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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 627 by chuckv, Wed Jul 16 21:49:59 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 >    int 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 );
45   #ifdef IS_MPI
46    
47    MPI_Datatype mpiAtomStructType;
# Line 48 | Line 53 | namespace EAM_NS{
53      LinkedAtomType(){
54        next = NULL;
55        name[0] = '\0';
56 +      eam_rvals    = NULL;
57 +      eam_rhovals  = NULL;
58 +      eam_Frhovals = NULL;
59      }
52 –    ~LinkedAtomType(){ if( next != NULL ) delete next; }
60  
61 +    ~LinkedAtomType(){
62 +      if( next != NULL ) delete next;
63 +      if( eam_rvals != NULL ) delete[] eam_rvals;
64 +      if( eam_rhovals != NULL ) delete[] eam_rhovals;
65 +      if( eam_Frhovals != NULL ) delete[] eam_Frhovals;
66 +    }
67 +
68      LinkedAtomType* find(char* key){
69        if( !strcmp(name, key) ) return this;
70        if( next != NULL ) return next->find(key);
# Line 58 | Line 72 | namespace EAM_NS{
72      }
73      
74  
75 <    void add( atomStruct &info ){
76 <    
75 >    void add( atomStruct &info, double *the_eam_rvals,
76 >              double *the_eam_rhovals,double *the_eam_Frhovals ){
77 >
78 >      int i;
79 >
80        // check for duplicates
81        
82        if( !strcmp( info.name, name ) ){
# Line 71 | Line 88 | namespace EAM_NS{
88          simError();
89        }
90        
91 <      if( next != NULL ) next->add(info);
91 >      if( next != NULL ) next->add(info, the_eam_rvals, the_eam_rhovals, the_eam_Frhovals);
92        else{
93          next = new LinkedAtomType();
94          strcpy(next->name, info.name);
95 <        next->mass     = info.mass;
96 <        next->epslon   = info.epslon;
97 <        next->sigma    = info.sigma;
98 <        next->ident    = info.ident;
95 >        next->mass             = info.mass;
96 >        next->lattice_constant = info.lattice_constant;
97 >        next->eam_nrho         = info.eam_nrho;
98 >        next->eam_drho         = info.eam_drho;
99 >        next->eam_nr           = info.eam_nr;
100 >        next->eam_dr           = info.eam_dr;
101 >        next->eam_rcut         = info.eam_rcut;
102 >        next->eam_ident        = info.eam_ident;
103 >        next->ident            = info.ident;
104 >
105 >        next->eam_rvals    = the_eam_rvals;
106 >        next->eam_rhovals  = the_eam_rhovals;
107 >        next->eam_Frhovals = the_eam_Frhovals;
108        }
109      }
110      
# Line 87 | Line 113 | namespace EAM_NS{
113      
114      void duplicate( atomStruct &info ){
115        strcpy(info.name, name);
116 <      info.mass     = mass;
117 <      info.epslon   = epslon;
118 <      info.sigma    = sigma;
119 <      info.ident    = ident;
120 <      info.last     = 0;
116 >      info.mass             = mass;
117 >      info.lattice_constant = lattice_constant;
118 >      info.eam_nrho         = eam_nrho;
119 >      info.eam_drho         = eam_drho;
120 >      info.eam_nr           = eam_nr;
121 >      info.eam_dr           = eam_dr;
122 >      info.eam_rcut         = eam_rcut;
123 >      info.eam_ident        = eam_ident;
124 >      info.ident            = ident;
125 >      info.last             = 0;
126      }
127  
128  
# Line 99 | Line 130 | namespace EAM_NS{
130  
131      char name[15];
132      double mass;
133 <    double epslon;
134 <    double sigma;
133 >    double lattice_constant;
134 >    int eam_nrho; // Number of points indexed by rho
135 >    double eam_drho; // The distance between each of the points indexed by rho.
136 >    int eam_nr;   // The number of points based on r (Both Phi(r) and Rho(r)).
137 >    double eam_dr;   // The distance between each of the rho points.
138 >    int eam_rcut; // The cutoff radius for eam.
