1 |
#include <cstdlib> |
2 |
#include <cstdio> |
3 |
#include <cstring> |
4 |
|
5 |
#include <iostream> |
6 |
using namespace std; |
7 |
|
8 |
#ifdef IS_MPI |
9 |
#include <mpi.h> |
10 |
#include <mpi++.h> |
11 |
#endif //is_mpi |
12 |
|
13 |
#include "ForceFields.hpp" |
14 |
#include "SRI.hpp" |
15 |
#include "simError.h" |
16 |
|
17 |
|
18 |
|
19 |
// Declare the structures that will be passed by the parser and MPI |
20 |
|
21 |
typedef struct{ |
22 |
char name[15]; |
23 |
double mass; |
24 |
double epslon; |
25 |
double sigma; |
26 |
double dipole; |
27 |
int isDipole; |
28 |
int ident; |
29 |
int last; // 0 -> default |
30 |
// 1 -> in MPI: tells nodes to stop listening |
31 |
} atomStruct; |
32 |
|
33 |
int parseAtomSSD( char *lineBuffer, int lineNum, atomStruct &info ); |
34 |
|
35 |
#ifdef IS_MPI |
36 |
#include "mpiForceField.h" |
37 |
|
38 |
MPI_Datatype mpiAtomStructType; |
39 |
|
40 |
#endif |
41 |
|
42 |
|
43 |
// declaration of functions needed to wrap the fortran module |
44 |
|
45 |
extern "C" { |
46 |
void forcefactory_( char* forceName, |
47 |
int* status, |
48 |
void (*wrapFunction)( void (*p1)( int* ident, |
49 |
double* mass, |
50 |
double* epslon, |
51 |
double* sigma, |
52 |
int* status ), |
53 |
void (*p2)( int *nLocal, |
54 |
int *identArray, |
55 |
int *isError ), |
56 |
void (*p3)( double* positionArray, |
57 |
double* forceArray, |
58 |
double* potentialEnergy, |
59 |
short int* doPotentialCalc )), |
60 |
int forceNameLength ); |
61 |
} |
62 |
|
63 |
|
64 |
void SSDfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, |
65 |
double* sigma, int* status ), |
66 |
void (*p2)( int *nLocal, int *identArray, |
67 |
int *isError ), |
68 |
void (*p3)( double* positionArray,double* forceArray, |
69 |
double* potentialEnergy, |
70 |
short int* doPotentialCalc ) ); |
71 |
|
72 |
void (*newSSDtype)( int* ident, double* mass, double* epslon, double* sigma, |
73 |
int* status ); |
74 |
|
75 |
void (*initSSDfortran) ( int *nLocal, int *identArray, int *isError ); |
76 |
|
77 |
SSD_FF* currentLJwrap; |
78 |
|
79 |
|
80 |
//**************************************************************** |
81 |
// begins the actual forcefield stuff. |
82 |
//**************************************************************** |
83 |
|
84 |
|
85 |
SSD_FF::SSD_FF(){ |
86 |
|
87 |
char fileName[200]; |
88 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
89 |
char* ffPath; |
90 |
char temp[200]; |
91 |
char errMsg[1000]; |
92 |
|
93 |
// do the funtion wrapping |
94 |
currentLJwrap = this; |
95 |
wrapMe(); |
96 |
|
97 |
#ifdef IS_MPI |
98 |
int i; |
99 |
|
100 |
// ********************************************************************** |
101 |
// Init the atomStruct mpi type |
102 |
|
103 |
atomStruct atomProto; // mpiPrototype |
104 |
int atomBC[3] = {15,4,3}; // block counts |
105 |
MPI_Aint atomDspls[3]; // displacements |
106 |
MPI_Datatype atomMbrTypes[3]; // member mpi types |
107 |
|
108 |
MPI_Address(&atomProto.name, &atomDspls[0]); |
109 |
MPI_Address(&atomProto.mass, &atomDspls[1]); |
110 |
MPI_Address(&atomProto.isDipole, &atomDspls[2]); |
111 |
|
112 |
atomMbrTypes[0] = MPI_CHAR; |
113 |
atomMbrTypes[1] = MPI_DOUBLE; |
114 |
atomMbrTypes[2] = MPI_INT; |
115 |
|
116 |
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
117 |
|
118 |
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
119 |
MPI_Type_commit(&mpiAtomStructType); |
120 |
|
121 |
// *********************************************************************** |
