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 "UseTheForce/ForceFields.hpp" |
13 |
#include "primitives/SRI.hpp" |
14 |
#include "utils/simError.h" |
15 |
#include "types/AtomType.hpp" |
16 |
#include "UseTheForce/DarkSide/eam_interface.h" |
17 |
|
18 |
//#include "UseTheForce/fortranWrappers.hpp" |
19 |
|
20 |
#ifdef IS_MPI |
21 |
#include "UseTheForce/mpiForceField.h" |
22 |
#endif // is_mpi |
23 |
|
24 |
|
25 |
|
26 |
namespace EAM_NS{ |
27 |
|
28 |
// Declare the structures that will be passed by the parser and MPI |
29 |
|
30 |
typedef struct{ |
31 |
char name[15]; |
32 |
double mass; |
33 |
double lattice_constant; |
34 |
double eam_drho; // The distance between each of the points indexed by rho. |
35 |
double eam_rcut; // The cutoff radius for eam. |
36 |
double eam_dr; // The distance between each of the rho points. |
37 |
int eam_nrho; // Number of points indexed by rho |
38 |
int eam_nr; // The number of points based on r (Both Phi(r) and Rho(r)). |
39 |
int eam_ident; // Atomic number |
40 |
int ident; |
41 |
int last; // 0 -> default |
42 |
// 1 -> in MPI: tells nodes to stop listening |
43 |
} atomStruct; |
44 |
|
45 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info, string eamPotFile ); |
46 |
int parseEAM( atomStruct &info, string eamPotFile, double **eam_rvals, |
47 |
double **eam_rhovals, double **eam_Frhovals); |
48 |
#ifdef IS_MPI |
49 |
|
50 |
MPI_Datatype mpiAtomStructType; |
51 |
|
52 |
#endif |
53 |
|
54 |
class LinkedAtomType { |
55 |
public: |
56 |
LinkedAtomType(){ |
57 |
next = NULL; |
58 |
name[0] = '\0'; |
59 |
eam_rvals = NULL; |
60 |
eam_rhovals = NULL; |
61 |
eam_Frhovals = NULL; |
62 |
} |
63 |
|
64 |
~LinkedAtomType(){ |
65 |
if( next != NULL ) delete next; |
66 |
if( eam_rvals != NULL ) delete[] eam_rvals; |
67 |
if( eam_rhovals != NULL ) delete[] eam_rhovals; |
68 |
if( eam_Frhovals != NULL ) delete[] eam_Frhovals; |
69 |
} |
70 |
|
71 |
LinkedAtomType* find(char* key){ |
72 |
if( !strcmp(name, key) ) return this; |
73 |
if( next != NULL ) return next->find(key); |
74 |
return NULL; |
75 |
} |
76 |
|
77 |
|
78 |
void add( atomStruct &info, double *the_eam_rvals, |
79 |
double *the_eam_rhovals,double *the_eam_Frhovals ){ |
80 |
|
81 |
// check for duplicates |
82 |
|
83 |
if( !strcmp( info.name, name ) ){ |
84 |
sprintf( painCave.errMsg, |
85 |
"Duplicate EAM atom type \"%s\" found in " |
86 |
"the EAM_FF param file./n", |
87 |
name ); |
88 |
painCave.isFatal = 1; |
89 |
simError(); |
90 |
} |
91 |
|
92 |
if( next != NULL ) next->add(info, the_eam_rvals, the_eam_rhovals, the_eam_Frhovals); |
93 |
else{ |
94 |
next = new LinkedAtomType(); |
95 |
strcpy(next->name, info.name); |
96 |
next->mass = info.mass; |
97 |
next->lattice_constant = info.lattice_constant; |
98 |
next->eam_nrho = info.eam_nrho; |
99 |
next->eam_drho = info.eam_drho; |
100 |
next->eam_nr = info.eam_nr; |
101 |
next->eam_dr = info.eam_dr; |
102 |
next->eam_rcut = info.eam_rcut; |
103 |
next->eam_ident = info.eam_ident; |
104 |
next->ident = info.ident; |
105 |
|
106 |
next->eam_rvals = the_eam_rvals; |
107 |
next->eam_rhovals = the_eam_rhovals; |
108 |
next->eam_Frhovals = the_eam_Frhovals; |
109 |
} |
110 |
} |
111 |
|
112 |
|
113 |
#ifdef IS_MPI |
114 |
|
115 |
void duplicate( atomStruct &info ){ |
116 |
strcpy(info.name, name); |
117 |
info.mass = mass; |
118 |
info.lattice_constant = lattice_constant; |
119 |
info.eam_nrho = eam_nrho; |
120 |
info.eam_drho = eam_drho; |
121 |
info.eam_nr = eam_nr; |
122 |
info.eam_dr = eam_dr; |
123 |
info.eam_rcut = eam_rcut; |
124 |
info.eam_ident = eam_ident; |
125 |
info.ident = ident; |
126 |
info.last = 0; |
127 |
} |
128 |
|
129 |
|
130 |
#endif |
131 |
|
132 |
