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 |
#include <fortranWrappers.hpp> |
13 |
|
14 |
#ifdef IS_MPI |
15 |
#include "mpiForceField.h" |
16 |
#endif // is_mpi |
17 |
|
18 |
namespace TPE { // restrict the access of the folowing to this file only. |
19 |
|
20 |
|
21 |
// Declare the structures that will be passed by MPI |
22 |
|
23 |
typedef struct{ |
24 |
char name[15]; |
25 |
double mass; |
26 |
double epslon; |
27 |
double sigma; |
28 |
double dipole; |
29 |
double w0; |
30 |
double v0; |
31 |
int isSSD; |
32 |
int isDipole; |
33 |
int ident; |
34 |
int last; // 0 -> default |
35 |
// 1 -> tells nodes to stop listening |
36 |
} atomStruct; |
37 |
|
38 |
|
39 |
typedef struct{ |
40 |
char nameA[15]; |
41 |
char nameB[15]; |
42 |
char type[30]; |
43 |
double d0; |
44 |
int last; // 0 -> default |
45 |
// 1 -> tells nodes to stop listening |
46 |
} bondStruct; |
47 |
|
48 |
|
49 |
typedef struct{ |
50 |
char nameA[15]; |
51 |
char nameB[15]; |
52 |
char nameC[15]; |
53 |
char type[30]; |
54 |
double k1, k2, k3, t0; |
55 |
int last; // 0 -> default |
56 |
// 1 -> tells nodes to stop listening |
57 |
} bendStruct; |
58 |
|
59 |
|
60 |
typedef struct{ |
61 |
char nameA[15]; |
62 |
char nameB[15]; |
63 |
char nameC[15]; |
64 |
char nameD[15]; |
65 |
char type[30]; |
66 |
double k1, k2, k3, k4; |
67 |
int last; // 0 -> default |
68 |
// 1 -> tells nodes to stop listening |
69 |
} torsionStruct; |
70 |
|
71 |
|
72 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
73 |
int parseBond( char *lineBuffer, int lineNum, bondStruct &info ); |
74 |
int parseBend( char *lineBuffer, int lineNum, bendStruct &info ); |
75 |
int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ); |
76 |
|
77 |
|
78 |
#ifdef IS_MPI |
79 |
|
80 |
MPI_Datatype mpiAtomStructType; |
81 |
MPI_Datatype mpiBondStructType; |
82 |
MPI_Datatype mpiBendStructType; |
83 |
MPI_Datatype mpiTorsionStructType; |
84 |
|
85 |
#endif |
86 |
|
87 |
} // namespace |
88 |
|
89 |
using namespace TPE; |
90 |
|
91 |
|
92 |
//**************************************************************** |
93 |
// begins the actual forcefield stuff. |
94 |
//**************************************************************** |
95 |
|
96 |
|
97 |
TraPPE_ExFF::TraPPE_ExFF(){ |
98 |
|
99 |
char fileName[200]; |
100 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
101 |
char* ffPath; |
102 |
char temp[200]; |
103 |
char errMsg[1000]; |
104 |
|
105 |
// do the funtion wrapping |
106 |
wrapMeFF( this ); |
107 |
|
108 |
|
109 |
#ifdef IS_MPI |
110 |
int i; |
111 |
|
112 |
// ********************************************************************** |
113 |
// Init the atomStruct mpi type |
114 |
|
115 |
atomStruct atomProto; // mpiPrototype |
116 |
int atomBC[3] = {15,6,4}; // block counts |
117 |
MPI_Aint atomDspls[3]; // displacements |
118 |
MPI_Datatype atomMbrTypes[3]; // member mpi types |
119 |
|
120 |
MPI_Address(&atomProto.name, &atomDspls[0]); |
121 |
MPI_Address(&atomProto.mass, &atomDspls[1]); |
122 |
MPI_Address(&atomProto.isSSD, &atomDspls[2]); |
123 |
|
124 |
atomMbrTypes[0] = MPI_CHAR; |
125 |
atomMbrTypes[1] = MPI_DOUBLE; |
126 |
atomMbrTypes[2] = MPI_INT; |
127 |
|
128 |
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
129 |
|
130 |
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
131 |
MPI_Type_commit(&mpiAtomStructType); |
132 |
|
133 |
|
134 |
// ********************************************************************** |
135 |
// Init the bondStruct mpi type |
136 |
|
137 |
bondStruct bondProto; // mpiPrototype |
138 |
int bondBC[3] = {60,1,1}; // block counts |
139 |
MPI_Aint bondDspls[3]; // displacements |
140 |
MPI_Datatype bondMbrTypes[3]; // member mpi types |
141 |
|
142 |
MPI_Address(&bondProto.nameA, &bondDspls[0]); |
143 |
MPI_Address(&bondProto.d0, &bondDspls[1]); |
144 |
MPI_Address(&bondProto.last, &bondDspls[2]); |
145 |
|
146 |
bondMbrTypes[0] = MPI_CHAR; |
147 |
bondMbrTypes[1] = MPI_DOUBLE; |
148 |
bondMbrTypes[2] = MPI_INT; |
149 |
|
150 |
for (i=2; i >= 0; i--) bondDspls[i] -= bondDspls[0]; |
151 |
|
152 |
MPI_Type_struct(3, bondBC, bondDspls, bondMbrTypes, &mpiBondStructType); |
153 |
MPI_Type_commit(&mpiBondStructType); |
154 |
|
155 |
|
156 |
// ********************************************************************** |
157 |
// Init the bendStruct mpi type |
158 |
|
159 |
bendStruct bendProto; // mpiPrototype |
160 |
int bendBC[3] = {75,4,1}; // block counts |
161 |
MPI_Aint bendDspls[3]; // displacements |
162 |
MPI_Datatype bendMbrTypes[3]; // member mpi types |
163 |
|
164 |
MPI_Address(&bendProto.nameA, &bendDspls[0]); |
165 |
MPI_Address(&bendProto.k1, &bendDspls[1]); |
166 |
MPI_Address(&bendProto.last, &bendDspls[2]); |
167 |
|
168 |
bendMbrTypes[0] = MPI_CHAR; |
169 |
bendMbrTypes[1] = MPI_DOUBLE; |
170 |
bendMbrTypes[2] = MPI_INT; |
171 |
|
172 |
for (i=2; i >= 0; i--) bendDspls[i] -= bendDspls[0]; |
173 |
|
174 |
MPI_Type_struct(3, bendBC, bendDspls, bendMbrTypes, &mpiBendStructType); |
175 |
MPI_Type_commit(&mpiBendStructType); |
176 |
|
177 |
|
178 |
// ********************************************************************** |
179 |
// Init the torsionStruct mpi type |
180 |
|
181 |
torsionStruct torsionProto; // mpiPrototype |
182 |
int torsionBC[3] = {90,4,1}; // block counts |
183 |
MPI_Aint torsionDspls[3]; // displacements |
184 |
MPI_Datatype torsionMbrTypes[3]; // member mpi types |
185 |
|
186 |
MPI_Address(&torsionProto.nameA, &torsionDspls[0]); |
187 |
MPI_Address(&torsionProto.k1, &torsionDspls[1]); |
188 |
MPI_Address(&torsionProto.last, &torsionDspls[2]); |
189 |
|
190 |
torsionMbrTypes[0] = MPI_CHAR; |
191 |
torsionMbrTypes[1] = MPI_DOUBLE; |
192 |
torsionMbrTypes[2] = MPI_INT; |
193 |
|
194 |
for (i=2; i >= 0; i--) torsionDspls[i] -= torsionDspls[0]; |
195 |
|
196 |
MPI_Type_struct(3, torsionBC, torsionDspls, torsionMbrTypes, |
197 |
&mpiTorsionStructType); |
198 |
MPI_Type_commit(&mpiTorsionStructType); |
199 |
|
200 |
// *********************************************************************** |
201 |
|
202 |
if( worldRank == 0 ){ |
203 |
#endif |
204 |
|
205 |
// generate the force file name |
206 |
|
207 |
strcpy( fileName, "TraPPE_Ex.frc" ); |
208 |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
209 |
|
210 |
