1 |
#include <stdlib.h> |
2 |
#include <stdio.h> |
3 |
#include <string.h> |
4 |
|
5 |
#include <iostream> |
6 |
using namespace std; |
7 |
|
8 |
#include "UseTheForce/ForceFields.hpp" |
9 |
#include "primitives/SRI.hpp" |
10 |
#include "utils/simError.h" |
11 |
#include "types/DirectionalAtomType.hpp" |
12 |
#include "UseTheForce/DarkSide/lj_interface.h" |
13 |
#include "UseTheForce/DarkSide/dipole_interface.h" |
14 |
#include "UseTheForce/DarkSide/sticky_interface.h" |
15 |
|
16 |
#ifdef IS_MPI |
17 |
#include "UseTheForce/mpiForceField.h" |
18 |
#endif // is_mpi |
19 |
|
20 |
|
21 |
// define some bond Types |
22 |
|
23 |
#define FIXED_BOND 0 |
24 |
#define HARMONIC_BOND 1 |
25 |
|
26 |
|
27 |
namespace DUFF_NS { // restrict the access of the folowing to this file only. |
28 |
|
29 |
|
30 |
// Declare the structures that will be passed by MPI |
31 |
|
32 |
typedef struct{ |
33 |
char name[15]; |
34 |
double mass; |
35 |
double epslon; |
36 |
double sigma; |
37 |
double charge; |
38 |
double dipole; |
39 |
double w0; |
40 |
double v0; |
41 |
double v0p; |
42 |
double rl; |
43 |
double ru; |
44 |
double rlp; |
45 |
double rup; |
46 |
int isSSD; |
47 |
int isCharge; |
48 |
int isDipole; |
49 |
int ident; |
50 |
int last; // 0 -> default |
51 |
// 1 -> tells nodes to stop listening |
52 |
} atomStruct; |
53 |
|
54 |
|
55 |
typedef struct{ |
56 |
char nameA[15]; |
57 |
char nameB[15]; |
58 |
double d0; |
59 |
double k0; |
60 |
int last; // 0 -> default |
61 |
// 1 -> tells nodes to stop listening |
62 |
int type; |
63 |
} bondStruct; |
64 |
|
65 |
|
66 |
typedef struct{ |
67 |
char nameA[15]; |
68 |
char nameB[15]; |
69 |
char nameC[15]; |
70 |
char type[30]; |
71 |
double k1, k2, k3, t0; |
72 |
int last; // 0 -> default |
73 |
// 1 -> tells nodes to stop listening |
74 |
} bendStruct; |
75 |
|
76 |
|
77 |
typedef struct{ |
78 |
char nameA[15]; |
79 |
char nameB[15]; |
80 |
char nameC[15]; |
81 |
char nameD[15]; |
82 |
char type[30]; |
83 |
double k1, k2, k3, k4; |
84 |
int last; // 0 -> default |
85 |
// 1 -> tells nodes to stop listening |
86 |
} torsionStruct; |
87 |
|
88 |
|
89 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
90 |
int parseBond( char *lineBuffer, int lineNum, bondStruct &info ); |
91 |
int parseBend( char *lineBuffer, int lineNum, bendStruct &info ); |
92 |
int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ); |
93 |
|
94 |
|
95 |
#ifdef IS_MPI |
96 |
|
97 |
MPI_Datatype mpiAtomStructType; |
98 |
MPI_Datatype mpiBondStructType; |
99 |
MPI_Datatype mpiBendStructType; |
100 |
MPI_Datatype mpiTorsionStructType; |
101 |
|
102 |
#endif |
103 |
|
104 |
class LinkedAtomType { |
105 |
public: |
106 |
LinkedAtomType(){ |
107 |
next = NULL; |
108 |
name[0] = '\0'; |
109 |
} |
110 |
~LinkedAtomType(){ if( next != NULL ) delete next; } |
111 |
|
112 |
LinkedAtomType* find(const char* key){ |
113 |
if( !strcmp(name, key) ) return this; |
114 |
if( next != NULL ) return next->find(key); |
115 |
return NULL; |
116 |
} |
117 |
|
118 |
void printMe( void ){ |
119 |
|
120 |
std::cerr << "LinkedAtype " << name << ": ident = " << ident << "\n"; |
121 |
// if( next != NULL ) next->printMe(); |
122 |
|
123 |
} |
124 |
|
125 |
void add( atomStruct &info ){ |
126 |
|
127 |
// check for duplicates |
128 |
|
129 |
if( !strcmp( info.name, name ) ){ |
130 |
sprintf( painCave.errMsg, |
131 |
"Duplicate DUFF atom type \"%s\" found in " |
132 |
"the DUFF param file./n", |
133 |
name ); |
134 |
painCave.isFatal = 1; |
135 |
simError(); |
136 |
} |
137 |
|
138 |
if( next != NULL ) next->add(info); |
139 |
else{ |
140 |
next = new LinkedAtomType(); |
141 |
strcpy(next->name, info.name); |
142 |
next->isDipole = info.isDipole; |
143 |
next->isSSD = info.isSSD; |
144 |
next->mass = info.mass; |
145 |
next->epslon = info.epslon; |
146 |
next->sigma = info.sigma; |
147 |
next->dipole = info.dipole; |
148 |
next->w0 = info.w0; |
149 |
next->v0 = info.v0; |
150 |
next->v0p = info.v0p; |
151 |
next->rl = info.rl; |
152 |
next->ru = info.ru; |
153 |
next->rlp = info.rlp; |
154 |
next->rup = info.rup; |
155 |
next->ident = info.ident; |
156 |
} |
157 |
} |
158 |
|
159 |
#ifdef IS_MPI |
160 |
|
161 |
void duplicate( atomStruct &info ){ |
162 |
strcpy(info.name, name); |
163 |
info.isDipole = isDipole; |
164 |
info.isSSD = isSSD; |
165 |
info.mass = mass; |
166 |
info.epslon = epslon; |
167 |
info.sigma = sigma; |
168 |
info.dipole = dipole; |
169 |
info.w0 = w0; |
170 |
info.v0 = v0; |
171 |
info.v0p = v0p; |
172 |
info.rl = rl; |
173 |
info.ru = ru; |
174 |
info.rlp = rlp; |
175 |
info.rup = rup; |
176 |
info.ident = ident; |
177 |
info.last = 0; |
178 |
} |
179 |
|
180 |
|
181 |
#endif |
182 |
|
183 |
char name[15]; |
184 |
int isDipole; |
185 |
int isSSD; |
186 |
double mass; |
187 |
double epslon; |
188 |
double sigma; |
189 |
double dipole; |
190 |
double w0; |
191 |
double v0; |
192 |
double v0p; |
193 |
double rl; |
194 |
double ru; |
195 |
double rlp; |
196 |
double rup; |
197 |
int ident; |
198 |
LinkedAtomType* next; |
199 |
}; |
200 |
|
201 |
class LinkedBondType { |
202 |
public: |
203 |
LinkedBondType(){ |
204 |
next = NULL; |
205 |
nameA[0] = '\0'; |
206 |
nameB[0] = '\0'; |
207 |
} |
208 |
~LinkedBondType(){ if( next != NULL ) delete next; } |
209 |
|
210 |
LinkedBondType* find(const char* key1, const char* key2){ |
211 |
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
212 |
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
213 |
if( next != NULL ) return next->find(key1, key2); |
214 |
return NULL; |
215 |
} |
216 |
|
217 |
|
218 |
void add( bondStruct &info ){ |
219 |
|
220 |
// check for duplicates |
221 |
int dup = 0; |
222 |
|
223 |
if( !strcmp(nameA, info.nameA ) && !strcmp( nameB, info.nameB ) ) dup = 1; |
224 |
if( !strcmp(nameA, info.nameB ) && !strcmp( nameB, info.nameA ) ) dup = 1; |
225 |
|
226 |
if(dup){ |
227 |
sprintf( painCave.errMsg, |
228 |
"Duplicate DUFF bond type \"%s - %s\" found in " |
229 |
"the DUFF param file./n", |
230 |
nameA, nameB ); |
231 |
painCave.isFatal = 1; |
232 |
simError(); |
233 |
} |
234 |
|
235 |
|
236 |
if( next != NULL ) next->add(info); |
237 |
else{ |
238 |
next = new LinkedBondType(); |
239 |
strcpy(next->nameA, info.nameA); |
240 |
strcpy(next->nameB, info.nameB); |
241 |
next->type = info.type; |
242 |
next->d0 = info.d0; |
243 |
next->k0 = info.k0; |
244 |
} |
245 |
} |
246 |
|
247 |
#ifdef IS_MPI |
248 |
void duplicate( bondStruct &info ){ |
249 |
strcpy(info.nameA, nameA); |
250 |
