StaticModelLoader::StaticModelLoader(char* path, char *mpath)
{
	m_infile.open(mpath);
	if (!m_infile) {
		cout << "Cannot open material file!\n";
		throw 1;
	}

	infile.open(path); //"res/car.obj"
	if (!infile) {
		cout << "Cannot open file!\n";
		throw 1;
	}

	mload();

	vload();

	infile.clear();
	infile.seekg(0, ios::beg);

	fload();

	infile.close();
	m_infile.close();

	//debug models
	std::cout << " verticies " << v_num
		<< " textures " << vt_num
		<< " normals " << vn_num
		<< " polygones " << f_num
		<< std::endl;
}
Пример #2
0
unint load_shader(const char *fname, GLenum type)
{
	int size=0; void *data=NULL;
	if(fload(fname,&size,&data))
	{
		const unint s=glCreateShader(type);
		int val=0;

		glShaderSource(s,1,(const char**)&data,&size);
		free(data);

		glCompileShader(s);
		glGetShaderiv(s,GL_INFO_LOG_LENGTH,&val);
		if(val>1)
		{
			char *log=(char*)malloc(val);
			glGetShaderInfoLog(s,val,NULL,log);
			info("Shader \"%s\" info:\n%s\n",fname,log);
			free((void*)log);
		}

		glGetShaderiv(s,GL_COMPILE_STATUS,&val);
		if(!val) info("Shader \"%s\" compiling failed\n",fname);

		return s;
	}
	else return 0;
}
Пример #3
0
static int
i82563reset(Ctlr* ctlr)
{
	int i, r;

	detach(ctlr);

	if(ctlr->type == i82566 || ctlr->type == i82567)
		r = fload(ctlr);
	else
		r = eeload(ctlr);
	if (r != 0 && r != 0xBABA){
		print("%s: bad EEPROM checksum - 0x%4.4ux\n",
			tname[ctlr->type], r);
		return -1;
	}

	for(i = Ea; i < Eaddrlen/2; i++){
		ctlr->ra[2*i]   = ctlr->eeprom[i];
		ctlr->ra[2*i+1] = ctlr->eeprom[i]>>8;
	}
	r = (csr32r(ctlr, Status) & Lanid) >> 2;
	ctlr->ra[5] += r;		/* ea ctlr[1] = ea ctlr[0]+1 */

	r = ctlr->ra[3]<<24 | ctlr->ra[2]<<16 | ctlr->ra[1]<<8 | ctlr->ra[0];
	csr32w(ctlr, Ral, r);
	r = 0x80000000 | ctlr->ra[5]<<8 | ctlr->ra[4];
	csr32w(ctlr, Rah, r);
	for(i = 1; i < 16; i++){
		csr32w(ctlr, Ral+i*8, 0);
		csr32w(ctlr, Rah+i*8, 0);
	}

	for(i = 0; i < 128; i++)
		csr32w(ctlr, Mta+i*4, 0);

	csr32w(ctlr, Fcal, 0x00C28001);
	csr32w(ctlr, Fcah, 0x00000100);
	csr32w(ctlr, Fct,  0x00008808);
	csr32w(ctlr, Fcttv, 0x00000100);

	csr32w(ctlr, Fcrtl, ctlr->fcrtl);
	csr32w(ctlr, Fcrth, ctlr->fcrth);

	ilock(&ctlr->imlock);
	csr32w(ctlr, Imc, ~0);
	ctlr->im = 0;		/* was = Lsc, which hangs some controllers */
	csr32w(ctlr, Ims, ctlr->im);
	iunlock(&ctlr->imlock);

	return 0;
}
Пример #4
0
byte load_tex(unint t, const char *fname, unshort w, unshort h, GLenum fmt, tex_filter tf)
{
	int size=0; void *data=NULL;
	if(fload(fname,&size,&data))
	{
		use_tex(t);
		glTexImage2D(GL_TEXTURE_2D,0,fmt,w,h,0,fmt,GL_UNSIGNED_BYTE,data);
		free(data);
		filter_tex(tf);

		return 1;
	}
	else return 0;
}
Пример #5
0
void BytecodeAssembler::load(BasicType bt, u4 index) {
  switch (bt) {
    case T_BOOLEAN:
    case T_CHAR:
    case T_BYTE:
    case T_SHORT:
    case T_INT:     iload(index); break;
    case T_FLOAT:   fload(index); break;
    case T_DOUBLE:  dload(index); break;
    case T_LONG:    lload(index); break;
    case T_OBJECT:
    case T_ARRAY:   aload(index); break;
    default:
      ShouldNotReachHere();
  }
}
Пример #6
0
void
rl_test(void)
{
  uchar *in, *out;
  size_t inlen;
  size_t outlen;

  while (1) {
    char *line = readline(">> ");

    in = (uchar*)fload(line, NULL, &inlen);
    printf("inlen: %zd\n", inlen);

    out = malloc(inlen);
    outlen = rl_encode1(out, in, inlen);
    printf("outlen: %zd\n", outlen);

    free(line);
    free(in);
    free(out);
  }
}
Пример #7
0
int main(int argc, char * argv[])
{

  //-o-o-o-o-o-o-o-o Declaring Variables o-o-o-o-o-o-o-o-o-//
  
  FILE * pmass , * phess , * pEqCrd , * poutDXDR , * poutFreq ; //, *pmo2ao;

  char massFileName[ 100 ] , hessFileName[ 100 ] , EqCrdFileName[ 100 ] ;
  
  char outDXDRFileName[ 100 ] , outFreqFileName[ 100 ] ;

  char massunit[ 100 ] , hessunit[ 100 ] , crdunit[ 100 ] ;
  
  int sdouble = sizeof(double);

  int natom , ncart , nmode ;
  
  int iatom , icart , imode ;

  int natomselect , natomprovide , ncartselect , ncartprovide ;

  int len_hess_cart, len_tri_hess_cart;

  int j,k,m;

  int itmp; double dtmp;

  char * keyword;

  int debuggingMode = NO ;

  //char gessname[ 100 ] ;

  double * hess_cart , * hess_cart_select ;
  
  double * freq , * vib_freq , * dxdr , * vib_dxdr ;
  
  double hessconvert , crdconvert , massconvert ;

  double * mass_provide , * mass; 

  char ** pcmd ; pcmd = argv ;

  int icmd = 1 ;
  
  
  int iline , iload ;
  
  int irow , icol ;
  
  int blank_signal , groinfo ;

  char buffer[ MAXCHARINLINE ] ;
  
  char cache[ MAXCHARINLINE ] ;
  
  char tmpString[ MAXCHARINLINE ] ;

  


  
  // ---> For debugging output 

  FILE * debug;



  //-o-o-o-o-o-o-o-o Recording cmd-line and time stamp o-o-o-o-o-o-o-o-o-//
  
  time_t current_time;

  time( &current_time );

  char now[ 300 ] ;

  strcpy( now , ctime( &current_time ) );

  int lennow = strlen( now ) ;

  *( now + lennow - 1 ) = ' ';

    
    
    printf("\n**********************************************************************\n");
      printf("* G_GMXFREQ_D : Stand-Alone Utility to Calculate Normal Modes        *\n");
      printf("* From Hessian File and Mass File.                                   *\n");
      printf("*                                                                    *\n");
      printf("*  ");
  for( icmd = 0 ; icmd < argc ; icmd ++ )
  {
    printf("%s " , *( pcmd + icmd ) );
  }
  printf("\n");
      printf("*                                                                    *\n");
      printf("*                                                                    *\n");
      printf("* Current Time : %s                           *\n" , now );
      printf("*                                                                    *\n");
      printf("*                                                                    *\n");
      printf("**********************************************************************\n");

 


  //-o-o-o-o-o-o-o Read input command-line arguments and input files while deciding some parameters ...o-o-o-o-o-o-o-o-o-o-//

  // -------> Parsing the Command Line Arguments ... 
  
  pcmd = argv ; 
  
  
  
  //int exn = 10 ; int exr  = 16 ; int exR = 18 ; int exH  = 22 ; int exM = 28 ; int exL = 30 ; 

  int exc = 20 ; 
  
  int exs = 18 ; int exm = 88 ;
  
  int exH = 70 ; 
  
  int exo = 22 , exw = 26 ;

  char * flag ;
  
  
  int internalOrNot = NO ;
  
  
  icmd = 1 ;
  
  printf("\n%d command-line arguments provided ...\n" , argc );
  
  if( argc == 1 )
  {
    printf("\n\nNo command-line arguments provided ... Mission aborting ...\n\n");
    
    printf("\nPlease refer to the usage by typing ' %s -h '\n\n" , * argv );
    
    exit(1); 
  
  
  }

  while( icmd < argc )
  {  
    pcmd ++ ; 

    flag = * pcmd ;

    printf("\nNo.%d argument , Currently @ flag = %s ...\n\n" , icmd , flag );

    if( ( * flag == '-' ) && ( strlen( flag ) == 2 ) )
    {
      switch ( *( flag + 1 ) )
      {
	      
	      case 'c' : strcpy( tmpString , *( ++ pcmd ) );
	      
	                 strcpy( buffer , *( ++ pcmd ) );
	                 
	                 if( strcmp( tmpString , "none" ) == 0 )
	                 {
	                   strcpy( EqCrdFileName , "dirtroad.anthem" ) ;
	                   
	                   internalOrNot = NO ;
	                   
	                   printf("\nCommand-line argument indicates : NO INPUT Eq. Coordinate ... Hence NO Internal Coordinate Transformation \n" ); 
	                 
	                 }
	                 else
	                 {
	                   strcpy( EqCrdFileName , tmpString ) ;
	                   
	                   strcpy( crdunit , buffer ) ;
	                   
	                   if( * crdunit == '-' )
	                   {
	                     printf("\nHey, you did not specify the unit of you Coordinate file ... !\n");
	                     
	                     exit( 11 ) ;
	                   
	                   }
	                 
	                   internalOrNot = YES ;
	                   
	                   printf("\nCommand-line argument indicates : Input Eq. Coordinate File name : %s . Format is %s ...\n" , EqCrdFileName , crdunit ); 
	                 
	                 
	                 }
	                 	                 	           
	                 exc = 21 ;	           
	                 	                 
	                 icmd = icmd + 3 ;
	                 
	                 break ;
	               
	      

	      case 'H' : strcpy( hessFileName , *( ++ pcmd ) );
	      
	                 strcpy( hessunit , *( ++ pcmd ) );
	      
	                 printf("\nCommand-line argument indicates : Input Hessian File name : %s . Unit is %s ...\n" , hessFileName , hessunit ); 
	                 
	                 if( * hessunit == '-' )
	                 {
	                   printf("\nHey, you did not specify the unit of you Hessian file ... !\n");
	                   
	                   exit( 11 );
	                 }
	                 	           
	                 exH = 71 ;	           
	                 	                 
	                 icmd = icmd + 3 ;
	                 
	                 break ;


	      case 'm' : strcpy( massFileName , *( ++ pcmd ) );
	      
	                 strcpy( massunit , *( ++ pcmd ) );
	      
	                 printf("\nCommand-line argument indicates : Input Mass File name : %s . Unit is %s ...\n" , massFileName , massunit ); 
	                 
	                 if( * crdunit == '-' )
	                 {
	                   printf("\nHey, you did not specify the unit of you Coordinate file ... !\n");
	                   
	                   exit( 11 );
	                 }
	                 	           
	                 exm = 89 ;	           
	                 	                 
	                 icmd = icmd + 3 ;
	                 
	                 break ;
	                 
               

	      case 's' : strcpy( tmpString , *( ++ pcmd ) ) ;
	      
	                 if( strcmp( tmpString , "all" ) == 0 || strcmp( tmpString , "All" ) == 0 )
	                 {
	                   exs = 20 ;
	                   
	                   printf("\nCommand-line argument indicates : All atoms will be chosen as solute ...\n" );
	                 }
	                 else
	                 {
	                   printf("\nReceived information : %s ...\n" , tmpString ) ;
	                   
	                   natomselect = atoi( tmpString ); 
	                  
	                   exs = 19 ;
	                   
	                   printf("\nCommand-line argument indicates : First %d atoms will be chosen as solute ...\n" , natomselect );
	                 }
	                 
	                 
	                 icmd = icmd + 2 ; 
	                 
	                 break ;
	      

	      case 'o' : strcpy( outDXDRFileName , *( ++ pcmd ) ); 
	      
	                 printf("\nCommand-line argument indicates : Output Normal Mode file name : %s ...\n" , outDXDRFileName ); 
	                 
	                 exo = 23 ;
	                 
	                 icmd = icmd + 2 ; 
	                 
	                 break ; 
	                 
	                 
	      case 'w' : strcpy( outFreqFileName , *( ++ pcmd ) ); 
	      
	                 printf("\nCommand-line argument indicates : Output frequency file name : %s ...\n" , outFreqFileName ); 
	                 
	                 exw = 27 ;
	                 
	                 icmd = icmd + 2 ; 
	                 
	                 break ; 


          case 'g' : strcpy( cache , *( ++ pcmd ) ) ;

                     printf("\nCommand-line argument indicates : Debugging Mode Invoking : %s ...\n" , cache );

                     if( strcmp( cache , "YES" ) == 0 || strcmp( cache , "Yes" ) == 0 || strcmp( cache , "yes" ) == 0 || strcmp( cache , "Y" ) == 0 || strcmp( cache , "y" ) == 0 )
                     {
                       debuggingMode = YES ;
                     }
                     else if( strcmp( cache , "NO" ) == 0 || strcmp( cache , "No" ) == 0 || strcmp( cache , "no" ) == 0 || strcmp( cache , "N" ) == 0 || strcmp( cache , "n" ) == 0 )
                     {
                       debuggingMode = NO ;
                     }
                     else
                     {
                       printf("\nInvalid choice of debugging mode ... Mission Aborted ...\n\n") ;

                       exit( 21 ) ;
                     }

                     icmd = icmd + 2 ;

                     break ;




		                 
	      case 'h' : printf("\nUsage:  % 15s [ -c 'input Equilibrium Geometry' ( gro / gmxcrd / g09crd )] [ -H 'Hessian file name' ' unit : au or gmx' ] [ -s # of atoms chosen as the solute ]" , * argv) ;
	                 printf("\n                        [ -m Mass file name & unit ( au or amu ) ] [ -w output frequency file name ] [ -o output dxdr file name ]\n\n");
	                 //printf("\n           [ -c 'input EqMD gro file of solvent' ][ -p P Group Name ][ -q Q Group Name ][ -N atom number of L-Shape reference atom ]");
	                 //printf("\n           [ -w whether to perform van der Waals contacting check ( YES / Yes / yes ) or ( NO / No / no ) or floating point number to indicate scaling factor ]");
	                 //printf("\n           [ -s # of atoms in solute molecule ] [ -t distance threshold to accept one alignment , unit = Angstrom ]\n\n" ); 
	                 
