/*
Returns the size of a BMP
*/
bmp_ret_t bmp_readSize(const char* file, uint16_t* width, uint16_t* height)
{
FILE *fp;
/* open the file */
if ((fp = fopen(file,"rb")) == NULL) {
return BMP_ERR_OPEN;
}
/* check to see if it is a valid bitmap file */
if (fgetc(fp)!='B' || fgetc(fp)!='M')
{
fclose(fp);
return BMP_ERR_INVALID;
}
fskip(fp,16);
fread(width, sizeof(uint16_t), 1, fp);
fskip(fp,2);
fread(height,sizeof(uint16_t), 1, fp);
#ifndef _WIN32
*width = flipOrder(*width);
*height = flipOrder(*height);
#endif
fclose(fp);
return BMP_OK;
}
void load_bmp(char *file,BITMAP *b)
{
FILE *fp;
long index;
word num_colors;
int x;
/* open the file */
if ((fp = fopen(file,"rb")) == NULL)
{
printf("Error opening file %s.\n",file);
exit(1);
}
/* check to see if it is a valid bitmap file */
if (fgetc(fp)!='B' || fgetc(fp)!='M')
{
fclose(fp);
printf("%s is not a bitmap file.\n",file);
exit(1);
}
/* read in the width and height of the image, and the
number of colors used; ignore the rest */
fskip(fp,16);
fread(&b->width, sizeof(word), 1, fp);
fskip(fp,2);
fread(&b->height,sizeof(word), 1, fp);
fskip(fp,22);
fread(&num_colors,sizeof(word), 1, fp);
fskip(fp,6);
/* assume we are working with an 8-bit file */
if (num_colors==0) num_colors=256;
/* try to allocate memory */
if ((b->data = (byte *) malloc((word)(b->width*b->height))) == NULL)
{
fclose(fp);
printf("Error allocating memory for file %s.\n",file);
exit(1);
}
/* read the palette information */
for(index=0;index<num_colors;index++)
{
b->palette[(int)(index*3+2)] = fgetc(fp) >> 2;
b->palette[(int)(index*3+1)] = fgetc(fp) >> 2;
b->palette[(int)(index*3+0)] = fgetc(fp) >> 2;
x=fgetc(fp);
}
/* read the bitmap */
for(index=(b->height-1)*b->width;index>=0;index-=b->width)
for(x=0;x<b->width;x++)
b->data[(word)(index+x)]=(byte)fgetc(fp);
fclose(fp);
}
/*-------------------------------------------------------------------
* CTReadCTF - read a slice from a ctf file
*-------------------------------------------------------------------
*/
static int CTReadCTF(FILE *fp, CTSlice slice, int x1, int y1, int x2, int y2)
{
unsigned short delta[512], row[512];
int i, del, left, right;
long off;
/*
CTSliceXSize(slice) = 512;
CTSliceYSize(slice) = 512;
*/
if (x1==-1)
{
slice->x1=slice->y1=x1=y1=0;
slice->x2=slice->y2=x2=y2=511;
slice->data = (unsigned short *)malloc(sizeof(unsigned short)*(x2-x1+1)*
(y2-y1+1));
memset(slice->data, '\0', sizeof(short)*(x2-x1+1)*(y2-y1+1));
CTSliceWidth(slice) = CTSliceHeight(slice) = 512;
}
/* skip past the 2048 byte header */
fskip(fp, 2048);
/* read the number of data values for each line */
fread(delta, 2, 512, fp);
/* compute offset for rows up to y1 */
for (off=0, i=0; i<x1; i++)
off+=delta[i]*2*2;
#ifdef DEBUG
printf("skipping %ld values\n", off);
#endif
/* skip to the x1'th row of data */
if (off != 0)
fskip(fp, off);
for (; x1<=x2; x1++)
{
/* skip to y1'th column of data in this row */
del=delta[x1];
/* compute how much data is present */
left = (512)/2 - del;
right = (512)/2 + del- 1;
memset(row, '\0', 512*sizeof(short));
fread(&row[left], 2, 2*del, fp);
