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