	                 //printf("\nNote : 1) For \"-w\" option, YES/Yes/yes will cause the vdw-check to perform with default scaling 1.00 while NO/No/no will shut down the vdw-check.\n");
	                 //printf("\n          Specifying a floating number will also cause the vdw-check to perform but the floating number will be the user-defined scaling factor (vdwFactor).\n");

	                 //printf("\n       2) For \"-t\" option, YES/Yes/yes will cause the universal-distance-check to perform with default threshold 1.20Å while NO/No/no will shut down the unidist-check.\n");
	                 //printf("\n          Specifying a floating number will also cause the unidist-check to perform but the floating number will be the user-defined distance threshold (vdwFactor).\n");

	                 printf("\nNote : 1) For \"-s\" option, [ -s all ] or [ -s All ] indicates all atoms chosen as solute;\n");
	                 printf("\n          Default for -s is all atoms when nresidue = 1  or natom in 1st residue when nresidue != 1 \n");
	                 
	                 printf("\n       2) For \"-c\" option, [ -c none none ] will turn off the internal coordinate transformation and perform regular Cartesian coordinate normal mode analysis ... \n\n\n");


	                 icmd = icmd + 1 ; 
	                 
	                 exit( 1 ) ;
	                 
	                 break ;



	      default : printf("\n\nInvalid option ' %s ' ... Please refer to the usage by typing ' %s -h '\n\n" , flag , * argv ); 
	      
	                icmd = argc ; 
	                
	                exit(1);

      
      
      
      }
    
    }
    else
    {
        printf("\n\nInvalid option ' %s ' ... Please refer to the usage by typing ' %s -h '\n\n" , flag , * argv );

	    exit(1);
      
      
    }
    
 
  } 

 
  // -------> Default File Names
  

  if( internalOrNot == YES && exc == 20 )
  {
    strcpy( crdunit , "gro" ) ;
    
    strcpy( EqCrdFileName , "system.gro" ) ;
    
    printf("\nNo input .gro file provided, default \"system.gro\" in play ...\n") ;
  
  }

  
  int lenEqGROFileName = strlen( EqCrdFileName ) ;
  
  if( exo == 22 )
  {
    strncpy( outDXDRFileName , EqCrdFileName , lenEqGROFileName - 4 ) ;
    
    *( outDXDRFileName + lenEqGROFileName - 4 ) = '\0' ;
    
    strcat( outDXDRFileName , ".dxdr" ) ;
    
    printf("\nBy default , output DXDR file name will be [ %s ] ...\n\n" , outDXDRFileName ) ;
  
  }
  
  
  
  if( exw == 26 )
  {
    strncpy( outFreqFileName , EqCrdFileName , lenEqGROFileName - 4 ) ;
    
    *( outFreqFileName + lenEqGROFileName - 4 ) = '\0' ;
    
    strcat( outFreqFileName , ".freq" ) ;
    
    printf("\nBy default , output DXDR file name will be [ %s ] ...\n\n" , outFreqFileName ) ;
  
  }

  

  if( exH == 70 )
  {
    strncpy( hessFileName , EqCrdFileName , lenEqGROFileName - 4 ) ;
    
    *( hessFileName + lenEqGROFileName - 4 ) = '\0' ;
    
    strcat( hessFileName , ".gess" ) ;
    
    printf("\nBy default , searching for Hessian file with the name %s ...\n\n" , hessFileName ) ;
    
    strcpy( hessunit , "gmx" ) ;
  
  }
  

  if( exm == 88 )
  {
    strncpy( massFileName , EqCrdFileName , lenEqGROFileName - 4 ) ;
    
    *( massFileName + lenEqGROFileName - 4 ) = '\0' ;
    
    strcat( massFileName , ".mass" ) ;
    
    printf("\nBy default , searching for Mass file with the name %s ...\n\n" , massFileName ) ;
    
    strcpy( massunit , "amu" ) ;
  
  }


 
  if( strcmp( hessunit , "au" ) == 0 )
  {
    printf("\nThe unit this Hessian file in is ATOMIC UNIT : Hartree/(Bohr^2) ... \n");
  
    hessconvert = 1.0000 ;
  }
  else if( strcmp( hessunit , "gmx" ) == 0 )
  {
    printf("\nThe unit this Hessian file in is GMX-Unit : kJ/mol/(nm^2) ... \n");
  
    hessconvert = HESSAU2GMX ;
  }
  else
  {
    printf("\nWhat did you say about the unit of you frequency again ??? \n");
  
    exit( 107 );
  }




  printf("\n===> Done Defining Default Fila Names <===\n\n\n") ;
  
  
  
  // -------> Confirming File Access ... 

  
  if( ( pmass = fopen( massFileName ,"r" ) ) == NULL )
  {  
    printf("\nUser defined mass-file [ %s ] does not exist...\n" , massFileName );

    exit( 63 );
  }
  
  
  
  if( ( pEqCrd = fopen( EqCrdFileName ,"r" ) ) == NULL && internalOrNot == YES )
  {  
    printf("\nUser defined Equilibrium Coordinate File [ %s ] does not exist...\n" , EqCrdFileName );

    exit( 63 );
  }
  


  if( ( phess = fopen( hessFileName ,"r" ) ) == NULL )
  {  
    printf("\nUser defined Hessian-file [ %s ] does not exist...\n" , hessFileName );

    exit( 63 );
  }
  


  printf("\n===> Done Confirming File Access <===\n\n\n") ;

  
  
  //-o-o-o-o-o-o-o Loading Eq. Coordinate , Hessian & Mass ...o-o-o-o-o-o-o-o-o-o-//
  
  //-----> Pre-Loading Equilibrium Geometry ...
  
  char grotitlestring[MAXLINE];
  
  iline = 3 ;
  
  iload = 0 ;
  
  int natomgroline , natomgrotitle ;
  
  int exVelocity = NO ;
  

  if( internalOrNot == YES && ( strcmp( crdunit , "gro" ) ) == 0 )
  {
    rewind( pEqCrd );
    
    //printf("\nCurrent character is %c ... \n" , fgetc( pEqGRO ) );
    
    fskip( pEqCrd , 1 );

    fscanf( pEqCrd , "%d" , &natomgrotitle );
    
    fskip( pEqCrd , 1 );
    
    printf("\n Second line of .gro file says it is describing %d atoms ... \n\n" , natomgrotitle );
    
    
    while( ( groinfo = freadline( buffer , MAXCHARINLINE , pEqCrd , ';' ) ) != 0 )
    {
      itmp = inLineWC( buffer ) ;
      
      break ;
    }
        
    if( itmp == 6 )
    {
      exVelocity = NO ;
      
      printf("\nI see there is no velocity information in .gro file ...\n\n") ;
      
    }
    else if( itmp == 9 )
    {
      exVelocity = YES ;
      
      printf("\nI see velocity information is also included in .gro file ...\n\n") ;
    
    }
    else
    {
      printf("\nPlease check the format of you .gro file ... There are %d words in one line of your molecular specification ... \n" , itmp ) ;
      
      exit( 456 );
    }
    
  
    printf("\nNow let's pre-load the .gro file ans see how many atoms it is describing ... \n");
    
    
    
    natomgroline = preLoadGRO( pEqCrd ) ;
  
    printf("\nIt can be seen that this .gro file is describing %d atoms ...\n" , natomgroline );
  
    
    
    if( natomgrotitle > natomgroline )
    {
      printf("\nYour .gro file is self-contradictory ... While the second line of your .gro file says there will be %d atoms, there are actually only %d atoms being described ... \n" ,  natomgrotitle , natomgroline );
  
      printf("\nWe will take all the atoms we can to procede ... \n");
    
      natom = natomgroline ;
    }
    else if( natomgrotitle == natomgroline )
    {
      printf("\nOkay ... Your .gro file is fine ... NAtom will be %d ... \n" , natomgrotitle );
    
      natom = natomgrotitle ;
    }
    else if( natomgrotitle < natomgroline )
    {
      printf("\nThe second line of your .gro file indicates there are %d atoms in this file but there are more atoms ( %d atoms ) being described insided ... We will take the first %d atoms ... \n" , natomgrotitle , natomgroline , natomgrotitle );
  
      natom = natomgrotitle ;
    }
    else
    {
      printf("\nSomething is wrong with checking the .gro file ... Please take a look at it ... \n");
    
      exit( 81 );
    }
  
    ncart = 3 * natom ;

    
    itmp = 0 ; 
   
    if( exs == 18 )
    {
      natomselect = natom ;
    }
    else if( exs == 19 && natomselect > natom ) // Will be dead ... 
    {
      printf("\nThere are only %d atoms in this system ... you cannot select more than that ... \n" , natom );
      
      if( natomgrotitle > natomgroline && natomselect <= natomgrotitle )
      {
        printf("\nAlthough ... the second line of your initial .gro file did indicate there were supposed to be %d atoms in system ... So go back and make sure what you are trying to do ... \n" , natomgrotitle );
      }
      else if( natomgrotitle < natomgroline && natomselect <= natomgroline )
      {
        printf("\nAlthough ... your initial .gro file did describe %d atoms in system ... So go back and make sure what you are trying to do ... \n" , natomgroline );
      }
      
      exit( 78 );
    }
    else if( exs == 19 && natomselect <= natom )
    {
      printf("\nYou have selected %d atoms as solute ... There are %d atoms en toto in this system ... \n" , natomselect , natom );    

    }
    else if( exs == 20 )
    {
      natomselect = natom ;
    }
    else
    {
      printf("\nSomething is wrong with the atom selection process ... NAtom = %d , NAtomSelect = %d ... \n" , natom , natomselect );
      
      exit( 78 );
    }
  
    ncartselect = 3 * natomselect ;
  
  
  
  }
  else if( internalOrNot == YES && ( ( strcmp( crdunit , "gmxcrd" ) ) == 0 || ( strcmp( crdunit , "g09crd" ) ) == 0 ) )
  {
    rewind( pEqCrd );
    
    itmp = flength( pEqCrd ) ;
    
    natom = itmp / 3 ;
    
    ncart = itmp ;
  
    if( exs == 18 )
    {
      natomselect = natom ;
    }
    else if( exs == 19 && natomselect > natom ) // Will be dead ... 
    {
      printf("\nThere are only %d atoms in this system ... you cannot select more than that ... \n" , natom );
            
      exit( 78 );
    }
    else if( exs == 19 && natomselect <= natom )
    {
      printf("\nYou have selected %d atoms as solute ... There are %d atoms en toto in this system ... \n" , natomselect , natom );    

    }
    else if( exs == 20 )
    {
      natomselect = natom ;
    }
    else
    {
      printf("\nSomething is wrong with the atom selection process ... NAtom = %d , NAtomSelect = %d ... \n" , natom , natomselect );
      
      exit( 78 );
    }
  
    ncartselect = 3 * natomselect ;
    
  }
  
  
  //-----> Pre-Loading Mass ...

  itmp = flength( pmass ) ;

   
  rewind( pmass ) ;

  
  if( internalOrNot == NO )
  {
    natom = itmp ;
    
    ncart = 3 * natom ;
    
    if( exs == 18 )
    {
      natomselect = natom ;
      
      printf("\nBy default, all available atoms will be chosen as solute ...\n\n") ;
    }
    else if( exs == 20 )
    {
      natomselect = natom ;
      
      printf("\nPer user's request, all available atoms will be chosen as solute ...\n\n") ;

    }
    else if( exs == 19 )
    {
      if( natomselect == natom )
      {
        printf("\nOKay ... I see you provided the mass for all the atom in this system ... \n"); 
      }
      else if( natomselect > natom ) // will be dead
      {
        printf("\nERROR : There are only %d atoms according to mass file, I cannot select that many atoms as solute ...\n\n" , natomselect ) ;
        
        exit( 89 ) ;
      }
      else if( natomselect < natom )
      {
        printf("\nOKay ... you provided %d floating-point numbers for mass so the total NAtom in system is %d while %d atoms are selected ...\n" , itmp , natom , natomselect );

        printf("\nSo ... I will assume the first %d numbers in your mass file correspond to the selected atoms ...\n" , natomselect );
      }
      else
      {
        printf("\nSomething is wrong with the mass file ... There are %d atomic mass in the file while the total NAtom in this system is %d and %d atoms are selected ... \n" , itmp , natom , natomselect );

        exit( 81 );

      }
    
    }
    
    ncartselect = natomselect * 3 ;
  
  
  }
  else if( internalOrNot == YES )
  {
    if( itmp == natomselect )
    {
      printf("\nOKay ... I see you provided the mass info for just the selected atoms ... \n");
    }
    else if( itmp == natom )
    {
      printf("\nOKay ... I see you provided the mass for all the atom in this system ... \n"); 
    }
    else if( itmp > natom )
    {
      printf("\nOKay ... you provided %d numbers for mass. The total NAtom in system is %d while %d atoms are selected ...\n" , itmp , natom , natomselect );

      printf("\nSo ... I will assume the first %d numbers in your mass file correspond to the selected atoms ...\n" , natomselect );
    }
    else
    {
      printf("\nSomething is wrong with the mass file ... There are %d atomic mass in the file while the total NAtom in this system is %d and %d atoms are selected ... \n" , itmp , natom , natomselect );

      exit( 81 );

    }
  
  }
  
  // ---> Loading Equilibrium Geometry ...
  