memcpy(&CTSliceShortData(slice, x1, y1), &row[y1],
sizeof(short)*(y2-y1+1));
}
CTSliceCompMinMaxD(slice);
return(0);
}
/*-------------------------------------------------------------------
* CTReadVol - read a slice from a volume file
*-------------------------------------------------------------------
*/
static int CTReadVol(FILE *fp, CTSlice slice, int num, int x1, int y1,
int x2, int y2)
{
/*
CTSliceXSize(slice) = 256;
CTSliceYSize(slice) = 256;
*/
CTSliceWidth(slice) = 256;
CTSliceHeight(slice) = 256;
if (x1==-1)
{
slice->x1=slice->y1=x1=y1=0;
slice->x2=x2=CTSliceXSize(slice)-1;
slice->y2=y2=CTSliceYSize(slice)-1;
slice->data=(unsigned short *)malloc(sizeof(short)*(x2-x1+1)*(y2-y1+1));
memset(slice->data, '\0', sizeof(short)*(x2-x1+1)*(y2-y1+1));
}
fskip(fp, 256*256*2*(num-1));
fread(slice->data, 2, 256*256, fp);
CTSliceCompMinMaxD(slice);
return(0);
}
int fread_byte(FILE * f, uint8_t * data)
{
if (data != NULL)
return (fread((void *) data, sizeof(uint8_t), 1, f) < 1) ? -1 : 0;
else
return fskip(f, 1);
return 0;
}
int fread_long(FILE * f, uint32_t * data)
{
int ret = 0;
if (data != NULL)
{
ret = (fread((void *) data, sizeof(uint32_t), 1, f) < 1) ? -1 : 0;
*data = GUINT32_FROM_LE(*data);
}
else
ret = fskip(f, 4);
return ret;
}
int fread_word(FILE * f, uint16_t * data)
{
int ret = 0;
if (data != NULL)
{
ret = (fread((void *) data, sizeof(uint16_t), 1, f) < 1) ? -1 : 0;
*data = GUINT16_FROM_LE(*data);
}
else
ret = fskip(f, 2);
return ret;
}
/*-------------------------------------------------------------------
* CTReadH3D - read a slice from an H3D file
*-------------------------------------------------------------------
*/
static int CTReadH3D(FILE *fp, CTSlice slice, int num, int x1, int y1,
int x2, int y2)
{
if (x1==-1)
{
slice->x1=slice->y1=x1=y1=0;
slice->x2=x2=CTSliceXSize(slice)-1;
slice->y2=y2=CTSliceYSize(slice)-1;
slice->fdata=(float *)malloc(sizeof(float)*(x2-x1+1)*(y2-y1+1));
memset(slice->fdata, '\0', sizeof(float)*(x2-x1+1)*(y2-y1+1));
}
CTSliceWidth(slice) = x2-x1+1;
CTSliceHeight(slice) = y2-y1+1;
fskip(fp, sizeof(int)*3 + sizeof(double)*3 +
CTVolXSize(slice->vol)*CTVolYSize(slice->vol)*(num-1)*sizeof(float));
fread(slice->fdata, sizeof(float), CTVolXSize(slice->vol)*
CTVolYSize(slice->vol), fp);
CTSliceCompMinMaxD(slice);
return(0);
}
int main( int argc, char * argv[] )
{
FILE * pgroinput , * pitpinput , * pCNDOoutput ;
char inpgroname[ MAXCHARINLINE ] , inpitpname[ MAXCHARINLINE ] , outCNDOname[ MAXCHARINLINE ] ;
int multiplicity , charge ;
int natom , ncart , natomselect , natomDump ;
int iatom ;
double dtmp ;
double dtmpArray[ MAXCHARINLINE ] ;
int itmp ;
char tmpString[ MAXCHARINLINE ] ;
// --------> Declaring utility functions ...
double tellmass( char * atomMDname ) ;
int tellatom( char * atomMDname ) ;
void dzeros( int dimrow, int dimcol, double *p ) ;
void izeros( int dimrow, int dimcol, int *p ) ;
// --------> Some default values ...
multiplicity = 1 ;
charge = 0 ;
// ==============> Handling the file names and Charge & Multiplicity ... <========= //
// -------> Parsing the Command Line Arguments ...
