85 |
|
|
86 |
|
#endif |
87 |
|
|
88 |
+ |
class LinkedAtomType { |
89 |
+ |
public: |
90 |
+ |
LinkedAtomType(){ |
91 |
+ |
next = NULL; |
92 |
+ |
name[0] = '\0'; |
93 |
+ |
} |
94 |
+ |
~LinkedAtomType(){ if( next != NULL ) delete next; } |
95 |
+ |
|
96 |
+ |
LinkedAtomType* find(char* key){ |
97 |
+ |
if( !strcmp(name, key) ) return this; |
98 |
+ |
if( next != NULL ) return next->find(key); |
99 |
+ |
return NULL; |
100 |
+ |
} |
101 |
+ |
|
102 |
+ |
void add( atomStruct &info ){ |
103 |
+ |
|
104 |
+ |
// check for duplicates |
105 |
+ |
|
106 |
+ |
if( !strcmp( info.name, name ) ){ |
107 |
+ |
sprintf( painCave.errMsg, |
108 |
+ |
"Duplicate TraPPE_Ex atom type \"%s\" found in " |
109 |
+ |
"the TraPPE_ExFF param file./n", |
110 |
+ |
name ); |
111 |
+ |
painCave.isFatal = 1; |
112 |
+ |
simError(); |
113 |
+ |
} |
114 |
+ |
|
115 |
+ |
if( next != NULL ) next->add(info); |
116 |
+ |
else{ |
117 |
+ |
next = new LinkedAtomType(); |
118 |
+ |
strcpy(next->name, info.name); |
119 |
+ |
next->isDipole = info.isDipole; |
120 |
+ |
next->isSSD = info.isSSD; |
121 |
+ |
next->mass = info.mass; |
122 |
+ |
next->epslon = info.epslon; |
123 |
+ |
next->sigma = info.sigma; |
124 |
+ |
next->dipole = info.dipole; |
125 |
+ |
next->w0 = info.w0; |
126 |
+ |
next->v0 = info.v0; |
127 |
+ |
next->ident = info.ident; |
128 |
+ |
} |
129 |
+ |
} |
130 |
+ |
|
131 |
+ |
#ifdef IS_MPI |
132 |
+ |
|
133 |
+ |
void duplicate( atomStruct &info ){ |
134 |
+ |
strcpy(info.name, name); |
135 |
+ |
info.isDipole = isDipole; |
136 |
+ |
info.isSSD = isSSD; |
137 |
+ |
info.mass = mass; |
138 |
+ |
info.epslon = epslon; |
139 |
+ |
info.sigma = sigma; |
140 |
+ |
info.dipole = dipole; |
141 |
+ |
info.w0 = w0; |
142 |
+ |
info.v0 = v0; |
143 |
+ |
info.last = 0; |
144 |
+ |
} |
145 |
+ |
|
146 |
+ |
|
147 |
+ |
#endif |
148 |
+ |
|
149 |
+ |
char name[15]; |
150 |
+ |
int isDipole; |
151 |
+ |
int isSSD; |
152 |
+ |
double mass; |
153 |
+ |
double epslon; |
154 |
+ |
double sigma; |
155 |
+ |
double dipole; |
156 |
+ |
double w0; |
157 |
+ |
double v0; |
158 |
+ |
int ident; |
159 |
+ |
LinkedAtomType* next; |
160 |
+ |
}; |
161 |
+ |
|
162 |
+ |
class LinkedBondType { |
163 |
+ |
public: |
164 |
+ |
LinkedBondType(){ |
165 |
+ |
next = NULL; |
166 |
+ |
nameA[0] = '\0'; |
167 |
+ |
nameB[0] = '\0'; |
168 |
+ |
type[0] = '\0'; |
169 |
+ |
} |
170 |
+ |
~LinkedBondType(){ if( next != NULL ) delete next; } |
171 |
+ |
|
172 |
+ |
LinkedBondType* find(char* key1, char* key2){ |
173 |
+ |
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
174 |
+ |
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
175 |
+ |
if( next != NULL ) return next->find(key1, key2); |
176 |
+ |
return NULL; |
177 |
+ |
} |
178 |
+ |
|
179 |
+ |
|
180 |
+ |
void add( bondStruct &info ){ |
181 |
+ |
|
182 |
+ |
// check for duplicates |
183 |
+ |
int dup = 0; |
184 |
+ |
|
185 |
+ |
if( !strcmp(nameA, info.nameA ) && !strcmp( nameB, info.nameB ) ) dup = 1; |
186 |
+ |
if( !strcmp(nameA, info.nameB ) && !strcmp( nameB, info.nameA ) ) dup = 1; |
187 |
+ |
|
188 |
+ |
if(dup){ |
189 |
+ |
sprintf( painCave.errMsg, |
190 |
+ |
"Duplicate TraPPE_Ex bond type \"%s - %s\" found in " |
191 |
+ |
"the TraPPE_ExFF param file./n", |
192 |
+ |
nameA, nameB ); |
193 |
+ |
painCave.isFatal = 1; |
194 |
+ |
simError(); |
195 |
+ |
} |
196 |
+ |
|
197 |
+ |
|
198 |
+ |
if( next != NULL ) next->add(info); |
199 |
+ |
else{ |
200 |
+ |
next = new LinkedBondType(); |
201 |
+ |
strcpy(next->nameA, info.nameA); |
202 |
+ |
strcpy(next->nameB, info.nameB); |
203 |
+ |
strcpy(next->type, info.type); |
204 |
+ |
next->d0 = info.d0; |
205 |
+ |
} |
206 |
+ |
} |
207 |
+ |
|
208 |
+ |
#ifdef IS_MPI |
209 |
+ |
void duplicate( bondStruct &info ){ |
210 |
+ |
strcpy(info.nameA, nameA); |
211 |
+ |
strcpy(info.nameB, nameB); |
212 |
+ |
strcpy(info.type, type); |
213 |
+ |
info.d0 = d0; |
214 |
+ |
info.last = 0; |
215 |
+ |
} |
216 |
+ |
|
217 |
+ |
|
218 |
+ |
#endif |
219 |
+ |
|
220 |
+ |
char nameA[15]; |
221 |
+ |
char nameB[15]; |
222 |
+ |
char type[30]; |
223 |
+ |
double d0; |
224 |
+ |
|
225 |
+ |
LinkedBondType* next; |
226 |
+ |
}; |
227 |
+ |
|
228 |
+ |
class LinkedBendType { |
229 |
+ |
public: |
230 |
+ |
LinkedBendType(){ |
231 |
+ |
next = NULL; |
232 |
+ |
nameA[0] = '\0'; |
233 |
+ |
nameB[0] = '\0'; |
234 |
+ |
nameC[0] = '\0'; |
235 |
+ |
type[0] = '\0'; |
236 |
+ |
} |
237 |
+ |
~LinkedBendType(){ if( next != NULL ) delete next; } |
238 |
+ |
|
239 |
+ |
LinkedBendType* find( char* key1, char* key2, char* key3 ){ |
240 |
+ |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
241 |
+ |
&& !strcmp( nameC, key3 ) ) return this; |
242 |
+ |
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
243 |
+ |
&& !strcmp( nameC, key1 ) ) return this; |
244 |
+ |
if( next != NULL ) return next->find(key1, key2, key3); |
245 |
+ |
return NULL; |
246 |
+ |
} |
247 |
+ |
|
248 |
+ |
void add( bendStruct &info ){ |
249 |
+ |
|
250 |
+ |
// check for duplicates |
251 |
+ |
int dup = 0; |
252 |
+ |
|
253 |
+ |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) |
254 |
+ |
&& !strcmp( nameC, info.nameC ) ) dup = 1; |
255 |
+ |
if( !strcmp( nameA, info.nameC ) && !strcmp( nameB, info.nameB ) |
256 |
+ |
&& !strcmp( nameC, info.nameA ) ) dup = 1; |
257 |
+ |
|
258 |
+ |
if(dup){ |
259 |
+ |
sprintf( painCave.errMsg, |
260 |
+ |
"Duplicate TraPPE_Ex bend type \"%s - %s - %s\" found in " |
261 |
+ |
"the TraPPE_ExFF param file./n", |
262 |
+ |
nameA, nameB, nameC ); |
263 |
+ |
painCave.isFatal = 1; |
264 |
+ |
simError(); |
265 |
+ |
} |
266 |
+ |
|
267 |
+ |
if( next != NULL ) next->add(info); |
268 |
+ |
else{ |
269 |
+ |
next = new LinkedBendType(); |
270 |
+ |
strcpy(next->nameA, info.nameA); |
271 |
+ |
strcpy(next->nameB, info.nameB); |
272 |
+ |
strcpy(next->nameC, info.nameC); |
273 |
+ |
strcpy(next->type, info.type); |
274 |
+ |
next->k1 = info.k1; |
275 |
+ |
next->k2 = info.k2; |
276 |
+ |
next->k3 = info.k3; |
277 |
+ |
next->t0 = info.t0; |
278 |
+ |
} |
279 |
+ |
} |
280 |
+ |
|
281 |
+ |
#ifdef IS_MPI |
282 |
+ |
|
283 |
+ |
void duplicate( bendStruct &info ){ |
284 |
+ |
strcpy(info.nameA, nameA); |
285 |
+ |
strcpy(info.nameB, nameB); |
286 |
+ |
strcpy(info.nameC, nameC); |
287 |
+ |
strcpy(info.type, type); |
288 |
+ |
info.k1 = k1; |