  GRO EqAtomList[ natomselect ] ; 
  
  double * EqCrd = calloc( ncartselect , sizeof( double ) ) ;
  
  dzeros( ncartselect , 1 , EqCrd ) ;
  
  double boxvector[ 3 ]; dzeros( 3 , 1 , boxvector ) ;
  
  char tmp_char ;
  
  if( internalOrNot == YES && ( strcmp( crdunit , "gro" ) ) == 0 ) // We want every coordinate to be in BOHR unit
  {
    crdconvert = NM2BOHR ;
    
    rewind( pEqCrd );
      
    fskip( pEqCrd , 1 );

    fskip( pEqCrd , 1 );
      
    printf("\nNow let's read the actual .gro file  ... \n");
    
    iload = 0 ; iline = 0 ;
    
    while( ( groinfo = freadline( buffer , MAXCHARINLINE , pEqCrd , ';' ) ) != 0 )
    { 
      //printf("\n//--------------> WORKING ON NO. %d LINE ... <-------------//\n" , iline );
      
      blank_signal = stellblank( buffer ) ;
      
      if( blank_signal == 0 )
      {
        //printf("\nNo.%d line is a blank line ... Moving on ...\n" , iline ) ;
        
        continue ;
      }
      else if( blank_signal == 1 )
      {  
        //printf("\nNo.%d line is NOT a blank line ... loading ...\n" , iline );
        
        if( ( tmp_char = getfirst( buffer ) ) == ';' )
        {
          //printf("\nThis is a comment line ... So nothing will be loaded ...\n");
          
          //fskip( pinputfile , 1 );
          
          continue ;
        }
        else
        {
          //printf("\nLine reads : %s ...\n" , buffer );
                
          sscanf( buffer , "%5d%5s" , &EqAtomList[ iload ].resnumber , EqAtomList[ iload ].resname );

          //printf( "%s\t" , EqAtomList[ iatom ].resname );

          //sscanf( pEqGRO , "%s" , EqAtomList[ iload ].atomname );
          
          strpickword( buffer , 2 , cache ) ;
          
          strcpy( EqAtomList[ iload ].atomname , cache ) ;

          //printf( "%s" , EqAtomList[ iatom ].atomname );

          //sscanf( pEqGRO , "%d" , &EqAtomList[ iload ].atomnumber );
          
          strpickword( buffer , 3 , cache ) ;
          
          EqAtomList[ iload ].atomnumber = atoi( cache ) ;

          //printf( "\nWorking on No. %d atom ...\n" , EqAtomList[ iatom ].atomnumber );

          //sscanf( pEqGRO , "%lf" , &EqAtomList[ iload ].cx ); //printf("\n Cx is %lf ...\t" , EqAtomList[ iatom ].cx);
          
          strpickword( buffer , 4 , cache ) ; EqAtomList[ iload ].cx = atof( cache ) ;
          
          *( EqCrd + 3 * iload + 0 ) = EqAtomList[ iload ].cx / crdconvert ;
          
          //sscanf( pEqGRO , "%lf" , &EqAtomList[ iload ].cy ); //printf("\n Cy is %lf ...\t" , EqAtomList[ iatom ].cy);
          
          strpickword( buffer , 5 , cache ) ; EqAtomList[ iload ].cy = atof( cache ) ;
          
          *( EqCrd + 3 * iload + 1 ) = EqAtomList[ iload ].cy / crdconvert ;
          
          //sscanf( pEqGRO , "%lf" , &EqAtomList[ iload ].cz ); //printf("\n Cz is %lf ...\n\n" , EqAtomList[ iatom ].cz);
          
          strpickword( buffer , 6 , cache ) ; EqAtomList[ iload ].cz = atof( cache ) ;
          
          *( EqCrd + 3 * iload + 2 ) = EqAtomList[ iload ].cz / crdconvert ;
          
          
          if( exVelocity == YES )
          {
            strpickword( buffer , 7 , cache ) ; EqAtomList[ iload ].vx = atof( cache ) ;
            
            strpickword( buffer , 8 , cache ) ; EqAtomList[ iload ].vy = atof( cache ) ;
            
            strpickword( buffer , 9 , cache ) ; EqAtomList[ iload ].vz = atof( cache ) ;
          
          }
          
          //fscanf( pgroinput , "%lf" , &EqAtomList[ iatom ].vx ); //printf("\n Vx is %lf ...\t" , EqAtomList[ iatom ].cx);

          //fscanf( pgroinput , "%lf" , &EqAtomList[ iatom ].vy ); //printf("\n Vy is %lf ...\t" , EqAtomList[ iatom ].cy);
    
          //fscanf( pgroinput , "%lf" , &EqAtomList[ iatom ].vz ); //printf("\n Vz is %lf ...\n\n" , EqAtomList[ iatom ].cz);

          
          iload ++ ;
          
        }
        
        //printf("\n%s\n" , buffer );
      }
      else
      {
        printf("\nSomething is wrong with the reading file part ...\n");
        
        exit(1);
      }
      
      iline ++ ;
      
      if( iload == natomselect ) break ;

    }
    
    
    /*
    if( iline < natomgroline )
    {
      fskip( pEqCrd , natomgroline - iline ) ;
    }
    
     
    
    fscanf( pgroinput , "%lf" , boxvector + 0 );

    fscanf( pgroinput , "%lf" , boxvector + 1 );

    fscanf( pgroinput , "%lf" , boxvector + 2 );
    */
    
    
  
  }
  else if( internalOrNot == YES && ( strcmp( crdunit , "grocrd" ) ) == 0 )
  {
    crdconvert = NM2BOHR ;
    
    rewind( pEqCrd ) ;
    
    for( icart = 0 ; icart < ncartselect ; icart ++ )
    {
      fscanf( pEqCrd , "%lf" , &dtmp ) ;
    
      *( EqCrd + icart ) = dtmp / crdconvert ;
    
    }
  
  }
  else if( internalOrNot == YES && ( strcmp( crdunit , "g09crd" ) ) == 0 )
  {
    crdconvert = 1.0000 ;
    
    rewind( pEqCrd ) ;
    
    for( icart = 0 ; icart < ncartselect ; icart ++ )
    {
      fscanf( pEqCrd , "%lf" , &dtmp ) ;
    
      *( EqCrd + icart ) = dtmp / crdconvert ;
    
    }
  
  }
  else if( internalOrNot == NO )
  {
    printf("\nAlready told you ... NO INTERNAL COORDINATE BUSINESS ...\n\n") ;
  }
  else
  {
    printf("\nUNKOWN ERROR : INVALID COORDINATE FILE FORMAT ...\n\n");
    
    exit( 73 ) ;
  }
  
  printf("\n===> Finished Loading Equilibrium Geometry <===\n\n\n") ;
  
  //dtranspose_nonsquare( natomselect , 3 , EqCrd , EqCrd ) ;
  
  
  /*
  debug = fopen("transposed_eqgeom.deb" , "wb+") ;
  
  doutput( debug , 3 , natomselect , EqCrd ) ;
  
  fclose( debug ) ;
  
  
  printf("\n===> Done Transposing Equilibrium Geometry <===\n\n\n") ;
  */
  
  // -------> Loading Mass ...  
  
  mass = calloc( natomselect , sizeof( double ) );
  
  dzeros( natomselect , 1 , mass );
  
  if( strcmp( massunit , "au" ) == 0 )
  {
    massconvert = AMU2AU ;
  }
  else if( strcmp( massunit , "amu" ) == 0 )
  {
    massconvert = 1.000 ;
  }
  else
  {
    printf("\nUNKOWN ERROR : INVALID MASS FILE FORMAT ...\n\n");
    
    exit( 75 ) ;
  }
  
  
  for( iatom = 0 ; iatom < natomselect ; iatom ++ )
  {
    fscanf( pmass , "%lf" , &dtmp ) ;
    
    *( mass + iatom ) = dtmp / massconvert ;
  }
   


  
  printf("\n===> Done Loading Mass ( in %s ) <===\n\n\n" , massunit ) ;

  
  //------> Hessian File :

  fskip( phess , 2 );

  len_hess_cart = flength( phess );

  if( len_hess_cart == ncart * ncart )
  {
    printf("\nOKay ... I see you provided the Hessian for all %d atom in system ... \n" , natom );
  }
  else if( len_hess_cart == ncartselect * ncartselect )
  {
    printf("\nOKay ... I see you only provided the Hessian for the %d selected atoms ... \n" , natomselect );
  }
  else if( len_hess_cart < ncart * ncart && len_hess_cart > ncartselect * ncartselect )
  {
    printf("\nThere are %d numbers in the Hessian file which is less than the square of total %d Cartesian coordinates in system but more than that of %d Cartesian coordinates of selected atoms ... \n" , len_hess_cart , ncart , ncartselect );

    printf("\nSo I am taking the first %d number ( %d * %d ) as the Hessian for selected atoms ...\n" , ncartselect * ncartselect , ncartselect , ncartselect );

  }
  else
  {
    printf("\nSomething is wrong with the Hessian file ... There are %d numbers in the Hessian file ... \n" , len_hess_cart );

    exit( 77 );

  }

  rewind( phess );

  //-------> Allocating space for Hessian and Diagonalization Process ...

  ncartprovide = sqrt( len_hess_cart ); 
  
  printf("\nWell ... the Hessian file you provided is a %d * %d square matrix ...\n" , ncartprovide , ncartprovide );

  hess_cart = calloc( len_hess_cart , sizeof(double));  dzeros( len_hess_cart , 1, hess_cart );

  hess_cart_select = calloc( ncartselect * ncartselect , sizeof(double) ) ; 
  
  dzeros( ncartselect , ncartselect , hess_cart_select );
  
  double * DMatrix = calloc( ncartselect * ncartselect , sizeof( double ) ) ;
  
  dzeros( ncartselect , ncartselect , DMatrix ) ;
  
  double * tmp_hessian = calloc( ncartselect * ncartselect , sizeof(double) ) ; 
  
  dzeros( ncartselect , ncartselect , tmp_hessian );


  //tri_hess_cart = calloc( ncart*(ncart+1)/2 , sizeof(double)); 
  //dzeros(ncart*(ncart+1)/2, 1, tri_hess_cart);



  //-------> Loading Hessian Matrix ...

  rewind( phess );

  fskip( phess , 2 );

  fload( phess , hess_cart );

  for( j = 0 ; j < len_hess_cart ; j ++ )
  {
    *( hess_cart + j ) = *( hess_cart + j ) / hessconvert ;
  }


  printf("\n===> Done Loading Whole Provided Hessian <===\n\n\n") ;


  //-------> Selecting the desired part of Hessian matrix 

  for( j = 0 ; j < ncartselect ; j ++ )
  {
    for( k = 0 ; k < ncartselect ; k ++ )
    {
      *( hess_cart_select + j * ncartselect + k ) = *( hess_cart + j * ncartprovide + k );
    }

  }

  printf("\n===> Done Picking The Selected Hessian <===\n\n\n") ;


  if( debuggingMode == YES )
  {
    debug = fopen("hess_cart.deb", "wb+");

    doutput( debug , ncart , ncart , hess_cart);

    fclose(debug);


    debug = fopen("hess_cart_select.deb", "wb+");

    doutput( debug , ncartselect , ncartselect , hess_cart_select );

    fclose(debug);
  }



  //-------> Transpose Hessian_cart_select to pass into gausvib_ ...
  
  
  
  dtranspose( ncartselect , hess_cart_select , hess_cart_select ) ;


  printf("\n===> Done Transposing Selected Hessian <===\n\n\n") ;


  //void gausvib_( int * , double * , double * , double * , double * , double * ) ;
  //            ( natom, mass, coordxyzinp, hessianinp, Dmatrix )




  //-------> Generate D-Matrix and transform into internal coord ...

  if( internalOrNot == YES )
  {
    gausvib_( &natomselect , mass , EqCrd , hess_cart_select , DMatrix ) ;
  
    dtranspose( ncartselect , DMatrix , DMatrix ) ;  
  
    printf("\n===> Done Generating D-Matrix ... Currently in C-Fashion <===\n\n\n") ;
  
  }
  else if( internalOrNot == NO )
  {
    for( icart = 0 ; icart < ncartselect ; icart ++ )
    {
      *( DMatrix + icart * ncartselect + icart ) = 1.000 ;
    }
  
  }
  else
  {
    printf("\nUNKNOWN ERROR : [ internalOrNot ] = %d \n\n" , internalOrNot ) ;
    
    exit( 15 ) ;
  
  }
  
  
  if( debuggingMode == YES )
  {
    debug = fopen( "DMatrix.deb" , "wb+") ;
  
    doutput( debug , ncartselect , ncartselect , DMatrix ) ;
  
    fclose( debug ) ;
  }

  


  for( j = 0 ; j < natomselect ; j ++ )   *( mass + j ) = ( *( mass + j ) ) * AMU2AU;

  
  printf("\n===> Done Putting Mass In AU <===\n\n\n") ;


  if( debuggingMode == YES )
  {
    debug = fopen("mass_au.deb", "wb+");

    doutput( debug , natomselect , 1 , mass );

    fclose(debug);
  }

  //-------> Performing mass-weighting for the Force constant matrix  

  dtranspose( ncartselect , hess_cart_select , hess_cart_select ) ; 
  
  //transpose back to C-Fashion
  

  masswt( natomselect , mass , hess_cart_select , hess_cart_select );

  
  
  printf("\n===> Done Mass-Weighting Selected Hessian <===\n\n\n") ;



  if( debuggingMode == YES )
  {
    debug = fopen("hess_masswt_select.deb", "wb+");

    doutput( debug , ncartselect , ncartselect , hess_cart_select );

    fclose(debug);
  }


  //-------> Calculating f_int = (D.') * f_mwc * D ;
  
  double done = 1.0000 ;
  
  double dzero = 0.0000 ;
  
  int nmode_trans_rot , nvibmodes ;
  
  if( natom == 2 )
  {
    nmode_trans_rot = 5 ;
  }
  else if( natom >= 3 )
  {
    nmode_trans_rot = 6 ;
  }
  
  nvibmodes = ncartselect - nmode_trans_rot ;
  
  double * hess_int_mwc = calloc( ncartselect * ncartselect , sizeof( double ) ) ;
  
  dzeros( ncartselect , ncartselect , hess_int_mwc ) ;
  
  double * vib_hess_int_mwc = calloc( nvibmodes * nvibmodes , sizeof( double ) ) ;
  
  dzeros( nvibmodes , nvibmodes , vib_hess_int_mwc ) ;
  
  
  
  dgemm_( "N" , "T" , &ncartselect , &ncartselect , &ncartselect , &done , DMatrix , &ncartselect , hess_cart_select , &ncartselect , &dzero , tmp_hessian , &ncartselect ) ;

  dgemm_( "N" , "T" , &ncartselect , &ncartselect , &ncartselect , &done , tmp_hessian , &ncartselect , DMatrix , &ncartselect , &dzero , hess_int_mwc , &ncartselect ) ;
  