char name[15]; |
133 |
double mass; |
134 |
double lattice_constant; |
135 |
int eam_nrho; // Number of points indexed by rho |
136 |
double eam_drho; // The distance between each of the points indexed by rho. |
137 |
int eam_nr; // The number of points based on r (Both Phi(r) and Rho(r)). |
138 |
double eam_dr; // The distance between each of the rho points. |
139 |
double eam_rcut; // The cutoff radius for eam. |
140 |
|
141 |
double *eam_rvals; // Z of r values |
142 |
double *eam_rhovals; // rho of r values |
143 |
double *eam_Frhovals; // F of rho values |
144 |
int eam_ident; // eam identity (atomic number) |
145 |
int ident; |
146 |
LinkedAtomType* next; |
147 |
}; |
148 |
|
149 |
LinkedAtomType* headAtomType; |
150 |
LinkedAtomType* currentAtomType; |
151 |
|
152 |
} |
153 |
|
154 |
using namespace EAM_NS; |
155 |
|
156 |
//**************************************************************** |
157 |
// begins the actual forcefield stuff. |
158 |
//**************************************************************** |
159 |
|
160 |
EAM_FF::EAM_FF() { |
161 |
EAM_FF(""); |
162 |
} |
163 |
|
164 |
EAM_FF::EAM_FF(string the_variant){ |
165 |
|
166 |
string fileName; |
167 |
string tempString; |
168 |
|
169 |
headAtomType = NULL; |
170 |
currentAtomType = NULL; |
171 |
|
172 |
// Set eamRcut to 0.0 |
173 |
eamRcut = 0.0; |
174 |
|
175 |
#ifdef IS_MPI |
176 |
int i; |
177 |
|
178 |
// ********************************************************************** |
179 |
// Init the atomStruct mpi type |
180 |
|
181 |
atomStruct atomProto; // mpiPrototype |
182 |
int atomBC[3] = {15,5,5}; // block counts |
183 |
MPI_Aint atomDspls[3]; // displacements |
184 |
MPI_Datatype atomMbrTypes[3]; // member mpi types |
185 |
|
186 |
MPI_Address(&atomProto.name, &atomDspls[0]); |
187 |
MPI_Address(&atomProto.mass, &atomDspls[1]); |
188 |
MPI_Address(&atomProto.eam_nrho, &atomDspls[2]); |
189 |
|
190 |
atomMbrTypes[0] = MPI_CHAR; |
191 |
atomMbrTypes[1] = MPI_DOUBLE; |
192 |
atomMbrTypes[2] = MPI_INT; |
193 |
|
194 |
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
195 |
|
196 |
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
197 |
MPI_Type_commit(&mpiAtomStructType); |
198 |
|
199 |
// *********************************************************************** |
200 |
|
201 |
if( worldRank == 0 ){ |
202 |
#endif |
203 |
|
204 |
// generate the force file name |
205 |
|
206 |
fileName = "EAM"; |
207 |
|
208 |
if (!the_variant.empty()) { |
209 |
has_variant = 1; |
210 |
fileName += "." + the_variant; |
211 |
|
212 |
sprintf( painCave.errMsg, |
213 |
"Using %s variant of EAM force field.\n", |
214 |
the_variant.c_str() ); |
215 |
painCave.severity = OOPSE_INFO; |
216 |
painCave.isFatal = 0; |
217 |
simError(); |
218 |
} |
219 |
|
220 |
fileName += ".frc"; |
221 |
|
222 |
//fprintf( stderr,"Trying to open %s\n", fileName ); |
223 |
|
224 |
// attempt to open the file in the current directory first. |
225 |
|
226 |
frcFile = fopen( fileName.c_str(), "r" ); |
227 |
|
228 |
if( frcFile == NULL ){ |
229 |
|
230 |
// next see if the force path enviorment variable is set |
231 |
|
232 |
tempString = ffPath + "/" + fileName; |
233 |
fileName = tempString; |
234 |
|
235 |
frcFile = fopen( fileName.c_str(), "r" ); |
236 |
|
237 |
if( frcFile == NULL ){ |
238 |
|
239 |
sprintf( painCave.errMsg, |
240 |
"Error opening the force field parameter file:\n" |
241 |
"\t%s\n" |
242 |
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
243 |
"variable?\n", |
244 |
fileName.c_str() ); |
245 |
painCave.severity = OOPSE_ERROR; |
246 |
painCave.isFatal = 1; |
247 |
simError(); |
248 |
} |
249 |
} |
250 |
|
251 |
|
252 |
#ifdef IS_MPI |
253 |
} |
254 |
|
255 |
