1 |
#include <stdlib.h> |
2 |
#include <stdio.h> |
3 |
#include <string.h> |
4 |
|
5 |
#include <iostream> |
6 |
using namespace std; |
7 |
|
8 |
#ifdef IS_MPI |
9 |
#include <mpi.h> |
10 |
#endif //is_mpi |
11 |
|
12 |
#include "ForceFields.hpp" |
13 |
#include "SRI.hpp" |
14 |
#include "simError.h" |
15 |
|
16 |
#include "fortranWrappers.hpp" |
17 |
|
18 |
#ifdef IS_MPI |
19 |
#include "mpiForceField.h" |
20 |
#endif // is_mpi |
21 |
|
22 |
|
23 |
|
24 |
namespace WATER_NS{ |
25 |
|
26 |
// Declare the structures that will be passed by the parser and MPI |
27 |
|
28 |
typedef struct{ |
29 |
char name[15]; |
30 |
double mass; |
31 |
double epslon; |
32 |
double sigma; |
33 |
double charge; |
34 |
int isDirectional; |
35 |
int isLJ; |
36 |
int isCharge; |
37 |
int ident; |
38 |
int last; // 0 -> default |
39 |
// 1 -> in MPI: tells nodes to stop listening |
40 |
} atomStruct; |
41 |
|
42 |
typedef struct{ |
43 |
char name[15]; |
44 |
double Ixx; |
45 |
double Iyy; |
46 |
double Izz; |
47 |
double dipole; |
48 |
double w0; |
49 |
double v0; |
50 |
double v0p; |
51 |
double rl; |
52 |
double ru; |
53 |
double rlp; |
54 |
double rup; |
55 |
int isDipole; |
56 |
int isSticky; |
57 |
int last; // 0 -> default |
58 |
// 1 -> in MPI: tells nodes to stop listening |
59 |
} directionalStruct; |
60 |
|
61 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
62 |
int parseDirectional( char *lineBuffer, int lineNum, directionalStruct &info ); |
63 |
|
64 |
|
65 |
#ifdef IS_MPI |
66 |
|
67 |
MPI_Datatype mpiAtomStructType; |
68 |
MPI_Datatype mpiDirectionalStructType; |
69 |
|
70 |
#endif |
71 |
|
72 |
class LinkedAtomType { |
73 |
public: |
74 |
LinkedAtomType(){ |
75 |
next = NULL; |
76 |
name[0] = '\0'; |
77 |
} |
78 |
~LinkedAtomType(){ if( next != NULL ) delete next; } |
79 |
|
80 |
LinkedAtomType* find(char* key){ |
81 |
if( !strcmp(name, key) ) return this; |
82 |
if( next != NULL ) return next->find(key); |
83 |
return NULL; |
84 |
} |
85 |
|
86 |
|
87 |
void add( atomStruct &info ){ |
88 |
|
89 |
// check for duplicates |
90 |
|
91 |
if( !strcmp( info.name, name ) ){ |
92 |
sprintf( painCave.errMsg, |
93 |
"Duplicate WATER atom type \"%s\" found in " |
94 |
"the WATER param file./n", |
95 |
name ); |
96 |
painCave.isFatal = 1; |
97 |
simError(); |
98 |
} |
99 |
|
100 |
if( next != NULL ) next->add(info); |
101 |
else{ |
102 |
next = new LinkedAtomType(); |
103 |
strcpy(next->name, info.name); |
104 |
next->isDirectional = info.isDirectional; |
105 |
next->isLJ = info.isLJ; |
106 |
next->isCharge = info.isCharge; |
107 |
next->mass = info.mass; |
108 |
next->epslon = info.epslon; |
109 |
next->sigma = info.sigma; |
110 |
next->charge = info.charge; |
111 |
next->ident = info.ident; |
112 |
} |
113 |
} |
114 |
|
115 |
#ifdef IS_MPI |
116 |
|
117 |
void duplicate( atomStruct &info ){ |
118 |
strcpy(info.name, name); |
119 |
info.isDirectional = isDirectional; |
120 |
info.isLJ = isLJ; |
121 |
info.isCharge = isCharge; |
122 |
info.mass = mass; |
123 |
info.epslon = epslon; |
124 |
info.sigma = sigma; |
125 |
info.charge = charge; |
126 |
info.ident = ident; |
127 |
info.last = 0; |
128 |
} |
129 |
|
130 |
#endif |
131 |
|
132 |
char name[15]; |
133 |
int isDirectional; |
134 |
int isLJ; |
135 |
int isCharge; |
136 |
double mass; |
137 |
double epslon; |
138 |
double sigma; |
139 |
double charge; |
140 |
int ident; |
141 |
LinkedAtomType* next; |
142 |
}; |
143 |
|
144 |
class LinkedDirectionalType { |
145 |
public: |
146 |
LinkedDirectionalType(){ |
147 |
next = NULL; |
148 |
name[0] = '\0'; |
149 |
} |
150 |
~LinkedDirectionalType(){ if( next != NULL ) delete next; } |
151 |
|
152 |
LinkedDirectionalType* find(char* key){ |
153 |
if( !strcmp(name, key) ) return this; |
154 |
if( next != NULL ) return next->find(key); |
155 |
return NULL; |
156 |
} |
157 |
|
158 |
|
159 |
void add( directionalStruct &info ){ |
160 |
|
161 |
// check for duplicates |
162 |
|
163 |
if( !strcmp( info.name, name ) ){ |
164 |
sprintf( painCave.errMsg, |
