ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/EAM_FF.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/EAM_FF.cpp (file contents):
Revision 499 by chuckv, Tue Apr 15 16:37:59 2003 UTC vs.
Revision 829 by gezelter, Tue Oct 28 16:03:37 2003 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
2 < #include <cstdio>
3 < #include <cstring>
1 > #include <stdlib.h>
2 > #include <stdio.h>
3 > #include <string.h>
4  
5   #include <iostream>
6   using namespace std;
# Line 28 | Line 28 | namespace EAM_NS{
28    typedef struct{
29      char name[15];
30      double mass;
31 <    double epslon;
32 <    double sigma;
31 >    double lattice_constant;
32 >    double eam_drho;  // The distance between each of the points indexed by rho.
33 >    double eam_rcut;  // The cutoff radius for eam.
34 >    double eam_dr;    // The distance between each of the rho points.    
35 >    int eam_nrho;  // Number of points indexed by rho
36 >    int eam_nr;    // The number of points based on r (Both Phi(r) and Rho(r)).
37 >    int eam_ident; // Atomic number
38      int ident;
39      int last;      //  0  -> default
40                     //  1  -> in MPI: tells nodes to stop listening
41    } atomStruct;
42  
43 <  int parseAtom( char *lineBuffer, int lineNum, atomStruct &info );
44 <  
43 >  int parseAtom( char *lineBuffer, int lineNum, atomStruct &info, char *eamPotFile );
44 >  int parseEAM( atomStruct &info, char *eamPotFile, double **eam_rvals,
45 >                double **eam_rhovals, double **eam_Frhovals);
46   #ifdef IS_MPI
47    
48    MPI_Datatype mpiAtomStructType;
# Line 48 | Line 54 | namespace EAM_NS{
54      LinkedAtomType(){
55        next = NULL;
56        name[0] = '\0';
57 +      eam_rvals    = NULL;
58 +      eam_rhovals  = NULL;
59 +      eam_Frhovals = NULL;
60      }
52 –    ~LinkedAtomType(){ if( next != NULL ) delete next; }
61  
62 +    ~LinkedAtomType(){
63 +      if( next != NULL ) delete next;
64 +      if( eam_rvals != NULL ) delete[] eam_rvals;
65 +      if( eam_rhovals != NULL ) delete[] eam_rhovals;
66 +      if( eam_Frhovals != NULL ) delete[] eam_Frhovals;
67 +    }
68 +
69      LinkedAtomType* find(char* key){
70        if( !strcmp(name, key) ) return this;
71        if( next != NULL ) return next->find(key);
# Line 58 | Line 73 | namespace EAM_NS{
73      }
74      
75  
76 <    void add( atomStruct &info ){
77 <    
76 >    void add( atomStruct &info, double *the_eam_rvals,
77 >              double *the_eam_rhovals,double *the_eam_Frhovals ){
78 >
79        // check for duplicates
80        
81        if( !strcmp( info.name, name ) ){
# Line 71 | Line 87 | namespace EAM_NS{
87          simError();
88        }
89        
90 <      if( next != NULL ) next->add(info);
90 >      if( next != NULL ) next->add(info, the_eam_rvals, the_eam_rhovals, the_eam_Frhovals);
91        else{
92          next = new LinkedAtomType();
93          strcpy(next->name, info.name);
94 <        next->mass     = info.mass;
95 <        next->epslon   = info.epslon;
96 <        next->sigma    = info.sigma;
97 <        next->ident    = info.ident;
94 >        next->mass             = info.mass;
95 >        next->lattice_constant = info.lattice_constant;
96 >        next->eam_nrho         = info.eam_nrho;
97 >        next->eam_drho         = info.eam_drho;
98 >        next->eam_nr           = info.eam_nr;
99 >        next->eam_dr           = info.eam_dr;
100 >        next->eam_rcut         = info.eam_rcut;
101 >        next->eam_ident        = info.eam_ident;
102 >        next->ident            = info.ident;
103 >
104 >        next->eam_rvals    = the_eam_rvals;
105 >        next->eam_rhovals  = the_eam_rhovals;
106 >        next->eam_Frhovals = the_eam_Frhovals;
107        }
108      }
109      
# Line 87 | Line 112 | namespace EAM_NS{
112      
113      void duplicate( atomStruct &info ){
114        strcpy(info.name, name);
115 <      info.mass     = mass;
116 <      info.epslon   = epslon;
117 <      info.sigma    = sigma;
118 <      info.ident    = ident;
119 <      info.last     = 0;
115 >      info.mass             = mass;
116 >      info.lattice_constant = lattice_constant;
117 >      info.eam_nrho         = eam_nrho;
118 >      info.eam_drho         = eam_drho;
119 >      info.eam_nr           = eam_nr;
120 >      info.eam_dr           = eam_dr;
121 >      info.eam_rcut         = eam_rcut;
122 >      info.eam_ident        = eam_ident;
123 >      info.ident            = ident;
124 >      info.last             = 0;
125      }
126  
127  
# Line 99 | Line 129 | namespace EAM_NS{
129  
130      char name[15];
131      double mass;
132 <    double epslon;
133 <    double sigma;
132 >    double lattice_constant;
133 >    int eam_nrho; // Number of points indexed by rho
134 >    double eam_drho; // The distance between each of the points indexed by rho.