strcpy(info.nameB, nameB); |
251 |
info.type = type; |
252 |
info.d0 = d0; |
253 |
info.k0 = k0; |
254 |
info.last = 0; |
255 |
} |
256 |
|
257 |
|
258 |
#endif |
259 |
|
260 |
char nameA[15]; |
261 |
char nameB[15]; |
262 |
int type; |
263 |
double d0; |
264 |
double k0; |
265 |
|
266 |
LinkedBondType* next; |
267 |
}; |
268 |
|
269 |
class LinkedBendType { |
270 |
public: |
271 |
LinkedBendType(){ |
272 |
next = NULL; |
273 |
nameA[0] = '\0'; |
274 |
nameB[0] = '\0'; |
275 |
nameC[0] = '\0'; |
276 |
type[0] = '\0'; |
277 |
} |
278 |
~LinkedBendType(){ if( next != NULL ) delete next; } |
279 |
|
280 |
LinkedBendType* find(const char* key1, const char* key2, const char* key3 ){ |
281 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
282 |
&& !strcmp( nameC, key3 ) ) return this; |
283 |
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
284 |
&& !strcmp( nameC, key1 ) ) return this; |
285 |
if( next != NULL ) return next->find(key1, key2, key3); |
286 |
return NULL; |
287 |
} |
288 |
|
289 |
void add( bendStruct &info ){ |
290 |
|
291 |
// check for duplicates |
292 |
int dup = 0; |
293 |
|
294 |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) |
295 |
&& !strcmp( nameC, info.nameC ) ) dup = 1; |
296 |
if( !strcmp( nameA, info.nameC ) && !strcmp( nameB, info.nameB ) |
297 |
&& !strcmp( nameC, info.nameA ) ) dup = 1; |
298 |
|
299 |
if(dup){ |
300 |
sprintf( painCave.errMsg, |
301 |
"Duplicate DUFF bend type \"%s - %s - %s\" found in " |
302 |
"the DUFF param file./n", |
303 |
nameA, nameB, nameC ); |
304 |
painCave.isFatal = 1; |
305 |
simError(); |
306 |
} |
307 |
|
308 |
if( next != NULL ) next->add(info); |
309 |
else{ |
310 |
next = new LinkedBendType(); |
311 |
strcpy(next->nameA, info.nameA); |
312 |
strcpy(next->nameB, info.nameB); |
313 |
strcpy(next->nameC, info.nameC); |
314 |
strcpy(next->type, info.type); |
315 |
next->k1 = info.k1; |
316 |
next->k2 = info.k2; |
317 |
next->k3 = info.k3; |
318 |
next->t0 = info.t0; |
319 |
} |
320 |
} |
321 |
|
322 |
#ifdef IS_MPI |
323 |
|
324 |
void duplicate( bendStruct &info ){ |
325 |
strcpy(info.nameA, nameA); |
326 |
strcpy(info.nameB, nameB); |
327 |
strcpy(info.nameC, nameC); |
328 |
strcpy(info.type, type); |
329 |
info.k1 = k1; |
330 |
info.k2 = k2; |
331 |
info.k3 = k3; |
332 |
info.t0 = t0; |
333 |
info.last = 0; |
334 |
} |
335 |
|
336 |
#endif // is_mpi |
337 |
|
338 |
char nameA[15]; |
339 |
char nameB[15]; |
340 |
char nameC[15]; |
341 |
char type[30]; |
342 |
double k1, k2, k3, t0; |
343 |
|
344 |
LinkedBendType* next; |
345 |
}; |
346 |
|
347 |
class LinkedTorsionType { |
348 |
public: |
349 |
LinkedTorsionType(){ |
350 |
next = NULL; |
351 |
nameA[0] = '\0'; |
352 |
nameB[0] = '\0'; |
353 |
nameC[0] = '\0'; |
354 |
type[0] = '\0'; |
355 |
} |
356 |
~LinkedTorsionType(){ if( next != NULL ) delete next; } |
357 |
|
358 |
LinkedTorsionType* find(const char* key1, const char* key2, const char* key3, const char* key4 ){ |
359 |
|
360 |
|
361 |
|
362 |
|
363 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
364 |
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
365 |
|
366 |
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
367 |
!strcmp( nameC, key2 ) && !strcmp( nameD, key1 ) ) return this; |
368 |
|
369 |
if( next != NULL ) return next->find(key1, key2, key3, key4); |
370 |
return NULL; |
371 |
} |
372 |
|
373 |
void add( torsionStruct &info ){ |
374 |
|
375 |
// check for duplicates |
376 |
int dup = 0; |
377 |
|
378 |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) && |
379 |
!strcmp( nameC, info.nameC ) && !strcmp( nameD, info.nameD ) ) dup = 1; |
380 |
|
381 |
if( !strcmp( nameA, info.nameD ) && !strcmp( nameB, info.nameC ) && |
382 |
!strcmp( nameC, info.nameB ) && !strcmp( nameD, info.nameA ) ) dup = 1; |
383 |
|
384 |
if(dup){ |
385 |
sprintf( painCave.errMsg, |
386 |
"Duplicate DUFF torsion type \"%s - %s - %s - %s\" found in " |
387 |
"the DUFF param file./n", nameA, nameB, nameC, nameD ); |
388 |
painCave.isFatal = 1; |
389 |
simError(); |
390 |
} |
391 |
|
392 |
if( next != NULL ) next->add(info); |
393 |
else{ |
394 |
next = new LinkedTorsionType(); |
395 |
strcpy(next->nameA, info.nameA); |
396 |
strcpy(next->nameB, info.nameB); |
397 |
strcpy(next->nameC, info.nameC); |
398 |
strcpy(next->nameD, info.nameD); |
399 |
strcpy(next->type, info.type); |
400 |
next->k1 = info.k1; |
401 |
next->k2 = info.k2; |
402 |
next->k3 = info.k3; |
403 |
next->k4 = info.k4; |
404 |
|
405 |
} |
406 |
} |
407 |
|
408 |
#ifdef IS_MPI |
409 |
|
410 |
void duplicate( torsionStruct &info ){ |
411 |
strcpy(info.nameA, nameA); |
412 |
strcpy(info.nameB, nameB); |
413 |
strcpy(info.nameC, nameC); |
414 |
strcpy(info.nameD, nameD); |
415 |
strcpy(info.type, type); |
416 |
info.k1 = k1; |
417 |
info.k2 = k2; |
418 |
info.k3 = k3; |
419 |
info.k4 = k4; |
420 |
info.last = 0; |
421 |
} |
422 |
|
423 |
#endif |
424 |
|
425 |
char nameA[15]; |
426 |
char nameB[15]; |
427 |
char nameC[15]; |
428 |
char nameD[15]; |
429 |
char type[30]; |
430 |
double k1, k2, k3, k4; |
431 |
|
432 |
LinkedTorsionType* next; |
433 |
}; |
434 |
|
435 |
|
436 |
LinkedAtomType* headAtomType; |
437 |
LinkedAtomType* currentAtomType; |
438 |
LinkedBondType* headBondType; |
439 |
LinkedBondType* currentBondType; |
440 |
LinkedBendType* headBendType; |
441 |
LinkedBendType* currentBendType; |
442 |
LinkedTorsionType* headTorsionType; |
443 |
LinkedTorsionType* currentTorsionType; |
444 |
|
445 |
} // namespace |
446 |
|
447 |
using namespace DUFF_NS; |
448 |
|
449 |
|
450 |
//**************************************************************** |
451 |
// begins the actual forcefield stuff. |
452 |
//**************************************************************** |
453 |
|
454 |
|
455 |
DUFF::DUFF(){ |
456 |
|
457 |
string fileName; |
458 |
string tempString; |
459 |
|
460 |
headAtomType = NULL; |
461 |
currentAtomType = NULL; |
462 |
headBondType = NULL; |
463 |
currentBondType = NULL; |
464 |
headBendType = NULL; |
465 |
currentBendType = NULL; |
466 |
headTorsionType = NULL; |
467 |
currentTorsionType = NULL; |
468 |
|
469 |
|
470 |
#ifdef IS_MPI |
471 |
int i; |
472 |
|
473 |
// ********************************************************************** |
474 |
// Init the atomStruct mpi type |
475 |
|
476 |
atomStruct atomProto; // mpiPrototype |
477 |
int atomBC[3] = {15,12,5}; // block counts |
478 |
MPI_Aint atomDspls[3]; // displacements |
479 |
MPI_Datatype atomMbrTypes[3]; // member mpi types |
480 |
|
481 |