289 |
+ |
info.k2 = k2; |
290 |
+ |
info.k3 = k3; |
291 |
+ |
info.t0 = t0; |
292 |
+ |
info.last = 0; |
293 |
+ |
} |
294 |
+ |
|
295 |
+ |
#endif // is_mpi |
296 |
+ |
|
297 |
+ |
char nameA[15]; |
298 |
+ |
char nameB[15]; |
299 |
+ |
char nameC[15]; |
300 |
+ |
char type[30]; |
301 |
+ |
double k1, k2, k3, t0; |
302 |
+ |
|
303 |
+ |
LinkedBendType* next; |
304 |
+ |
}; |
305 |
+ |
|
306 |
+ |
class LinkedTorsionType { |
307 |
+ |
public: |
308 |
+ |
LinkedTorsionType(){ |
309 |
+ |
next = NULL; |
310 |
+ |
nameA[0] = '\0'; |
311 |
+ |
nameB[0] = '\0'; |
312 |
+ |
nameC[0] = '\0'; |
313 |
+ |
type[0] = '\0'; |
314 |
+ |
} |
315 |
+ |
~LinkedTorsionType(){ if( next != NULL ) delete next; } |
316 |
+ |
|
317 |
+ |
LinkedTorsionType* find( char* key1, char* key2, char* key3, char* key4 ){ |
318 |
+ |
|
319 |
+ |
|
320 |
+ |
|
321 |
+ |
|
322 |
+ |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
323 |
+ |
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
324 |
+ |
|
325 |
+ |
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
326 |
+ |
!strcmp( nameC, key2 ) && !strcmp( nameD, key1 ) ) return this; |
327 |
+ |
|
328 |
+ |
if( next != NULL ) return next->find(key1, key2, key3, key4); |
329 |
+ |
return NULL; |
330 |
+ |
} |
331 |
+ |
|
332 |
+ |
void add( torsionStruct &info ){ |
333 |
+ |
|
334 |
+ |
// check for duplicates |
335 |
+ |
int dup = 0; |
336 |
+ |
|
337 |
+ |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) && |
338 |
+ |
!strcmp( nameC, info.nameC ) && !strcmp( nameD, info.nameD ) ) dup = 1; |
339 |
+ |
|
340 |
+ |
if( !strcmp( nameA, info.nameD ) && !strcmp( nameB, info.nameC ) && |
341 |
+ |
!strcmp( nameC, info.nameB ) && !strcmp( nameD, info.nameA ) ) dup = 1; |
342 |
+ |
|
343 |
+ |
if(dup){ |
344 |
+ |
sprintf( painCave.errMsg, |
345 |
+ |
"Duplicate TraPPE_Ex torsion type \"%s - %s - %s - %s\" found in " |
346 |
+ |
"the TraPPE_ExFF param file./n", nameA, nameB, nameC, nameD ); |
347 |
+ |
painCave.isFatal = 1; |
348 |
+ |
simError(); |
349 |
+ |
} |
350 |
+ |
|
351 |
+ |
if( next != NULL ) next->add(info); |
352 |
+ |
else{ |
353 |
+ |
next = new LinkedTorsionType(); |
354 |
+ |
strcpy(next->nameA, info.nameA); |
355 |
+ |
strcpy(next->nameB, info.nameB); |
356 |
+ |
strcpy(next->nameC, info.nameC); |
357 |
+ |
strcpy(next->nameD, info.nameD); |
358 |
+ |
strcpy(next->type, info.type); |
359 |
+ |
next->k1 = info.k1; |
360 |
+ |
next->k2 = info.k2; |
361 |
+ |
next->k3 = info.k3; |
362 |
+ |
next->k4 = info.k4; |
363 |
+ |
|
364 |
+ |
} |
365 |
+ |
} |
366 |
+ |
|
367 |
+ |
#ifdef IS_MPI |
368 |
+ |
|
369 |
+ |
void duplicate( torsionStruct &info ){ |
370 |
+ |
strcpy(info.nameA, nameA); |
371 |
+ |
strcpy(info.nameB, nameB); |
372 |
+ |
strcpy(info.nameC, nameC); |
373 |
+ |
strcpy(info.nameD, nameD); |
374 |
+ |
strcpy(info.type, type); |
375 |
+ |
info.k1 = k1; |
376 |
+ |
info.k2 = k2; |
377 |
+ |
info.k3 = k3; |
378 |
+ |
info.k4 = k4; |
379 |
+ |
info.last = 0; |
380 |
+ |
} |
381 |
+ |
|
382 |
+ |
#endif |
383 |
+ |
|
384 |
+ |
char nameA[15]; |
385 |
+ |
char nameB[15]; |
386 |
+ |
char nameC[15]; |
387 |
+ |
char nameD[15]; |
388 |
+ |
char type[30]; |
389 |
+ |
double k1, k2, k3, k4; |
390 |
+ |
|
391 |
+ |
LinkedTorsionType* next; |
392 |
+ |
}; |
393 |
+ |
|
394 |
+ |
|
395 |
+ |
LinkedAtomType* headAtomType; |
396 |
+ |
LinkedAtomType* currentAtomType; |
397 |
+ |
LinkedBondType* headBondType; |
398 |
+ |
LinkedBondType* currentBondType; |
399 |
+ |
LinkedBendType* headBendType; |
400 |
+ |
LinkedBendType* currentBendType; |
401 |
+ |
LinkedTorsionType* headTorsionType; |
402 |
+ |
LinkedTorsionType* currentTorsionType; |
403 |
+ |
|
404 |
|
} // namespace |
405 |
|
|
406 |
|
using namespace TPE; |
419 |
|
char temp[200]; |
420 |
|
char errMsg[1000]; |
421 |
|
|
422 |
+ |
headAtomType = NULL; |
423 |
+ |
currentAtomType = NULL; |
424 |
+ |
headBondType = NULL; |
425 |
+ |
currentBondType = NULL; |
426 |
+ |
headBendType = NULL; |
427 |
+ |
currentBendType = NULL; |
428 |
+ |
headTorsionType = NULL; |
429 |
+ |
currentTorsionType = NULL; |
430 |
+ |
|
431 |
|
// do the funtion wrapping |
432 |
|
wrapMeFF( this ); |
433 |
|
|
578 |
|
|
579 |
|
TraPPE_ExFF::~TraPPE_ExFF(){ |
580 |
|
|
581 |
+ |
if( headAtomType != NULL ) delete headAtomType; |
582 |
+ |
if( headBondType != NULL ) delete headBondType; |
583 |
+ |
if( headBendType != NULL ) delete headBendType; |
584 |
+ |
if( headTorsionType != NULL ) delete headTorsionType; |
585 |
+ |
|
586 |
|
#ifdef IS_MPI |
587 |
|
if( worldRank == 0 ){ |
588 |
|
#endif // is_mpi |
594 |
|
#endif // is_mpi |
595 |
|
} |
596 |
|
|
597 |
+ |
void TraPPE_ExFF::cleanMe( void ){ |
598 |
+ |
|
599 |
+ |
#ifdef IS_MPI |
600 |
+ |
|
601 |
+ |
// keep the linked lists in the mpi version |
602 |
+ |
|
603 |
+ |
#else // is_mpi |
604 |
+ |
|
605 |
+ |
// delete the linked lists in the single processor version |
606 |
+ |
|
607 |
+ |
if( headAtomType != NULL ) delete headAtomType; |
608 |
+ |
if( headBondType != NULL ) delete headBondType; |
609 |
+ |
if( headBendType != NULL ) delete headBendType; |
610 |
+ |
if( headTorsionType != NULL ) delete headTorsionType; |
611 |
+ |
|
612 |
+ |
#endif // is_mpi |
613 |
+ |
} |
614 |
+ |
|
615 |
+ |
|
616 |
|
void TraPPE_ExFF::initForceField( int ljMixRule ){ |
617 |
|
|
618 |
|
initFortran( ljMixRule, entry_plug->useReactionField ); |
619 |
|
} |
620 |
|
|
621 |
|
|
622 |
< |
void TraPPE_ExFF::initializeAtoms( void ){ |
623 |
< |
|
624 |
< |
class LinkedType { |
276 |
< |
public: |
277 |
< |
LinkedType(){ |
278 |
< |
next = NULL; |
279 |
< |
name[0] = '\0'; |
280 |
< |
} |
281 |
< |
~LinkedType(){ if( next != NULL ) delete next; } |
282 |
< |
|
283 |
< |
LinkedType* find(char* key){ |
284 |
< |
if( !strcmp(name, key) ) return this; |
285 |
< |
if( next != NULL ) return next->find(key); |
286 |
< |
return NULL; |
287 |
< |
} |
288 |
< |
|
289 |
< |
void add( atomStruct &info ){ |
290 |
< |
|
291 |
< |
// check for duplicates |
292 |
< |
|
293 |
< |
if( !strcmp( info.name, name ) ){ |
294 |
< |
sprintf( painCave.errMsg, |
295 |
< |
"Duplicate TraPPE_Ex atom type \"%s\" found in " |
296 |
< |
"the TraPPE_ExFF param file./n", |
297 |
< |
name ); |
298 |
< |
painCave.isFatal = 1; |
299 |
< |
simError(); |
300 |
< |
} |
301 |
< |
|
302 |
< |
if( next != NULL ) next->add(info); |
303 |