  //dtransopose

  //    SUBROUTINE DGEMM ( TRANSA, TRANSB, M, N, K, ALPHA, A, LDA, B, LDB, BETA, C, LDC )



  printf("\n===> Done Calculating f_int = (D.') * f_mwc * D <===\n\n\n") ;
  
  
  if( debuggingMode == YES )
  {
    debug = fopen( "hess_int_mwc.deb" , "wb+") ;
  
    doutput( debug , ncartselect , ncartselect , hess_int_mwc ) ;
  
    fclose( debug ) ;
  }
  
  
  
  
  //-------> Performing matrix-diagonalization for Hess_Cart and l=D*L ( for internalOrNot == YES )
  
  
  freq = calloc( ncartselect , sizeof( double ) ) ; dzeros( ncartselect , 1 , freq );

  vib_freq = calloc( nvibmodes , sizeof(double));  dzeros( nvibmodes , 1 , vib_freq );

  dxdr = calloc( ncartselect * ncartselect , sizeof(double));  
  
  dzeros( ncartselect * ncartselect , 1 , dxdr );
  
  vib_dxdr = calloc( ncartselect * nvibmodes , sizeof( double ) );  
  
  dzeros( ncartselect * nvibmodes , 1 , vib_dxdr ) ;
  
  double * tmp_dxdr = calloc( nvibmodes * nvibmodes , sizeof( double ) ) ;
  
  dzeros( nvibmodes , nvibmodes , tmp_dxdr ) ;
  
  double * tmp_dxdr_2 = calloc( nvibmodes * nvibmodes , sizeof( double ) ) ;
  
  dzeros( nvibmodes , nvibmodes , tmp_dxdr_2 ) ;
  

  if( internalOrNot == YES )
  {
    
    // ---> Taking the vibrational ( 3N - 6 )-by-( 3N - 6 ) block 
    
    for( icart = nmode_trans_rot ; icart < ncartselect ; icart ++ )
    {
      for( itmp = nmode_trans_rot ; itmp < ncartselect ; itmp ++ ) 
      {
        *( vib_hess_int_mwc + ( icart - nmode_trans_rot ) * nvibmodes + ( itmp - nmode_trans_rot ) ) = *( hess_int_mwc + icart * ncartselect + itmp ) ;
    
      }
  
    }

    if( debuggingMode == YES )
    {
      debug = fopen( "vib_hess_int_mwc.deb" , "wb+" ) ;
  
      doutput( debug , nvibmodes , nvibmodes , vib_hess_int_mwc ) ;
  
      fclose( debug ) ;
    }
  
    // ---> Diagonalization
  
    dsyev_f2c( nvibmodes , vib_hess_int_mwc , tmp_dxdr, vib_freq  );

    dtranspose( nvibmodes , tmp_dxdr , tmp_dxdr );
  
    
    
    if( debuggingMode == YES )
    {
      
      /*
      debug = fopen( "vib_dxdr_internal.deb" , "wb+" ) ;
  
      doutput( debug , nvibmodes , nvibmodes , tmp_dxdr ) ;
  
      fclose( debug ) ;
      */
      
      debug = fopen( "vib_freq_internal.deb" , "wb+" ) ;
      
      doutput( debug , nvibmodes , 1 , vib_freq ) ;
      
      fclose( debug ) ;
      
    }



  
    printf("\n===> Done Diagonalizing ( 3N - 6 )-by-( 3N - 6 ) internal coordinate mass-weighted Hessian and transpose 3N-6 normal modes back to C <===\n\n\n") ;
    
  
    // ---> Putting ( 3N - 6 )-by-( 3N - 6 ) dxdr into vib_dxdr which is 3N-by-( 3N - 6 )

    for( icart = nmode_trans_rot ; icart < ncartselect ; icart ++ )
    {
      for( imode = 0 ; imode < nvibmodes ; imode ++ ) 
      {
        *( vib_dxdr + icart * nvibmodes + imode ) = *( tmp_dxdr + ( icart - nmode_trans_rot ) * nvibmodes + imode ) ;
    
      }
  
    }
  
  
    printf("\n===> Done Putting ( 3N - 6 )-by-( 3N - 6 ) dxdr into vib_dxdr which is 3N-by-( 3N - 6 ) <===\n\n\n") ;
  
  
    if( debuggingMode == YES )
    {
      debug = fopen( "vib_dxdr_internal.deb" , "wb+" ) ;
  
      doutput( debug , ncartselect , nvibmodes , vib_dxdr ) ;
      
      printf("\n[===> Debug <===] [\t%lf\t%lf\t%lf\t]" , *( vib_dxdr + 10 ) , *( vib_dxdr + 19 ) , *( vib_dxdr + 38 ) ) ;
  
      fclose( debug ) ;
    }
  
    //---> Performing l = D*L
  
  
    dtranspose_nonsquare( ncartselect , nvibmodes , vib_dxdr , vib_dxdr ) ;

    dgemm_( "T" , "N" , &ncartselect , &nvibmodes , &ncartselect , &done , DMatrix , &ncartselect , vib_dxdr , &ncartselect , &dzero , tmp_dxdr_2 , &ncartselect ) ;
  
    dtranspose_nonsquare( nvibmodes , ncartselect , tmp_dxdr_2 , tmp_dxdr_2 ) ;


    if( debuggingMode == YES )
    {
      debug = fopen( "vib_dxdr_Cartesian.deb" , "wb+" ) ;
  
      doutput( debug , ncartselect , nvibmodes , tmp_dxdr_2 ) ;
  
      fclose( debug ) ;
    }
  
   // ---> Putting l into the 3N-by-3N dxdr matrix ...


  
    for( icart = 0 ; icart < ncartselect ; icart ++ )
    {
      for( imode = nmode_trans_rot ; imode < ncartselect ; imode ++ ) 
      {
        *( dxdr + icart * ncartselect + imode ) = *( tmp_dxdr_2 + icart * nvibmodes + ( imode - nmode_trans_rot ) ) ;
    
      }
  
    }
  
  
    printf("\n===> Done Calculating l = D * L <===\n\n\n") ;
    
    
    // ---> Assemble variable "freq" from "vib_freq"
    
    for( imode = nmode_trans_rot ; imode < ncartselect ; imode ++ ) 
    {
      *( freq + imode ) = *( vib_freq + imode - nmode_trans_rot ) ;
    
    }
  
  
  
  } 
  else if( internalOrNot == NO )
  {
    dsyev_f2c( ncartselect , hess_int_mwc , dxdr, freq  );

    dtranspose( ncartselect , dxdr , dxdr );
  
  
  
  } ////////// ________________________  //////////
  
  
  if( debuggingMode == YES )
  {
    /*
    debug = fopen( "dxdr.deb" , "wb+" ) ;
  
    doutput( debug , ncartselect , ncartselect , dxdr ) ;
  
    fclose( debug ) ;
  
    */


    debug = fopen("allfrequency.deb", "wb+");

    doutput( debug , ncartselect , 1 , freq );

    fclose( debug );
  
  }
  
  
  
  
  
  
  //-------> Arranging frequencies and w=sqrt(lambda) ... 

  if( natomselect == 1 )
  {
    printf("\nSeriously? Only one atom ? NO WAYYYYYY ... \n");

    exit( 90 );
  }
  else if( natomselect == 2  )
  {
    *( freq + 5 ) = sqrt( *( freq + 5 ) ) * 219474.6313705 ;
  }

  else
  {
    for( j = 0 ; j < ncartselect ; j ++ )
    {
      if( *( freq + j ) >= 0.000 )
	    
	      *( freq + j ) = sqrt( *( freq + j ) ) * 219474.6313705 ;
      else
	      //*( freq + j ) = -1.000 * sqrt( -1.0000 * ( *( freq + j ) ) ) * 219474.6313705 ;
	      *( freq + j ) = 0.0000 ;
  
    }

  }

  
  // Here, no matter it is internal or not, after unit change, we will need to assign freq into vib_freq again ...
  
  for( imode = 0 ; imode < nvibmodes ; imode ++ )
  {
    *( vib_freq + imode ) = *( freq + imode + nmode_trans_rot ) ;
  }

  printf("\n===> Done Putting Vib-Frequencies Together <===\n\n\n") ;

  


  poutDXDR = fopen( outDXDRFileName , "wb+" ) ;
  
  doutput( poutDXDR , ncartselect , ncartselect , dxdr ) ;

  fclose( poutDXDR ) ;


  poutFreq = fopen( outFreqFileName, "wb+");

  doutput( poutFreq , ncartselect , 1 , freq );

  fclose( poutFreq );




  printf("\n\nI assume it's Allllllll Done   ...\n\n");




/*

  FILE * pmass , * phess , * pEqCrd , * poutDXDR , * poutFreq ; //, *pmo2ao;

  char massFileName[ 100 ] , hessFileName[ 100 ] , EqCrdFileName[ 100 ] ;
  
  char outDXDRFileName[ 100 ] , outFreqFileName[ 100 ] ;




*/


















  return( 0 ) ;

}
Пример #8
0
	void system::read_binary(const char *filename, const int n_files) 
	{
#if 1
		assert(n_files == 1);

		vec3 rmin, rmax;
		if (myproc == 0) 
		{

			FILE *fin; 
			if (!(fin = fopen(filename, "r"))) 
			{
				std::cerr << "Cannot open file " << filename << std::endl;
				exit(-1);
			}

			std::cerr << "proc= " << myproc << " read snapshot: " << filename << std::endl;

			int ival;
			float fval;

#define fload(x) { myfread(&fval, sizeof(float), 1, fin); x = fval; }
#define iload(x) { myfread(&ival, sizeof(int),   1, fin); x = ival;}

			float ftmp;
			int itmp, np0, npx, npy, npz;
			iload(itmp); // 20*4
			assert(itmp == 20*4);
			iload(itmp); // myid
			iload(np0);
			iload(npx);

			union 
			{
				unsigned long long uint_long;
				unsigned int       uint[2];
			} data;
			iload(data.uint[0]);
			iload(data.uint[1]);
			scheduler.tsysU = data.uint_long;

			float courant_No;
			int nglob, nloc, ndim;
			iload(nglob);
			iload(nloc);
			iload(ndim);  
			assert(ndim == 3);
			fload(t_global);
			fload(dt_global);
			iload(iteration);
			fload(courant_No);
			fload(gamma_gas);

			int periodic_on;
			iload(periodic_on);
			assert(periodic_on == -1);
			
			fload(rmin.x);
			fload(rmin.y);
			fload(rmin.z);
			fload(rmax.x);
			fload(rmax.y);
			fload(rmax.z);
			iload(itmp);     // 20*4
			assert(itmp == 20*4);

			ptcl_local.resize(nglob);
			U_local.resize(nglob);
			dU_local.resize(nglob);

			fprintf(stderr, "np =%d   nglob= %d \n", np0, nglob);

			int pc = 0;
			for (int pr = 0; pr < np0; pr++) 
			{
				fprintf(stderr, " p= %d out of %d; nloc= %d\n", pr, np0, nloc);
				for (int i = 0; i < nloc; i++) 
				{
					Particle p;
          p.tend  = t_global;
          p.rung  = 0.0;
          p.new_dt = 0.0;
          p.local_id = i;
					Fluid W(0.0);

					iload(ival);    
					assert(ival == 26*4);
					iload(ival); p.idx = ival;
				
					fload(p.pos.x); 
					fload(p.pos.y);
					fload(p.pos.z);

					p.pos = periodic(p.pos);

					assert(rmin.x <= p.pos.x);
					assert(rmax.x >= p.pos.x);
					assert(rmin.y <= p.pos.y);
					assert(rmax.y >= p.pos.y);
					assert(rmin.z <= p.pos.z);
					assert(rmax.z >= p.pos.z);
          p.orig_pos = p.pos;
          p.pot = 0;


					fload(p.vel.x);
					fload(p.vel.y);
					fload(p.vel.z);
          p.orig_vel = p.vel;
					fload(W[Fluid::DENS]);
					fload(W[Fluid::ETHM]);
					fload(ftmp); // compute_pressure(m.dens, m.ethm));
					fload(p.rmax);     //dump(    (sqr(m.B.x  ) + sqr(m.B.y  ) + sqr(m.B.z  ))*0.5f);
					iload(p.boundary); //				fload(ftmp); //dump(sqrt(sqr(m.vel.x) + sqr(m.vel.y) + sqr(m.vel.z))); 
					fload(W[Fluid::VELX]);
					fload(W[Fluid::VELY]);
					fload(W[Fluid::VELZ]);
					fload(W[Fluid::BX]);
					fload(W[Fluid::BY]);
					fload(W[Fluid::BZ]);
					float h;
					fload(h);
					fload(p.volume);
          p.volume_new = p.volume;
					fload(W[Fluid::PSI]);
					fload(ftmp); //L*divB_i[i]);
					fload(W[Fluid::ENTR]);
					fload(ftmp); // Jx
					fload(ftmp); // Jy
					fload(ftmp); // Jz
					iload(ival); 
					assert(ival == 26*4);

					p.tlast = t_global;

					ptcl_local[pc] = p;
					U_local    [pc] = W;
          dU_local   [pc] = 0.0;
          dU_local   [pc] = 0.0;
					pc++;
				}

				fprintf(stderr, "p= %d  np0= %d size= %d %d\n",
						pr, np0, (int)U_local.size(), (int)ptcl_local.size());
				if (!(pr < np0-1)) break;
				iload(itmp); // 20*4
				assert(itmp == 20*4);
				iload(itmp); // myid
				iload(np0);
				iload(npx);
				iload(npy);
				iload(npz);

				int nglob1;
				iload(nglob1);
				if (nglob != nglob1) {
					fprintf(stderr, "np; npx, npy, npz = %d; %d %d %d \n", 
							np0, npx, npy, npz);
					fprintf(stderr, "nglob= %d  nglob1= %d\n", nglob, nglob1);
				}
				assert(nglob == nglob1);
				iload(nloc);
				iload(ndim);
				fload(t_global);
				fload(dt_global);
				iload(iteration);
				fload(courant_No);
				fload(gamma_gas);

				iload(periodic_on);

				fload(rmin.x);
				fload(rmin.y);
				fload(rmin.z);
				fload(rmax.x);
				fload(rmax.y);
				fload(rmax.z);
				iload(itmp);     // 20*4
			}
			assert(pc == nglob);
			assert(nglob == (int)U_local.size());
			fclose(fin);


			local_n = U_local.size();
		}

		global_n = U_local.size();		      
		local_n = global_n;

