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 <mpi++.h> |
16 |
#include "mpiForceField.h" |
17 |
#endif // is_mpi |
18 |
|
19 |
namespace TPE { // restrict the access of the folowing to this file only. |
20 |
|
21 |
|
22 |
// Declare the structures that will be passed by MPI |
23 |
|
24 |
typedef struct{ |
25 |
char name[15]; |
26 |
double mass; |
27 |
double epslon; |
28 |
double sigma; |
29 |
double dipole; |
30 |
double w0; |
31 |
double v0; |
32 |
int isSSD; |
33 |
int isDipole; |
34 |
int ident; |
35 |
int last; // 0 -> default |
36 |
// 1 -> tells nodes to stop listening |
37 |
} atomStruct; |
38 |
|
39 |
|
40 |
typedef struct{ |
41 |
char nameA[15]; |
42 |
char nameB[15]; |
43 |
char type[30]; |
44 |
double d0; |
45 |
int last; // 0 -> default |
46 |
// 1 -> tells nodes to stop listening |
47 |
} bondStruct; |
48 |
|
49 |
|
50 |
typedef struct{ |
51 |
char nameA[15]; |
52 |
char nameB[15]; |
53 |
char nameC[15]; |
54 |
char type[30]; |
55 |
double k1, k2, k3, t0; |
56 |
int last; // 0 -> default |
57 |
// 1 -> tells nodes to stop listening |
58 |
} bendStruct; |
59 |
|
60 |
|
61 |
typedef struct{ |
62 |
char nameA[15]; |
63 |
char nameB[15]; |
64 |
char nameC[15]; |
65 |
char nameD[15]; |
66 |
char type[30]; |
67 |
double k1, k2, k3, k4; |
68 |
int last; // 0 -> default |
69 |
// 1 -> tells nodes to stop listening |
70 |
} torsionStruct; |
71 |
|
72 |
|
73 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
74 |
int parseBond( char *lineBuffer, int lineNum, bondStruct &info ); |
75 |
int parseBend( char *lineBuffer, int lineNum, bendStruct &info ); |
76 |
int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ); |
77 |
|
78 |
|
79 |
#ifdef IS_MPI |
80 |
|
81 |
MPI_Datatype mpiAtomStructType; |
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 ){ |
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|
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// 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 |
|
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if( next != NULL ) next->add(info); |
116 |
else{ |
117 |
next = new LinkedAtomType(); |
118 |
strcpy(next->name, info.name); |
119 |
next->isDipole = info.isDipole; |
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next->isSSD = info.isSSD; |
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next->mass = info.mass; |
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next->epslon = info.epslon; |
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next->sigma = info.sigma; |
124 |
next->dipole = info.dipole; |
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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); |
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info.isDipole = isDipole; |
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info.isSSD = isSSD; |
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info.mass = mass; |
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info.epslon = epslon; |
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info.sigma = sigma; |
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info.dipole = dipole; |
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info.w0 = w0; |
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info.v0 = v0; |
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info.last = 0; |
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} |
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|
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 { |
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public: |
164 |
LinkedBondType(){ |
165 |
next = NULL; |
166 |
nameA[0] = '\0'; |
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nameB[0] = '\0'; |
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type[0] = '\0'; |
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} |
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); |
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return NULL; |
177 |
} |
178 |
|
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|
180 |
void add( bondStruct &info ){ |
181 |
|
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// 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 |
|
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|
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if( next != NULL ) next->add(info); |
199 |
else{ |
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next = new LinkedBondType(); |
201 |