< |
else{ |
304 |
< |
next = new LinkedType(); |
305 |
< |
strcpy(next->name, info.name); |
306 |
< |
next->isDipole = info.isDipole; |
307 |
< |
next->isSSD = info.isSSD; |
308 |
< |
next->mass = info.mass; |
309 |
< |
next->epslon = info.epslon; |
310 |
< |
next->sigma = info.sigma; |
311 |
< |
next->dipole = info.dipole; |
312 |
< |
next->w0 = info.w0; |
313 |
< |
next->v0 = info.v0; |
314 |
< |
next->ident = info.ident; |
315 |
< |
} |
316 |
< |
} |
317 |
< |
|
318 |
< |
#ifdef IS_MPI |
319 |
< |
|
320 |
< |
void duplicate( atomStruct &info ){ |
321 |
< |
strcpy(info.name, name); |
322 |
< |
info.isDipole = isDipole; |
323 |
< |
info.isSSD = isSSD; |
324 |
< |
info.mass = mass; |
325 |
< |
info.epslon = epslon; |
326 |
< |
info.sigma = sigma; |
327 |
< |
info.dipole = dipole; |
328 |
< |
info.w0 = w0; |
329 |
< |
info.v0 = v0; |
330 |
< |
info.last = 0; |
331 |
< |
} |
332 |
< |
|
333 |
< |
|
334 |
< |
#endif |
335 |
< |
|
336 |
< |
char name[15]; |
337 |
< |
int isDipole; |
338 |
< |
int isSSD; |
339 |
< |
double mass; |
340 |
< |
double epslon; |
341 |
< |
double sigma; |
342 |
< |
double dipole; |
343 |
< |
double w0; |
344 |
< |
double v0; |
345 |
< |
int ident; |
346 |
< |
LinkedType* next; |
347 |
< |
}; |
348 |
< |
|
349 |
< |
LinkedType* headAtomType; |
350 |
< |
LinkedType* currentAtomType; |
351 |
< |
atomStruct info; |
352 |
< |
info.last = 1; // initialize last to have the last set. |
353 |
< |
// if things go well, last will be set to 0 |
354 |
< |
|
355 |
< |
|
356 |
< |
|
357 |
< |
int i; |
622 |
> |
void TraPPE_ExFF::readParams( void ){ |
623 |
> |
|
624 |
> |
int i, a, b, c, d; |
625 |
|
int identNum; |
626 |
+ |
char* atomA; |
627 |
+ |
char* atomB; |
628 |
+ |
char* atomC; |
629 |
+ |
char* atomD; |
630 |
|
|
631 |
< |
Atom** the_atoms; |
632 |
< |
int nAtoms; |
633 |
< |
the_atoms = entry_plug->atoms; |
634 |
< |
nAtoms = entry_plug->n_atoms; |
631 |
> |
atomStruct atomInfo; |
632 |
> |
bondStruct bondInfo; |
633 |
> |
bendStruct bendInfo; |
634 |
> |
torsionStruct torsionInfo; |
635 |
|
|
636 |
< |
////////////////////////////////////////////////// |
366 |
< |
// a quick water fix |
636 |
> |
bigSigma = 0.0; |
637 |
|
|
638 |
< |
double waterI[3][3]; |
639 |
< |
waterI[0][0] = 1.76958347772500; |
640 |
< |
waterI[0][1] = 0.0; |
641 |
< |
waterI[0][2] = 0.0; |
638 |
> |
atomInfo.last = 1; |
639 |
> |
bondInfo.last = 1; |
640 |
> |
bendInfo.last = 1; |
641 |
> |
torsionInfo.last = 1; |
642 |
|
|
643 |
< |
waterI[1][0] = 0.0; |
374 |
< |
waterI[1][1] = 0.614537057924513; |
375 |
< |
waterI[1][2] = 0.0; |
376 |
< |
|
377 |
< |
waterI[2][0] = 0.0; |
378 |
< |
waterI[2][1] = 0.0; |
379 |
< |
waterI[2][2] = 1.15504641980049; |
380 |
< |
|
381 |
< |
|
382 |
< |
double headI[3][3]; |
383 |
< |
headI[0][0] = 1125; |
384 |
< |
headI[0][1] = 0.0; |
385 |
< |
headI[0][2] = 0.0; |
386 |
< |
|
387 |
< |
headI[1][0] = 0.0; |
388 |
< |
headI[1][1] = 1125; |
389 |
< |
headI[1][2] = 0.0; |
390 |
< |
|
391 |
< |
headI[2][0] = 0.0; |
392 |
< |
headI[2][1] = 0.0; |
393 |
< |
headI[2][2] = 250; |
394 |
< |
|
643 |
> |
// read in the atom info |
644 |
|
|
396 |
– |
|
397 |
– |
////////////////////////////////////////////////// |
398 |
– |
|
399 |
– |
|
645 |
|
#ifdef IS_MPI |
646 |
|
if( worldRank == 0 ){ |
647 |
|
#endif |
648 |
|
|
649 |
|
// read in the atom types. |
405 |
– |
|
406 |
– |
headAtomType = new LinkedType; |
650 |
|
|
651 |
+ |
headAtomType = new LinkedAtomType; |
652 |
+ |
|
653 |
|
fastForward( "AtomTypes", "initializeAtoms" ); |
654 |
|
|
655 |
|
// we are now at the AtomTypes section. |
676 |
|
if( readLine[0] != '!' ){ |
677 |
|
|
678 |
|
// the parser returns 0 if the line was blank |
679 |
< |
if( parseAtom( readLine, lineNum, info ) ){ |
680 |
< |
info.ident = identNum; |
681 |
< |
headAtomType->add( info );; |
679 |
> |
if( parseAtom( readLine, lineNum, atomInfo ) ){ |
680 |
> |
atomInfo.ident = identNum; |
681 |
> |
headAtomType->add( atomInfo );; |
682 |
|
identNum++; |
683 |
|
} |
684 |
|
} |
696 |
|
|
697 |
|
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
698 |
|
while( currentAtomType != NULL ){ |
699 |
< |
currentAtomType->duplicate( info ); |
699 |
> |
currentAtomType->duplicate( atomInfo ); |
700 |
|
|
701 |
|
|
702 |
|
|
703 |
< |
sendFrcStruct( &info, mpiAtomStructType ); |
703 |
> |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
704 |
|
|
705 |
|
sprintf( checkPointMsg, |
706 |
|
"successfully sent TraPPE_Ex force type: \"%s\"\n", |
707 |
< |
info.name ); |
707 |
> |
atomInfo.name ); |
708 |
|
MPIcheckPoint(); |
709 |
|
|
710 |
|
currentAtomType = currentAtomType->next; |
711 |
|
} |
712 |
< |
info.last = 1; |
713 |
< |
sendFrcStruct( &info, mpiAtomStructType ); |
712 |
> |
atomInfo.last = 1; |
713 |
> |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
714 |
|
|
715 |
|
} |
716 |
|
|
720 |
|
|
721 |
|
MPIcheckPoint(); |
722 |
|
|
723 |
< |
headAtomType = new LinkedType; |
724 |
< |
recieveFrcStruct( &info, mpiAtomStructType ); |
723 |
> |
headAtomType = new LinkedAtomType; |
724 |
> |
recieveFrcStruct( &atomInfo, mpiAtomStructType ); |
725 |
|
|
726 |
< |
while( !info.last ){ |
726 |
> |
while( !atomInfo.last ){ |
727 |
|
|
728 |
|
|
729 |
|
|
730 |
< |
headAtomType->add( info ); |
730 |
> |
headAtomType->add( atomInfo ); |
731 |
|
|
732 |
|
MPIcheckPoint(); |
733 |
|
|
734 |
< |
recieveFrcStruct( &info, mpiAtomStructType ); |
734 |
> |
recieveFrcStruct( &atomInfo, mpiAtomStructType ); |
735 |
|
} |
736 |
|
} |
737 |
|
#endif // is_mpi |
750 |
|
currentAtomType = headAtomType; |
751 |
|
while( currentAtomType != NULL ){ |
752 |
|
|
508 |
– |
if(currentAtomType->isDipole) entry_plug->useReactionField = 1; |
753 |
|
if(currentAtomType->isDipole) entry_plug->useDipole = 1; |
754 |
|
if(currentAtomType->isSSD) entry_plug->useSticky = 1; |
755 |
|
|
790 |
|
#endif // is_mpi |
791 |
|
|
792 |
|
|
549 |
– |
// initialize the atoms |
550 |
– |
|
551 |
– |
double bigSigma = 0.0; |
552 |
– |
DirectionalAtom* dAtom; |
793 |
|
|
794 |
< |
for( i=0; i<nAtoms; i++ ){ |
555 |
< |
|
556 |
< |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
557 |
< |
if( currentAtomType == NULL ){ |
558 |
< |
sprintf( painCave.errMsg, |
559 |
< |
"AtomType error, %s not found in force file.\n", |
560 |
< |
the_atoms[i]->getType() ); |
561 |
< |
painCave.isFatal = 1; |