165 |
"Duplicate WATER directional type \"%s\" found in " |
166 |
"the WATER param file./n", |
167 |
name ); |
168 |
painCave.isFatal = 1; |
169 |
simError(); |
170 |
} |
171 |
|
172 |
if( next != NULL ) next->add(info); |
173 |
else{ |
174 |
next = new LinkedDirectionalType(); |
175 |
strcpy(next->name, info.name); |
176 |
next->isDipole = info.isDipole; |
177 |
next->isSticky = info.isSticky; |
178 |
next->Ixx = info.Ixx; |
179 |
next->Iyy = info.Iyy; |
180 |
next->Izz = info.Izz; |
181 |
next->dipole = info.dipole; |
182 |
next->w0 = info.w0; |
183 |
next->v0 = info.v0; |
184 |
next->v0p = info.v0p; |
185 |
next->rl = info.rl; |
186 |
next->ru = info.ru; |
187 |
next->rlp = info.rlp; |
188 |
next->rup = info.rup; |
189 |
} |
190 |
} |
191 |
|
192 |
#ifdef IS_MPI |
193 |
|
194 |
void duplicate( directionalStruct &info ){ |
195 |
strcpy(info.name, name); |
196 |
info.isDipole = isDipole; |
197 |
info.isSticky = isSticky; |
198 |
info.Ixx = Ixx; |
199 |
info.Iyy = Iyy; |
200 |
info.Izz = Izz; |
201 |
info.dipole = dipole; |
202 |
info.w0 = w0; |
203 |
info.v0 = v0; |
204 |
info.v0p = v0p; |
205 |
info.rl = rl; |
206 |
info.ru = ru; |
207 |
info.rlp = rlp; |
208 |
info.rup = rup; |
209 |
info.last = 0; |
210 |
} |
211 |
|
212 |
#endif |
213 |
|
214 |
char name[15]; |
215 |
int isDipole; |
216 |
int isSticky; |
217 |
double Ixx; |
218 |
double Iyy; |
219 |
double Izz; |
220 |
double dipole; |
221 |
double w0; |
222 |
double v0; |
223 |
double v0p; |
224 |
double rl; |
225 |
double ru; |
226 |
double rlp; |
227 |
double rup; |
228 |
LinkedDirectionalType* next; |
229 |
}; |
230 |
|
231 |
LinkedAtomType* headAtomType; |
232 |
LinkedAtomType* currentAtomType; |
233 |
LinkedDirectionalType* headDirectionalType; |
234 |
LinkedDirectionalType* currentDirectionalType; |
235 |
} // namespace |
236 |
|
237 |
using namespace WATER_NS; |
238 |
|
239 |
//**************************************************************** |
240 |
// begins the actual forcefield stuff. |
241 |
//**************************************************************** |
242 |
|
243 |
|
244 |
WATER::WATER(){ |
245 |
|
246 |
char fileName[200]; |
247 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
248 |
char* ffPath; |
249 |
char temp[200]; |
250 |
|
251 |
headAtomType = NULL; |
252 |
currentAtomType = NULL; |
253 |
headDirectionalType = NULL; |
254 |
currentDirectionalType = NULL; |
255 |
|
256 |
// do the funtion wrapping |
257 |
wrapMeFF( this ); |
258 |
|
259 |
#ifdef IS_MPI |
260 |
int i; |
261 |
|
262 |
// ********************************************************************** |
263 |
// Init the atomStruct mpi type |
264 |
|
265 |
atomStruct atomProto; // mpiPrototype |
266 |
int atomBC[3] = {15,4,5}; // block counts |
267 |
MPI_Aint atomDspls[3]; // displacements |
268 |
MPI_Datatype atomMbrTypes[3]; // member mpi types |
269 |
|
270 |
MPI_Address(&atomProto.name, &atomDspls[0]); |
271 |
MPI_Address(&atomProto.mass, &atomDspls[1]); |
272 |
MPI_Address(&atomProto.isDirectional, &atomDspls[2]); |
273 |
|
274 |
atomMbrTypes[0] = MPI_CHAR; |
275 |
atomMbrTypes[1] = MPI_DOUBLE; |
276 |
atomMbrTypes[2] = MPI_INT; |
277 |
|
278 |
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
279 |
|
280 |
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
281 |
MPI_Type_commit(&mpiAtomStructType); |
282 |
|
283 |
// *********************************************************************** |
284 |
|
285 |
// ********************************************************************** |
286 |
// Init the directionalStruct mpi type |
287 |
|
288 |
directionalStruct directionalProto; // mpiPrototype |
289 |
int directionalBC[3] = {15,11,3}; // block counts |
290 |
MPI_Aint directionalDspls[3]; // displacements |
291 |
MPI_Datatype directionalMbrTypes[3]; // member mpi types |
292 |
|
293 |
MPI_Address(&directionalProto.name, &directionalDspls[0]); |
294 |
MPI_Address(&directionalProto.Ixx, &directionalDspls[1]); |
295 |
MPI_Address(&directionalProto.isDipole, &directionalDspls[2]); |