139 >
140 >    double *eam_rvals;    // Z of r values
141 >    double *eam_rhovals;  // rho of r values
142 >    double *eam_Frhovals; // F of rho values
143 >    int eam_ident;        // eam identity (atomic number)
144      int ident;
145      LinkedAtomType* next;
146    };
# Line 138 | Line 178 | EAM_FF::EAM_FF(){
178    // Init the atomStruct mpi type
179  
180    atomStruct atomProto; // mpiPrototype
181 <  int atomBC[3] = {15,3,2};  // block counts
181 >  int atomBC[3] = {15,4,6};  // block counts
182    MPI_Aint atomDspls[3];           // displacements
183    MPI_Datatype atomMbrTypes[3];    // member mpi types
184  
185    MPI_Address(&atomProto.name, &atomDspls[0]);
186    MPI_Address(&atomProto.mass, &atomDspls[1]);
187 <  MPI_Address(&atomProto.ident, &atomDspls[2]);
187 >  MPI_Address(&atomProto.eam_nrho, &atomDspls[2]);
188    
189    atomMbrTypes[0] = MPI_CHAR;
190    atomMbrTypes[1] = MPI_DOUBLE;
# Line 201 | Line 241 | EAM_FF::EAM_FF(){
241   #ifdef IS_MPI
242    }
243    
244 <  sprintf( checkPointMsg, "LJ_FF file opened sucessfully." );
244 >  sprintf( checkPointMsg, "EAM_FF file opened sucessfully." );
245    MPIcheckPoint();
246    
247   #endif // is_mpi
# Line 251 | Line 291 | void EAM_FF::readParams( void ){
291  
292    int i;
293    int identNum;
294 +  double *eam_rvals;    // Z of r values
295 +  double *eam_rhovals;  // rho of r values
296 +  double *eam_Frhovals; // F of rho values
297 +  char eamPotFile[1000];
298    
299  
300    bigSigma = 0.0;
# Line 262 | Line 306 | void EAM_FF::readParams( void ){
306  
307      headAtomType = new LinkedAtomType;
308      
309 <    fastForward( "AtomTypes", "initializeAtoms" );
309 >    fastForward( "AtomTypes", "eam atom readParams" );
310  
311      // we are now at the AtomTypes section.
312      
# Line 282 | Line 326 | void EAM_FF::readParams( void ){
326      
327      identNum = 1;
328      // stop reading at end of file, or at next section
329 +
330      while( readLine[0] != '#' && eof_test != NULL ){
331  
332        // toss comment lines
333        if( readLine[0] != '!' ){
334          
335          // the parser returns 0 if the line was blank
336 <        if( parseAtom( readLine, lineNum, info ) ){
336 >        if( parseAtom( readLine, lineNum, info, eamPotFile ) ){
337 >          parseEAM(info,eamPotFile, &eam_rvals,
338 >                   &eam_rhovals, &eam_Frhovals)){
339            info.ident = identNum;
340 <          headAtomType->add( info );;
340 >          headAtomType->add( info, eam_rvals,
341 >                             eam_rhovals,eam_Frhovals );
342            identNum++;
343          }
344        }
345        eof_test = fgets( readLine, sizeof(readLine), frcFile );
346        lineNum++;
347      }
348 +    
349 +    
350  
351   #ifdef IS_MPI
352 +  
353      
354      // send out the linked list to all the other processes
355  
356      sprintf( checkPointMsg,
357 <             "LJ_FF atom structures read successfully." );
357 >             "EAM_FF atom structures read successfully." );
358      MPIcheckPoint();
359  
360      currentAtomType = headAtomType->next; //skip the first element who is a place holder.