strcpy(next->nameA, info.nameA); |
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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 |
|
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class LinkedBendType { |
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public: |
230 |
LinkedBendType(){ |
231 |
next = NULL; |
232 |
nameA[0] = '\0'; |
233 |
nameB[0] = '\0'; |
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nameC[0] = '\0'; |
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type[0] = '\0'; |
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} |
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; |
407 |
|
408 |
|
409 |
//**************************************************************** |
410 |
// begins the actual forcefield stuff. |
411 |
//**************************************************************** |
412 |
|
413 |
|
414 |
TraPPE_ExFF::TraPPE_ExFF(){ |
415 |
|
416 |
char fileName[200]; |
417 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
418 |
char* ffPath; |
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 |
|
434 |
|
435 |
#ifdef IS_MPI |
436 |
int i; |
437 |
|
438 |
// ********************************************************************** |
439 |
// Init the atomStruct mpi type |
440 |
|
441 |
atomStruct atomProto; // mpiPrototype |
442 |
int atomBC[3] = {15,6,4}; // block counts |
443 |
MPI_Aint atomDspls[3]; // displacements |
444 |
MPI_Datatype atomMbrTypes[3]; // member mpi types |
445 |
|
446 |
MPI_Address(&atomProto.name, &atomDspls[0]); |
447 |
MPI_Address(&atomProto.mass, &atomDspls[1]); |
448 |
MPI_Address(&atomProto.isSSD, &atomDspls[2]); |
449 |
|
450 |
atomMbrTypes[0] = MPI_CHAR; |
451 |
atomMbrTypes[1] = MPI_DOUBLE; |
452 |
atomMbrTypes[2] = MPI_INT; |
453 |
|
454 |
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
455 |
|
456 |
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
457 |
MPI_Type_commit(&mpiAtomStructType); |
458 |
|
459 |
|
460 |
// ********************************************************************** |
461 |
// Init the bondStruct mpi type |
462 |
|
463 |
bondStruct bondProto; // mpiPrototype |
464 |
int bondBC[3] = {60,1,1}; // block counts |
465 |
MPI_Aint bondDspls[3]; // displacements |
466 |
MPI_Datatype bondMbrTypes[3]; // member mpi types |
467 |
|
468 |
MPI_Address(&bondProto.nameA, &bondDspls[0]); |
469 |
MPI_Address(&bondProto.d0, &bondDspls[1]); |
470 |
MPI_Address(&bondProto.last, &bondDspls[2]); |
471 |
|
472 |
bondMbrTypes[0] = MPI_CHAR; |
473 |
bondMbrTypes[1] = MPI_DOUBLE; |
474 |
bondMbrTypes[2] = MPI_INT; |
475 |
|
476 |
for (i=2; i >= 0; i--) bondDspls[i] -= bondDspls[0]; |
477 |
|
478 |
MPI_Type_struct(3, bondBC, bondDspls, bondMbrTypes, &mpiBondStructType); |
479 |
MPI_Type_commit(&mpiBondStructType); |
480 |
|
481 |
|
482 |
// ********************************************************************** |
483 |
// Init the bendStruct mpi type |
484 |
|
485 |
bendStruct bendProto; // mpiPrototype |
486 |
int bendBC[3] = {75,4,1}; // block counts |
487 |
MPI_Aint bendDspls[3]; // displacements |
488 |
MPI_Datatype bendMbrTypes[3]; // member mpi types |
489 |
|
490 |
MPI_Address(&bendProto.nameA, &bendDspls[0]); |
491 |
MPI_Address(&bendProto.k1, &bendDspls[1]); |
492 |
MPI_Address(&bendProto.last, &bendDspls[2]); |
493 |
|
494 |
bendMbrTypes[0] = MPI_CHAR; |
495 |
bendMbrTypes[1] = MPI_DOUBLE; |
496 |
bendMbrTypes[2] = MPI_INT; |
497 |
|
498 |
for (i=2; i >= 0; i--) bendDspls[i] -= bendDspls[0]; |
499 |
|
500 |
MPI_Type_struct(3, bendBC, bendDspls, bendMbrTypes, &mpiBendStructType); |
501 |
MPI_Type_commit(&mpiBendStructType); |
502 |
|
503 |
|
504 |
// ********************************************************************** |
505 |
// Init the torsionStruct mpi type |
506 |
|
507 |
torsionStruct torsionProto; // mpiPrototype |
508 |
int torsionBC[3] = {90,4,1}; // block counts |
509 |
MPI_Aint torsionDspls[3]; // displacements |
510 |
MPI_Datatype torsionMbrTypes[3]; // member mpi types |
511 |
|
512 |
MPI_Address(&torsionProto.nameA, &torsionDspls[0]); |
513 |
MPI_Address(&torsionProto.k1, &torsionDspls[1]); |
514 |
MPI_Address(&torsionProto.last, &torsionDspls[2]); |
515 |
|
516 |
torsionMbrTypes[0] = MPI_CHAR; |
517 |
torsionMbrTypes[1] = MPI_DOUBLE; |
518 |
torsionMbrTypes[2] = MPI_INT; |
519 |
|
520 |
for (i=2; i >= 0; i--) torsionDspls[i] -= torsionDspls[0]; |
521 |
|
522 |
MPI_Type_struct(3, torsionBC, torsionDspls, torsionMbrTypes, |
523 |