char ** pcmd ;
pcmd = argv ; //pcmd ++ ;
int icmd = 1 ;
//int exn = 10 ; int exr = 16 ; int exR = 18 ; int exH = 22 ; int exM = 28 ; int exL = 30 ;
int exf = 1 ; int exo = 3 ; int exx = 36 ;
int exs = 18 ; int exD = 28 ;
char * flag ;
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 'f' : strcpy( inpgroname , *( ++ pcmd ) ) ;
printf("\nCommand-line argument indicates : Input File name : %s ...\n" , inpgroname );
exf = 7 ;
icmd = icmd + 2 ;
break ;
case 'o' : strcpy( outCNDOname , *( ++ pcmd ) ) ;
printf("\nCommand-line argument indicates : Output File name : %s ...\n" , outCNDOname );
exo = 9 ;
icmd = icmd + 2 ;
break ;
case 'x' : strcpy( inpitpname , *( ++ pcmd ) ) ;
if( strcmp( inpitpname , "dummy") == 0 || strcmp( inpitpname , "none") == 0 || strcmp( inpitpname , "None") == 0 )
{
exx = 99 ;
printf("\nLooks like we are not using point charge here ... \n") ;
}
else
{
printf("\nCommand-line argument indicates : Input .itp File name : %s ...\n" , inpitpname );
exx = 37 ;
}
icmd = icmd + 2 ;
break ;
case 's' : strcpy( tmpString , *( ++ pcmd ) ) ;
if( strcmp( tmpString , "all" ) == 0 || 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 'D' : strcpy( tmpString , *( ++ pcmd ) ) ;
if( strcmp( tmpString , "all" ) == 0 || strcmp( tmpString , "All" ) == 0 || strcmp( tmpString , "ALL" ) == 0 )
{
exD = 30 ;
printf("\nCommand-line argument indicates : All atoms will be chosen to be dumped in output file ...\n" );
}
else if( strcmp( tmpString , "solute" ) == 0 || strcmp( tmpString , "Solute" ) == 0 || strcmp( tmpString , "SOLUTE" ) == 0 )
{
exD = 31 ;
printf("\nCommand-line argument indicates : Only selected solute atoms will be chosen to be dumped in output file ...\n" );
}
else
{
printf("\nReceived information : %s ...\n" , tmpString ) ;
natomDump = atoi( tmpString );
exD = 29 ;
printf("\nCommand-line argument indicates : First %d atoms will be dumped into output file ...\n" , natomDump );
}
icmd = icmd + 2 ;
break ;
/*
case 'r' : radiusM = atof( *( ++ pcmd ) );
exr = 17 ;
printf("\nCommand-line argument indicates : User defined radius for middle layer : %12.8f ...\n" , radiusM );
icmd = icmd + 2 ;
break ;
case 'R' : radiusL = atof( *( ++ pcmd ) );
exR = 19 ;
printf("\nCommand-line argument indicates : User defined radius for lower layer : %12.8f ...\n" , radiusL );
icmd = icmd + 2 ;
break ;
case 'H' : strcpy( highest_method , *( ++ pcmd ) );
exH = 23 ;
printf("\nCommand-line argument indicates : User defined method for Highest layer : %s ...\n" , highest_method );
icmd = icmd + 2 ;
break ;
case 'M' : strcpy( middle_method , *( ++ pcmd ) );
exM = 29 ;
printf("\nCommand-line argument indicates : User defined method for Middle layer : %s ...\n" , middle_method );
icmd = icmd + 2 ;
break ;
case 'L' : strcpy( lower_method , *( ++ pcmd ) );
exL = 31 ;
printf("\nCommand-line argument indicates : User defined method for Lower layer : %s ...\n" , lower_method );
icmd = icmd + 2 ;
break ;
*/
case 'h' : printf("\nUsage: %s [ -f 'input gro file name' ] [(optional) -o 'output CNDO input file name' ] [ -x input GMX .itp file ] [ -s # of atoms chosen as the solute ] [ -D # of atoms chosen to be Dumped in output file ]\n\n" , * argv );
printf("\nNOTE : 1) [ -s all ] or [ -s All ] indicates all atoms chosen as solute;\n\n 2) Default for -s is all atoms when nresidue = 1 or natom in 1st residue when nresidue != 1 \n");
printf("\n 3) User can use [ -x none / None / dummy ] to indicate all selected atoms ( may be less than total number of atoms ) will be treated as solute \n\n");
//printf("\m 3) ") ;
//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);
}
}
// --------> Setting DEFAULT value for important variables ...