MPI_Address(&atomProto.name, &atomDspls[0]); |
482 |
MPI_Address(&atomProto.mass, &atomDspls[1]); |
483 |
MPI_Address(&atomProto.isSSD, &atomDspls[2]); |
484 |
|
485 |
atomMbrTypes[0] = MPI_CHAR; |
486 |
atomMbrTypes[1] = MPI_DOUBLE; |
487 |
atomMbrTypes[2] = MPI_INT; |
488 |
|
489 |
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
490 |
|
491 |
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
492 |
MPI_Type_commit(&mpiAtomStructType); |
493 |
|
494 |
|
495 |
// ********************************************************************** |
496 |
// Init the bondStruct mpi type |
497 |
|
498 |
bondStruct bondProto; // mpiPrototype |
499 |
int bondBC[3] = {30,2,2}; // block counts |
500 |
MPI_Aint bondDspls[3]; // displacements |
501 |
MPI_Datatype bondMbrTypes[3]; // member mpi types |
502 |
|
503 |
MPI_Address(&bondProto.nameA, &bondDspls[0]); |
504 |
MPI_Address(&bondProto.d0, &bondDspls[1]); |
505 |
MPI_Address(&bondProto.last, &bondDspls[2]); |
506 |
|
507 |
bondMbrTypes[0] = MPI_CHAR; |
508 |
bondMbrTypes[1] = MPI_DOUBLE; |
509 |
bondMbrTypes[2] = MPI_INT; |
510 |
|
511 |
for (i=2; i >= 0; i--) bondDspls[i] -= bondDspls[0]; |
512 |
|
513 |
MPI_Type_struct(3, bondBC, bondDspls, bondMbrTypes, &mpiBondStructType); |
514 |
MPI_Type_commit(&mpiBondStructType); |
515 |
|
516 |
|
517 |
// ********************************************************************** |
518 |
// Init the bendStruct mpi type |
519 |
|
520 |
bendStruct bendProto; // mpiPrototype |
521 |
int bendBC[3] = {75,4,1}; // block counts |
522 |
MPI_Aint bendDspls[3]; // displacements |
523 |
MPI_Datatype bendMbrTypes[3]; // member mpi types |
524 |
|
525 |
MPI_Address(&bendProto.nameA, &bendDspls[0]); |
526 |
MPI_Address(&bendProto.k1, &bendDspls[1]); |
527 |
MPI_Address(&bendProto.last, &bendDspls[2]); |
528 |
|
529 |
bendMbrTypes[0] = MPI_CHAR; |
530 |
bendMbrTypes[1] = MPI_DOUBLE; |
531 |
bendMbrTypes[2] = MPI_INT; |
532 |
|
533 |
for (i=2; i >= 0; i--) bendDspls[i] -= bendDspls[0]; |
534 |
|
535 |
MPI_Type_struct(3, bendBC, bendDspls, bendMbrTypes, &mpiBendStructType); |
536 |
MPI_Type_commit(&mpiBendStructType); |
537 |
|
538 |
|
539 |
// ********************************************************************** |
540 |
// Init the torsionStruct mpi type |
541 |
|
542 |
torsionStruct torsionProto; // mpiPrototype |
543 |
int torsionBC[3] = {90,4,1}; // block counts |
544 |
MPI_Aint torsionDspls[3]; // displacements |
545 |
MPI_Datatype torsionMbrTypes[3]; // member mpi types |
546 |
|
547 |
MPI_Address(&torsionProto.nameA, &torsionDspls[0]); |
548 |
MPI_Address(&torsionProto.k1, &torsionDspls[1]); |
549 |
MPI_Address(&torsionProto.last, &torsionDspls[2]); |
550 |
|
551 |
torsionMbrTypes[0] = MPI_CHAR; |
552 |
torsionMbrTypes[1] = MPI_DOUBLE; |
553 |
torsionMbrTypes[2] = MPI_INT; |
554 |
|
555 |
for (i=2; i >= 0; i--) torsionDspls[i] -= torsionDspls[0]; |
556 |
|
557 |
MPI_Type_struct(3, torsionBC, torsionDspls, torsionMbrTypes, |
558 |
&mpiTorsionStructType); |
559 |
MPI_Type_commit(&mpiTorsionStructType); |
560 |
|
561 |
// *********************************************************************** |
562 |
|
563 |
if( worldRank == 0 ){ |
564 |
#endif |
565 |
|
566 |
// generate the force file name |
567 |
|
568 |
fileName = "DUFF.frc"; |
569 |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
570 |
|
571 |
// attempt to open the file in the current directory first. |
572 |
|
573 |
frcFile = fopen( fileName.c_str(), "r" ); |
574 |
|
575 |
if( frcFile == NULL ){ |
576 |
|
577 |
// next see if the force path enviorment variable is set |
578 |
|
579 |
tempString = ffPath + "/" + fileName; |
580 |
fileName = tempString; |
581 |
|
582 |
frcFile = fopen( fileName.c_str(), "r" ); |
583 |
|
584 |
if( frcFile == NULL ){ |
585 |
|
586 |
sprintf( painCave.errMsg, |
587 |
"Error opening the force field parameter file:\n" |
588 |
"\t%s\n" |
589 |
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
590 |
"variable?\n", |
591 |
fileName.c_str() ); |
592 |
painCave.severity = OOPSE_ERROR; |
593 |
painCave.isFatal = 1; |
594 |
simError(); |
595 |
} |
596 |
} |
597 |
|
598 |
#ifdef IS_MPI |
599 |
} |
600 |
|
601 |
sprintf( checkPointMsg, "DUFF file opened sucessfully." ); |
602 |
MPIcheckPoint(); |
603 |
|
604 |
#endif // is_mpi |
605 |
} |
606 |
|
607 |
|
608 |
DUFF::~DUFF(){ |
609 |
|
610 |
if( headAtomType != NULL ) delete headAtomType; |
611 |
if( headBondType != NULL ) delete headBondType; |
612 |
if( headBendType != NULL ) delete headBendType; |
613 |
if( headTorsionType != NULL ) delete headTorsionType; |
614 |
|
615 |
#ifdef IS_MPI |
616 |
if( worldRank == 0 ){ |
617 |
#endif // is_mpi |
618 |
|
619 |
fclose( frcFile ); |
620 |
|
621 |
#ifdef IS_MPI |
622 |
} |
623 |
#endif // is_mpi |
624 |
} |
625 |
|
626 |
void DUFF::cleanMe( void ){ |
627 |
|
628 |
#ifdef IS_MPI |
629 |
|
630 |
// keep the linked lists in the mpi version |
631 |
|
632 |
#else // is_mpi |
633 |
|
634 |
// delete the linked lists in the single processor version |
635 |
|
636 |
if( headAtomType != NULL ) delete headAtomType; |
637 |
if( headBondType != NULL ) delete headBondType; |
638 |
if( headBendType != NULL ) delete headBendType; |
639 |
if( headTorsionType != NULL ) delete headTorsionType; |
640 |
|
641 |
#endif // is_mpi |
642 |
} |
643 |
|
644 |
|
645 |
void DUFF::initForceField(){ |
646 |
|
647 |
initFortran( entry_plug->useReactionField ); |
648 |
} |
649 |
|
650 |
|
651 |
void DUFF::readParams( void ){ |
652 |
|
653 |
int identNum, isError; |
654 |
|
655 |
atomStruct atomInfo; |
656 |
bondStruct bondInfo; |
657 |
bendStruct bendInfo; |
658 |
torsionStruct torsionInfo; |
659 |
|
660 |
AtomType* at; |
661 |
|
662 |
bigSigma = 0.0; |
663 |
|
664 |
atomInfo.last = 1; |
665 |
bondInfo.last = 1; |
666 |
bendInfo.last = 1; |
667 |
torsionInfo.last = 1; |
668 |
|
669 |
// read in the atom info |
670 |
|
671 |
#ifdef IS_MPI |
672 |
if( worldRank == 0 ){ |
673 |
#endif |
674 |
|
675 |
// read in the atom types. |
676 |
|
677 |
headAtomType = new LinkedAtomType; |
678 |
|
679 |
fastForward( "AtomTypes", "initializeAtoms" ); |
680 |
|
681 |
// we are now at the AtomTypes section. |
682 |
|
683 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
684 |
lineNum++; |
685 |
|
686 |
|
687 |
// read a line, and start parseing out the atom types |
688 |
|
689 |
if( eof_test == NULL ){ |
690 |
sprintf( painCave.errMsg, |
691 |
"Error in reading Atoms from force file at line %d.\n", |
692 |
lineNum ); |
693 |
painCave.isFatal = 1; |
694 |