&mpiTorsionStructType); |
524 |
MPI_Type_commit(&mpiTorsionStructType); |
525 |
|
526 |
// *********************************************************************** |
527 |
|
528 |
if( worldRank == 0 ){ |
529 |
#endif |
530 |
|
531 |
// generate the force file name |
532 |
|
533 |
strcpy( fileName, "TraPPE_Ex.frc" ); |
534 |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
535 |
|
536 |
// attempt to open the file in the current directory first. |
537 |
|
538 |
frcFile = fopen( fileName, "r" ); |
539 |
|
540 |
if( frcFile == NULL ){ |
541 |
|
542 |
// next see if the force path enviorment variable is set |
543 |
|
544 |
ffPath = getenv( ffPath_env ); |
545 |
if( ffPath == NULL ) { |
546 |
STR_DEFINE(ffPath, FRC_PATH ); |
547 |
} |
548 |
|
549 |
|
550 |
strcpy( temp, ffPath ); |
551 |
strcat( temp, "/" ); |
552 |
strcat( temp, fileName ); |
553 |
strcpy( fileName, temp ); |
554 |
|
555 |
frcFile = fopen( fileName, "r" ); |
556 |
|
557 |
if( frcFile == NULL ){ |
558 |
|
559 |
sprintf( painCave.errMsg, |
560 |
"Error opening the force field parameter file: %s\n" |
561 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
562 |
"vairable?\n", |
563 |
fileName ); |
564 |
painCave.isFatal = 1; |
565 |
simError(); |
566 |
} |
567 |
} |
568 |
|
569 |
#ifdef IS_MPI |
570 |
} |
571 |
|
572 |
sprintf( checkPointMsg, "TraPPE_ExFF file opened sucessfully." ); |
573 |
MPIcheckPoint(); |
574 |
|
575 |
#endif // is_mpi |
576 |
} |
577 |
|
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 |
589 |
|
590 |
fclose( frcFile ); |
591 |
|
592 |
#ifdef IS_MPI |
593 |
} |
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::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 |
atomStruct atomInfo; |
632 |
bondStruct bondInfo; |
633 |
bendStruct bendInfo; |
634 |
torsionStruct torsionInfo; |
635 |
|
636 |
bigSigma = 0.0; |
637 |
|
638 |
atomInfo.last = 1; |
639 |
bondInfo.last = 1; |
640 |
bendInfo.last = 1; |
641 |
torsionInfo.last = 1; |
642 |
|
643 |
// read in the atom info |
644 |
|
645 |
#ifdef IS_MPI |
646 |
if( worldRank == 0 ){ |
647 |
#endif |
648 |
|
649 |
// read in the atom types. |
650 |
|
651 |
headAtomType = new LinkedAtomType; |
652 |
|
653 |
fastForward( "AtomTypes", "initializeAtoms" ); |
654 |
|
655 |
// we are now at the AtomTypes section. |
656 |
|
657 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
658 |
lineNum++; |
659 |
|
660 |
|
661 |
// read a line, and start parseing out the atom types |
662 |
|
663 |
if( eof_test == NULL ){ |
664 |
sprintf( painCave.errMsg, |
665 |
"Error in reading Atoms from force file at line %d.\n", |
666 |
lineNum ); |
667 |
painCave.isFatal = 1; |
668 |
simError(); |
669 |
} |
670 |
|
671 |
identNum = 1; |
672 |
// stop reading at end of file, or at next section |
673 |
while( readLine[0] != '#' && eof_test != NULL ){ |
674 |
|
675 |
// toss comment lines |
676 |
if( readLine[0] != '!' ){ |
677 |
|
678 |
// the parser returns 0 if the line was blank |
679 |
if( parseAtom( readLine, lineNum, atomInfo ) ){ |
680 |
atomInfo.ident = identNum; |
681 |
headAtomType->add( atomInfo );; |
682 |
identNum++; |
683 |
} |
684 |
} |
685 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
686 |
lineNum++; |
687 |
} |
688 |
|
689 |
#ifdef IS_MPI |
690 |
|
691 |
// send out the linked list to all the other processes |
692 |
|
693 |
sprintf( checkPointMsg, |
694 |
"TraPPE_ExFF atom structures read successfully." ); |
695 |
MPIcheckPoint(); |
696 |
|
697 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
698 |
while( currentAtomType != NULL ){ |
699 |
currentAtomType->duplicate( atomInfo ); |
700 |
|
701 |
|
702 |
|
703 |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
704 |
|
705 |
sprintf( checkPointMsg, |
706 |
"successfully sent TraPPE_Ex force type: \"%s\"\n", |
707 |
atomInfo.name ); |
708 |
MPIcheckPoint(); |
709 |
|
710 |
currentAtomType = currentAtomType->next; |
711 |
} |
712 |
atomInfo.last = 1; |
713 |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
714 |
|
715 |
} |
716 |
|
717 |
else{ |
718 |
|
719 |
// listen for node 0 to send out the force params |
720 |
|
721 |
MPIcheckPoint(); |
722 |
|
723 |
headAtomType = new LinkedAtomType; |
724 |
recieveFrcStruct( &atomInfo, mpiAtomStructType ); |
725 |
|
726 |
while( !atomInfo.last ){ |
727 |
|
728 |
|
729 |
|
730 |
headAtomType->add( atomInfo ); |
731 |
|
732 |
MPIcheckPoint(); |
733 |
|
734 |
recieveFrcStruct( &atomInfo, mpiAtomStructType ); |
735 |
} |
736 |
} |