		MPI_Bcast(&global_n,   1, MPI_UNSIGNED_LONG_LONG, 0, MPI_COMM_WORLD);
		MPI_Bcast(&iteration,  1, MPI_INT, 0, MPI_COMM_WORLD);

		double dt_glob = dt_global;
		double  t_glob =  t_global;
		MPI_Bcast(& t_glob,  1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
		MPI_Bcast(&dt_glob,  1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
		MPI_Bcast(&scheduler.tsysU, 1, MPI_UNSIGNED_LONG_LONG, 0, MPI_COMM_WORLD);
		dt_global = dt_glob;
		t_global  =  t_glob;
    scheduler.set_tsys(t_global);
		assert(t_global == scheduler.get_tsys());


//		scheduler.tsysU = (unsigned long long)(t_global / scheduler.dt_tick);
		scheduler.min_rung = 0;

		dt_global = 0.0f;
		
    distribute_data(true, false, true);
	
#if 1	
		fit_vec(ptcl_local);
		fit_vec(U_local);
		fit_vec(dU_local);
		fit_vec(Wrec_local);
#endif

		all_active = true;
		
		MPI_Barrier(MPI_COMM_WORLD);

		for (int i = 0; i < (int)local_n; i++)
		{
			ptcl_local[i].tlast = t_global;
//      ptcl_local[i].volume = cell_local[i].Volume;

      Wrec_local[i] = Fluid_rec(U_local[i]);
      U_local[i] = U_local[i].to_conservative(ptcl_local[i].volume);
      dU_local[i] = 0.0;
		}
    
    MPI_Barrier(MPI_COMM_WORLD);
    if (myproc == 0)
      fprintf(stderr , " pvel ... \n");

    get_active_ptcl(true);

    MPI_Barrier(MPI_COMM_WORLD);
    if (myproc == 0)
      fprintf(stderr , " pvel ... \n");


    cell_list.swap(cell_local);
    ptcl_import.swap(ptcl_local);
    U_import.swap(U_local);
    site_active_list.swap(active_ptcl);

    compute_pvel();
    compute_timesteps(true);

    cell_list.swap(cell_local);
    ptcl_import.swap(ptcl_local);
    U_import.swap(U_local);
    site_active_list.swap(active_ptcl);

    for (int i = 0; i < (int)local_n; i++)
    {
      ptcl_local[i].rung += 1;
      ptcl_local[i].tend  = ptcl_local[i].tlast + scheduler.get_dt(ptcl_local[i].rung);
      ptcl_local[i].orig_vel = ptcl_local[i].vel;
      ptcl_local[i].unset_active();
    }
    all_active = true;
    scheduler.flush_list();
    boundary_n = 0;
    for (int i = 0; i < (int)local_n; i++)
    {
      scheduler.push_particle(i, (int)ptcl_local[i].rung);
      if (ptcl_local[i].is_boundary())
        boundary_n++;
    }

    unsigned long long boundary_glb;
    MPI_Allreduce(&boundary_n, &boundary_glb, 1, MPI_UNSIGNED_LONG_LONG, MPI_SUM, MPI_COMM_WORLD);

    if (myproc == 0)
      fprintf(stderr, "boundary_glb= %lld\n", boundary_glb);

    clear_mesh(true);

    MPI_Barrier(MPI_COMM_WORLD);
    if (myproc == 0) fprintf(stderr, " proc= %d: complete read_binary \n", myproc);
#endif
  }
Пример #9
0
int main( int argc , char * argv[ ] )
{
  FILE * pndx , * pdxdr , * pfreq , * patomlist , * passgn ;
  
  FILE * debug ;
  
  char dxdrname [ 50 ] , ndxname [ 50 ] , atomlistname [ 50 ] , freqname [ 50 ], outassgnname [ 50 ] ;
  
  char ** pcmd ; pcmd = argv ;
  
  int icmd , itmp ;
  
  int ncart , natom , nmode , nfreqprovide;
  
  int icart , iatom , imode , ifreq ;
  
  int exfreq , exatomlist ;
  
  int fakeOrNot = 0 ;

  time_t current_time;

  time( &current_time );

  char now[ 300 ] ;

  strcpy( now , ctime( &current_time ) );

  int lennow = strlen( now ) ;

  *( now + lennow - 1 ) = ' ';

   
  // ========> Recording Command-Line Arguments ...
  
    printf("\n**********************************************************************\n");
      printf("* G_NMASSGN_D : Listing the localization of all vibrational modes.   *\n");
      printf("*                                                                    *\n");
      printf("*  ");
  for( icmd = 0 ; icmd < argc ; icmd ++ )
  {
    printf("%s " , *( pcmd + icmd ) );
  }
  printf("\n");
      printf("*                                                                    *\n");
      printf("*                                                                    *\n");
      printf("* Current Time : %s                           *\n" , now );
      printf("*                                                                    *\n");
      printf("*                                                                    *\n");
      printf("**********************************************************************\n");

 

  // =====> Setting up default file names ... 
  
  
  strcpy( dxdrname , "dxdr.deb" );
  
  strcpy( ndxname , "system.index" );
  
  strcpy( freqname , "vibfrequency.deb" );
  
  strcpy( outassgnname , "system.assgn" );
  
  strcpy( atomlistname , "atom.list" );
  
  // =====> Parsing command line input arguments ...
  
  if( argc == 1 )
  {
    printf("\n\nNo command-line arguments provided ... Mission aborting ...\n\n");
    
    printf("\nPlease refer to the usage by typing ' %s -h '\n\n" , * argv );
    
    exit(1); 

  }

  char * flag ;
  
  icmd = 1 ;

  while( icmd < argc )
  {  
    pcmd ++ ; 

    flag = * pcmd ;

    printf("\nNo.%d argument , Currently @ flag = %s ...\n\n" , icmd , flag );

    if( ( * flag == '-' ) && ( strlen( flag ) == 2 ) )
    {
      switch ( *( flag + 1 ) )
      {
	      
	      case 'f' : strcpy( dxdrname , *( ++ pcmd ) ) ; 
			 
			         printf("\nCommand-line argument indicates : Input dxdr File name : %s ...\n" , dxdrname ); 
	      
	                 icmd = icmd + 2 ; 
	                 
	                 break ;

	      case 'o' : strcpy( outassgnname , *( ++ pcmd ) ); 
	      
	                 printf("\nCommand-line argument indicates : Output File name : %s ...\n" , outassgnname ); 
	                 
	                 icmd = icmd + 2 ; 
	                 
	                 break ; 
	                 
	      case 'w' : strcpy( freqname , *( ++ pcmd ) );
	      
	                 printf("\nCommand-line argument indicates : Input frequency File name : %s ...\n" , freqname ); 
	                 
	                 icmd = icmd + 2 ;
	                 
	                 break ;

	      case 'n' : strcpy( ndxname , *( ++ pcmd ) );
	      
	                 printf("\nCommand-line argument indicates : Input index File name : %s ...\n" , ndxname ); 
	                 
	                 icmd = icmd + 2 ;
	                 
	                 break ;

	      case 'l' : strcpy( atomlistname , *( ++ pcmd ) );
	      
	                 if( ( strcmp( atomlistname , "none" ) ) == 0 )
	                 {
	                   printf("\nCommand-line argument indicates : No AtomList needed ... Will not produce fake frequency file ...\n" );
	                   
	                   fakeOrNot = 0 ; 
	                 }
	                 else
	                 {
	                   printf("\nCommand-line argument indicates : Input atom list File name : %s ...\n" , atomlistname ); 
	                   
	                   fakeOrNot = 1 ;
	                 }
	                 
	                 icmd = icmd + 2 ;
	                 
	                 break ;
          
	      case 'h' : printf("\nUsage:  %s [ -f 'input dxdr file name' ] [ -n 'input index file name (in GROMACS .ndx format)' ] [(optional) -o 'output NM assignment file name' ] [ -l atom list file (listing the atomic number of all atoms in system ; \"none\" if no frequency file desired)][ -w 'input vibrational frequency file ; best case length = nmode' ]\n\n" , * argv ); 
	                 
	                 printf("\n\n==> NOTE : In order to be fool-proof , if there is mis-match on the NAtom between dxdr file and any other file , this code will set NAtom to be the number from dxdr automatically ...\n\n");
	                 
	                 //printf("\nUsage:  %s [ -t G09 calculation type : 1=ONIOM ; 2=Point Charge ] [ -f 'input gro file name' ] [(optional) -o 'output g09 file name' ] [ -n # of layers (integer) ] [ (optional) -r radius of middle layer (real) ] [-R radius of lower layer (real) ] [ -H method for Highest layer (string) ] [ (optional) -M method for Middle layer (string) ] [ -L method for Lower layer (string) ] [ -x input GMX .itp file ]\n\n" , * argv ); 
	      
	                 //exh = 9 ;
	                 
	                 icmd = icmd + 1 ; 
	                 
	                 exit(1) ;

	      default : printf("\n\nInvalid option ' %s ' ... Please refer to the usage by typing ' %s -h '\n\n" , flag , * argv ); 
	      
	                icmd = argc ; 
	                
	                exit(1);

      
      
      
      }
    
    }
    else
    {
        printf("\n\nInvalid option ' %s ' ... Please refer to the usage by typing ' %s -h '\n\n" , flag , * argv );

	    exit(1);
      
      
    }
    
 
  } 
  

  // =====> Open the files ...
  
  if( ( pndx = fopen( ndxname , "r" ) ) == NULL )
  {
    printf("\nUser-defined index file %s does not exist ...\n\n" , ndxname );
    
    exit( 1 );
  
  }

  if( ( pdxdr = fopen( dxdrname , "r" ) ) == NULL )
  {
    printf("\nUser-defined dxdr file %s does not exist ...\n\n" , dxdrname );
    
    exit( 1 );
  
  }

  double * freq ;

  if( ( pfreq = fopen( freqname , "r" ) ) == NULL )
  {
    printf("\nUser-defined frequency file %s does not exist ...\n\n" , freqname );
    
    printf("\nBut it's OK , we will procede without frequency information ... \n");
    
    exfreq = 0 ;
  
  }
  else
  {
    nfreqprovide = flength( pfreq );
    
    rewind( pfreq ) ;
    
    freq = ( double * ) calloc( nfreqprovide , sizeof( double ) ) ;
    
    fload( pfreq , freq );
    
    rewind( pfreq );
    
    exfreq = 1 ;

  }


  int * atomlist , natomlistprovide ;
  
  if( fakeOrNot == 1 )
  {
    if( ( patomlist = fopen( atomlistname , "r" ) ) == NULL )
    {
      printf("\nUser-defined atom list file %s does not exist ...\n\n" , atomlistname );
      
      printf("\nMeaning ... All of your atoms will be carbon ...\n");
    
      exatomlist = 0 ;
  
    }
    else
    {
      natomlistprovide = flength( patomlist );
      
      rewind( patomlist );
    
      atomlist = ( int * ) calloc( natomlistprovide , sizeof( int ) ) ;
    
      int_fload( patomlist , atomlist );
    
      exatomlist = 1 ;
    }
  
  }



  // =====> Read the index file (*****.ndx) ... 
  
  int countlrb , countrrb ;
  
  int ngroup ;
  
  int ilrb , irrb , igroup ;
  
  char c ;
  
  char ** groupnames ;
  
  char tmpstring[ 100 ] ;
  
  char tmpchar ;
  
  // -----> Finding out how many groups are defined in index file ...
  
  ilrb = 0 ; irrb = 0 ; 
  
  //fsearch( pndx , "begin" );
  
  //fscanf( pndx , "%s" , tmpstring );
  
  //if( strcmp( tmpstring , "]" ) != 0 )
  //{
  //  printf("\nSomething is wrong with the ndx file format at the beginning ... Mission Aborting ... \n") ;
  //  
  //  exit(3);
  //
  //}
  
  //fskip( pndx , 1 ) ;
  
  rewind( pndx ) ;
  
  while( ( c = fgetc( pndx ) ) != EOF )
  {
    if( c == '[' )
    {
      ilrb ++ ;
    }
    else if( c == ']')
    {
      irrb ++ ;
    }
    else
    {
      continue ;
    }
  
  }
  
  if( ilrb == irrb )
  {
    ngroup = ilrb ;
    
    printf("\nThere are %d defined groups in the index file ...\n" , ngroup );
    
  }
  else  
  {
    printf("\nSomething is wrong in the index file ... There are unmatched brackets or broken entries ...\n");
    
    exit( 2 );
    
  }
  
  if( ngroup == 0 )
  {
    printf("\nThis index file is an empty file ... Mission Aborting ...\n");
    
    exit(4);
  }
  

  // -----> Finding out how many atoms are in each group 
  
  int * natom_in_each_group = calloc( ngroup , sizeof( int ) ) ;
  
  int current_atom_index , next_atom_index ;
  
  int info ;
  
  rewind( pndx ) ;
  
  //fsearch( pndx , "begin" );
  
  //fskip( pndx , 1 ) ;
  
  for( igroup = 0 ; igroup < ngroup ; igroup ++ )
  {
    printf("\n--------------------------> GROUP #%d <----------------------------" , igroup + 1 );
    
    //itmp = 0 ;
    
    fsearch( pndx , "]" ) ;
    
    //fskip( pndx , 1 ) ;
    
    //printf("\nHere we are ... : %c " , fgetc( pndx ) );
    
    fscanf( pndx , "%s" , tmpstring );
    
    //printf("\nFor this group , the 1st grabbed tmpstring is %s ... \n" , tmpstring );
    
    //while( strcmp( tmpstring , "[") != 0 )
   
    for( itmp = 0 ; strcmp( tmpstring , "[" ) != 0 && info != EOF ;   )
    {
      //printf("\nGrabbed tmpstring is %s ... \n" , tmpstring ) ;
      
      if( strcmp( tmpstring , "-" ) == 0 )
      {
        //printf("\nThe '-' situation happened ... before '-' we are at No.%d atom ... \n" , current_atom_index );
        
        fscanf( pndx , "%d" , &next_atom_index );
        
        //printf("\nAnd after '-' we are at No.%d atom ... \n" , next_atom_index );
        
        itmp = itmp + ( next_atom_index - current_atom_index );
        
        *( natom_in_each_group + igroup ) = itmp ;
        
        current_atom_index = next_atom_index ;
        
        info = fscanf( pndx , "%s" , tmpstring ) ;
      }
      else
      {
        itmp ++ ;
        