562 |
< |
simError(); |
563 |
< |
} |
564 |
< |
|
565 |
< |
the_atoms[i]->setMass( currentAtomType->mass ); |
566 |
< |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
567 |
< |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
568 |
< |
the_atoms[i]->setIdent( currentAtomType->ident ); |
569 |
< |
the_atoms[i]->setLJ(); |
570 |
< |
|
571 |
< |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
572 |
< |
|
573 |
< |
if( currentAtomType->isDipole ){ |
574 |
< |
if( the_atoms[i]->isDirectional() ){ |
575 |
< |
|
576 |
< |
dAtom = (DirectionalAtom *) the_atoms[i]; |
577 |
< |
dAtom->setMu( currentAtomType->dipole ); |
578 |
< |
dAtom->setHasDipole( 1 ); |
579 |
< |
dAtom->setJx( 0.0 ); |
580 |
< |
dAtom->setJy( 0.0 ); |
581 |
< |
dAtom->setJz( 0.0 ); |
582 |
< |
|
583 |
< |
if(!strcmp("SSD",the_atoms[i]->getType())){ |
584 |
< |
dAtom->setI( waterI ); |
585 |
< |
dAtom->setSSD( 1 ); |
586 |
< |
} |
587 |
< |
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
588 |
< |
dAtom->setI( headI ); |
589 |
< |
dAtom->setSSD( 0 ); |
590 |
< |
} |
591 |
< |
else{ |
592 |
< |
sprintf(painCave.errMsg, |
593 |
< |
"AtmType error, %s does not have a moment of inertia set.\n", |
594 |
< |
the_atoms[i]->getType() ); |
595 |
< |
painCave.isFatal = 1; |
596 |
< |
simError(); |
597 |
< |
} |
598 |
< |
entry_plug->n_dipoles++; |
599 |
< |
} |
600 |
< |
else{ |
601 |
< |
|
602 |
< |
sprintf( painCave.errMsg, |
603 |
< |
"TraPPE_ExFF error: Atom \"%s\" is a dipole, yet no standard" |
604 |
< |
" orientation was specifed in the BASS file.\n", |
605 |
< |
currentAtomType->name ); |
606 |
< |
painCave.isFatal = 1; |
607 |
< |
simError(); |
608 |
< |
} |
609 |
< |
} |
610 |
< |
else{ |
611 |
< |
if( the_atoms[i]->isDirectional() ){ |
612 |
< |
sprintf( painCave.errMsg, |
613 |
< |
"TraPPE_ExFF error: Atom \"%s\" was given a standard" |
614 |
< |
"orientation in the BASS file, yet it is not a dipole.\n", |
615 |
< |
currentAtomType->name); |
616 |
< |
painCave.isFatal = 1; |
617 |
< |
simError(); |
618 |
< |
} |
619 |
< |
} |
620 |
< |
} |
621 |
< |
|
622 |
< |
#ifdef IS_MPI |
623 |
< |
double tempBig = bigSigma; |
624 |
< |
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
625 |
< |
#endif //is_mpi |
626 |
< |
|
627 |
< |
//calc rCut and rList |
628 |
< |
|
629 |
< |
entry_plug->rCut = 2.5 * bigSigma; |
630 |
< |
|
631 |
< |
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) |
632 |
< |
entry_plug->rCut = entry_plug->box_x / 2.0; |
633 |
< |
|
634 |
< |
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) |
635 |
< |
entry_plug->rCut = entry_plug->box_y / 2.0; |
636 |
< |
|
637 |
< |
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) |
638 |
< |
entry_plug->rCut = entry_plug->box_z / 2.0; |
639 |
< |
|
640 |
< |
entry_plug->rList = entry_plug->rCut + 1.0; |
641 |
< |
|
642 |
< |
entry_plug->useLJ = 1; // use Lennard Jones is on by default |
643 |
< |
|
644 |
< |
// clean up the memory |
645 |
< |
|
646 |
< |
delete headAtomType; |
647 |
< |
|
648 |
< |
#ifdef IS_MPI |
649 |
< |
sprintf( checkPointMsg, "TraPPE_Ex atoms initialized succesfully" ); |
650 |
< |
MPIcheckPoint(); |
651 |
< |
#endif // is_mpi |
652 |
< |
|
653 |
< |
} |
654 |
< |
|
655 |
< |
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
656 |
< |
|
657 |
< |
class LinkedType { |
658 |
< |
public: |
659 |
< |
LinkedType(){ |
660 |
< |
next = NULL; |
661 |
< |
nameA[0] = '\0'; |
662 |
< |
nameB[0] = '\0'; |
663 |
< |
type[0] = '\0'; |
664 |
< |
} |
665 |
< |
~LinkedType(){ if( next != NULL ) delete next; } |
666 |
< |
|
667 |
< |
LinkedType* find(char* key1, char* key2){ |
668 |
< |
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
669 |
< |
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
670 |
< |
if( next != NULL ) return next->find(key1, key2); |
671 |
< |
return NULL; |
672 |
< |
} |
673 |
< |
|
674 |
< |
|
675 |
< |
void add( bondStruct &info ){ |
676 |
< |
|
677 |
< |
// check for duplicates |
678 |
< |
int dup = 0; |
679 |
< |
|
680 |
< |
if( !strcmp(nameA, info.nameA ) && !strcmp( nameB, info.nameB ) ) dup = 1; |
681 |
< |
if( !strcmp(nameA, info.nameB ) && !strcmp( nameB, info.nameA ) ) dup = 1; |
682 |
< |
|
683 |
< |
if(dup){ |
684 |
< |
sprintf( painCave.errMsg, |
685 |
< |
"Duplicate TraPPE_Ex bond type \"%s - %s\" found in " |
686 |
< |
"the TraPPE_ExFF param file./n", |
687 |
< |
nameA, nameB ); |
688 |
< |
painCave.isFatal = 1; |
689 |
< |
simError(); |
690 |
< |
} |
691 |
< |
|
692 |
< |
|
693 |
< |
if( next != NULL ) next->add(info); |
694 |
< |
else{ |
695 |
< |
next = new LinkedType(); |
696 |
< |
strcpy(next->nameA, info.nameA); |
697 |
< |
strcpy(next->nameB, info.nameB); |
698 |
< |
strcpy(next->type, info.type); |
699 |
< |
next->d0 = info.d0; |
700 |
< |
} |
701 |
< |
} |
702 |
< |
|
703 |
< |
#ifdef IS_MPI |
704 |
< |
void duplicate( bondStruct &info ){ |
705 |
< |
strcpy(info.nameA, nameA); |
706 |
< |
strcpy(info.nameB, nameB); |
707 |
< |
strcpy(info.type, type); |
708 |
< |
info.d0 = d0; |
709 |
< |
info.last = 0; |
710 |
< |
} |
711 |
< |
|
712 |
< |
|
713 |
< |
#endif |
714 |
< |
|
715 |
< |
char nameA[15]; |
716 |
< |
char nameB[15]; |
717 |
< |
char type[30]; |
718 |
< |
double d0; |
719 |
< |
|
720 |
< |
LinkedType* next; |
721 |
< |
}; |
722 |
< |
|
723 |
< |
|
724 |
< |
|
725 |
< |
LinkedType* headBondType; |
726 |
< |
LinkedType* currentBondType; |
727 |
< |
bondStruct info; |
728 |
< |
info.last = 1; // initialize last to have the last set. |
729 |
< |
// if things go well, last will be set to 0 |
730 |
< |
|
731 |
< |
SRI **the_sris; |
732 |
< |
Atom** the_atoms; |
733 |
< |
int nBonds; |
734 |
< |
the_sris = entry_plug->sr_interactions; |
735 |
< |
the_atoms = entry_plug->atoms; |
736 |
< |
nBonds = entry_plug->n_bonds; |
737 |
< |
|
738 |
< |
int i, a, b; |
739 |
< |
char* atomA; |
740 |
< |
char* atomB; |
794 |
> |
// read in the bonds |
795 |
|
|
796 |
|
#ifdef IS_MPI |
797 |
|
if( worldRank == 0 ){ |
799 |
|
|
800 |
|
// read in the bond types. |
801 |
|
|
802 |
< |
headBondType = new LinkedType; |
802 |
> |
headBondType = new LinkedBondType; |
803 |
|
|
804 |
|
fastForward( "BondTypes", "initializeBonds" ); |
805 |
|
|
826 |
|
if( readLine[0] != '!' ){ |
827 |
|
|
828 |
|
// the parser returns 0 if the line was blank |
829 |
< |
if( parseBond( readLine, lineNum, info ) ){ |