sprintf( checkPointMsg, "EAM_FF file opened sucessfully." ); |
256 |
MPIcheckPoint(); |
257 |
|
258 |
#endif // is_mpi |
259 |
} |
260 |
|
261 |
|
262 |
EAM_FF::~EAM_FF(){ |
263 |
|
264 |
if( headAtomType != NULL ) delete headAtomType; |
265 |
|
266 |
#ifdef IS_MPI |
267 |
if( worldRank == 0 ){ |
268 |
#endif // is_mpi |
269 |
|
270 |
fclose( frcFile ); |
271 |
|
272 |
#ifdef IS_MPI |
273 |
} |
274 |
#endif // is_mpi |
275 |
} |
276 |
|
277 |
|
278 |
void EAM_FF::calcRcut( void ){ |
279 |
|
280 |
#ifdef IS_MPI |
281 |
double tempEamRcut = eamRcut; |
282 |
MPI_Allreduce( &tempEamRcut, &eamRcut, 1, MPI_DOUBLE, MPI_MAX, |
283 |
MPI_COMM_WORLD); |
284 |
#endif //is_mpi |
285 |
entry_plug->setDefaultRcut(eamRcut); |
286 |
} |
287 |
|
288 |
|
289 |
void EAM_FF::initForceField( ){ |
290 |
initFortran(0); |
291 |
} |
292 |
|
293 |
void EAM_FF::cleanMe( void ){ |
294 |
|
295 |
#ifdef IS_MPI |
296 |
|
297 |
// keep the linked list in the mpi version |
298 |
|
299 |
#else // is_mpi |
300 |
|
301 |
// delete the linked list in the single processor version |
302 |
|
303 |
if( headAtomType != NULL ) delete headAtomType; |
304 |
|
305 |
#endif // is_mpi |
306 |
} |
307 |
|
308 |
|
309 |
void EAM_FF::readParams( void ){ |
310 |
|
311 |
atomStruct info; |
312 |
info.last = 1; // initialize last to have the last set. |
313 |
// if things go well, last will be set to 0 |
314 |
|
315 |
int identNum; |
316 |
double *eam_rvals; // Z of r values |
317 |
double *eam_rhovals; // rho of r values |
318 |
double *eam_Frhovals; // F of rho values |
319 |
string eamPotFile; |
320 |
|
321 |
|
322 |
|
323 |
bigSigma = 0.0; |
324 |
#ifdef IS_MPI |
325 |
if( worldRank == 0 ){ |
326 |
#endif |
327 |
|
328 |
// read in the atom types. |
329 |
|
330 |
headAtomType = new LinkedAtomType; |
331 |
|
332 |
fastForward( "AtomTypes", "eam atom readParams" ); |
333 |
|
334 |
// we are now at the AtomTypes section. |
335 |
|
336 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
337 |
lineNum++; |
338 |
|
339 |
|
340 |
// read a line, and start parseing out the atom types |
341 |
|
342 |
if( eof_test == NULL ){ |
343 |
sprintf( painCave.errMsg, |
344 |
"Error in reading Atoms from force file at line %d.\n", |
345 |
lineNum ); |
346 |
painCave.isFatal = 1; |
347 |
simError(); |
348 |
} |
349 |
|
350 |
identNum = 1; |
351 |
// stop reading at end of file, or at next section |
352 |
|
353 |
while( readLine[0] != '#' && eof_test != NULL ){ |
354 |
|
355 |
// toss comment lines |
356 |
if( readLine[0] != '!' ){ |
357 |
|
358 |
// the parser returns 0 if the line was blank |
359 |
if( parseAtom( readLine, lineNum, info, eamPotFile ) ){ |
360 |
parseEAM(info,eamPotFile, &eam_rvals, |
361 |
&eam_rhovals, &eam_Frhovals); |
362 |
info.ident = identNum; |
363 |
headAtomType->add( info, eam_rvals, |
364 |
eam_rhovals,eam_Frhovals ); |
365 |
identNum++; |
366 |
} |
367 |
} |
368 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
369 |
lineNum++; |
370 |
} |
371 |
|
372 |
|
373 |
|
374 |
#ifdef IS_MPI |
375 |
|
376 |
|
377 |
// send out the linked list to all the other processes |
378 |
|
379 |
sprintf( checkPointMsg, |
380 |
"EAM_FF atom structures read successfully." ); |
381 |
MPIcheckPoint(); |
382 |
|
383 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
384 |
while( currentAtomType != NULL ){ |
385 |
currentAtomType->duplicate( info ); |
386 |
|
387 |
|
388 |
|
389 |
sendFrcStruct( &info, mpiAtomStructType ); |
390 |
|
391 |
// We have to now broadcast the Arrays |
392 |
MPI_Bcast(currentAtomType->eam_rvals, |
393 |
currentAtomType->eam_nr, |
394 |
MPI_DOUBLE,0,MPI_COMM_WORLD); |
395 |
MPI_Bcast(currentAtomType->eam_rhovals, |
396 |
currentAtomType->eam_nr, |
397 |
