1 |
#include <cstdlib> |
2 |
#include <cstdio> |
3 |
#include <cstring> |
4 |
|
5 |
#include <iostream> |
6 |
using namespace std; |
7 |
|
8 |
#include "ForceFields.hpp" |
9 |
#include "SRI.hpp" |
10 |
#include "simError.h" |
11 |
|
12 |
#include "fortranWrappers.hpp" |
13 |
|
14 |
#ifdef IS_MPI |
15 |
#include "mpiForceField.h" |
16 |
#endif // is_mpi |
17 |
|
18 |
|
19 |
// define some bond Types |
20 |
|
21 |
#define FIXED_BOND 0 |
22 |
#define HARMONIC_BOND 1 |
23 |
|
24 |
|
25 |
namespace DUFF_NS { // restrict the access of the folowing to this file only. |
26 |
|
27 |
|
28 |
// Declare the structures that will be passed by MPI |
29 |
|
30 |
typedef struct{ |
31 |
char name[15]; |
32 |
double mass; |
33 |
double epslon; |
34 |
double sigma; |
35 |
double dipole; |
36 |
double w0; |
37 |
double v0; |
38 |
int isSSD; |
39 |
int isDipole; |
40 |
int ident; |
41 |
int last; // 0 -> default |
42 |
// 1 -> tells nodes to stop listening |
43 |
} atomStruct; |
44 |
|
45 |
|
46 |
typedef struct{ |
47 |
char nameA[15]; |
48 |
char nameB[15]; |
49 |
double d0; |
50 |
double k0; |
51 |
int last; // 0 -> default |
52 |
// 1 -> tells nodes to stop listening |
53 |
int type; |
54 |
} bondStruct; |
55 |
|
56 |
|
57 |
typedef struct{ |
58 |
char nameA[15]; |
59 |
char nameB[15]; |
60 |
char nameC[15]; |
61 |
char type[30]; |
62 |
double k1, k2, k3, t0; |
63 |
int last; // 0 -> default |
64 |
// 1 -> tells nodes to stop listening |
65 |
} bendStruct; |
66 |
|
67 |
|
68 |
typedef struct{ |
69 |
char nameA[15]; |
70 |
char nameB[15]; |
71 |
char nameC[15]; |
72 |
char nameD[15]; |
73 |
char type[30]; |
74 |
double k1, k2, k3, k4; |
75 |
int last; // 0 -> default |
76 |
// 1 -> tells nodes to stop listening |
77 |
} torsionStruct; |
78 |
|
79 |
|
80 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
81 |
int parseBond( char *lineBuffer, int lineNum, bondStruct &info ); |
82 |
int parseBend( char *lineBuffer, int lineNum, bendStruct &info ); |
83 |
int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ); |
84 |
|
85 |
|
86 |
#ifdef IS_MPI |
87 |
|
88 |
MPI_Datatype mpiAtomStructType; |
89 |
MPI_Datatype mpiBondStructType; |
90 |
MPI_Datatype mpiBendStructType; |
91 |
MPI_Datatype mpiTorsionStructType; |
92 |
|
93 |
#endif |
94 |
|
95 |
class LinkedAtomType { |
96 |
public: |
97 |
LinkedAtomType(){ |
98 |
next = NULL; |
99 |
name[0] = '\0'; |
100 |
} |
101 |
~LinkedAtomType(){ if( next != NULL ) delete next; } |
102 |
|
103 |
LinkedAtomType* find(char* key){ |
104 |
if( !strcmp(name, key) ) return this; |
105 |
if( next != NULL ) return next->find(key); |
106 |
return NULL; |
107 |
} |
108 |
|
109 |
void printMe( void ){ |
110 |
|
111 |
std::cerr << "LinkedAtype " << name << ": ident = " << ident << "\n"; |
112 |
if( next != NULL ) next->printMe(); |
113 |
|
114 |
} |
115 |
|
116 |
void add( atomStruct &info ){ |
117 |
|
118 |
// check for duplicates |
119 |
|
120 |
if( !strcmp( info.name, name ) ){ |
121 |
sprintf( painCave.errMsg, |
122 |
"Duplicate DUFF atom type \"%s\" found in " |
123 |
"the DUFF param file./n", |
124 |
name ); |
125 |
painCave.isFatal = 1; |
126 |
simError(); |
127 |
} |
128 |
|
129 |
if( next != NULL ) next->add(info); |
130 |
else{ |
131 |
next = new LinkedAtomType(); |
132 |
strcpy(next->name, info.name); |
133 |
next->isDipole = info.isDipole; |
134 |
next->isSSD = info.isSSD; |
135 |
next->mass = info.mass; |
136 |
next->epslon = info.epslon; |
137 |
next->sigma = info.sigma; |
138 |
next->dipole = info.dipole; |
139 |
next->w0 = info.w0; |
140 |
next->v0 = info.v0; |
141 |
next->ident = info.ident; |
142 |
} |
143 |
} |
144 |
|
145 |
#ifdef IS_MPI |
146 |
|
147 |
void duplicate( atomStruct &info ){ |
148 |
strcpy(info.name, name); |
149 |
info.isDipole = isDipole; |
150 |
info.isSSD = isSSD; |
151 |
info.mass = mass; |
152 |
info.epslon = epslon; |
153 |
info.sigma = sigma; |
154 |
info.dipole = dipole; |
155 |
info.w0 = w0; |
156 |
info.v0 = v0; |
157 |
info.ident = ident; |
158 |
info.last = 0; |
159 |
} |
160 |
|
161 |
|
162 |
#endif |
163 |
|
164 |
char name[15]; |
165 |
int isDipole; |
166 |
int isSSD; |
167 |
double mass; |
168 |
double epslon; |
169 |
double sigma; |
170 |
double dipole; |
171 |
double w0; |
172 |
double v0; |
173 |
int ident; |
174 |
LinkedAtomType* next; |
175 |
}; |
176 |
|
177 |
class LinkedBondType { |
178 |
public: |
179 |
LinkedBondType(){ |
180 |
next = NULL; |
181 |
nameA[0] = '\0'; |
182 |
nameB[0] = '\0'; |
183 |
} |
184 |
~LinkedBondType(){ if( next != NULL ) delete next; } |
185 |
|
186 |
LinkedBondType* find(char* key1, char* key2){ |
187 |
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
188 |
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
189 |
if( next != NULL ) return next->find(key1, key2); |
190 |
return NULL; |
191 |
} |
192 |
|
193 |
|
194 |
void add( bondStruct &info ){ |
195 |
|
196 |
// check for duplicates |
197 |
int dup = 0; |
198 |
|
199 |
if( !strcmp(nameA, info.nameA ) && !strcmp( nameB, info.nameB ) ) dup = 1; |
200 |
if( !strcmp(nameA, info.nameB ) && !strcmp( nameB, info.nameA ) ) dup = 1; |
201 |
|
202 |
if(dup){ |
203 |
sprintf( painCave.errMsg, |
204 |
"Duplicate DUFF bond type \"%s - %s\" found in " |
205 |
"the DUFF param file./n", |
206 |
nameA, nameB ); |
207 |
painCave.isFatal = 1; |
208 |
simError(); |
209 |
} |
210 |
|
211 |
|
212 |
if( next != NULL ) next->add(info); |
213 |
else{ |
214 |
next = new LinkedBondType(); |
215 |
strcpy(next->nameA, info.nameA); |
216 |
strcpy(next->nameB, info.nameB); |
217 |
next->type = info.type; |
218 |
next->d0 = info.d0; |
219 |
next->k0 = info.k0; |
220 |
} |
221 |
} |
222 |
|
223 |
#ifdef IS_MPI |
224 |
void duplicate( bondStruct &info ){ |
225 |
strcpy(info.nameA, nameA); |
226 |
strcpy(info.nameB, nameB); |
227 |
info.type = type; |
228 |
info.d0 = d0; |
229 |
info.k0 = k0; |
230 |
info.last = 0; |
231 |
} |
232 |
|
233 |
|
234 |
#endif |
235 |
|
236 |
char nameA[15]; |
237 |
char nameB[15]; |
238 |
int type; |
239 |
double d0; |
240 |
double k0; |
241 |
|
242 |
LinkedBondType* next; |
243 |
}; |
244 |
|
245 |
class LinkedBendType { |
246 |
public: |
247 |
LinkedBendType(){ |
248 |
next = NULL; |
249 |
nameA[0] = '\0'; |
