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 |
TraPPEFF::TraPPEFF(){ |
13 |
|
14 |
#ifdef IS_MPI |
15 |
sprintf( painCave.errMsg, |
16 |
"TraPPE ForceField does not currently support mpi" ); |
17 |
painCave.isFatal = 1; |
18 |
simError(); |
19 |
#endif // is_mpi |
20 |
|
21 |
|
22 |
char fileName[200]; |
23 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
24 |
char* ffPath; |
25 |
char temp[200]; |
26 |
|
27 |
// generate the force file name |
28 |
|
29 |
strcpy( fileName, "TraPPE.frc" ); |
30 |
|
31 |
// attempt to open the file in the current directory first. |
32 |
|
33 |
frcFile = fopen( fileName, "r" ); |
34 |
|
35 |
if( frcFile == NULL ){ |
36 |
|
37 |
// next see if the force path enviorment variable is set |
38 |
|
39 |
ffPath = getenv( ffPath_env ); |
40 |
strcpy( temp, ffPath ); |
41 |
strcat( temp, "/" ); |
42 |
strcat( temp, fileName ); |
43 |
strcpy( fileName, temp ); |
44 |
|
45 |
frcFile = fopen( fileName, "r" ); |
46 |
|
47 |
if( frcFile == NULL ){ |
48 |
|
49 |
fprintf( stderr, |
50 |
"Error opening the force field parameter file: %s\n" |
51 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
52 |
"vairable?\n", |
53 |
fileName ); |
54 |
exit( 8 ); |
55 |
} |
56 |
} |
57 |
} |
58 |
|
59 |
TraPPEFF::~TraPPEFF(){ |
60 |
|
61 |
fclose( frcFile ); |
62 |
} |
63 |
|
64 |
void TraPPEFF::initializeAtoms( void ){ |
65 |
|
66 |
class LinkedType { |
67 |
public: |
68 |
LinkedType(){ |
69 |
next = NULL; |
70 |
name[0] = '\0'; |
71 |
} |
72 |
~LinkedType(){ if( next != NULL ) delete next; } |
73 |
|
74 |
LinkedType* find(char* key){ |
75 |
if( !strcmp(name, key) ) return this; |
76 |
if( next != NULL ) return next->find(key); |
77 |
return NULL; |
78 |
} |
79 |
|
80 |
char name[15]; |
81 |
double mass; |
82 |
double epslon; |
83 |
double sigma; |
84 |
LinkedType* next; |
85 |
}; |
86 |
|
87 |
LinkedType* headAtomType; |
88 |
LinkedType* currentAtomType; |
89 |
LinkedType* tempAtomType; |
90 |
|
91 |
char readLine[500]; |
92 |
char* the_token; |
93 |
char* eof_test; |
94 |
int foundAtom = 0; |
95 |
int lineNum = 0; |
96 |
int i; |
97 |
|
98 |
Atom** the_atoms; |
99 |
int nAtoms; |
100 |
the_atoms = entry_plug->atoms; |
101 |
nAtoms = entry_plug->n_atoms; |
102 |
|
103 |
// read in the atom types. |
104 |
|
105 |
rewind( frcFile ); |
106 |
headAtomType = new LinkedType; |
107 |
currentAtomType = headAtomType; |
108 |
|
109 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
110 |
lineNum++; |
111 |
if( eof_test == NULL ){ |
112 |
fprintf( stderr, "Error in reading Atoms from force file.\n" ); |
113 |
exit(8); |
114 |
} |
115 |
|
116 |
|
117 |
while( !foundAtom ){ |
118 |
while( eof_test != NULL && readLine[0] != '#' ){ |
119 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
120 |
lineNum++; |
121 |
} |
122 |
if( eof_test == NULL ){ |
123 |
fprintf( stderr, |
124 |
"Error in reading Atoms from force file at line %d.\n", |
125 |
lineNum ); |
126 |
exit(8); |
127 |
} |
128 |
|
129 |
the_token = strtok( readLine, " ,;\t#\n" ); |
130 |
foundAtom = !strcmp( "AtomTypes", the_token ); |
131 |
|
132 |
if( !foundAtom ){ |
133 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
134 |
lineNum++; |
135 |
|
136 |
if( eof_test == NULL ){ |
137 |
fprintf( stderr, |
138 |
"Error in reading Atoms from force file at line %d.\n", |
139 |
lineNum ); |
140 |
exit(8); |
141 |
} |
142 |