MPI_DOUBLE,0,MPI_COMM_WORLD); |
398 |
MPI_Bcast(currentAtomType->eam_Frhovals, |
399 |
currentAtomType->eam_nrho, |
400 |
MPI_DOUBLE,0,MPI_COMM_WORLD); |
401 |
|
402 |
sprintf( checkPointMsg, |
403 |
"successfully sent EAM force type: \"%s\"\n", |
404 |
info.name ); |
405 |
MPIcheckPoint(); |
406 |
|
407 |
currentAtomType = currentAtomType->next; |
408 |
} |
409 |
info.last = 1; |
410 |
sendFrcStruct( &info, mpiAtomStructType ); |
411 |
|
412 |
} |
413 |
|
414 |
else{ |
415 |
|
416 |
// listen for node 0 to send out the force params |
417 |
|
418 |
MPIcheckPoint(); |
419 |
|
420 |
headAtomType = new LinkedAtomType; |
421 |
receiveFrcStruct( &info, mpiAtomStructType ); |
422 |
|
423 |
while( !info.last ){ |
424 |
|
425 |
// allocate the arrays |
426 |
|
427 |
eam_rvals = new double[info.eam_nr]; |
428 |
eam_rhovals = new double[info.eam_nr]; |
429 |
eam_Frhovals = new double[info.eam_nrho]; |
430 |
|
431 |
// We have to now broadcast the Arrays |
432 |
MPI_Bcast(eam_rvals, |
433 |
info.eam_nr, |
434 |
MPI_DOUBLE,0,MPI_COMM_WORLD); |
435 |
MPI_Bcast(eam_rhovals, |
436 |
info.eam_nr, |
437 |
MPI_DOUBLE,0,MPI_COMM_WORLD); |
438 |
MPI_Bcast(eam_Frhovals, |
439 |
info.eam_nrho, |
440 |
MPI_DOUBLE,0,MPI_COMM_WORLD); |
441 |
|
442 |
|
443 |
headAtomType->add( info, eam_rvals, eam_rhovals, eam_Frhovals ); |
444 |
|
445 |
MPIcheckPoint(); |
446 |
|
447 |
receiveFrcStruct( &info, mpiAtomStructType ); |
448 |
|
449 |
|
450 |
} |
451 |
} |
452 |
#endif // is_mpi |
453 |
|
454 |
// call new A_types in fortran |
455 |
|
456 |
int isError; |
457 |
|
458 |
// dummy variables |
459 |
|
460 |
currentAtomType = headAtomType->next; |
461 |
while( currentAtomType != NULL ){ |
462 |
|
463 |
if( currentAtomType->name[0] != '\0' ){ |
464 |
|
465 |
AtomType* at = new AtomType(); |
466 |
at->setIdent(currentAtomType->ident); |
467 |
at->setName(currentAtomType->name); |
468 |
at->setEAM(); |
469 |
at->complete(); |
470 |
|
471 |
} |
472 |
|
473 |
currentAtomType = currentAtomType->next; |
474 |
} |
475 |
|
476 |
entry_plug->useLennardJones = 0; |
477 |
entry_plug->useEAM = 1; |
478 |
// Walk down again and send out EAM type |
479 |
currentAtomType = headAtomType->next; |
480 |
while( currentAtomType != NULL ){ |
481 |
|
482 |
if( currentAtomType->name[0] != '\0' ){ |
483 |
isError = 0; |
484 |
|
485 |
newEAMtype( &(currentAtomType->lattice_constant), |
486 |
&(currentAtomType->eam_nrho), |
487 |
&(currentAtomType->eam_drho), |
488 |
&(currentAtomType->eam_nr), |
489 |
&(currentAtomType->eam_dr), |
490 |
&(currentAtomType->eam_rcut), |
491 |
currentAtomType->eam_rvals, |
492 |
currentAtomType->eam_rhovals, |
493 |
currentAtomType->eam_Frhovals, |
494 |
&(currentAtomType->eam_ident), |
495 |
&isError); |
496 |
|
497 |
if( isError ){ |
498 |
sprintf( painCave.errMsg, |
499 |
"Error initializing the \"%s\" atom type in fortran EAM\n", |
500 |
currentAtomType->name ); |
501 |
painCave.isFatal = 1; |
502 |
simError(); |
503 |
} |
504 |
} |
505 |
currentAtomType = currentAtomType->next; |
506 |
} |
507 |
|
508 |
|
509 |
|
510 |
#ifdef IS_MPI |
511 |
sprintf( checkPointMsg, |
512 |
"EAM_FF atom structures successfully sent to fortran\n" ); |
513 |
MPIcheckPoint(); |
514 |
#endif // is_mpi |
515 |
|
516 |
|
517 |
|
518 |
} |
519 |
|
520 |
|
521 |
void EAM_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
522 |
|
523 |
int i; |
524 |
|
525 |
// initialize the atoms |
526 |
|
527 |
for( i=0; i<nAtoms; i++ ){ |
528 |
|
529 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
530 |
if( currentAtomType == NULL ){ |
531 |
sprintf( painCave.errMsg, |
532 |
"AtomType error, %s not found in force file.\n", |
533 |
the_atoms[i]->getType() ); |
534 |
painCave.isFatal = 1; |