// attempt to open the file in the current directory first. |
211 |
|
212 |
frcFile = fopen( fileName, "r" ); |
213 |
|
214 |
if( frcFile == NULL ){ |
215 |
|
216 |
// next see if the force path enviorment variable is set |
217 |
|
218 |
ffPath = getenv( ffPath_env ); |
219 |
if( ffPath == NULL ) { |
220 |
sprintf( painCave.errMsg, |
221 |
"Error opening the force field parameter file: %s\n" |
222 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
223 |
"vairable?\n", |
224 |
fileName ); |
225 |
painCave.isFatal = 1; |
226 |
simError(); |
227 |
} |
228 |
|
229 |
|
230 |
strcpy( temp, ffPath ); |
231 |
strcat( temp, "/" ); |
232 |
strcat( temp, fileName ); |
233 |
strcpy( fileName, temp ); |
234 |
|
235 |
frcFile = fopen( fileName, "r" ); |
236 |
|
237 |
if( frcFile == NULL ){ |
238 |
|
239 |
sprintf( painCave.errMsg, |
240 |
"Error opening the force field parameter file: %s\n" |
241 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
242 |
"vairable?\n", |
243 |
fileName ); |
244 |
painCave.isFatal = 1; |
245 |
simError(); |
246 |
} |
247 |
} |
248 |
|
249 |
#ifdef IS_MPI |
250 |
} |
251 |
|
252 |
sprintf( checkPointMsg, "TraPPE_ExFF file opened sucessfully." ); |
253 |
MPIcheckPoint(); |
254 |
|
255 |
#endif // is_mpi |
256 |
} |
257 |
|
258 |
|
259 |
TraPPE_ExFF::~TraPPE_ExFF(){ |
260 |
|
261 |
#ifdef IS_MPI |
262 |
if( worldRank == 0 ){ |
263 |
#endif // is_mpi |
264 |
|
265 |
fclose( frcFile ); |
266 |
|
267 |
#ifdef IS_MPI |
268 |
} |
269 |
#endif // is_mpi |
270 |
} |
271 |
|
272 |
void TraPPE_ExFF::doForces( int calcPot ){ |
273 |
|
274 |
int i, isError; |
275 |
double* frc; |
276 |
double* pos; |
277 |
double* tau; |
278 |
short int passedCalcPot = (short int)calcPot; |
279 |
|
280 |
// forces are zeroed here, before any are acumulated. |
281 |
// NOTE: do not rezero the forces in Fortran. |
282 |
|
283 |
for(i=0; i<entry_plug->n_atoms; i++){ |
284 |
entry_plug->atoms[i]->zeroForces(); |
285 |
} |
286 |
|
287 |
frc = Atom::getFrcArray(); |
288 |
pos = Atom::getPosArray(); |
289 |
tau = entry_plug->tau; |
290 |
|
291 |
isError = 0; |
292 |
fortranForceLoop( pos, frc, &(entry_plug->lrPot), tau, |
293 |
&passedCalcPot, &isError ); |
294 |
|
295 |
|
296 |
if( isError ){ |
297 |
sprintf( painCave.errMsg, |
298 |
"Error returned from the fortran force calculation.\n" ); |
299 |
painCave.isFatal = 1; |
300 |
simError(); |
301 |
} |
302 |
|
303 |
#ifdef IS_MPI |
304 |
sprintf( checkPointMsg, |
305 |
"successfully returned from the force calculation.\n" ); |
306 |
MPIcheckPoint(); |
307 |
#endif // is_mpi |
308 |
|
309 |
} |
310 |
|
311 |
void TraPPE_ExFF::initFortran( void ){ |
312 |
|
313 |
int nLocal = entry_plug->n_atoms; |
314 |
int *ident; |
315 |
int isError; |
316 |
int i; |
317 |
|
318 |
ident = new int[nLocal]; |
319 |
|
320 |
for(i=0; i<nLocal; i++){ |
321 |
ident[i] = entry_plug->atoms[i]->getIdent(); |
322 |
} |
323 |
|
324 |
isError = 0; |
325 |
initfortran( &nLocal, ident, &isError ); |
326 |
|
327 |
if(isError){ |
328 |
sprintf( painCave.errMsg, |
329 |
"TraPPE_ExFF error: There was an error initializing the component list in fortran.\n" ); |
330 |
painCave.isFatal = 1; |
331 |
simError(); |
332 |
} |
333 |
|
334 |
|
335 |
#ifdef IS_MPI |
336 |
sprintf( checkPointMsg, "TraPPE_ExFF successfully initialized the fortran component list.\n" ); |
337 |
MPIcheckPoint(); |
338 |
#endif // is_mpi |
339 |
|
340 |
delete[] ident; |
341 |
|
342 |
} |
343 |
|
344 |
|
345 |
|
346 |
|
347 |
void TraPPE_ExFF::initializeAtoms( void ){ |
348 |
|
349 |
class LinkedType { |
350 |
public: |
351 |
LinkedType(){ |
352 |
next = NULL; |
353 |
name[0] = '\0'; |
354 |
} |
355 |
~LinkedType(){ if( next != NULL ) delete next; } |
356 |
|
357 |
LinkedType* find(char* key){ |
358 |
if( !strcmp(name, key) ) return this; |
359 |
if( next != NULL ) return next->find(key); |
360 |
return NULL; |
361 |
} |
362 |
|
363 |
void add( atomStruct &info ){ |
364 |
|
365 |
// check for duplicates |
366 |
|
367 |
if( !strcmp( info.name, name ) ){ |
368 |
sprintf( painCave.errMsg, |
369 |
"Duplicate TraPPE_Ex atom type \"%s\" found in " |
370 |
"the TraPPE_ExFF param file./n", |
371 |
name ); |
372 |
painCave.isFatal = 1; |
373 |
simError(); |
374 |
} |
375 |
|
376 |
if( next != NULL ) next->add(info); |
377 |
else{ |
378 |
next = new LinkedType(); |
379 |
strcpy(next->name, info.name); |
380 |
next->isDipole = info.isDipole; |
381 |
next->isSSD = info.isSSD; |
382 |
next->mass = info.mass; |
383 |
next->epslon = info.epslon; |
384 |
next->sigma = info.sigma; |
385 |
next->dipole = info.dipole; |
386 |
next->w0 = info.w0; |
387 |
next->v0 = info.v0; |
388 |
next->ident = info.ident; |
389 |
} |
390 |
} |
391 |
|
392 |
#ifdef IS_MPI |
393 |
|
394 |
void duplicate( atomStruct &info ){ |
395 |
strcpy(info.name, name); |
396 |
info.isDipole = isDipole; |
397 |
info.isSSD = isSSD; |
398 |
info.mass = mass; |
399 |
info.epslon = epslon; |
400 |
info.sigma = sigma; |
401 |
info.dipole = dipole; |
402 |
info.w0 = w0; |
403 |
info.v0 = v0; |
404 |
info.last = 0; |
405 |
} |
406 |
|
407 |
|
408 |
#endif |
409 |
|
410 |
char name[15]; |
411 |
int isDipole; |
412 |
int isSSD; |
413 |
double mass; |
414 |
double epslon; |
415 |
double sigma; |
416 |
double dipole; |
417 |
double w0; |
418 |
double v0; |
419 |
int ident; |
420 |
LinkedType* next; |
421 |
}; |
422 |
|
423 |
LinkedType* headAtomType; |
424 |
LinkedType* currentAtomType; |
425 |
atomStruct info; |
426 |
info.last = 1; // initialize last to have the last set. |
427 |
// if things go well, last will be set to 0 |
428 |
|
429 |
|
430 |
|
431 |
int i; |
432 |
int identNum; |
433 |
|
434 |
Atom** the_atoms; |
435 |
int nAtoms; |
436 |
the_atoms = entry_plug->atoms; |
437 |
nAtoms = entry_plug->n_atoms; |
438 |
|
439 |
|
440 |
////////////////////////////////////////////////// |
441 |
// a quick water fix |
442 |
|
443 |
double waterI[3][3]; |
444 |
waterI[0][0] = 1.76958347772500; |
445 |
waterI[0][1] = 0.0; |
446 |
waterI[0][2] = 0.0; |
447 |
|
448 |
waterI[1][0] = 0.0; |
449 |
waterI[1][1] = 0.614537057924513; |
450 |
waterI[1][2] = 0.0; |
451 |
|
452 |
waterI[2][0] = 0.0; |
453 |
waterI[2][1] = 0.0; |
454 |
waterI[2][2] = 1.15504641980049; |
455 |
|
456 |
|
457 |
double headI[3][3]; |
458 |
headI[0][0] = 1125; |
459 |