122 |
|
123 |
if( worldRank == 0 ){ |
124 |
#endif |
125 |
|
126 |
// generate the force file name |
127 |
|
128 |
strcpy( fileName, "SSD_FF.frc" ); |
129 |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
130 |
|
131 |
// attempt to open the file in the current directory first. |
132 |
|
133 |
frcFile = fopen( fileName, "r" ); |
134 |
|
135 |
if( frcFile == NULL ){ |
136 |
|
137 |
// next see if the force path enviorment variable is set |
138 |
|
139 |
ffPath = getenv( ffPath_env ); |
140 |
if( ffPath == NULL ) { |
141 |
sprintf( painCave.errMsg, |
142 |
"Error opening the force field parameter file: %s\n" |
143 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
144 |
"vairable?\n", |
145 |
fileName ); |
146 |
painCave.isFatal = 1; |
147 |
simError(); |
148 |
} |
149 |
|
150 |
|
151 |
strcpy( temp, ffPath ); |
152 |
strcat( temp, "/" ); |
153 |
strcat( temp, fileName ); |
154 |
strcpy( fileName, temp ); |
155 |
|
156 |
frcFile = fopen( fileName, "r" ); |
157 |
|
158 |
if( frcFile == NULL ){ |
159 |
|
160 |
sprintf( painCave.errMsg, |
161 |
"Error opening the force field parameter file: %s\n" |
162 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
163 |
"vairable?\n", |
164 |
fileName ); |
165 |
painCave.isFatal = 1; |
166 |
simError(); |
167 |
} |
168 |
} |
169 |
|
170 |
#ifdef IS_MPI |
171 |
} |
172 |
|
173 |
sprintf( checkPointMsg, "SSD_FF file opened sucessfully." ); |
174 |
MPIcheckPoint(); |
175 |
|
176 |
#endif // is_mpi |
177 |
} |
178 |
|
179 |
|
180 |
SSD_FF::~SSD_FF(){ |
181 |
|
182 |
#ifdef IS_MPI |
183 |
if( worldRank == 0 ){ |
184 |
#endif // is_mpi |
185 |
|
186 |
fclose( frcFile ); |
187 |
|
188 |
#ifdef IS_MPI |
189 |
} |
190 |
#endif // is_mpi |
191 |
} |
192 |
|
193 |
|
194 |
void SSD_FF::wrapMe( void ){ |
195 |
|
196 |
char* currentFF = "SSD"; |
197 |
int isError = 0; |
198 |
|
199 |
forcefactory_( currentFF, &isError, SSDfunctionWrapper, strlen(currentFF) ); |
200 |
|
201 |
if( isError ){ |
202 |
|
203 |
sprintf( painCave.errMsg, |
204 |
"SSD_FF error: an error was returned from fortran when the " |
205 |
"the functions were being wrapped.\n" ); |
206 |
painCave.isFatal = 1; |
207 |
simError(); |
208 |
} |
209 |
|
210 |
#ifdef IS_MPI |
211 |
sprintf( checkPointMsg, "SSD_FF functions succesfully wrapped." ); |
212 |
MPIcheckPoint(); |
213 |
#endif // is_mpi |
214 |
} |
215 |
|
216 |
|
217 |
void LJfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, |
218 |
double* sigma, int* status ), |
219 |
void (*p2)( int*, int*, int* ), |
220 |
void (*p3)( double* positionArray,double* forceArray, |
221 |
double* potentialEnergy, |
222 |
short int* doPotentialCalc ) ){ |
223 |
|
224 |
|
225 |
newSSDtype = p1; |
226 |
initSSDfortran = p2; |
227 |
currentLJwrap->setSSDfortran( p3 ); |
228 |
} |
229 |
|
230 |
|
231 |
|
232 |
void SSD_FF::initializeAtoms( void ){ |
233 |
|
234 |
class LinkedType { |
235 |
public: |
236 |
LinkedType(){ |
237 |
next = NULL; |
238 |
name[0] = '\0'; |
239 |
} |
240 |
~LinkedType(){ if( next != NULL ) delete next; } |
241 |
|
242 |
LinkedType* find(char* key){ |
243 |
if( !strcmp(name, key) ) return this; |
244 |
if( next != NULL ) return next->find(key); |
245 |
return NULL; |
246 |
} |
247 |
|
248 |
|
249 |
void add( atomStruct &info ){ |
250 |
|
251 |
// check for duplicates |
252 |
|
253 |
if( !strcmp( info.name, name ) ){ |
254 |
sprintf( painCave.errMsg, |
255 |
"Duplicate LJ atom type \"%s\" found in " |
256 |
"the SSD_FF param file./n", |
257 |
name ); |
258 |