char defoutname[ MAXCHARINLINE ] , definpname[ MAXCHARINLINE ] , defitpname[ MAXCHARINLINE ];
int inputnamelength , outputnamelength , inputitpnamelength;
printf("\nID = %d ...\n" , exo * exf * exx );
switch( exo * exf * exx ) // File Names ... int exf = 1 / 7 ; int exo = 3 / 9; int exx = 36 / 37 - 99 ;
{
case 108 : strcpy( inpgroname , "sys.gro" );
strcpy( inpitpname , "sys.itp" );
strcpy( outCNDOname , "sys.dat" );
break ;
case 1*3*99 : strcpy( inpgroname , "sys.gro" );
//strcpy( inpitpname , "sys.itp" );
strcpy( outCNDOname , "sys.dat" );
break ;
case 756 : inputnamelength = strlen( inpgroname ) ;
strncpy( defoutname, inpgroname , inputnamelength - 4 ) ;
*( defoutname + inputnamelength - 4 ) = '\0' ;
strcat( defoutname, ".dat") ;
strcpy( outCNDOname , defoutname ) ;
strncpy( defitpname , inpgroname , inputnamelength - 4 );
*( defitpname + inputnamelength - 4 ) = '\0' ;
strcat( defitpname , ".itp" );
strcpy( inpitpname , defitpname );
break ;
case 3*7*99 : inputnamelength = strlen( inpgroname ) ;
strncpy( defoutname, inpgroname , inputnamelength - 4 ) ;
*( defoutname + inputnamelength - 4 ) = '\0' ;
strcat( defoutname, ".dat") ;
strcpy( outCNDOname , defoutname ) ;
break ;
case 7*9*99 : printf("\n\nHoorayyyyyyyy ... Both input and output name are specified !!!\n\n");
printf("\nAnd ... We don't need itp file ! \n");
break ;
case 324 : outputnamelength = strlen( outCNDOname ) ;
strncpy( definpname, outCNDOname , outputnamelength - 4 ) ;
*( definpname + outputnamelength - 4 ) = '\0' ;
strcat( definpname, ".gro") ;
strcpy( inpgroname , definpname );
strncpy( defitpname , outCNDOname , outputnamelength - 4 );
*( defitpname + outputnamelength - 4 ) = '\0' ;
strcat( defitpname , ".itp" );
strcpy( inpitpname , defitpname );
break ;
case 1*9*99 : outputnamelength = strlen( outCNDOname ) ;
strncpy( definpname, outCNDOname , outputnamelength - 4 ) ;
*( definpname + outputnamelength - 4 ) = '\0' ;
strcat( definpname, ".gro") ;
strcpy( inpgroname , definpname );
break ;
case 111 : strcpy( inpgroname , "sys.gro" );
strcpy( outCNDOname , "sys.inp" );
break ;
case 777 : inputnamelength = strlen( inpgroname ) ;
strncpy( defoutname, inpgroname , inputnamelength - 4 ) ;
*( defoutname + inputnamelength - 4 ) = '\0' ;
strcat( defoutname, ".dat") ;
strcpy( outCNDOname , defoutname ) ;
break ;
case 2331 : printf("\n\nHoorayyyyyyyy ... All file names are specified !!!\n\n");
break ;
case 333 : outputnamelength = strlen( outCNDOname ) ;
strncpy( definpname, outCNDOname , outputnamelength - 4 ) ;
*( definpname + outputnamelength - 4 ) = '\0' ;
strcat( definpname, ".gro") ;
strcpy( inpgroname , definpname );
break ;
}
// --------------> Summarizing and File Access ...