        *( natom_in_each_group + igroup ) = itmp ;
        
        current_atom_index = atoi( tmpstring );
        
        //printf("\nNormal situation ... current_atom_index is %d ... \n" , current_atom_index );
        
        info = fscanf( pndx , "%s" , tmpstring );
      }
      
      
    
    }
    
    if( info == EOF )
    {
      printf("\nHit the bottom of file ...\n\n") ;
      
      break ;
    }
  
    printf("\nDone with #%d group ... \n" , igroup + 1 );
    

  }

  printf("\n--------------------------> Done checking up groups <----------------------------");


  /* Debugging output for this part ... */
  
  printf("\n== Group Information Summary ==\n");
  
  for( igroup = 0 ; igroup < ngroup ; igroup ++ )
  {
    printf("\nNo.%d Group Has %d atoms ...\n" , igroup + 1 , *( natom_in_each_group + igroup ) );
  
  }

  // -----> Recording the name of each group ...
  
  groupnames = ( char ** ) calloc( ngroup , sizeof( char * ) ) ;
  
  int tmp_groupname_length ;
  
  rewind( pndx ) ;
  
  //fsearch( pndx , "begin" );
  
  //fskip( pndx , 1 );
  
  for( igroup = 0 ; igroup < ngroup ; igroup ++ )
  {
    fsearch( pndx , "[" ) ;
    
    fscanf( pndx , "%s" , tmpstring );
    
    tmp_groupname_length = strlen( tmpstring ) ;
    
    *( groupnames + igroup ) = ( char * ) calloc( tmp_groupname_length + 3 , sizeof( char ) ) ;
    
    strcpy( *( groupnames + igroup ) , tmpstring ) ;
    
    printf("\nName of %d group is %s ...\n" , igroup + 1 , *( groupnames + igroup ) );
  
  }

  
  
  // =====> Loading the eigenvectors ( dxdr file ) ... 
  
  printf("\n--------------------------> Begin reading dxdr file ...  <----------------------------" );
  
  int len_dxdr = flength( pdxdr ) ;
  
  printf("\nThere are %d numbers in eigenvectors file ... \n" , len_dxdr );
  
  ncart = sqrt( len_dxdr );
  
  natom = ncart / 3 ;
  
  double * dxdr = calloc( len_dxdr , sizeof( double ) ) ;
  
  rewind( pdxdr );
  
  fload( pdxdr , dxdr ) ;
  
  rewind( pdxdr ) ;  
  
  printf("\nDone with loading dxdr file ... \n");
  
  switch( natom )
  {
    case 1 : printf("\nSeriously? Only ONE atom? ...\n") ; exit( 9 ) ; break ;
    
    case 2 : nmode = 6 ; break ;
    
    default : nmode = ncart - 0 ; break ;
  
  }

  if( exfreq == 0 )
  {
    freq = ( double * ) calloc( nmode , sizeof( double ) ) ;
    
    dzeros( nmode , 1 , freq ) ;
  }
  else
  {
    if( nfreqprovide > nmode )
    {
      printf("\nOkay ... The number of vibrational frequency you provided is more than the normal mode we have from eigenvectors ...\n");
      
      printf("\nSo I will take only the first #_of_eigenvectors frequencies from the file you provided ...\n");
    }
    else if( nfreqprovide < nmode )
    {
      printf("\nOkay ... The number of vibrational frequency you provided is less than the normal mode we have from eigenvectors ...\n");
      
      printf("\nThe rest will be padded with zeros ... Sorry, I really don't want to do the diagonalization ...\n");
      
      free( freq ) ;
      
      freq = ( double * ) calloc( nmode , sizeof( double ) ) ;
      
      rewind( pfreq );
      
      fload( pfreq , freq ) ;
      
      dzeros( nmode - nfreqprovide , 1 , freq + nfreqprovide ) ;

    }
  
  
  }
  
  
  
  if( exatomlist == 0 )
  {
    if( fakeOrNot == 1 )
    {
      for( iatom = 0 ; iatom < natom ; iatom ++ ) 
      {
        *( atomlist + iatom ) = 6 ;
      }
    }
  }
  else
  {
    if( natomlistprovide > natom )
    {
      printf("\nOkay ... The number of atom you provided is more than the NAtom we have from eigenvectors ...\n");
      
      printf("\nSo I will take only the first #_of_atoms from the file you provided ...\n");
    
    }
    else if( natomlistprovide < natom )
    {
      printf("\nOkay ... The number of atom you provided is less than the NAtom we have from eigenvectors ...\n");
      
      printf("\nSo all the rest will be automatically set as Carbon ... \n");
      
      free( atomlist );
      
      atomlist = ( int * ) calloc( natom , sizeof( int ) ) ;
      
      rewind( patomlist );
      
      int_fload( patomlist , atomlist );
      
      for( iatom = natom - natomlistprovide ; iatom < natom ; iatom ++ )
      {
        *( atomlist + iatom ) = 6 ;
      }
      
      
    
    }
  
  }
  
  
  
  
  // =====> Loading the eigenvectors ( dxdr file ) ... 
  
  
  
  // -----> Based on group information, prepare the recording structures (array) ... 
  
  printf("\n=================================> _ <=====================================\n");
  
  printf("\nStarting from here, we will actually read index file and give the assignment ... \n");
  
  double * assgninfo = calloc( ngroup * nmode , sizeof( double ) ) ;
  
  rewind( pndx ) ;
  
  //fsearch( pndx , "begin" );
  
  //fskip( pndx , 1 ) ;
  
  double tmp_xcomponent , tmp_ycomponent , tmp_zcomponent , tmp_magnitude ;
  
  //printf("\nDebugging ... Debugging ... % 12.8E\t% 12.8E\t% 12.8E\n\n" , *( dxdr + 3 ) , *( dxdr + 4 ) , *( dxdr + 5 ) );


  info = 9 ;
  
  for( igroup = 0 ; igroup < ngroup ; igroup ++ )
  { 
    printf("\n--------------------------> GROUP #%d : %s <----------------------------" , igroup + 1 , *( groupnames + igroup ) );
    
    fsearch( pndx , "]" ) ;
    
    fscanf( pndx , "%s" , tmpstring );
    
    //printf("\nFor this group , the 1st grabbed tmpstring is %s ... \n" , tmpstring );
    
    for( itmp = 0 ; strcmp( tmpstring , "[" ) != 0 && info != EOF ;   )
    {   
      //printf("\nGrabbed tmpstring is %s ... \n" , tmpstring ) ;
      
      if( strcmp( tmpstring , "-" ) == 0 )
      {
        //printf("\nThe '-' situation happened ... before '-' we are at No.%d atom ... \n" , current_atom_index );
        
        fscanf( pndx , "%d" , &next_atom_index );
        
        //printf("\nAnd after '-' we are at No.%d atom ... \n" , next_atom_index );
        
        itmp = itmp + ( next_atom_index - current_atom_index );
        
        for( iatom = current_atom_index ; iatom < next_atom_index ; iatom ++ )
        {  
           //tmp_xcomponent = 0.0000 ; tmp_ycomponent = 0.0000 ; tmp_zcomponent = 0.0000 ; 
      
           //tmp_magnitude = tmp_xcomponent * tmp_xcomponent + tmp_ycomponent * tmp_ycomponent + tmp_zcomponent * tmp_zcomponent ;
           
           printf("\nWorking on No.%d atom ... in No.%d group ...\n" , iatom + 1 , igroup + 1 );
           
           for( imode = 0 ; imode < nmode ; imode ++ )
           {
             tmp_xcomponent = *( dxdr + ( 3 * ( iatom - 0 ) + 0 ) * nmode + imode ) ;
             
             //printf("\nNO.%d mode has % 12.8E on #%d atom X ... \n" , imode + 1 , tmp_xcomponent , iatom + 1 );
             
             tmp_ycomponent = *( dxdr + ( 3 * ( iatom - 0 ) + 1 ) * nmode + imode ) ;
             
             //printf("\nNO.%d mode has % 12.8E on #%d atom Y ... \n" , imode + 1 , tmp_ycomponent , iatom + 1 );
           
             tmp_zcomponent = *( dxdr + ( 3 * ( iatom - 0 ) + 2 ) * nmode + imode ) ;
             
             //printf("\nNO.%d mode has % 12.8E on #%d atom Z ... \n" , imode + 1 , tmp_zcomponent , iatom + 1 );
             
             tmp_magnitude = tmp_xcomponent * tmp_xcomponent + tmp_ycomponent * tmp_ycomponent + tmp_zcomponent * tmp_zcomponent ;
             
             //printf("\nNO.%d mode has % 12.8E on #%d atom ... \n" , imode + 1 , tmp_magnitude , iatom + 1 ) ;
             
             *( assgninfo + igroup * nmode + imode ) = *( assgninfo + igroup * nmode + imode ) + tmp_magnitude ;
             
             printf("\nUp to No.%d atom , No.%d mode has % 12.8E on #%d group ...\n" , iatom + 1 , imode + 1 , *( assgninfo + igroup * nmode + imode ) , igroup + 1 );
           
           }

        }
        
        current_atom_index = next_atom_index ;
        
        info = fscanf( pndx , "%s" , tmpstring ) ;
      }
      else
      {
        itmp ++ ;
        
        current_atom_index = atoi( tmpstring );
        
        //printf("\nNormal situation ... current_atom_index is %d ... \n" , current_atom_index );
        
        printf("\nWorking on No.%d atom ... in No.%d group ...\n" , current_atom_index  , igroup + 1 );
        
        for( imode = 0 ; imode < nmode ; imode ++ )
        {
          tmp_xcomponent = *( dxdr + ( 3 * ( current_atom_index - 1 ) + 0 ) * nmode + imode ) ;
          
          //printf("\nNO.%d mode has % 12.8E on #%d atom X ... \n" , imode + 1 , tmp_xcomponent , current_atom_index );
          
          tmp_ycomponent = *( dxdr + ( 3 * ( current_atom_index - 1 ) + 1 ) * nmode + imode ) ;
          
          //printf("\nNO.%d mode has % 12.8E on #%d atom Y ... \n" , imode + 1 , tmp_ycomponent , current_atom_index );
          
          tmp_zcomponent = *( dxdr + ( 3 * ( current_atom_index - 1 ) + 2 ) * nmode + imode ) ;
          
          //printf("\nNO.%d mode has % 12.8E on #%d atom Z ... \n" , imode + 1 , tmp_zcomponent , current_atom_index );
          
          tmp_magnitude = tmp_xcomponent * tmp_xcomponent + tmp_ycomponent * tmp_ycomponent + tmp_zcomponent * tmp_zcomponent ;
          
          //printf("\nNO.%d mode has % 12.8E on #%d atom ... \n" , imode + 1 , tmp_magnitude , current_atom_index ) ;
          
          *( assgninfo + igroup * nmode + imode ) = *( assgninfo + igroup * nmode + imode ) + tmp_magnitude ;
          
          printf("\nUp to No.%d atom , No.%d mode has % 12.8E on #%d group ...\n" , current_atom_index , imode + 1 , *( assgninfo + igroup * nmode + imode ) , igroup + 1 );
        
        }
        
        info = fscanf( pndx , "%s" , tmpstring );
        
      }
      
    }
    
    if( info == EOF )
    {
      printf("\nHit the bottom of file ...\n\n") ;
      
      break ;
    }
  
    printf("\nDone Loading Information of [ % 5d ] group ... \n" , igroup + 1 );
    
  
  }


  /* Debugging output ... */
  
  debug = fopen( "assgnfull.info" , "wb+" );
  
  fprintf( debug , "Mode#\t" ) ;
  
  for( igroup = 0 ; igroup < ngroup ; igroup ++ )
  {
    fprintf( debug , "% 12s\t" , *( groupnames + igroup ) ) ;
  
  }
  
  fprintf( debug , "vib-Frequencies" );
  
  fprintf( debug , "\n\n" );
  
  for( imode = 0 ; imode < nmode ; imode ++ )
  {
    fprintf( debug , "%d\t" , imode + 1 );
    
    for( igroup = 0 ; igroup < ngroup ; igroup ++ )
    {
      fprintf( debug , "% 12.8E\t" , *( assgninfo + igroup * nmode + imode ) );
    
    }
  
    fprintf( debug , "% 12.8E\n\n" , *( freq + imode ) ) ;
  
  }




  // =====> Writing the output file ( MATLAB loadable pure number array file ) ... 
  
  
  passgn = fopen( outassgnname , "wb+" ) ;
  
  fprintf( passgn , "\n\n" );
  
  for( imode = 0 ; imode < nmode ; imode ++ )
  {
    fprintf( passgn , "%d\t" , imode + 1 );
    
    for( igroup = 0 ; igroup < ngroup ; igroup ++ )
    {
      fprintf( passgn , "% 12.8E\t" , *( assgninfo + igroup * nmode + imode ) );
    
    }
  
    fprintf( passgn , "% 12.8E\n\n" , *( freq + imode ) ) ;
  
  }


  // =====> Writing the output file ( MATLAB loadable pure number array file ) ... 

