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