737 |
#endif // is_mpi |
738 |
|
739 |
// call new A_types in fortran |
740 |
|
741 |
int isError; |
742 |
|
743 |
// dummy variables |
744 |
|
745 |
int isGB = 0; |
746 |
int isLJ = 1; |
747 |
double GB_dummy = 0.0; |
748 |
|
749 |
|
750 |
currentAtomType = headAtomType; |
751 |
while( currentAtomType != NULL ){ |
752 |
|
753 |
if(currentAtomType->isDipole) entry_plug->useDipole = 1; |
754 |
if(currentAtomType->isSSD) entry_plug->useSticky = 1; |
755 |
|
756 |
if( currentAtomType->name[0] != '\0' ){ |
757 |
isError = 0; |
758 |
makeAtype( &(currentAtomType->ident), |
759 |
&isLJ, |
760 |
&(currentAtomType->isSSD), |
761 |
&(currentAtomType->isDipole), |
762 |
&isGB, |
763 |
&(currentAtomType->epslon), |
764 |
&(currentAtomType->sigma), |
765 |
&(currentAtomType->dipole), |
766 |
&(currentAtomType->w0), |
767 |
&(currentAtomType->v0), |
768 |
&GB_dummy, |
769 |
&GB_dummy, |
770 |
&GB_dummy, |
771 |
&GB_dummy, |
772 |
&GB_dummy, |
773 |
&GB_dummy, |
774 |
&isError ); |
775 |
if( isError ){ |
776 |
sprintf( painCave.errMsg, |
777 |
"Error initializing the \"%s\" atom type in fortran\n", |
778 |
currentAtomType->name ); |
779 |
painCave.isFatal = 1; |
780 |
simError(); |
781 |
} |
782 |
} |
783 |
currentAtomType = currentAtomType->next; |
784 |
} |
785 |
|
786 |
#ifdef IS_MPI |
787 |
sprintf( checkPointMsg, |
788 |
"TraPPE_ExFF atom structures successfully sent to fortran\n" ); |
789 |
MPIcheckPoint(); |
790 |
#endif // is_mpi |
791 |
|
792 |
|
793 |
|
794 |
// read in the bonds |
795 |
|
796 |
#ifdef IS_MPI |
797 |
if( worldRank == 0 ){ |
798 |
#endif |
799 |
|
800 |
// read in the bond types. |
801 |
|
802 |
headBondType = new LinkedBondType; |
803 |
|
804 |
fastForward( "BondTypes", "initializeBonds" ); |
805 |
|
806 |
// we are now at the bondTypes section |
807 |
|
808 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
809 |
lineNum++; |
810 |
|
811 |
|
812 |
// read a line, and start parseing out the atom types |
813 |
|
814 |
if( eof_test == NULL ){ |
815 |
sprintf( painCave.errMsg, |
816 |
"Error in reading bonds from force file at line %d.\n", |
817 |
lineNum ); |
818 |
painCave.isFatal = 1; |
819 |
simError(); |
820 |
} |
821 |
|
822 |
// stop reading at end of file, or at next section |
823 |
while( readLine[0] != '#' && eof_test != NULL ){ |
824 |
|
825 |
// toss comment lines |
826 |
if( readLine[0] != '!' ){ |
827 |
|
828 |
// the parser returns 0 if the line was blank |
829 |
if( parseBond( readLine, lineNum, bondInfo ) ){ |
830 |
headBondType->add( bondInfo ); |
831 |
} |
832 |
} |
833 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
834 |
lineNum++; |
835 |
} |
836 |
|
837 |
#ifdef IS_MPI |
838 |
|
839 |
// send out the linked list to all the other processes |
840 |
|
841 |
sprintf( checkPointMsg, |
842 |
"TraPPE_Ex bond structures read successfully." ); |
843 |
MPIcheckPoint(); |
844 |
|
845 |
currentBondType = headBondType; |
846 |
while( currentBondType != NULL ){ |
847 |
currentBondType->duplicate( bondInfo ); |
848 |
sendFrcStruct( &bondInfo, mpiBondStructType ); |
849 |
currentBondType = currentBondType->next; |
850 |
} |
851 |
bondInfo.last = 1; |
852 |
sendFrcStruct( &bondInfo, mpiBondStructType ); |
853 |
|
854 |
} |
855 |
|
856 |
else{ |
857 |
|
858 |
// listen for node 0 to send out the force params |
859 |
|
860 |
MPIcheckPoint(); |
861 |
|
862 |
headBondType = new LinkedBondType; |
863 |
recieveFrcStruct( &bondInfo, mpiBondStructType ); |
864 |
while( !bondInfo.last ){ |
865 |
|
866 |
headBondType->add( bondInfo ); |
867 |
recieveFrcStruct( &bondInfo, mpiBondStructType ); |
868 |
} |
869 |
} |
870 |
#endif // is_mpi |
871 |
|
872 |
|
873 |
// read in the bends |
874 |
|
875 |
#ifdef IS_MPI |
876 |
if( worldRank == 0 ){ |
877 |
#endif |
878 |
|
879 |
// read in the bend types. |
880 |
|
881 |
headBendType = new LinkedBendType; |
882 |
|
883 |
fastForward( "BendTypes", "initializeBends" ); |
884 |
|
885 |
// we are now at the bendTypes section |
886 |
|
887 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
888 |
lineNum++; |
889 |
|
890 |
// read a line, and start parseing out the bend types |
891 |
|
892 |
if( eof_test == NULL ){ |
893 |
sprintf( painCave.errMsg, |
894 |
"Error in reading bends from force file at line %d.\n", |
895 |
lineNum ); |
896 |
painCave.isFatal = 1; |
897 |
simError(); |
898 |
} |
899 |
|
900 |
// stop reading at end of file, or at next section |
901 |
while( readLine[0] != '#' && eof_test != NULL ){ |