# Line 314 | Line 365 | void EAM_FF::readParams( void ){
365  
366        sendFrcStruct( &info, mpiAtomStructType );
367  
368 +      // We have to now broadcast the Arrays
369 +      MPI_Bcast(currentAtomType->eam_rvals,
370 +                currentAtomType->eam_nr,
371 +                MPI_DOUBLE,0,MPI_COMM_WORLD);
372 +      MPI_Bcast(currentAtomType->eam_rhovals,
373 +                currentAtomType->eam_nr,
374 +                MPI_DOUBLE,0,MPI_COMM_WORLD);
375 +      MPI_Bcast(currentAtomType->eam_Frhovals,
376 +                currentAtomType->eam_nrho,
377 +                MPI_DOUBLE,0,MPI_COMM_WORLD);
378 +
379        sprintf( checkPointMsg,
380 <               "successfully sent lJ force type: \"%s\"\n",
380 >               "successfully sent EAM force type: \"%s\"\n",
381                 info.name );
382        MPIcheckPoint();
383  
# Line 334 | Line 396 | void EAM_FF::readParams( void ){
396  
397      headAtomType = new LinkedAtomType;
398      recieveFrcStruct( &info, mpiAtomStructType );
399 <    
399 >
400      while( !info.last ){
401 +      
402 +      // allocate the arrays
403  
404 +      eam_rvals    = new double[info.eam_nr];
405 +      eam_rhovals  = new double[info.eam_nr];
406 +      eam_Frhovals = new double[info.eam_nrho];
407  
408 +      // We have to now broadcast the Arrays
409 +      MPI_Bcast(eam_rvals,
410 +                info.eam_nr,
411 +                MPI_DOUBLE,0,MPI_COMM_WORLD);
412 +      MPI_Bcast(eam_rhovals,
413 +                info.eam_nr,
414 +                MPI_DOUBLE,0,MPI_COMM_WORLD);
415 +      MPI_Bcast(eam_Frhovals,
416 +                info.eam_nrho,
417 +                MPI_DOUBLE,0,MPI_COMM_WORLD);
418 +      
419  
420 <      headAtomType->add( info );
420 >      headAtomType->add( info, eam_rvals, eam_rhovals, eam_Frhovals );
421        
422        MPIcheckPoint();
423  
424        recieveFrcStruct( &info, mpiAtomStructType );
425 +
426 +
427      }
428    }
429   #endif // is_mpi
# Line 353 | Line 433 | void EAM_FF::readParams( void ){
433    int isError;
434  
435    // dummy variables
436 <  int isLJ = 1;
436 >  int isLJ = 0;
437    int isDipole = 0;
438    int isSSD = 0;
439    int isGB = 0;
440 +  int isEam = 1;
441    double dipole = 0.0;
442    
443 <  currentAtomType = headAtomType;
443 >  currentAtomType = headAtomType->next;
444    while( currentAtomType != NULL ){
445      
446      if( currentAtomType->name[0] != '\0' ){
# Line 369 | Line 450 | void EAM_FF::readParams( void ){
450                   &isSSD,
451                   &isDipole,
452                   &isGB,
453 +                 &isEAM,
454                   &(currentAtomType->epslon),
455                   &(currentAtomType->sigma),
456                   &dipole,
# Line 384 | Line 466 | void EAM_FF::readParams( void ){
466      currentAtomType = currentAtomType->next;
467    }
468        
469 <  entry_plug->useLJ = 1;
469 >  entry_plug->useLJ = 0;
470  
471 +  // Walk down again and send out EAM type
472 +  currentAtomType = headAtomType->next;
473 +  while( currentAtomType != NULL ){
474 +    
475 +    if( currentAtomType->name[0] != '\0' ){
476 +      isError = 0;
477 +      newEAMtype( &(currentAtomType->lattice_constant),
478 +                  &(currentAtomType->eam_nrho),
479 +                  &(currentAtomType->eam_drho),
480 +                  &(currentAtomType->eam_nr),
481 +                  &(currentAtomType->eam_dr),
482 +                  currentAtomType->eam_rvals,
483 +                  currentAtomType->eam_rhovals,
484 +                  currentAtomType->eam_Frhovals,
485 +                  &(currentAtomType->eam_ident),
486 +                  &isError);
487 +      if( isError ){
488 +        sprintf( painCave.errMsg,
489 +                 "Error initializing the \"%s\" atom type in fortran EAM\n",
490 +                 currentAtomType->name );
491 +        painCave.isFatal = 1;
492 +        simError();
493 +      }
494 +    }
495 +    currentAtomType = currentAtomType->next;
496 +  }
497 +
498 +
499 +
500   #ifdef IS_MPI
501    sprintf( checkPointMsg,
502 <           "LJ_FF atom structures successfully sent to fortran\n" );
502 >           "EAM_FF atom structures successfully sent to fortran\n" );
503    MPIcheckPoint();