printf("\n\nInput GMX .gro file name is : %s ...\n" , inpgroname );
printf("\nOutput CNDO dat file name is %s ...\n" , outCNDOname );
if( ( pitpinput = fopen( inpitpname , "r" ) ) == NULL && exx != 99 )
{
printf("\nUser defined .itp file %s does not exist ... \n" , inpitpname );
exit( 3 );
}
// ==============> Reading information from GMX .gro file ... <========= //
char grotitlestring[MAXLINE];
int iline = 3 ;
int iload = 0 ;
int blank_signal , groinfo ;
char buffer[ MAXCHARINLINE ] ;
char cache[ MAXCHARINLINE ] ;
char tmp_char ;
int natomgroline , natomgrotitle ;
int exVelocity = 0 ;
if( ( pgroinput = fopen( inpgroname , "r" ) ) == NULL )
{
printf("\nUser defined .gro file %s does not exist ... \n" , inpgroname );
exit( 3 );
}
else
{
rewind( pgroinput );
//printf("\nCurrent character is %c ... \n" , fgetc( pEqGRO ) );
fskip( pgroinput , 1 );
fscanf( pgroinput , "%d" , &natomgrotitle );
fskip( pgroinput , 1 );
printf("\n Second line of .gro file says it is describing %d atoms ... \n\n" , natomgrotitle );
while( ( groinfo = freadline( buffer , MAXCHARINLINE , pgroinput , ';' ) ) != 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");
rewind( pgroinput ) ;
fskip( pgroinput , 2 ) ;
while( ( groinfo = freadline( buffer , MAXCHARINLINE , pgroinput , ';' ) ) != 0 )
{
//printf("\n//--------------> WORKING ON NO. %d LINE ... <-------------//\n" , iline );
//info = freadline( buffer , MAXCHARINLINE , pinputfile , ';' );
//printf("\nNow we are at : %s\n" , buffer );
//printf("\n INFO is %d ...\n" , info );
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 );
iload ++ ;
}
//printf("\n%s\n" , buffer );
}
else
{
printf("\nSomething is wrong with the reading file part ...\n");
exit(1);
}
iline ++ ;
}//while( info != 0 );
natomgroline = iload - 1 ; // Because the last line is boxvector line .
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 ;
// =====> Actually Reading the GRO File ...
GRO atomlist[ natom ] ;
rewind( pgroinput );
fskip( pgroinput , 1 );
fskip( pgroinput , 1 );
printf("\nNow let's read the actual .gro file ... \n");
iload = 0 ; iline = 0 ;
while( ( groinfo = freadline( buffer , MAXCHARINLINE , pgroinput , ';' ) ) != 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" , &atomlist[ iload ].resnumber , atomlist[ iload ].resname );
//printf( "%s\t" , atomlist[ iatom ].resname );
//sscanf( pEqGRO , "%s" , EqAtomList[ iload ].atomname );
strpickword( buffer , 2 , cache ) ;
strcpy( atomlist[ iload ].atomname , cache ) ;
//printf( "%s" , atomlist[ iatom ].atomname );
//sscanf( pEqGRO , "%d" , &EqAtomList[ iload ].atomnumber );
strpickword( buffer , 3 , cache ) ;
atomlist[ 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 ) ; atomlist[ iload ].cx = atof( cache ) ;
//sscanf( pEqGRO , "%lf" , &EqAtomList[ iload ].cy ); //printf("\n Cy is %lf ...\t" , EqAtomList[ iatom ].cy);
strpickword( buffer , 5 , cache ) ; atomlist[ iload ].cy = atof( cache ) ;
//sscanf( pEqGRO , "%lf" , &EqAtomList[ iload ].cz ); //printf("\n Cz is %lf ...\n\n" , EqAtomList[ iatom ].cz);
strpickword( buffer , 6 , cache ) ; atomlist[ iload ].cz = atof( cache ) ;
if( exVelocity == YES )
{
strpickword( buffer , 7 , cache ) ; atomlist[ iload ].vx = atof( cache ) ;
strpickword( buffer , 8 , cache ) ; atomlist[ iload ].vy = atof( cache ) ;
strpickword( buffer , 9 , cache ) ; atomlist[ 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);
}
if( iload == natom ) break ;
iline ++ ;
}
if( natomgrotitle < natomgroline )
{
fskip( pgroinput , natomgroline - natomgrotitle ) ;
}
double boxvector[ 3 ];
fscanf( pgroinput , "%lf" , boxvector + 0 );
fscanf( pgroinput , "%lf" , boxvector + 1 );
fscanf( pgroinput , "%lf" , boxvector + 2 );
// ---------------> Figuring out how many solvent molecules (residues) are in the system ...
