82 |
|
MPI_Datatype mpiBondStructType; |
83 |
|
MPI_Datatype mpiBendStructType; |
84 |
|
MPI_Datatype mpiTorsionStructType; |
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 LinkedType(); |
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 LinkedType(); |
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 LinkedType(); |
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 LinkedType(); |
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::initForceField( int ljMixRule ){ |
268 |
< |
|
269 |
< |
initFortran( ljMixRule, entry_plug->useReactionField ); |
270 |
< |
} |
597 |
> |
void TraPPE_ExFF::cleanMe( void ){ |
598 |
|
|
599 |
< |
|
273 |
< |
void TraPPE_ExFF::initializeAtoms( void ){ |
599 |
> |
#ifdef IS_MPI |
600 |
|
|
601 |
< |
class LinkedType { |
276 |
< |
public: |
277 |
< |
LinkedType(){ |
278 |
< |
next = NULL; |
279 |
< |
name[0] = '\0'; |
280 |
< |
} |
281 |
< |
~LinkedType(){ if( next != NULL ) delete next; } |
601 |
> |
// keep the linked lists in the mpi version |
602 |
|
|
603 |
< |
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 ){ |
603 |
> |
#else // is_mpi |
604 |
|
|
605 |
< |
// 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 |
< |
} |
605 |
> |
// delete the linked lists in the single processor version |
606 |
|
|
607 |
< |
if( next != NULL ) next->add(info); |
608 |
< |
else{ |
609 |
< |
next = new LinkedType(); |
610 |
< |
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 |
< |
} |
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 |
< |
#ifdef IS_MPI |
613 |
< |
|
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 |
< |
} |
612 |
> |
#endif // is_mpi |
613 |
> |
} |
614 |
|
|
615 |
|
|
616 |
< |
#endif |
616 |
> |
void TraPPE_ExFF::initForceField( int ljMixRule ){ |
617 |
> |
|
618 |
> |
initFortran( ljMixRule, entry_plug->useReactionField ); |
619 |
> |
} |
620 |
|
|
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 |
621 |
|
|
622 |
< |
|
622 |
> |
void TraPPE_ExFF::readParams( void ){ |
623 |
|
|
624 |
|
int i; |
625 |
|
int identNum; |
626 |
|
|
627 |
< |
Atom** the_atoms; |
628 |
< |
int nAtoms; |
629 |
< |
the_atoms = entry_plug->atoms; |
630 |
< |
nAtoms = entry_plug->n_atoms; |
627 |
> |
atomStruct atomInfo; |
628 |
> |
bondStruct bondInfo; |
629 |
> |
bendStruct bendInfo; |
630 |
> |
torsionStruct torsionInfo; |
631 |
|
|
365 |
– |
////////////////////////////////////////////////// |
366 |
– |
// a quick water fix |
367 |
– |
|
368 |
– |
double waterI[3][3]; |
369 |
– |
waterI[0][0] = 1.76958347772500; |
370 |
– |
waterI[0][1] = 0.0; |
371 |
– |
waterI[0][2] = 0.0; |
372 |
– |
|
373 |
– |
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 |
– |
|
632 |
|
|
633 |
+ |
atomInfo.last = 1; |
634 |
+ |
bondInfo.last = 1; |
635 |
+ |
bendInfo.last = 1; |
636 |
+ |
torsionInfo.last = 1; |
637 |
|
|
638 |
< |
////////////////////////////////////////////////// |
639 |
< |
|
399 |
< |
|
638 |
> |
// read in the atom info |
639 |
> |
|
640 |
|
#ifdef IS_MPI |
641 |
|
if( worldRank == 0 ){ |
642 |
|
#endif |
643 |
|
|
644 |
|
// read in the atom types. |
405 |
– |
|
406 |
– |
headAtomType = new LinkedType; |
645 |
|
|
646 |
+ |
headAtomType = new LinkedAtomType; |
647 |
+ |
|
648 |
|
fastForward( "AtomTypes", "initializeAtoms" ); |
649 |
|
|
650 |
|
// we are now at the AtomTypes section. |
671 |
|
if( readLine[0] != '!' ){ |
672 |
|
|
673 |
|
// the parser returns 0 if the line was blank |
674 |
< |
if( parseAtom( readLine, lineNum, info ) ){ |
675 |
< |
info.ident = identNum; |
676 |
< |
headAtomType->add( info );; |
674 |
> |
if( parseAtom( readLine, lineNum, atomInfo ) ){ |
675 |
> |
atomInfo.ident = identNum; |
676 |
> |
headAtomType->add( atomInfo );; |
677 |
|
identNum++; |
678 |
|
} |
679 |
|
} |
691 |
|
|
692 |
|
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
693 |
|
while( currentAtomType != NULL ){ |
694 |
< |
currentAtomType->duplicate( info ); |
694 |
> |
currentAtomType->duplicate( atomInfo ); |
695 |
|
|
696 |
|
|
697 |
|
|
698 |
< |
sendFrcStruct( &info, mpiAtomStructType ); |
698 |
> |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
699 |
|
|
700 |
|
sprintf( checkPointMsg, |
701 |
|
"successfully sent TraPPE_Ex force type: \"%s\"\n", |
702 |
< |
info.name ); |