296 |
|
297 |
directionalMbrTypes[0] = MPI_CHAR; |
298 |
directionalMbrTypes[1] = MPI_DOUBLE; |
299 |
directionalMbrTypes[2] = MPI_INT; |
300 |
|
301 |
for (i=2; i >= 0; i--) directionalDspls[i] -= directionalDspls[0]; |
302 |
|
303 |
MPI_Type_struct(3, directionalBC, directionalDspls, directionalMbrTypes, |
304 |
&mpiDirectionalStructType); |
305 |
MPI_Type_commit(&mpiDirectionalStructType); |
306 |
|
307 |
// *********************************************************************** |
308 |
|
309 |
if( worldRank == 0 ){ |
310 |
#endif |
311 |
|
312 |
// generate the force file name |
313 |
|
314 |
strcpy( fileName, "WATER.frc" ); |
315 |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
316 |
|
317 |
// attempt to open the file in the current directory first. |
318 |
|
319 |
frcFile = fopen( fileName, "r" ); |
320 |
|
321 |
if( frcFile == NULL ){ |
322 |
|
323 |
// next see if the force path enviorment variable is set |
324 |
|
325 |
ffPath = getenv( ffPath_env ); |
326 |
if( ffPath == NULL ) { |
327 |
STR_DEFINE(ffPath, FRC_PATH ); |
328 |
} |
329 |
|
330 |
|
331 |
strcpy( temp, ffPath ); |
332 |
strcat( temp, "/" ); |
333 |
strcat( temp, fileName ); |
334 |
strcpy( fileName, temp ); |
335 |
|
336 |
frcFile = fopen( fileName, "r" ); |
337 |
|
338 |
if( frcFile == NULL ){ |
339 |
|
340 |
sprintf( painCave.errMsg, |
341 |
"Error opening the force field parameter file: %s\n" |
342 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
343 |
"variable?\n", |
344 |
fileName ); |
345 |
painCave.isFatal = 1; |
346 |
simError(); |
347 |
} |
348 |
} |
349 |
|
350 |
#ifdef IS_MPI |
351 |
} |
352 |
|
353 |
sprintf( checkPointMsg, "WATER file opened sucessfully." ); |
354 |
MPIcheckPoint(); |
355 |
|
356 |
#endif // is_mpi |
357 |
} |
358 |
|
359 |
|
360 |
WATER::~WATER(){ |
361 |
|
362 |
if( headAtomType != NULL ) delete headAtomType; |
363 |
if( headDirectionalType != NULL ) delete headDirectionalType; |
364 |
|
365 |
#ifdef IS_MPI |
366 |
if( worldRank == 0 ){ |
367 |
#endif // is_mpi |
368 |
|
369 |
fclose( frcFile ); |
370 |
|
371 |
#ifdef IS_MPI |
372 |
} |
373 |
#endif // is_mpi |
374 |
} |
375 |
|
376 |
void WATER::cleanMe( void ){ |
377 |
|
378 |
#ifdef IS_MPI |
379 |
|
380 |
// keep the linked list in the mpi version |
381 |
|
382 |
#else // is_mpi |
383 |
|
384 |
// delete the linked list in the single processor version |
385 |
|
386 |
if( headAtomType != NULL ) delete headAtomType; |
387 |
if( headDirectionalType != NULL ) delete headDirectionalType; |
388 |
|
389 |
#endif // is_mpi |
390 |
} |
391 |
|
392 |
|
393 |
void WATER::initForceField( int ljMixRule ){ |
394 |
|
395 |
initFortran( ljMixRule, entry_plug->useReactionField ); |
396 |
} |
397 |
|
398 |
|
399 |
void WATER::readParams( void ){ |
400 |
|
401 |
int identNum; |
402 |
|
403 |
atomStruct atomInfo; |
404 |
directionalStruct directionalInfo; |
405 |
fpos_t *atomPos; |
406 |
|
407 |
atomInfo.last = 1; // initialize last to have the last set. |
408 |
directionalInfo.last = 1; // if things go well, last will be set to 0 |
409 |
|
410 |
atomPos = new fpos_t; |
411 |
bigSigma = 0.0; |
412 |
|
413 |
#ifdef IS_MPI |
414 |
if( worldRank == 0 ){ |
415 |
#endif |
416 |
|
417 |
// read in the atom types. |
418 |
|
419 |
headAtomType = new LinkedAtomType; |
420 |
headDirectionalType = new LinkedDirectionalType; |
421 |
|
422 |
fastForward( "AtomTypes", "initializeAtoms" ); |
423 |
|
424 |
// we are now at the AtomTypes section. |
425 |
|
426 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
427 |
lineNum++; |
428 |
|
429 |
|
430 |
// read a line, and start parsing out the atom types |
431 |
|
432 |
if( eof_test == NULL ){ |
433 |
sprintf( painCave.errMsg, |
434 |
"Error in reading Atoms from force file at line %d.\n", |
435 |
lineNum ); |
436 |
painCave.isFatal = 1; |
437 |
simError(); |
438 |
} |
439 |
|
440 |
identNum = 1; |
441 |
// stop reading at end of file, or at next section |
442 |
while( readLine[0] != '#' && eof_test != NULL ){ |
443 |
|
444 |