902 |
|
903 |
// toss comment lines |
904 |
if( readLine[0] != '!' ){ |
905 |
|
906 |
// the parser returns 0 if the line was blank |
907 |
if( parseBend( readLine, lineNum, bendInfo ) ){ |
908 |
headBendType->add( bendInfo ); |
909 |
} |
910 |
} |
911 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
912 |
lineNum++; |
913 |
} |
914 |
|
915 |
#ifdef IS_MPI |
916 |
|
917 |
// send out the linked list to all the other processes |
918 |
|
919 |
sprintf( checkPointMsg, |
920 |
"TraPPE_Ex bend structures read successfully." ); |
921 |
MPIcheckPoint(); |
922 |
|
923 |
currentBendType = headBendType; |
924 |
while( currentBendType != NULL ){ |
925 |
currentBendType->duplicate( bendInfo ); |
926 |
sendFrcStruct( &bendInfo, mpiBendStructType ); |
927 |
currentBendType = currentBendType->next; |
928 |
} |
929 |
bendInfo.last = 1; |
930 |
sendFrcStruct( &bendInfo, mpiBendStructType ); |
931 |
|
932 |
} |
933 |
|
934 |
else{ |
935 |
|
936 |
// listen for node 0 to send out the force params |
937 |
|
938 |
MPIcheckPoint(); |
939 |
|
940 |
headBendType = new LinkedBendType; |
941 |
recieveFrcStruct( &bendInfo, mpiBendStructType ); |
942 |
while( !bendInfo.last ){ |
943 |
|
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 |
|
1037 |
|
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 |
#ifdef IS_MPI |
1145 |
sprintf( checkPointMsg, "TraPPE_Ex atoms initialized succesfully" ); |
1146 |
MPIcheckPoint(); |
1147 |
#endif // is_mpi |
1148 |
|
1149 |
} |
1150 |
|
1151 |
void TraPPE_ExFF::initializeBonds( int nBonds, Bond** bondArray, |
1152 |
bond_pair* the_bonds ){ |
1153 |
int i,a,b; |
1154 |
char* atomA; |
1155 |
char* atomB; |
1156 |
|
1157 |
Atom** the_atoms; |
1158 |
the_atoms = entry_plug->atoms; |
1159 |
|
1160 |
|
1161 |
// initialize the Bonds |
1162 |
|
1163 |
for( i=0; i<nBonds; i++ ){ |
1164 |
|
1165 |
a = the_bonds[i].a; |
1166 |
b = the_bonds[i].b; |
1167 |
|
1168 |
atomA = the_atoms[a]->getType(); |
1169 |
atomB = the_atoms[b]->getType(); |
1170 |
currentBondType = headBondType->find( atomA, atomB ); |
1171 |
if( currentBondType == NULL ){ |
1172 |
sprintf( painCave.errMsg, |
1173 |
"BondType error, %s - %s not found in force file.\n", |
1174 |
atomA, atomB ); |
1175 |
painCave.isFatal = 1; |
1176 |
simError(); |
1177 |
} |
1178 |
|
1179 |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
1180 |
|
1181 |
bondArray[i] = new ConstrainedBond( *the_atoms[a], |
1182 |
*the_atoms[b], |
1183 |
currentBondType->d0 ); |
1184 |
entry_plug->n_constraints++; |
1185 |
} |
1186 |
} |
1187 |
|
1188 |
#ifdef IS_MPI |
1189 |
sprintf( checkPointMsg, "TraPPE_Ex bonds initialized succesfully" ); |
1190 |
MPIcheckPoint(); |
1191 |
#endif // is_mpi |
1192 |
|
1193 |
} |
1194 |
|
1195 |
void TraPPE_ExFF::initializeBends( int nBends, Bend** bendArray, |
1196 |
bend_set* the_bends ){ |
1197 |
|
1198 |
QuadraticBend* qBend; |
1199 |
GhostBend* gBend; |
1200 |
Atom** the_atoms; |
1201 |
the_atoms = entry_plug->atoms; |
1202 |
|
1203 |
int i, a, b, c; |
1204 |
char* atomA; |
1205 |
char* atomB; |
1206 |
char* atomC; |
1207 |
|
1208 |
// initialize the Bends |
1209 |
|
1210 |
for( i=0; i<nBends; i++ ){ |
1211 |
|
1212 |
a = the_bends[i].a; |
1213 |
b = the_bends[i].b; |
1214 |
c = the_bends[i].c; |
1215 |
|
1216 |
atomA = the_atoms[a]->getType(); |
1217 |
atomB = the_atoms[b]->getType(); |
1218 |
|
1219 |
if( the_bends[i].isGhost ) atomC = "GHOST"; |
1220 |
else atomC = the_atoms[c]->getType(); |
1221 |
|
1222 |
currentBendType = headBendType->find( atomA, atomB, atomC ); |
1223 |
if( currentBendType == NULL ){ |
1224 |
sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found" |
1225 |
" in force file.\n", |
1226 |
atomA, atomB, atomC ); |
1227 |
painCave.isFatal = 1; |
1228 |
simError(); |
1229 |
} |
1230 |
|
1231 |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1232 |
|
1233 |
if( the_bends[i].isGhost){ |
1234 |
|
1235 |
if( the_bends[i].ghost == b ){ |
1236 |
// do nothing |
1237 |
} |
1238 |
else if( the_bends[i].ghost == a ){ |
1239 |
c = a; |
1240 |
a = b; |
1241 |
b = a; |
1242 |
} |
1243 |
else{ |
1244 |
sprintf( painCave.errMsg, |
1245 |
"BendType error, %s - %s - %s,\n" |
1246 |
" --> central atom is not " |
1247 |
"correctly identified with the " |
1248 |
"\"ghostVectorSource = \" tag.\n", |
1249 |
atomA, atomB, atomC ); |
1250 |
painCave.isFatal = 1; |
1251 |
simError(); |
1252 |
} |
1253 |
|
1254 |
gBend = new GhostBend( *the_atoms[a], |
1255 |
