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 |
#include <fortranWrappers.hpp> |
18 |
|
19 |
#ifdef IS_MPI |
20 |
#include "mpiForceField.h" |
21 |
#endif // is_mpi |
22 |
|
23 |
|
24 |
|
25 |
namespace LJ_NS{ |
26 |
|
27 |
// Declare the structures that will be passed by the parser and MPI |
28 |
|
29 |
typedef struct{ |
30 |
char name[15]; |
31 |
double mass; |
32 |
double epslon; |
33 |
double sigma; |
34 |
int ident; |
35 |
int last; // 0 -> default |
36 |
// 1 -> in MPI: tells nodes to stop listening |
37 |
} atomStruct; |
38 |
|
39 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
40 |
|
41 |
#ifdef IS_MPI |
42 |
|
43 |
MPI_Datatype mpiAtomStructType; |
44 |
|
45 |
#endif |
46 |
} |
47 |
|
48 |
using namespace LJ_NS; |
49 |
|
50 |
//**************************************************************** |
51 |
// begins the actual forcefield stuff. |
52 |
//**************************************************************** |
53 |
|
54 |
|
55 |
LJ_FF::LJ_FF(){ |
56 |
|
57 |
char fileName[200]; |
58 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
59 |
char* ffPath; |
60 |
char temp[200]; |
61 |
char errMsg[1000]; |
62 |
|
63 |
// do the funtion wrapping |
64 |
wrapMeFF( this ); |
65 |
|
66 |
#ifdef IS_MPI |
67 |
int i; |
68 |
|
69 |
// ********************************************************************** |
70 |
// Init the atomStruct mpi type |
71 |
|
72 |
atomStruct atomProto; // mpiPrototype |
73 |
int atomBC[3] = {15,3,2}; // block counts |
74 |
MPI_Aint atomDspls[3]; // displacements |
75 |
MPI_Datatype atomMbrTypes[3]; // member mpi types |
76 |
|
77 |
MPI_Address(&atomProto.name, &atomDspls[0]); |
78 |
MPI_Address(&atomProto.mass, &atomDspls[1]); |
79 |
MPI_Address(&atomProto.ident, &atomDspls[2]); |
80 |
|
81 |
atomMbrTypes[0] = MPI_CHAR; |
82 |
atomMbrTypes[1] = MPI_DOUBLE; |
83 |
atomMbrTypes[2] = MPI_INT; |
84 |
|
85 |
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
86 |
|
87 |
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
88 |
MPI_Type_commit(&mpiAtomStructType); |
89 |
|
90 |
// *********************************************************************** |
91 |
|
92 |
if( worldRank == 0 ){ |
93 |
#endif |
94 |
|
95 |
// generate the force file name |
96 |
|
97 |
strcpy( fileName, "LJ_FF.frc" ); |
98 |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
99 |
|
100 |
// attempt to open the file in the current directory first. |
101 |
|
102 |
frcFile = fopen( fileName, "r" ); |
103 |
|
104 |
if( frcFile == NULL ){ |
105 |
|
106 |
// next see if the force path enviorment variable is set |
107 |
|
108 |
ffPath = getenv( ffPath_env ); |
109 |
if( ffPath == NULL ) { |
110 |
STR_DEFINE(ffPath, FRC_PATH ); |
111 |
} |
112 |
|
113 |
|
114 |
strcpy( temp, ffPath ); |
115 |
strcat( temp, "/" ); |
116 |
strcat( temp, fileName ); |
117 |
strcpy( fileName, temp ); |
118 |
|
119 |
frcFile = fopen( fileName, "r" ); |
120 |
|
121 |
if( frcFile == NULL ){ |
122 |
|
123 |
sprintf( painCave.errMsg, |
124 |
"Error opening the force field parameter file: %s\n" |
125 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
126 |
"vairable?\n", |
127 |
fileName ); |
128 |
painCave.isFatal = 1; |
129 |
simError(); |
130 |
} |
131 |
} |
132 |
|
133 |
#ifdef IS_MPI |
134 |
} |
135 |
|
136 |
sprintf( checkPointMsg, "LJ_FF file opened sucessfully." ); |
137 |
MPIcheckPoint(); |
138 |
|
139 |
#endif // is_mpi |
140 |
} |
141 |
|
142 |
|
143 |
LJ_FF::~LJ_FF(){ |
144 |
|
145 |
#ifdef IS_MPI |
146 |
if( worldRank == 0 ){ |
147 |
#endif // is_mpi |
148 |
|
149 |
fclose( frcFile ); |
150 |
|
151 |
#ifdef IS_MPI |
152 |
} |
153 |
#endif // is_mpi |