135 >    int eam_nr;   // The number of points based on r (Both Phi(r) and Rho(r)).
136 >    double eam_dr;   // The distance between each of the rho points.
137 >    double eam_rcut; // The cutoff radius for eam.
138 >
139 >    double *eam_rvals;    // Z of r values
140 >    double *eam_rhovals;  // rho of r values
141 >    double *eam_Frhovals; // F of rho values
142 >    int eam_ident;        // eam identity (atomic number)
143      int ident;
144      LinkedAtomType* next;
145    };
# Line 110 | Line 149 | using namespace LJ_NS;
149  
150   }
151  
152 < using namespace LJ_NS;
152 > using namespace EAM_NS;
153  
154   //****************************************************************
155   // begins the actual forcefield stuff.  
# Line 123 | Line 162 | EAM_FF::EAM_FF(){
162    char* ffPath_env = "FORCE_PARAM_PATH";
163    char* ffPath;
164    char temp[200];
126 –  char errMsg[1000];
165  
166    headAtomType = NULL;
167    currentAtomType = NULL;
168  
169 +  // Set eamRcut to 0.0
170 +  eamRcut = 0.0;
171 +
172    // do the funtion wrapping
173    wrapMeFF( this );
174  
# Line 138 | Line 179 | EAM_FF::EAM_FF(){
179    // Init the atomStruct mpi type
180  
181    atomStruct atomProto; // mpiPrototype
182 <  int atomBC[3] = {15,3,2};  // block counts
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.ident, &atomDspls[2]);
188 >  MPI_Address(&atomProto.eam_nrho, &atomDspls[2]);
189    
190    atomMbrTypes[0] = MPI_CHAR;
191    atomMbrTypes[1] = MPI_DOUBLE;
# Line 201 | Line 242 | EAM_FF::EAM_FF(){
242   #ifdef IS_MPI
243    }
244    
245 <  sprintf( checkPointMsg, "LJ_FF file opened sucessfully." );
245 >  sprintf( checkPointMsg, "EAM_FF file opened sucessfully." );
246    MPIcheckPoint();
247    
248   #endif // is_mpi
# Line 223 | Line 264 | void EAM_FF::initForceField( int ljMixRule ){
264   #endif // is_mpi
265   }
266  
267 < void EAM_FF::initForceField( int ljMixRule ){
267 >
268 > void EAM_FF::calcRcut( void ){
269    
270 +  #ifdef IS_MPI
271 +  double tempEamRcut = eamRcut;
272 +  MPI_Allreduce( &tempEamRcut, &eamRcut, 1, MPI_DOUBLE, MPI_MAX,
273 +                 MPI_COMM_WORLD);
274 + #endif  //is_mpi
275 +  entry_plug->setRcut(eamRcut);
276 + }
277 +
278 +
279 + void EAM_FF::initForceField( int ljMixRule ){
280    initFortran( ljMixRule, 0 );
281   }
282  
# Line 243 | Line 295 | void EAM_FF::readParams( void ){
295   #endif // is_mpi
296   }
297  
298 +
299   void EAM_FF::readParams( void ){
300  
301    atomStruct info;
302    info.last = 1; // initialize last to have the last set.
