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