504   #endif // is_mpi
505  
# Line 416 | Line 527 | void EAM_FF::initializeAtoms( int nAtoms, Atom** the_a
527      }
528      
529      the_atoms[i]->setMass( currentAtomType->mass );
419 –    the_atoms[i]->setEpslon( currentAtomType->epslon );
420 –    the_atoms[i]->setSigma( currentAtomType->sigma );
530      the_atoms[i]->setIdent( currentAtomType->ident );
531 <    the_atoms[i]->setLJ();
531 >    the_atoms[i]->setEAM();
532  
424 –    if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
533    }
534   }
535  
# Line 514 | Line 622 | int EAM_NS::parseAtom( char *lineBuffer, int lineNum,
622  
623  
624  
625 < int EAM_NS::parseAtom( char *lineBuffer, int lineNum,  atomStruct &info ){
625 > int EAM_NS::parseAtom( char *lineBuffer, int lineNum,   atomStruct &info, char *eamPotFile ){
626  
627    char* the_token;
628    
# Line 539 | Line 647 | int EAM_NS::parseAtom( char *lineBuffer, int lineNum,
647        simError();
648      }
649          
650 <    info.epslon = atof( the_token );
651 <          
652 <    if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
653 <      sprintf( painCave.errMsg,
654 <               "Error parseing AtomTypes: line %d\n", lineNum );
650 >    strcpy( eamPotFile, the_token );
651 >    return 1;
652 >  }
653 >  else return 0;
654 > }
655 >
656 > int EAM_NS::parseEAM(atomStruct &info, char *eamPotFile,
657 >                     double **eam_rvals,
658 >                     double **eam_rhovals,
659 >                     double **eam_Frhovals){
660 >  
661 >  char* ffPath_env = "FORCE_PARAM_PATH";
662 >  char* ffPath;
663 >  char* the_token;
664 >  FILE *eamFile;
665 >  char temp[200];
666 >  int linenumber;
667 >  int nReadLines;
668 >
669 >  int i,j;
670 >
671 >  linenumber = 0;
672 >
673 >  // Open eam file
674 >  eamFile = fopen( eamPotFile, "r" );
675 >  
676 >  
677 >  if( frcFile == NULL ){
678 >    
679 >      // next see if the force path enviorment variable is set
680 >    
681 >    ffPath = getenv( ffPath_env );
682 >    if( ffPath == NULL ) {
683 >      STR_DEFINE(ffPath, FRC_PATH );
684 >    }
685 >    
686 >    
687 >    strcpy( temp, ffPath );
688 >    strcat( temp, "/" );
689 >    strcat( temp, eamPotFile );
690 >    strcpy( eamPotFile, temp );
691 >    
692 >    eamFile = fopen( eamPotFile, "r" );
693 >
694 >    
695 >    
696 >    if( frcFile == NULL ){
697 >      
698 >      sprintf( painCave.errMsg,
699 >               "Error opening the EAM force parameter file: %s\n"
700 >               "Have you tried setting the FORCE_PARAM_PATH environment "
701 >               "vairable?\n",
702 >               eamPotFile );
703        painCave.isFatal = 1;
704        simError();
705      }
706 <        
707 <    info.sigma = atof( the_token );
706 >  }
707 >
708 >  // First line is a comment line, read and toss it....
709 >  eof_test = fgets(read_buffer, sizeof(read_buffer),eamFile);
710 >  linenumber++;
711 >  if(eof_test == NULL){
712 >    sprintf( painCave.errMsg,
713 >             "error in reading commment in %s\n", eamPotFile);
714 >    painCave.isFatal = 1;
715 >    simError();
716 >  }
717 >
718 >
719 >
720 >  // The Second line contains atomic number, atomic mass and a lattice constant
721 >  eof_test = fgets(read_buffer, sizeof(read_buffer),eamFile);
722 >  linenumber++;
723 >  if(eof_test == NULL){
724 >    sprintf( painCave.errMsg,
725 >             "error in reading Identifier line in %s\n", eamPotFile);
726 >    painCave.isFatal = 1;
727 >    simError();
728 >  }
729 >
730 >
731 >
732      
733 <    return 1;
733 >  if ( (the_token = strtok( read_buffer, " \n\t,;")) == NULL){
734 >    sprintf( painCave.errMsg,
735 >             "Error parseing EAM ident  line in %s\n", eamPotFile );
736 >    painCave.isFatal = 1;
737 >    simError();
738    }
739 <  else return 0;
739 >  
740 >  info.eam_ident = atoi( the_token );
741 >
742 >  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
743 >    sprintf( painCave.errMsg,
744 >             "Error parseing EAM mass in %s\n", eamPotFile );
745 >    painCave.isFatal = 1;
746 >    simError();
747 >  }
748 >  info.mass = atof( the_token);
749 >
750 >  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
751 >    sprintf( painCave.errMsg,
752 >             "Error parseing EAM Lattice Constant %s\n", eamPotFile );