 FILE * pfakefreq ;
 
 int ibatch = 0 ;
 
 int nbatch = nmode / 3 ;
 
 
 

 if( fakeOrNot == 1 )
 {
   pfakefreq = fopen( "fakeg09.freq" , "wb+" );
   
   if( natom == 1 )
   {
     printf("\nReally? Really?? Really???\n\n");
   
     exit( 1 ) ;
   }
   else if( natom == 2 )
   {
     fprintf( pfakefreq , "                  1\n                    A\nFrequencies -- %10.4f\n" , *( freq + 5 ) ) ;
   
     fprintf( pfakefreq , "Red. masses -- %10.4f\nFrc consts  -- %10.4f\nIR Inten    -- %10.4f\n Atom  AN      X      Y      Z     \n" , 1.00 , 1.00 , 1.00 );
 
     for( iatom = 0 ; iatom < natom ; iatom ++ )
     {
       fprintf( pfakefreq , "%5d%4d  % 8.4f  % 8.4f  %8.4f\n" , iatom + 1 , *( atomlist + iatom ) , *( dxdr + 3 * iatom + 0 ) , *( dxdr + 3 * iatom + 1 ) , *( dxdr + 3 * iatom + 2 ) );
   
     }
 
   }
   else
   {
     for( ibatch = 2 ; ibatch < nbatch ; ibatch ++ )
     {
       fprintf( pfakefreq , "                      %5d                             %5d                             %5d\n" , 3 * ( ibatch - 2 ) + 1 , 3 * ( ibatch - 2 ) + 2 , 3 * ( ibatch - 2 ) + 3 );
       
       fprintf( pfakefreq , "                      %5c                             %5c                             %5c\n" , 'A' , 'A', 'A' );
     
       fprintf( pfakefreq , "%-12s --  %10.4f                        %10.4f                        %10.4f\n" , " Frequencies" , *( freq + 3 * ibatch + 0 ) , *( freq + 3 * ibatch + 1 ) , *( freq + 3 * ibatch + 2 ) );
     
       fprintf( pfakefreq , "%-12s --  %10.4f                        %10.4f                        %10.4f\n" , " Red. masses" , 1.00 , 1.00 , 1.00 );
     
       fprintf( pfakefreq , "%-12s --  %10.4f                        %10.4f                        %10.4f\n" , " Frc consts" , 10.00 , 10.00 , 10.00 );
     
       fprintf( pfakefreq , "%-12s --  %10.4f                        %10.4f                        %10.4f\n" , " IR Inten" , 10.00 , 10.00 , 10.00 );
     
       fprintf( pfakefreq , "   Atom  AN     X         Y         Z             X         Y         Z             X         Y         Z\n");
     
       for( iatom = 0 ; iatom < natom ; iatom ++ )
       {
         fprintf( pfakefreq , "%5d%4d" , iatom + 1 , *( atomlist + iatom ) ) ;
     
         fprintf( pfakefreq , "   % 8.4f  % 8.4f  %8.4f" , *( dxdr + nmode * ( 3 * iatom + 0 ) + ( 3 * ( ibatch + 0 ) + 0 ) ) , *( dxdr + nmode * ( 3 * iatom + 1 ) + ( 3 * ( ibatch + 0 ) + 0 ) ) , *( dxdr + nmode * ( 3 * iatom + 2 ) + ( 3 * ( ibatch + 0 ) + 0 ) )  ) ;
       
         fprintf( pfakefreq , "      % 8.4f  % 8.4f  %8.4f" , *( dxdr + nmode * ( 3 * iatom + 0 ) + ( 3 * ( ibatch + 0 ) + 1 ) ) , *( dxdr + nmode * ( 3 * iatom + 1 ) + ( 3 * ( ibatch + 0 ) + 1 ) ) , *( dxdr + nmode * ( 3 * iatom + 2 ) + ( 3 * ( ibatch + 0 ) + 1 ) )  ) ;    

         fprintf( pfakefreq , "      % 8.4f  % 8.4f  %8.4f\n" , *( dxdr + nmode * ( 3 * iatom + 0 ) + ( 3 * ( ibatch + 0 ) + 2 ) ) , *( dxdr + nmode * ( 3 * iatom + 1 ) + ( 3 * ( ibatch + 0 ) + 2 ) ) , *( dxdr + nmode * ( 3 * iatom + 2 ) + ( 3 * ( ibatch + 0 ) + 2 ) )  ) ;    
       
       }
   
     }
   

   }

 }









  return( 0 );

} // The End ... 
Пример #10
0
Файл: app.c Проект: youka2/fx
void init(void)
{
	if(init_mblur() && init_vig() && init_quad())
	{
		int size=0; void *data=NULL;

		/*glClearColor(1.0f,1.0f,1.0f,1.0f);*/
		glClearColor(0.04f,0.0f,0.04f,1.0f);

		use_mblur();
		send_mblur_samples(16.0f); /* adjust motion blur samples here */

		use_vig();
		send_vig_size((float)sw(),(float)sh());
		vigmode(0);

		use_basic();
		persp(proj,75.0f,asp(),0.1f,24.0f);

		if(fload("data/area-model.bin",&size,&data))
		{
			add_to_vbo(&area_mod,data,size);
			free(data);

			update_vbo();

			gen_texs(1,&area_tex);
			//if(load_tex_compressed(area_tex,"data/area-ao-texture.bin",tf_mipmap))
			if(load_tex_compressed(area_tex,"data/area-texture.bin",tf_mipmap))
			{
				const int downsample=1; /* adjust fb down-sizing here */
				texmode(1);

				nsw=sw()/downsample;
				nsh=sh()/downsample;

				gen_texs(4,texs);
				gen_rbs(3,rbs);
				gen_fbs(4,fbos);

				use_fb(fbos[0]);
				add_fb_rb(0,rbs[0],nsw,nsh,GL_RGB8,4); /* adjust renderbuffer samples here */
				add_fb_rb(0,rbs[1],nsw,nsh,GL_DEPTH_COMPONENT24,4); /* adjust renderbuffer samples here */

				use_fb(fbos[1]);
				add_fb_tex(0,texs[0],nsw,nsh,GL_RGB8,tf_linear);
				add_fb_rb(0,rbs[2],nsw,nsh,GL_DEPTH_COMPONENT24,0);

				use_fb(fbos[2]);
				add_fb_tex(0,texs[1],nsw,nsh,GL_RGB8,tf_linear);
				add_fb_tex(1,texs[2],nsw,nsh,GL_RGBA32F,tf_linear);
				add_fb_rb(0,rbs[2],nsw,nsh,GL_DEPTH_COMPONENT24,0);

				use_fb(fbos[3]);
				add_fb_tex(0,texs[3],nsw,nsh,GL_RGB8,tf_linear);

				use_fb(0);
				use_rb(0);
				use_tex(0);
			}
			else quit();
		}
		else quit();
	}
	else quit();
}
Пример #11
0
void vsmcreate(int argc, char *argv[])
{
    TVSMHeader head;    // VSM file header
    TVSMResource res;   // resource
    char *fdir = NULL;  // working directory
    char *fn = NULL;    // target file name
    TCRC csum;          // checksum
    int i;
    FILE *f;
    char *tmp, *tmp2;
    char ch;

    // command line parameters
    int vendor_id = -1;
    bool dont_load_header = false;
    bool dont_incl_footer = false;
    int ins_version = 0;
    unsigned short int version[4];

    // process arguments passed by command line
    for (i=2; i<argc; i++)
    {
        // -vid
        if (strcasecmp(argv[i], "-vid") == 0)
        {
            // there is no argument after -vid
            if (i+1 >= argc) errexit("Wrong parameter format '-vid'");
            sscanf(argv[++i], "%u", &vendor_id);
        }

        // -dh
        else if (strcasecmp(argv[i], "-dh") == 0)
            dont_load_header = true;

        // -df
        else if (strcasecmp(argv[i], "-df") == 0)
            dont_incl_footer = true;

        // -v
        else if (strcasecmp(argv[i], "-v") == 0)
        {
            if (i+1 >= argc) errexit("Wrong parameter format '-v'");

            ins_version = 1;
            if (sscanf(argv[++i], "%hd.%hd.%hd.%hd", &version[3], &version[2],
                       &version[1], &version[0]) != 4)
            errexit("Wrong parameter format '-v'\nShould be '-v a.b.c.d'");
        }

        // File or directory name
        else if (i+2 >= argc)
        {
            if (fdir == NULL) fdir = argv[i];
            else fn = argv[i];
        }

        // Incorrect parameter
        else
        {
            printf("Unknown argument: %s\n", argv[i]);
            errexit("Wrong parameter format");
        }
    }

    // Directory not specified
    if (fdir == NULL) errexit("Input folder not specified");

    // Target file not specified - generating filename from input folder
    if (fn == NULL)
    {
        fn = new char[strlen(fdir) + 5];
        strcpy(fn, fdir);
        if (isSlash(fn)) fn[strlen(fn) -1] = '\0';
        strcat(fn, ".vsm");
    }

    // End directory path by '\' char:
    if (isSlash(fdir) == 0)
    {
        tmp = new char[strlen(fdir) + 2];
        strcpy(tmp, fdir);
        strcat(tmp, "\\");
        fdir = tmp;
    }

    // File information
    printf("Input  folder:  %s\n", fdir);
    printf("Output file:    %s\n", fn);

    // Load header
    if (dont_load_header == false)
    {
        // open file
        tmp = new char[strlen(fdir) + 12];
        strcpy(tmp, fdir);
        strcat(tmp, "header.bin");
        i = fload(tmp, &head, sizeof(head));
        delete [] tmp;

        // file doesn't exists
        if (i < 0)
            errexit("\nCan't open file 'header.bin'.\n"
                    "Use '-dh' switch to generate default header");
        else if (i != sizeof(head))
            errexit("\nIncorrect file 'header.bin'.\n"
                    "Use '-dh' switch to generate default header");
    }

    // generate header
    else
    {
        memset(&head, 0, sizeof(head));
        head.signature = VSMSignature;
    }

    // change vendor id
    if (vendor_id >= 0) head.vendor_id = vendor_id;

    // change version number
    if (ins_version)
    {
        for (i=0; i<4; i++)
        head.version[i] = version[i];
    }

    // Show header info
    printf("Vendor ID:      %d\n\n", head.vendor_id);

    // Check if output file already exists
    if (FileExist(fn))
    {
        printf("File %s already exist. Overwrite? (y/N)\n\n", fn);
        ch = getch();
        if ((ch != 'y') && (ch != 'Y')) exit(0);
    }

    // Open output file
    f = fopen(fn, "wb");
    if (f == NULL) errexit("Can't create output file!");

    // Write header
    puts("writing header");
    if (fwrite(&head, sizeof(head), 1, f) <= 0)
    {
        fclose(f);
        errexit("Write error!");
    }

    // Prepare to listing files
    tmp = new char[8192];
    strcpy(tmp, fdir);
    tmp2 = tmp + strlen(tmp);
    strcat(tmp, "res*");
    TFileList fl;
    char *fname = FLFindFirst(&fl, tmp);
    res.data = new char[VSMMaxResSize+1];
    csum.newCRC32();
    head.ressize = 0;

    // Write file
    while (fname)
    {
        i = ParseResName(fname);

        // given file is not a resource file - skip
        if (i < 0) continue;

        res.id = i;
        printf("writing resource 0x%04x from %s\n", res.id, fname);

        // read resource file
        strcpy(tmp2, fname);
        i = fload(tmp, res.data, VSMMaxResSize+1);
        if (i < 0) errexit("Can't read resource file!");
        res.size = i;
        if (i >= VSMMaxResSize+1) errexit("Resource file is too big!");

        // write to output file
        if (fwrite(&res, RHSIZE, 1, f) <= 0) errexit("Write error!");
        if (fwrite(res.data, res.size, 1, f) <= 0) errexit("Write error!");
        csum.add(&res, RHSIZE);
        csum.add(res.data, res.size);
        head.ressize += RHSIZE + res.size;

        // make sure that file end up with even address
        if (head.ressize & 1)
        {
            if (fwrite("\0", 1, 1, f) <= 0) errexit("Write error!");
            head.ressize++;
            csum.add(0);
        }

        fname = FLFind(&fl);
    }

    // Writing footer
    if (dont_incl_footer == false)
    {
        // footer address (divided by 4)
        i = head.ressize & 3;
        if (i)
        {
            i = 4 - i;
            if (fwrite("\0\0\0", i, 1, f) <= 0) errexit("Write error!");
        }

        // load footer
        strcpy(tmp2, "footer.bin");
        i = fload(tmp, res.data, VSMMaxResSize);

        // if footer exists
        if (i != -1)
        {
            puts("writing footer");

            // can't read footer.bin
            if (i < 0) errexit("\nCan't open file 'footer.bin'.\n"
                               "Use '-df' switch if you don't need footer");

            // footer.bin length is 0
            if (i == 0) printf("\nFile 'footer.bin' is empty.");

            // write footer and check for errors
            else if (fwrite(res.data, i, 1, f) <= 0) errexit("Write error!");
        }
    }

    // Update header checksum
    head.checksum = csum.getCRC32() ^ 0xffffffff;
    puts("updating header (checksum and resources size)\n");
    fseek(f, 0, SEEK_SET);
    if (fwrite(&head, sizeof(head), 1, f) <= 0) errexit("Write error!");

    fclose(f);
    fileinfo(&head, head.checksum);

    delete [] tmp;
    delete [] res.data;
} // void vsmcreate(int argc, char *argv[])
Пример #12
0
int main( int argc , char * argv[ ] )
{
  FILE * pdxdr , * pfreq , * patomlist , * pfakefreq ;
  
  FILE * debug ;
  
  char dxdrname [ 50 ] , atomlistname [ 50 ] , freqname [ 50 ], outfreqname [ 50 ] ;
  
  char ** pcmd ; pcmd = argv ;
  
  int icmd , itmp ;
  
  int natom , ncart , nmode , nfreqprovide;
  
  int natomSelect , ncartSelect , nmodeSelect ;
  
  int icart , iatom , imode , ifreq ;
  
  int exfreq , exatomlist , exselect ;
  
  
  char buffer[ MAXCHARINLINE ] ;

  int lenBuff ;

  char cache[ MAXCHARINLINE ] ;

  char stmp[ 150 ] , stmp2[ 150 ] , tmpString[ 150 ];
  
  

  time_t current_time;

  time( &current_time );

  char now[ 300 ] ;

  strcpy( now , ctime( &current_time ) );

  int lennow = strlen( now ) ;

  *( now + lennow - 1 ) = ' ';

   
  // ========> Recording Command-Line Arguments ...
  
    printf("\n**********************************************************************\n");
      printf("* G_FAKEFREQ_D : Organize (DX/DR) into G09 Format for visualization. *\n");
      printf("*                                                                    *\n");
      printf("*  ");
  for( icmd = 0 ; icmd < argc ; icmd ++ )
  {
    printf("%s " , *( pcmd + icmd ) );
  }
  printf("\n");
      printf("*                                                                    *\n");
      printf("*                                                                    *\n");
      printf("* Current Time : %s                           *\n" , now );
      printf("*                                                                    *\n");
      printf("*                                                                    *\n");
      printf("**********************************************************************\n");

 

  // =====> Setting up default file names ... 
  
  
  strcpy( dxdrname , "dxdr.deb" );
  
  strcpy( freqname , "vibfrequency.deb" );
  
  strcpy( outfreqname , "fakeg09.freq" );
  
  strcpy( atomlistname , "atom.list" );
  
  // =====> Parsing command line input arguments ...
  
  exselect = 20 ;
  
  if( argc == 1 )
  {
    printf("\n\nNo command-line arguments provided ... Mission aborting ...\n\n");
    
    printf("\nPlease refer to the usage by typing ' %s -h '\n\n" , * argv );
    
    exit(1); 