250 |
nameB[0] = '\0'; |
251 |
nameC[0] = '\0'; |
252 |
type[0] = '\0'; |
253 |
} |
254 |
~LinkedBendType(){ if( next != NULL ) delete next; } |
255 |
|
256 |
LinkedBendType* find( char* key1, char* key2, char* key3 ){ |
257 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
258 |
&& !strcmp( nameC, key3 ) ) return this; |
259 |
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
260 |
&& !strcmp( nameC, key1 ) ) return this; |
261 |
if( next != NULL ) return next->find(key1, key2, key3); |
262 |
return NULL; |
263 |
} |
264 |
|
265 |
void add( bendStruct &info ){ |
266 |
|
267 |
// check for duplicates |
268 |
int dup = 0; |
269 |
|
270 |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) |
271 |
&& !strcmp( nameC, info.nameC ) ) dup = 1; |
272 |
if( !strcmp( nameA, info.nameC ) && !strcmp( nameB, info.nameB ) |
273 |
&& !strcmp( nameC, info.nameA ) ) dup = 1; |
274 |
|
275 |
if(dup){ |
276 |
sprintf( painCave.errMsg, |
277 |
"Duplicate DUFF bend type \"%s - %s - %s\" found in " |
278 |
"the DUFF param file./n", |
279 |
nameA, nameB, nameC ); |
280 |
painCave.isFatal = 1; |
281 |
simError(); |
282 |
} |
283 |
|
284 |
if( next != NULL ) next->add(info); |
285 |
else{ |
286 |
next = new LinkedBendType(); |
287 |
strcpy(next->nameA, info.nameA); |
288 |
strcpy(next->nameB, info.nameB); |
289 |
strcpy(next->nameC, info.nameC); |
290 |
strcpy(next->type, info.type); |
291 |
next->k1 = info.k1; |
292 |
next->k2 = info.k2; |
293 |
next->k3 = info.k3; |
294 |
next->t0 = info.t0; |
295 |
} |
296 |
} |
297 |
|
298 |
#ifdef IS_MPI |
299 |
|
300 |
void duplicate( bendStruct &info ){ |
301 |
strcpy(info.nameA, nameA); |
302 |
strcpy(info.nameB, nameB); |
303 |
strcpy(info.nameC, nameC); |
304 |
strcpy(info.type, type); |
305 |
info.k1 = k1; |
306 |
info.k2 = k2; |
307 |
info.k3 = k3; |
308 |
info.t0 = t0; |
309 |
info.last = 0; |
310 |
} |
311 |
|
312 |
#endif // is_mpi |
313 |
|
314 |
char nameA[15]; |
315 |
char nameB[15]; |
316 |
char nameC[15]; |
317 |
char type[30]; |
318 |
double k1, k2, k3, t0; |
319 |
|
320 |
LinkedBendType* next; |
321 |
}; |
322 |
|
323 |
class LinkedTorsionType { |
324 |
public: |
325 |
LinkedTorsionType(){ |
326 |
next = NULL; |
327 |
nameA[0] = '\0'; |
328 |
nameB[0] = '\0'; |
329 |
nameC[0] = '\0'; |
330 |
type[0] = '\0'; |
331 |
} |
332 |
~LinkedTorsionType(){ if( next != NULL ) delete next; } |
333 |
|
334 |
LinkedTorsionType* find( char* key1, char* key2, char* key3, char* key4 ){ |
335 |
|
336 |
|
337 |
|
338 |
|
339 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
340 |
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
341 |
|
342 |
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
343 |
!strcmp( nameC, key2 ) && !strcmp( nameD, key1 ) ) return this; |
344 |
|
345 |
if( next != NULL ) return next->find(key1, key2, key3, key4); |
346 |
return NULL; |
347 |
} |
348 |
|
349 |
void add( torsionStruct &info ){ |
350 |
|
351 |
// check for duplicates |
352 |
int dup = 0; |
353 |
|
354 |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) && |
355 |
!strcmp( nameC, info.nameC ) && !strcmp( nameD, info.nameD ) ) dup = 1; |
356 |
|
357 |
if( !strcmp( nameA, info.nameD ) && !strcmp( nameB, info.nameC ) && |
358 |
!strcmp( nameC, info.nameB ) && !strcmp( nameD, info.nameA ) ) dup = 1; |
359 |
|
360 |
if(dup){ |
361 |
sprintf( painCave.errMsg, |
362 |
"Duplicate DUFF torsion type \"%s - %s - %s - %s\" found in " |
363 |
"the DUFF param file./n", nameA, nameB, nameC, nameD ); |
364 |
painCave.isFatal = 1; |
365 |
simError(); |
366 |
} |
367 |
|
368 |
if( next != NULL ) next->add(info); |
369 |
else{ |
370 |
next = new LinkedTorsionType(); |
371 |
strcpy(next->nameA, info.nameA); |
372 |
strcpy(next->nameB, info.nameB); |
373 |
strcpy(next->nameC, info.nameC); |
374 |
strcpy(next->nameD, info.nameD); |
375 |
strcpy(next->type, info.type); |
376 |
next->k1 = info.k1; |
377 |
next->k2 = info.k2; |
378 |
next->k3 = info.k3; |
379 |
next->k4 = info.k4; |
380 |
|
381 |
} |
382 |
} |
383 |
|
384 |
#ifdef IS_MPI |
385 |
|
386 |
void duplicate( torsionStruct &info ){ |
387 |
strcpy(info.nameA, nameA); |
388 |
strcpy(info.nameB, nameB); |
389 |
strcpy(info.nameC, nameC); |
390 |
strcpy(info.nameD, nameD); |
391 |
strcpy(info.type, type); |
392 |
info.k1 = k1; |
393 |
info.k2 = k2; |
394 |
info.k3 = k3; |
395 |
info.k4 = k4; |
396 |
info.last = 0; |
397 |
} |
398 |
|
399 |
#endif |
400 |
|
401 |
char nameA[15]; |
402 |
char nameB[15]; |
403 |
char nameC[15]; |
404 |
char nameD[15]; |
405 |
char type[30]; |
406 |
double k1, k2, k3, k4; |
407 |
|
408 |
LinkedTorsionType* next; |
409 |
}; |
410 |
|
411 |
|
412 |
LinkedAtomType* headAtomType; |
413 |
LinkedAtomType* currentAtomType; |
414 |
LinkedBondType* headBondType; |
415 |
LinkedBondType* currentBondType; |
416 |
LinkedBendType* headBendType; |
417 |
LinkedBendType* currentBendType; |
418 |
LinkedTorsionType* headTorsionType; |
419 |
LinkedTorsionType* currentTorsionType; |
420 |
|
421 |
} // namespace |
422 |
|
423 |
using namespace DUFF_NS; |
424 |
|
425 |
|
426 |
//**************************************************************** |
427 |
// begins the actual forcefield stuff. |
428 |
//**************************************************************** |
429 |
|
430 |
|
431 |
DUFF::DUFF(){ |
432 |
|
433 |
char fileName[200]; |
434 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
435 |
char* ffPath; |
436 |
char temp[200]; |
437 |
char errMsg[1000]; |
438 |
|
439 |
headAtomType = NULL; |
440 |
currentAtomType = NULL; |
441 |
headBondType = NULL; |
442 |
currentBondType = NULL; |
443 |
headBendType = NULL; |
444 |
currentBendType = NULL; |
445 |
headTorsionType = NULL; |
446 |
currentTorsionType = NULL; |
447 |
|
448 |
// do the funtion wrapping |
449 |
wrapMeFF( this ); |
450 |
|
451 |
|
452 |
#ifdef IS_MPI |
453 |
int i; |
454 |
|
455 |
// ********************************************************************** |
456 |
// Init the atomStruct mpi type |
457 |
|
458 |
atomStruct atomProto; // mpiPrototype |
459 |
int atomBC[3] = {15,6,4}; // block counts |
460 |
MPI_Aint atomDspls[3]; // displacements |
461 |
MPI_Datatype atomMbrTypes[3]; // member mpi types |
462 |
|
463 |