headI[0][1] = 0.0; |
460 |
headI[0][2] = 0.0; |
461 |
|
462 |
headI[1][0] = 0.0; |
463 |
headI[1][1] = 1125; |
464 |
headI[1][2] = 0.0; |
465 |
|
466 |
headI[2][0] = 0.0; |
467 |
headI[2][1] = 0.0; |
468 |
headI[2][2] = 250; |
469 |
|
470 |
|
471 |
|
472 |
////////////////////////////////////////////////// |
473 |
|
474 |
|
475 |
#ifdef IS_MPI |
476 |
if( worldRank == 0 ){ |
477 |
#endif |
478 |
|
479 |
// read in the atom types. |
480 |
|
481 |
headAtomType = new LinkedType; |
482 |
|
483 |
fastForward( "AtomTypes", "initializeAtoms" ); |
484 |
|
485 |
// we are now at the AtomTypes section. |
486 |
|
487 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
488 |
lineNum++; |
489 |
|
490 |
|
491 |
// read a line, and start parseing out the atom types |
492 |
|
493 |
if( eof_test == NULL ){ |
494 |
sprintf( painCave.errMsg, |
495 |
"Error in reading Atoms from force file at line %d.\n", |
496 |
lineNum ); |
497 |
painCave.isFatal = 1; |
498 |
simError(); |
499 |
} |
500 |
|
501 |
identNum = 1; |
502 |
// stop reading at end of file, or at next section |
503 |
while( readLine[0] != '#' && eof_test != NULL ){ |
504 |
|
505 |
// toss comment lines |
506 |
if( readLine[0] != '!' ){ |
507 |
|
508 |
// the parser returns 0 if the line was blank |
509 |
if( parseAtom( readLine, lineNum, info ) ){ |
510 |
info.ident = identNum; |
511 |
headAtomType->add( info );; |
512 |
identNum++; |
513 |
} |
514 |
} |
515 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
516 |
lineNum++; |
517 |
} |
518 |
|
519 |
#ifdef IS_MPI |
520 |
|
521 |
// send out the linked list to all the other processes |
522 |
|
523 |
sprintf( checkPointMsg, |
524 |
"TraPPE_ExFF atom structures read successfully." ); |
525 |
MPIcheckPoint(); |
526 |
|
527 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
528 |
while( currentAtomType != NULL ){ |
529 |
currentAtomType->duplicate( info ); |
530 |
|
531 |
|
532 |
|
533 |
sendFrcStruct( &info, mpiAtomStructType ); |
534 |
|
535 |
sprintf( checkPointMsg, |
536 |
"successfully sent TraPPE_Ex force type: \"%s\"\n", |
537 |
info.name ); |
538 |
MPIcheckPoint(); |
539 |
|
540 |
currentAtomType = currentAtomType->next; |
541 |
} |
542 |
info.last = 1; |
543 |
sendFrcStruct( &info, mpiAtomStructType ); |
544 |
|
545 |
} |
546 |
|
547 |
else{ |
548 |
|
549 |
// listen for node 0 to send out the force params |
550 |
|
551 |
MPIcheckPoint(); |
552 |
|
553 |
headAtomType = new LinkedType; |
554 |
recieveFrcStruct( &info, mpiAtomStructType ); |
555 |
|
556 |
while( !info.last ){ |
557 |
|
558 |
|
559 |
|
560 |
headAtomType->add( info ); |
561 |
|
562 |
MPIcheckPoint(); |
563 |
|
564 |
recieveFrcStruct( &info, mpiAtomStructType ); |
565 |
} |
566 |
} |
567 |
#endif // is_mpi |
568 |
|
569 |
// call new A_types in fortran |
570 |
|
571 |
int isError; |
572 |
|
573 |
// dummy variables |
574 |
|
575 |
int isGB = 0; |
576 |
int isLJ = 1; |
577 |
|
578 |
|
579 |
currentAtomType = headAtomType; |
580 |
while( currentAtomType != NULL ){ |
581 |
|
582 |
if( currentAtomType->name[0] != '\0' ){ |
583 |
isError = 0; |
584 |
newTPEtype( &(currentAtomType->ident), |
585 |
&(currentAtomType->mass), |
586 |
&(currentAtomType->epslon), |
587 |
&(currentAtomType->sigma), |
588 |
&isLJ, |
589 |
&(currentAtomType->isSSD), |
590 |
&(currentAtomType->isDipole), |
591 |
&isGB, |
592 |
&(currentAtomType->w0), |
593 |
&(currentAtomType->v0), |
594 |
&(currentAtomType->dipole), |
595 |
&isError ); |
596 |
if( isError ){ |
597 |
sprintf( painCave.errMsg, |
598 |
"Error initializing the \"%s\" atom type in fortran\n", |
599 |
currentAtomType->name ); |
600 |
painCave.isFatal = 1; |
601 |
simError(); |
602 |
} |
603 |
} |
604 |
currentAtomType = currentAtomType->next; |
605 |
} |
606 |
|
607 |
#ifdef IS_MPI |
608 |
sprintf( checkPointMsg, |
609 |
"TraPPE_ExFF atom structures successfully sent to fortran\n" ); |
610 |
MPIcheckPoint(); |
611 |
#endif // is_mpi |
612 |
|
613 |
|
614 |
// initialize the atoms |
615 |
|
616 |
double bigSigma = 0.0; |
617 |
DirectionalAtom* dAtom; |
618 |
|
619 |
for( i=0; i<nAtoms; i++ ){ |
620 |
|
621 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
622 |
if( currentAtomType == NULL ){ |
623 |
sprintf( painCave.errMsg, |
624 |
"AtomType error, %s not found in force file.\n", |
625 |
the_atoms[i]->getType() ); |
626 |
painCave.isFatal = 1; |
627 |
simError(); |
628 |
} |
629 |
|
630 |
the_atoms[i]->setMass( currentAtomType->mass ); |
631 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
632 |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
633 |
the_atoms[i]->setLJ(); |
634 |
|
635 |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
636 |
|
637 |
if( currentAtomType->isDipole ){ |
638 |
if( the_atoms[i]->isDirectional() ){ |
639 |
|
640 |
dAtom = (DirectionalAtom *) the_atoms[i]; |
641 |
dAtom->setMu( currentAtomType->dipole ); |
642 |
dAtom->setHasDipole( 1 ); |
643 |
dAtom->setJx( 0.0 ); |
644 |
dAtom->setJy( 0.0 ); |
645 |
dAtom->setJz( 0.0 ); |
646 |
|
647 |
if(!strcmp("SSD",the_atoms[i]->getType())){ |
648 |
dAtom->setI( waterI ); |
649 |
dAtom->setSSD( 1 ); |
650 |
} |
651 |
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
652 |
dAtom->setI( headI ); |
653 |
dAtom->setSSD( 0 ); |
654 |
} |
655 |
else{ |
656 |
sprintf(painCave.errMsg, |
657 |
"AtmType error, %s does not have a moment of inertia set.\n", |
658 |
the_atoms[i]->getType() ); |
659 |
painCave.isFatal = 1; |
660 |
simError(); |
661 |
} |
662 |
entry_plug->n_dipoles++; |
663 |
} |
664 |
else{ |
665 |
|
666 |
sprintf( painCave.errMsg, |
667 |
"TraPPE_ExFF error: Atom \"%s\" is a dipole, yet no standard" |
668 |
" orientation was specifed in the BASS file.\n", |
669 |
currentAtomType->name ); |
670 |
painCave.isFatal = 1; |
671 |
simError(); |
672 |
} |
673 |
} |
674 |
else{ |
675 |
if( the_atoms[i]->isDirectional() ){ |
676 |
sprintf( painCave.errMsg, |
677 |
"TraPPE_ExFF error: Atom \"%s\" was given a standard" |
678 |
"orientation in the BASS file, yet it is not a dipole.\n", |
679 |
currentAtomType->name); |
680 |
painCave.isFatal = 1; |
681 |
simError(); |
682 |
} |
683 |
} |
684 |
} |
685 |
|
686 |
#ifdef IS_MPI |
687 |
double tempBig = bigSigma; |
688 |
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
689 |
#endif //is_mpi |
690 |
|