// toss comment lines |
445 |
if( readLine[0] != '!' ){ |
446 |
|
447 |
// the parser returns 0 if the line was blank |
448 |
if( parseAtom( readLine, lineNum, atomInfo ) ){ |
449 |
atomInfo.ident = identNum; |
450 |
headAtomType->add( atomInfo ); |
451 |
if ( atomInfo.isDirectional ) { |
452 |
|
453 |
// if the atom is directional, skip to the directional section |
454 |
// and parse directional info. |
455 |
fgetpos( frcFile, atomPos ); |
456 |
sectionSearch( "DirectionalTypes", atomInfo.name, |
457 |
"initializeDirectional" ); |
458 |
parseDirectional( readLine, lineNum, directionalInfo ); |
459 |
headDirectionalType->add( directionalInfo ); |
460 |
|
461 |
// return to the AtomTypes section |
462 |
fsetpos( frcFile, atomPos ); |
463 |
} |
464 |
identNum++; |
465 |
} |
466 |
} |
467 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
468 |
lineNum++; |
469 |
} |
470 |
|
471 |
#ifdef IS_MPI |
472 |
|
473 |
// send out the linked list to all the other processes |
474 |
|
475 |
sprintf( checkPointMsg, |
476 |
"WATER atom structures read successfully." ); |
477 |
MPIcheckPoint(); |
478 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
479 |
while( currentAtomType != NULL ){ |
480 |
currentAtomType->duplicate( atomInfo ); |
481 |
|
482 |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
483 |
|
484 |
sprintf( checkPointMsg, |
485 |
"successfully sent WATER force type: \"%s\"\n", |
486 |
atomInfo.name ); |
487 |
MPIcheckPoint(); |
488 |
|
489 |
currentAtomType = currentAtomType->next; |
490 |
} |
491 |
|
492 |
atomInfo.last = 1; |
493 |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
494 |
|
495 |
if ( atomInfo.isDirectional ){ |
496 |
// send out the linked list to all the other processes |
497 |
|
498 |
sprintf( checkPointMsg, |
499 |
"WATER directional structures read successfully." ); |
500 |
MPIcheckPoint(); |
501 |
|
502 |
currentDirectionalType = headDirectionalType->next; |
503 |
while( currentDirectionalType != NULL ){ |
504 |
currentDirectionalType->duplicate( directionalInfo ); |
505 |
sendFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
506 |
currentDirectionalType = currentDirectionalType->next; |
507 |
} |
508 |
directionalInfo.last = 1; |
509 |
sendFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
510 |
} |
511 |
} |
512 |
|
513 |
else{ |
514 |
|
515 |
// listen for node 0 to send out the force params |
516 |
|
517 |
MPIcheckPoint(); |
518 |
|
519 |
headAtomType = new LinkedAtomType; |
520 |
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
521 |
|
522 |
while( !atomInfo.last ){ |
523 |
|
524 |
headAtomType->add( atomInfo ); |
525 |
|
526 |
MPIcheckPoint(); |
527 |
|
528 |
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
529 |
} |
530 |
|
531 |
if ( atomInfo.isDirectional ) { |
532 |
// listen for node 0 to send out the force params |
533 |
|
534 |
MPIcheckPoint(); |
535 |
|
536 |
headDirectionalType = new LinkedDirectionalType; |
537 |
receiveFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
538 |
while( !directionalInfo.last ){ |
539 |
|
540 |
headDirectionalType->add( directionalInfo ); |
541 |
receiveFrcStruct( &directionalInfo, mpiDirectionalStructType ); |
542 |
} |
543 |
|
544 |
sprintf( checkPointMsg, |
545 |
"WATER directional structures broadcast successfully." ); |
546 |
MPIcheckPoint(); |
547 |
} |
548 |
} |
549 |
|
550 |
#endif // is_mpi |
551 |
|
552 |
// call new A_types in fortran |
553 |
|
554 |
int isError; |
555 |
|
556 |
// dummy variables |
557 |
int isGB = 0; |
558 |
int isEAM = 0; |
559 |
int notDipole = 0; |
560 |
int notSSD = 0; |
561 |
double noDipMoment = 0.0; |
562 |
|
563 |
|
564 |
currentAtomType = headAtomType->next; |
565 |
currentDirectionalType = headDirectionalType->next; |
566 |
|
567 |
while( currentAtomType != NULL ){ |
568 |
|
569 |
if( currentAtomType->isLJ ) entry_plug->useLJ = 1; |
570 |
if( currentAtomType->isCharge ) entry_plug->useCharges = 1; |
571 |
if( currentAtomType->isDirectional ){ |
572 |
// only directional atoms can have dipoles or be sticky |