*the_atoms[b] ); |
1256 |
gBend->setConstants( currentBendType->k1, |
1257 |
currentBendType->k2, |
1258 |
currentBendType->k3, |
1259 |
currentBendType->t0 ); |
1260 |
bendArray[i] = gBend; |
1261 |
} |
1262 |
else{ |
1263 |
qBend = new QuadraticBend( *the_atoms[a], |
1264 |
*the_atoms[b], |
1265 |
*the_atoms[c] ); |
1266 |
qBend->setConstants( currentBendType->k1, |
1267 |
currentBendType->k2, |
1268 |
currentBendType->k3, |
1269 |
currentBendType->t0 ); |
1270 |
bendArray[i] = qBend; |
1271 |
} |
1272 |
} |
1273 |
} |
1274 |
|
1275 |
#ifdef IS_MPI |
1276 |
sprintf( checkPointMsg, "TraPPE_Ex bends initialized succesfully" ); |
1277 |
MPIcheckPoint(); |
1278 |
#endif // is_mpi |
1279 |
|
1280 |
} |
1281 |
|
1282 |
void TraPPE_ExFF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
1283 |
torsion_set* the_torsions ){ |
1284 |
|
1285 |
int i, a, b, c, d; |
1286 |
char* atomA; |
1287 |
char* atomB; |
1288 |
char* atomC; |
1289 |
char* atomD; |
1290 |
|
1291 |
CubicTorsion* cTors; |
1292 |
Atom** the_atoms; |
1293 |
the_atoms = entry_plug->atoms; |
1294 |
|
1295 |
// initialize the Torsions |
1296 |
|
1297 |
for( i=0; i<nTorsions; i++ ){ |
1298 |
|
1299 |
a = the_torsions[i].a; |
1300 |
b = the_torsions[i].b; |
1301 |
c = the_torsions[i].c; |
1302 |
d = the_torsions[i].d; |
1303 |
|
1304 |
atomA = the_atoms[a]->getType(); |
1305 |
atomB = the_atoms[b]->getType(); |
1306 |
atomC = the_atoms[c]->getType(); |
1307 |
atomD = the_atoms[d]->getType(); |
1308 |
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1309 |
if( currentTorsionType == NULL ){ |
1310 |
sprintf( painCave.errMsg, |
1311 |
"TorsionType error, %s - %s - %s - %s not found" |
1312 |
" in force file.\n", |
1313 |
atomA, atomB, atomC, atomD ); |
1314 |
painCave.isFatal = 1; |
1315 |
simError(); |
1316 |
} |
1317 |
|
1318 |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1319 |
|
1320 |
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1321 |
*the_atoms[c], *the_atoms[d] ); |
1322 |
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1323 |
currentTorsionType->k3, currentTorsionType->k4 ); |
1324 |
torsionArray[i] = cTors; |
1325 |
} |
1326 |
} |
1327 |
|
1328 |
#ifdef IS_MPI |
1329 |
sprintf( checkPointMsg, "TraPPE_Ex torsions initialized succesfully" ); |
1330 |
MPIcheckPoint(); |
1331 |
#endif // is_mpi |
1332 |
|
1333 |
} |
1334 |
|
1335 |
void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){ |
1336 |
|
1337 |
int foundText = 0; |
1338 |
char* the_token; |
1339 |
|
1340 |
rewind( frcFile ); |
1341 |
lineNum = 0; |
1342 |
|
1343 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1344 |
lineNum++; |
1345 |
if( eof_test == NULL ){ |
1346 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
1347 |
" file is empty.\n", |
1348 |
searchOwner ); |
1349 |
painCave.isFatal = 1; |
1350 |
simError(); |
1351 |
} |
1352 |
|
1353 |
|
1354 |
while( !foundText ){ |
1355 |
while( eof_test != NULL && readLine[0] != '#' ){ |
1356 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1357 |
lineNum++; |
1358 |
} |
1359 |
if( eof_test == NULL ){ |
1360 |
sprintf( painCave.errMsg, |
1361 |
"Error fast forwarding force file for %s at " |
1362 |
"line %d: file ended unexpectedly.\n", |
1363 |
searchOwner, |
1364 |
lineNum ); |
1365 |
painCave.isFatal = 1; |
1366 |
simError(); |
1367 |
} |
1368 |
|
1369 |
the_token = strtok( readLine, " ,;\t#\n" ); |
1370 |
foundText = !strcmp( stopText, the_token ); |
1371 |
|
1372 |
if( !foundText ){ |
1373 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1374 |
lineNum++; |
1375 |
|
1376 |
if( eof_test == NULL ){ |
1377 |
sprintf( painCave.errMsg, |
1378 |
"Error fast forwarding force file for %s at " |
1379 |
"line %d: file ended unexpectedly.\n", |
1380 |
searchOwner, |
1381 |
lineNum ); |
1382 |
painCave.isFatal = 1; |
1383 |
simError(); |
1384 |
} |
1385 |
} |
1386 |
} |
1387 |
} |
1388 |
|
1389 |
|
1390 |
int TPE::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1391 |
|
1392 |
char* the_token; |
1393 |
|
1394 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1395 |
if( the_token != NULL ){ |
1396 |
|
1397 |
strcpy( info.name, the_token ); |
1398 |
|
1399 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1400 |
sprintf( painCave.errMsg, |
1401 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1402 |
painCave.isFatal = 1; |
1403 |
simError(); |
1404 |
} |
1405 |
|
1406 |
info.isDipole = atoi( the_token ); |
1407 |
|