691 |
//calc rCut and rList |
692 |
|
693 |
entry_plug->rCut = 2.5 * bigSigma; |
694 |
|
695 |
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) |
696 |
entry_plug->rCut = entry_plug->box_x / 2.0; |
697 |
|
698 |
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) |
699 |
entry_plug->rCut = entry_plug->box_y / 2.0; |
700 |
|
701 |
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) |
702 |
entry_plug->rCut = entry_plug->box_z / 2.0; |
703 |
|
704 |
entry_plug->rList = entry_plug->rCut + 1.0; |
705 |
|
706 |
|
707 |
// clean up the memory |
708 |
|
709 |
delete headAtomType; |
710 |
|
711 |
#ifdef IS_MPI |
712 |
sprintf( checkPointMsg, "TraPPE_Ex atoms initialized succesfully" ); |
713 |
MPIcheckPoint(); |
714 |
#endif // is_mpi |
715 |
|
716 |
initFortran(); |
717 |
entry_plug->refreshSim(); |
718 |
|
719 |
} |
720 |
|
721 |
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
722 |
|
723 |
class LinkedType { |
724 |
public: |
725 |
LinkedType(){ |
726 |
next = NULL; |
727 |
nameA[0] = '\0'; |
728 |
nameB[0] = '\0'; |
729 |
type[0] = '\0'; |
730 |
} |
731 |
~LinkedType(){ if( next != NULL ) delete next; } |
732 |
|
733 |
LinkedType* find(char* key1, char* key2){ |
734 |
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
735 |
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
736 |
if( next != NULL ) return next->find(key1, key2); |
737 |
return NULL; |
738 |
} |
739 |
|
740 |
|
741 |
void add( bondStruct &info ){ |
742 |
|
743 |
// check for duplicates |
744 |
int dup = 0; |
745 |
|
746 |
if( !strcmp(nameA, info.nameA ) && !strcmp( nameB, info.nameB ) ) dup = 1; |
747 |
if( !strcmp(nameA, info.nameB ) && !strcmp( nameB, info.nameA ) ) dup = 1; |
748 |
|
749 |
if(dup){ |
750 |
sprintf( painCave.errMsg, |
751 |
"Duplicate TraPPE_Ex bond type \"%s - %s\" found in " |
752 |
"the TraPPE_ExFF param file./n", |
753 |
nameA, nameB ); |
754 |
painCave.isFatal = 1; |
755 |
simError(); |
756 |
} |
757 |
|
758 |
|
759 |
if( next != NULL ) next->add(info); |
760 |
else{ |
761 |
next = new LinkedType(); |
762 |
strcpy(next->nameA, info.nameA); |
763 |
strcpy(next->nameB, info.nameB); |
764 |
strcpy(next->type, info.type); |
765 |
next->d0 = info.d0; |
766 |
} |
767 |
} |
768 |
|
769 |
#ifdef IS_MPI |
770 |
void duplicate( bondStruct &info ){ |
771 |
strcpy(info.nameA, nameA); |
772 |
strcpy(info.nameB, nameB); |
773 |
strcpy(info.type, type); |
774 |
info.d0 = d0; |
775 |
info.last = 0; |
776 |
} |
777 |
|
778 |
|
779 |
#endif |
780 |
|
781 |
char nameA[15]; |
782 |
char nameB[15]; |
783 |
char type[30]; |
784 |
double d0; |
785 |
|
786 |
LinkedType* next; |
787 |
}; |
788 |
|
789 |
|
790 |
|
791 |
LinkedType* headBondType; |
792 |
LinkedType* currentBondType; |
793 |
bondStruct info; |
794 |
info.last = 1; // initialize last to have the last set. |
795 |
// if things go well, last will be set to 0 |
796 |
|
797 |
SRI **the_sris; |
798 |
Atom** the_atoms; |
799 |
int nBonds; |
800 |
the_sris = entry_plug->sr_interactions; |
801 |
the_atoms = entry_plug->atoms; |
802 |
nBonds = entry_plug->n_bonds; |
803 |
|
804 |
int i, a, b; |
805 |
char* atomA; |
806 |
char* atomB; |
807 |
|
808 |
#ifdef IS_MPI |
809 |
if( worldRank == 0 ){ |
810 |
#endif |
811 |
|
812 |
// read in the bond types. |
813 |
|
814 |
headBondType = new LinkedType; |
815 |
|
816 |
fastForward( "BondTypes", "initializeBonds" ); |
817 |
|
818 |
// we are now at the bondTypes section |
819 |
|
820 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
821 |
lineNum++; |
822 |
|
823 |
|
824 |
// read a line, and start parseing out the atom types |
825 |
|
826 |
if( eof_test == NULL ){ |
827 |
sprintf( painCave.errMsg, |
828 |
"Error in reading bonds from force file at line %d.\n", |
829 |
lineNum ); |
830 |
painCave.isFatal = 1; |
831 |
simError(); |
832 |
} |
833 |
|
834 |
// stop reading at end of file, or at next section |
835 |
while( readLine[0] != '#' && eof_test != NULL ){ |
836 |
|
837 |
// toss comment lines |
838 |
if( readLine[0] != '!' ){ |
839 |
|
840 |
// the parser returns 0 if the line was blank |
841 |
if( parseBond( readLine, lineNum, info ) ){ |
842 |
headBondType->add( info ); |
843 |
} |
844 |
} |
845 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
846 |
lineNum++; |
847 |
} |
848 |
|
849 |
#ifdef IS_MPI |
850 |
|
851 |
// send out the linked list to all the other processes |
852 |
|
853 |
sprintf( checkPointMsg, |
854 |
"TraPPE_Ex bond structures read successfully." ); |
855 |
MPIcheckPoint(); |
856 |
|
857 |
currentBondType = headBondType; |
858 |
while( currentBondType != NULL ){ |
859 |
currentBondType->duplicate( info ); |
860 |
sendFrcStruct( &info, mpiBondStructType ); |
861 |
currentBondType = currentBondType->next; |
862 |
} |
863 |
info.last = 1; |
864 |
sendFrcStruct( &info, mpiBondStructType ); |
865 |
|
866 |
} |
867 |
|
868 |
else{ |
869 |
|
870 |
// listen for node 0 to send out the force params |
871 |
|
872 |
MPIcheckPoint(); |
873 |
|
874 |
headBondType = new LinkedType; |
875 |
recieveFrcStruct( &info, mpiBondStructType ); |
876 |
while( !info.last ){ |
877 |
|
878 |
headBondType->add( info ); |
879 |
recieveFrcStruct( &info, mpiBondStructType ); |
880 |
} |
881 |
} |
882 |
#endif // is_mpi |
883 |
|
884 |
|
885 |
// initialize the Bonds |
886 |
|
887 |
|
888 |
for( i=0; i<nBonds; i++ ){ |
889 |
|
890 |
a = the_bonds[i].a; |
891 |
b = the_bonds[i].b; |
892 |
|
893 |
atomA = the_atoms[a]->getType(); |
894 |
atomB = the_atoms[b]->getType(); |
895 |
currentBondType = headBondType->find( atomA, atomB ); |
896 |
if( currentBondType == NULL ){ |
897 |
sprintf( painCave.errMsg, |
898 |
"BondType error, %s - %s not found in force file.\n", |
899 |
atomA, atomB ); |
900 |
painCave.isFatal = 1; |
901 |
simError(); |
902 |
} |
903 |
|
904 |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
905 |
|
906 |
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
907 |
*the_atoms[b], |
908 |
currentBondType->d0 ); |
909 |
entry_plug->n_constraints++; |
910 |
} |
911 |
} |
912 |
|
913 |
|
914 |
// clean up the memory |
915 |
|
916 |
delete headBondType; |
917 |
|
918 |
#ifdef IS_MPI |
919 |
sprintf( checkPointMsg, "TraPPE_Ex bonds initialized succesfully" ); |
920 |
MPIcheckPoint(); |
921 |
#endif // is_mpi |
922 |
|
923 |
} |
924 |
|
925 |