753 >    painCave.isFatal = 1;
754 >    simError();
755 >  }
756 >  info.lattice_constant = atof( the_token);
757 >
758 >  // Next line is nrho, drho, nr, dr and rcut
759 >  eof_test = fgets(read_buffer, sizeof(read_buffer),eamFile)
760 >  if(eof_test == NULL){
761 >    sprintf( painCave.errMsg,
762 >             "error in reading number of points line in %s\n", eamPotFile);
763 >    painCave.isFatal = 1;
764 >    simError();
765 >  }
766 >
767 >  if ( (the_token = strtok( read_buffer, " \n\t,;")) == NULL){
768 >    sprintf( painCave.errMsg,
769 >             "Error parseing EAM nrho: line in %s\n", eamPotFile );
770 >    painCave.isFatal = 1;
771 >    simError();
772 >  }
773 >  
774 >  info.eam_nrho = atoi( the_token );
775 >  
776 >  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
777 >    sprintf( painCave.errMsg,
778 >             "Error parseing EAM drho in %s\n", eamPotFile );
779 >    painCave.isFatal = 1;
780 >    simError();
781 >  }
782 >  info.eam_drho = atof( the_token);
783 >
784 >  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
785 >    sprintf( painCave.errMsg,
786 >             "Error parseing EAM # r in %s\n", eamPotFile );
787 >    painCave.isFatal = 1;
788 >    simError();
789 >  }
790 >  info.eam_nr = atoi( the_token);
791 >  
792 >  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
793 >    sprintf( painCave.errMsg,
794 >             "Error parseing EAM dr in %s\n", eamPotFile );
795 >    painCave.isFatal = 1;
796 >    simError();
797 >  }
798 >  info.eam_dr = atof( the_token);
799 >
800 >  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
801 >    sprintf( painCave.errMsg,
802 >             "Error parseing EAM rcut in %s\n", eamPotFile );
803 >    painCave.isFatal = 1;
804 >    simError();
805 >  }
806 >  info.eam_rcut = atof( the_token);
807 >
808 >
809 >  // Ok now we have to allocate point arrays and read in number of points
810 >  // Index the arrays for fortran, starting at 1
811 >  *eam_Frhovals = new double[info.nrho];
812 >  *eam_rvals    = new double[info.nr];
813 >  *eam_rhovals  = new double[info.nr];
814 >
815 >  // Parse F of rho vals.
816 >
817 >  // Assume for now that we have a complete number of lines
818 >  nReadLines = int(info.nrho/5);
819 >
820 >  for (i=0;i<nReadLines;i++){
821 >    j = i*5;
822 >    
823 >    // Read next line
824 >    eof_test = fgets(read_buffer, sizeof(read_buffer),eamFile);
825 >    linenumber++;
826 >    if(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( read_buffer, " \n\t,;")) == NULL){
837 >      sprintf( painCave.errMsg,
838 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
839 >      painCave.isFatal = 1;
840 >      simError();
841 >    }
842 >    
843 >    *eam_Frhovals[j+0] = atof( the_token );
844 >    
845 >    // Value 2
846 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
847 >      sprintf( painCave.errMsg,
848 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
849 >      painCave.isFatal = 1;
850 >      simError();
851 >    }
852 >  
853 >    *eam_Frhovals[j+1] = atof( the_token );
854 >    
855 >    // Value 3
856 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
857 >      sprintf( painCave.errMsg,
858 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
859 >      painCave.isFatal = 1;
860 >      simError();
861 >    }
862 >    
863 >    *eam_Frhovals[j+2] = atof( the_token );
864 >    
865 >    // Value 4
866 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
867 >      sprintf( painCave.errMsg,
868 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
869 >      painCave.isFatal = 1;
870 >      simError();
871 >    }
872 >    
873 >    *eam_Frhovals[j+3] = atof( the_token );
874 >
875 >    // Value 5
876 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
877 >      sprintf( painCave.errMsg,
878 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
879 >      painCave.isFatal = 1;
880 >      simError();
881 >    }
882 >    
883 >    *eam_Frhovals[j+4] = atof( the_token );
884 >    
885 >  }
886 >  // Parse Z of r vals
887 >  
888 >  // Assume for now that we have a complete number of lines
889 >  nReadLines = int(info.nr/5);
890 >
891 >  for (i=0;i<nReadLines;i++){
892 >    j = i*5;
893 >
894 >    // Read next line