painCave.isFatal = 1; |
259 |
simError(); |
260 |
} |
261 |
|
262 |
if( next != NULL ) next->add(info); |
263 |
else{ |
264 |
next = new LinkedType(); |
265 |
strcpy(next->name, info.name); |
266 |
next->isDipole = info.isDipole; |
267 |
next->mass = info.mass; |
268 |
next->epslon = info.epslon; |
269 |
next->sigma = info.sigma; |
270 |
next->dipole = info.dipole; |
271 |
next->ident = info.ident; |
272 |
} |
273 |
} |
274 |
|
275 |
|
276 |
#ifdef IS_MPI |
277 |
|
278 |
void duplicate( atomStruct &info ){ |
279 |
strcpy(info.name, name); |
280 |
info.isDipole = isDipole; |
281 |
info.mass = mass; |
282 |
info.epslon = epslon; |
283 |
info.sigma = sigma; |
284 |
info.ident = ident; |
285 |
info.dipole = dipole; |
286 |
info.last = 0; |
287 |
} |
288 |
|
289 |
|
290 |
#endif |
291 |
|
292 |
char name[15]; |
293 |
int isDipole; |
294 |
double dipole; |
295 |
double mass; |
296 |
double epslon; |
297 |
double sigma; |
298 |
int ident; |
299 |
LinkedType* next; |
300 |
}; |
301 |
|
302 |
LinkedType* headAtomType; |
303 |
LinkedType* currentAtomType; |
304 |
atomStruct info; |
305 |
info.last = 1; // initialize last to have the last set. |
306 |
// if things go well, last will be set to 0 |
307 |
|
308 |
int i; |
309 |
int identNum; |
310 |
|
311 |
Atom** the_atoms; |
312 |
int nAtoms; |
313 |
the_atoms = entry_plug->atoms; |
314 |
nAtoms = entry_plug->n_atoms; |
315 |
|
316 |
|
317 |
#ifdef IS_MPI |
318 |
if( worldRank == 0 ){ |
319 |
#endif |
320 |
|
321 |
// read in the atom types. |
322 |
|
323 |
headAtomType = new LinkedType; |
324 |
|
325 |
fastForward( "AtomTypes", "initializeAtoms" ); |
326 |
|
327 |
// we are now at the AtomTypes section. |
328 |
|
329 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
330 |
lineNum++; |
331 |
|
332 |
|
333 |
// read a line, and start parseing out the atom types |
334 |
|
335 |
if( eof_test == NULL ){ |
336 |
sprintf( painCave.errMsg, |
337 |
"Error in reading Atoms from force file at line %d.\n", |
338 |
lineNum ); |
339 |
painCave.isFatal = 1; |
340 |
simError(); |
341 |
} |
342 |
|
343 |
identNum = 1; |
344 |
// stop reading at end of file, or at next section |
345 |
while( readLine[0] != '#' && eof_test != NULL ){ |
346 |
|
347 |
// toss comment lines |
348 |
if( readLine[0] != '!' ){ |
349 |
|
350 |
// the parser returns 0 if the line was blank |
351 |
if( parseAtomLJ( readLine, lineNum, info ) ){ |
352 |
info.ident = identNum; |
353 |
headAtomType->add( info );; |
354 |
identNum++; |
355 |
} |
356 |
} |
357 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
358 |
lineNum++; |
359 |
} |
360 |
|
361 |
#ifdef IS_MPI |
362 |
|
363 |
// send out the linked list to all the other processes |
364 |
|
365 |
sprintf( checkPointMsg, |
366 |
"SSD_FF atom structures read successfully." ); |
367 |
MPIcheckPoint(); |
368 |
|
369 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
370 |
while( currentAtomType != NULL ){ |
371 |
currentAtomType->duplicate( info ); |
372 |
|
373 |
|
374 |
|
375 |
sendFrcStruct( &info, mpiAtomStructType ); |
376 |
|
377 |
sprintf( checkPointMsg, |
378 |
"successfully sent ssd force type: \"%s\"\n", |
379 |
info.name ); |
380 |
MPIcheckPoint(); |
381 |
|
382 |
currentAtomType = currentAtomType->next; |
383 |
} |
384 |
info.last = 1; |
385 |
sendFrcStruct( &info, mpiAtomStructType ); |
386 |
|
387 |
} |
388 |
|
389 |
else{ |
390 |
|
391 |
// listen for node 0 to send out the force params |
392 |
|
393 |
MPIcheckPoint(); |
394 |
|
395 |
headAtomType = new LinkedType; |