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
926 |
|
927 |
class LinkedType { |
928 |
public: |
929 |
LinkedType(){ |
930 |
next = NULL; |
931 |
nameA[0] = '\0'; |
932 |
nameB[0] = '\0'; |
933 |
nameC[0] = '\0'; |
934 |
type[0] = '\0'; |
935 |
} |
936 |
~LinkedType(){ if( next != NULL ) delete next; } |
937 |
|
938 |
LinkedType* find( char* key1, char* key2, char* key3 ){ |
939 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
940 |
&& !strcmp( nameC, key3 ) ) return this; |
941 |
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
942 |
&& !strcmp( nameC, key1 ) ) return this; |
943 |
if( next != NULL ) return next->find(key1, key2, key3); |
944 |
return NULL; |
945 |
} |
946 |
|
947 |
void add( bendStruct &info ){ |
948 |
|
949 |
// check for duplicates |
950 |
int dup = 0; |
951 |
|
952 |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) |
953 |
&& !strcmp( nameC, info.nameC ) ) dup = 1; |
954 |
if( !strcmp( nameA, info.nameC ) && !strcmp( nameB, info.nameB ) |
955 |
&& !strcmp( nameC, info.nameA ) ) dup = 1; |
956 |
|
957 |
if(dup){ |
958 |
sprintf( painCave.errMsg, |
959 |
"Duplicate TraPPE_Ex bend type \"%s - %s - %s\" found in " |
960 |
"the TraPPE_ExFF param file./n", |
961 |
nameA, nameB, nameC ); |
962 |
painCave.isFatal = 1; |
963 |
simError(); |
964 |
} |
965 |
|
966 |
if( next != NULL ) next->add(info); |
967 |
else{ |
968 |
next = new LinkedType(); |
969 |
strcpy(next->nameA, info.nameA); |
970 |
strcpy(next->nameB, info.nameB); |
971 |
strcpy(next->nameC, info.nameC); |
972 |
strcpy(next->type, info.type); |
973 |
next->k1 = info.k1; |
974 |
next->k2 = info.k2; |
975 |
next->k3 = info.k3; |
976 |
next->t0 = info.t0; |
977 |
} |
978 |
} |
979 |
|
980 |
#ifdef IS_MPI |
981 |
|
982 |
void duplicate( bendStruct &info ){ |
983 |
strcpy(info.nameA, nameA); |
984 |
strcpy(info.nameB, nameB); |
985 |
strcpy(info.nameC, nameC); |
986 |
strcpy(info.type, type); |
987 |
info.k1 = k1; |
988 |
info.k2 = k2; |
989 |
info.k3 = k3; |
990 |
info.t0 = t0; |
991 |
info.last = 0; |
992 |
} |
993 |
|
994 |
#endif // is_mpi |
995 |
|
996 |
char nameA[15]; |
997 |
char nameB[15]; |
998 |
char nameC[15]; |
999 |
char type[30]; |
1000 |
double k1, k2, k3, t0; |
1001 |
|
1002 |
LinkedType* next; |
1003 |
}; |
1004 |
|
1005 |
LinkedType* headBendType; |
1006 |
LinkedType* currentBendType; |
1007 |
bendStruct info; |
1008 |
info.last = 1; // initialize last to have the last set. |
1009 |
// if things go well, last will be set to 0 |
1010 |
|
1011 |
QuadraticBend* qBend; |
1012 |
GhostBend* gBend; |
1013 |
SRI **the_sris; |
1014 |
Atom** the_atoms; |
1015 |
int nBends; |
1016 |
the_sris = entry_plug->sr_interactions; |
1017 |
the_atoms = entry_plug->atoms; |
1018 |
nBends = entry_plug->n_bends; |
1019 |
|
1020 |
int i, a, b, c; |
1021 |
char* atomA; |
1022 |
char* atomB; |
1023 |
char* atomC; |
1024 |
|
1025 |
|
1026 |
#ifdef IS_MPI |
1027 |
if( worldRank == 0 ){ |
1028 |
#endif |
1029 |
|
1030 |
// read in the bend types. |
1031 |
|
1032 |
headBendType = new LinkedType; |
1033 |
|
1034 |
fastForward( "BendTypes", "initializeBends" ); |
1035 |
|
1036 |
// we are now at the bendTypes section |
1037 |
|
1038 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1039 |
lineNum++; |
1040 |
|
1041 |
// read a line, and start parseing out the bend types |
1042 |
|
1043 |
if( eof_test == NULL ){ |
1044 |
sprintf( painCave.errMsg, |
1045 |
"Error in reading bends from force file at line %d.\n", |
1046 |
lineNum ); |
1047 |
painCave.isFatal = 1; |
1048 |
simError(); |
1049 |
} |
1050 |
|
1051 |
// stop reading at end of file, or at next section |
1052 |
while( readLine[0] != '#' && eof_test != NULL ){ |
1053 |
|
1054 |
// toss comment lines |
1055 |
if( readLine[0] != '!' ){ |
1056 |
|
1057 |
// the parser returns 0 if the line was blank |
1058 |
if( parseBend( readLine, lineNum, info ) ){ |
1059 |
headBendType->add( info ); |
1060 |
} |
1061 |
} |
1062 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1063 |
lineNum++; |
1064 |
} |
1065 |
|
1066 |
#ifdef IS_MPI |
1067 |
|
1068 |
// send out the linked list to all the other processes |
1069 |
|
1070 |
sprintf( checkPointMsg, |
1071 |
"TraPPE_Ex bend structures read successfully." ); |
1072 |
MPIcheckPoint(); |
1073 |
|
1074 |
currentBendType = headBendType; |
1075 |
while( currentBendType != NULL ){ |
1076 |
currentBendType->duplicate( info ); |
1077 |
sendFrcStruct( &info, mpiBendStructType ); |
1078 |
currentBendType = currentBendType->next; |
1079 |
} |
1080 |
info.last = 1; |
1081 |
sendFrcStruct( &info, mpiBendStructType ); |
1082 |
|
1083 |
} |
1084 |
|
1085 |
else{ |
1086 |
|
1087 |
// listen for node 0 to send out the force params |
1088 |
|
1089 |
MPIcheckPoint(); |
1090 |
|
1091 |
headBendType = new LinkedType; |
1092 |
recieveFrcStruct( &info, mpiBendStructType ); |
1093 |
while( !info.last ){ |
1094 |
|
1095 |
headBendType->add( info ); |
1096 |
recieveFrcStruct( &info, mpiBendStructType ); |
1097 |
} |
1098 |
} |
1099 |
#endif // is_mpi |
1100 |
|
1101 |
// initialize the Bends |
1102 |
|
1103 |
int index; |
1104 |
|
1105 |
for( i=0; i<nBends; i++ ){ |
1106 |
|
1107 |
a = the_bends[i].a; |
1108 |
b = the_bends[i].b; |
1109 |
c = the_bends[i].c; |
1110 |
|
1111 |
atomA = the_atoms[a]->getType(); |
1112 |
atomB = the_atoms[b]->getType(); |
1113 |
|
1114 |
if( the_bends[i].isGhost ) atomC = "GHOST"; |
1115 |
else atomC = the_atoms[c]->getType(); |
1116 |
|
1117 |
currentBendType = headBendType->find( atomA, atomB, atomC ); |
1118 |
if( currentBendType == NULL ){ |
1119 |
sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found" |
1120 |
" in force file.\n", |
1121 |
atomA, atomB, atomC ); |
1122 |
painCave.isFatal = 1; |
1123 |
simError(); |
1124 |
} |
1125 |
|
1126 |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1127 |
|
1128 |
index = i + entry_plug->n_bonds; |
1129 |
|
1130 |
if( the_bends[i].isGhost){ |
1131 |
|
1132 |
if( the_bends[i].ghost == b ){ |
1133 |
// do nothing |
1134 |
} |
1135 |
else if( the_bends[i].ghost == a ){ |
1136 |
c = a; |
1137 |
a = b; |
1138 |
b = a; |
1139 |
} |
1140 |
else{ |
1141 |
sprintf( painCave.errMsg, |
1142 |
"BendType error, %s - %s - %s,\n" |
1143 |
" --> central atom is not " |
1144 |
"correctly identified with the " |
1145 |