int nresidue = atomlist[ natom - 1 ].resnumber ;
// ---------------> Figuring out how many atoms are in each residue ...
int * n_of_atom_in_residues = calloc( nresidue , sizeof( int ) ) ;
izeros( nresidue , 1 , n_of_atom_in_residues );
//double * molecularmass = calloc( nresidue , sizeof( double ) ) ;
//dzeros( nresidue , 1 , molecularmass );
int iresidue = 1 ;
for( iatom = 0 ; iatom < natom ; iatom ++ )
{
if( atomlist[ iatom ].resnumber == ( iresidue + 1 ) )
{
//printf("\n#%d residue has %d atoms ...\n" , iresidue , *( n_of_atom_in_residues + iresidue - 1 ) );
iresidue ++ ;
//printf("\n\nStarting ... # %d residue (molecule) ... \n\n" , iresidue );
}
else if( atomlist[ iatom ].resnumber == iresidue )
{
//printf("\nStill in this residue ... \n");
//continue ;
}
else
{
printf("\nSomething is wrong with the atomlist or atomcast ... Mission Aborting ...\n\n");
exit(1);
}
*( n_of_atom_in_residues + iresidue - 1 ) = *( n_of_atom_in_residues + iresidue - 1 ) + 1 ;
///*( molecularmass + iresidue - 1 ) = *( molecularmass + iresidue - 1 ) + atomcast[ iatom ].atommass ;
}
//Just debugging ...
for( iresidue = 1 ; ( iresidue - 1 ) < nresidue ; iresidue ++ )
{
printf("\nThere are %d atoms in No. %d residue ... \n" , *( n_of_atom_in_residues + iresidue - 1 ) , iresidue );
//printf("\nThe molecular mass of No. %d residue is %lf ...\n" , iresidue , *( molecularmass + iresidue - 1 ) );
}
//---> Dealing with the "Default senario " of Chosen Atoms ...
if( exs == 18 && nresidue == 1 )
{
natomselect = natom ;
}
else if( exs == 18 && nresidue > 1 )
{
natomselect = *( n_of_atom_in_residues + 0 ) ;
}
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 for rotation ... 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 );
}
if( exD == 28 )
{
natomDump = natom ;
}
else if( exD == 30 )
{
natomDump = natom ;
}
else if( exD == 31 )
{
natomDump = natomselect ;
printf("\nBased on command-line input , only [ %d ] solute atoms will be dumped ...\n\n" , natomselect ) ;
}
else if( exD == 29 )
{
if( natomDump <= natom && natomDump > natomselect )
{
printf("\nBased on command-line input , besides solute , [ %d ] atoms from solvent will be dumped ...\n\n" , natomDump - natomselect ) ;
}
else if( natomDump == natomselect )
{
printf("\nBased on command-line input , only [ %d ] solute atoms will be dumped ...\n\n" , natomselect ) ;
}
else if( natomDump < natomselect && natomDump >= 0 )
{
printf("\nWARNING : You chose to dump ONLY PART OF SOLUTE atoms [ %d ] into your cndo .dat file ...\n\n" , natomDump ) ;
}
else if( natomDump < 0 )
{
natomDump = natomselect ;
printf("\nBased on command-line input , only [ %d ] solute atoms will be dumped ...\n\n" , natomselect ) ;
}
else if( natomDump > natom )
{
printf("\nWARNING : There are in total only [ %d ] atoms in the system , so you cannot request more than [ %d ] atoms dumped ...\n\n" , natom , natom ) ;
printf("\nNow we re-set the natomDump to be natom ...\n\n" ) ;
natomDump = natom ;
}
}
// -------------------------------> Reading ITP File ... <---------------------------------- //
int itpinfo , natomITP ;
if( exx != 99 )
{
// =====> Pre-Loading ...
