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