simError(); |
695 |
} |
696 |
|
697 |
identNum = 1; |
698 |
// stop reading at end of file, or at next section |
699 |
while( readLine[0] != '#' && eof_test != NULL ){ |
700 |
|
701 |
// toss comment lines |
702 |
if( readLine[0] != '!' ){ |
703 |
|
704 |
// the parser returns 0 if the line was blank |
705 |
if( parseAtom( readLine, lineNum, atomInfo ) ){ |
706 |
atomInfo.ident = identNum; |
707 |
headAtomType->add( atomInfo );; |
708 |
identNum++; |
709 |
} |
710 |
} |
711 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
712 |
lineNum++; |
713 |
} |
714 |
|
715 |
#ifdef IS_MPI |
716 |
|
717 |
// send out the linked list to all the other processes |
718 |
|
719 |
sprintf( checkPointMsg, |
720 |
"DUFF atom structures read successfully." ); |
721 |
MPIcheckPoint(); |
722 |
|
723 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
724 |
while( currentAtomType != NULL ){ |
725 |
currentAtomType->duplicate( atomInfo ); |
726 |
|
727 |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
728 |
|
729 |
sprintf( checkPointMsg, |
730 |
"successfully sent DUFF force type: \"%s\"\n", |
731 |
atomInfo.name ); |
732 |
MPIcheckPoint(); |
733 |
|
734 |
currentAtomType = currentAtomType->next; |
735 |
} |
736 |
atomInfo.last = 1; |
737 |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
738 |
|
739 |
} |
740 |
|
741 |
else{ |
742 |
|
743 |
// listen for node 0 to send out the force params |
744 |
|
745 |
MPIcheckPoint(); |
746 |
|
747 |
headAtomType = new LinkedAtomType; |
748 |
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
749 |
|
750 |
while( !atomInfo.last ){ |
751 |
|
752 |
headAtomType->add( atomInfo ); |
753 |
|
754 |
MPIcheckPoint(); |
755 |
|
756 |
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
757 |
} |
758 |
} |
759 |
|
760 |
#endif // is_mpi |
761 |
|
762 |
// dummy variables |
763 |
|
764 |
currentAtomType = headAtomType->next;; |
765 |
while( currentAtomType != NULL ){ |
766 |
|
767 |
if( currentAtomType->name[0] != '\0' ){ |
768 |
|
769 |
if (currentAtomType->isSSD || currentAtomType->isDipole) |
770 |
at = new DirectionalAtomType(); |
771 |
else |
772 |
at = new AtomType(); |
773 |
|
774 |
if (currentAtomType->isSSD) { |
775 |
((DirectionalAtomType*)at)->setSticky(); |
776 |
entry_plug->useSticky = 1; |
777 |
} |
778 |
|
779 |
if (currentAtomType->isDipole) { |
780 |
((DirectionalAtomType*)at)->setDipole(); |
781 |
entry_plug->useDipoles = 1; |
782 |
} |
783 |
|
784 |
at->setIdent(currentAtomType->ident); |
785 |
at->setName(currentAtomType->name); |
786 |
at->setLennardJones(); |
787 |
at->complete(); |
788 |
} |
789 |
currentAtomType = currentAtomType->next; |
790 |
} |
791 |
|
792 |
currentAtomType = headAtomType->next;; |
793 |
while( currentAtomType != NULL ){ |
794 |
|
795 |
if( currentAtomType->name[0] != '\0' ){ |
796 |
isError = 0; |
797 |
newLJtype( &(currentAtomType->ident), &(currentAtomType->sigma), |
798 |
&(currentAtomType->epslon), &isError); |
799 |
if( isError ){ |
800 |
sprintf( painCave.errMsg, |
801 |
"Error initializing the \"%s\" LJ type in fortran\n", |
802 |
currentAtomType->name ); |
803 |
painCave.isFatal = 1; |
804 |
simError(); |
805 |
} |
806 |
|
807 |
if (currentAtomType->isDipole) { |
808 |
newDipoleType(&(currentAtomType->ident), &(currentAtomType->dipole), |
809 |
&isError); |
810 |
if( isError ){ |
811 |
sprintf( painCave.errMsg, |
812 |
"Error initializing the \"%s\" dipole type in fortran\n", |
813 |
currentAtomType->name ); |
814 |
painCave.isFatal = 1; |
815 |
simError(); |
816 |
} |
817 |
} |
818 |
|
819 |
if(currentAtomType->isSSD) { |
820 |
makeStickyType( &(currentAtomType->w0), &(currentAtomType->v0), |
821 |
&(currentAtomType->v0p), |
822 |
&(currentAtomType->rl), &(currentAtomType->ru), |
823 |
&(currentAtomType->rlp), &(currentAtomType->rup)); |
824 |
} |
825 |
|
826 |
} |
827 |
currentAtomType = currentAtomType->next; |
828 |
} |
829 |
|
830 |
#ifdef IS_MPI |
831 |
sprintf( checkPointMsg, |
832 |
"DUFF atom structures successfully sent to fortran\n" ); |
833 |
MPIcheckPoint(); |
834 |
#endif // is_mpi |
835 |
|
836 |
|
837 |
|
838 |
// read in the bonds |
839 |
|
840 |
#ifdef IS_MPI |
841 |
if( worldRank == 0 ){ |
842 |
#endif |
843 |
|
844 |
// read in the bond types. |
845 |
|
846 |
headBondType = new LinkedBondType; |
847 |
|
848 |
fastForward( "BondTypes", "initializeBonds" ); |
849 |
|
850 |
// we are now at the bondTypes section |
851 |
|
852 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
853 |
lineNum++; |
854 |
|
855 |
|
856 |
// read a line, and start parseing out the atom types |
857 |
|
858 |
if( eof_test == NULL ){ |
859 |
sprintf( painCave.errMsg, |
860 |
"Error in reading bonds from force file at line %d.\n", |
861 |
lineNum ); |
862 |
painCave.isFatal = 1; |
863 |
simError(); |
864 |
} |
865 |
|
866 |
// stop reading at end of file, or at next section |
867 |
while( readLine[0] != '#' && eof_test != NULL ){ |
868 |
|
869 |
// toss comment lines |
870 |
if( readLine[0] != '!' ){ |
871 |
|
872 |
// the parser returns 0 if the line was blank |
873 |
if( parseBond( readLine, lineNum, bondInfo ) ){ |
874 |
headBondType->add( bondInfo ); |
875 |
} |
876 |
} |
877 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
878 |
lineNum++; |
879 |
} |
880 |
|
881 |
#ifdef IS_MPI |
882 |
|
883 |
// send out the linked list to all the other processes |
884 |
|
885 |
sprintf( checkPointMsg, |
886 |
"DUFF bond structures read successfully." ); |
887 |
MPIcheckPoint(); |
888 |
|
889 |
currentBondType = headBondType->next; |
890 |
while( currentBondType != NULL ){ |
891 |
currentBondType->duplicate( bondInfo ); |
892 |
sendFrcStruct( &bondInfo, mpiBondStructType ); |
893 |
currentBondType = currentBondType->next; |
894 |
} |
895 |
bondInfo.last = 1; |
896 |
sendFrcStruct( &bondInfo, mpiBondStructType ); |
897 |
|
898 |
} |
899 |
|
900 |
else{ |
901 |
|
902 |
// listen for node 0 to send out the force params |
903 |
|
904 |
MPIcheckPoint(); |
905 |
|
906 |
headBondType = new LinkedBondType; |
907 |
receiveFrcStruct( &bondInfo, mpiBondStructType ); |
908 |
while( !bondInfo.last ){ |
909 |
|
910 |
headBondType->add( bondInfo ); |
911 |
receiveFrcStruct( &bondInfo, mpiBondStructType ); |
912 |
} |
913 |
} |
914 |
|
915 |
sprintf( checkPointMsg, |
916 |
"DUFF bond structures broadcast successfully." ); |
917 |
MPIcheckPoint(); |
918 |
|
919 |
#endif // is_mpi |
920 |
|
921 |
|
922 |
// read in the bends |
923 |
|
924 |
#ifdef IS_MPI |
925 |
if( worldRank == 0 ){ |
926 |
#endif |
927 |
|
928 |