396 |
recieveFrcStruct( &info, mpiAtomStructType ); |
397 |
|
398 |
while( !info.last ){ |
399 |
|
400 |
|
401 |
|
402 |
headAtomType->add( info ); |
403 |
|
404 |
MPIcheckPoint(); |
405 |
|
406 |
recieveFrcStruct( &info, mpiAtomStructType ); |
407 |
} |
408 |
} |
409 |
#endif // is_mpi |
410 |
|
411 |
// call new A_types in fortran |
412 |
|
413 |
int isError; |
414 |
currentAtomType = headAtomType; |
415 |
while( currentAtomType != NULL ){ |
416 |
|
417 |
if( currentAtomType->name[0] != '\0' ){ |
418 |
isError = 0; |
419 |
newSSDtype( &(currentAtomType->ident), |
420 |
&(currentAtomType->mass), |
421 |
&(currentAtomType->epslon), |
422 |
&(currentAtomType->sigma), |
423 |
&isError ); |
424 |
if( isError ){ |
425 |
sprintf( painCave.errMsg, |
426 |
"Error initializing the \"%s\" atom type in fortran\n", |
427 |
currentAtomType->name ); |
428 |
painCave.isFatal = 1; |
429 |
simError(); |
430 |
} |
431 |
} |
432 |
currentAtomType = currentAtomType->next; |
433 |
} |
434 |
|
435 |
#ifdef IS_MPI |
436 |
sprintf( checkPointMsg, |
437 |
"SSD_FF atom structures successfully sent to fortran\n" ); |
438 |
MPIcheckPoint(); |
439 |
#endif // is_mpi |
440 |
|
441 |
|
442 |
|
443 |
// initialize the atoms |
444 |
|
445 |
////////////////////////////////////////////////// |
446 |
// a quick water fix |
447 |
|
448 |
double waterI[3][3]; |
449 |
waterI[0][0] = 1.76958347772500; |
450 |
waterI[0][1] = 0.0; |
451 |
waterI[0][2] = 0.0; |
452 |
|
453 |
waterI[1][0] = 0.0; |
454 |
waterI[1][1] = 0.614537057924513; |
455 |
waterI[1][2] = 0.0; |
456 |
|
457 |
waterI[2][0] = 0.0; |
458 |
waterI[2][1] = 0.0; |
459 |
waterI[2][2] = 1.15504641980049; |
460 |
|
461 |
double bigSigma = 0.0; |
462 |
Atom* thisAtom; |
463 |
DirectionalAtom* dAtom; |
464 |
|
465 |
for( i=0; i<nAtoms; i++ ){ |
466 |
|
467 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
468 |
if( currentAtomType == NULL ){ |
469 |
sprintf( painCave.errMsg, |
470 |
"AtomType error, %s not found in force file.\n", |
471 |
the_atoms[i]->getType() ); |
472 |
painCave.isFatal = 1; |
473 |
simError(); |
474 |
} |
475 |
|
476 |
the_atoms[i]->setMass( currentAtomType->mass ); |
477 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
478 |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
479 |
the_atoms[i]->setIdent( currentAtomType->ident ); |
480 |
the_atoms[i]->setLJ(); |
481 |
|
482 |
if( currentAtomType->isDipole ){ |
483 |
if( the_atoms[i]->isDirectional() ){ |
484 |
|
485 |
dAtom = (DirectionalAtom *) the_atoms[i]; |
486 |
dAtom->setMu( currentAtomType->dipole ); |
487 |
dAtom->setHasDipole( 1 ); |
488 |
dAtom->setJx( 0.0 ); |
489 |
dAtom->setJy( 0.0 ); |
490 |
dAtom->setJz( 0.0 ); |
491 |
|
492 |
if(!strcmp("SSD",the_atoms[i]->getType())){ |
493 |
dAtom->setI( waterI ); |
494 |
dAtom->setSSD( 1 ); |
495 |
} |
496 |
else{ |
497 |
sprintf(painCave.errMsg, |
498 |
"AtmType error, %s does not have a moment of inertia set.\n", |
499 |
the_atoms[i]->getType() ); |
500 |
painCave.isFatal = 1; |
501 |
simError(); |
502 |
} |
503 |
entry_plug->n_dipoles++; |
504 |
} |
505 |
else{ |
506 |
|
507 |
sprintf( painCave.errMsg, |
508 |
"SSD_FF error: Atom \"%s\" is a dipole, yet no standard" |
509 |
" orientation was specifed in the BASS file.\n", |
510 |
currentAtomType->name ); |
511 |
painCave.isFatal = 1; |
512 |
simError(); |
513 |
} |
514 |
} |
515 |
else{ |
516 |
if( the_atoms[i]->isDirectional() ){ |
517 |
sprintf( painCave.errMsg, |
518 |
"SSD_FF error: Atom \"%s\" was given a standard" |