154 |
} |
155 |
|
156 |
|
157 |
|
158 |
void LJ_FF::initializeAtoms( void ){ |
159 |
|
160 |
class LinkedType { |
161 |
public: |
162 |
LinkedType(){ |
163 |
next = NULL; |
164 |
name[0] = '\0'; |
165 |
} |
166 |
~LinkedType(){ if( next != NULL ) delete next; } |
167 |
|
168 |
LinkedType* find(char* key){ |
169 |
if( !strcmp(name, key) ) return this; |
170 |
if( next != NULL ) return next->find(key); |
171 |
return NULL; |
172 |
} |
173 |
|
174 |
|
175 |
void add( atomStruct &info ){ |
176 |
|
177 |
// check for duplicates |
178 |
|
179 |
if( !strcmp( info.name, name ) ){ |
180 |
sprintf( painCave.errMsg, |
181 |
"Duplicate LJ atom type \"%s\" found in " |
182 |
"the LJ_FF param file./n", |
183 |
name ); |
184 |
painCave.isFatal = 1; |
185 |
simError(); |
186 |
} |
187 |
|
188 |
if( next != NULL ) next->add(info); |
189 |
else{ |
190 |
next = new LinkedType(); |
191 |
strcpy(next->name, info.name); |
192 |
next->mass = info.mass; |
193 |
next->epslon = info.epslon; |
194 |
next->sigma = info.sigma; |
195 |
next->ident = info.ident; |
196 |
} |
197 |
} |
198 |
|
199 |
|
200 |
#ifdef IS_MPI |
201 |
|
202 |
void duplicate( atomStruct &info ){ |
203 |
strcpy(info.name, name); |
204 |
info.mass = mass; |
205 |
info.epslon = epslon; |
206 |
info.sigma = sigma; |
207 |
info.ident = ident; |
208 |
info.last = 0; |
209 |
} |
210 |
|
211 |
|
212 |
#endif |
213 |
|
214 |
char name[15]; |
215 |
double mass; |
216 |
double epslon; |
217 |
double sigma; |
218 |
int ident; |
219 |
LinkedType* next; |
220 |
}; |
221 |
|
222 |
LinkedType* headAtomType; |
223 |
LinkedType* currentAtomType; |
224 |
atomStruct info; |
225 |
info.last = 1; // initialize last to have the last set. |
226 |
// if things go well, last will be set to 0 |
227 |
|
228 |
int i; |
229 |
int identNum; |
230 |
|
231 |
Atom** the_atoms; |
232 |
int nAtoms; |
233 |
the_atoms = entry_plug->atoms; |
234 |
nAtoms = entry_plug->n_atoms; |
235 |
|
236 |
|
237 |
#ifdef IS_MPI |
238 |
if( worldRank == 0 ){ |
239 |
#endif |
240 |
|
241 |
// read in the atom types. |
242 |
|
243 |
headAtomType = new LinkedType; |
244 |
|
245 |
fastForward( "AtomTypes", "initializeAtoms" ); |
246 |
|
247 |
// we are now at the AtomTypes section. |
248 |
|
249 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
250 |
lineNum++; |
251 |
|
252 |
|
253 |
// read a line, and start parseing out the atom types |
254 |
|
255 |
if( eof_test == NULL ){ |
256 |
sprintf( painCave.errMsg, |
257 |
"Error in reading Atoms from force file at line %d.\n", |
258 |
lineNum ); |
259 |
painCave.isFatal = 1; |
260 |
simError(); |
261 |
} |
262 |
|
263 |
identNum = 1; |
264 |
// stop reading at end of file, or at next section |
265 |
while( readLine[0] != '#' && eof_test != NULL ){ |
266 |
|
267 |
// toss comment lines |
268 |
if( readLine[0] != '!' ){ |
269 |
|
270 |
// the parser returns 0 if the line was blank |
271 |
if( parseAtom( readLine, lineNum, info ) ){ |
272 |
info.ident = identNum; |
273 |
headAtomType->add( info );; |
274 |
identNum++; |
275 |
} |
276 |
} |
277 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
278 |
lineNum++; |
279 |
} |
280 |
|
281 |
#ifdef IS_MPI |
282 |
|
283 |
// send out the linked list to all the other processes |
284 |
|
285 |
sprintf( checkPointMsg, |
286 |
"LJ_FF atom structures read successfully." ); |
287 |
MPIcheckPoint(); |
288 |
|
289 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
290 |
while( currentAtomType != NULL ){ |
291 |
currentAtomType->duplicate( info ); |
292 |
|
293 |
|
294 |
|
295 |
sendFrcStruct( &info, mpiAtomStructType ); |
296 |
|
297 |
sprintf( checkPointMsg, |
298 |