303                   // if things go well, last will be set to 0
304  
252 –  int i;
305    int identNum;
306 +  double *eam_rvals;    // Z of r values
307 +  double *eam_rhovals;  // rho of r values
308 +  double *eam_Frhovals; // F of rho values
309 +  char eamPotFile[1000];
310    
311  
312    bigSigma = 0.0;
# Line 262 | Line 318 | void EAM_FF::readParams( void ){
318  
319      headAtomType = new LinkedAtomType;
320      
321 <    fastForward( "AtomTypes", "initializeAtoms" );
321 >    fastForward( "AtomTypes", "eam atom readParams" );
322  
323      // we are now at the AtomTypes section.
324      
# Line 282 | Line 338 | void EAM_FF::readParams( void ){
338      
339      identNum = 1;
340      // stop reading at end of file, or at next section
341 +
342      while( readLine[0] != '#' && eof_test != NULL ){
343  
344        // toss comment lines
345        if( readLine[0] != '!' ){
346          
347          // the parser returns 0 if the line was blank
348 <        if( parseAtom( readLine, lineNum, info ) ){
348 >        if( parseAtom( readLine, lineNum, info, eamPotFile ) ){
349 >          parseEAM(info,eamPotFile, &eam_rvals,
350 >                   &eam_rhovals, &eam_Frhovals);
351            info.ident = identNum;
352 <          headAtomType->add( info );;
352 >          headAtomType->add( info, eam_rvals,
353 >                             eam_rhovals,eam_Frhovals );
354            identNum++;
355          }
356        }
357        eof_test = fgets( readLine, sizeof(readLine), frcFile );
358        lineNum++;
359      }
360 +    
361 +    
362  
363   #ifdef IS_MPI
364 +  
365      
366      // send out the linked list to all the other processes
367  
368      sprintf( checkPointMsg,
369 <             "LJ_FF atom structures read successfully." );
369 >             "EAM_FF atom structures read successfully." );
370      MPIcheckPoint();
371  
372      currentAtomType = headAtomType->next; //skip the first element who is a place holder.
# Line 314 | Line 377 | void EAM_FF::readParams( void ){
377  
378        sendFrcStruct( &info, mpiAtomStructType );
379  
380 +      // We have to now broadcast the Arrays
381 +      MPI_Bcast(currentAtomType->eam_rvals,
382 +                currentAtomType->eam_nr,
383 +                MPI_DOUBLE,0,MPI_COMM_WORLD);
384 +      MPI_Bcast(currentAtomType->eam_rhovals,
385 +                currentAtomType->eam_nr,
386 +                MPI_DOUBLE,0,MPI_COMM_WORLD);
387 +      MPI_Bcast(currentAtomType->eam_Frhovals,
388 +                currentAtomType->eam_nrho,
389 +                MPI_DOUBLE,0,MPI_COMM_WORLD);
390 +
391        sprintf( checkPointMsg,
392 <               "successfully sent lJ force type: \"%s\"\n",
392 >               "successfully sent EAM force type: \"%s\"\n",
393                 info.name );
394        MPIcheckPoint();
395  
# Line 334 | Line 408 | void EAM_FF::readParams( void ){
408  
409      headAtomType = new LinkedAtomType;
410      recieveFrcStruct( &info, mpiAtomStructType );
411 <    
411 >
412      while( !info.last ){
413 +      
414 +      // allocate the arrays
415  
416 +      eam_rvals    = new double[info.eam_nr];
417 +      eam_rhovals  = new double[info.eam_nr];
418 +      eam_Frhovals = new double[info.eam_nrho];
419  
420 +      // We have to now broadcast the Arrays
421 +      MPI_Bcast(eam_rvals,
422 +                info.eam_nr,
423 +                MPI_DOUBLE,0,MPI_COMM_WORLD);
424 +      MPI_Bcast(eam_rhovals,
425 +                info.eam_nr,
426 +                MPI_DOUBLE,0,MPI_COMM_WORLD);
427 +      MPI_Bcast(eam_Frhovals,
428 +                info.eam_nrho,
429 +                MPI_DOUBLE,0,MPI_COMM_WORLD);
430 +      
431  
432 <      headAtomType->add( info );
432 >      headAtomType->add( info, eam_rvals, eam_rhovals, eam_Frhovals );
433        
434        MPIcheckPoint();
435  
436        recieveFrcStruct( &info, mpiAtomStructType );
437 +
438 +
439      }
440    }
441   #endif // is_mpi
# Line 353 | Line 445 | void EAM_FF::readParams( void ){
445    int isError;
446  
447    // dummy variables
448 <  int isLJ = 1;
448 >  int isLJ = 0;
449    int isDipole = 0;
450    int isSSD = 0;
451    int isGB = 0;
452 +  int isEAM= 1;