519 |
"orientation in the BASS file, yet it is not a dipole.\n", |
520 |
currentAtomType->name); |
521 |
painCave.isFatal = 1; |
522 |
simError(); |
523 |
} |
524 |
} |
525 |
|
526 |
|
527 |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
528 |
} |
529 |
|
530 |
|
531 |
#ifdef IS_MPI |
532 |
double tempBig = bigSigma; |
533 |
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
534 |
#endif //is_mpi |
535 |
|
536 |
//calc rCut and rList |
537 |
|
538 |
entry_plug->rCut = 2.5 * bigSigma; |
539 |
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) entry_plug->rCut = entry_plug->box_x / 2.0; |
540 |
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) entry_plug->rCut = entry_plug->box_y / 2.0; |
541 |
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) entry_plug->rCut = entry_plug->box_z / 2.0; |
542 |
|
543 |
entry_plug->rList = entry_plug->rCut + 1.0; |
544 |
|
545 |
// clean up the memory |
546 |
|
547 |
delete headAtomType; |
548 |
|
549 |
#ifdef IS_MPI |
550 |
sprintf( checkPointMsg, "SSD_FF atoms initialized succesfully" ); |
551 |
MPIcheckPoint(); |
552 |
#endif // is_mpi |
553 |
|
554 |
initFortran(); |
555 |
entry_plug->refreshSim(); |
556 |
|
557 |
} |
558 |
|
559 |
void SSD_FF::initializeBonds( bond_pair* the_bonds ){ |
560 |
|
561 |
if( entry_plug->n_bonds ){ |
562 |
sprintf( painCave.errMsg, |
563 |
"SSD_FF does not support bonds.\n" ); |
564 |
painCave.isFatal = 1; |
565 |
simError(); |
566 |
} |
567 |
#ifdef IS_MPI |
568 |
MPIcheckPoint(); |
569 |
#endif // is_mpi |
570 |
|
571 |
} |
572 |
|
573 |
void SSD_FF::initializeBends( bend_set* the_bends ){ |
574 |
|
575 |
if( entry_plug->n_bends ){ |
576 |
sprintf( painCave.errMsg, |
577 |
"SSD_FF does not support bends.\n" ); |
578 |
painCave.isFatal = 1; |
579 |
simError(); |
580 |
} |
581 |
#ifdef IS_MPI |
582 |
MPIcheckPoint(); |
583 |
#endif // is_mpi |
584 |
|
585 |
} |
586 |
|
587 |
void SSD_FF::initializeTorsions( torsion_set* the_torsions ){ |
588 |
|
589 |
if( entry_plug->n_torsions ){ |
590 |
sprintf( painCave.errMsg, |
591 |
"SSD_FF does not support torsions.\n" ); |
592 |
painCave.isFatal = 1; |
593 |
simError(); |
594 |
} |
595 |
#ifdef IS_MPI |
596 |
MPIcheckPoint(); |
597 |
#endif // is_mpi |
598 |
|
599 |
} |
600 |
|
601 |
|
602 |
void SSD_FF::fastForward( char* stopText, char* searchOwner ){ |
603 |
|
604 |
int foundText = 0; |
605 |
char* the_token; |
606 |
|
607 |
rewind( frcFile ); |
608 |
lineNum = 0; |
609 |
|
610 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
611 |
lineNum++; |
612 |
if( eof_test == NULL ){ |
613 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
614 |
" file is empty.\n", |
615 |
searchOwner ); |
616 |
painCave.isFatal = 1; |
617 |
simError(); |
618 |
} |
619 |
|
620 |
|
621 |
while( !foundText ){ |
622 |
while( eof_test != NULL && readLine[0] != '#' ){ |
623 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
624 |
lineNum++; |
625 |
} |
626 |
if( eof_test == NULL ){ |
627 |
sprintf( painCave.errMsg, |
628 |
"Error fast forwarding force file for %s at " |
629 |
"line %d: file ended unexpectedly.\n", |
630 |
searchOwner, |
631 |
lineNum ); |
632 |
painCave.isFatal = 1; |
633 |
simError(); |
634 |
} |
635 |
|
636 |
the_token = strtok( readLine, " ,;\t#\n" ); |
637 |
foundText = !strcmp( stopText, the_token ); |
638 |
|
639 |
if( !foundText ){ |
640 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
641 |
lineNum++; |
642 |
|
643 |
if( eof_test == NULL ){ |
644 |