MPI_Address(&atomProto.name, &atomDspls[0]); |
464 |
MPI_Address(&atomProto.mass, &atomDspls[1]); |
465 |
MPI_Address(&atomProto.isSSD, &atomDspls[2]); |
466 |
|
467 |
atomMbrTypes[0] = MPI_CHAR; |
468 |
atomMbrTypes[1] = MPI_DOUBLE; |
469 |
atomMbrTypes[2] = MPI_INT; |
470 |
|
471 |
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
472 |
|
473 |
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
474 |
MPI_Type_commit(&mpiAtomStructType); |
475 |
|
476 |
|
477 |
// ********************************************************************** |
478 |
// Init the bondStruct mpi type |
479 |
|
480 |
bondStruct bondProto; // mpiPrototype |
481 |
int bondBC[3] = {30,2,2}; // block counts |
482 |
MPI_Aint bondDspls[3]; // displacements |
483 |
MPI_Datatype bondMbrTypes[3]; // member mpi types |
484 |
|
485 |
MPI_Address(&bondProto.nameA, &bondDspls[0]); |
486 |
MPI_Address(&bondProto.d0, &bondDspls[1]); |
487 |
MPI_Address(&bondProto.last, &bondDspls[2]); |
488 |
|
489 |
bondMbrTypes[0] = MPI_CHAR; |
490 |
bondMbrTypes[1] = MPI_DOUBLE; |
491 |
bondMbrTypes[2] = MPI_INT; |
492 |
|
493 |
for (i=2; i >= 0; i--) bondDspls[i] -= bondDspls[0]; |
494 |
|
495 |
MPI_Type_struct(3, bondBC, bondDspls, bondMbrTypes, &mpiBondStructType); |
496 |
MPI_Type_commit(&mpiBondStructType); |
497 |
|
498 |
|
499 |
// ********************************************************************** |
500 |
// Init the bendStruct mpi type |
501 |
|
502 |
bendStruct bendProto; // mpiPrototype |
503 |
int bendBC[3] = {75,4,1}; // block counts |
504 |
MPI_Aint bendDspls[3]; // displacements |
505 |
MPI_Datatype bendMbrTypes[3]; // member mpi types |
506 |
|
507 |
MPI_Address(&bendProto.nameA, &bendDspls[0]); |
508 |
MPI_Address(&bendProto.k1, &bendDspls[1]); |
509 |
MPI_Address(&bendProto.last, &bendDspls[2]); |
510 |
|
511 |
bendMbrTypes[0] = MPI_CHAR; |
512 |
bendMbrTypes[1] = MPI_DOUBLE; |
513 |
bendMbrTypes[2] = MPI_INT; |
514 |
|
515 |
for (i=2; i >= 0; i--) bendDspls[i] -= bendDspls[0]; |
516 |
|
517 |
MPI_Type_struct(3, bendBC, bendDspls, bendMbrTypes, &mpiBendStructType); |
518 |
MPI_Type_commit(&mpiBendStructType); |
519 |
|
520 |
|
521 |
// ********************************************************************** |
522 |
// Init the torsionStruct mpi type |
523 |
|
524 |
torsionStruct torsionProto; // mpiPrototype |
525 |
int torsionBC[3] = {90,4,1}; // block counts |
526 |
MPI_Aint torsionDspls[3]; // displacements |
527 |
MPI_Datatype torsionMbrTypes[3]; // member mpi types |
528 |
|
529 |
MPI_Address(&torsionProto.nameA, &torsionDspls[0]); |
530 |
MPI_Address(&torsionProto.k1, &torsionDspls[1]); |
531 |
MPI_Address(&torsionProto.last, &torsionDspls[2]); |
532 |
|
533 |
torsionMbrTypes[0] = MPI_CHAR; |
534 |
torsionMbrTypes[1] = MPI_DOUBLE; |
535 |
torsionMbrTypes[2] = MPI_INT; |
536 |
|
537 |
for (i=2; i >= 0; i--) torsionDspls[i] -= torsionDspls[0]; |
538 |
|
539 |
MPI_Type_struct(3, torsionBC, torsionDspls, torsionMbrTypes, |
540 |
&mpiTorsionStructType); |
541 |
MPI_Type_commit(&mpiTorsionStructType); |
542 |
|
543 |
// *********************************************************************** |
544 |
|
545 |
if( worldRank == 0 ){ |
546 |
#endif |
547 |
|
548 |
// generate the force file name |
549 |
|
550 |
strcpy( fileName, "DUFF.frc" ); |
551 |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
552 |
|
553 |
// attempt to open the file in the current directory first. |
554 |
|
555 |
frcFile = fopen( fileName, "r" ); |
556 |
|
557 |
if( frcFile == NULL ){ |
558 |
|
559 |
// next see if the force path enviorment variable is set |
560 |
|
561 |
ffPath = getenv( ffPath_env ); |
562 |
if( ffPath == NULL ) { |
563 |
STR_DEFINE(ffPath, FRC_PATH ); |
564 |
} |
565 |
|
566 |
|
567 |
strcpy( temp, ffPath ); |
568 |
strcat( temp, "/" ); |
569 |
strcat( temp, fileName ); |
570 |
strcpy( fileName, temp ); |
571 |
|
572 |
frcFile = fopen( fileName, "r" ); |
573 |
|
574 |
if( frcFile == NULL ){ |
575 |
|
576 |
sprintf( painCave.errMsg, |
577 |
"Error opening the force field parameter file: %s\n" |
578 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
579 |
"vairable?\n", |
580 |
fileName ); |
581 |
painCave.isFatal = 1; |
582 |
simError(); |
583 |
} |
584 |
} |
585 |
|
586 |
#ifdef IS_MPI |
587 |
} |
588 |
|
589 |
sprintf( checkPointMsg, "DUFF file opened sucessfully." ); |
590 |
MPIcheckPoint(); |
591 |
|
592 |
#endif // is_mpi |
593 |
} |
594 |
|
595 |
|
596 |
DUFF::~DUFF(){ |
597 |
|
598 |
if( headAtomType != NULL ) delete headAtomType; |
599 |
if( headBondType != NULL ) delete headBondType; |
600 |
if( headBendType != NULL ) delete headBendType; |
601 |
if( headTorsionType != NULL ) delete headTorsionType; |
602 |
|
603 |
#ifdef IS_MPI |
604 |
if( worldRank == 0 ){ |
605 |
#endif // is_mpi |
606 |
|
607 |
fclose( frcFile ); |
608 |
|
609 |
#ifdef IS_MPI |
610 |
} |
611 |
#endif // is_mpi |
612 |
} |
613 |
|
614 |
void DUFF::cleanMe( void ){ |
615 |
|
616 |
#ifdef IS_MPI |
617 |
|
618 |
// keep the linked lists in the mpi version |
619 |
|
620 |
#else // is_mpi |
621 |
|
622 |
// delete the linked lists in the single processor version |
623 |
|
624 |
if( headAtomType != NULL ) delete headAtomType; |
625 |
if( headBondType != NULL ) delete headBondType; |
626 |
if( headBendType != NULL ) delete headBendType; |
627 |
if( headTorsionType != NULL ) delete headTorsionType; |
628 |
|
629 |
#endif // is_mpi |
630 |
} |
631 |
|
632 |
|
633 |
void DUFF::initForceField( int ljMixRule ){ |
634 |
|
635 |
initFortran( ljMixRule, entry_plug->useReactionField ); |
636 |
} |
637 |
|
638 |
|
639 |
void DUFF::readParams( void ){ |
640 |
|
641 |
int i, a, b, c, d; |
642 |
int identNum; |
643 |
char* atomA; |
644 |
char* atomB; |
645 |
char* atomC; |
646 |
char* atomD; |
647 |
|
648 |
atomStruct atomInfo; |
649 |
bondStruct bondInfo; |
650 |
bendStruct bendInfo; |
651 |
torsionStruct torsionInfo; |
652 |
|
653 |
bigSigma = 0.0; |
654 |
|
655 |
atomInfo.last = 1; |
656 |
bondInfo.last = 1; |
657 |
bendInfo.last = 1; |
658 |
torsionInfo.last = 1; |
659 |
|
660 |
// read in the atom info |
661 |
|
662 |
#ifdef IS_MPI |
663 |
if( worldRank == 0 ){ |
664 |
#endif |
665 |
|
666 |
// read in the atom types. |
667 |
|
668 |