453    double dipole = 0.0;
454 +  double eamSigma = 0.0;
455 +  double eamEpslon = 0.0;
456    
457 <  currentAtomType = headAtomType;
457 >  currentAtomType = headAtomType->next;
458    while( currentAtomType != NULL ){
459      
460      if( currentAtomType->name[0] != '\0' ){
# Line 369 | Line 464 | void EAM_FF::readParams( void ){
464                   &isSSD,
465                   &isDipole,
466                   &isGB,
467 <                 &(currentAtomType->epslon),
468 <                 &(currentAtomType->sigma),
467 >                 &isEAM,
468 >                 &eamEpslon,
469 >                 &eamSigma,
470                   &dipole,
471                   &isError );
472        if( isError ){
# Line 384 | Line 480 | void EAM_FF::readParams( void ){
480      currentAtomType = currentAtomType->next;
481    }
482        
483 <  entry_plug->useLJ = 1;
483 >  entry_plug->useLJ = 0;
484 >  entry_plug->useEAM = 1;
485 >  // Walk down again and send out EAM type
486 >  currentAtomType = headAtomType->next;
487 >  while( currentAtomType != NULL ){
488 >    
489 >    if( currentAtomType->name[0] != '\0' ){
490 >      isError = 0;
491  
492 +      newEAMtype( &(currentAtomType->lattice_constant),
493 +                  &(currentAtomType->eam_nrho),
494 +                  &(currentAtomType->eam_drho),
495 +                  &(currentAtomType->eam_nr),
496 +                  &(currentAtomType->eam_dr),
497 +                  &(currentAtomType->eam_rcut),
498 +                  currentAtomType->eam_rvals,
499 +                  currentAtomType->eam_rhovals,
500 +                  currentAtomType->eam_Frhovals,
501 +                  &(currentAtomType->eam_ident),
502 +                  &isError);
503 +
504 +      if( isError ){
505 +        sprintf( painCave.errMsg,
506 +                 "Error initializing the \"%s\" atom type in fortran EAM\n",
507 +                 currentAtomType->name );
508 +        painCave.isFatal = 1;
509 +        simError();
510 +      }
511 +    }
512 +    currentAtomType = currentAtomType->next;
513 +  }
514 +
515 +
516 +
517   #ifdef IS_MPI
518    sprintf( checkPointMsg,
519 <           "LJ_FF atom structures successfully sent to fortran\n" );
519 >           "EAM_FF atom structures successfully sent to fortran\n" );
520    MPIcheckPoint();
521   #endif // is_mpi
522  
523 +
524 +
525   }
526  
527  
528   void EAM_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){
529    
530    int i;
531 <
531 >  
532    // initialize the atoms
533    
404 –
405 –  Atom* thisAtom;
406 –
534    for( i=0; i<nAtoms; i++ ){
535      
536      currentAtomType = headAtomType->find( the_atoms[i]->getType() );
# Line 416 | Line 543 | void EAM_FF::initializeAtoms( int nAtoms, Atom** the_a
543      }
544      
545      the_atoms[i]->setMass( currentAtomType->mass );
419 –    the_atoms[i]->setEpslon( currentAtomType->epslon );
420 –    the_atoms[i]->setSigma( currentAtomType->sigma );
546      the_atoms[i]->setIdent( currentAtomType->ident );
547 <    the_atoms[i]->setLJ();
547 >    the_atoms[i]->setEAM();
548 >    the_atoms[i]->setEamRcut( currentAtomType->eam_rcut);
549  
550 <    if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
550 >    if (eamRcut < currentAtomType->eam_rcut) eamRcut = currentAtomType->eam_rcut;
551 >
552    }
553   }
554  
555 < void LJ_FF::initializeBonds( int nBonds, Bond** BondArray,
555 > void EAM_FF::initializeBonds( int nBonds, Bond** BondArray,
556                               bond_pair* the_bonds ){
557    
558      if( nBonds ){
# Line 514 | Line 641 | int EAM_NS::parseAtom( char *lineBuffer, int lineNum,
641  
642  
643  
644 < int EAM_NS::parseAtom( char *lineBuffer, int lineNum,  atomStruct &info ){
644 > int EAM_NS::parseAtom( char *lineBuffer, int lineNum,   atomStruct &info, char *eamPotFile ){
645  
646    char* the_token;
647    
# Line 532 | Line 659 | int EAM_NS::parseAtom( char *lineBuffer, int lineNum,
659      
660      info.mass = atof( the_token );
661      
535 –    if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
536 –      sprintf( painCave.errMsg,
537 –               "Error parseing AtomTypes: line %d\n", lineNum );
538 –      painCave.isFatal = 1;