"successfully sent lJ force type: \"%s\"\n", |
299 |
info.name ); |
300 |
MPIcheckPoint(); |
301 |
|
302 |
currentAtomType = currentAtomType->next; |
303 |
} |
304 |
info.last = 1; |
305 |
sendFrcStruct( &info, mpiAtomStructType ); |
306 |
|
307 |
} |
308 |
|
309 |
else{ |
310 |
|
311 |
// listen for node 0 to send out the force params |
312 |
|
313 |
MPIcheckPoint(); |
314 |
|
315 |
headAtomType = new LinkedType; |
316 |
recieveFrcStruct( &info, mpiAtomStructType ); |
317 |
|
318 |
while( !info.last ){ |
319 |
|
320 |
|
321 |
|
322 |
headAtomType->add( info ); |
323 |
|
324 |
MPIcheckPoint(); |
325 |
|
326 |
recieveFrcStruct( &info, mpiAtomStructType ); |
327 |
} |
328 |
} |
329 |
#endif // is_mpi |
330 |
|
331 |
// call new A_types in fortran |
332 |
|
333 |
int isError; |
334 |
|
335 |
// dummy variables |
336 |
int isLJ = 1; |
337 |
int isDipole = 0; |
338 |
int isSSD = 0; |
339 |
int isGB = 0; |
340 |
double w0 = 0.0; |
341 |
double v0 = 0.0; |
342 |
double dipole = 0.0; |
343 |
|
344 |
|
345 |
currentAtomType = headAtomType; |
346 |
while( currentAtomType != NULL ){ |
347 |
|
348 |
if( currentAtomType->name[0] != '\0' ){ |
349 |
isError = 0; |
350 |
makeAtype( &(currentAtomType->ident), |
351 |
&(currentAtomType->mass), |
352 |
&(currentAtomType->epslon), |
353 |
&(currentAtomType->sigma), |
354 |
&isLJ, &isSSD, &isDipole, &isGB, &w0, &v0, &dipole, |
355 |
&isError ); |
356 |
if( isError ){ |
357 |
sprintf( painCave.errMsg, |
358 |
"Error initializing the \"%s\" atom type in fortran\n", |
359 |
currentAtomType->name ); |
360 |
painCave.isFatal = 1; |
361 |
simError(); |
362 |
} |
363 |
} |
364 |
currentAtomType = currentAtomType->next; |
365 |
} |
366 |
|
367 |
#ifdef IS_MPI |
368 |
sprintf( checkPointMsg, |
369 |
"LJ_FF atom structures successfully sent to fortran\n" ); |
370 |
MPIcheckPoint(); |
371 |
#endif // is_mpi |
372 |
|
373 |
|
374 |
|
375 |
// initialize the atoms |
376 |
|
377 |
double bigSigma = 0.0; |
378 |
Atom* thisAtom; |
379 |
|
380 |
for( i=0; i<nAtoms; i++ ){ |
381 |
|
382 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
383 |
if( currentAtomType == NULL ){ |
384 |
sprintf( painCave.errMsg, |
385 |
"AtomType error, %s not found in force file.\n", |
386 |
the_atoms[i]->getType() ); |
387 |
painCave.isFatal = 1; |
388 |
simError(); |
389 |
} |
390 |
|
391 |
the_atoms[i]->setMass( currentAtomType->mass ); |
392 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
393 |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
394 |
the_atoms[i]->setIdent( currentAtomType->ident ); |
395 |
the_atoms[i]->setLJ(); |
396 |
|
397 |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
398 |
} |
399 |
|
400 |
|
401 |
#ifdef IS_MPI |
402 |
double tempBig = bigSigma; |
403 |
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
404 |
#endif //is_mpi |
405 |
|
406 |
//calc rCut and rList |
407 |
|
408 |
entry_plug->rCut = 2.5 * bigSigma; |
409 |
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) entry_plug->rCut = entry_plug->box_x / 2.0; |
410 |
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) entry_plug->rCut = entry_plug->box_y / 2.0; |
411 |
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) entry_plug->rCut = entry_plug->box_z / 2.0; |
412 |
|
413 |
entry_plug->rList = entry_plug->rCut + 1.0; |
414 |
|
415 |
// clean up the memory |
416 |
|
417 |
delete headAtomType; |
418 |
|
419 |
#ifdef IS_MPI |
420 |
sprintf( checkPointMsg, "LJ_FF atoms initialized succesfully" ); |
421 |
MPIcheckPoint(); |
422 |
#endif // is_mpi |
423 |
|
424 |
this->initFortran(); |
425 |
entry_plug->refreshSim(); |
426 |
|
427 |
} |
428 |
|
429 |