headAtomType = new LinkedAtomType; |
669 |
|
670 |
fastForward( "AtomTypes", "initializeAtoms" ); |
671 |
|
672 |
// we are now at the AtomTypes section. |
673 |
|
674 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
675 |
lineNum++; |
676 |
|
677 |
|
678 |
// read a line, and start parseing out the atom types |
679 |
|
680 |
if( eof_test == NULL ){ |
681 |
sprintf( painCave.errMsg, |
682 |
"Error in reading Atoms from force file at line %d.\n", |
683 |
lineNum ); |
684 |
painCave.isFatal = 1; |
685 |
simError(); |
686 |
} |
687 |
|
688 |
identNum = 1; |
689 |
// stop reading at end of file, or at next section |
690 |
while( readLine[0] != '#' && eof_test != NULL ){ |
691 |
|
692 |
// toss comment lines |
693 |
if( readLine[0] != '!' ){ |
694 |
|
695 |
// the parser returns 0 if the line was blank |
696 |
if( parseAtom( readLine, lineNum, atomInfo ) ){ |
697 |
atomInfo.ident = identNum; |
698 |
headAtomType->add( atomInfo );; |
699 |
identNum++; |
700 |
} |
701 |
} |
702 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
703 |
lineNum++; |
704 |
} |
705 |
|
706 |
#ifdef IS_MPI |
707 |
|
708 |
// send out the linked list to all the other processes |
709 |
|
710 |
sprintf( checkPointMsg, |
711 |
"DUFF atom structures read successfully." ); |
712 |
MPIcheckPoint(); |
713 |
|
714 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
715 |
while( currentAtomType != NULL ){ |
716 |
currentAtomType->duplicate( atomInfo ); |
717 |
|
718 |
|
719 |
|
720 |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
721 |
|
722 |
sprintf( checkPointMsg, |
723 |
"successfully sent DUFF force type: \"%s\"\n", |
724 |
atomInfo.name ); |
725 |
MPIcheckPoint(); |
726 |
|
727 |
currentAtomType = currentAtomType->next; |
728 |
} |
729 |
atomInfo.last = 1; |
730 |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
731 |
|
732 |
} |
733 |
|
734 |
else{ |
735 |
|
736 |
// listen for node 0 to send out the force params |
737 |
|
738 |
MPIcheckPoint(); |
739 |
|
740 |
headAtomType = new LinkedAtomType; |
741 |
recieveFrcStruct( &atomInfo, mpiAtomStructType ); |
742 |
|
743 |
while( !atomInfo.last ){ |
744 |
|
745 |
|
746 |
|
747 |
headAtomType->add( atomInfo ); |
748 |
|
749 |
MPIcheckPoint(); |
750 |
|
751 |
recieveFrcStruct( &atomInfo, mpiAtomStructType ); |
752 |
} |
753 |
} |
754 |
|
755 |
#endif // is_mpi |
756 |
|
757 |
|
758 |
|
759 |
// call new A_types in fortran |
760 |
|
761 |
int isError; |
762 |
|
763 |
// dummy variables |
764 |
|
765 |
int isGB = 0; |
766 |
int isLJ = 1; |
767 |
int isEAM =0; |
768 |
double GB_dummy = 0.0; |
769 |
|
770 |
|
771 |
currentAtomType = headAtomType->next;; |
772 |
while( currentAtomType != NULL ){ |
773 |
|
774 |
if(currentAtomType->isDipole) entry_plug->useDipole = 1; |
775 |
if(currentAtomType->isSSD) { |
776 |
entry_plug->useSticky = 1; |
777 |
set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0)); |
778 |
} |
779 |
|
780 |
if( currentAtomType->name[0] != '\0' ){ |
781 |
isError = 0; |
782 |
makeAtype( &(currentAtomType->ident), |
783 |
&isLJ, |
784 |
&(currentAtomType->isSSD), |
785 |
&(currentAtomType->isDipole), |
786 |
&isGB, |
787 |
&isEAM, |
788 |
&(currentAtomType->epslon), |
789 |
&(currentAtomType->sigma), |
790 |
&(currentAtomType->dipole), |
791 |
&isError ); |
792 |
if( isError ){ |
793 |
sprintf( painCave.errMsg, |
794 |
"Error initializing the \"%s\" atom type in fortran\n", |
795 |
currentAtomType->name ); |
796 |
painCave.isFatal = 1; |
797 |
simError(); |
798 |
} |
799 |
} |
800 |
currentAtomType = currentAtomType->next; |
801 |
} |
802 |
|
803 |
#ifdef IS_MPI |
804 |
sprintf( checkPointMsg, |
805 |
"DUFF atom structures successfully sent to fortran\n" ); |
806 |
MPIcheckPoint(); |
807 |
#endif // is_mpi |
808 |
|
809 |
|
810 |
|
811 |
// read in the bonds |
812 |
|
813 |
#ifdef IS_MPI |
814 |
if( worldRank == 0 ){ |
815 |
#endif |
816 |
|
817 |
// read in the bond types. |
818 |
|
819 |
headBondType = new LinkedBondType; |
820 |
|
821 |
fastForward( "BondTypes", "initializeBonds" ); |
822 |
|
823 |
// we are now at the bondTypes section |
824 |
|
825 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
826 |
lineNum++; |
827 |
|
828 |
|
829 |
// read a line, and start parseing out the atom types |
830 |
|
831 |
if( eof_test == NULL ){ |
832 |
sprintf( painCave.errMsg, |
833 |
"Error in reading bonds from force file at line %d.\n", |
834 |
lineNum ); |
835 |
painCave.isFatal = 1; |
836 |
simError(); |
837 |
} |
838 |
|
839 |
// stop reading at end of file, or at next section |
840 |
while( readLine[0] != '#' && eof_test != NULL ){ |
841 |
|
842 |
// toss comment lines |
843 |
if( readLine[0] != '!' ){ |
844 |
|
845 |
// the parser returns 0 if the line was blank |
846 |
if( parseBond( readLine, lineNum, bondInfo ) ){ |
847 |
headBondType->add( bondInfo ); |
848 |
} |
849 |
} |
850 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
851 |
lineNum++; |
852 |
} |
853 |
|
854 |
#ifdef IS_MPI |
855 |
|
856 |
// send out the linked list to all the other processes |
857 |
|
858 |
sprintf( checkPointMsg, |
859 |
"DUFF bond structures read successfully." ); |
860 |
MPIcheckPoint(); |
861 |
|
862 |
currentBondType = headBondType->next; |
863 |
while( currentBondType != NULL ){ |
864 |
currentBondType->duplicate( bondInfo ); |
865 |
sendFrcStruct( &bondInfo, mpiBondStructType ); |
866 |
currentBondType = currentBondType->next; |
867 |
} |
868 |
bondInfo.last = 1; |
869 |
sendFrcStruct( &bondInfo, mpiBondStructType ); |
870 |
|
871 |
} |
872 |
|
873 |
else{ |
874 |
|
875 |
// listen for node 0 to send out the force params |
876 |
|
877 |
MPIcheckPoint(); |
878 |
|
879 |
headBondType = new LinkedBondType; |
880 |
recieveFrcStruct( &bondInfo, mpiBondStructType ); |
881 |
while( !bondInfo.last ){ |
882 |
|
883 |
headBondType->add( bondInfo ); |
884 |
recieveFrcStruct( &bondInfo, mpiBondStructType ); |
885 |
} |
886 |
} |
887 |
|
888 |
sprintf( checkPointMsg, |
889 |
"DUFF bond structures broadcast successfully." ); |
890 |
MPIcheckPoint(); |
891 |
|
892 |
#endif // is_mpi |
893 |
|
894 |
|
895 |
// read in the bends |
896 |
|
897 |
#ifdef IS_MPI |
898 |
if( worldRank == 0 ){ |
899 |
#endif |
900 |
|
901 |