539 –      simError();
540 –    }
541 –        
542 –    info.epslon = atof( the_token );
543 –          
662      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
663        sprintf( painCave.errMsg,
664                 "Error parseing AtomTypes: line %d\n", lineNum );
# Line 548 | Line 666 | int EAM_NS::parseAtom( char *lineBuffer, int lineNum,
666        simError();
667      }
668          
669 <    info.sigma = atof( the_token );
552 <    
669 >    strcpy( eamPotFile, the_token );
670      return 1;
671    }
672    else return 0;
673 + }
674 +
675 + int EAM_NS::parseEAM(atomStruct &info, char *eamPotFile,
676 +                     double **eam_rvals,
677 +                     double **eam_rhovals,
678 +                     double **eam_Frhovals){
679 +  double* myEam_rvals;
680 +  double* myEam_rhovals;
681 +  double* myEam_Frhovals;
682 +
683 +  char* ffPath_env = "FORCE_PARAM_PATH";
684 +  char* ffPath;
685 +  char* the_token;
686 +  char* eam_eof_test;
687 +  FILE *eamFile;
688 +  const int BUFFERSIZE = 3000;
689 +
690 +  char temp[200];
691 +  int linenumber;
692 +  int nReadLines;
693 +  char eam_read_buffer[BUFFERSIZE];
694 +
695 +
696 +  int i,j;
697 +
698 +  linenumber = 0;
699 +
700 +  // Open eam file
701 +  eamFile = fopen( eamPotFile, "r" );
702 +  
703 +  
704 +  if( eamFile == NULL ){
705 +    
706 +      // next see if the force path enviorment variable is set
707 +    
708 +    ffPath = getenv( ffPath_env );
709 +    if( ffPath == NULL ) {
710 +      STR_DEFINE(ffPath, FRC_PATH );
711 +    }
712 +    
713 +    
714 +    strcpy( temp, ffPath );
715 +    strcat( temp, "/" );
716 +    strcat( temp, eamPotFile );
717 +    strcpy( eamPotFile, temp );
718 +    
719 +    eamFile = fopen( eamPotFile, "r" );
720 +
721 +    
722 +    
723 +    if( eamFile == NULL ){
724 +      
725 +      sprintf( painCave.errMsg,
726 +               "Error opening the EAM force parameter file: %s\n"
727 +               "Have you tried setting the FORCE_PARAM_PATH environment "
728 +               "vairable?\n",
729 +               eamPotFile );
730 +      painCave.isFatal = 1;
731 +      simError();
732 +    }
733 +  }
734 +
735 +  // First line is a comment line, read and toss it....
736 +  eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile);
737 +  linenumber++;
738 +  if(eam_eof_test == NULL){
739 +    sprintf( painCave.errMsg,
740 +             "error in reading commment in %s\n", eamPotFile);
741 +    painCave.isFatal = 1;
742 +    simError();
743 +  }
744 +
745 +
746 +
747 +  // The Second line contains atomic number, atomic mass and a lattice constant
748 +  eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile);
749 +  linenumber++;
750 +  if(eam_eof_test == NULL){
751 +    sprintf( painCave.errMsg,
752 +             "error in reading Identifier line in %s\n", eamPotFile);
753 +    painCave.isFatal = 1;
754 +    simError();
755 +  }
756 +
757 +
758 +
759 +    
760 +  if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
761 +    sprintf( painCave.errMsg,
762 +             "Error parseing EAM ident  line in %s\n", eamPotFile );
763 +    painCave.isFatal = 1;
764 +    simError();
765 +  }
766 +  
767 +  info.eam_ident = atoi( the_token );
768 +
769 +  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
770 +    sprintf( painCave.errMsg,
771 +             "Error parseing EAM mass in %s\n", eamPotFile );
772 +    painCave.isFatal = 1;
773 +    simError();
774 +  }
775 +  info.mass = atof( the_token);
776 +
777 +  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
778 +    sprintf( painCave.errMsg,
779 +             "Error parseing EAM Lattice Constant %s\n", eamPotFile );
780 +    painCave.isFatal = 1;
781 +    simError();
782 +  }
783 +  info.lattice_constant = atof( the_token);
784 +
785 +  // Next line is nrho, drho, nr, dr and rcut
786 +  eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile);
787 +  if(eam_eof_test == NULL){
788 +    sprintf( painCave.errMsg,
789 +             "error in reading number of points line in %s\n", eamPotFile);
790 +    painCave.isFatal = 1;
791 +    simError();
792 +  }
793 +
794 +  if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
795 +    sprintf( painCave.errMsg,