535 |
simError(); |
536 |
} |
537 |
|
538 |
the_atoms[i]->setMass( currentAtomType->mass ); |
539 |
the_atoms[i]->setIdent( currentAtomType->ident ); |
540 |
|
541 |
if (eamRcut < currentAtomType->eam_rcut) eamRcut = currentAtomType->eam_rcut; |
542 |
|
543 |
} |
544 |
} |
545 |
|
546 |
void EAM_FF::initializeBonds( int nBonds, Bond** BondArray, |
547 |
bond_pair* the_bonds ){ |
548 |
|
549 |
if( nBonds ){ |
550 |
sprintf( painCave.errMsg, |
551 |
"LJ_FF does not support bonds.\n" ); |
552 |
painCave.isFatal = 1; |
553 |
simError(); |
554 |
} |
555 |
} |
556 |
|
557 |
void EAM_FF::initializeBends( int nBends, Bend** bendArray, |
558 |
bend_set* the_bends ){ |
559 |
|
560 |
if( nBends ){ |
561 |
sprintf( painCave.errMsg, |
562 |
"LJ_FF does not support bends.\n" ); |
563 |
painCave.isFatal = 1; |
564 |
simError(); |
565 |
} |
566 |
} |
567 |
|
568 |
void EAM_FF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
569 |
torsion_set* the_torsions ){ |
570 |
|
571 |
if( nTorsions ){ |
572 |
sprintf( painCave.errMsg, |
573 |
"LJ_FF does not support torsions.\n" ); |
574 |
painCave.isFatal = 1; |
575 |
simError(); |
576 |
} |
577 |
} |
578 |
|
579 |
void EAM_FF::fastForward( char* stopText, char* searchOwner ){ |
580 |
|
581 |
int foundText = 0; |
582 |
char* the_token; |
583 |
|
584 |
rewind( frcFile ); |
585 |
lineNum = 0; |
586 |
|
587 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
588 |
lineNum++; |
589 |
if( eof_test == NULL ){ |
590 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
591 |
" file is empty.\n", |
592 |
searchOwner ); |
593 |
painCave.isFatal = 1; |
594 |
simError(); |
595 |
} |
596 |
|
597 |
|
598 |
while( !foundText ){ |
599 |
while( eof_test != NULL && readLine[0] != '#' ){ |
600 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
601 |
lineNum++; |
602 |
} |
603 |
if( eof_test == NULL ){ |
604 |
sprintf( painCave.errMsg, |
605 |
"Error fast forwarding force file for %s at " |
606 |
"line %d: file ended unexpectedly.\n", |
607 |
searchOwner, |
608 |
lineNum ); |
609 |
painCave.isFatal = 1; |
610 |
simError(); |
611 |
} |
612 |
|
613 |
the_token = strtok( readLine, " ,;\t#\n" ); |
614 |
foundText = !strcmp( stopText, the_token ); |
615 |
|
616 |
if( !foundText ){ |
617 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
618 |
lineNum++; |
619 |
|
620 |
if( eof_test == NULL ){ |
621 |
sprintf( painCave.errMsg, |
622 |
"Error fast forwarding force file for %s at " |
623 |
"line %d: file ended unexpectedly.\n", |
624 |
searchOwner, |
625 |
lineNum ); |
626 |
painCave.isFatal = 1; |
627 |
simError(); |
628 |
} |
629 |
} |
630 |
} |
631 |
} |
632 |
|
633 |
|
634 |
|
635 |
int EAM_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info, string eamPotFile ){ |
636 |
|
637 |
char* the_token; |
638 |
|
639 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
640 |
if( the_token != NULL ){ |
641 |
|
642 |
strcpy( info.name, the_token ); |
643 |
|
644 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
645 |
sprintf( painCave.errMsg, |
646 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
647 |
painCave.isFatal = 1; |
648 |
simError(); |
649 |
} |
650 |
|
651 |
info.mass = atof( the_token ); |
652 |
|
653 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
654 |
sprintf( painCave.errMsg, |
655 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
656 |
painCave.isFatal = 1; |
657 |
simError(); |
658 |
} |
659 |
|
660 |
eamPotFile = the_token; |
661 |
|
662 |
return 1; |
663 |
} |
664 |
else return 0; |
665 |
} |
666 |
|
667 |
int EAM_NS::parseEAM(atomStruct &info, string eamPotFile, |
668 |
double **eam_rvals, |
669 |
double **eam_rhovals, |
670 |
double **eam_Frhovals){ |
671 |
