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 |
|
11 |
|
12 |
TraPPE_ExFF::TraPPE_ExFF(){ |
13 |
|
14 |
char fileName[200]; |
15 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
16 |
char* ffPath; |
17 |
char temp[200]; |
18 |
|
19 |
// generate the force file name |
20 |
|
21 |
strcpy( fileName, "TraPPE_Ex.frc" ); |
22 |
|
23 |
// attempt to open the file in the current directory first. |
24 |
|
25 |
frcFile = fopen( fileName, "r" ); |
26 |
|
27 |
if( frcFile == NULL ){ |
28 |
|
29 |
// next see if the force path enviorment variable is set |
30 |
|
31 |
ffPath = getenv( ffPath_env ); |
32 |
strcpy( temp, ffPath ); |
33 |
strcat( temp, "/" ); |
34 |
strcat( temp, fileName ); |
35 |
strcpy( fileName, temp ); |
36 |
|
37 |
frcFile = fopen( fileName, "r" ); |
38 |
|
39 |
if( frcFile == NULL ){ |
40 |
|
41 |
fprintf( stderr, |
42 |
"Error opening the force field parameter file: %s\n" |
43 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
44 |
"vairable?\n", |
45 |
fileName ); |
46 |
exit( 8 ); |
47 |
} |
48 |
} |
49 |
} |
50 |
|
51 |
TraPPE_ExFF::~TraPPE_ExFF(){ |
52 |
|
53 |
fclose( frcFile ); |
54 |
} |
55 |
|
56 |
void TraPPE_ExFF::initializeAtoms( void ){ |
57 |
|
58 |
class LinkedType { |
59 |
public: |
60 |
LinkedType(){ |
61 |
next = NULL; |
62 |
name[0] = '\0'; |
63 |
} |
64 |
~LinkedType(){ if( next != NULL ) delete next; } |
65 |
|
66 |
LinkedType* find(char* key){ |
67 |
if( !strcmp(name, key) ) return this; |
68 |
if( next != NULL ) return next->find(key); |
69 |
return NULL; |
70 |
} |
71 |
|
72 |
char name[15]; |
73 |
int isDipole; |
74 |
double mass; |
75 |
double epslon; |
76 |
double sigma; |
77 |
double dipole; |
78 |
LinkedType* next; |
79 |
}; |
80 |
|
81 |
LinkedType* headAtomType; |
82 |
LinkedType* currentAtomType; |
83 |
LinkedType* tempAtomType; |
84 |
|
85 |
char readLine[500]; |
86 |
char* the_token; |
87 |
char* eof_test; |
88 |
int foundAtom = 0; |
89 |
int lineNum = 0; |
90 |
int i; |
91 |
|
92 |
////////////////////////////////////////////////// |
93 |
// a quick water fix |
94 |
|
95 |
double waterI[3][3]; |
96 |
waterI[0][0] = 1.76958347772500; |
97 |
waterI[0][1] = 0.0; |
98 |
waterI[0][2] = 0.0; |
99 |
|
100 |
waterI[1][0] = 0.0; |
101 |
waterI[1][1] = 0.614537057924513; |
102 |
waterI[1][2] = 0.0; |
103 |
|
104 |
waterI[2][0] = 0.0; |
105 |
waterI[2][1] = 0.0; |
106 |
waterI[2][2] = 1.15504641980049; |
107 |
|
108 |
|
109 |
double headI[3][3]; |
110 |
headI[0][0] = 1125; |
111 |
headI[0][1] = 0.0; |
112 |
headI[0][2] = 0.0; |
113 |
|
114 |
headI[1][0] = 0.0; |
115 |
headI[1][1] = 1125; |
116 |
headI[1][2] = 0.0; |
117 |
|
118 |
headI[2][0] = 0.0; |
119 |
headI[2][1] = 0.0; |
120 |
headI[2][2] = 250; |
121 |
|
122 |
|
123 |
|
124 |
////////////////////////////////////////////////// |
125 |
|
126 |
Atom** the_atoms; |
127 |
int nAtoms; |
128 |
the_atoms = entry_plug->atoms; |
129 |
nAtoms = entry_plug->n_atoms; |
130 |
|
131 |
// read in the atom types. |
132 |
|
133 |
rewind( frcFile ); |
134 |
headAtomType = new LinkedType; |
135 |
currentAtomType = headAtomType; |
136 |
|
137 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
138 |
lineNum++; |
139 |
if( eof_test == NULL ){ |
140 |
fprintf( stderr, "Error in reading Atoms from force file.\n" ); |
141 |
exit(8); |
142 |
} |
143 |
|
144 |
|
145 |
while( !foundAtom ){ |
146 |
while( eof_test != NULL && readLine[0] != '#' ){ |
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 |
the_token = strtok( readLine, " ,;\t#\n" ); |
158 |
foundAtom = !strcmp( "AtomTypes", the_token ); |
159 |
|
160 |
if( !foundAtom ){ |
161 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
162 |
lineNum++; |
163 |
|
164 |
if( eof_test == NULL ){ |