830 |
< |
headBondType->add( info ); |
829 |
> |
if( parseBond( readLine, lineNum, bondInfo ) ){ |
830 |
> |
headBondType->add( bondInfo ); |
831 |
|
} |
832 |
|
} |
833 |
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
844 |
|
|
845 |
|
currentBondType = headBondType; |
846 |
|
while( currentBondType != NULL ){ |
847 |
< |
currentBondType->duplicate( info ); |
848 |
< |
sendFrcStruct( &info, mpiBondStructType ); |
847 |
> |
currentBondType->duplicate( bondInfo ); |
848 |
> |
sendFrcStruct( &bondInfo, mpiBondStructType ); |
849 |
|
currentBondType = currentBondType->next; |
850 |
|
} |
851 |
< |
info.last = 1; |
852 |
< |
sendFrcStruct( &info, mpiBondStructType ); |
851 |
> |
bondInfo.last = 1; |
852 |
> |
sendFrcStruct( &bondInfo, mpiBondStructType ); |
853 |
|
|
854 |
|
} |
855 |
|
|
859 |
|
|
860 |
|
MPIcheckPoint(); |
861 |
|
|
862 |
< |
headBondType = new LinkedType; |
863 |
< |
recieveFrcStruct( &info, mpiBondStructType ); |
864 |
< |
while( !info.last ){ |
862 |
> |
headBondType = new LinkedBondType; |
863 |
> |
recieveFrcStruct( &bondInfo, mpiBondStructType ); |
864 |
> |
while( !bondInfo.last ){ |
865 |
|
|
866 |
< |
headBondType->add( info ); |
867 |
< |
recieveFrcStruct( &info, mpiBondStructType ); |
866 |
> |
headBondType->add( bondInfo ); |
867 |
> |
recieveFrcStruct( &bondInfo, mpiBondStructType ); |
868 |
|
} |
869 |
|
} |
870 |
|
#endif // is_mpi |
871 |
|
|
818 |
– |
|
819 |
– |
// initialize the Bonds |
820 |
– |
|
872 |
|
|
873 |
< |
for( i=0; i<nBonds; i++ ){ |
823 |
< |
|
824 |
< |
a = the_bonds[i].a; |
825 |
< |
b = the_bonds[i].b; |
826 |
< |
|
827 |
< |
atomA = the_atoms[a]->getType(); |
828 |
< |
atomB = the_atoms[b]->getType(); |
829 |
< |
currentBondType = headBondType->find( atomA, atomB ); |
830 |
< |
if( currentBondType == NULL ){ |
831 |
< |
sprintf( painCave.errMsg, |
832 |
< |
"BondType error, %s - %s not found in force file.\n", |
833 |
< |
atomA, atomB ); |
834 |
< |
painCave.isFatal = 1; |
835 |
< |
simError(); |
836 |
< |
} |
837 |
< |
|
838 |
< |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
839 |
< |
|
840 |
< |
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
841 |
< |
*the_atoms[b], |
842 |
< |
currentBondType->d0 ); |
843 |
< |
entry_plug->n_constraints++; |
844 |
< |
} |
845 |
< |
} |
846 |
< |
|
847 |
< |
|
848 |
< |
// clean up the memory |
849 |
< |
|
850 |
< |
delete headBondType; |
851 |
< |
|
852 |
< |
#ifdef IS_MPI |
853 |
< |
sprintf( checkPointMsg, "TraPPE_Ex bonds initialized succesfully" ); |
854 |
< |
MPIcheckPoint(); |
855 |
< |
#endif // is_mpi |
856 |
< |
|
857 |
< |
} |
858 |
< |
|
859 |
< |
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
860 |
< |
|
861 |
< |
class LinkedType { |
862 |
< |
public: |
863 |
< |
LinkedType(){ |
864 |
< |
next = NULL; |
865 |
< |
nameA[0] = '\0'; |
866 |
< |
nameB[0] = '\0'; |
867 |
< |
nameC[0] = '\0'; |
868 |
< |
type[0] = '\0'; |
869 |
< |
} |
870 |
< |
~LinkedType(){ if( next != NULL ) delete next; } |
871 |
< |
|
872 |
< |
LinkedType* find( char* key1, char* key2, char* key3 ){ |
873 |
< |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
874 |
< |
&& !strcmp( nameC, key3 ) ) return this; |
875 |
< |
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
876 |
< |
&& !strcmp( nameC, key1 ) ) return this; |
877 |
< |
if( next != NULL ) return next->find(key1, key2, key3); |
878 |
< |
return NULL; |
879 |
< |
} |
880 |
< |
|
881 |
< |
void add( bendStruct &info ){ |
882 |
< |
|
883 |
< |
// check for duplicates |
884 |
< |
int dup = 0; |
885 |
< |
|
886 |
< |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) |
887 |
< |
&& !strcmp( nameC, info.nameC ) ) dup = 1; |
888 |
< |
if( !strcmp( nameA, info.nameC ) && !strcmp( nameB, info.nameB ) |
889 |
< |
&& !strcmp( nameC, info.nameA ) ) dup = 1; |
890 |
< |
|
891 |
< |
if(dup){ |
892 |
< |
sprintf( painCave.errMsg, |
893 |
< |
"Duplicate TraPPE_Ex bend type \"%s - %s - %s\" found in " |
894 |
< |
"the TraPPE_ExFF param file./n", |
895 |
< |
nameA, nameB, nameC ); |
896 |
< |
painCave.isFatal = 1; |
897 |
< |
simError(); |
898 |
< |
} |
899 |
< |
|
900 |
< |
if( next != NULL ) next->add(info); |
901 |
< |
else{ |
902 |
< |
next = new LinkedType(); |
903 |
< |
strcpy(next->nameA, info.nameA); |
904 |
< |
strcpy(next->nameB, info.nameB); |
905 |
< |
strcpy(next->nameC, info.nameC); |
906 |
< |
strcpy(next->type, info.type); |
907 |
< |
next->k1 = info.k1; |
908 |
< |
next->k2 = info.k2; |
909 |
< |
next->k3 = info.k3; |
910 |
< |
next->t0 = info.t0; |
911 |
< |
} |
912 |
< |
} |
913 |
< |
|
914 |
< |
#ifdef IS_MPI |
915 |
< |
|
916 |
< |
void duplicate( bendStruct &info ){ |
917 |
< |
strcpy(info.nameA, nameA); |
918 |
< |
strcpy(info.nameB, nameB); |
919 |
< |
strcpy(info.nameC, nameC); |
920 |
< |
strcpy(info.type, type); |
921 |
< |
info.k1 = k1; |
922 |
< |
info.k2 = k2; |
923 |
< |
info.k3 = k3; |
924 |
< |
info.t0 = t0; |
925 |
< |
info.last = 0; |
926 |
< |
} |
927 |
< |
|
928 |
< |
#endif // is_mpi |
929 |
< |
|
930 |
< |
char nameA[15]; |
931 |
< |
char nameB[15]; |
932 |
< |
char nameC[15]; |
933 |
< |
char type[30]; |
934 |
< |
double k1, k2, k3, t0; |
935 |
< |
|
936 |
< |
LinkedType* next; |
937 |
< |
}; |
938 |
< |
|
939 |
< |
LinkedType* headBendType; |
940 |
< |
LinkedType* currentBendType; |
941 |
< |
bendStruct info; |
942 |
< |
info.last = 1; // initialize last to have the last set. |
943 |
< |
// if things go well, last will be set to 0 |
944 |
< |
|
945 |
< |
QuadraticBend* qBend; |
946 |
< |
GhostBend* gBend; |
947 |
< |
SRI **the_sris; |
948 |
< |
Atom** the_atoms; |
949 |
< |
int nBends; |
950 |
< |
the_sris = entry_plug->sr_interactions; |
951 |
< |
the_atoms = entry_plug->atoms; |
952 |
< |
nBends = entry_plug->n_bends; |
873 |
> |
// read in the bends |
874 |
|
|
954 |
– |
int i, a, b, c; |
955 |
– |
char* atomA; |
956 |
– |
char* atomB; |
957 |
– |
char* atomC; |
958 |
– |
|
959 |
– |
|
875 |
|
#ifdef IS_MPI |
876 |
|
if( worldRank == 0 ){ |
877 |
|
#endif |
878 |
|
|
879 |
|
// read in the bend types. |
880 |
|
|
881 |
< |
headBendType = new LinkedType; |
881 |
> |
headBendType = new LinkedBendType; |
882 |
|
|
883 |
|
fastForward( "BendTypes", "initializeBends" ); |
884 |
|
|
904 |
|
if( readLine[0] != '!' ){ |
905 |
|
|
906 |
|
// the parser returns 0 if the line was blank |
907 |
< |