573 |
if ( currentDirectionalType->isDipole ) entry_plug->useDipoles = 1; |
574 |
if ( currentDirectionalType->isSticky ) { |
575 |
entry_plug->useSticky = 1; |
576 |
set_sticky_params( &(currentDirectionalType->w0), |
577 |
&(currentDirectionalType->v0), |
578 |
&(currentDirectionalType->v0p), |
579 |
&(currentDirectionalType->rl), |
580 |
&(currentDirectionalType->ru), |
581 |
&(currentDirectionalType->rlp), |
582 |
&(currentDirectionalType->rup)); |
583 |
} |
584 |
if( currentAtomType->name[0] != '\0' ){ |
585 |
isError = 0; |
586 |
makeAtype( &(currentAtomType->ident), |
587 |
&(currentAtomType->isLJ), |
588 |
&(currentDirectionalType->isSticky), |
589 |
&(currentDirectionalType->isDipole), |
590 |
&isGB, |
591 |
&isEAM, |
592 |
&(currentAtomType->isCharge), |
593 |
&(currentAtomType->epslon), |
594 |
&(currentAtomType->sigma), |
595 |
&(currentAtomType->charge), |
596 |
&(currentDirectionalType->dipole), |
597 |
&isError ); |
598 |
if( isError ){ |
599 |
sprintf( painCave.errMsg, |
600 |
"Error initializing the \"%s\" atom type in fortran\n", |
601 |
currentAtomType->name ); |
602 |
painCave.isFatal = 1; |
603 |
simError(); |
604 |
} |
605 |
} |
606 |
currentDirectionalType->next; |
607 |
} |
608 |
|
609 |
else { |
610 |
// use all dummy variables if this is not a directional atom |
611 |
if( currentAtomType->name[0] != '\0' ){ |
612 |
isError = 0; |
613 |
makeAtype( &(currentAtomType->ident), |
614 |
&(currentAtomType->isLJ), |
615 |
¬SSD, |
616 |
¬Dipole, |
617 |
&isGB, |
618 |
&isEAM, |
619 |
&(currentAtomType->isCharge), |
620 |
&(currentAtomType->epslon), |
621 |
&(currentAtomType->sigma), |
622 |
&(currentAtomType->charge), |
623 |
&noDipMoment, |
624 |
&isError ); |
625 |
if( isError ){ |
626 |
sprintf( painCave.errMsg, |
627 |
"Error initializing the \"%s\" atom type in fortran\n", |
628 |
currentAtomType->name ); |
629 |
painCave.isFatal = 1; |
630 |
simError(); |
631 |
} |
632 |
} |
633 |
} |
634 |
currentAtomType = currentAtomType->next; |
635 |
} |
636 |
|
637 |
#ifdef IS_MPI |
638 |
sprintf( checkPointMsg, |
639 |
"WATER atom structures successfully sent to fortran\n" ); |
640 |
MPIcheckPoint(); |
641 |
#endif // is_mpi |
642 |
|
643 |
} |
644 |
|
645 |
|
646 |
void WATER::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
647 |
|
648 |
int i,j; |
649 |
|
650 |
// initialize the atoms |
651 |
DirectionalAtom* dAtom; |
652 |
double inertialMat[3][3]; |
653 |
|
654 |
for( i=0; i<nAtoms; i++ ){ |
655 |
fprintf(stderr, "flag 1\n"); |
656 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
657 |
fprintf(stderr, "%s is the type\n", the_atoms[i]->getType()); |
658 |
if( currentAtomType == NULL ){ |
659 |
sprintf( painCave.errMsg, |
660 |
"AtomType error, %s not found in force file.\n", |
661 |
the_atoms[i]->getType() ); |
662 |
painCave.isFatal = 1; |
663 |
simError(); |
664 |
} |
665 |
fprintf(stderr, "flag 2\n"); |
666 |
if( currentAtomType->isLJ ) the_atoms[i]->setLJ(); |
667 |
if( currentAtomType->isCharge ) the_atoms[i]->setCharged(); |
668 |
the_atoms[i]->setMass( currentAtomType->mass ); |
669 |
the_atoms[i]->setIdent( currentAtomType->ident ); |
670 |
fprintf(stderr, "flag 3\n"); |
671 |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
672 |
|
673 |
if( currentAtomType->isDirectional ){ |
674 |
fprintf(stderr, "flag 4\n"); |
675 |
currentDirectionalType = |
676 |
headDirectionalType->find( the_atoms[i]->getType() ); |
677 |
fprintf(stderr, "%s is the type\n", the_atoms[i]->getType()); |
678 |
if( currentDirectionalType == NULL ){ |
679 |
sprintf( painCave.errMsg, |
680 |
"DirectionalType error, %s not found in force file.\n", |
681 |
the_atoms[i]->getType() ); |
682 |
painCave.isFatal = 1; |
683 |
simError(); |
684 |
} |
685 |
|
686 |
// zero out the moments of inertia matrix |
687 |
for( i=0; i<3; i++ ) |
688 |
for( j=0; j<3; j++ ) |
689 |
inertialMat[i][j] = 0.0; |
690 |
|
691 |
// load the force file moments of inertia |
692 |
inertialMat[0][0] = currentDirectionalType->Ixx; |