printf("\nNow let's pre-load the .itp file and see how many atoms it is describing ... \n");
iline = 1 ;
iload = 0 ;
fsearch( pitpinput , "atoms" ) ;
fskip( pitpinput , 1 );
while( ( itpinfo = freadline( buffer , MAXCHARINLINE , pitpinput , ';' ) ) != 0 )
{
//printf("\n//--------------> WORKING ON NO. %d LINE ... <-------------//\n" , iline );
//info = freadline( buffer , MAXCHARINLINE , pinputfile , ';' );
//printf("\nNow we are at : %s\n" , buffer );
//printf("\n INFO is %d ...\n" , info );
blank_signal = stellblank( buffer ) ;
if( blank_signal == 0 )
{
printf("\nNo.%d line is a blank line ... Moving on ...\n" , iline ) ;
}
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 );
}
else if( ( tmp_char = getfirst( buffer ) ) == '[' )
{
printf("\nSTARTING OF NEW DIRECTIVE ... END READING ... \n\n");
break ;
}
else
{
//printf("\nLine reads : %s ...\n" , buffer );
iload ++ ;
}
//printf("\n%s\n" , buffer );
}
else
{
printf("\nSomething is wrong with the reading file part ...\n");
exit(1);
}
iline ++ ;
}//while( info != 0 );
natomITP = iload ;
printf("\nThere are %d atoms described in itp file ...\n" , natomITP );
/*
if( natomITP != natomselect )
{
printf("\nWhile you specified you wanted %d atoms as the solute, in your itp file, there are only %d atoms being described ...\n" , natomsoluteSelect , natomITP );
printf("\nPlease check your itp file and make sure the # of atoms match ...\n");
printf("\nWe will continue anyway but once we find any required info does not exist in your itp file , we will terminate this process immediately ...\n\n") ;
}
*/
}
else
{
natomITP = natom ;
natomselect = natom ;
}
ITP atomdatabase[ natomITP ];
if( exx != 99 )
{
// =====> Loading ...
printf("\nNow let's actually load the .itp file ... \n");
iline = 1 ;
iload = 0 ;
//ITP atomdatabase[ natomITP ];
rewind( pitpinput ) ;
fsearch( pitpinput , "atoms" ) ;
fskip( pitpinput , 1 );
while( ( itpinfo = freadline( buffer , MAXCHARINLINE , pitpinput , ';' ) ) != 0 )
{
//printf("\n//--------------> WORKING ON NO. %d LINE ... <-------------//\n" , iline );
//info = freadline( buffer , MAXCHARINLINE , pinputfile , ';' );
//printf("\nNow we are at : %s\n" , buffer );
//printf("\n INFO is %d ...\n" , info );
blank_signal = stellblank( buffer ) ;
if( blank_signal == 0 )
{
//printf("\nNo.%d line is a blank line ... Moving on ...\n" , iline ) ;
}
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 );
}
else if( ( tmp_char = getfirst( buffer ) ) == '[' )
{
//printf("\nSTARTING OF NEW DIRECTIVE ... END READING ... \n\n");
break ;
}
else
{
//printf("\nLine reads : %s ...\n" , buffer );
iload ++ ;
strpickword( buffer , 1 , cache );
atomdatabase[ iload -1 ].nr = atoi( cache ) ;
strpickword( buffer , 2 , cache );
strcpy( atomdatabase[ iload -1 ].type , cache );
strpickword( buffer , 3 , cache );
atomdatabase[ iload -1 ].resnr = atoi( cache ) ;
strpickword( buffer , 4 , cache );
strcpy( atomdatabase[ iload -1 ].residue , cache );
strpickword( buffer , 5 , cache );
strcpy( atomdatabase[ iload -1 ].atomname , cache );
strpickword( buffer , 6 , cache );
atomdatabase[ iload -1 ].cgnr = atoi( cache ) ;
strpickword( buffer , 7 , cache );
atomdatabase[ iload -1 ].charge = atof( cache ) ;
strpickword( buffer , 8 , cache );
atomdatabase[ iload -1 ].mass = atof( cache ) ;
printf("\nCharge of this atom is %lf ...\n" , atomdatabase[ iload -1 ].charge ) ;
}
//printf("\n%s\n" , buffer );
}
else
{
printf("\nSomething is wrong with the reading file part ...\n");
exit(1);
}
iline ++ ;
}
}
// ==============> Organizing Info and Defining Layers ... <========= //
// ---------------> Allocating mem for dat array ...