// read in the bend types. |
929 |
|
930 |
headBendType = new LinkedBendType; |
931 |
|
932 |
fastForward( "BendTypes", "initializeBends" ); |
933 |
|
934 |
// we are now at the bendTypes section |
935 |
|
936 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
937 |
lineNum++; |
938 |
|
939 |
// read a line, and start parseing out the bend types |
940 |
|
941 |
if( eof_test == NULL ){ |
942 |
sprintf( painCave.errMsg, |
943 |
"Error in reading bends from force file at line %d.\n", |
944 |
lineNum ); |
945 |
painCave.isFatal = 1; |
946 |
simError(); |
947 |
} |
948 |
|
949 |
// stop reading at end of file, or at next section |
950 |
while( readLine[0] != '#' && eof_test != NULL ){ |
951 |
|
952 |
// toss comment lines |
953 |
if( readLine[0] != '!' ){ |
954 |
|
955 |
// the parser returns 0 if the line was blank |
956 |
if( parseBend( readLine, lineNum, bendInfo ) ){ |
957 |
headBendType->add( bendInfo ); |
958 |
} |
959 |
} |
960 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
961 |
lineNum++; |
962 |
} |
963 |
|
964 |
#ifdef IS_MPI |
965 |
|
966 |
// send out the linked list to all the other processes |
967 |
|
968 |
sprintf( checkPointMsg, |
969 |
"DUFF bend structures read successfully." ); |
970 |
MPIcheckPoint(); |
971 |
|
972 |
currentBendType = headBendType->next; |
973 |
while( currentBendType != NULL ){ |
974 |
currentBendType->duplicate( bendInfo ); |
975 |
sendFrcStruct( &bendInfo, mpiBendStructType ); |
976 |
currentBendType = currentBendType->next; |
977 |
} |
978 |
bendInfo.last = 1; |
979 |
sendFrcStruct( &bendInfo, mpiBendStructType ); |
980 |
|
981 |
} |
982 |
|
983 |
else{ |
984 |
|
985 |
// listen for node 0 to send out the force params |
986 |
|
987 |
MPIcheckPoint(); |
988 |
|
989 |
headBendType = new LinkedBendType; |
990 |
receiveFrcStruct( &bendInfo, mpiBendStructType ); |
991 |
while( !bendInfo.last ){ |
992 |
|
993 |
headBendType->add( bendInfo ); |
994 |
receiveFrcStruct( &bendInfo, mpiBendStructType ); |
995 |
} |
996 |
} |
997 |
|
998 |
sprintf( checkPointMsg, |
999 |
"DUFF bend structures broadcast successfully." ); |
1000 |
MPIcheckPoint(); |
1001 |
|
1002 |
#endif // is_mpi |
1003 |
|
1004 |
|
1005 |
// read in the torsions |
1006 |
|
1007 |
#ifdef IS_MPI |
1008 |
if( worldRank == 0 ){ |
1009 |
#endif |
1010 |
|
1011 |
// read in the torsion types. |
1012 |
|
1013 |
headTorsionType = new LinkedTorsionType; |
1014 |
|
1015 |
fastForward( "TorsionTypes", "initializeTorsions" ); |
1016 |
|
1017 |
// we are now at the torsionTypes section |
1018 |
|
1019 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1020 |
lineNum++; |
1021 |
|
1022 |
|
1023 |
// read a line, and start parseing out the atom types |
1024 |
|
1025 |
if( eof_test == NULL ){ |
1026 |
sprintf( painCave.errMsg, |
1027 |
"Error in reading torsions from force file at line %d.\n", |
1028 |
lineNum ); |
1029 |
painCave.isFatal = 1; |
1030 |
simError(); |
1031 |
} |
1032 |
|
1033 |
// stop reading at end of file, or at next section |
1034 |
while( readLine[0] != '#' && eof_test != NULL ){ |
1035 |
|
1036 |
// toss comment lines |
1037 |
if( readLine[0] != '!' ){ |
1038 |
|
1039 |
// the parser returns 0 if the line was blank |
1040 |
if( parseTorsion( readLine, lineNum, torsionInfo ) ){ |
1041 |
headTorsionType->add( torsionInfo ); |
1042 |
|
1043 |
} |
1044 |
} |
1045 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1046 |
lineNum++; |
1047 |
} |
1048 |
|
1049 |
#ifdef IS_MPI |
1050 |
|
1051 |
// send out the linked list to all the other processes |
1052 |
|
1053 |
sprintf( checkPointMsg, |
1054 |
"DUFF torsion structures read successfully." ); |
1055 |
MPIcheckPoint(); |
1056 |
|
1057 |
currentTorsionType = headTorsionType->next; |
1058 |
while( currentTorsionType != NULL ){ |
1059 |
currentTorsionType->duplicate( torsionInfo ); |
1060 |
sendFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1061 |
currentTorsionType = currentTorsionType->next; |
1062 |
} |
1063 |
torsionInfo.last = 1; |
1064 |
sendFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1065 |
|
1066 |
} |
1067 |
|
1068 |
else{ |
1069 |
|
1070 |
// listen for node 0 to send out the force params |
1071 |
|
1072 |
MPIcheckPoint(); |
1073 |
|
1074 |
headTorsionType = new LinkedTorsionType; |
1075 |
receiveFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1076 |
while( !torsionInfo.last ){ |
1077 |
|
1078 |
headTorsionType->add( torsionInfo ); |
1079 |
receiveFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1080 |
} |
1081 |
} |
1082 |
|
1083 |
sprintf( checkPointMsg, |
1084 |
"DUFF torsion structures broadcast successfully." ); |
1085 |
MPIcheckPoint(); |
1086 |
|
1087 |
#endif // is_mpi |
1088 |
|
1089 |
entry_plug->useLennardJones = 1; |
1090 |
} |
1091 |
|
1092 |
|
1093 |
|
1094 |
void DUFF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
1095 |
|
1096 |
|
1097 |
////////////////////////////////////////////////// |
1098 |
// a quick water fix |
1099 |
|
1100 |
double waterI[3][3]; |
1101 |
waterI[0][0] = 1.76958347772500; |
1102 |
waterI[0][1] = 0.0; |
1103 |
waterI[0][2] = 0.0; |
1104 |
|
1105 |
waterI[1][0] = 0.0; |
1106 |
waterI[1][1] = 0.614537057924513; |
1107 |
waterI[1][2] = 0.0; |
1108 |
|
1109 |
waterI[2][0] = 0.0; |
1110 |
waterI[2][1] = 0.0; |
1111 |
waterI[2][2] = 1.15504641980049; |
1112 |
|
1113 |
|
1114 |
double headI[3][3]; |
1115 |
headI[0][0] = 1125; |
1116 |
headI[0][1] = 0.0; |
1117 |
headI[0][2] = 0.0; |
1118 |
|
1119 |
headI[1][0] = 0.0; |
1120 |
headI[1][1] = 1125; |
1121 |
headI[1][2] = 0.0; |
1122 |
|
1123 |
headI[2][0] = 0.0; |
1124 |
headI[2][1] = 0.0; |
1125 |
headI[2][2] = 250; |
1126 |
|
1127 |
////////////////////////////////////////////////// |
1128 |
|
1129 |
|
1130 |
// initialize the atoms |
1131 |
|
1132 |
DirectionalAtom* dAtom; |
1133 |
double ji[3]; |
1134 |
|
1135 |
for(int i=0; i<nAtoms; i++ ){ |
1136 |
|
1137 |
currentAtomType = headAtomType->find(the_atoms[i]->getType().c_str() ); |
1138 |
if( currentAtomType == NULL ){ |
1139 |
sprintf( painCave.errMsg, |
1140 |
"AtomType error, %s not found in force file.\n", |
1141 |
the_atoms[i]->getType().c_str() ); |
1142 |
painCave.isFatal = 1; |
1143 |
simError(); |
1144 |
} |
1145 |
|
1146 |
the_atoms[i]->setMass( currentAtomType->mass ); |
1147 |
the_atoms[i]->setIdent( currentAtomType->ident ); |
1148 |
|
1149 |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
1150 |
|
1151 |
if( currentAtomType->isDipole ){ |
1152 |
if( the_atoms[i]->isDirectional() ){ |
1153 |
|
1154 |