} |
143 |
} |
144 |
|
145 |
// we are now at the AtomTypes section. |
146 |
|
147 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
148 |
lineNum++; |
149 |
|
150 |
if( eof_test == NULL ){ |
151 |
fprintf( stderr, |
152 |
"Error in reading Atoms from force file at line %d.\n", |
153 |
lineNum ); |
154 |
exit(8); |
155 |
} |
156 |
|
157 |
while( readLine[0] != '#' && eof_test != NULL ){ |
158 |
|
159 |
if( readLine[0] != '!' ){ |
160 |
|
161 |
the_token = strtok( readLine, " \n\t,;" ); |
162 |
if( the_token != NULL ){ |
163 |
|
164 |
strcpy( currentAtomType->name, the_token ); |
165 |
|
166 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
167 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
168 |
exit(8); |
169 |
} |
170 |
|
171 |
sscanf( the_token, "%lf", ¤tAtomType->mass ); |
172 |
|
173 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
174 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
175 |
exit(8); |
176 |
} |
177 |
|
178 |
sscanf( the_token, "%lf", ¤tAtomType->epslon ); |
179 |
|
180 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
181 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
182 |
exit(8); |
183 |
} |
184 |
|
185 |
sscanf( the_token, "%lf", ¤tAtomType->sigma ); |
186 |
} |
187 |
} |
188 |
|
189 |
tempAtomType = new LinkedType; |
190 |
currentAtomType->next = tempAtomType; |
191 |
currentAtomType = tempAtomType; |
192 |
|
193 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
194 |
lineNum++; |
195 |
} |
196 |
|
197 |
|
198 |
// initialize the atoms |
199 |
|
200 |
for( i=0; i<nAtoms; i++ ){ |
201 |
|
202 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
203 |
if( currentAtomType == NULL ){ |
204 |
fprintf( stderr, "AtomType error, %s not found in force file.\n", |
205 |
the_atoms[i]->getType() ); |
206 |
exit(8); |
207 |
} |
208 |
|
209 |
the_atoms[i]->setMass( currentAtomType->mass ); |
210 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
211 |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
212 |
the_atoms[i]->setLJ(); |
213 |
} |
214 |
|
215 |
|
216 |
// clean up the memory |
217 |
|
218 |
delete headAtomType; |
219 |
} |
220 |
|
221 |
void TraPPEFF::initializeBonds( bond_pair* the_bonds ){ |
222 |
|
223 |
class LinkedType { |
224 |
public: |
225 |
LinkedType(){ |
226 |
next = NULL; |
227 |
nameA[0] = '\0'; |
228 |
nameB[0] = '\0'; |
229 |
type[0] = '\0'; |
230 |
} |
231 |
~LinkedType(){ if( next != NULL ) delete next; } |
232 |
|
233 |
LinkedType* find(char* key1, char* key2){ |
234 |
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
235 |
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
236 |
if( next != NULL ) return next->find(key1, key2); |
237 |
return NULL; |
238 |
} |
239 |
|
240 |
char nameA[15]; |
241 |
char nameB[15]; |
242 |
char type[30]; |
243 |
double d0; |
244 |
|
245 |
LinkedType* next; |
246 |
}; |
247 |
|
248 |
|
249 |
|
250 |
LinkedType* headBondType; |
251 |
LinkedType* currentBondType; |
252 |
LinkedType* tempBondType; |
253 |
|
254 |
char readLine[500]; |
255 |
char* the_token; |
256 |
char* eof_test; |
257 |
int foundBond = 0; |
258 |
int lineNum = 0; |
259 |
int i, a, b; |
260 |
char* atomA; |
261 |
char* atomB; |
262 |
|
263 |
SRI **the_sris; |
264 |
Atom** the_atoms; |
265 |
int nBonds; |
266 |
the_sris = entry_plug->sr_interactions; |
267 |
the_atoms = entry_plug->atoms; |
268 |