165 |
fprintf( stderr, |
166 |
"Error in reading Atoms from force file at line %d.\n", |
167 |
lineNum ); |
168 |
exit(8); |
169 |
} |
170 |
} |
171 |
} |
172 |
|
173 |
// we are now at the AtomTypes section. |
174 |
|
175 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
176 |
lineNum++; |
177 |
|
178 |
if( eof_test == NULL ){ |
179 |
fprintf( stderr, |
180 |
"Error in reading Atoms from force file at line %d.\n", |
181 |
lineNum ); |
182 |
exit(8); |
183 |
} |
184 |
|
185 |
while( readLine[0] != '#' && eof_test != NULL ){ |
186 |
|
187 |
if( readLine[0] != '!' ){ |
188 |
|
189 |
the_token = strtok( readLine, " \n\t,;" ); |
190 |
if( the_token != NULL ){ |
191 |
|
192 |
strcpy( currentAtomType->name, the_token ); |
193 |
|
194 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
195 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
196 |
exit(8); |
197 |
} |
198 |
|
199 |
sscanf( the_token, "%d", ¤tAtomType->isDipole ); |
200 |
|
201 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
202 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
203 |
exit(8); |
204 |
} |
205 |
|
206 |
sscanf( the_token, "%lf", ¤tAtomType->mass ); |
207 |
|
208 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
209 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
210 |
exit(8); |
211 |
} |
212 |
|
213 |
sscanf( the_token, "%lf", ¤tAtomType->epslon ); |
214 |
|
215 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
216 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
217 |
exit(8); |
218 |
} |
219 |
|
220 |
sscanf( the_token, "%lf", ¤tAtomType->sigma ); |
221 |
|
222 |
if( currentAtomType->isDipole ){ |
223 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
224 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
225 |
exit(8); |
226 |
} |
227 |
|
228 |
sscanf( the_token, "%lf", ¤tAtomType->dipole ); |
229 |
} |
230 |
} |
231 |
} |
232 |
|
233 |
tempAtomType = new LinkedType; |
234 |
currentAtomType->next = tempAtomType; |
235 |
currentAtomType = tempAtomType; |
236 |
|
237 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
238 |
lineNum++; |
239 |
} |
240 |
|
241 |
|
242 |
// initialize the atoms |
243 |
|
244 |
DirectionalAtom* dAtom; |
245 |
|
246 |
for( i=0; i<nAtoms; i++ ){ |
247 |
|
248 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
249 |
if( currentAtomType == NULL ){ |
250 |
fprintf( stderr, "AtomType error, %s not found in force file.\n", |
251 |
the_atoms[i]->getType() ); |
252 |
exit(8); |
253 |
} |
254 |
|
255 |
the_atoms[i]->setMass( currentAtomType->mass ); |
256 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
257 |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
258 |
the_atoms[i]->setLJ(); |
259 |
|
260 |
if( currentAtomType->isDipole ){ |
261 |
if( the_atoms[i]->isDirectional() ){ |
262 |
|
263 |
dAtom = (DirectionalAtom *) the_atoms[i]; |
264 |
dAtom->setMu( currentAtomType->dipole ); |
265 |
dAtom->setHasDipole( 1 ); |
266 |
dAtom->setJx( 0.0 ); |
267 |
dAtom->setJy( 0.0 ); |
268 |
dAtom->setJz( 0.0 ); |
269 |
|
270 |
if(!strcmp("SSD",the_atoms[i]->getType())){ |
271 |
dAtom->setI( waterI ); |
272 |
dAtom->setSSD( 1 ); |
273 |
} |
274 |
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
275 |
dAtom->setI( headI ); |
276 |
dAtom->setSSD( 0 ); |
277 |
} |
278 |
else{ |
279 |
fprintf(stderr, |
280 |
"AtmType error, %s does not have a moment of inertia set.\n", |
281 |
the_atoms[i]->getType() ); |
282 |
exit(8); |
283 |
} |
284 |
entry_plug->n_dipoles++; |
285 |
} |
286 |
else{ |
287 |
std::cerr |
288 |
<< "TraPPE_ExFF error: Atom \"" |
289 |
<< currentAtomType->name << "\" is a dipole, yet no standard" |
290 |
<< " orientation was specifed in the BASS file.\n"; |