if( parseBend( readLine, lineNum, info ) ){ |
908 |
< |
headBendType->add( info ); |
907 |
> |
if( parseBend( readLine, lineNum, bendInfo ) ){ |
908 |
> |
headBendType->add( bendInfo ); |
909 |
|
} |
910 |
|
} |
911 |
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
922 |
|
|
923 |
|
currentBendType = headBendType; |
924 |
|
while( currentBendType != NULL ){ |
925 |
< |
currentBendType->duplicate( info ); |
926 |
< |
sendFrcStruct( &info, mpiBendStructType ); |
925 |
> |
currentBendType->duplicate( bendInfo ); |
926 |
> |
sendFrcStruct( &bendInfo, mpiBendStructType ); |
927 |
|
currentBendType = currentBendType->next; |
928 |
|
} |
929 |
< |
info.last = 1; |
930 |
< |
sendFrcStruct( &info, mpiBendStructType ); |
929 |
> |
bendInfo.last = 1; |
930 |
> |
sendFrcStruct( &bendInfo, mpiBendStructType ); |
931 |
|
|
932 |
|
} |
933 |
|
|
937 |
|
|
938 |
|
MPIcheckPoint(); |
939 |
|
|
940 |
< |
headBendType = new LinkedType; |
941 |
< |
recieveFrcStruct( &info, mpiBendStructType ); |
942 |
< |
while( !info.last ){ |
940 |
> |
headBendType = new LinkedBendType; |
941 |
> |
recieveFrcStruct( &bendInfo, mpiBendStructType ); |
942 |
> |
while( !bendInfo.last ){ |
943 |
|
|
944 |
< |
headBendType->add( info ); |
945 |
< |
recieveFrcStruct( &info, mpiBendStructType ); |
944 |
> |
headBendType->add( bendInfo ); |
945 |
> |
recieveFrcStruct( &bendInfo, mpiBendStructType ); |
946 |
|
} |
947 |
|
} |
948 |
|
#endif // is_mpi |
949 |
+ |
|
950 |
+ |
|
951 |
+ |
// read in the torsions |
952 |
+ |
|
953 |
+ |
#ifdef IS_MPI |
954 |
+ |
if( worldRank == 0 ){ |
955 |
+ |
#endif |
956 |
+ |
|
957 |
+ |
// read in the torsion types. |
958 |
+ |
|
959 |
+ |
headTorsionType = new LinkedTorsionType; |
960 |
+ |
|
961 |
+ |
fastForward( "TorsionTypes", "initializeTorsions" ); |
962 |
+ |
|
963 |
+ |
// we are now at the torsionTypes section |
964 |
+ |
|
965 |
+ |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
966 |
+ |
lineNum++; |
967 |
+ |
|
968 |
+ |
|
969 |
+ |
// read a line, and start parseing out the atom types |
970 |
+ |
|
971 |
+ |
if( eof_test == NULL ){ |
972 |
+ |
sprintf( painCave.errMsg, |
973 |
+ |
"Error in reading torsions from force file at line %d.\n", |
974 |
+ |
lineNum ); |
975 |
+ |
painCave.isFatal = 1; |
976 |
+ |
simError(); |
977 |
+ |
} |
978 |
+ |
|
979 |
+ |
// stop reading at end of file, or at next section |
980 |
+ |
while( readLine[0] != '#' && eof_test != NULL ){ |
981 |
+ |
|
982 |
+ |
// toss comment lines |
983 |
+ |
if( readLine[0] != '!' ){ |
984 |
+ |
|
985 |
+ |
// the parser returns 0 if the line was blank |
986 |
+ |
if( parseTorsion( readLine, lineNum, torsionInfo ) ){ |
987 |
+ |
headTorsionType->add( torsionInfo ); |
988 |
+ |
|
989 |
+ |
} |
990 |
+ |
} |
991 |
+ |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
992 |
+ |
lineNum++; |
993 |
+ |
} |
994 |
+ |
|
995 |
+ |
#ifdef IS_MPI |
996 |
+ |
|
997 |
+ |
// send out the linked list to all the other processes |
998 |
+ |
|
999 |
+ |
sprintf( checkPointMsg, |
1000 |
+ |
"TraPPE_Ex torsion structures read successfully." ); |
1001 |
+ |
MPIcheckPoint(); |
1002 |
+ |
|
1003 |
+ |
currentTorsionType = headTorsionType; |
1004 |
+ |
while( currentTorsionType != NULL ){ |
1005 |
+ |
currentTorsionType->duplicate( torsionInfo ); |
1006 |
+ |
sendFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1007 |
+ |
currentTorsionType = currentTorsionType->next; |
1008 |
+ |
} |
1009 |
+ |
torsionInfo.last = 1; |
1010 |
+ |
sendFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1011 |
+ |
|
1012 |
+ |
} |
1013 |
+ |
|
1014 |
+ |
else{ |
1015 |
+ |
|
1016 |
+ |
// listen for node 0 to send out the force params |
1017 |
+ |
|
1018 |
+ |
MPIcheckPoint(); |
1019 |
+ |
|
1020 |
+ |
headTorsionType = new LinkedTorsionType; |
1021 |
+ |
recieveFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1022 |
+ |
while( !torsionInfo.last ){ |
1023 |
+ |
|
1024 |
+ |
headTorsionType->add( torsionInfo ); |
1025 |
+ |
recieveFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1026 |
+ |
} |
1027 |
+ |
} |
1028 |
+ |
#endif // is_mpi |
1029 |
+ |
|
1030 |
+ |
entry_plug->useLJ = 1; |
1031 |
+ |
} |
1032 |
+ |
|
1033 |
+ |
|
1034 |
+ |
|
1035 |
+ |
void TraPPE_ExFF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
1036 |
|
|
1035 |
– |
// initialize the Bends |
1037 |
|
|
1038 |
< |
int index; |
1038 |
> |
////////////////////////////////////////////////// |
1039 |
> |
// a quick water fix |
1040 |
|
|
1041 |
+ |
double waterI[3][3]; |
1042 |
+ |
waterI[0][0] = 1.76958347772500; |
1043 |
+ |
waterI[0][1] = 0.0; |
1044 |
+ |
waterI[0][2] = 0.0; |
1045 |
+ |
|
1046 |
+ |
waterI[1][0] = 0.0; |
1047 |
+ |
waterI[1][1] = 0.614537057924513; |
1048 |
+ |
waterI[1][2] = 0.0; |
1049 |
+ |
|
1050 |
+ |
waterI[2][0] = 0.0; |
1051 |
+ |
waterI[2][1] = 0.0; |
1052 |
+ |
waterI[2][2] = 1.15504641980049; |
1053 |
+ |
|
1054 |
+ |
|
1055 |
+ |
double headI[3][3]; |
1056 |
+ |
headI[0][0] = 1125; |
1057 |
+ |
headI[0][1] = 0.0; |
1058 |
+ |
headI[0][2] = 0.0; |
1059 |
+ |
|
1060 |
+ |
headI[1][0] = 0.0; |
1061 |
+ |
headI[1][1] = 1125; |
1062 |
+ |
headI[1][2] = 0.0; |
1063 |
+ |
|
1064 |
+ |
headI[2][0] = 0.0; |
1065 |
+ |
headI[2][1] = 0.0; |
1066 |
+ |
headI[2][2] = 250; |
1067 |
+ |
|
1068 |
+ |
////////////////////////////////////////////////// |
1069 |
+ |
|
1070 |
+ |
|
1071 |
+ |
// initialize the atoms |
1072 |
+ |
|
1073 |
+ |
DirectionalAtom* dAtom; |
1074 |
+ |
|
1075 |
+ |
for(int i=0; i<nAtoms; i++ ){ |
1076 |
+ |
|
1077 |
+ |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
1078 |
+ |
if( currentAtomType == NULL ){ |
1079 |
+ |
sprintf( painCave.errMsg, |
1080 |
+ |
"AtomType error, %s not found in force file.\n", |
1081 |
+ |
the_atoms[i]->getType() ); |
1082 |
+ |
painCave.isFatal = 1; |
1083 |
+ |
simError(); |
1084 |
+ |
} |
1085 |
+ |
|
1086 |
+ |
the_atoms[i]->setMass( currentAtomType->mass ); |
1087 |
+ |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
1088 |
+ |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
1089 |
+ |
the_atoms[i]->setIdent( currentAtomType->ident ); |
1090 |
+ |
the_atoms[i]->setLJ(); |
1091 |
+ |
|
1092 |
+ |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
1093 |
+ |
|
1094 |
+ |
if( currentAtomType->isDipole ){ |
1095 |
+ |
if( the_atoms[i]->isDirectional() ){ |
1096 |
+ |
|
1097 |
+ |
