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