291 |
exit(8); |
292 |
} |
293 |
} |
294 |
else{ |
295 |
if( the_atoms[i]->isDirectional() ){ |
296 |
std::cerr |
297 |
<< "TraPPE_ExFF error: Atom \"" |
298 |
<< currentAtomType->name << "\" was given a standard orientation" |
299 |
<< " in the BASS file, yet it is not a dipole.\n"; |
300 |
exit(8); |
301 |
} |
302 |
} |
303 |
} |
304 |
|
305 |
|
306 |
// clean up the memory |
307 |
|
308 |
delete headAtomType; |
309 |
} |
310 |
|
311 |
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
312 |
|
313 |
class LinkedType { |
314 |
public: |
315 |
LinkedType(){ |
316 |
next = NULL; |
317 |
nameA[0] = '\0'; |
318 |
nameB[0] = '\0'; |
319 |
type[0] = '\0'; |
320 |
} |
321 |
~LinkedType(){ if( next != NULL ) delete next; } |
322 |
|
323 |
LinkedType* find(char* key1, char* key2){ |
324 |
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
325 |
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
326 |
if( next != NULL ) return next->find(key1, key2); |
327 |
return NULL; |
328 |
} |
329 |
|
330 |
char nameA[15]; |
331 |
char nameB[15]; |
332 |
char type[30]; |
333 |
double d0; |
334 |
|
335 |
LinkedType* next; |
336 |
}; |
337 |
|
338 |
|
339 |
|
340 |
LinkedType* headBondType; |
341 |
LinkedType* currentBondType; |
342 |
LinkedType* tempBondType; |
343 |
|
344 |
char readLine[500]; |
345 |
char* the_token; |
346 |
char* eof_test; |
347 |
int foundBond = 0; |
348 |
int lineNum = 0; |
349 |
int i, a, b; |
350 |
char* atomA; |
351 |
char* atomB; |
352 |
|
353 |
SRI **the_sris; |
354 |
Atom** the_atoms; |
355 |
int nBonds; |
356 |
the_sris = entry_plug->sr_interactions; |
357 |
the_atoms = entry_plug->atoms; |
358 |
nBonds = entry_plug->n_bonds; |
359 |
|
360 |
// read in the bond types. |
361 |
|
362 |
rewind( frcFile ); |
363 |
headBondType = new LinkedType; |
364 |
currentBondType = headBondType; |
365 |
|
366 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
367 |
lineNum++; |
368 |
if( eof_test == NULL ){ |
369 |
fprintf( stderr, "Error in reading Bonds from force file.\n" ); |
370 |
exit(8); |
371 |
} |
372 |
|
373 |
|
374 |
while( !foundBond ){ |
375 |
while( eof_test != NULL && readLine[0] != '#' ){ |
376 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
377 |
lineNum++; |
378 |
} |
379 |
if( eof_test == NULL ){ |
380 |
fprintf( stderr, |
381 |
"Error in reading Bonds from force file at line %d.\n", |
382 |
lineNum ); |
383 |
exit(8); |
384 |
} |
385 |
|
386 |
the_token = strtok( readLine, " ,;\t#\n" ); |
387 |
foundBond = !strcmp( "BondTypes", the_token ); |
388 |
|
389 |
if( !foundBond ){ |
390 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
391 |
lineNum++; |
392 |
|
393 |
if( eof_test == NULL ){ |
394 |
fprintf( stderr, |
395 |
"Error in reading Bonds from force file at line %d.\n", |
396 |
lineNum ); |
397 |
exit(8); |
398 |
} |
399 |
} |
400 |
} |
401 |
|
402 |
// we are now at the BondTypes section. |
403 |
|
404 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
405 |
lineNum++; |
406 |
|
407 |
if( eof_test == NULL ){ |
408 |
fprintf( stderr, |
409 |
"Error in reading Bonds from force file at line %d.\n", |
410 |
lineNum ); |
411 |
exit(8); |
412 |
} |
413 |
|
414 |
while( readLine[0] != '#' && eof_test != NULL ){ |
415 |
|
416 |
if( readLine[0] != '!' ){ |
417 |
|
418 |
the_token = strtok( readLine, " \n\t,;" ); |
419 |
if( the_token != NULL ){ |
420 |
|
421 |
strcpy( currentBondType->nameA, the_token ); |
422 |
|
423 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
424 |
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
425 |
exit(8); |
426 |
} |
427 |
|
428 |
strcpy( currentBondType->nameB, the_token ); |
429 |
|
430 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