693 |
inertialMat[1][1] = currentDirectionalType->Iyy; |
694 |
inertialMat[2][2] = currentDirectionalType->Izz; |
695 |
fprintf(stderr, "Let's try pointing to isDirectional\n"); |
696 |
fprintf(stderr, "%i what is this\n",the_atoms[i]->isDirectional()); |
697 |
dAtom = (DirectionalAtom *) the_atoms[i]; |
698 |
fprintf(stderr, "%i is isDipole\n", currentDirectionalType->isDipole); |
699 |
dAtom->setHasDipole( currentDirectionalType->isDipole ); |
700 |
dAtom->setMu( currentDirectionalType->dipole ); |
701 |
fprintf(stderr, "flag 5\n"); |
702 |
dAtom->setMu( currentDirectionalType->dipole ); |
703 |
fprintf(stderr,"flag 6\n"); |
704 |
// if it's sticky then it's an SSD type |
705 |
dAtom->setSSD( currentDirectionalType->isSticky ); |
706 |
dAtom->setJx( 0.0 ); |
707 |
dAtom->setJy( 0.0 ); |
708 |
dAtom->setJz( 0.0 ); |
709 |
dAtom->setI( inertialMat ); |
710 |
fprintf(stderr, "flag 7\n"); |
711 |
entry_plug->n_dipoles++; |
712 |
fprintf(stderr, "flag 8\n"); |
713 |
} |
714 |
else{ |
715 |
sprintf( painCave.errMsg, |
716 |
"WATER error: Atom \"%s\" is directional, yet no standard" |
717 |
" orientation was specifed in the BASS file.\n", |
718 |
currentAtomType->name ); |
719 |
painCave.isFatal = 1; |
720 |
simError(); |
721 |
} |
722 |
} |
723 |
} |
724 |
|
725 |
void WATER::initializeBonds( int nBonds, Bond** BondArray, |
726 |
bond_pair* the_bonds ){ |
727 |
|
728 |
if( nBonds ){ |
729 |
sprintf( painCave.errMsg, |
730 |
"WATER does not support bonds.\n" ); |
731 |
painCave.isFatal = 1; |
732 |
simError(); |
733 |
} |
734 |
} |
735 |
|
736 |
void WATER::initializeBends( int nBends, Bend** bendArray, |
737 |
bend_set* the_bends ){ |
738 |
|
739 |
if( nBends ){ |
740 |
sprintf( painCave.errMsg, |
741 |
"WATER does not support bends.\n" ); |
742 |
painCave.isFatal = 1; |
743 |
simError(); |
744 |
} |
745 |
} |
746 |
|
747 |
void WATER::initializeTorsions( int nTorsions, Torsion** torsionArray, |
748 |
torsion_set* the_torsions ){ |
749 |
|
750 |
if( nTorsions ){ |
751 |
sprintf( painCave.errMsg, |
752 |
"WATER does not support torsions.\n" ); |
753 |
painCave.isFatal = 1; |
754 |
simError(); |
755 |
} |
756 |
} |
757 |
|
758 |
void WATER::fastForward( char* stopText, char* searchOwner ){ |
759 |
|
760 |
int foundText = 0; |
761 |
char* the_token; |
762 |
|
763 |
rewind( frcFile ); |
764 |
lineNum = 0; |
765 |
|
766 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
767 |
lineNum++; |
768 |
if( eof_test == NULL ){ |
769 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
770 |
" file is empty.\n", |
771 |
searchOwner ); |
772 |
painCave.isFatal = 1; |
773 |
simError(); |
774 |
} |
775 |
|
776 |
|
777 |
while( !foundText ){ |
778 |
while( eof_test != NULL && readLine[0] != '#' ){ |
779 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
780 |
lineNum++; |
781 |
} |
782 |
if( eof_test == NULL ){ |
783 |
sprintf( painCave.errMsg, |
784 |
"Error fast forwarding force file for %s at " |
785 |
"line %d: file ended unexpectedly.\n", |
786 |
searchOwner, |
787 |
lineNum ); |
788 |
painCave.isFatal = 1; |
789 |
simError(); |
790 |
} |
791 |
|
792 |
the_token = strtok( readLine, " ,;\t#\n" ); |
793 |
foundText = !strcmp( stopText, the_token ); |
794 |
|
795 |
if( !foundText ){ |
796 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
797 |
lineNum++; |
798 |
|
799 |
if( eof_test == NULL ){ |
800 |
sprintf( painCave.errMsg, |
801 |
"Error fast forwarding force file for %s at " |
802 |
"line %d: file ended unexpectedly.\n", |
803 |
searchOwner, |
804 |
lineNum ); |
805 |
painCave.isFatal = 1; |
806 |
simError(); |
807 |
} |
808 |
} |
809 |
} |
810 |
} |
811 |
|
812 |
void WATER::sectionSearch( char* secHead, char* stopText, char* searchOwner ){ |
813 |
|
814 |
int foundSection = 0; |
815 |
int foundText = 0; |
816 |
char* the_token; |
817 |
fpos_t *tempPos; |
818 |
|
819 |
rewind( frcFile ); |
820 |
lineNum = 0; |
821 |
tempPos = new fpos_t; |
822 |
|
823 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
824 |
lineNum++; |