// read in the bend types. |
902 |
|
903 |
headBendType = new LinkedBendType; |
904 |
|
905 |
fastForward( "BendTypes", "initializeBends" ); |
906 |
|
907 |
// we are now at the bendTypes section |
908 |
|
909 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
910 |
lineNum++; |
911 |
|
912 |
// read a line, and start parseing out the bend types |
913 |
|
914 |
if( eof_test == NULL ){ |
915 |
sprintf( painCave.errMsg, |
916 |
"Error in reading bends from force file at line %d.\n", |
917 |
lineNum ); |
918 |
painCave.isFatal = 1; |
919 |
simError(); |
920 |
} |
921 |
|
922 |
// stop reading at end of file, or at next section |
923 |
while( readLine[0] != '#' && eof_test != NULL ){ |
924 |
|
925 |
// toss comment lines |
926 |
if( readLine[0] != '!' ){ |
927 |
|
928 |
// the parser returns 0 if the line was blank |
929 |
if( parseBend( readLine, lineNum, bendInfo ) ){ |
930 |
headBendType->add( bendInfo ); |
931 |
} |
932 |
} |
933 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
934 |
lineNum++; |
935 |
} |
936 |
|
937 |
#ifdef IS_MPI |
938 |
|
939 |
// send out the linked list to all the other processes |
940 |
|
941 |
sprintf( checkPointMsg, |
942 |
"DUFF bend structures read successfully." ); |
943 |
MPIcheckPoint(); |
944 |
|
945 |
currentBendType = headBendType->next; |
946 |
while( currentBendType != NULL ){ |
947 |
currentBendType->duplicate( bendInfo ); |
948 |
sendFrcStruct( &bendInfo, mpiBendStructType ); |
949 |
currentBendType = currentBendType->next; |
950 |
} |
951 |
bendInfo.last = 1; |
952 |
sendFrcStruct( &bendInfo, mpiBendStructType ); |
953 |
|
954 |
} |
955 |
|
956 |
else{ |
957 |
|
958 |
// listen for node 0 to send out the force params |
959 |
|
960 |
MPIcheckPoint(); |
961 |
|
962 |
headBendType = new LinkedBendType; |
963 |
recieveFrcStruct( &bendInfo, mpiBendStructType ); |
964 |
while( !bendInfo.last ){ |
965 |
|
966 |
headBendType->add( bendInfo ); |
967 |
recieveFrcStruct( &bendInfo, mpiBendStructType ); |
968 |
} |
969 |
} |
970 |
|
971 |
sprintf( checkPointMsg, |
972 |
"DUFF bend structures broadcast successfully." ); |
973 |
MPIcheckPoint(); |
974 |
|
975 |
#endif // is_mpi |
976 |
|
977 |
|
978 |
// read in the torsions |
979 |
|
980 |
#ifdef IS_MPI |
981 |
if( worldRank == 0 ){ |
982 |
#endif |
983 |
|
984 |
// read in the torsion types. |
985 |
|
986 |
headTorsionType = new LinkedTorsionType; |
987 |
|
988 |
fastForward( "TorsionTypes", "initializeTorsions" ); |
989 |
|
990 |
// we are now at the torsionTypes section |
991 |
|
992 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
993 |
lineNum++; |
994 |
|
995 |
|
996 |
// read a line, and start parseing out the atom types |
997 |
|
998 |
if( eof_test == NULL ){ |
999 |
sprintf( painCave.errMsg, |
1000 |
"Error in reading torsions from force file at line %d.\n", |
1001 |
lineNum ); |
1002 |
painCave.isFatal = 1; |
1003 |
simError(); |
1004 |
} |
1005 |
|
1006 |
// stop reading at end of file, or at next section |
1007 |
while( readLine[0] != '#' && eof_test != NULL ){ |
1008 |
|
1009 |
// toss comment lines |
1010 |
if( readLine[0] != '!' ){ |
1011 |
|
1012 |
// the parser returns 0 if the line was blank |
1013 |
if( parseTorsion( readLine, lineNum, torsionInfo ) ){ |
1014 |
headTorsionType->add( torsionInfo ); |
1015 |
|
1016 |
} |
1017 |
} |
1018 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1019 |
lineNum++; |
1020 |
} |
1021 |
|
1022 |
#ifdef IS_MPI |
1023 |
|
1024 |
// send out the linked list to all the other processes |
1025 |
|
1026 |
sprintf( checkPointMsg, |
1027 |
"DUFF torsion structures read successfully." ); |
1028 |
MPIcheckPoint(); |
1029 |
|
1030 |
currentTorsionType = headTorsionType->next; |
1031 |
while( currentTorsionType != NULL ){ |
1032 |
currentTorsionType->duplicate( torsionInfo ); |
1033 |
sendFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1034 |
currentTorsionType = currentTorsionType->next; |
1035 |
} |
1036 |
torsionInfo.last = 1; |
1037 |
sendFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1038 |
|
1039 |
} |
1040 |
|
1041 |
else{ |
1042 |
|
1043 |
// listen for node 0 to send out the force params |
1044 |
|
1045 |
MPIcheckPoint(); |
1046 |
|
1047 |
headTorsionType = new LinkedTorsionType; |
1048 |
recieveFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1049 |
while( !torsionInfo.last ){ |
1050 |
|
1051 |
headTorsionType->add( torsionInfo ); |
1052 |
recieveFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1053 |
} |
1054 |
} |
1055 |
|
1056 |
sprintf( checkPointMsg, |
1057 |
"DUFF torsion structures broadcast successfully." ); |
1058 |
MPIcheckPoint(); |
1059 |
|
1060 |
#endif // is_mpi |
1061 |
|
1062 |
entry_plug->useLJ = 1; |
1063 |
} |
1064 |
|
1065 |
|
1066 |
|
1067 |
void DUFF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
1068 |
|
1069 |
|
1070 |
////////////////////////////////////////////////// |
1071 |
// a quick water fix |
1072 |
|
1073 |
double waterI[3][3]; |
1074 |
waterI[0][0] = 1.76958347772500; |
1075 |
waterI[0][1] = 0.0; |
1076 |
waterI[0][2] = 0.0; |
1077 |
|
1078 |
waterI[1][0] = 0.0; |
1079 |
waterI[1][1] = 0.614537057924513; |
1080 |
waterI[1][2] = 0.0; |
1081 |
|
1082 |
waterI[2][0] = 0.0; |
1083 |
waterI[2][1] = 0.0; |
1084 |
waterI[2][2] = 1.15504641980049; |
1085 |
|
1086 |
|
1087 |
double headI[3][3]; |
1088 |
headI[0][0] = 1125; |
1089 |
headI[0][1] = 0.0; |
1090 |
headI[0][2] = 0.0; |
1091 |
|
1092 |
headI[1][0] = 0.0; |
1093 |
headI[1][1] = 1125; |
1094 |
headI[1][2] = 0.0; |
1095 |
|
1096 |
headI[2][0] = 0.0; |
1097 |
headI[2][1] = 0.0; |
1098 |
headI[2][2] = 250; |
1099 |
|
1100 |
////////////////////////////////////////////////// |
1101 |
|
1102 |
|
1103 |
// initialize the atoms |
1104 |
|
1105 |
DirectionalAtom* dAtom; |
1106 |
|
1107 |
for(int i=0; i<nAtoms; i++ ){ |
1108 |
|
1109 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
1110 |
if( currentAtomType == NULL ){ |
1111 |
sprintf( painCave.errMsg, |
1112 |
"AtomType error, %s not found in force file.\n", |
1113 |
the_atoms[i]->getType() ); |
1114 |
painCave.isFatal = 1; |
1115 |
simError(); |
1116 |
} |
1117 |
|
1118 |
the_atoms[i]->setMass( currentAtomType->mass ); |
1119 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