nBonds = entry_plug->n_bonds; |
269 |
|
270 |
// read in the bond types. |
271 |
|
272 |
rewind( frcFile ); |
273 |
headBondType = new LinkedType; |
274 |
currentBondType = headBondType; |
275 |
|
276 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
277 |
lineNum++; |
278 |
if( eof_test == NULL ){ |
279 |
fprintf( stderr, "Error in reading Bonds from force file.\n" ); |
280 |
exit(8); |
281 |
} |
282 |
|
283 |
|
284 |
while( !foundBond ){ |
285 |
while( eof_test != NULL && readLine[0] != '#' ){ |
286 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
287 |
lineNum++; |
288 |
} |
289 |
if( eof_test == NULL ){ |
290 |
fprintf( stderr, |
291 |
"Error in reading Bonds from force file at line %d.\n", |
292 |
lineNum ); |
293 |
exit(8); |
294 |
} |
295 |
|
296 |
the_token = strtok( readLine, " ,;\t#\n" ); |
297 |
foundBond = !strcmp( "BondTypes", the_token ); |
298 |
|
299 |
if( !foundBond ){ |
300 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
301 |
lineNum++; |
302 |
|
303 |
if( eof_test == NULL ){ |
304 |
fprintf( stderr, |
305 |
"Error in reading Bonds from force file at line %d.\n", |
306 |
lineNum ); |
307 |
exit(8); |
308 |
} |
309 |
} |
310 |
} |
311 |
|
312 |
// we are now at the BondTypes section. |
313 |
|
314 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
315 |
lineNum++; |
316 |
|
317 |
if( eof_test == NULL ){ |
318 |
fprintf( stderr, |
319 |
"Error in reading Bonds from force file at line %d.\n", |
320 |
lineNum ); |
321 |
exit(8); |
322 |
} |
323 |
|
324 |
while( readLine[0] != '#' && eof_test != NULL ){ |
325 |
|
326 |
if( readLine[0] != '!' ){ |
327 |
|
328 |
the_token = strtok( readLine, " \n\t,;" ); |
329 |
if( the_token != NULL ){ |
330 |
|
331 |
strcpy( currentBondType->nameA, the_token ); |
332 |
|
333 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
334 |
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
335 |
exit(8); |
336 |
} |
337 |
|
338 |
strcpy( currentBondType->nameB, the_token ); |
339 |
|
340 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
341 |
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
342 |
exit(8); |
343 |
} |
344 |
|
345 |
strcpy( currentBondType->type, the_token ); |
346 |
|
347 |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
348 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
349 |
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
350 |
exit(8); |
351 |
} |
352 |
|
353 |
sscanf( the_token, "%lf", ¤tBondType->d0 ); |
354 |
} |
355 |
|
356 |
else{ |
357 |
fprintf(stderr, |
358 |
"Unknown TraPPE bond type \"%s\" at line %d\n", |
359 |
currentBondType->type, |
360 |
lineNum ); |
361 |
exit(8); |
362 |
} |
363 |
} |
364 |
} |
365 |
|
366 |
tempBondType = new LinkedType; |
367 |
currentBondType->next = tempBondType; |
368 |
currentBondType = tempBondType; |
369 |
|
370 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
371 |
lineNum++; |
372 |
} |
373 |
|
374 |
|
375 |
// initialize the Bonds |
376 |
|
377 |
|
378 |
for( i=0; i<nBonds; i++ ){ |
379 |
|
380 |
a = the_bonds[i].a; |
381 |
b = the_bonds[i].b; |
382 |
|
383 |
atomA = the_atoms[a]->getType(); |
384 |
atomB = the_atoms[b]->getType(); |
385 |
currentBondType = headBondType->find( atomA, atomB ); |
386 |
if( currentBondType == NULL ){ |
387 |
fprintf( stderr, "BondType error, %s - %s not found in force file.\n", |
388 |
atomA, atomB ); |