dAtom = (DirectionalAtom *) the_atoms[i]; |
1098 |
+ |
dAtom->setMu( currentAtomType->dipole ); |
1099 |
+ |
dAtom->setHasDipole( 1 ); |
1100 |
+ |
dAtom->setJx( 0.0 ); |
1101 |
+ |
dAtom->setJy( 0.0 ); |
1102 |
+ |
dAtom->setJz( 0.0 ); |
1103 |
+ |
|
1104 |
+ |
if(!strcmp("SSD",the_atoms[i]->getType())){ |
1105 |
+ |
dAtom->setI( waterI ); |
1106 |
+ |
dAtom->setSSD( 1 ); |
1107 |
+ |
} |
1108 |
+ |
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
1109 |
+ |
dAtom->setI( headI ); |
1110 |
+ |
dAtom->setSSD( 0 ); |
1111 |
+ |
} |
1112 |
+ |
else{ |
1113 |
+ |
sprintf(painCave.errMsg, |
1114 |
+ |
"AtmType error, %s does not have a moment of inertia set.\n", |
1115 |
+ |
the_atoms[i]->getType() ); |
1116 |
+ |
painCave.isFatal = 1; |
1117 |
+ |
simError(); |
1118 |
+ |
} |
1119 |
+ |
entry_plug->n_dipoles++; |
1120 |
+ |
} |
1121 |
+ |
else{ |
1122 |
+ |
|
1123 |
+ |
sprintf( painCave.errMsg, |
1124 |
+ |
"TraPPE_ExFF error: Atom \"%s\" is a dipole, yet no standard" |
1125 |
+ |
" orientation was specifed in the BASS file.\n", |
1126 |
+ |
currentAtomType->name ); |
1127 |
+ |
painCave.isFatal = 1; |
1128 |
+ |
simError(); |
1129 |
+ |
} |
1130 |
+ |
} |
1131 |
+ |
else{ |
1132 |
+ |
if( the_atoms[i]->isDirectional() ){ |
1133 |
+ |
sprintf( painCave.errMsg, |
1134 |
+ |
"TraPPE_ExFF error: Atom \"%s\" was given a standard" |
1135 |
+ |
"orientation in the BASS file, yet it is not a dipole.\n", |
1136 |
+ |
currentAtomType->name); |
1137 |
+ |
painCave.isFatal = 1; |
1138 |
+ |
simError(); |
1139 |
+ |
} |
1140 |
+ |
} |
1141 |
+ |
} |
1142 |
+ |
} |
1143 |
+ |
|
1144 |
+ |
void TraPPE_ExFF::initializeBonds( int nBonds, Bond** bondArray, |
1145 |
+ |
bond_pair* the_bonds ){ |
1146 |
+ |
int i,a,b; |
1147 |
+ |
char* atomA; |
1148 |
+ |
char* atomB; |
1149 |
+ |
|
1150 |
+ |
Atom** the_atoms; |
1151 |
+ |
the_atoms = entry_plug->atoms; |
1152 |
+ |
|
1153 |
+ |
|
1154 |
+ |
// initialize the Bonds |
1155 |
+ |
|
1156 |
+ |
for( i=0; i<nBonds; i++ ){ |
1157 |
+ |
|
1158 |
+ |
a = the_bonds[i].a; |
1159 |
+ |
b = the_bonds[i].b; |
1160 |
+ |
|
1161 |
+ |
atomA = the_atoms[a]->getType(); |
1162 |
+ |
atomB = the_atoms[b]->getType(); |
1163 |
+ |
currentBondType = headBondType->find( atomA, atomB ); |
1164 |
+ |
if( currentBondType == NULL ){ |
1165 |
+ |
sprintf( painCave.errMsg, |
1166 |
+ |
"BondType error, %s - %s not found in force file.\n", |
1167 |
+ |
atomA, atomB ); |
1168 |
+ |
painCave.isFatal = 1; |
1169 |
+ |
simError(); |
1170 |
+ |
} |
1171 |
+ |
|
1172 |
+ |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
1173 |
+ |
|
1174 |
+ |
bondArray[i] = new ConstrainedBond( *the_atoms[a], |
1175 |
+ |
*the_atoms[b], |
1176 |
+ |
currentBondType->d0 ); |
1177 |
+ |
entry_plug->n_constraints++; |
1178 |
+ |
} |
1179 |
+ |
} |
1180 |
+ |
} |
1181 |
+ |
|
1182 |
+ |
void TraPPE_ExFF::initializeBends( int nBends, Bend** bendArray, |
1183 |
+ |
bend_set* the_bends ){ |
1184 |
+ |
|
1185 |
+ |
QuadraticBend* qBend; |
1186 |
+ |
GhostBend* gBend; |
1187 |
+ |
Atom** the_atoms; |
1188 |
+ |
the_atoms = entry_plug->atoms; |
1189 |
+ |
|
1190 |
+ |
int i, a, b, c; |
1191 |
+ |
char* atomA; |
1192 |
+ |
char* atomB; |
1193 |
+ |
char* atomC; |
1194 |
+ |
|
1195 |
+ |
// initialize the Bends |
1196 |
+ |
|
1197 |
|
for( i=0; i<nBends; i++ ){ |
1198 |
|
|
1199 |
|
a = the_bends[i].a; |
1217 |
|
|
1218 |
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1219 |
|
|
1062 |
– |
index = i + entry_plug->n_bonds; |
1063 |
– |
|
1220 |
|
if( the_bends[i].isGhost){ |
1221 |
|
|
1222 |
|
if( the_bends[i].ghost == b ){ |
1244 |
|
currentBendType->k2, |
1245 |
|
currentBendType->k3, |
1246 |
|
currentBendType->t0 ); |
1247 |
< |
the_sris[index] = gBend; |
1247 |
> |
bendArray[i] = gBend; |
1248 |
|
} |
1249 |
|
else{ |
1250 |
|
qBend = new QuadraticBend( *the_atoms[a], |
1254 |
|
currentBendType->k2, |
1255 |
|
currentBendType->k3, |
1256 |
|
currentBendType->t0 ); |
1257 |
< |
the_sris[index] = qBend; |
1257 |
> |
bendArray[i] = qBend; |
1258 |
|
} |
1259 |
|
} |
1260 |
|
} |
1105 |
– |
|
1106 |
– |
|
1107 |
– |
// clean up the memory |
1108 |
– |
|
1109 |
– |
delete headBendType; |
1110 |
– |
|
1111 |
– |
#ifdef IS_MPI |
1112 |
– |
sprintf( checkPointMsg, "TraPPE_Ex bends initialized succesfully" ); |
1113 |
– |
MPIcheckPoint(); |
1114 |
– |
#endif // is_mpi |
1115 |
– |
|
1261 |
|
} |
1262 |
|
|
1263 |
< |
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
1263 |
> |
void TraPPE_ExFF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
1264 |
> |
torsion_set* the_torsions ){ |
1265 |
|
|
1266 |
< |
class LinkedType { |
1121 |
< |
public: |
1122 |
< |
LinkedType(){ |
1123 |
< |
next = NULL; |
1124 |
< |
nameA[0] = '\0'; |
1125 |
< |
nameB[0] = '\0'; |
1126 |
< |
nameC[0] = '\0'; |
1127 |
< |
type[0] = '\0'; |
1128 |
< |
} |
1129 |
< |
~LinkedType(){ if( next != NULL ) delete next; } |
1130 |
< |
|
1131 |
< |
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
1132 |
< |
|
1133 |
< |
|
1134 |
< |
|
1135 |
< |
|
1136 |
< |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
1137 |
< |
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
1138 |
< |
|
1139 |
< |
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
1140 |
< |
!strcmp( nameC, key2 ) && !strcmp( nameD, key1 ) ) return this; |
1141 |
< |
|
1142 |
< |
if( next != NULL ) return next->find(key1, key2, key3, key4); |
1143 |
< |
return NULL; |
1144 |
< |
} |
1145 |
< |
|
1146 |
< |
void add( torsionStruct &info ){ |
1147 |
< |
|
1148 |
< |
// check for duplicates |
1149 |
< |
int dup = 0; |
1150 |
< |
|
1151 |
< |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) && |
1152 |
< |
!strcmp( nameC, info.nameC ) && !strcmp( nameD, info.nameD ) ) dup = 1; |
1153 |
< |
|
1154 |
< |
if( !strcmp( nameA, info.nameD ) && !strcmp( nameB, info.nameC ) && |
1155 |
< |
!strcmp( nameC, info.nameB ) && !strcmp( nameD, info.nameA ) ) dup = 1; |
1156 |
< |
|
1157 |
< |
if(dup){ |
1158 |
< |
sprintf( painCave.errMsg, |
1159 |
< |
"Duplicate TraPPE_Ex torsion type \"%s - %s - %s - %s\" found in " |
1160 |
< |
"the TraPPE_ExFF param file./n", nameA, nameB, nameC, nameD ); |
1161 |
< |
painCave.isFatal = 1; |
1162 |
< |
simError(); |
1163 |
< |
} |
1164 |
< |
|
1165 |
< |
if( next != NULL ) next->add(info); |
1166 |
< |
else{ |
1167 |
< |
next = new LinkedType(); |
1168 |