895 >    eof_test = fgets(read_buffer, sizeof(read_buffer),eamFile);
896 >    linenumber++;
897 >    if(eof_test == NULL){
898 >      sprintf( painCave.errMsg,
899 >               "error in reading EAM file %s at line %d\n",
900 >               eamPotFile,linenumber);
901 >      painCave.isFatal = 1;
902 >      simError();
903 >    }
904 >    
905 >    // Parse 5 values on each line into array
906 >    // Value 1
907 >    if ( (the_token = strtok( read_buffer, " \n\t,;")) == NULL){
908 >      sprintf( painCave.errMsg,
909 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
910 >      painCave.isFatal = 1;
911 >      simError();
912 >    }
913 >    
914 >    *eam_rvals[j+0] = atof( the_token );
915 >
916 >    // Value 2
917 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
918 >      sprintf( painCave.errMsg,
919 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
920 >      painCave.isFatal = 1;
921 >      simError();
922 >    }
923 >  
924 >    *eam_rvals[j+1] = atof( the_token );
925 >
926 >    // Value 3
927 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
928 >      sprintf( painCave.errMsg,
929 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
930 >      painCave.isFatal = 1;
931 >      simError();
932 >    }
933 >  
934 >    *eam_rvals[j+2] = atof( the_token );
935 >
936 >    // Value 4
937 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
938 >      sprintf( painCave.errMsg,
939 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
940 >      painCave.isFatal = 1;
941 >      simError();
942 >    }
943 >  
944 >    *eam_rvals[j+3] = atof( the_token );
945 >
946 >    // Value 5
947 >    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
948 >      sprintf( painCave.errMsg,
949 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
950 >      painCave.isFatal = 1;
951 >      simError();
952 >    }
953 >  
954 >    *eam_rvals[j+4] = atof( the_token );
955 >
956 >  }
957 >  // Parse rho of r vals
958 >
959 >  // Assume for now that we have a complete number of lines
960 >
961 >  for (i=0;i<nReadLines;i++){
962 >    j = i*5;
963 >
964 >    // Read next line
965 >    eof_test = fgets(read_buffer, sizeof(read_buffer),eamFile);
966 >    linenumber++;
967 >    if(eof_test == NULL){
968 >      sprintf( painCave.errMsg,
969 >               "error in reading EAM file %s at line %d\n",
970 >               eamPotFile,linenumber);
971 >      painCave.isFatal = 1;
972 >      simError();
973 >    }
974 >  
975 >    // Parse 5 values on each line into array
976 >    // Value 1
977 >    if ( (the_token = strtok( read_buffer, " \n\t,;")) == NULL){
978 >      sprintf( painCave.errMsg,
979 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
980 >      painCave.isFatal = 1;
981 >      simError();
982 >    }
983 >  
984 >    *eam_rhovals[j+0] = atof( the_token );
985 >
986 >    // Value 2
987 >    if ( (the_token = strtok( read_buffer, " \n\t,;")) == NULL){
988 >      sprintf( painCave.errMsg,
989 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
990 >      painCave.isFatal = 1;
991 >      simError();
992 >    }
993 >  
994 >    *eam_rhovals[j+1] = atof( the_token );
995 >
996 >    // Value 3
997 >    if ( (the_token = strtok( read_buffer, " \n\t,;")) == NULL){
998 >      sprintf( painCave.errMsg,
999 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
1000 >      painCave.isFatal = 1;
1001 >      simError();
1002 >    }
1003 >  
1004 >    *eam_rhovals[j+2] = atof( the_token );
1005 >
1006 >    // Value 4
1007 >    if ( (the_token = strtok( read_buffer, " \n\t,;")) == NULL){
1008 >      sprintf( painCave.errMsg,
1009 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
1010 >      painCave.isFatal = 1;
1011 >      simError();
1012 >    }
1013 >  
1014 >    *eam_rhovals[j+3] = atof( the_token );
1015 >
1016 >    // Value 5
1017 >    if ( (the_token = strtok( read_buffer, " \n\t,;")) == NULL){
1018 >      sprintf( painCave.errMsg,
1019 >               "Error parseing EAM nrho: line in %s\n", eamPotFile );
1020 >      painCave.isFatal = 1;
1021 >      simError();
1022 >    }
1023 >  
1024 >    *eam_rhovals[j+4] = atof( the_token );
1025 >
1026 >  }
1027 >
1028 >  fclose(eamFile);
1029 >  return 0;
1030   }

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