389 |
exit(8); |
390 |
} |
391 |
|
392 |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
393 |
|
394 |
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
395 |
*the_atoms[b], |
396 |
currentBondType->d0 ); |
397 |
entry_plug->n_constraints++; |
398 |
} |
399 |
} |
400 |
|
401 |
|
402 |
// clean up the memory |
403 |
|
404 |
delete headBondType; |
405 |
} |
406 |
|
407 |
void TraPPEFF::initializeBends( bend_set* the_bends ){ |
408 |
|
409 |
class LinkedType { |
410 |
public: |
411 |
LinkedType(){ |
412 |
next = NULL; |
413 |
nameA[0] = '\0'; |
414 |
nameB[0] = '\0'; |
415 |
nameC[0] = '\0'; |
416 |
type[0] = '\0'; |
417 |
} |
418 |
~LinkedType(){ if( next != NULL ) delete next; } |
419 |
|
420 |
LinkedType* find( char* key1, char* key2, char* key3 ){ |
421 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
422 |
&& !strcmp( nameC, key3 ) ) return this; |
423 |
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
424 |
&& !strcmp( nameC, key1 ) ) return this; |
425 |
if( next != NULL ) return next->find(key1, key2, key3); |
426 |
return NULL; |
427 |
} |
428 |
|
429 |
char nameA[15]; |
430 |
char nameB[15]; |
431 |
char nameC[15]; |
432 |
char type[30]; |
433 |
double k1, k2, k3, t0; |
434 |
|
435 |
LinkedType* next; |
436 |
}; |
437 |
|
438 |
LinkedType* headBendType; |
439 |
LinkedType* currentBendType; |
440 |
LinkedType* tempBendType; |
441 |
|
442 |
char readLine[500]; |
443 |
char* the_token; |
444 |
char* eof_test; |
445 |
int foundBend = 0; |
446 |
int lineNum = 0; |
447 |
int i, a, b, c, index; |
448 |
char* atomA; |
449 |
char* atomB; |
450 |
char* atomC; |
451 |
QuadraticBend* qBend; |
452 |
|
453 |
SRI **the_sris; |
454 |
Atom** the_atoms; |
455 |
int nBends; |
456 |
the_sris = entry_plug->sr_interactions; |
457 |
the_atoms = entry_plug->atoms; |
458 |
nBends = entry_plug->n_bends; |
459 |
|
460 |
// read in the bend types. |
461 |
|
462 |
rewind( frcFile ); |
463 |
headBendType = new LinkedType; |
464 |
currentBendType = headBendType; |
465 |
|
466 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
467 |
lineNum++; |
468 |
if( eof_test == NULL ){ |
469 |
fprintf( stderr, "Error in reading Bends from force file.\n" ); |
470 |
exit(8); |
471 |
} |
472 |
|
473 |
|
474 |
while( !foundBend ){ |
475 |
while( eof_test != NULL && readLine[0] != '#' ){ |
476 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
477 |
lineNum++; |
478 |
} |
479 |
if( eof_test == NULL ){ |
480 |
fprintf( stderr, |
481 |
"Error in reading Bends from force file at line %d.\n", |
482 |
lineNum ); |
483 |
exit(8); |
484 |
} |
485 |
|
486 |
the_token = strtok( readLine, " ,;\t#\n" ); |
487 |
foundBend = !strcmp( "BendTypes", the_token ); |
488 |
|
489 |
if( !foundBend ){ |
490 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
491 |
lineNum++; |
492 |
|
493 |
if( eof_test == NULL ){ |
494 |
fprintf( stderr, |
495 |
"Error in reading Bends from force file at line %d.\n", |
496 |
lineNum ); |
497 |
exit(8); |
498 |
} |
499 |
} |
500 |
} |
501 |
|
502 |
// we are now at the BendTypes section. |
503 |
|
504 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
505 |
lineNum++; |
506 |
|
507 |
if( eof_test == NULL ){ |
508 |
fprintf( stderr, |
509 |
"Error in reading Bends from force file at line %d.\n", |
510 |
lineNum ); |
511 |
exit(8); |
512 |
} |
513 |
|
514 |
while( readLine[0] != '#' && eof_test != NULL ){ |
515 |
|
516 |
if( readLine[0] != '!' ){ |
517 |
|
518 |
the_token = strtok( readLine, " \n\t,;" ); |
519 |
if( the_token != NULL ){ |
520 |
|
521 |
strcpy( currentBendType->nameA, the_token ); |
522 |
|
523 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
524 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
525 |
exit(8); |
526 |
} |
527 |
|
528 |
strcpy( currentBendType->nameB, the_token ); |
529 |
|
530 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
531 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
532 |
exit(8); |
533 |
} |
534 |
|
535 |
strcpy( currentBendType->nameC, the_token ); |
536 |
|
537 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
538 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
539 |
exit(8); |
540 |
} |
541 |
|
542 |
strcpy( currentBendType->type, the_token ); |
543 |
|
544 |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
545 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
546 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
547 |
exit(8); |
548 |
} |
549 |
|
550 |
sscanf( the_token, "%lf", ¤tBendType->k1 ); |
551 |
|
552 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
553 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
554 |
exit(8); |
555 |
} |
556 |
|
557 |
sscanf( the_token, "%lf", ¤tBendType->k2 ); |
558 |
|
559 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
560 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
561 |
exit(8); |
562 |
} |
563 |
|
564 |
sscanf( the_token, "%lf", ¤tBendType->k3 ); |
565 |
|
566 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
567 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
568 |
exit(8); |
569 |
} |
570 |
|
571 |
sscanf( the_token, "%lf", ¤tBendType->t0 ); |
572 |
} |
573 |
|
574 |
else{ |
575 |
fprintf(stderr, |
576 |
"Unknown TraPPE bend type \"%s\" at line %d\n", |
577 |
currentBendType->type, |
578 |
lineNum ); |
579 |
exit(8); |
580 |
} |
581 |
} |
582 |
} |
583 |
|
584 |
tempBendType = new LinkedType; |
585 |
currentBendType->next = tempBendType; |
586 |
currentBendType = tempBendType; |
587 |
|
588 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
589 |
lineNum++; |
590 |
} |
591 |
|
592 |
|
593 |
// initialize the Bends |
594 |
|
595 |
for( i=0; i<nBends; i++ ){ |
596 |
|
597 |
a = the_bends[i].a; |
598 |
b = the_bends[i].b; |
599 |
c = the_bends[i].c; |
600 |
|
601 |
atomA = the_atoms[a]->getType(); |
602 |
atomB = the_atoms[b]->getType(); |
603 |
atomC = the_atoms[c]->getType(); |
604 |
currentBendType = headBendType->find( atomA, atomB, atomC ); |
605 |
if( currentBendType == NULL ){ |
606 |
fprintf( stderr, "BendType error, %s - %s - %s not found" |
607 |
" in force file.\n", |
608 |
atomA, atomB, atomC ); |
609 |
exit(8); |
610 |
} |
611 |
|
612 |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
613 |
|
614 |
index = i + entry_plug->n_bonds; |
615 |
qBend = new QuadraticBend( *the_atoms[a], |
616 |
*the_atoms[b], |
617 |
*the_atoms[c] ); |
618 |
qBend->setConstants( currentBendType->k1, |
619 |
currentBendType->k2, |
620 |
currentBendType->k3, |
621 |
currentBendType->t0 ); |
622 |
the_sris[index] = qBend; |
623 |
} |
624 |
} |
625 |
|
626 |
|
627 |
// clean up the memory |
628 |
|
629 |
delete headBendType; |
630 |
} |
631 |
|
632 |
void TraPPEFF::initializeTorsions( torsion_set* the_torsions ){ |
633 |
|
634 |
class LinkedType { |
635 |
public: |
636 |
LinkedType(){ |
637 |
next = NULL; |
638 |
nameA[0] = '\0'; |
639 |
nameB[0] = '\0'; |
640 |
nameC[0] = '\0'; |
641 |
type[0] = '\0'; |
642 |
} |
643 |
~LinkedType(){ if( next != NULL ) delete next; } |
644 |
|
645 |
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
646 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
647 |
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
648 |
|
649 |
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
650 |
!strcmp( nameC, key2 ) && !strcmp( nameD, key4 ) ) return this; |
651 |
|
652 |
if( next != NULL ) return next->find(key1, key2, key3, key4); |
653 |
return NULL; |
654 |
} |
655 |
|
656 |
char nameA[15]; |
657 |
char nameB[15]; |
658 |
char nameC[15]; |
659 |
char nameD[15]; |
660 |
char type[30]; |
661 |
double k1, k2, k3, k4; |
662 |
|
663 |
LinkedType* next; |
664 |
}; |
665 |
|
666 |
LinkedType* headTorsionType; |
667 |
LinkedType* currentTorsionType; |
668 |
LinkedType* tempTorsionType; |
669 |
|
670 |
char readLine[500]; |
671 |
char* the_token; |
672 |
char* eof_test; |
673 |
int foundTorsion = 0; |
674 |
int lineNum = 0; |
675 |
int i, a, b, c, d, index; |
676 |
char* atomA; |
677 |
char* atomB; |
678 |
char* atomC; |
679 |
char* atomD; |
680 |
CubicTorsion* cTors; |
681 |
|
682 |
SRI **the_sris; |
683 |
Atom** the_atoms; |
684 |
int nTorsions; |
685 |
the_sris = entry_plug->sr_interactions; |
686 |
the_atoms = entry_plug->atoms; |
687 |
nTorsions = entry_plug->n_torsions; |
688 |
|
689 |
// read in the torsion types. |
690 |
|
691 |
rewind( frcFile ); |
692 |
headTorsionType = new LinkedType; |
693 |
currentTorsionType = headTorsionType; |
694 |
|
695 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
696 |
lineNum++; |
697 |
if( eof_test == NULL ){ |
698 |
fprintf( stderr, "Error in reading Torsions from force file.\n" ); |
699 |
exit(8); |
700 |
} |
701 |
|
702 |
|
703 |
while( !foundTorsion ){ |
704 |
while( eof_test != NULL && readLine[0] != '#' ){ |
705 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
706 |
lineNum++; |
707 |
} |
708 |
if( eof_test == NULL ){ |
709 |
fprintf( stderr, |
710 |
"Error in reading Torsions from force file at line %d.\n", |
711 |
lineNum ); |
712 |
exit(8); |
713 |
} |
714 |
|
715 |
the_token = strtok( readLine, " ,;\t#\n" ); |
716 |
foundTorsion = !strcmp( "TorsionTypes", the_token ); |
717 |
|
718 |
if( !foundTorsion ){ |
719 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
720 |
lineNum++; |
721 |
|
722 |
if( eof_test == NULL ){ |
723 |
fprintf( stderr, |
724 |
"Error in reading Torsions from force file at line %d.\n", |
725 |
lineNum ); |
726 |
exit(8); |
727 |
} |
728 |
} |
729 |
} |
730 |
|
731 |
// we are now at the TorsionTypes section. |
732 |
|
733 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
734 |
lineNum++; |
735 |
|
736 |
if( eof_test == NULL ){ |
737 |
fprintf( stderr, |
738 |
"Error in reading Torsions from force file at line %d.\n", |
739 |
lineNum ); |
740 |
exit(8); |
741 |
} |
742 |
|
743 |
while( readLine[0] != '#' && eof_test != NULL ){ |
744 |
|
745 |
if( readLine[0] != '!' ){ |
746 |
|
747 |
the_token = strtok( readLine, " \n\t,;" ); |
748 |
if( the_token != NULL ){ |
749 |
|
750 |
strcpy( currentTorsionType->nameA, the_token ); |
751 |
|
752 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
753 |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
754 |
exit(8); |
755 |
} |
756 |
|
757 |
strcpy( currentTorsionType->nameB, the_token ); |
758 |
|
759 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
760 |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
761 |
exit(8); |
762 |
} |
763 |
|
764 |
strcpy( currentTorsionType->nameC, the_token ); |
765 |
|
766 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
767 |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
768 |
exit(8); |
769 |
} |
770 |
|
771 |
strcpy( currentTorsionType->nameD, the_token ); |
772 |
|
773 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
774 |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
775 |
exit(8); |
776 |
} |
777 |
|
778 |
strcpy( currentTorsionType->type, the_token ); |
779 |
|
780 |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
781 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
782 |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
783 |
exit(8); |
784 |
} |
785 |
|
786 |
sscanf( the_token, "%lf", ¤tTorsionType->k1 ); |
787 |
|
788 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
789 |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
790 |
exit(8); |
791 |
} |
792 |
|
793 |
sscanf( the_token, "%lf", ¤tTorsionType->k2 ); |
794 |
|
795 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
796 |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
797 |
exit(8); |
798 |
} |
799 |
|
800 |
sscanf( the_token, "%lf", ¤tTorsionType->k3 ); |
801 |
|
802 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
803 |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
804 |
exit(8); |
805 |
} |
806 |
|
807 |
sscanf( the_token, "%lf", ¤tTorsionType->k4 ); |
808 |
} |
809 |
|
810 |
else{ |
811 |
fprintf(stderr, |
812 |
"Unknown TraPPE torsion type \"%s\" at line %d\n", |
813 |
currentTorsionType->type, |
814 |
lineNum ); |
815 |
exit(8); |
816 |
} |
817 |
} |
818 |
} |
819 |
|
820 |
tempTorsionType = new LinkedType; |
821 |
currentTorsionType->next = tempTorsionType; |
822 |
currentTorsionType = tempTorsionType; |
823 |
|
824 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
825 |
lineNum++; |
826 |
} |
827 |
|
828 |
|
829 |
// initialize the Torsions |
830 |
|
831 |
for( i=0; i<nTorsions; i++ ){ |
832 |
|
833 |
a = the_torsions[i].a; |
834 |
b = the_torsions[i].b; |
835 |
c = the_torsions[i].c; |
836 |
d = the_torsions[i].d; |
837 |
|
838 |
atomA = the_atoms[a]->getType(); |
839 |
atomB = the_atoms[b]->getType(); |
840 |
atomC = the_atoms[c]->getType(); |
841 |
atomD = the_atoms[d]->getType(); |
842 |
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
843 |
if( currentTorsionType == NULL ){ |
844 |
fprintf( stderr, "TorsionType error, %s - %s - %s - %s not found" |
845 |
" in force file.\n", |
846 |
atomA, atomB, atomC, atomD ); |
847 |
exit(8); |
848 |
} |
849 |
|
850 |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
851 |
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
852 |
|
853 |
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
854 |
*the_atoms[c], *the_atoms[d] ); |
855 |
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
856 |
currentTorsionType->k3, currentTorsionType->k4 ); |
857 |
the_sris[index] = cTors; |
858 |
} |
859 |
} |
860 |
|
861 |
|
862 |
// clean up the memory |
863 |
|
864 |
delete headTorsionType; |
865 |
} |