< |
strcpy(next->nameA, info.nameA); |
1169 |
< |
strcpy(next->nameB, info.nameB); |
1170 |
< |
strcpy(next->nameC, info.nameC); |
1171 |
< |
strcpy(next->nameD, info.nameD); |
1172 |
< |
strcpy(next->type, info.type); |
1173 |
< |
next->k1 = info.k1; |
1174 |
< |
next->k2 = info.k2; |
1175 |
< |
next->k3 = info.k3; |
1176 |
< |
next->k4 = info.k4; |
1177 |
< |
|
1178 |
< |
} |
1179 |
< |
} |
1180 |
< |
|
1181 |
< |
#ifdef IS_MPI |
1182 |
< |
|
1183 |
< |
void duplicate( torsionStruct &info ){ |
1184 |
< |
strcpy(info.nameA, nameA); |
1185 |
< |
strcpy(info.nameB, nameB); |
1186 |
< |
strcpy(info.nameC, nameC); |
1187 |
< |
strcpy(info.nameD, nameD); |
1188 |
< |
strcpy(info.type, type); |
1189 |
< |
info.k1 = k1; |
1190 |
< |
info.k2 = k2; |
1191 |
< |
info.k3 = k3; |
1192 |
< |
info.k4 = k4; |
1193 |
< |
info.last = 0; |
1194 |
< |
} |
1195 |
< |
|
1196 |
< |
#endif |
1197 |
< |
|
1198 |
< |
char nameA[15]; |
1199 |
< |
char nameB[15]; |
1200 |
< |
char nameC[15]; |
1201 |
< |
char nameD[15]; |
1202 |
< |
char type[30]; |
1203 |
< |
double k1, k2, k3, k4; |
1204 |
< |
|
1205 |
< |
LinkedType* next; |
1206 |
< |
}; |
1207 |
< |
|
1208 |
< |
LinkedType* headTorsionType; |
1209 |
< |
LinkedType* currentTorsionType; |
1210 |
< |
torsionStruct info; |
1211 |
< |
info.last = 1; // initialize last to have the last set. |
1212 |
< |
// if things go well, last will be set to 0 |
1213 |
< |
|
1214 |
< |
int i, a, b, c, d, index; |
1266 |
> |
int i, a, b, c, d; |
1267 |
|
char* atomA; |
1268 |
|
char* atomB; |
1269 |
|
char* atomC; |
1270 |
|
char* atomD; |
1219 |
– |
CubicTorsion* cTors; |
1271 |
|
|
1272 |
< |
SRI **the_sris; |
1272 |
> |
CubicTorsion* cTors; |
1273 |
|
Atom** the_atoms; |
1223 |
– |
int nTorsions; |
1224 |
– |
the_sris = entry_plug->sr_interactions; |
1274 |
|
the_atoms = entry_plug->atoms; |
1226 |
– |
nTorsions = entry_plug->n_torsions; |
1275 |
|
|
1228 |
– |
#ifdef IS_MPI |
1229 |
– |
if( worldRank == 0 ){ |
1230 |
– |
#endif |
1231 |
– |
|
1232 |
– |
// read in the torsion types. |
1233 |
– |
|
1234 |
– |
headTorsionType = new LinkedType; |
1235 |
– |
|
1236 |
– |
fastForward( "TorsionTypes", "initializeTorsions" ); |
1237 |
– |
|
1238 |
– |
// we are now at the torsionTypes section |
1239 |
– |
|
1240 |
– |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1241 |
– |
lineNum++; |
1242 |
– |
|
1243 |
– |
|
1244 |
– |
// read a line, and start parseing out the atom types |
1245 |
– |
|
1246 |
– |
if( eof_test == NULL ){ |
1247 |
– |
sprintf( painCave.errMsg, |
1248 |
– |
"Error in reading torsions from force file at line %d.\n", |
1249 |
– |
lineNum ); |
1250 |
– |
painCave.isFatal = 1; |
1251 |
– |
simError(); |
1252 |
– |
} |
1253 |
– |
|
1254 |
– |
// stop reading at end of file, or at next section |
1255 |
– |
while( readLine[0] != '#' && eof_test != NULL ){ |
1256 |
– |
|
1257 |
– |
// toss comment lines |
1258 |
– |
if( readLine[0] != '!' ){ |
1259 |
– |
|
1260 |
– |
// the parser returns 0 if the line was blank |
1261 |
– |
if( parseTorsion( readLine, lineNum, info ) ){ |
1262 |
– |
headTorsionType->add( info ); |
1263 |
– |
|
1264 |
– |
} |
1265 |
– |
} |
1266 |
– |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1267 |
– |
lineNum++; |
1268 |
– |
} |
1269 |
– |
|
1270 |
– |
#ifdef IS_MPI |
1271 |
– |
|
1272 |
– |
// send out the linked list to all the other processes |
1273 |
– |
|
1274 |
– |
sprintf( checkPointMsg, |
1275 |
– |
"TraPPE_Ex torsion structures read successfully." ); |
1276 |
– |
MPIcheckPoint(); |
1277 |
– |
|
1278 |
– |
currentTorsionType = headTorsionType; |
1279 |
– |
while( currentTorsionType != NULL ){ |
1280 |
– |
currentTorsionType->duplicate( info ); |
1281 |
– |
sendFrcStruct( &info, mpiTorsionStructType ); |
1282 |
– |
currentTorsionType = currentTorsionType->next; |
1283 |
– |
} |
1284 |
– |
info.last = 1; |
1285 |
– |
sendFrcStruct( &info, mpiTorsionStructType ); |
1286 |
– |
|
1287 |
– |
} |
1288 |
– |
|
1289 |
– |
else{ |
1290 |
– |
|
1291 |
– |
// listen for node 0 to send out the force params |
1292 |
– |
|
1293 |
– |
MPIcheckPoint(); |
1294 |
– |
|
1295 |
– |
headTorsionType = new LinkedType; |
1296 |
– |
recieveFrcStruct( &info, mpiTorsionStructType ); |
1297 |
– |
while( !info.last ){ |
1298 |
– |
|
1299 |
– |
headTorsionType->add( info ); |
1300 |
– |
recieveFrcStruct( &info, mpiTorsionStructType ); |
1301 |
– |
} |
1302 |
– |
} |
1303 |
– |
#endif // is_mpi |
1304 |
– |
|
1276 |
|
// initialize the Torsions |
1277 |
|
|
1278 |
|
for( i=0; i<nTorsions; i++ ){ |
1297 |
|
} |
1298 |
|
|
1299 |
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1329 |
– |
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
1300 |
|
|
1301 |
|
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1302 |
|
*the_atoms[c], *the_atoms[d] ); |
1303 |
|
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1304 |
|
currentTorsionType->k3, currentTorsionType->k4 ); |
1305 |
< |
the_sris[index] = cTors; |
1305 |
> |
torsionArray[i] = cTors; |
1306 |
|
} |
1307 |
|
} |
1338 |
– |
|
1339 |
– |
|
1340 |
– |
// clean up the memory |
1341 |
– |
|
1342 |
– |
delete headTorsionType; |
1343 |
– |
|
1344 |
– |
#ifdef IS_MPI |
1345 |
– |
sprintf( checkPointMsg, "TraPPE_Ex torsions initialized succesfully" ); |
1346 |
– |
MPIcheckPoint(); |
1347 |
– |
#endif // is_mpi |
1348 |
– |
|
1308 |
|
} |
1309 |
|
|
1310 |
|
void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){ |
1519 |
|
|
1520 |
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1521 |
|
sprintf( painCave.errMsg, |
1522 |
< |
"Error parseing BondTypes: line %d\n", lineNum ); |
1522 |
> |
"Error parseing BendTypes: line %d\n", lineNum ); |
1523 |
|
painCave.isFatal = 1; |
1524 |
|
simError(); |
1525 |
|
} |
1528 |
|
|
1529 |
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1530 |
|
sprintf( painCave.errMsg, |
1531 |
< |
"Error parseing BondTypes: line %d\n", lineNum ); |
1531 |
> |
"Error parseing BendTypes: line %d\n", lineNum ); |
1532 |
|
painCave.isFatal = 1; |
1533 |
|
simError(); |
1534 |
|
} |
1537 |
|
|
1538 |
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1539 |
|
sprintf( painCave.errMsg, |
1540 |
< |
"Error parseing BondTypes: line %d\n", lineNum ); |
1540 |
> |
"Error parseing BendTypes: line %d\n", lineNum ); |
1541 |
|
painCave.isFatal = 1; |
1542 |
|
simError(); |
1543 |
|
} |