double* myEam_rvals; |
672 |
double* myEam_rhovals; |
673 |
double* myEam_Frhovals; |
674 |
|
675 |
char* the_token; |
676 |
char* eam_eof_test; |
677 |
FILE *eamFile; |
678 |
const int BUFFERSIZE = 3000; |
679 |
|
680 |
string tempString; |
681 |
int linenumber; |
682 |
int nReadLines; |
683 |
char eam_read_buffer[BUFFERSIZE]; |
684 |
|
685 |
int i,j; |
686 |
|
687 |
linenumber = 0; |
688 |
|
689 |
// Open eam file |
690 |
eamFile = fopen( eamPotFile.c_str(), "r" ); |
691 |
|
692 |
if( eamFile == NULL ){ |
693 |
|
694 |
// next see if the force path enviorment variable is set |
695 |
|
696 |
tempString = ffPath + "/" + eamPotFile; |
697 |
eamPotFile = tempString; |
698 |
|
699 |
eamFile = fopen( eamPotFile.c_str(), "r" ); |
700 |
|
701 |
if( eamFile == NULL ){ |
702 |
|
703 |
sprintf( painCave.errMsg, |
704 |
"Error opening the EAM force parameter file: %s\n" |
705 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
706 |
"variable?\n", |
707 |
eamPotFile.c_str() ); |
708 |
painCave.isFatal = 1; |
709 |
simError(); |
710 |
} |
711 |
} |
712 |
|
713 |
// First line is a comment line, read and toss it.... |
714 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
715 |
linenumber++; |
716 |
if(eam_eof_test == NULL){ |
717 |
sprintf( painCave.errMsg, |
718 |
"error in reading commment in %s\n", eamPotFile.c_str()); |
719 |
painCave.isFatal = 1; |
720 |
simError(); |
721 |
} |
722 |
|
723 |
|
724 |
|
725 |
// The Second line contains atomic number, atomic mass and a lattice constant |
726 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
727 |
linenumber++; |
728 |
if(eam_eof_test == NULL){ |
729 |
sprintf( painCave.errMsg, |
730 |
"error in reading Identifier line in %s\n", eamPotFile.c_str()); |
731 |
painCave.isFatal = 1; |
732 |
simError(); |
733 |
} |
734 |
|
735 |
|
736 |
|
737 |
|
738 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
739 |
sprintf( painCave.errMsg, |
740 |
"Error parsing EAM ident line in %s\n", eamPotFile.c_str() ); |
741 |
painCave.isFatal = 1; |
742 |
simError(); |
743 |
} |
744 |
|
745 |
info.eam_ident = atoi( the_token ); |
746 |
|
747 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
748 |
sprintf( painCave.errMsg, |
749 |
"Error parsing EAM mass in %s\n", eamPotFile.c_str() ); |
750 |
painCave.isFatal = 1; |
751 |
simError(); |
752 |
} |
753 |
info.mass = atof( the_token); |
754 |
|
755 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
756 |
sprintf( painCave.errMsg, |
757 |
"Error parsing EAM Lattice Constant %s\n", eamPotFile.c_str() ); |
758 |
painCave.isFatal = 1; |
759 |
simError(); |
760 |
} |
761 |
info.lattice_constant = atof( the_token); |
762 |
|
763 |
// Next line is nrho, drho, nr, dr and rcut |
764 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
765 |
if(eam_eof_test == NULL){ |
766 |
sprintf( painCave.errMsg, |
767 |
"error in reading number of points line in %s\n", |
768 |
eamPotFile.c_str()); |
769 |
painCave.isFatal = 1; |
770 |
simError(); |
771 |
} |
772 |
|
773 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
774 |
sprintf( painCave.errMsg, |
775 |
"Error parseing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
776 |
painCave.isFatal = 1; |
777 |
simError(); |
778 |
} |
779 |
|
780 |
info.eam_nrho = atoi( the_token ); |
781 |
|
782 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
783 |
sprintf( painCave.errMsg, |
784 |
"Error parsing EAM drho in %s\n", eamPotFile.c_str() ); |
785 |
painCave.isFatal = 1; |
786 |
simError(); |
787 |
} |
788 |
info.eam_drho = atof( the_token); |
789 |
|
790 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
791 |
sprintf( painCave.errMsg, |
792 |
"Error parsing EAM # r in %s\n", eamPotFile.c_str() ); |
793 |
