
932 |
next->k1 = info.k1; |
933 |
next->k2 = info.k2; |
934 |
next->k3 = info.k3; |
935 |
next->t0 = info.t0; |
936 |
} |
937 |
} |
938 |
|
939 |
#ifdef IS_MPI |
940 |
|
941 |
void duplicate( bendStruct &info ){ |
942 |
strcpy(info.nameA, nameA); |
943 |
strcpy(info.nameB, nameB); |
944 |
strcpy(info.nameC, nameC); |
945 |
strcpy(info.type, type); |
946 |
info.k1 = k1; |
947 |
info.k2 = k2; |
948 |
info.k3 = k3; |
949 |
info.t0 = t0; |
950 |
info.last = 0; |
951 |
} |
952 |
|
953 |
#endif // is_mpi |
954 |
|
955 |
char nameA[15]; |
956 |
char nameB[15]; |
957 |
char nameC[15]; |
958 |
char type[30]; |
959 |
double k1, k2, k3, t0; |
960 |
|
961 |
LinkedType* next; |
962 |
}; |
963 |
|
964 |
LinkedType* headBendType; |
965 |
LinkedType* currentBendType; |
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 |
969 |
|
970 |
QuadraticBend* qBend; |
971 |
SRI **the_sris; |
972 |
Atom** the_atoms; |
973 |
int nBends; |
974 |
the_sris = entry_plug->sr_interactions; |
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 |
|
990 |
headBendType = new LinkedType; |
991 |
|
992 |
fastForward( "BendTypes", "initializeBends" ); |
993 |
|
994 |
// we are now at the bendTypes section |
995 |
|
996 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
997 |
lineNum++; |
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", |
1004 |
lineNum ); |
1005 |
painCave.isFatal = 1; |
1006 |
simError(); |
1007 |
} |
1008 |
|
1009 |
// stop reading at end of file, or at next section |
1010 |
while( readLine[0] != '#' && eof_test != NULL ){ |
1011 |
|
1012 |
// toss comment lines |
1013 |
if( readLine[0] != '!' ){ |
1014 |
|
1015 |
// the parser returns 0 if the line was blank |
1016 |
if( parseBend( readLine, lineNum, info ) ){ |
1017 |
headBendType->add( info ); |
1018 |
} |
1019 |
} |
1020 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1021 |
lineNum++; |
1022 |
} |
1023 |
|
1024 |
#ifdef IS_MPI |
1025 |
|
1026 |
// send out the linked list to all the other processes |
1027 |
|
1028 |
sprintf( checkPointMsg, |
1029 |
"TraPPE_Ex bend structures read successfully." ); |
1030 |
MPIcheckPoint(); |
1031 |
|
1032 |
currentBendType = headBendType; |
1033 |
while( currentBendType != NULL ){ |
1034 |
currentBendType->duplicate( info ); |
1035 |
sendFrcStruct( &info, mpiBendStructType ); |
1036 |
currentBendType = currentBendType->next; |
1037 |
} |
1038 |
info.last = 1; |
1039 |
sendFrcStruct( &info, mpiBendStructType ); |
1040 |
|
1041 |
} |
1042 |
|
1043 |
else{ |
1044 |
|
1045 |
// listen for node 0 to send out the force params |
1046 |
|
1047 |
MPIcheckPoint(); |
1048 |
|
1049 |
headBendType = new LinkedType; |
1050 |
recieveFrcStruct( &info, mpiBendStructType ); |
1051 |
while( !info.last ){ |
1052 |
|
1053 |
headBendType->add( info ); |
1054 |
recieveFrcStruct( &info, mpiBendStructType ); |
1055 |
} |
1056 |
} |
1057 |
#endif // is_mpi |
1058 |
|
1059 |
// initialize the Bends |
1060 |
|
1061 |
int index; |
1062 |
|
1063 |
for( i=0; i<nBends; i++ ){ |
1064 |
|
1065 |
a = the_bends[i].a; |
1066 |
b = the_bends[i].b; |
1067 |
c = the_bends[i].c; |
1068 |
|
1069 |
atomA = the_atoms[a]->getType(); |
1070 |
atomB = the_atoms[b]->getType(); |
1071 |
atomC = the_atoms[c]->getType(); |
