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