painCave.isFatal = 1; |
794 |
simError(); |
795 |
} |
796 |
info.eam_nr = atoi( the_token); |
797 |
|
798 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
799 |
sprintf( painCave.errMsg, |
800 |
"Error parsing EAM dr in %s\n", eamPotFile.c_str() ); |
801 |
painCave.isFatal = 1; |
802 |
simError(); |
803 |
} |
804 |
info.eam_dr = atof( the_token); |
805 |
|
806 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
807 |
sprintf( painCave.errMsg, |
808 |
"Error parsing EAM rcut in %s\n", eamPotFile.c_str() ); |
809 |
painCave.isFatal = 1; |
810 |
simError(); |
811 |
} |
812 |
info.eam_rcut = atof( the_token); |
813 |
|
814 |
|
815 |
|
816 |
|
817 |
|
818 |
// Ok now we have to allocate point arrays and read in number of points |
819 |
// Index the arrays for fortran, starting at 1 |
820 |
myEam_Frhovals = new double[info.eam_nrho]; |
821 |
myEam_rvals = new double[info.eam_nr]; |
822 |
myEam_rhovals = new double[info.eam_nr]; |
823 |
|
824 |
// Parse F of rho vals. |
825 |
|
826 |
// Assume for now that we have a complete number of lines |
827 |
nReadLines = int(info.eam_nrho/5); |
828 |
|
829 |
|
830 |
|
831 |
for (i=0;i<nReadLines;i++){ |
832 |
j = i*5; |
833 |
|
834 |
// Read next line |
835 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
836 |
linenumber++; |
837 |
if(eam_eof_test == NULL){ |
838 |
sprintf( painCave.errMsg, |
839 |
"error in reading EAM file %s at line %d\n", |
840 |
eamPotFile.c_str(), linenumber); |
841 |
painCave.isFatal = 1; |
842 |
simError(); |
843 |
} |
844 |
|
845 |
// Parse 5 values on each line into array |
846 |
// Value 1 |
847 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
848 |
sprintf( painCave.errMsg, |
849 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
850 |
painCave.isFatal = 1; |
851 |
simError(); |
852 |
} |
853 |
|
854 |
myEam_Frhovals[j+0] = atof( the_token ); |
855 |
|
856 |
// Value 2 |
857 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
858 |
sprintf( painCave.errMsg, |
859 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
860 |
painCave.isFatal = 1; |
861 |
simError(); |
862 |
} |
863 |
|
864 |
myEam_Frhovals[j+1] = atof( the_token ); |
865 |
|
866 |
// Value 3 |
867 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
868 |
sprintf( painCave.errMsg, |
869 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
870 |
painCave.isFatal = 1; |
871 |
simError(); |
872 |
} |
873 |
|
874 |
myEam_Frhovals[j+2] = atof( the_token ); |
875 |
|
876 |
// Value 4 |
877 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
878 |
sprintf( painCave.errMsg, |
879 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
880 |
painCave.isFatal = 1; |
881 |
simError(); |
882 |
} |
883 |
|
884 |
myEam_Frhovals[j+3] = atof( the_token ); |
885 |
|
886 |
// Value 5 |
887 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
888 |
sprintf( painCave.errMsg, |
889 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
890 |
painCave.isFatal = 1; |
891 |
simError(); |
892 |
} |
893 |
|
894 |
myEam_Frhovals[j+4] = atof( the_token ); |
895 |
|
896 |
} |
897 |
// Parse Z of r vals |
898 |
|
899 |
// Assume for now that we have a complete number of lines |
900 |
nReadLines = int(info.eam_nr/5); |
901 |
|
902 |
for (i=0;i<nReadLines;i++){ |
903 |
j = i*5; |
904 |
|
905 |
// Read next line |
906 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
907 |
linenumber++; |
908 |
if(eam_eof_test == NULL){ |
909 |
sprintf( painCave.errMsg, |
910 |
"error in reading EAM file %s at line %d\n", |
911 |
eamPotFile.c_str(), linenumber); |
912 |
painCave.isFatal = 1; |
913 |
simError(); |
914 |
} |
915 |
|
916 |
// Parse 5 values on each line into array |
917 |
// Value 1 |