1120 |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
1121 |
the_atoms[i]->setIdent( currentAtomType->ident ); |
1122 |
the_atoms[i]->setLJ(); |
1123 |
|
1124 |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
1125 |
|
1126 |
if( currentAtomType->isDipole ){ |
1127 |
if( the_atoms[i]->isDirectional() ){ |
1128 |
|
1129 |
dAtom = (DirectionalAtom *) the_atoms[i]; |
1130 |
dAtom->setMu( currentAtomType->dipole ); |
1131 |
dAtom->setHasDipole( 1 ); |
1132 |
dAtom->setJx( 0.0 ); |
1133 |
dAtom->setJy( 0.0 ); |
1134 |
dAtom->setJz( 0.0 ); |
1135 |
|
1136 |
if(!strcmp("SSD",the_atoms[i]->getType())){ |
1137 |
dAtom->setI( waterI ); |
1138 |
dAtom->setSSD( 1 ); |
1139 |
} |
1140 |
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
1141 |
dAtom->setI( headI ); |
1142 |
dAtom->setSSD( 0 ); |
1143 |
} |
1144 |
else{ |
1145 |
sprintf(painCave.errMsg, |
1146 |
"AtmType error, %s does not have a moment of inertia set.\n", |
1147 |
the_atoms[i]->getType() ); |
1148 |
painCave.isFatal = 1; |
1149 |
simError(); |
1150 |
} |
1151 |
entry_plug->n_dipoles++; |
1152 |
} |
1153 |
else{ |
1154 |
|
1155 |
sprintf( painCave.errMsg, |
1156 |
"DUFF error: Atom \"%s\" is a dipole, yet no standard" |
1157 |
" orientation was specifed in the BASS file.\n", |
1158 |
currentAtomType->name ); |
1159 |
painCave.isFatal = 1; |
1160 |
simError(); |
1161 |
} |
1162 |
} |
1163 |
else{ |
1164 |
if( the_atoms[i]->isDirectional() ){ |
1165 |
sprintf( painCave.errMsg, |
1166 |
"DUFF error: Atom \"%s\" was given a standard" |
1167 |
"orientation in the BASS file, yet it is not a dipole.\n", |
1168 |
currentAtomType->name); |
1169 |
painCave.isFatal = 1; |
1170 |
simError(); |
1171 |
} |
1172 |
} |
1173 |
} |
1174 |
} |
1175 |
|
1176 |
void DUFF::initializeBonds( int nBonds, Bond** bondArray, |
1177 |
bond_pair* the_bonds ){ |
1178 |
int i,a,b; |
1179 |
char* atomA; |
1180 |
char* atomB; |
1181 |
|
1182 |
Atom** the_atoms; |
1183 |
the_atoms = entry_plug->atoms; |
1184 |
|
1185 |
|
1186 |
// initialize the Bonds |
1187 |
|
1188 |
for( i=0; i<nBonds; i++ ){ |
1189 |
|
1190 |
a = the_bonds[i].a; |
1191 |
b = the_bonds[i].b; |
1192 |
|
1193 |
atomA = the_atoms[a]->getType(); |
1194 |
atomB = the_atoms[b]->getType(); |
1195 |
currentBondType = headBondType->find( atomA, atomB ); |
1196 |
if( currentBondType == NULL ){ |
1197 |
sprintf( painCave.errMsg, |
1198 |
"BondType error, %s - %s not found in force file.\n", |
1199 |
atomA, atomB ); |
1200 |
painCave.isFatal = 1; |
1201 |
simError(); |
1202 |
} |
1203 |
|
1204 |
switch( currentBondType->type ){ |
1205 |
|
1206 |
case FIXED_BOND: |
1207 |
|
1208 |
bondArray[i] = new ConstrainedBond( *the_atoms[a], |
1209 |
*the_atoms[b], |
1210 |
currentBondType->d0 ); |
1211 |
entry_plug->n_constraints++; |
1212 |
break; |
1213 |
|
1214 |
case HARMONIC_BOND: |
1215 |
|
1216 |
bondArray[i] = new HarmonicBond( *the_atoms[a], |
1217 |
*the_atoms[b], |
1218 |
currentBondType->d0, |
1219 |
currentBondType->k0 ); |
1220 |
break; |
1221 |
|
1222 |
default: |
1223 |
|
1224 |
break; |
1225 |
// do nothing |
1226 |
} |
1227 |
} |
1228 |
} |
1229 |
|
1230 |
void DUFF::initializeBends( int nBends, Bend** bendArray, |
1231 |
bend_set* the_bends ){ |
1232 |
|
1233 |
QuadraticBend* qBend; |
1234 |
GhostBend* gBend; |
1235 |
Atom** the_atoms; |
1236 |
the_atoms = entry_plug->atoms; |
1237 |
|
1238 |
int i, a, b, c; |
1239 |
char* atomA; |
1240 |
char* atomB; |
1241 |
char* atomC; |
1242 |
|
1243 |
// initialize the Bends |
1244 |
|
1245 |
for( i=0; i<nBends; i++ ){ |
1246 |
|
1247 |
a = the_bends[i].a; |
1248 |
b = the_bends[i].b; |
1249 |
c = the_bends[i].c; |
1250 |
|
1251 |
atomA = the_atoms[a]->getType(); |
1252 |
atomB = the_atoms[b]->getType(); |
1253 |
|
1254 |
if( the_bends[i].isGhost ) atomC = "GHOST"; |
1255 |
else atomC = the_atoms[c]->getType(); |
1256 |
|
1257 |
currentBendType = headBendType->find( atomA, atomB, atomC ); |
1258 |
if( currentBendType == NULL ){ |
1259 |
sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found" |
1260 |
" in force file.\n", |
1261 |
atomA, atomB, atomC ); |
1262 |
painCave.isFatal = 1; |
1263 |
simError(); |
1264 |
} |
1265 |
|
1266 |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1267 |
|
1268 |
if( the_bends[i].isGhost){ |
1269 |
|
1270 |
if( the_bends[i].ghost == b ){ |
1271 |
// do nothing |
1272 |
} |
1273 |
else if( the_bends[i].ghost == a ){ |
1274 |
c = a; |
1275 |
a = b; |
1276 |
b = c; |
1277 |
} |
1278 |
else{ |
1279 |
sprintf( painCave.errMsg, |
1280 |
"BendType error, %s - %s - %s,\n" |
1281 |
" --> central atom is not " |
1282 |
"correctly identified with the " |
1283 |
"\"ghostVectorSource = \" tag.\n", |
1284 |
atomA, atomB, atomC ); |
1285 |
painCave.isFatal = 1; |
1286 |
simError(); |
1287 |
} |
1288 |
|
1289 |
gBend = new GhostBend( *the_atoms[a], |
1290 |
*the_atoms[b] ); |
1291 |
gBend->setConstants( currentBendType->k1, |
1292 |
currentBendType->k2, |
1293 |
currentBendType->k3, |
1294 |
currentBendType->t0 ); |
1295 |
bendArray[i] = gBend; |
1296 |
} |
1297 |
else{ |
1298 |
qBend = new QuadraticBend( *the_atoms[a], |
1299 |
*the_atoms[b], |
1300 |
*the_atoms[c] ); |
1301 |
qBend->setConstants( currentBendType->k1, |
1302 |
currentBendType->k2, |
1303 |
currentBendType->k3, |
1304 |
currentBendType->t0 ); |
1305 |
bendArray[i] = qBend; |
1306 |
} |
1307 |
} |
1308 |
} |
1309 |
} |
1310 |
|
1311 |
void DUFF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
1312 |
torsion_set* the_torsions ){ |
1313 |
|
1314 |
int i, a, b, c, d; |
1315 |
char* atomA; |
1316 |
char* atomB; |
1317 |
char* atomC; |
1318 |
char* atomD; |
1319 |
|
1320 |
CubicTorsion* cTors; |
1321 |
Atom** the_atoms; |
1322 |
the_atoms = entry_plug->atoms; |
1323 |
|
1324 |
// initialize the Torsions |
1325 |
|
1326 |
for( i=0; i<nTorsions; i++ ){ |
1327 |
|
1328 |
a = the_torsions[i].a; |
1329 |
b = the_torsions[i].b; |
1330 |
c = the_torsions[i].c; |
1331 |
d = the_torsions[i].d; |
1332 |
|
1333 |
atomA = the_atoms[a]->getType(); |
1334 |
atomB = the_atoms[b]->getType(); |
1335 |
atomC = the_atoms[c]->getType(); |
1336 |
atomD = the_atoms[d]->getType(); |
1337 |
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1338 |