702 |
> |
atomInfo.name ); |
703 |
|
MPIcheckPoint(); |
704 |
|
|
705 |
|
currentAtomType = currentAtomType->next; |
706 |
|
} |
707 |
< |
info.last = 1; |
708 |
< |
sendFrcStruct( &info, mpiAtomStructType ); |
707 |
> |
atomInfo.last = 1; |
708 |
> |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
709 |
|
|
710 |
|
} |
711 |
|
|
716 |
|
MPIcheckPoint(); |
717 |
|
|
718 |
|
headAtomType = new LinkedType; |
719 |
< |
recieveFrcStruct( &info, mpiAtomStructType ); |
719 |
> |
recieveFrcStruct( &atomInfo, mpiAtomStructType ); |
720 |
|
|
721 |
< |
while( !info.last ){ |
721 |
> |
while( !atomInfo.last ){ |
722 |
|
|
723 |
|
|
724 |
|
|
725 |
< |
headAtomType->add( info ); |
725 |
> |
headAtomType->add( atomInfo ); |
726 |
|
|
727 |
|
MPIcheckPoint(); |
728 |
|
|
729 |
< |
recieveFrcStruct( &info, mpiAtomStructType ); |
729 |
> |
recieveFrcStruct( &atomInfo, mpiAtomStructType ); |
730 |
|
} |
731 |
|
} |
732 |
|
#endif // is_mpi |
783 |
|
"TraPPE_ExFF atom structures successfully sent to fortran\n" ); |
784 |
|
MPIcheckPoint(); |
785 |
|
#endif // is_mpi |
786 |
+ |
|
787 |
+ |
|
788 |
|
|
789 |
+ |
// read in the bonds |
790 |
+ |
|
791 |
|
|
792 |
+ |
|
793 |
+ |
|
794 |
+ |
} |
795 |
+ |
|
796 |
+ |
|
797 |
+ |
|
798 |
+ |
void TraPPE_ExFF::initializeAtoms( void ){ |
799 |
+ |
|
800 |
+ |
|
801 |
+ |
|
802 |
+ |
|
803 |
+ |
|
804 |
+ |
|
805 |
+ |
Atom** the_atoms; |
806 |
+ |
int nAtoms; |
807 |
+ |
the_atoms = entry_plug->atoms; |
808 |
+ |
nAtoms = entry_plug->n_atoms; |
809 |
+ |
|
810 |
+ |
////////////////////////////////////////////////// |
811 |
+ |
// a quick water fix |
812 |
+ |
|
813 |
+ |
double waterI[3][3]; |
814 |
+ |
waterI[0][0] = 1.76958347772500; |
815 |
+ |
waterI[0][1] = 0.0; |
816 |
+ |
waterI[0][2] = 0.0; |
817 |
+ |
|
818 |
+ |
waterI[1][0] = 0.0; |
819 |
+ |
waterI[1][1] = 0.614537057924513; |
820 |
+ |
waterI[1][2] = 0.0; |
821 |
+ |
|
822 |
+ |
waterI[2][0] = 0.0; |
823 |
+ |
waterI[2][1] = 0.0; |
824 |
+ |
waterI[2][2] = 1.15504641980049; |
825 |
+ |
|
826 |
+ |
|
827 |
+ |
double headI[3][3]; |
828 |
+ |
headI[0][0] = 1125; |
829 |
+ |
headI[0][1] = 0.0; |
830 |
+ |
headI[0][2] = 0.0; |
831 |
+ |
|
832 |
+ |
headI[1][0] = 0.0; |
833 |
+ |
headI[1][1] = 1125; |
834 |
+ |
headI[1][2] = 0.0; |
835 |
+ |
|
836 |
+ |
headI[2][0] = 0.0; |
837 |
+ |
headI[2][1] = 0.0; |
838 |
+ |
headI[2][2] = 250; |
839 |
+ |
|
840 |
+ |
|
841 |
+ |
|
842 |
+ |
////////////////////////////////////////////////// |
843 |
+ |
|
844 |
+ |
|
845 |
+ |
|
846 |
+ |
|
847 |
|
// initialize the atoms |
848 |
|
|
849 |
|
double bigSigma = 0.0; |
953 |
|
|
954 |
|
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
955 |
|
|
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; } |
956 |
|
|
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 |
– |
|
957 |
|
|
675 |
– |
void add( bondStruct &info ){ |
676 |
– |
|
677 |
– |
// check for duplicates |
678 |
– |
int dup = 0; |
958 |
|
|
959 |
< |
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 |
< |
} |
959 |
> |
|
960 |
|
|
961 |
|
|
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; |
962 |
|
info.last = 1; // initialize last to have the last set. |
963 |
|
// if things go well, last will be set to 0 |
964 |
|
|
1092 |
|
|
1093 |
|
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
1094 |
|
|
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; } |
1095 |
|
|
1096 |
< |
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; |
1096 |
> |
|
1097 |
|
|
936 |
– |
LinkedType* next; |
937 |
– |
}; |
938 |
– |
|
939 |
– |
LinkedType* headBendType; |
940 |
– |
LinkedType* currentBendType; |
1098 |
|
bendStruct info; |
1099 |
|
info.last = 1; // initialize last to have the last set. |
1100 |
|
// if things go well, last will be set to 0 |
1274 |
|
|
1275 |
|
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
1276 |
|
|
1120 |
– |
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; } |
1277 |
|
|
1278 |
< |
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 |
< |
} |
1278 |
> |
|
1279 |
|
|
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; |
1280 |
|
torsionStruct info; |
1281 |
|
info.last = 1; // initialize last to have the last set. |
1282 |
|
// if things go well, last will be set to 0 |