796 +             "Error parseing EAM nrho: line in %s\n", eamPotFile );
797 +    painCave.isFatal = 1;
798 +    simError();
799 +  }
800 +  
801 +  info.eam_nrho = atoi( the_token );
802 +  
803 +  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
804 +    sprintf( painCave.errMsg,
805 +             "Error parseing EAM drho in %s\n", eamPotFile );
806 +    painCave.isFatal = 1;
807 +    simError();
808 +  }
809 +  info.eam_drho = atof( the_token);
810 +
811 +  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
812 +    sprintf( painCave.errMsg,
813 +             "Error parseing EAM # r in %s\n", eamPotFile );
814 +    painCave.isFatal = 1;
815 +    simError();
816 +  }
817 +  info.eam_nr = atoi( the_token);
818 +  
819 +  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
820 +    sprintf( painCave.errMsg,
821 +             "Error parseing EAM dr in %s\n", eamPotFile );
822 +    painCave.isFatal = 1;
823 +    simError();
824 +  }
825 +  info.eam_dr = atof( the_token);
826 +
827 +  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
828 +    sprintf( painCave.errMsg,
829 +             "Error parseing EAM rcut in %s\n", eamPotFile );
830 +    painCave.isFatal = 1;
831 +    simError();
832 +  }
833 +  info.eam_rcut = atof( the_token);
834 +
835 +
836 +
837 +
838 +
839 +  // Ok now we have to allocate point arrays and read in number of points
840 +  // Index the arrays for fortran, starting at 1
841 +  myEam_Frhovals = new double[info.eam_nrho];
842 +  myEam_rvals    = new double[info.eam_nr];
843 +  myEam_rhovals  = new double[info.eam_nr];
844 +
845 +  // Parse F of rho vals.
846 +
847 +  // Assume for now that we have a complete number of lines
848 +  nReadLines = int(info.eam_nrho/5);
849 +  
850 +
851 +
852 +  for (i=0;i<nReadLines;i++){
853 +    j = i*5;
854 +
855 +    // Read next line
856 +    eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile);
857 +    linenumber++;
858 +    if(eam_eof_test == NULL){
859 +      sprintf( painCave.errMsg,
860 +               "error in reading EAM file %s at line %d\n",
861 +               eamPotFile,linenumber);
862 +      painCave.isFatal = 1;
863 +      simError();
864 +    }
865 +    
866 +    // Parse 5 values on each line into array
867 +    // Value 1
868 +    if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
869 +      sprintf( painCave.errMsg,
870 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
871 +      painCave.isFatal = 1;
872 +      simError();
873 +    }
874 +
875 +    myEam_Frhovals[j+0] = atof( the_token );
876 +    
877 +    // Value 2
878 +    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
879 +      sprintf( painCave.errMsg,
880 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
881 +      painCave.isFatal = 1;
882 +      simError();
883 +    }
884 +
885 +    myEam_Frhovals[j+1] = atof( the_token );
886 +    
887 +    // Value 3
888 +    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
889 +      sprintf( painCave.errMsg,
890 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
891 +      painCave.isFatal = 1;
892 +      simError();
893 +    }
894 +
895 +    myEam_Frhovals[j+2] = atof( the_token );
896 +    
897 +    // Value 4
898 +    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
899 +      sprintf( painCave.errMsg,
900 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
901 +      painCave.isFatal = 1;
902 +      simError();
903 +    }
904 +
905 +    myEam_Frhovals[j+3] = atof( the_token );
906 +
907 +    // Value 5
908 +    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
909 +      sprintf( painCave.errMsg,
910 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
911 +      painCave.isFatal = 1;
912 +      simError();
913 +    }
914 +
915 +    myEam_Frhovals[j+4] = atof( the_token );
916 +    
917 +  }
918 +  // Parse Z of r vals
919 +  
920 +  // Assume for now that we have a complete number of lines
921 +  nReadLines = int(info.eam_nr/5);
922 +
923 +  for (i=0;i<nReadLines;i++){
924 +    j = i*5;
925 +
926 +    // Read next line
927 +    eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile);
928 +    linenumber++;
929 +    if(eam_eof_test == NULL){
930 +      sprintf( painCave.errMsg,