if( currentTorsionType == NULL ){ |
1339 |
sprintf( painCave.errMsg, |
1340 |
"TorsionType error, %s - %s - %s - %s not found" |
1341 |
" in force file.\n", |
1342 |
atomA, atomB, atomC, atomD ); |
1343 |
painCave.isFatal = 1; |
1344 |
simError(); |
1345 |
} |
1346 |
|
1347 |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1348 |
|
1349 |
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1350 |
*the_atoms[c], *the_atoms[d] ); |
1351 |
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1352 |
currentTorsionType->k3, currentTorsionType->k4 ); |
1353 |
torsionArray[i] = cTors; |
1354 |
} |
1355 |
} |
1356 |
} |
1357 |
|
1358 |
void DUFF::fastForward( char* stopText, char* searchOwner ){ |
1359 |
|
1360 |
int foundText = 0; |
1361 |
char* the_token; |
1362 |
|
1363 |
rewind( frcFile ); |
1364 |
lineNum = 0; |
1365 |
|
1366 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1367 |
lineNum++; |
1368 |
if( eof_test == NULL ){ |
1369 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
1370 |
" file is empty.\n", |
1371 |
searchOwner ); |
1372 |
painCave.isFatal = 1; |
1373 |
simError(); |
1374 |
} |
1375 |
|
1376 |
|
1377 |
while( !foundText ){ |
1378 |
while( eof_test != NULL && readLine[0] != '#' ){ |
1379 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1380 |
lineNum++; |
1381 |
} |
1382 |
if( eof_test == NULL ){ |
1383 |
sprintf( painCave.errMsg, |
1384 |
"Error fast forwarding force file for %s at " |
1385 |
"line %d: file ended unexpectedly.\n", |
1386 |
searchOwner, |
1387 |
lineNum ); |
1388 |
painCave.isFatal = 1; |
1389 |
simError(); |
1390 |
} |
1391 |
|
1392 |
the_token = strtok( readLine, " ,;\t#\n" ); |
1393 |
foundText = !strcmp( stopText, the_token ); |
1394 |
|
1395 |
if( !foundText ){ |
1396 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1397 |
lineNum++; |
1398 |
|
1399 |
if( eof_test == NULL ){ |
1400 |
sprintf( painCave.errMsg, |
1401 |
"Error fast forwarding force file for %s at " |
1402 |
"line %d: file ended unexpectedly.\n", |
1403 |
searchOwner, |
1404 |
lineNum ); |
1405 |
painCave.isFatal = 1; |
1406 |
simError(); |
1407 |
} |
1408 |
} |
1409 |
} |
1410 |
} |
1411 |
|
1412 |
|
1413 |
int DUFF_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1414 |
|
1415 |
char* the_token; |
1416 |
|
1417 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1418 |
if( the_token != NULL ){ |
1419 |
|
1420 |
strcpy( info.name, the_token ); |
1421 |
|
1422 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1423 |
sprintf( painCave.errMsg, |
1424 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1425 |
painCave.isFatal = 1; |
1426 |
simError(); |
1427 |
} |
1428 |
|
1429 |
info.isDipole = atoi( the_token ); |
1430 |
|
1431 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1432 |
sprintf( painCave.errMsg, |
1433 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1434 |
painCave.isFatal = 1; |
1435 |
simError(); |
1436 |
} |
1437 |
|
1438 |
info.isSSD = atoi( the_token ); |
1439 |
|
1440 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1441 |
sprintf( painCave.errMsg, |
1442 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1443 |
painCave.isFatal = 1; |
1444 |
simError(); |
1445 |
} |
1446 |
|
1447 |
info.mass = atof( the_token ); |
1448 |
|
1449 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1450 |
sprintf( painCave.errMsg, |
1451 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1452 |
painCave.isFatal = 1; |
1453 |
simError(); |
1454 |
} |
1455 |
|
1456 |
info.epslon = atof( the_token ); |
1457 |
|
1458 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1459 |
sprintf( painCave.errMsg, |
1460 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1461 |
painCave.isFatal = 1; |
1462 |
simError(); |
1463 |
} |
1464 |
|
1465 |
info.sigma = atof( the_token ); |
1466 |
|
1467 |
if( info.isDipole ){ |
1468 |
|
1469 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1470 |
sprintf( painCave.errMsg, |
1471 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1472 |
painCave.isFatal = 1; |
1473 |
simError(); |
1474 |
} |
1475 |
|
1476 |
info.dipole = atof( the_token ); |
1477 |
} |
1478 |
else info.dipole = 0.0; |
1479 |
|
1480 |
if( info.isSSD ){ |
1481 |
|
1482 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1483 |
sprintf( painCave.errMsg, |
1484 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1485 |
painCave.isFatal = 1; |
1486 |
simError(); |
1487 |
} |
1488 |
|
1489 |
info.w0 = atof( the_token ); |
1490 |
|
1491 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1492 |
sprintf( painCave.errMsg, |
1493 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1494 |
painCave.isFatal = 1; |
1495 |
simError(); |
1496 |
} |
1497 |
|
1498 |
info.v0 = atof( the_token ); |
1499 |
} |
1500 |
else info.v0 = info.w0 = 0.0; |
1501 |
|
1502 |
return 1; |
1503 |
} |
1504 |
else return 0; |
1505 |
} |
1506 |
|
1507 |
int DUFF_NS::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1508 |
|
1509 |
char* the_token; |
1510 |
char bondType[30]; |
1511 |
|
1512 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1513 |
if( the_token != NULL ){ |
1514 |
|
1515 |
strcpy( info.nameA, the_token ); |
1516 |
|
1517 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1518 |
sprintf( painCave.errMsg, |
1519 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1520 |
painCave.isFatal = 1; |
1521 |
simError(); |
1522 |
} |
1523 |
|
1524 |
strcpy( info.nameB, the_token ); |
1525 |
|
1526 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1527 |
sprintf( painCave.errMsg, |
1528 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1529 |
painCave.isFatal = 1; |
1530 |
simError(); |
1531 |
} |
1532 |
|
1533 |
strcpy( bondType, the_token ); |
1534 |
|
1535 |
if( !strcmp( bondType, "fixed" ) ){ |
1536 |
info.type = FIXED_BOND; |
1537 |
|
1538 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1539 |
sprintf( painCave.errMsg, |
1540 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1541 |
painCave.isFatal = 1; |
1542 |
simError(); |
1543 |
} |
1544 |
|
1545 |
info.d0 = atof( the_token ); |
1546 |
} |
1547 |
else if( !strcmp( bondType, "harmonic" ) ){ |
1548 |
info.type = HARMONIC_BOND; |
1549 |
|