dAtom = (DirectionalAtom *) the_atoms[i]; |
1155 |
dAtom->setHasDipole( 1 ); |
1156 |
|
1157 |
ji[0] = 0.0; |
1158 |
ji[1] = 0.0; |
1159 |
ji[2] = 0.0; |
1160 |
|
1161 |
dAtom->setJ( ji ); |
1162 |
|
1163 |
if(!strcmp("SSD",the_atoms[i]->getType().c_str())){ |
1164 |
dAtom->setI( waterI ); |
1165 |
} |
1166 |
else if(!strcmp("HEAD",the_atoms[i]->getType().c_str())){ |
1167 |
dAtom->setI( headI ); |
1168 |
} |
1169 |
else{ |
1170 |
sprintf(painCave.errMsg, |
1171 |
"AtmType error, %s does not have a moment of inertia set.\n", |
1172 |
the_atoms[i]->getType().c_str() ); |
1173 |
painCave.isFatal = 1; |
1174 |
simError(); |
1175 |
} |
1176 |
entry_plug->n_dipoles++; |
1177 |
} |
1178 |
else{ |
1179 |
|
1180 |
sprintf( painCave.errMsg, |
1181 |
"DUFF error: Atom \"%s\" is a dipole, yet no standard" |
1182 |
" orientation was specifed in the meta-data file.\n", |
1183 |
currentAtomType->name ); |
1184 |
painCave.isFatal = 1; |
1185 |
simError(); |
1186 |
} |
1187 |
} |
1188 |
else{ |
1189 |
if( the_atoms[i]->isDirectional() ){ |
1190 |
sprintf( painCave.errMsg, |
1191 |
"DUFF error: Atom \"%s\" was given a standard " |
1192 |
"orientation in the meta-data file, yet it is not a dipole.\n", |
1193 |
currentAtomType->name); |
1194 |
painCave.isFatal = 1; |
1195 |
simError(); |
1196 |
} |
1197 |
} |
1198 |
} |
1199 |
} |
1200 |
|
1201 |
void DUFF::initializeBonds( int nBonds, Bond** bondArray, |
1202 |
bond_pair* the_bonds ){ |
1203 |
int i,a,b; |
1204 |
|
1205 |
Atom** the_atoms; |
1206 |
the_atoms = entry_plug->atoms; |
1207 |
|
1208 |
|
1209 |
// initialize the Bonds |
1210 |
|
1211 |
for( i=0; i<nBonds; i++ ){ |
1212 |
|
1213 |
a = the_bonds[i].a; |
1214 |
b = the_bonds[i].b; |
1215 |
|
1216 |
currentBondType = headBondType->find( the_atoms[a]->getType().c_str(), the_atoms[b]->getType().c_str() ); |
1217 |
if( currentBondType == NULL ){ |
1218 |
sprintf( painCave.errMsg, |
1219 |
"BondType error, %s - %s not found in force file.\n", |
1220 |
the_atoms[a]->getType().c_str(), the_atoms[b]->getType().c_str() ); |
1221 |
painCave.isFatal = 1; |
1222 |
simError(); |
1223 |
} |
1224 |
|
1225 |
switch( currentBondType->type ){ |
1226 |
|
1227 |
case FIXED_BOND: |
1228 |
|
1229 |
bondArray[i] = new ConstrainedBond( *the_atoms[a], |
1230 |
*the_atoms[b], |
1231 |
currentBondType->d0 ); |
1232 |
entry_plug->n_constraints++; |
1233 |
break; |
1234 |
|
1235 |
case HARMONIC_BOND: |
1236 |
|
1237 |
bondArray[i] = new HarmonicBond( *the_atoms[a], |
1238 |
*the_atoms[b], |
1239 |
currentBondType->d0, |
1240 |
currentBondType->k0 ); |
1241 |
break; |
1242 |
|
1243 |
default: |
1244 |
|
1245 |
break; |
1246 |
// do nothing |
1247 |
} |
1248 |
} |
1249 |
} |
1250 |
|
1251 |
void DUFF::initializeBends( int nBends, Bend** bendArray, |
1252 |
bend_set* the_bends ){ |
1253 |
|
1254 |
QuadraticBend* qBend; |
1255 |
GhostBend* gBend; |
1256 |
Atom** the_atoms; |
1257 |
the_atoms = entry_plug->atoms; |
1258 |
|
1259 |
int i, a, b, c; |
1260 |
string atomA; |
1261 |
string atomB; |
1262 |
string atomC; |
1263 |
|
1264 |
// initialize the Bends |
1265 |
|
1266 |
for( i=0; i<nBends; i++ ){ |
1267 |
|
1268 |
a = the_bends[i].a; |
1269 |
b = the_bends[i].b; |
1270 |
c = the_bends[i].c; |
1271 |
|
1272 |
atomA = the_atoms[a]->getType(); |
1273 |
atomB = the_atoms[b]->getType(); |
1274 |
|
1275 |
if( the_bends[i].isGhost ) atomC = "GHOST"; |
1276 |
else atomC = the_atoms[c]->getType(); |
1277 |
|
1278 |
currentBendType = headBendType->find( atomA.c_str(), atomB.c_str(), atomC.c_str()); |
1279 |
if( currentBendType == NULL ){ |
1280 |
sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found" |
1281 |
" in force file.\n", |
1282 |
atomA.c_str(), atomB.c_str(), atomC.c_str() ); |
1283 |
painCave.isFatal = 1; |
1284 |
simError(); |
1285 |
} |
1286 |
|
1287 |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1288 |
|
1289 |
if( the_bends[i].isGhost){ |
1290 |
|
1291 |
if( the_bends[i].ghost == b ){ |
1292 |
// do nothing |
1293 |
} |
1294 |
else if( the_bends[i].ghost == a ){ |
1295 |
c = a; |
1296 |
a = b; |
1297 |
b = c; |
1298 |
} |
1299 |
else{ |
1300 |
sprintf( painCave.errMsg, |
1301 |
"BendType error, %s - %s - %s,\n" |
1302 |
" --> central atom is not " |
1303 |
"correctly identified with the " |
1304 |
"\"ghostVectorSource = \" tag.\n", |
1305 |
atomA.c_str(), atomB.c_str(), atomC.c_str() ); |
1306 |
painCave.isFatal = 1; |
1307 |
simError(); |
1308 |
} |
1309 |
|
1310 |
gBend = new GhostBend( *the_atoms[a], |
1311 |
*the_atoms[b]); |
1312 |
|
1313 |
gBend->setConstants( currentBendType->k1, |
1314 |
currentBendType->k2, |
1315 |
currentBendType->k3, |
1316 |
currentBendType->t0 ); |
1317 |
bendArray[i] = gBend; |
1318 |
} |
1319 |
else{ |
1320 |
qBend = new QuadraticBend( *the_atoms[a], |
1321 |
*the_atoms[b], |
1322 |
*the_atoms[c] ); |
1323 |
qBend->setConstants( currentBendType->k1, |
1324 |
currentBendType->k2, |
1325 |
currentBendType->k3, |
1326 |
currentBendType->t0 ); |
1327 |
bendArray[i] = qBend; |
1328 |
} |
1329 |
} |
1330 |
} |
1331 |
} |
1332 |
|
1333 |
void DUFF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
1334 |
torsion_set* the_torsions ){ |
1335 |
|
1336 |
int i, a, b, c, d; |
1337 |
|
1338 |
CubicTorsion* cTors; |
1339 |
Atom** the_atoms; |
1340 |
the_atoms = entry_plug->atoms; |
1341 |
|
1342 |
// initialize the Torsions |
1343 |
|
1344 |
for( i=0; i<nTorsions; i++ ){ |
1345 |
|
1346 |
a = the_torsions[i].a; |
1347 |
b = the_torsions[i].b; |
1348 |
c = the_torsions[i].c; |
1349 |
d = the_torsions[i].d; |
1350 |
|
1351 |
currentTorsionType = headTorsionType->find( the_atoms[a]->getType().c_str(), |
1352 |
the_atoms[b]->getType().c_str(), |
1353 |
the_atoms[c]->getType().c_str(), |
1354 |
the_atoms[d]->getType().c_str() ); |
1355 |
if( currentTorsionType == NULL ){ |
1356 |
sprintf( painCave.errMsg, |
1357 |
"TorsionType error, %s - %s - %s - %s not found" |
1358 |
" in force file.\n", |
1359 |
the_atoms[a]->getType().c_str(), |
1360 |
the_atoms[b]->getType().c_str(), |
1361 |
the_atoms[c]->getType().c_str(), |
1362 |
the_atoms[d]->getType().c_str() ); |
1363 |
painCave.isFatal = 1; |
1364 |
simError(); |
1365 |
} |
1366 |
|
1367 |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1368 |
|
1369 |
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1370 |
*the_atoms[c], *the_atoms[d] ); |
1371 |
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1372 |
currentTorsionType->k3, currentTorsionType->k4 ); |
1373 |
torsionArray[i] = cTors; |
1374 |
} |
1375 |