931 +               "error in reading EAM file %s at line %d\n",
932 +               eamPotFile,linenumber);
933 +      painCave.isFatal = 1;
934 +      simError();
935 +    }
936 +    
937 +    // Parse 5 values on each line into array
938 +    // Value 1
939 +    if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
940 +      sprintf( painCave.errMsg,
941 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
942 +      painCave.isFatal = 1;
943 +      simError();
944 +    }
945 +    
946 +    myEam_rvals[j+0] = atof( the_token );
947 +
948 +    // Value 2
949 +    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
950 +      sprintf( painCave.errMsg,
951 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
952 +      painCave.isFatal = 1;
953 +      simError();
954 +    }
955 +  
956 +    myEam_rvals[j+1] = atof( the_token );
957 +
958 +    // Value 3
959 +    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
960 +      sprintf( painCave.errMsg,
961 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
962 +      painCave.isFatal = 1;
963 +      simError();
964 +    }
965 +  
966 +    myEam_rvals[j+2] = atof( the_token );
967 +
968 +    // Value 4
969 +    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
970 +      sprintf( painCave.errMsg,
971 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
972 +      painCave.isFatal = 1;
973 +      simError();
974 +    }
975 +  
976 +    myEam_rvals[j+3] = atof( the_token );
977 +
978 +    // Value 5
979 +    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
980 +      sprintf( painCave.errMsg,
981 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
982 +      painCave.isFatal = 1;
983 +      simError();
984 +    }
985 +  
986 +    myEam_rvals[j+4] = atof( the_token );
987 +
988 +  }
989 +  // Parse rho of r vals
990 +
991 +  // Assume for now that we have a complete number of lines
992 +
993 +  for (i=0;i<nReadLines;i++){
994 +    j = i*5;
995 +
996 +    // Read next line
997 +    eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile);
998 +    linenumber++;
999 +    if(eam_eof_test == NULL){
1000 +      sprintf( painCave.errMsg,
1001 +               "error in reading EAM file %s at line %d\n",
1002 +               eamPotFile,linenumber);
1003 +      painCave.isFatal = 1;
1004 +      simError();
1005 +    }
1006 +  
1007 +    // Parse 5 values on each line into array
1008 +    // Value 1
1009 +    if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
1010 +      sprintf( painCave.errMsg,
1011 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
1012 +      painCave.isFatal = 1;
1013 +      simError();
1014 +    }
1015 +  
1016 +    myEam_rhovals[j+0] = atof( the_token );
1017 +
1018 +    // Value 2
1019 +    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
1020 +      sprintf( painCave.errMsg,
1021 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
1022 +      painCave.isFatal = 1;
1023 +      simError();
1024 +    }
1025 +  
1026 +    myEam_rhovals[j+1] = atof( the_token );
1027 +
1028 +    // Value 3
1029 +    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
1030 +      sprintf( painCave.errMsg,
1031 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
1032 +      painCave.isFatal = 1;
1033 +      simError();
1034 +    }
1035 +  
1036 +    myEam_rhovals[j+2] = atof( the_token );
1037 +
1038 +    // Value 4
1039 +    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
1040 +      sprintf( painCave.errMsg,
1041 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
1042 +      painCave.isFatal = 1;
1043 +      simError();
1044 +    }
1045 +  
1046 +    myEam_rhovals[j+3] = atof( the_token );
1047 +
1048 +    // Value 5
1049 +    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
1050 +      sprintf( painCave.errMsg,
1051 +               "Error parseing EAM nrho: line in %s\n", eamPotFile );
1052 +      painCave.isFatal = 1;
1053 +      simError();
1054 +    }
1055 +  
1056 +    myEam_rhovals[j+4] = atof( the_token );
1057 +
1058 +  }
1059 +  *eam_rvals = myEam_rvals;
1060 +  *eam_rhovals = myEam_rhovals;
1061 +  *eam_Frhovals = myEam_Frhovals;
1062 +
1063 +  fclose(eamFile);
1064 +  return 0;
1065   }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines