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root/group/trunk/OOPSE/libmdtools/EAM_FF.cpp
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Comparing trunk/OOPSE/libmdtools/EAM_FF.cpp (file contents):
Revision 499 by chuckv, Tue Apr 15 16:37:59 2003 UTC vs.
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC

# 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_dr;    // The distance between each of the rho points.    
34 >    int eam_nrho;  // Number of points indexed by rho
35 >    int eam_nr;    // The number of points based on r (Both Phi(r) and Rho(r)).
36 >    double eam_rcut;  // The cutoff radius for eam.
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 );
# 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] = {15,4,6};  // 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 539 | Line 666 | int EAM_NS::parseAtom( char *lineBuffer, int lineNum,
666        simError();
667      }
668          
669 <    info.epslon = atof( the_token );
670 <          
671 <    if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
672 <      sprintf( painCave.errMsg,
673 <               "Error parseing AtomTypes: line %d\n", lineNum );
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      }
550 –        
551 –    info.sigma = atof( the_token );
552 –    
553 –    return 1;
733    }
734 <  else return 0;
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   }

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