431 |
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
432 |
exit(8); |
433 |
} |
434 |
|
435 |
strcpy( currentBondType->type, the_token ); |
436 |
|
437 |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
438 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
439 |
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
440 |
exit(8); |
441 |
} |
442 |
|
443 |
sscanf( the_token, "%lf", ¤tBondType->d0 ); |
444 |
} |
445 |
|
446 |
else{ |
447 |
fprintf(stderr, |
448 |
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
449 |
currentBondType->type, |
450 |
lineNum ); |
451 |
exit(8); |
452 |
} |
453 |
} |
454 |
} |
455 |
|
456 |
tempBondType = new LinkedType; |
457 |
currentBondType->next = tempBondType; |
458 |
currentBondType = tempBondType; |
459 |
|
460 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
461 |
lineNum++; |
462 |
} |
463 |
|
464 |
|
465 |
// initialize the Bonds |
466 |
|
467 |
|
468 |
for( i=0; i<nBonds; i++ ){ |
469 |
|
470 |
a = the_bonds[i].a; |
471 |
b = the_bonds[i].b; |
472 |
|
473 |
atomA = the_atoms[a]->getType(); |
474 |
atomB = the_atoms[b]->getType(); |
475 |
currentBondType = headBondType->find( atomA, atomB ); |
476 |
if( currentBondType == NULL ){ |
477 |
fprintf( stderr, "BondType error, %s - %s not found in force file.\n", |
478 |
atomA, atomB ); |
479 |
exit(8); |
480 |
} |
481 |
|
482 |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
483 |
|
484 |
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
485 |
*the_atoms[b], |
486 |
currentBondType->d0 ); |
487 |
entry_plug->n_constraints++; |
488 |
} |
489 |
} |
490 |
|
491 |
|
492 |
// clean up the memory |
493 |
|
494 |
delete headBondType; |
495 |
|
496 |
} |
497 |
|
498 |
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
499 |
|
500 |
class LinkedType { |
501 |
public: |
502 |
LinkedType(){ |
503 |
next = NULL; |
504 |
nameA[0] = '\0'; |
505 |
nameB[0] = '\0'; |
506 |
nameC[0] = '\0'; |
507 |
type[0] = '\0'; |
508 |
} |
509 |
~LinkedType(){ if( next != NULL ) delete next; } |
510 |
|
511 |
LinkedType* find( char* key1, char* key2, char* key3 ){ |
512 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
513 |
&& !strcmp( nameC, key3 ) ) return this; |
514 |
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
515 |
&& !strcmp( nameC, key1 ) ) return this; |
516 |
if( next != NULL ) return next->find(key1, key2, key3); |
517 |
return NULL; |
518 |
} |
519 |
|
520 |
char nameA[15]; |
521 |
char nameB[15]; |
522 |
char nameC[15]; |
523 |
char type[30]; |
524 |
double k1, k2, k3, t0; |
525 |
|
526 |
LinkedType* next; |
527 |
}; |
528 |
|
529 |
LinkedType* headBendType; |
530 |
LinkedType* currentBendType; |
531 |
LinkedType* tempBendType; |
532 |
|
533 |
char readLine[500]; |
534 |
char* the_token; |
535 |
char* eof_test; |
536 |
int foundBend = 0; |
537 |
int lineNum = 0; |
538 |
int i, a, b, c, index; |
539 |
char* atomA; |
540 |
char* atomB; |
541 |
char* atomC; |
542 |
QuadraticBend* qBend; |
543 |
|
544 |
SRI **the_sris; |
545 |
Atom** the_atoms; |
546 |
int nBends; |
547 |
the_sris = entry_plug->sr_interactions; |
548 |
the_atoms = entry_plug->atoms; |
549 |
nBends = entry_plug->n_bends; |
550 |
|
551 |
// read in the bend types. |
552 |
|
553 |
rewind( frcFile ); |
554 |
headBendType = new LinkedType; |
555 |
currentBendType = headBendType; |
556 |
|
557 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
558 |
lineNum++; |
559 |
if( eof_test == NULL ){ |
560 |
fprintf( stderr, "Error in reading Bends from force file.\n" ); |
561 |
exit(8); |
562 |
} |
563 |
|
564 |
|
565 |
while( !foundBend ){ |
566 |
while( eof_test != NULL && readLine[0] != '#' ){ |
567 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
568 |
lineNum++; |
569 |
} |
570 |
if( eof_test == NULL ){ |
571 |
fprintf( stderr, |
572 |
"Error in reading Bends from force file at line %d.\n", |
573 |
lineNum ); |
574 |
exit(8); |
575 |
} |
576 |
|
577 |
the_token = strtok( readLine, " ,;\t#\n" ); |
578 |
foundBend = !strcmp( "BendTypes", the_token ); |
579 |
|
580 |
if( !foundBend ){ |
581 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
582 |
lineNum++; |
583 |
|
584 |
if( eof_test == NULL ){ |
585 |
fprintf( stderr, |
586 |
"Error in reading Bends from force file at line %d.\n", |
587 |
lineNum ); |
588 |
exit(8); |
589 |
} |
590 |
} |
591 |
} |
592 |
|
593 |
// we are now at the BendTypes section. |
594 |
|
595 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
596 |
lineNum++; |
597 |
|
598 |
if( eof_test == NULL ){ |
599 |
fprintf( stderr, |
600 |
"Error in reading Bends from force file at line %d.\n", |
601 |
lineNum ); |
602 |
exit(8); |
603 |
} |
604 |
|
605 |
while( readLine[0] != '#' && eof_test != NULL ){ |
606 |
|
607 |
if( readLine[0] != '!' ){ |
608 |
|
609 |
the_token = strtok( readLine, " \n\t,;" ); |
610 |
if( the_token != NULL ){ |
611 |
|
612 |
strcpy( currentBendType->nameA, the_token ); |
613 |
|
614 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
615 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
616 |
exit(8); |
617 |
} |
618 |
|
619 |
strcpy( currentBendType->nameB, the_token ); |
620 |
|
621 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
622 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
623 |
exit(8); |
624 |
} |
625 |
|
626 |
strcpy( currentBendType->nameC, the_token ); |
627 |
|
628 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
629 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
630 |
exit(8); |
631 |
} |
632 |
|
633 |
strcpy( currentBendType->type, the_token ); |
634 |
|
635 |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
636 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
637 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
638 |
exit(8); |
639 |
} |
640 |
|
641 |
sscanf( the_token, "%lf", ¤tBendType->k1 ); |
642 |
|
643 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
644 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
645 |
exit(8); |
646 |
} |
647 |
|
648 |
sscanf( the_token, "%lf", ¤tBendType->k2 ); |
649 |
|
650 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
651 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
652 |
exit(8); |
653 |
} |
654 |
|
655 |
sscanf( the_token, "%lf", ¤tBendType->k3 ); |
656 |
|
657 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
658 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
659 |
exit(8); |
660 |
} |
661 |
|
662 |
sscanf( the_token, "%lf", ¤tBendType->t0 ); |
663 |
} |
664 |
|
665 |
else{ |
666 |
fprintf(stderr, |
667 |
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
668 |
currentBendType->type, |
669 |
lineNum ); |
670 |
exit(8); |
671 |
} |
672 |
} |
673 |
} |
674 |
|
675 |
tempBendType = new LinkedType; |
676 |
currentBendType->next = tempBendType; |
677 |
currentBendType = tempBendType; |
678 |
|
679 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
680 |
lineNum++; |
681 |
} |
682 |
|
683 |
|
684 |
// initialize the Bends |
685 |
|
686 |
for( i=0; i<nBends; i++ ){ |
687 |
|
688 |
a = the_bends[i].a; |
689 |
b = the_bends[i].b; |
690 |
c = the_bends[i].c; |
691 |
|
692 |
atomA = the_atoms[a]->getType(); |
693 |
atomB = the_atoms[b]->getType(); |
694 |
atomC = the_atoms[c]->getType(); |
695 |
currentBendType = headBendType->find( atomA, atomB, atomC ); |
696 |
if( currentBendType == NULL ){ |
697 |
fprintf( stderr, "BendType error, %s - %s - %s not found" |
698 |
" in force file.\n", |
699 |
atomA, atomB, atomC ); |
700 |
exit(8); |
701 |
} |
702 |
|
703 |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
704 |
|
705 |
index = i + entry_plug->n_bonds; |
706 |
qBend = new QuadraticBend( *the_atoms[a], |
707 |
*the_atoms[b], |
708 |
*the_atoms[c] ); |
709 |
qBend->setConstants( currentBendType->k1, |
710 |
currentBendType->k2, |
711 |
currentBendType->k3, |
712 |
currentBendType->t0 ); |
713 |
the_sris[index] = qBend; |
714 |
} |
715 |
} |
716 |
|
717 |
|
718 |
// clean up the memory |
719 |
|
720 |
delete headBendType; |
721 |
|
722 |
} |
723 |
|
724 |
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
725 |
|
726 |
class LinkedType { |
727 |
public: |
728 |
LinkedType(){ |
729 |
next = NULL; |
730 |
nameA[0] = '\0'; |
731 |
nameB[0] = '\0'; |
732 |
nameC[0] = '\0'; |
733 |
type[0] = '\0'; |
734 |
} |
735 |
~LinkedType(){ if( next != NULL ) delete next; } |
736 |
|
737 |
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
738 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
739 |
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
740 |
|
741 |
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
742 |
!strcmp( nameC, key2 ) && !strcmp( nameD, key4 ) ) return this; |
743 |
|
744 |
if( next != NULL ) return next->find(key1, key2, key3, key4); |
745 |
return NULL; |
746 |
} |
747 |
|
748 |
char nameA[15]; |
749 |
char nameB[15]; |
750 |
char nameC[15]; |
751 |
char nameD[15]; |
752 |
char type[30]; |
753 |
double k1, k2, k3, k4; |
754 |
|
755 |
LinkedType* next; |
756 |
}; |
757 |
|
758 |
LinkedType* headTorsionType; |
759 |
LinkedType* currentTorsionType; |
760 |
LinkedType* tempTorsionType; |
761 |
|
762 |
char readLine[500]; |
763 |
char* the_token; |
764 |
char* eof_test; |
765 |
int foundTorsion = 0; |
766 |
int lineNum = 0; |
767 |
int i, a, b, c, d, index; |
768 |
char* atomA; |
769 |
char* atomB; |
770 |
char* atomC; |
771 |
char* atomD; |
772 |
CubicTorsion* cTors; |
773 |
|
774 |
SRI **the_sris; |
775 |
Atom** the_atoms; |
776 |
int nTorsions; |
777 |
the_sris = entry_plug->sr_interactions; |
778 |
the_atoms = entry_plug->atoms; |
779 |
nTorsions = entry_plug->n_torsions; |
780 |
|
781 |
// read in the torsion types. |
782 |
|
783 |
rewind( frcFile ); |
784 |
headTorsionType = new LinkedType; |
785 |
currentTorsionType = headTorsionType; |
786 |
|
787 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
788 |
lineNum++; |
789 |
if( eof_test == NULL ){ |
790 |
fprintf( stderr, "Error in reading Torsions from force file.\n" ); |
791 |
exit(8); |
792 |
} |
793 |
|
794 |
|
795 |
while( !foundTorsion ){ |
796 |
while( eof_test != NULL && readLine[0] != '#' ){ |
797 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
798 |
lineNum++; |
799 |
} |
800 |
if( eof_test == NULL ){ |
801 |
fprintf( stderr, |
802 |
"Error in reading Torsions from force file at line %d.\n", |
803 |
lineNum ); |
804 |
exit(8); |
805 |
} |
806 |
|
807 |
the_token = strtok( readLine, " ,;\t#\n" ); |
808 |
foundTorsion = !strcmp( "TorsionTypes", the_token ); |
809 |
|
810 |
if( !foundTorsion ){ |
811 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
812 |
lineNum++; |
813 |
|
814 |
if( eof_test == NULL ){ |
815 |
fprintf( stderr, |
816 |
"Error in reading Torsions from force file at line %d.\n", |
817 |
lineNum ); |
818 |
exit(8); |
819 |
} |
820 |
} |
821 |
} |
822 |
|
823 |
// we are now at the TorsionTypes section. |
824 |
|
825 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
826 |
lineNum++; |
827 |
|
828 |
if( eof_test == NULL ){ |
829 |
fprintf( stderr, |
830 |
"Error in reading Torsions from force file at line %d.\n", |
831 |
lineNum ); |
832 |
exit(8); |
833 |
} |
834 |
|
835 |
while( readLine[0] != '#' && eof_test != NULL ){ |
836 |
|
837 |
if( readLine[0] != '!' ){ |
838 |
|
839 |
the_token = strtok( readLine, " \n\t,;" ); |
840 |
if( the_token != NULL ){ |
841 |
|
842 |
strcpy( currentTorsionType->nameA, the_token ); |
843 |
|
844 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
845 |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
846 |
exit(8); |
847 |
} |
848 |
|
849 |
strcpy( currentTorsionType->nameB, the_token ); |
850 |
|
851 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
852 |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
853 |
exit(8); |
854 |
} |
855 |
|
856 |
strcpy( currentTorsionType->nameC, the_token ); |
857 |
|
858 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
859 |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
860 |
exit(8); |
861 |
} |
862 |
|
863 |
strcpy( currentTorsionType->nameD, the_token ); |
864 |
|
865 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
866 |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
867 |
exit(8); |
868 |
} |
869 |
|
870 |
strcpy( currentTorsionType->type, the_token ); |
871 |
|
872 |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
873 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
874 |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
875 |
exit(8); |
876 |
} |
877 |
|
878 |
sscanf( the_token, "%lf", ¤tTorsionType->k1 ); |
879 |
|
880 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
881 |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
882 |
exit(8); |
883 |
} |
884 |
|
885 |
sscanf( the_token, "%lf", ¤tTorsionType->k2 ); |
886 |
|
887 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
888 |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
889 |
exit(8); |
890 |
} |
891 |
|
892 |
sscanf( the_token, "%lf", ¤tTorsionType->k3 ); |
893 |
|
894 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
895 |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
896 |
exit(8); |
897 |
} |
898 |
|
899 |
sscanf( the_token, "%lf", ¤tTorsionType->k4 ); |
900 |
} |
901 |
|
902 |
else{ |
903 |
fprintf(stderr, |
904 |
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
905 |
currentTorsionType->type, |
906 |
lineNum ); |
907 |
exit(8); |
908 |
} |
909 |
} |
910 |
} |
911 |
|
912 |
tempTorsionType = new LinkedType; |
913 |
currentTorsionType->next = tempTorsionType; |
914 |
currentTorsionType = tempTorsionType; |
915 |
|
916 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
917 |
lineNum++; |
918 |
} |
919 |
|
920 |
|
921 |
// initialize the Torsions |
922 |
|
923 |
for( i=0; i<nTorsions; i++ ){ |
924 |
|
925 |
a = the_torsions[i].a; |
926 |
b = the_torsions[i].b; |
927 |
c = the_torsions[i].c; |
928 |
d = the_torsions[i].d; |
929 |
|
930 |
atomA = the_atoms[a]->getType(); |
931 |
atomB = the_atoms[b]->getType(); |
932 |
atomC = the_atoms[c]->getType(); |
933 |
atomD = the_atoms[d]->getType(); |
934 |
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
935 |
if( currentTorsionType == NULL ){ |
936 |
fprintf( stderr, "TorsionType error, %s - %s - %s - %s not found" |
937 |
" in force file.\n", |
938 |
atomA, atomB, atomC, atomD ); |
939 |
exit(8); |
940 |
} |
941 |
|
942 |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
943 |
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
944 |
|
945 |
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
946 |
*the_atoms[c], *the_atoms[d] ); |
947 |
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
948 |
currentTorsionType->k3, currentTorsionType->k4 ); |
949 |
the_sris[index] = cTors; |
950 |
} |
951 |
} |
952 |
|
953 |
|
954 |
// clean up the memory |
955 |
|
956 |
delete headTorsionType; |
957 |
|
958 |
} |