825 |
if( eof_test == NULL ){ |
826 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
827 |
" file is empty.\n", |
828 |
searchOwner ); |
829 |
painCave.isFatal = 1; |
830 |
simError(); |
831 |
} |
832 |
|
833 |
while( !foundSection ){ |
834 |
while( eof_test != NULL && readLine[0] != '#' ){ |
835 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
836 |
lineNum++; |
837 |
} |
838 |
if( eof_test == NULL ){ |
839 |
sprintf( painCave.errMsg, |
840 |
"Error fast forwarding force file for %s at " |
841 |
"line %d: file ended unexpectedly.\n", |
842 |
searchOwner, |
843 |
lineNum ); |
844 |
painCave.isFatal = 1; |
845 |
simError(); |
846 |
} |
847 |
the_token = strtok( readLine, " ,;\t#\n" ); |
848 |
foundSection = !strcmp( secHead, the_token ); |
849 |
|
850 |
if( !foundSection ){ |
851 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
852 |
lineNum++; |
853 |
|
854 |
if( eof_test == NULL ){ |
855 |
sprintf( painCave.errMsg, |
856 |
"Error section searching force file for %s at " |
857 |
"line %d: file ended unexpectedly.\n", |
858 |
searchOwner, |
859 |
lineNum ); |
860 |
painCave.isFatal = 1; |
861 |
simError(); |
862 |
} |
863 |
} |
864 |
} |
865 |
|
866 |
while( !foundText ){ |
867 |
|
868 |
fgetpos( frcFile, tempPos ); |
869 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
870 |
lineNum++; |
871 |
|
872 |
if( eof_test == NULL ){ |
873 |
sprintf( painCave.errMsg, |
874 |
"Error fast forwarding force file for %s at " |
875 |
"line %d: file ended unexpectedly.\n", |
876 |
searchOwner, |
877 |
lineNum ); |
878 |
painCave.isFatal = 1; |
879 |
simError(); |
880 |
} |
881 |
|
882 |
the_token = strtok( readLine, " ,;\t#\n" ); |
883 |
if( the_token != NULL ){ |
884 |
foundText = !strcmp( stopText, the_token ); |
885 |
} |
886 |
} |
887 |
fsetpos( frcFile, tempPos ); |
888 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
889 |
lineNum++; |
890 |
} |
891 |
|
892 |
|
893 |
int WATER_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
894 |
|
895 |
char* the_token; |
896 |
|
897 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
898 |
if( the_token != NULL ){ |
899 |
|
900 |
strcpy( info.name, the_token ); |
901 |
|
902 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
903 |
sprintf( painCave.errMsg, |
904 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
905 |
painCave.isFatal = 1; |
906 |
simError(); |
907 |
} |
908 |
|
909 |
info.isDirectional = atoi( the_token ); |
910 |
|
911 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
912 |
sprintf( painCave.errMsg, |
913 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
914 |
painCave.isFatal = 1; |
915 |
simError(); |
916 |
} |
917 |
|
918 |
info.isLJ = atoi( the_token ); |
919 |
|
920 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
921 |
sprintf( painCave.errMsg, |
922 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
923 |
painCave.isFatal = 1; |
924 |
simError(); |
925 |
} |
926 |
|
927 |
info.isCharge = atoi( the_token ); |
928 |
|
929 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
930 |
sprintf( painCave.errMsg, |
931 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
932 |
painCave.isFatal = 1; |
933 |
simError(); |
934 |
} |
935 |
|
936 |
info.mass = atof( the_token ); |
937 |
|
938 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
939 |
sprintf( painCave.errMsg, |
940 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
941 |
painCave.isFatal = 1; |
942 |
simError(); |
943 |
} |
944 |
|
945 |
info.epslon = atof( the_token ); |
946 |
|
947 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
948 |
sprintf( painCave.errMsg, |
949 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
950 |
painCave.isFatal = 1; |
951 |
simError(); |
952 |
} |
953 |
|
954 |
info.sigma = atof( the_token ); |
955 |
|
956 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
957 |
sprintf( painCave.errMsg, |
958 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
959 |
painCave.isFatal = 1; |
960 |
simError(); |
961 |
} |
962 |
|
963 |