1072 |
currentBendType = headBendType->find( atomA, atomB, atomC ); |
1073 |
if( currentBendType == NULL ){ |
1074 |
sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found" |
1075 |
" in force file.\n", |
1076 |
atomA, atomB, atomC ); |
1077 |
painCave.isFatal = 1; |
1078 |
simError(); |
1079 |
} |
1080 |
|
1081 |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1082 |
|
1083 |
index = i + entry_plug->n_bonds; |
1084 |
qBend = new QuadraticBend( *the_atoms[a], |
1085 |
*the_atoms[b], |
1086 |
*the_atoms[c] ); |
1087 |
qBend->setConstants( currentBendType->k1, |
1088 |
currentBendType->k2, |
1089 |
currentBendType->k3, |
1090 |
currentBendType->t0 ); |
1091 |
the_sris[index] = qBend; |
1092 |
} |
1093 |
} |
1094 |
|
1095 |
|
1096 |
// clean up the memory |
1097 |
|
1098 |
delete headBendType; |
1099 |
|
1100 |
#ifdef IS_MPI |
1101 |
sprintf( checkPointMsg, "TraPPE_Ex bends initialized succesfully" ); |
1102 |
MPIcheckPoint(); |
1103 |
#endif // is_mpi |
1104 |
|
1105 |
} |
1106 |
|
1107 |
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
1108 |
|
1109 |
class LinkedType { |
1110 |
public: |
1111 |
LinkedType(){ |
1112 |
next = NULL; |
1113 |
nameA[0] = '\0'; |
1114 |
nameB[0] = '\0'; |
1115 |
nameC[0] = '\0'; |
1116 |
type[0] = '\0'; |
1117 |
} |
1118 |
~LinkedType(){ if( next != NULL ) delete next; } |
1119 |
|
1120 |
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
1121 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
1122 |
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
1123 |
|
1124 |
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
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 |
} |
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(); |
1153 |
strcpy(next->nameA, info.nameA); |
1154 |
strcpy(next->nameB, info.nameB); |
1155 |
strcpy(next->nameC, info.nameC); |
1156 |
strcpy(next->type, info.type); |
1157 |
next->k1 = info.k1; |
1158 |
next->k2 = info.k2; |
1159 |
next->k3 = info.k3; |
1160 |
next->k4 = info.k4; |
1161 |
} |
1162 |
} |
1163 |
|
1164 |
#ifdef IS_MPI |
1165 |
|
1166 |
void duplicate( torsionStruct &info ){ |
1167 |
strcpy(info.nameA, nameA); |
1168 |
strcpy(info.nameB, nameB); |
1169 |
strcpy(info.nameC, nameC); |
1170 |
strcpy(info.nameD, nameD); |
1171 |
strcpy(info.type, type); |
1172 |
info.k1 = k1; |
1173 |
info.k2 = k2; |
1174 |
info.k3 = k3; |
1175 |
info.k4 = k4; |
1176 |
info.last = 0; |
1177 |
} |
1178 |
|
1179 |
#endif |
1180 |
|
1181 |
char nameA[15]; |
1182 |
char nameB[15]; |
1183 |
char nameC[15]; |
1184 |
char nameD[15]; |
1185 |
char type[30]; |
1186 |
double k1, k2, k3, k4; |
1187 |
|
1188 |
LinkedType* next; |
1189 |
}; |
1190 |
|
1191 |
LinkedType* headTorsionType; |
1192 |
LinkedType* currentTorsionType; |
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 |
1196 |
|
1197 |
int i, a, b, c, d, index; |
1198 |
char* atomA; |
1199 |
char* atomB; |
1200 |
char* atomC; |
1201 |
char* atomD; |
1202 |
CubicTorsion* cTors; |
1203 |
|
1204 |
SRI **the_sris; |
1205 |
Atom** the_atoms; |
1206 |
int nTorsions; |
1207 |
the_sris = entry_plug->sr_interactions; |
1208 |
the_atoms = entry_plug->atoms; |
1209 |
nTorsions = entry_plug->n_torsions; |
1210 |
|
1211 |
#ifdef IS_MPI |
1212 |
if( worldRank == 0 ){ |
1213 |
#endif |
1214 |
|
1215 |
// read in the torsion types. |
1216 |
|
1217 |
headTorsionType = new LinkedType; |
1218 |
|
1219 |
fastForward( "TorsionTypes", "initializeTorsions" ); |
1220 |
|
1221 |
// we are now at the torsionTypes section |
1222 |
|
1223 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1224 |
lineNum++; |
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", |
1232 |
lineNum ); |
1233 |
painCave.isFatal = 1; |
1234 |
simError(); |
1235 |
} |
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] != '!' ){ |
1242 |
|
1243 |
// the parser returns 0 if the line was blank |
1244 |
if( parseTorsion( readLine, lineNum, info ) ){ |
1245 |
headTorsionType->add( info ); |
1246 |
} |
1247 |
} |
1248 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1249 |
lineNum++; |
1250 |
} |
1251 |
|
1252 |
#ifdef IS_MPI |
1253 |
|
1254 |
// send out the linked list to all the other processes |
1255 |
|
1256 |
sprintf( checkPointMsg, |
1257 |
"TraPPE_Ex torsion structures read successfully." ); |
1258 |
MPIcheckPoint(); |
1259 |
|
1260 |
currentTorsionType = headTorsionType; |
1261 |
while( currentTorsionType != NULL ){ |
1262 |
currentTorsionType->duplicate( info ); |
1263 |
sendFrcStruct( &info, mpiTorsionStructType ); |
1264 |
currentTorsionType = currentTorsionType->next; |
1265 |
} |
1266 |
info.last = 1; |
1267 |
sendFrcStruct( &info, mpiTorsionStructType ); |
1268 |
|
1269 |
} |
1270 |
|
1271 |
else{ |
1272 |
|
1273 |
// listen for node 0 to send out the force params |
1274 |
|
1275 |
MPIcheckPoint(); |
1276 |
|
1277 |
headTorsionType = new LinkedType; |
1278 |
recieveFrcStruct( &info, mpiTorsionStructType ); |
1279 |
while( !info.last ){ |
1280 |
|
1281 |
headTorsionType->add( info ); |
1282 |
recieveFrcStruct( &info, mpiTorsionStructType ); |
1283 |
} |
1284 |
} |
1285 |
#endif // is_mpi |
1286 |
|
1287 |
// initialize the Torsions |
1288 |
|
1289 |
for( i=0; i<nTorsions; i++ ){ |
1290 |
|
1291 |
a = the_torsions[i].a; |
1292 |
b = the_torsions[i].b; |
1293 |
c = the_torsions[i].c; |
1294 |
d = the_torsions[i].d; |
1295 |
|
1296 |
atomA = the_atoms[a]->getType(); |
1297 |
atomB = the_atoms[b]->getType(); |
1298 |
atomC = the_atoms[c]->getType(); |
1299 |
atomD = the_atoms[d]->getType(); |
1300 |
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1301 |
if( currentTorsionType == NULL ){ |
1302 |
sprintf( painCave.errMsg, |
1303 |
"TorsionType error, %s - %s - %s - %s not found" |
1304 |
" in force file.\n", |
1305 |
atomA, atomB, atomC, atomD ); |
1306 |
painCave.isFatal = 1; |
1307 |
simError(); |
1308 |
} |
1309 |
|
1310 |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1311 |
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
1312 |
|
1313 |
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1314 |
*the_atoms[c], *the_atoms[d] ); |
1315 |
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1316 |
currentTorsionType->k3, currentTorsionType->k4 ); |
1317 |
the_sris[index] = cTors; |
1318 |
} |
1319 |
} |
1320 |
|
1321 |
|
1322 |
// clean up the memory |
1323 |
|
1324 |
delete headTorsionType; |
1325 |
|
1326 |
#ifdef IS_MPI |
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 |
} |