"\"ghostVectorSource = \" tag.\n", |
1146 |
atomA, atomB, atomC ); |
1147 |
painCave.isFatal = 1; |
1148 |
simError(); |
1149 |
} |
1150 |
|
1151 |
gBend = new GhostBend( *the_atoms[a], |
1152 |
*the_atoms[b] ); |
1153 |
gBend->setConstants( currentBendType->k1, |
1154 |
currentBendType->k2, |
1155 |
currentBendType->k3, |
1156 |
currentBendType->t0 ); |
1157 |
the_sris[index] = gBend; |
1158 |
} |
1159 |
else{ |
1160 |
qBend = new QuadraticBend( *the_atoms[a], |
1161 |
*the_atoms[b], |
1162 |
*the_atoms[c] ); |
1163 |
qBend->setConstants( currentBendType->k1, |
1164 |
currentBendType->k2, |
1165 |
currentBendType->k3, |
1166 |
currentBendType->t0 ); |
1167 |
the_sris[index] = qBend; |
1168 |
} |
1169 |
} |
1170 |
} |
1171 |
|
1172 |
|
1173 |
// clean up the memory |
1174 |
|
1175 |
delete headBendType; |
1176 |
|
1177 |
#ifdef IS_MPI |
1178 |
sprintf( checkPointMsg, "TraPPE_Ex bends initialized succesfully" ); |
1179 |
MPIcheckPoint(); |
1180 |
#endif // is_mpi |
1181 |
|
1182 |
} |
1183 |
|
1184 |
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
1185 |
|
1186 |
class LinkedType { |
1187 |
public: |
1188 |
LinkedType(){ |
1189 |
next = NULL; |
1190 |
nameA[0] = '\0'; |
1191 |
nameB[0] = '\0'; |
1192 |
nameC[0] = '\0'; |
1193 |
type[0] = '\0'; |
1194 |
} |
1195 |
~LinkedType(){ if( next != NULL ) delete next; } |
1196 |
|
1197 |
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
1198 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
1199 |
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
1200 |
|
1201 |
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
1202 |
!strcmp( nameC, key2 ) && !strcmp( nameD, key1 ) ) return this; |
1203 |
|
1204 |
if( next != NULL ) return next->find(key1, key2, key3, key4); |
1205 |
return NULL; |
1206 |
} |
1207 |
|
1208 |
void add( torsionStruct &info ){ |
1209 |
|
1210 |
// check for duplicates |
1211 |
int dup = 0; |
1212 |
|
1213 |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) && |
1214 |
!strcmp( nameC, info.nameC ) && !strcmp( nameD, info.nameD ) ) dup = 1; |
1215 |
|
1216 |
if( !strcmp( nameA, info.nameD ) && !strcmp( nameB, info.nameC ) && |
1217 |
!strcmp( nameC, info.nameB ) && !strcmp( nameD, info.nameA ) ) dup = 1; |
1218 |
|
1219 |
if(dup){ |
1220 |
sprintf( painCave.errMsg, |
1221 |
"Duplicate TraPPE_Ex torsion type \"%s - %s - %s - %s\" found in " |
1222 |
"the TraPPE_ExFF param file./n", nameA, nameB, nameC, nameD ); |
1223 |
painCave.isFatal = 1; |
1224 |
simError(); |
1225 |
} |
1226 |
|
1227 |
if( next != NULL ) next->add(info); |
1228 |
else{ |
1229 |
next = new LinkedType(); |
1230 |
strcpy(next->nameA, info.nameA); |
1231 |
strcpy(next->nameB, info.nameB); |
1232 |
strcpy(next->nameC, info.nameC); |
1233 |
strcpy(next->type, info.type); |
1234 |
next->k1 = info.k1; |
1235 |
next->k2 = info.k2; |
1236 |
next->k3 = info.k3; |
1237 |
next->k4 = info.k4; |
1238 |
} |
1239 |
} |
1240 |
|
1241 |
#ifdef IS_MPI |
1242 |
|
1243 |
void duplicate( torsionStruct &info ){ |
1244 |
strcpy(info.nameA, nameA); |
1245 |
strcpy(info.nameB, nameB); |
1246 |
strcpy(info.nameC, nameC); |
1247 |
strcpy(info.nameD, nameD); |
1248 |
strcpy(info.type, type); |
1249 |
info.k1 = k1; |
1250 |
info.k2 = k2; |
1251 |
info.k3 = k3; |
1252 |
info.k4 = k4; |
1253 |
info.last = 0; |
1254 |
} |
1255 |
|
1256 |
#endif |
1257 |
|
1258 |
char nameA[15]; |
1259 |
char nameB[15]; |
1260 |
char nameC[15]; |
1261 |
char nameD[15]; |
1262 |
char type[30]; |
1263 |
double k1, k2, k3, k4; |
1264 |
|
1265 |
LinkedType* next; |
1266 |
}; |
1267 |
|
1268 |
LinkedType* headTorsionType; |
1269 |
LinkedType* currentTorsionType; |
1270 |
torsionStruct info; |
1271 |
info.last = 1; // initialize last to have the last set. |
1272 |
// if things go well, last will be set to 0 |
1273 |
|
1274 |
int i, a, b, c, d, index; |
1275 |
char* atomA; |
1276 |
char* atomB; |
1277 |
char* atomC; |
1278 |
char* atomD; |
1279 |
CubicTorsion* cTors; |
1280 |
|
1281 |
SRI **the_sris; |
1282 |
Atom** the_atoms; |
1283 |
int nTorsions; |
1284 |
the_sris = entry_plug->sr_interactions; |
1285 |
the_atoms = entry_plug->atoms; |
1286 |
nTorsions = entry_plug->n_torsions; |
1287 |
|
1288 |
#ifdef IS_MPI |
1289 |
if( worldRank == 0 ){ |
1290 |
#endif |
1291 |
|
1292 |
// read in the torsion types. |
1293 |
|
1294 |
headTorsionType = new LinkedType; |
1295 |
|
1296 |
fastForward( "TorsionTypes", "initializeTorsions" ); |
1297 |
|
1298 |
// we are now at the torsionTypes section |
1299 |
|
1300 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1301 |
lineNum++; |
1302 |
|
1303 |
|
1304 |
// read a line, and start parseing out the atom types |
1305 |
|
1306 |
if( eof_test == NULL ){ |
1307 |
sprintf( painCave.errMsg, |
1308 |
"Error in reading torsions from force file at line %d.\n", |
1309 |
lineNum ); |
1310 |
painCave.isFatal = 1; |
1311 |
simError(); |
1312 |
} |
1313 |
|
1314 |
// stop reading at end of file, or at next section |
1315 |
while( readLine[0] != '#' && eof_test != NULL ){ |
1316 |
|
1317 |
// toss comment lines |
1318 |
if( readLine[0] != '!' ){ |
1319 |
|
1320 |
// the parser returns 0 if the line was blank |
1321 |
if( parseTorsion( readLine, lineNum, info ) ){ |
1322 |
headTorsionType->add( info ); |
1323 |
} |
1324 |
} |
1325 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1326 |
lineNum++; |
1327 |
} |
1328 |
|
1329 |
#ifdef IS_MPI |
1330 |
|
1331 |
// send out the linked list to all the other processes |
1332 |
|
1333 |
sprintf( checkPointMsg, |
1334 |
"TraPPE_Ex torsion structures read successfully." ); |
1335 |
MPIcheckPoint(); |
1336 |
|
1337 |
currentTorsionType = headTorsionType; |
1338 |
while( currentTorsionType != NULL ){ |
1339 |
currentTorsionType->duplicate( info ); |
1340 |
sendFrcStruct( &info, mpiTorsionStructType ); |
1341 |
currentTorsionType = currentTorsionType->next; |
1342 |
} |
1343 |
info.last = 1; |
1344 |
sendFrcStruct( &info, mpiTorsionStructType ); |
1345 |
|
1346 |
} |
1347 |
|
1348 |
else{ |
1349 |
|
1350 |
// listen for node 0 to send out the force params |
1351 |
|
1352 |
MPIcheckPoint(); |
1353 |
|
1354 |
headTorsionType = new LinkedType; |
1355 |
recieveFrcStruct( &info, mpiTorsionStructType ); |
1356 |
while( !info.last ){ |
1357 |
|
1358 |
headTorsionType->add( info ); |