info.charge = atof( the_token ); |
964 |
|
965 |
return 1; |
966 |
} |
967 |
else return 0; |
968 |
} |
969 |
|
970 |
int WATER_NS::parseDirectional( char *lineBuffer, int lineNum, directionalStruct &info ){ |
971 |
|
972 |
char* the_token; |
973 |
|
974 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
975 |
if( the_token != NULL ){ |
976 |
|
977 |
strcpy( info.name, the_token ); |
978 |
|
979 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
980 |
sprintf( painCave.errMsg, |
981 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
982 |
painCave.isFatal = 1; |
983 |
simError(); |
984 |
} |
985 |
|
986 |
info.isDipole = atoi( the_token ); |
987 |
|
988 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
989 |
sprintf( painCave.errMsg, |
990 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
991 |
painCave.isFatal = 1; |
992 |
simError(); |
993 |
} |
994 |
|
995 |
info.isSticky = atoi( the_token ); |
996 |
|
997 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
998 |
sprintf( painCave.errMsg, |
999 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1000 |
painCave.isFatal = 1; |
1001 |
simError(); |
1002 |
} |
1003 |
|
1004 |
info.Ixx = atof( the_token ); |
1005 |
|
1006 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1007 |
sprintf( painCave.errMsg, |
1008 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1009 |
painCave.isFatal = 1; |
1010 |
simError(); |
1011 |
} |
1012 |
|
1013 |
info.Iyy = atof( the_token ); |
1014 |
|
1015 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1016 |
sprintf( painCave.errMsg, |
1017 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1018 |
painCave.isFatal = 1; |
1019 |
simError(); |
1020 |
} |
1021 |
|
1022 |
info.Izz = atof( the_token ); |
1023 |
|
1024 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1025 |
sprintf( painCave.errMsg, |
1026 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1027 |
painCave.isFatal = 1; |
1028 |
simError(); |
1029 |
} |
1030 |
|
1031 |
|
1032 |
info.dipole = atof( the_token ); |
1033 |
|
1034 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1035 |
sprintf( painCave.errMsg, |
1036 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1037 |
painCave.isFatal = 1; |
1038 |
simError(); |
1039 |
} |
1040 |
|
1041 |
info.w0 = atof( the_token ); |
1042 |
|
1043 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1044 |
sprintf( painCave.errMsg, |
1045 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1046 |
painCave.isFatal = 1; |
1047 |
simError(); |
1048 |
} |
1049 |
|
1050 |
info.v0 = atof( the_token ); |
1051 |
|
1052 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1053 |
sprintf( painCave.errMsg, |
1054 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1055 |
painCave.isFatal = 1; |
1056 |
simError(); |
1057 |
} |
1058 |
|
1059 |
info.v0p = atof( the_token ); |
1060 |
|
1061 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1062 |
sprintf( painCave.errMsg, |
1063 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1064 |
painCave.isFatal = 1; |
1065 |
simError(); |
1066 |
} |
1067 |
|
1068 |
info.rl = atof( the_token ); |
1069 |
|
1070 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1071 |
sprintf( painCave.errMsg, |
1072 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1073 |
painCave.isFatal = 1; |
1074 |
simError(); |
1075 |
} |
1076 |
|
1077 |
info.ru = atof( the_token ); |
1078 |
|
1079 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1080 |
sprintf( painCave.errMsg, |
1081 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1082 |
painCave.isFatal = 1; |
1083 |
simError(); |
1084 |
} |
1085 |
|
1086 |
info.rlp = atof( the_token ); |
1087 |
|
1088 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1089 |
sprintf( painCave.errMsg, |
1090 |
"Error parseing DirectionalTypes: line %d\n", lineNum ); |
1091 |
painCave.isFatal = 1; |
1092 |
simError(); |
1093 |
} |
1094 |
|
1095 |
info.rup = atof( the_token ); |
1096 |
|
1097 |
return 1; |
1098 |
} |
1099 |
else return 0; |
1100 |
} |