void LJ_FF::initializeBonds( bond_pair* the_bonds ){ |
430 |
|
431 |
if( entry_plug->n_bonds ){ |
432 |
sprintf( painCave.errMsg, |
433 |
"LJ_FF does not support bonds.\n" ); |
434 |
painCave.isFatal = 1; |
435 |
simError(); |
436 |
} |
437 |
#ifdef IS_MPI |
438 |
MPIcheckPoint(); |
439 |
#endif // is_mpi |
440 |
|
441 |
} |
442 |
|
443 |
void LJ_FF::initializeBends( bend_set* the_bends ){ |
444 |
|
445 |
if( entry_plug->n_bends ){ |
446 |
sprintf( painCave.errMsg, |
447 |
"LJ_FF does not support bends.\n" ); |
448 |
painCave.isFatal = 1; |
449 |
simError(); |
450 |
} |
451 |
#ifdef IS_MPI |
452 |
MPIcheckPoint(); |
453 |
#endif // is_mpi |
454 |
|
455 |
} |
456 |
|
457 |
void LJ_FF::initializeTorsions( torsion_set* the_torsions ){ |
458 |
|
459 |
if( entry_plug->n_torsions ){ |
460 |
sprintf( painCave.errMsg, |
461 |
"LJ_FF does not support torsions.\n" ); |
462 |
painCave.isFatal = 1; |
463 |
simError(); |
464 |
} |
465 |
#ifdef IS_MPI |
466 |
MPIcheckPoint(); |
467 |
#endif // is_mpi |
468 |
|
469 |
} |
470 |
|
471 |
void LJ_FF::fastForward( char* stopText, char* searchOwner ){ |
472 |
|
473 |
int foundText = 0; |
474 |
char* the_token; |
475 |
|
476 |
rewind( frcFile ); |
477 |
lineNum = 0; |
478 |
|
479 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
480 |
lineNum++; |
481 |
if( eof_test == NULL ){ |
482 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
483 |
" file is empty.\n", |
484 |
searchOwner ); |
485 |
painCave.isFatal = 1; |
486 |
simError(); |
487 |
} |
488 |
|
489 |
|
490 |
while( !foundText ){ |
491 |
while( eof_test != NULL && readLine[0] != '#' ){ |
492 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
493 |
lineNum++; |
494 |
} |
495 |
if( eof_test == NULL ){ |
496 |
sprintf( painCave.errMsg, |
497 |
"Error fast forwarding force file for %s at " |
498 |
"line %d: file ended unexpectedly.\n", |
499 |
searchOwner, |
500 |
lineNum ); |
501 |
painCave.isFatal = 1; |
502 |
simError(); |
503 |
} |
504 |
|
505 |
the_token = strtok( readLine, " ,;\t#\n" ); |
506 |
foundText = !strcmp( stopText, the_token ); |
507 |
|
508 |
if( !foundText ){ |
509 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
510 |
lineNum++; |
511 |
|
512 |
if( eof_test == NULL ){ |
513 |
sprintf( painCave.errMsg, |
514 |
"Error fast forwarding force file for %s at " |
515 |
"line %d: file ended unexpectedly.\n", |
516 |
searchOwner, |
517 |
lineNum ); |
518 |
painCave.isFatal = 1; |
519 |
simError(); |
520 |
} |
521 |
} |
522 |
} |
523 |
} |
524 |
|
525 |
|
526 |
|
527 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
528 |
|
529 |
char* the_token; |
530 |
|
531 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
532 |
if( the_token != NULL ){ |
533 |
|
534 |
strcpy( info.name, the_token ); |
535 |
|
536 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
537 |
sprintf( painCave.errMsg, |
538 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
539 |
painCave.isFatal = 1; |
540 |
simError(); |
541 |
} |
542 |
|
543 |
info.mass = atof( the_token ); |
544 |
|
545 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
546 |
sprintf( painCave.errMsg, |
547 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
548 |
painCave.isFatal = 1; |
549 |
simError(); |
550 |
} |
551 |
|
552 |
info.epslon = atof( the_token ); |
553 |
|
554 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
555 |
sprintf( painCave.errMsg, |
556 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
557 |
painCave.isFatal = 1; |
558 |
simError(); |
559 |
} |
560 |
|
561 |
info.sigma = atof( the_token ); |
562 |
|
563 |
return 1; |
564 |
} |
565 |
else return 0; |
566 |
} |