1359 |
recieveFrcStruct( &info, mpiTorsionStructType ); |
1360 |
} |
1361 |
} |
1362 |
#endif // is_mpi |
1363 |
|
1364 |
// initialize the Torsions |
1365 |
|
1366 |
for( i=0; i<nTorsions; i++ ){ |
1367 |
|
1368 |
a = the_torsions[i].a; |
1369 |
b = the_torsions[i].b; |
1370 |
c = the_torsions[i].c; |
1371 |
d = the_torsions[i].d; |
1372 |
|
1373 |
atomA = the_atoms[a]->getType(); |
1374 |
atomB = the_atoms[b]->getType(); |
1375 |
atomC = the_atoms[c]->getType(); |
1376 |
atomD = the_atoms[d]->getType(); |
1377 |
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1378 |
if( currentTorsionType == NULL ){ |
1379 |
sprintf( painCave.errMsg, |
1380 |
"TorsionType error, %s - %s - %s - %s not found" |
1381 |
" in force file.\n", |
1382 |
atomA, atomB, atomC, atomD ); |
1383 |
painCave.isFatal = 1; |
1384 |
simError(); |
1385 |
} |
1386 |
|
1387 |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1388 |
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
1389 |
|
1390 |
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1391 |
*the_atoms[c], *the_atoms[d] ); |
1392 |
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1393 |
currentTorsionType->k3, currentTorsionType->k4 ); |
1394 |
the_sris[index] = cTors; |
1395 |
} |
1396 |
} |
1397 |
|
1398 |
|
1399 |
// clean up the memory |
1400 |
|
1401 |
delete headTorsionType; |
1402 |
|
1403 |
#ifdef IS_MPI |
1404 |
sprintf( checkPointMsg, "TraPPE_Ex torsions initialized succesfully" ); |
1405 |
MPIcheckPoint(); |
1406 |
#endif // is_mpi |
1407 |
|
1408 |
} |
1409 |
|
1410 |
void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){ |
1411 |
|
1412 |
int foundText = 0; |
1413 |
char* the_token; |
1414 |
|
1415 |
rewind( frcFile ); |
1416 |
lineNum = 0; |
1417 |
|
1418 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1419 |
lineNum++; |
1420 |
if( eof_test == NULL ){ |
1421 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
1422 |
" file is empty.\n", |
1423 |
searchOwner ); |
1424 |
painCave.isFatal = 1; |
1425 |
simError(); |
1426 |
} |
1427 |
|
1428 |
|
1429 |
while( !foundText ){ |
1430 |
while( eof_test != NULL && readLine[0] != '#' ){ |
1431 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1432 |
lineNum++; |
1433 |
} |
1434 |
if( eof_test == NULL ){ |
1435 |
sprintf( painCave.errMsg, |
1436 |
"Error fast forwarding force file for %s at " |
1437 |
"line %d: file ended unexpectedly.\n", |
1438 |
searchOwner, |
1439 |
lineNum ); |
1440 |
painCave.isFatal = 1; |
1441 |
simError(); |
1442 |
} |
1443 |
|
1444 |
the_token = strtok( readLine, " ,;\t#\n" ); |
1445 |
foundText = !strcmp( stopText, the_token ); |
1446 |
|
1447 |
if( !foundText ){ |
1448 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1449 |
lineNum++; |
1450 |
|
1451 |
if( eof_test == NULL ){ |
1452 |
sprintf( painCave.errMsg, |
1453 |
"Error fast forwarding force file for %s at " |
1454 |
"line %d: file ended unexpectedly.\n", |
1455 |
searchOwner, |
1456 |
lineNum ); |
1457 |
painCave.isFatal = 1; |
1458 |
simError(); |
1459 |
} |
1460 |
} |
1461 |
} |
1462 |
} |
1463 |
|
1464 |
|
1465 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1466 |
|
1467 |
char* the_token; |
1468 |
|
1469 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1470 |
if( the_token != NULL ){ |
1471 |
|
1472 |
strcpy( info.name, the_token ); |
1473 |
|
1474 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1475 |
sprintf( painCave.errMsg, |
1476 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1477 |
painCave.isFatal = 1; |
1478 |
simError(); |
1479 |
} |
1480 |
|
1481 |
info.isDipole = atoi( the_token ); |
1482 |
|
1483 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1484 |
sprintf( painCave.errMsg, |
1485 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1486 |
painCave.isFatal = 1; |
1487 |
simError(); |
1488 |
} |
1489 |
|
1490 |
info.isSSD = atoi( the_token ); |
1491 |
|
1492 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1493 |
sprintf( painCave.errMsg, |
1494 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1495 |
painCave.isFatal = 1; |
1496 |
simError(); |
1497 |
} |
1498 |
|
1499 |
info.mass = atof( the_token ); |
1500 |
|
1501 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1502 |
sprintf( painCave.errMsg, |
1503 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1504 |
painCave.isFatal = 1; |
1505 |
simError(); |
1506 |
} |
1507 |
|
1508 |
info.epslon = atof( the_token ); |
1509 |
|
1510 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1511 |
sprintf( painCave.errMsg, |
1512 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1513 |
painCave.isFatal = 1; |
1514 |
simError(); |
1515 |
} |
1516 |
|
1517 |
info.sigma = atof( the_token ); |
1518 |
|
1519 |
if( info.isDipole ){ |
1520 |
|
1521 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1522 |
sprintf( painCave.errMsg, |
1523 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1524 |
painCave.isFatal = 1; |
1525 |
simError(); |
1526 |
} |
1527 |
|
1528 |
info.dipole = atof( the_token ); |
1529 |
} |
1530 |
else info.dipole = 0.0; |
1531 |
|
1532 |
if( info.isSSD ){ |
1533 |
|
1534 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1535 |
sprintf( painCave.errMsg, |
1536 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1537 |
painCave.isFatal = 1; |
1538 |
simError(); |
1539 |
} |
1540 |
|
1541 |
info.w0 = atof( the_token ); |
1542 |
|
1543 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1544 |
sprintf( painCave.errMsg, |
1545 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1546 |
painCave.isFatal = 1; |
1547 |
simError(); |
1548 |
} |
1549 |
|
1550 |
info.v0 = atof( the_token ); |
1551 |
} |
1552 |
else info.v0 = info.w0 = 0.0; |
1553 |
|
1554 |
return 1; |
1555 |
} |
1556 |
else return 0; |
1557 |
} |
1558 |
|
1559 |
int parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1560 |
|
1561 |
char* the_token; |
1562 |
|
1563 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1564 |
if( the_token != NULL ){ |
1565 |
|
1566 |
strcpy( info.nameA, the_token ); |
1567 |
|
1568 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1569 |
sprintf( painCave.errMsg, |
1570 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1571 |
painCave.isFatal = 1; |
1572 |
simError(); |
1573 |
} |
1574 |
|
1575 |