1408 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1409 |
sprintf( painCave.errMsg, |
1410 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1411 |
painCave.isFatal = 1; |
1412 |
simError(); |
1413 |
} |
1414 |
|
1415 |
info.isSSD = atoi( the_token ); |
1416 |
|
1417 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1418 |
sprintf( painCave.errMsg, |
1419 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1420 |
painCave.isFatal = 1; |
1421 |
simError(); |
1422 |
} |
1423 |
|
1424 |
info.mass = atof( the_token ); |
1425 |
|
1426 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1427 |
sprintf( painCave.errMsg, |
1428 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1429 |
painCave.isFatal = 1; |
1430 |
simError(); |
1431 |
} |
1432 |
|
1433 |
info.epslon = atof( the_token ); |
1434 |
|
1435 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1436 |
sprintf( painCave.errMsg, |
1437 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1438 |
painCave.isFatal = 1; |
1439 |
simError(); |
1440 |
} |
1441 |
|
1442 |
info.sigma = atof( the_token ); |
1443 |
|
1444 |
if( info.isDipole ){ |
1445 |
|
1446 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1447 |
sprintf( painCave.errMsg, |
1448 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1449 |
painCave.isFatal = 1; |
1450 |
simError(); |
1451 |
} |
1452 |
|
1453 |
info.dipole = atof( the_token ); |
1454 |
} |
1455 |
else info.dipole = 0.0; |
1456 |
|
1457 |
if( info.isSSD ){ |
1458 |
|
1459 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1460 |
sprintf( painCave.errMsg, |
1461 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1462 |
painCave.isFatal = 1; |
1463 |
simError(); |
1464 |
} |
1465 |
|
1466 |
info.w0 = atof( the_token ); |
1467 |
|
1468 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1469 |
sprintf( painCave.errMsg, |
1470 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1471 |
painCave.isFatal = 1; |
1472 |
simError(); |
1473 |
} |
1474 |
|
1475 |
info.v0 = atof( the_token ); |
1476 |
} |
1477 |
else info.v0 = info.w0 = 0.0; |
1478 |
|
1479 |
return 1; |
1480 |
} |
1481 |
else return 0; |
1482 |
} |
1483 |
|
1484 |
int TPE::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1485 |
|
1486 |
char* the_token; |
1487 |
|
1488 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1489 |
if( the_token != NULL ){ |
1490 |
|
1491 |
strcpy( info.nameA, the_token ); |
1492 |
|
1493 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1494 |
sprintf( painCave.errMsg, |
1495 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1496 |
painCave.isFatal = 1; |
1497 |
simError(); |
1498 |
} |
1499 |
|
1500 |
strcpy( info.nameB, the_token ); |
1501 |
|
1502 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1503 |
sprintf( painCave.errMsg, |
1504 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1505 |
painCave.isFatal = 1; |
1506 |
simError(); |
1507 |
} |
1508 |
|
1509 |
strcpy( info.type, the_token ); |
1510 |
|
1511 |
if( !strcmp( info.type, "fixed" ) ){ |
1512 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1513 |
sprintf( painCave.errMsg, |
1514 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1515 |
painCave.isFatal = 1; |
1516 |
simError(); |
1517 |
} |
1518 |
|
1519 |
info.d0 = atof( the_token ); |
1520 |
} |
1521 |
else{ |
1522 |
sprintf( painCave.errMsg, |
1523 |
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
1524 |
info.type, |
1525 |
lineNum ); |
1526 |
painCave.isFatal = 1; |
1527 |
simError(); |
1528 |
} |
1529 |
|
1530 |
return 1; |
1531 |
} |
1532 |
else return 0; |
1533 |
} |
1534 |
|
1535 |
|
1536 |
int TPE::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1537 |
|
1538 |
char* the_token; |
1539 |
|
1540 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1541 |
if( the_token != NULL ){ |
1542 |
|
1543 |
strcpy( info.nameA, the_token ); |
1544 |
|
1545 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1546 |
sprintf( painCave.errMsg, |
1547 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1548 |
painCave.isFatal = 1; |
1549 |
simError(); |
1550 |
} |
1551 |
|
1552 |
strcpy( info.nameB, the_token ); |
1553 |
|
1554 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1555 |
sprintf( painCave.errMsg, |
1556 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1557 |
painCave.isFatal = 1; |
1558 |
simError(); |
1559 |
} |
1560 |
|
1561 |
strcpy( info.nameC, the_token ); |
1562 |
|
1563 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1564 |