1550 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1551 |
sprintf( painCave.errMsg, |
1552 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1553 |
painCave.isFatal = 1; |
1554 |
simError(); |
1555 |
} |
1556 |
|
1557 |
info.d0 = atof( the_token ); |
1558 |
|
1559 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1560 |
sprintf( painCave.errMsg, |
1561 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1562 |
painCave.isFatal = 1; |
1563 |
simError(); |
1564 |
} |
1565 |
|
1566 |
info.k0 = atof( the_token ); |
1567 |
} |
1568 |
|
1569 |
else{ |
1570 |
sprintf( painCave.errMsg, |
1571 |
"Unknown DUFF bond type \"%s\" at line %d\n", |
1572 |
info.type, |
1573 |
lineNum ); |
1574 |
painCave.isFatal = 1; |
1575 |
simError(); |
1576 |
} |
1577 |
|
1578 |
return 1; |
1579 |
} |
1580 |
else return 0; |
1581 |
} |
1582 |
|
1583 |
|
1584 |
int DUFF_NS::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1585 |
|
1586 |
char* the_token; |
1587 |
|
1588 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1589 |
if( the_token != NULL ){ |
1590 |
|
1591 |
strcpy( info.nameA, the_token ); |
1592 |
|
1593 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1594 |
sprintf( painCave.errMsg, |
1595 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1596 |
painCave.isFatal = 1; |
1597 |
simError(); |
1598 |
} |
1599 |
|
1600 |
strcpy( info.nameB, the_token ); |
1601 |
|
1602 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1603 |
sprintf( painCave.errMsg, |
1604 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1605 |
painCave.isFatal = 1; |
1606 |
simError(); |
1607 |
} |
1608 |
|
1609 |
strcpy( info.nameC, the_token ); |
1610 |
|
1611 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1612 |
sprintf( painCave.errMsg, |
1613 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1614 |
painCave.isFatal = 1; |
1615 |
simError(); |
1616 |
} |
1617 |
|
1618 |
strcpy( info.type, the_token ); |
1619 |
|
1620 |
if( !strcmp( info.type, "quadratic" ) ){ |
1621 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1622 |
sprintf( painCave.errMsg, |
1623 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1624 |
painCave.isFatal = 1; |
1625 |
simError(); |
1626 |
} |
1627 |
|
1628 |
info.k1 = atof( the_token ); |
1629 |
|
1630 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1631 |
sprintf( painCave.errMsg, |
1632 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1633 |
painCave.isFatal = 1; |
1634 |
simError(); |
1635 |
} |
1636 |
|
1637 |
info.k2 = atof( the_token ); |
1638 |
|
1639 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1640 |
sprintf( painCave.errMsg, |
1641 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1642 |
painCave.isFatal = 1; |
1643 |
simError(); |
1644 |
} |
1645 |
|
1646 |
info.k3 = atof( the_token ); |
1647 |
|
1648 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1649 |
sprintf( painCave.errMsg, |
1650 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1651 |
painCave.isFatal = 1; |
1652 |
simError(); |
1653 |
} |
1654 |
|
1655 |
info.t0 = atof( the_token ); |
1656 |
} |
1657 |
|
1658 |
else{ |
1659 |
sprintf( painCave.errMsg, |
1660 |
"Unknown DUFF bend type \"%s\" at line %d\n", |
1661 |
info.type, |
1662 |
lineNum ); |
1663 |
painCave.isFatal = 1; |
1664 |
simError(); |
1665 |
} |
1666 |
|
1667 |
return 1; |
1668 |
} |
1669 |
else return 0; |
1670 |
} |
1671 |
|
1672 |
int DUFF_NS::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1673 |
|
1674 |
char* the_token; |
1675 |
|
1676 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1677 |
if( the_token != NULL ){ |
1678 |
|
1679 |
strcpy( info.nameA, the_token ); |
1680 |
|
1681 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1682 |
sprintf( painCave.errMsg, |
1683 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1684 |
painCave.isFatal = 1; |
1685 |
simError(); |
1686 |
} |
1687 |
|
1688 |
strcpy( info.nameB, the_token ); |
1689 |
|
1690 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1691 |
sprintf( painCave.errMsg, |
1692 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1693 |
painCave.isFatal = 1; |
1694 |
simError(); |
1695 |
} |
1696 |
|
1697 |
strcpy( info.nameC, the_token ); |
1698 |
|
1699 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1700 |
sprintf( painCave.errMsg, |
1701 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1702 |
painCave.isFatal = 1; |
1703 |
simError(); |
1704 |
} |
1705 |
|
1706 |
strcpy( info.nameD, the_token ); |
1707 |
|
1708 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1709 |
sprintf( painCave.errMsg, |
1710 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1711 |
painCave.isFatal = 1; |
1712 |
simError(); |
1713 |
} |
1714 |
|
1715 |
strcpy( info.type, the_token ); |
1716 |
|
1717 |
if( !strcmp( info.type, "cubic" ) ){ |
1718 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1719 |
sprintf( painCave.errMsg, |
1720 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1721 |
painCave.isFatal = 1; |
1722 |
simError(); |
1723 |
} |
1724 |
|
1725 |
info.k1 = atof( the_token ); |
1726 |
|
1727 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1728 |
sprintf( painCave.errMsg, |
1729 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1730 |
painCave.isFatal = 1; |
1731 |
simError(); |
1732 |
} |
1733 |
|
1734 |
info.k2 = atof( the_token ); |
1735 |
|
1736 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1737 |
sprintf( painCave.errMsg, |
1738 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1739 |
painCave.isFatal = 1; |
1740 |
simError(); |
1741 |
} |
1742 |
|
1743 |
info.k3 = atof( the_token ); |
1744 |
|
1745 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1746 |
sprintf( painCave.errMsg, |
1747 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1748 |
painCave.isFatal = 1; |
1749 |
simError(); |
1750 |
} |
1751 |
|
1752 |
info.k4 = atof( the_token ); |
1753 |
|
1754 |
} |
1755 |
|
1756 |
else{ |
1757 |
sprintf( painCave.errMsg, |
1758 |
"Unknown DUFF torsion type \"%s\" at line %d\n", |
1759 |
info.type, |
1760 |
lineNum ); |
1761 |
painCave.isFatal = 1; |
1762 |
simError(); |
1763 |
} |
1764 |
|
1765 |
return 1; |
1766 |
} |
1767 |
|
1768 |
else return 0; |
1769 |
} |