strcpy( info.nameB, the_token ); |
1576 |
|
1577 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1578 |
sprintf( painCave.errMsg, |
1579 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1580 |
painCave.isFatal = 1; |
1581 |
simError(); |
1582 |
} |
1583 |
|
1584 |
strcpy( info.type, the_token ); |
1585 |
|
1586 |
if( !strcmp( info.type, "fixed" ) ){ |
1587 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1588 |
sprintf( painCave.errMsg, |
1589 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1590 |
painCave.isFatal = 1; |
1591 |
simError(); |
1592 |
} |
1593 |
|
1594 |
info.d0 = atof( the_token ); |
1595 |
} |
1596 |
else{ |
1597 |
sprintf( painCave.errMsg, |
1598 |
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
1599 |
info.type, |
1600 |
lineNum ); |
1601 |
painCave.isFatal = 1; |
1602 |
simError(); |
1603 |
} |
1604 |
|
1605 |
return 1; |
1606 |
} |
1607 |
else return 0; |
1608 |
} |
1609 |
|
1610 |
|
1611 |
int parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1612 |
|
1613 |
char* the_token; |
1614 |
|
1615 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1616 |
if( the_token != NULL ){ |
1617 |
|
1618 |
strcpy( info.nameA, the_token ); |
1619 |
|
1620 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1621 |
sprintf( painCave.errMsg, |
1622 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1623 |
painCave.isFatal = 1; |
1624 |
simError(); |
1625 |
} |
1626 |
|
1627 |
strcpy( info.nameB, the_token ); |
1628 |
|
1629 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1630 |
sprintf( painCave.errMsg, |
1631 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1632 |
painCave.isFatal = 1; |
1633 |
simError(); |
1634 |
} |
1635 |
|
1636 |
strcpy( info.nameC, the_token ); |
1637 |
|
1638 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1639 |
sprintf( painCave.errMsg, |
1640 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1641 |
painCave.isFatal = 1; |
1642 |
simError(); |
1643 |
} |
1644 |
|
1645 |
strcpy( info.type, the_token ); |
1646 |
|
1647 |
if( !strcmp( info.type, "quadratic" ) ){ |
1648 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1649 |
sprintf( painCave.errMsg, |
1650 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1651 |
painCave.isFatal = 1; |
1652 |
simError(); |
1653 |
} |
1654 |
|
1655 |
info.k1 = atof( the_token ); |
1656 |
|
1657 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1658 |
sprintf( painCave.errMsg, |
1659 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1660 |
painCave.isFatal = 1; |
1661 |
simError(); |
1662 |
} |
1663 |
|
1664 |
info.k2 = atof( the_token ); |
1665 |
|
1666 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1667 |
sprintf( painCave.errMsg, |
1668 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1669 |
painCave.isFatal = 1; |
1670 |
simError(); |
1671 |
} |
1672 |
|
1673 |
info.k3 = atof( the_token ); |
1674 |
|
1675 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1676 |
sprintf( painCave.errMsg, |
1677 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1678 |
painCave.isFatal = 1; |
1679 |
simError(); |
1680 |
} |
1681 |
|
1682 |
info.t0 = atof( the_token ); |
1683 |
} |
1684 |
|
1685 |
else{ |
1686 |
sprintf( painCave.errMsg, |
1687 |
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
1688 |
info.type, |
1689 |
lineNum ); |
1690 |
painCave.isFatal = 1; |
1691 |
simError(); |
1692 |
} |
1693 |
|
1694 |
return 1; |
1695 |
} |
1696 |
else return 0; |
1697 |
} |
1698 |
|
1699 |
int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1700 |
|
1701 |
char* the_token; |
1702 |
|
1703 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1704 |
if( the_token != NULL ){ |
1705 |
|
1706 |
strcpy( info.nameA, the_token ); |
1707 |
|
1708 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1709 |
sprintf( painCave.errMsg, |
1710 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1711 |
painCave.isFatal = 1; |
1712 |
simError(); |
1713 |
} |
1714 |
|
1715 |
strcpy( info.nameB, the_token ); |
1716 |
|
1717 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1718 |
sprintf( painCave.errMsg, |
1719 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1720 |
painCave.isFatal = 1; |
1721 |
simError(); |
1722 |
} |
1723 |
|
1724 |
strcpy( info.nameC, the_token ); |
1725 |
|
1726 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1727 |
sprintf( painCave.errMsg, |
1728 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1729 |
painCave.isFatal = 1; |
1730 |
simError(); |
1731 |
} |
1732 |
|
1733 |
strcpy( info.nameD, the_token ); |
1734 |
|
1735 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1736 |
sprintf( painCave.errMsg, |
1737 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1738 |
painCave.isFatal = 1; |
1739 |
simError(); |
1740 |
} |
1741 |
|
1742 |
strcpy( info.type, the_token ); |
1743 |
|
1744 |
if( !strcmp( info.type, "cubic" ) ){ |
1745 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1746 |
sprintf( painCave.errMsg, |
1747 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1748 |
painCave.isFatal = 1; |
1749 |
simError(); |
1750 |
} |
1751 |
|
1752 |
info.k1 = atof( the_token ); |
1753 |
|
1754 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1755 |
sprintf( painCave.errMsg, |
1756 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1757 |
painCave.isFatal = 1; |
1758 |
simError(); |
1759 |
} |
1760 |
|
1761 |
info.k2 = atof( the_token ); |
1762 |
|
1763 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1764 |
sprintf( painCave.errMsg, |
1765 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1766 |
painCave.isFatal = 1; |
1767 |
simError(); |
1768 |
} |
1769 |
|
1770 |
info.k3 = atof( the_token ); |
1771 |
|
1772 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1773 |
sprintf( painCave.errMsg, |
1774 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1775 |
painCave.isFatal = 1; |
1776 |
simError(); |
1777 |
} |
1778 |
|
1779 |
info.k4 = atof( the_token ); |
1780 |
|
1781 |
} |
1782 |
|
1783 |
else{ |
1784 |
sprintf( painCave.errMsg, |
1785 |
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
1786 |
info.type, |
1787 |
lineNum ); |
1788 |
painCave.isFatal = 1; |
1789 |
simError(); |
1790 |
} |
1791 |
|
1792 |
return 1; |
1793 |
} |
1794 |
|
1795 |
else return 0; |
1796 |
} |