} |
1376 |
} |
1377 |
|
1378 |
void DUFF::fastForward( char* stopText, char* searchOwner ){ |
1379 |
|
1380 |
int foundText = 0; |
1381 |
char* the_token; |
1382 |
|
1383 |
rewind( frcFile ); |
1384 |
lineNum = 0; |
1385 |
|
1386 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1387 |
lineNum++; |
1388 |
if( eof_test == NULL ){ |
1389 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
1390 |
" file is empty.\n", |
1391 |
searchOwner ); |
1392 |
painCave.isFatal = 1; |
1393 |
simError(); |
1394 |
} |
1395 |
|
1396 |
|
1397 |
while( !foundText ){ |
1398 |
while( eof_test != NULL && readLine[0] != '#' ){ |
1399 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1400 |
lineNum++; |
1401 |
} |
1402 |
if( eof_test == NULL ){ |
1403 |
sprintf( painCave.errMsg, |
1404 |
"Error fast forwarding force file for %s at " |
1405 |
"line %d: file ended unexpectedly.\n", |
1406 |
searchOwner, |
1407 |
lineNum ); |
1408 |
painCave.isFatal = 1; |
1409 |
simError(); |
1410 |
} |
1411 |
|
1412 |
the_token = strtok( readLine, " ,;\t#\n" ); |
1413 |
foundText = !strcmp( stopText, the_token ); |
1414 |
|
1415 |
if( !foundText ){ |
1416 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1417 |
lineNum++; |
1418 |
|
1419 |
if( eof_test == NULL ){ |
1420 |
sprintf( painCave.errMsg, |
1421 |
"Error fast forwarding force file for %s at " |
1422 |
"line %d: file ended unexpectedly.\n", |
1423 |
searchOwner, |
1424 |
lineNum ); |
1425 |
painCave.isFatal = 1; |
1426 |
simError(); |
1427 |
} |
1428 |
} |
1429 |
} |
1430 |
} |
1431 |
|
1432 |
|
1433 |
int DUFF_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1434 |
|
1435 |
char* the_token; |
1436 |
|
1437 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1438 |
if( the_token != NULL ){ |
1439 |
|
1440 |
strcpy( info.name, the_token ); |
1441 |
|
1442 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1443 |
sprintf( painCave.errMsg, |
1444 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1445 |
painCave.isFatal = 1; |
1446 |
simError(); |
1447 |
} |
1448 |
|
1449 |
info.isDipole = atoi( the_token ); |
1450 |
|
1451 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1452 |
sprintf( painCave.errMsg, |
1453 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1454 |
painCave.isFatal = 1; |
1455 |
simError(); |
1456 |
} |
1457 |
|
1458 |
info.isSSD = atoi( the_token ); |
1459 |
|
1460 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1461 |
sprintf( painCave.errMsg, |
1462 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1463 |
painCave.isFatal = 1; |
1464 |
simError(); |
1465 |
} |
1466 |
|
1467 |
info.mass = atof( the_token ); |
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.epslon = atof( the_token ); |
1477 |
|
1478 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1479 |
sprintf( painCave.errMsg, |
1480 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1481 |
painCave.isFatal = 1; |
1482 |
simError(); |
1483 |
} |
1484 |
|
1485 |
info.sigma = atof( the_token ); |
1486 |
|
1487 |
if( info.isDipole ){ |
1488 |
|
1489 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1490 |
sprintf( painCave.errMsg, |
1491 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1492 |
painCave.isFatal = 1; |
1493 |
simError(); |
1494 |
} |
1495 |
|
1496 |
info.dipole = atof( the_token ); |
1497 |
} |
1498 |
else info.dipole = 0.0; |
1499 |
|
1500 |
if( info.isSSD ){ |
1501 |
|
1502 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1503 |
sprintf( painCave.errMsg, |
1504 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1505 |
painCave.isFatal = 1; |
1506 |
simError(); |
1507 |
} |
1508 |
|
1509 |
info.w0 = atof( the_token ); |
1510 |
|
1511 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1512 |
sprintf( painCave.errMsg, |
1513 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1514 |
painCave.isFatal = 1; |
1515 |
simError(); |
1516 |
} |
1517 |
|
1518 |
info.v0 = atof( the_token ); |
1519 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1520 |
sprintf( painCave.errMsg, |
1521 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1522 |
painCave.isFatal = 1; |
1523 |
simError(); |
1524 |
} |
1525 |
|
1526 |
info.v0p = atof( the_token ); |
1527 |
|
1528 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1529 |
sprintf( painCave.errMsg, |
1530 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1531 |
painCave.isFatal = 1; |
1532 |
simError(); |
1533 |
} |
1534 |
|
1535 |
info.rl = atof( the_token ); |
1536 |
|
1537 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1538 |
sprintf( painCave.errMsg, |
1539 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1540 |
painCave.isFatal = 1; |
1541 |
simError(); |
1542 |
} |
1543 |
|
1544 |
info.ru = atof( the_token ); |
1545 |
|
1546 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1547 |
sprintf( painCave.errMsg, |
1548 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1549 |
painCave.isFatal = 1; |
1550 |
simError(); |
1551 |
} |
1552 |
|
1553 |
info.rlp = atof( the_token ); |
1554 |
|
1555 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1556 |
sprintf( painCave.errMsg, |
1557 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1558 |
painCave.isFatal = 1; |
1559 |
simError(); |
1560 |
} |
1561 |
|
1562 |
info.rup = atof( the_token ); |
1563 |
} |
1564 |
else info.v0 = info.w0 = info.v0p = info.rl = info.ru = info.rlp = info.rup = 0.0; |
1565 |
|
1566 |
return 1; |
1567 |
} |
1568 |
else return 0; |
1569 |
} |
1570 |
|
1571 |
int DUFF_NS::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1572 |
|
1573 |
char* the_token; |
1574 |
char bondType[30]; |
1575 |
|
1576 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1577 |
if( the_token != NULL ){ |
1578 |
|
1579 |
strcpy( info.nameA, the_token ); |
1580 |
|
1581 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1582 |
sprintf( painCave.errMsg, |
1583 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1584 |
painCave.isFatal = 1; |
1585 |
simError(); |
1586 |
} |
1587 |
|
1588 |
strcpy( info.nameB, the_token ); |
1589 |
|
1590 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1591 |
sprintf( painCave.errMsg, |
1592 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1593 |
painCave.isFatal = 1; |
1594 |
simError(); |
1595 |
} |
1596 |
|
1597 |
strcpy( bondType, the_token ); |
1598 |
|
1599 |
if( !strcmp( bondType, "fixed" ) ){ |
1600 |
info.type = FIXED_BOND; |
1601 |
|
1602 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1603 |
sprintf( painCave.errMsg, |