sprintf( painCave.errMsg, |
1565 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1566 |
painCave.isFatal = 1; |
1567 |
simError(); |
1568 |
} |
1569 |
|
1570 |
strcpy( info.type, the_token ); |
1571 |
|
1572 |
if( !strcmp( info.type, "quadratic" ) ){ |
1573 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1574 |
sprintf( painCave.errMsg, |
1575 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1576 |
painCave.isFatal = 1; |
1577 |
simError(); |
1578 |
} |
1579 |
|
1580 |
info.k1 = atof( the_token ); |
1581 |
|
1582 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1583 |
sprintf( painCave.errMsg, |
1584 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1585 |
painCave.isFatal = 1; |
1586 |
simError(); |
1587 |
} |
1588 |
|
1589 |
info.k2 = atof( the_token ); |
1590 |
|
1591 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1592 |
sprintf( painCave.errMsg, |
1593 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1594 |
painCave.isFatal = 1; |
1595 |
simError(); |
1596 |
} |
1597 |
|
1598 |
info.k3 = atof( the_token ); |
1599 |
|
1600 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1601 |
sprintf( painCave.errMsg, |
1602 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1603 |
painCave.isFatal = 1; |
1604 |
simError(); |
1605 |
} |
1606 |
|
1607 |
info.t0 = atof( the_token ); |
1608 |
} |
1609 |
|
1610 |
else{ |
1611 |
sprintf( painCave.errMsg, |
1612 |
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
1613 |
info.type, |
1614 |
lineNum ); |
1615 |
painCave.isFatal = 1; |
1616 |
simError(); |
1617 |
} |
1618 |
|
1619 |
return 1; |
1620 |
} |
1621 |
else return 0; |
1622 |
} |
1623 |
|
1624 |
int TPE::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1625 |
|
1626 |
char* the_token; |
1627 |
|
1628 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1629 |
if( the_token != NULL ){ |
1630 |
|
1631 |
strcpy( info.nameA, the_token ); |
1632 |
|
1633 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1634 |
sprintf( painCave.errMsg, |
1635 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1636 |
painCave.isFatal = 1; |
1637 |
simError(); |
1638 |
} |
1639 |
|
1640 |
strcpy( info.nameB, the_token ); |
1641 |
|
1642 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1643 |
sprintf( painCave.errMsg, |
1644 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1645 |
painCave.isFatal = 1; |
1646 |
simError(); |
1647 |
} |
1648 |
|
1649 |
strcpy( info.nameC, the_token ); |
1650 |
|
1651 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1652 |
sprintf( painCave.errMsg, |
1653 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1654 |
painCave.isFatal = 1; |
1655 |
simError(); |
1656 |
} |
1657 |
|
1658 |
strcpy( info.nameD, the_token ); |
1659 |
|
1660 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1661 |
sprintf( painCave.errMsg, |
1662 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1663 |
painCave.isFatal = 1; |
1664 |
simError(); |
1665 |
} |
1666 |
|
1667 |
strcpy( info.type, the_token ); |
1668 |
|
1669 |
if( !strcmp( info.type, "cubic" ) ){ |
1670 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1671 |
sprintf( painCave.errMsg, |
1672 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1673 |
painCave.isFatal = 1; |
1674 |
simError(); |
1675 |
} |
1676 |
|
1677 |
info.k1 = atof( the_token ); |
1678 |
|
1679 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1680 |
sprintf( painCave.errMsg, |
1681 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1682 |
painCave.isFatal = 1; |
1683 |
simError(); |
1684 |
} |
1685 |
|
1686 |
info.k2 = atof( the_token ); |
1687 |
|
1688 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1689 |
sprintf( painCave.errMsg, |
1690 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1691 |
painCave.isFatal = 1; |
1692 |
simError(); |
1693 |
} |
1694 |
|
1695 |
info.k3 = atof( the_token ); |
1696 |
|
1697 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1698 |
sprintf( painCave.errMsg, |
1699 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1700 |
painCave.isFatal = 1; |
1701 |
simError(); |
1702 |
} |
1703 |
|
1704 |
info.k4 = atof( the_token ); |
1705 |
|
1706 |
} |
1707 |
|
1708 |
else{ |
1709 |
sprintf( painCave.errMsg, |
1710 |
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
1711 |
info.type, |
1712 |
lineNum ); |
1713 |
painCave.isFatal = 1; |
1714 |
simError(); |
1715 |
} |
1716 |
|
1717 |
return 1; |
1718 |
} |
1719 |
|
1720 |
else return 0; |
1721 |
} |