sprintf( painCave.errMsg, |
645 |
"Error fast forwarding force file for %s at " |
646 |
"line %d: file ended unexpectedly.\n", |
647 |
searchOwner, |
648 |
lineNum ); |
649 |
painCave.isFatal = 1; |
650 |
simError(); |
651 |
} |
652 |
} |
653 |
} |
654 |
} |
655 |
|
656 |
|
657 |
|
658 |
int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info ){ |
659 |
|
660 |
char* the_token; |
661 |
|
662 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
663 |
if( the_token != NULL ){ |
664 |
|
665 |
strcpy( info.name, the_token ); |
666 |
|
667 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
668 |
sprintf( painCave.errMsg, |
669 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
670 |
painCave.isFatal = 1; |
671 |
simError(); |
672 |
} |
673 |
|
674 |
info.isDipole = atoi( the_token ); |
675 |
|
676 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
677 |
sprintf( painCave.errMsg, |
678 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
679 |
painCave.isFatal = 1; |
680 |
simError(); |
681 |
} |
682 |
|
683 |
info.mass = atof( the_token ); |
684 |
|
685 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
686 |
sprintf( painCave.errMsg, |
687 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
688 |
painCave.isFatal = 1; |
689 |
simError(); |
690 |
} |
691 |
|
692 |
info.epslon = atof( the_token ); |
693 |
|
694 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
695 |
sprintf( painCave.errMsg, |
696 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
697 |
painCave.isFatal = 1; |
698 |
simError(); |
699 |
} |
700 |
|
701 |
info.sigma = atof( the_token ); |
702 |
|
703 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
704 |
sprintf( painCave.errMsg, |
705 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
706 |
painCave.isFatal = 1; |
707 |
simError(); |
708 |
} |
709 |
|
710 |
info.dipole = atof( the_token ); |
711 |
|
712 |
return 1; |
713 |
} |
714 |
else return 0; |
715 |
} |
716 |
|
717 |
|
718 |
void SSD_FF::doForces( int calcPot ){ |
719 |
|
720 |
int i; |
721 |
double* frc; |
722 |
double* pos; |
723 |
short int passedCalcPot = (short int)calcPot; |
724 |
|
725 |
// forces are zeroed here, before any are acumulated. |
726 |
// NOTE: do not rezero the forces in Fortran. |
727 |
|
728 |
for(i=0; i<entry_plug->n_atoms; i++){ |
729 |
entry_plug->atoms[i]->zeroForces(); |
730 |
} |
731 |
|
732 |
frc = Atom::getFrcArray(); |
733 |
pos = Atom::getPosArray(); |
734 |
|
735 |
// entry_plug->lrPot = -1; |
736 |
doSSDfortran( pos, frc, &(entry_plug->lrPot), &passedCalcPot ); |
737 |
|
738 |
|
739 |
// fprintf( stderr, |
740 |
// "lrPot = %lf\n", entry_plug->lrPot ); |
741 |
|
742 |
} |
743 |
|
744 |
void SSD_FF::initFortran( void ){ |
745 |
|
746 |
int nLocal = entry_plug->n_atoms; |
747 |
int *ident; |
748 |
int isError; |
749 |
int i; |
750 |
|
751 |
ident = new int[nLocal]; |
752 |
|
753 |
for(i=0; i<nLocal; i++){ |
754 |
ident[i] = entry_plug->atoms[i]->getIdent(); |
755 |
} |
756 |
|
757 |
isError = 0; |
758 |
initSSDfortran( &nLocal, ident, &isError ); |
759 |
|
760 |
if(isError){ |
761 |
sprintf( painCave.errMsg, |
762 |
"SSD_FF error: There was an error initializing the component list in fortran.\n" ); |
763 |
painCave.isFatal = 1; |
764 |
simError(); |
765 |
} |
766 |
|
767 |
|
768 |
#ifdef IS_MPI |
769 |
sprintf( checkPointMsg, "SSD_FF successfully initialized the fortran component list.\n" ); |
770 |
MPIcheckPoint(); |
771 |
#endif // is_mpi |
772 |
|
773 |
delete[] ident; |
774 |
|
775 |
} |