1604 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1605 |
painCave.isFatal = 1; |
1606 |
simError(); |
1607 |
} |
1608 |
|
1609 |
info.d0 = atof( the_token ); |
1610 |
|
1611 |
info.k0=0.0; |
1612 |
} |
1613 |
else if( !strcmp( bondType, "harmonic" ) ){ |
1614 |
info.type = HARMONIC_BOND; |
1615 |
|
1616 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1617 |
sprintf( painCave.errMsg, |
1618 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1619 |
painCave.isFatal = 1; |
1620 |
simError(); |
1621 |
} |
1622 |
|
1623 |
info.d0 = atof( the_token ); |
1624 |
|
1625 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1626 |
sprintf( painCave.errMsg, |
1627 |
"Error parseing BondTypes: line %d\n", lineNum ); |
1628 |
painCave.isFatal = 1; |
1629 |
simError(); |
1630 |
} |
1631 |
|
1632 |
info.k0 = atof( the_token ); |
1633 |
} |
1634 |
|
1635 |
else{ |
1636 |
sprintf( painCave.errMsg, |
1637 |
"Unknown DUFF bond type \"%s\" at line %d\n", |
1638 |
bondType, |
1639 |
lineNum ); |
1640 |
painCave.isFatal = 1; |
1641 |
simError(); |
1642 |
} |
1643 |
|
1644 |
return 1; |
1645 |
} |
1646 |
else return 0; |
1647 |
} |
1648 |
|
1649 |
|
1650 |
int DUFF_NS::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1651 |
|
1652 |
char* the_token; |
1653 |
|
1654 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1655 |
if( the_token != NULL ){ |
1656 |
|
1657 |
strcpy( info.nameA, the_token ); |
1658 |
|
1659 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1660 |
sprintf( painCave.errMsg, |
1661 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1662 |
painCave.isFatal = 1; |
1663 |
simError(); |
1664 |
} |
1665 |
|
1666 |
strcpy( info.nameB, the_token ); |
1667 |
|
1668 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1669 |
sprintf( painCave.errMsg, |
1670 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1671 |
painCave.isFatal = 1; |
1672 |
simError(); |
1673 |
} |
1674 |
|
1675 |
strcpy( info.nameC, the_token ); |
1676 |
|
1677 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1678 |
sprintf( painCave.errMsg, |
1679 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1680 |
painCave.isFatal = 1; |
1681 |
simError(); |
1682 |
} |
1683 |
|
1684 |
strcpy( info.type, the_token ); |
1685 |
|
1686 |
if( !strcmp( info.type, "quadratic" ) ){ |
1687 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1688 |
sprintf( painCave.errMsg, |
1689 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1690 |
painCave.isFatal = 1; |
1691 |
simError(); |
1692 |
} |
1693 |
|
1694 |
info.k1 = atof( the_token ); |
1695 |
|
1696 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1697 |
sprintf( painCave.errMsg, |
1698 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1699 |
painCave.isFatal = 1; |
1700 |
simError(); |
1701 |
} |
1702 |
|
1703 |
info.k2 = atof( the_token ); |
1704 |
|
1705 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1706 |
sprintf( painCave.errMsg, |
1707 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1708 |
painCave.isFatal = 1; |
1709 |
simError(); |
1710 |
} |
1711 |
|
1712 |
info.k3 = atof( the_token ); |
1713 |
|
1714 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1715 |
sprintf( painCave.errMsg, |
1716 |
"Error parseing BendTypes: line %d\n", lineNum ); |
1717 |
painCave.isFatal = 1; |
1718 |
simError(); |
1719 |
} |
1720 |
|
1721 |
info.t0 = atof( the_token ); |
1722 |
} |
1723 |
|
1724 |
else{ |
1725 |
sprintf( painCave.errMsg, |
1726 |
"Unknown DUFF bend type \"%s\" at line %d\n", |
1727 |
info.type, |
1728 |
lineNum ); |
1729 |
painCave.isFatal = 1; |
1730 |
simError(); |
1731 |
} |
1732 |
|
1733 |
return 1; |
1734 |
} |
1735 |
else return 0; |
1736 |
} |
1737 |
|
1738 |
int DUFF_NS::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1739 |
|
1740 |
char* the_token; |
1741 |
|
1742 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1743 |
if( the_token != NULL ){ |
1744 |
|
1745 |
strcpy( info.nameA, the_token ); |
1746 |
|
1747 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1748 |
sprintf( painCave.errMsg, |
1749 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1750 |
painCave.isFatal = 1; |
1751 |
simError(); |
1752 |
} |
1753 |
|
1754 |
strcpy( info.nameB, the_token ); |
1755 |
|
1756 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1757 |
sprintf( painCave.errMsg, |
1758 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1759 |
painCave.isFatal = 1; |
1760 |
simError(); |
1761 |
} |
1762 |
|
1763 |
strcpy( info.nameC, the_token ); |
1764 |
|
1765 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1766 |
sprintf( painCave.errMsg, |
1767 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1768 |
painCave.isFatal = 1; |
1769 |
simError(); |
1770 |
} |
1771 |
|
1772 |
strcpy( info.nameD, the_token ); |
1773 |
|
1774 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1775 |
sprintf( painCave.errMsg, |
1776 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1777 |
painCave.isFatal = 1; |
1778 |
simError(); |
1779 |
} |
1780 |
|
1781 |
strcpy( info.type, the_token ); |
1782 |
|
1783 |
if( !strcmp( info.type, "cubic" ) ){ |
1784 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1785 |
sprintf( painCave.errMsg, |
1786 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1787 |
painCave.isFatal = 1; |
1788 |
simError(); |
1789 |
} |
1790 |
|
1791 |
info.k1 = atof( the_token ); |
1792 |
|
1793 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1794 |
sprintf( painCave.errMsg, |
1795 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1796 |
painCave.isFatal = 1; |
1797 |
simError(); |
1798 |
} |
1799 |
|
1800 |
info.k2 = atof( the_token ); |
1801 |
|
1802 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1803 |
sprintf( painCave.errMsg, |
1804 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1805 |
painCave.isFatal = 1; |
1806 |
simError(); |
1807 |
} |
1808 |
|
1809 |
info.k3 = atof( the_token ); |
1810 |
|
1811 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1812 |
sprintf( painCave.errMsg, |
1813 |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1814 |
painCave.isFatal = 1; |
1815 |
simError(); |
1816 |
} |
1817 |
|
1818 |
info.k4 = atof( the_token ); |
1819 |
|
1820 |
} |
1821 |
|
1822 |
else{ |
1823 |
sprintf( painCave.errMsg, |
1824 |
"Unknown DUFF torsion type \"%s\" at line %d\n", |
1825 |
info.type, |
1826 |
lineNum ); |
1827 |
painCave.isFatal = 1; |
1828 |
simError(); |
1829 |
} |
1830 |
|
1831 |
return 1; |
1832 |
} |
1833 |
|
1834 |
else return 0; |
1835 |
} |