918 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
919 |
sprintf( painCave.errMsg, |
920 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
921 |
painCave.isFatal = 1; |
922 |
simError(); |
923 |
} |
924 |
|
925 |
myEam_rvals[j+0] = atof( the_token ); |
926 |
|
927 |
// Value 2 |
928 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
929 |
sprintf( painCave.errMsg, |
930 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
931 |
painCave.isFatal = 1; |
932 |
simError(); |
933 |
} |
934 |
|
935 |
myEam_rvals[j+1] = atof( the_token ); |
936 |
|
937 |
// Value 3 |
938 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
939 |
sprintf( painCave.errMsg, |
940 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
941 |
painCave.isFatal = 1; |
942 |
simError(); |
943 |
} |
944 |
|
945 |
myEam_rvals[j+2] = atof( the_token ); |
946 |
|
947 |
// Value 4 |
948 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
949 |
sprintf( painCave.errMsg, |
950 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
951 |
painCave.isFatal = 1; |
952 |
simError(); |
953 |
} |
954 |
|
955 |
myEam_rvals[j+3] = atof( the_token ); |
956 |
|
957 |
// Value 5 |
958 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
959 |
sprintf( painCave.errMsg, |
960 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
961 |
painCave.isFatal = 1; |
962 |
simError(); |
963 |
} |
964 |
|
965 |
myEam_rvals[j+4] = atof( the_token ); |
966 |
|
967 |
} |
968 |
// Parse rho of r vals |
969 |
|
970 |
// Assume for now that we have a complete number of lines |
971 |
|
972 |
for (i=0;i<nReadLines;i++){ |
973 |
j = i*5; |
974 |
|
975 |
// Read next line |
976 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
977 |
linenumber++; |
978 |
if(eam_eof_test == NULL){ |
979 |
sprintf( painCave.errMsg, |
980 |
"error in reading EAM file %s at line %d\n", |
981 |
eamPotFile.c_str(), linenumber); |
982 |
painCave.isFatal = 1; |
983 |
simError(); |
984 |
} |
985 |
|
986 |
// Parse 5 values on each line into array |
987 |
// Value 1 |
988 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
989 |
sprintf( painCave.errMsg, |
990 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
991 |
painCave.isFatal = 1; |
992 |
simError(); |
993 |
} |
994 |
|
995 |
myEam_rhovals[j+0] = atof( the_token ); |
996 |
|
997 |
// Value 2 |
998 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
999 |
sprintf( painCave.errMsg, |
1000 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
1001 |
painCave.isFatal = 1; |
1002 |
simError(); |
1003 |
} |
1004 |
|
1005 |
myEam_rhovals[j+1] = atof( the_token ); |
1006 |
|
1007 |
// Value 3 |
1008 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
1009 |
sprintf( painCave.errMsg, |
1010 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
1011 |
painCave.isFatal = 1; |
1012 |
simError(); |
1013 |
} |
1014 |
|
1015 |
myEam_rhovals[j+2] = atof( the_token ); |
1016 |
|
1017 |
// Value 4 |
1018 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
1019 |
sprintf( painCave.errMsg, |
1020 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
1021 |
painCave.isFatal = 1; |
1022 |
simError(); |
1023 |
} |
1024 |
|
1025 |
myEam_rhovals[j+3] = atof( the_token ); |
1026 |
|
1027 |
// Value 5 |
1028 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
1029 |
sprintf( painCave.errMsg, |
1030 |
"Error parsing EAM nrho: line in %s\n", eamPotFile.c_str() ); |
1031 |
painCave.isFatal = 1; |
1032 |
simError(); |
1033 |
} |
1034 |
|
1035 |
myEam_rhovals[j+4] = atof( the_token ); |
1036 |
|
1037 |
} |
1038 |
*eam_rvals = myEam_rvals; |
1039 |
*eam_rhovals = myEam_rhovals; |
1040 |
*eam_Frhovals = myEam_Frhovals; |
1041 |
|
1042 |
fclose(eamFile); |
1043 |
return 0; |
1044 |
} |