  }

  char * flag ;
  
  icmd = 1 ;

  while( icmd < argc )
  {  
    pcmd ++ ; 

    flag = * pcmd ;

    printf("\nNo.%d argument , Currently @ flag = %s ...\n\n" , icmd , flag );

    if( ( * flag == '-' ) && ( strlen( flag ) == 2 ) )
    {
      switch ( *( flag + 1 ) )
      {
	      
	      case 'f' : strcpy( dxdrname , *( ++ pcmd ) ) ; 
			 
			         printf("\nCommand-line argument indicates : Input dxdr File name : %s ...\n" , dxdrname ); 
	      
	                 icmd = icmd + 2 ; 
	                 
	                 break ;

	      case 'o' : strcpy( outfreqname , *( ++ pcmd ) ); 
	      
	                 printf("\nCommand-line argument indicates : Output File name : %s ...\n" , outfreqname ); 
	                 
	                 icmd = icmd + 2 ; 
	                 
	                 break ; 
	                 
	      case 'w' : strcpy( freqname , *( ++ pcmd ) );
	      
	                 printf("\nCommand-line argument indicates : Input frequency File name : %s ...\n" , freqname ); 
	                 
	                 icmd = icmd + 2 ;
	                 
	                 break ;

	      case 'l' : strcpy( atomlistname , *( ++ pcmd ) );
	      
	                 printf("\nCommand-line argument indicates : Input atom list File name : %s ...\n" , atomlistname ); 
	                 
	                 icmd = icmd + 2 ;
	                 
	                 break ;
	      
	      case 's' : strcpy( tmpString , *( ++ pcmd ) ) ;
	      
	                 if( strcmp( tmpString , "all" ) == 0 || strcmp( tmpString , "All" ) == 0 )
	                 {
	                   exselect = 22 ;
	                   
	                   printf("\nCommand-line argument indicates : All atoms will be chosen as solute ...\n" );
	                 }
	                 else
	                 {
	                   printf("\nReceived information : %s ...\n" , tmpString ) ;
	                   
	                   natomSelect = atoi( tmpString ); 
	                  
	                   exselect = 21 ;
	                   
	                   printf("\nCommand-line argument indicates : First %d atoms will be chosen as solute ...\n" , natomSelect );
	                 
	                 }

	                 
	                 icmd = icmd + 2 ; 
	                 
	                 break ;
          

          
	      case 'h' : printf("\nUsage:  %s [ -f 'input dxdr file name' ] [(optional) -o 'output NM assignment file name' ] [ -l atom list file (listing the atomic number of all atoms in system)] [ -s # of atom selected to output ] [ -w 'input vibrational frequency file' ]\n\n" , * argv ); 
	                 
	                 printf("\n\n==> NOTE : In order to be fool-proof , if there is mis-match on the NAtom between dxdr file and any other file , this code will set NAtom to be the number from dxdr automatically ...\n\n");
	                 
	                 //printf("\nUsage:  %s [ -t G09 calculation type : 1=ONIOM ; 2=Point Charge ] [ -f 'input gro file name' ] [(optional) -o 'output g09 file name' ] [ -n # of layers (integer) ] [ (optional) -r radius of middle layer (real) ] [-R radius of lower layer (real) ] [ -H method for Highest layer (string) ] [ (optional) -M method for Middle layer (string) ] [ -L method for Lower layer (string) ] [ -x input GMX .itp file ]\n\n" , * argv ); 
	      
	                 //exh = 9 ;
	                 
	                 icmd = icmd + 1 ; 
	                 
	                 exit(1) ;

	      default : printf("\n\nInvalid option ' %s ' ... Please refer to the usage by typing ' %s -h '\n\n" , flag , * argv ); 
	      
	                icmd = argc ; 
	                
	                exit(1);

      
      
      
      }
    
    }
    else
    {
        printf("\n\nInvalid option ' %s ' ... Please refer to the usage by typing ' %s -h '\n\n" , flag , * argv );

	    exit(1);
      
      
    }
    
 
  } 
  

  // =====> Open the files ...


  if( ( pdxdr = fopen( dxdrname , "r" ) ) == NULL )
  {
    printf("\nUser-defined dxdr file %s does not exist ...\n\n" , dxdrname );
    
    exit( 1 );
  
  }

  double * freq ;

  if( ( pfreq = fopen( freqname , "r" ) ) == NULL )
  {
    printf("\nUser-defined frequency file %s does not exist ...\n\n" , freqname );
    
    printf("\nBut it's OK , we will procede without frequency information ... \n");
    
    exfreq = 0 ;
  
  }
  else
  {
    nfreqprovide = flength( pfreq );
    
    rewind( pfreq ) ;
    
    freq = ( double * ) calloc( nfreqprovide , sizeof( double ) ) ;
    
    fload( pfreq , freq );
    
    rewind( pfreq );
    
    exfreq = 1 ;

  }


  int * atomlist , natomlistprovide ;
  

  if( ( patomlist = fopen( atomlistname , "r" ) ) == NULL )
  {
    printf("\nUser-defined atom list file %s does not exist ...\n\n" , atomlistname );
    
    printf("\nMeaning ... All of your atoms will be carbon ...\n");
    
    exatomlist = 0 ;
  
  }
  else
  {
    natomlistprovide = flength( patomlist );
    
    rewind( patomlist );
    
    atomlist = ( int * ) calloc( natomlistprovide , sizeof( int ) ) ;
    
    int_fload( patomlist , atomlist );
    
    exatomlist = 1 ;
  }




  
  // =====> Loading the eigenvectors ( dxdr file ) ... 
  
  printf("\n--------------------------> Begin reading dxdr file ...  <----------------------------" );
  
  int len_dxdr = flength( pdxdr ) ;
  
  printf("\nThere are %d numbers in eigenvectors file ... \n" , len_dxdr );
  
  ncart = sqrt( len_dxdr );
  
  natom = ncart / 3 ;
  
  double * dxdr = calloc( len_dxdr , sizeof( double ) ) ;
  
  rewind( pdxdr );
  
  fload( pdxdr , dxdr ) ;
  
  rewind( pdxdr ) ;  
  
  printf("\nDone with loading dxdr file ... \n");
  
  switch( natom )
  {
    case 1 : printf("\nSeriously? Only ONE atom? ...\n") ; exit( 9 ) ; break ;
    
    case 2 : nmode = 6 ; break ;
    
    default : nmode = ncart - 0 ; break ;
  
  }

  if( exfreq == 0 )
  {
    freq = ( double * ) calloc( nmode , sizeof( double ) ) ;
    
    dzeros( nmode , 1 , freq ) ;
  }
  else
  {
    if( nfreqprovide > nmode )
    {
      printf("\nOkay ... The number of vibrational frequency you provided is more than the normal mode we have from eigenvectors ...\n");
      
      printf("\nSo I will take only the first #_of_eigenvectors frequencies from the file you provided ...\n");
    }
    else if( nfreqprovide < nmode )
    {
      printf("\nOkay ... The number of vibrational frequency you provided is less than the normal mode we have from eigenvectors ...\n");
      
      printf("\nThe rest will be padded with zeros ... Sorry, I really don't want to do the diagonalization ...\n");
      
      free( freq ) ;
      
      freq = ( double * ) calloc( nmode , sizeof( double ) ) ;
      
      rewind( pfreq );
      
      fload( pfreq , freq ) ;
      
      dzeros( nmode - nfreqprovide , 1 , freq + nfreqprovide ) ;

    }
  
  
  }
  
  
  
  if( exatomlist == 0 )
  {
    for( iatom = 0 ; iatom < natom ; iatom ++ ) 
    {
      *( atomlist + iatom ) = 6 ;
    }
    
  }
  else
  {
    if( natomlistprovide > natom )
    {
      printf("\nOkay ... The number of atom you provided is more than the NAtom we have from eigenvectors ...\n");
      
      printf("\nSo I will take only the first #_of_atoms from the file you provided ...\n");
    
    }
    else if( natomlistprovide < natom )
    {
      printf("\nOkay ... The number of atom you provided is less than the NAtom we have from eigenvectors ...\n");
      
      printf("\nSo all the rest will be automatically set as Carbon ... \n");
      
      free( atomlist );
      
      atomlist = ( int * ) calloc( natom , sizeof( int ) ) ;
      
      rewind( patomlist );
      
      int_fload( patomlist , atomlist );
      
      for( iatom = natom - natomlistprovide ; iatom < natom ; iatom ++ )
      {
        *( atomlist + iatom ) = 6 ;
      }
      
      
    
    }
  
  }
  
  if( exselect == 20 )
  {
    printf("\nBy default , all %d atoms are selected as solute ... \n\n" , natom ) ;

    natomSelect = natom ;

  }
  else if( exselect == 22 )
  {
    printf("\nPer user's request , all %d atoms are selected as solute ... \n\n" , natom ) ;

    natomSelect = natom ;
  }
  else if( exselect == 21 )
  {
    if( natomSelect > natom )
    {
      printf("\nOops ... you requested %d atoms as solute but we only have %d atoms in G09 .inp file ... By default , all atoms are selected as solute ... \n\n" , natomSelect , natom ) ;

      natomSelect = natom ;

    }
    else if( natomSelect <= natom && natomSelect > 0 )
    {
      printf("\nPer user's request , the first %d atoms are selected as solute ... \n\n" , natomSelect ) ;
    }
    else if( natomSelect <= 0 )
    {
      printf("\n# of solute atom must be a positive integer!!!\n\n") ;

      exit( 52 ) ;
    }


  }
  
  
  ncartSelect = natomSelect * 3 ;
  
  switch( natomSelect )
  {
    case 1 : printf("\nSeriously? Only ONE atom selected ? ...\n") ; exit( 9 ) ; break ;
    
    case 2 : nmodeSelect = 6 ; break ;
    
    default : nmodeSelect = ncartSelect - 0 ; break ;
  
  }

  

  // =====> Writing the output file ( MATLAB loadable pure number array file ) ... 
  
 printf("\n--------------------------> Begin organizing dxdr file into G09 format...  <----------------------------\n\n\n" );

 pfakefreq = fopen( outfreqname , "wb+" );
 
 int ibatch = 0 ;  
 
 int nbatch = nmodeSelect / 3 ;
 
 
 
 if( natomSelect == 1 )
 {
   printf("\nReally? Really?? Really???\n\n");
   
   exit( 1 ) ;
 }
 else if( natomSelect == 2 )
 {
   fprintf( pfakefreq , "                  1\n                    A\nFrequencies -- %10.4f\n" , *( freq + 5 ) ) ;
   
   fprintf( pfakefreq , "Red. masses -- %10.4f\nFrc consts  -- %10.4f\nIR Inten    -- %10.4f\n Atom  AN      X      Y      Z     \n" , 1.00 , 1.00 , 1.00 );
 
   for( iatom = 0 ; iatom < natomSelect ; iatom ++ )
   {
     fprintf( pfakefreq , "%5d%4d  % 8.4f  % 8.4f  %8.4f\n" , iatom + 1 , *( atomlist + iatom ) , *( dxdr + 3 * iatom + 0 ) , *( dxdr + 3 * iatom + 1 ) , *( dxdr + 3 * iatom + 2 ) );
   
   }
 
 }
 else
 {
   for( ibatch = 2 ; ibatch < nbatch ; ibatch ++ )
   {
     fprintf( pfakefreq , "                      %5d                             %5d                             %5d\n" , 3 * ( ibatch - 2 ) + 1 , 3 * ( ibatch - 2 ) + 2 , 3 * ( ibatch - 2 ) + 3 );
     
     fprintf( pfakefreq , "                      %5c                             %5c                             %5c\n" , 'A' , 'A', 'A' );
     
     fprintf( pfakefreq , "%-12s --  %10.4f                        %10.4f                        %10.4f\n" , " Frequencies" , *( freq + 3 * ibatch + 0 ) , *( freq + 3 * ibatch + 1 ) , *( freq + 3 * ibatch + 2 ) );
     
     fprintf( pfakefreq , "%-12s --  %10.4f                        %10.4f                        %10.4f\n" , " Red. masses" , 1.00 , 1.00 , 1.00 );
     
     fprintf( pfakefreq , "%-12s --  %10.4f                        %10.4f                        %10.4f\n" , " Frc consts" , 10.00 , 10.00 , 10.00 );
     
     fprintf( pfakefreq , "%-12s --  %10.4f                        %10.4f                        %10.4f\n" , " IR Inten" , 10.00 , 10.00 , 10.00 );
     
     fprintf( pfakefreq , "   Atom  AN     X         Y         Z             X         Y         Z             X         Y         Z\n");
     
     for( iatom = 0 ; iatom < natomSelect ; iatom ++ )
     {
       fprintf( pfakefreq , "%5d%4d" , iatom + 1 , *( atomlist + iatom ) ) ;
     
       fprintf( pfakefreq , "   % 8.4f  % 8.4f  %8.4f" , *( dxdr + nmode * ( 3 * iatom + 0 ) + ( 3 * ( ibatch + 0 ) + 0 ) ) , *( dxdr + nmode * ( 3 * iatom + 1 ) + ( 3 * ( ibatch + 0 ) + 0 ) ) , *( dxdr + nmode * ( 3 * iatom + 2 ) + ( 3 * ( ibatch + 0 ) + 0 ) )  ) ;
       
       fprintf( pfakefreq , "      % 8.4f  % 8.4f  %8.4f" , *( dxdr + nmode * ( 3 * iatom + 0 ) + ( 3 * ( ibatch + 0 ) + 1 ) ) , *( dxdr + nmode * ( 3 * iatom + 1 ) + ( 3 * ( ibatch + 0 ) + 1 ) ) , *( dxdr + nmode * ( 3 * iatom + 2 ) + ( 3 * ( ibatch + 0 ) + 1 ) )  ) ;    

       fprintf( pfakefreq , "      % 8.4f  % 8.4f  %8.4f\n" , *( dxdr + nmode * ( 3 * iatom + 0 ) + ( 3 * ( ibatch + 0 ) + 2 ) ) , *( dxdr + nmode * ( 3 * iatom + 1 ) + ( 3 * ( ibatch + 0 ) + 2 ) ) , *( dxdr + nmode * ( 3 * iatom + 2 ) + ( 3 * ( ibatch + 0 ) + 2 ) )  ) ;    
       
     }
   
   }

   
 }

  printf("\n==============> ALL DONE !!! ^-^ !!! <===============\n\n\n\n\n\n");


  return( 0 );

} // The End ...