DAT atomcast[ natom ];
for( iatom = 0 ; iatom < natom ; iatom ++ )
{
atomcast[ iatom ].cx = atomlist[ iatom ].cx * 10.00 ;
atomcast[ iatom ].cy = atomlist[ iatom ].cy * 10.00 ;
atomcast[ iatom ].cz = atomlist[ iatom ].cz * 10.00 ;
atomcast[ iatom ].atomlabel = tellatom( atomlist[ iatom ].atomname );
//atomcast[ iatom ].atommass = tellmass( atomlist[ iatom ].atomname );
atomcast[ iatom ].atomcharge = 0.00 ;
//printf("\nNo. %d atom ; X = %lf ; Y = %lf ; Z = %lf ; Atom = %d Mass = %lf ...\n" , iatom+1 , atomcast[ iatom ].cx , atomcast[ iatom ].cy , atomcast[ iatom ].cz , atomcast[ iatom ].atomlabel , atomcast[ iatom ].atommass );
}
// ==============> Loading information into atomcast ... <========= //
int itype = 0 ;
/*
FILE * debug ;
debug = fopen( "atomnames.deb" , "wb+" );
for( iatom = 0 ; iatom < natom ; iatom ++ )
{
fprintf( debug , "\n%d\t%s\n" , iatom + 1 , atomlist[ iatom ].atomname );
}
fclose( debug );
debug = fopen( "atomtypes.deb" , "wb+");
for( itype = 0 ; itype < ntype ; itype ++ )
{
fprintf( debug , "%8d %s %lf\t\n" , atomdatabase[ itype ].nr , atomdatabase[ itype ].atomname , atomdatabase[ itype ].charge );
}
fclose( debug );
*/
int info_res , info_atomname ;
int ntype ;
if( exx != 99 )
{
ntype = natomITP ;
for( iatom = natomselect ; iatom < natom ; iatom ++ )
{
for( itype = 0 ; itype < ntype ; itype ++ )
{
if( ( info_res = strcmp( atomlist[ iatom ].resname , atomdatabase[ itype ].residue ) ) == 0 && ( info_atomname = strcmp( atomlist[ iatom ].atomname , atomdatabase[ itype ].atomname ) ) == 0 )
{
atomcast[ iatom ].atomcharge = atomdatabase[ itype ].charge ;
//printf("\nNo.%d atom , charge is %lf ...\n" , iatom + 1 , atomcast[ iatom ].atomcharge );
break ;
}
}
}
}
// ---------------> Outputing ...
pCNDOoutput = fopen( outCNDOname , "wb+" );
fprintf( pCNDOoutput , "%s\n" , inpgroname );
fprintf( pCNDOoutput , "%s\n" , "HAMILT= INDO" );
fprintf( pCNDOoutput , "%s\n" , "STOP= CI" );
fprintf( pCNDOoutput , "%s\n" , "ROTINV= YES" );
//fprintf( pCNDOoutput , "%s\n" , "SHIFT= 20" );
fprintf( pCNDOoutput , "%s\n" , "BETA= INDO/S" );
fprintf( pCNDOoutput , "%s\n" , "POINTGRP= C1" );
fprintf( pCNDOoutput , "%s\n" , "EX_FROM= 60" );
fprintf( pCNDOoutput , "%s\n" , "MAX_CI= 60" );
fprintf( pCNDOoutput , "%s\n" , "CI_DUMP= 60" );
//fprintf( pCNDOoutput , "%s\n" , "DUMP= MAX" );
fprintf( pCNDOoutput , "%s%d\n" , "CHARGE= " , charge );
fprintf( pCNDOoutput , "%s%d\n" , "MULT_CI= " , multiplicity );
fprintf( pCNDOoutput , "%s\n" , "MAX_ITS= 300" );
fprintf( pCNDOoutput , "%s\n\n" , "RESTART= MO" );
if( natomDump >= natomselect )
{
for( iatom = 0 ; iatom < natomselect ; iatom ++ )
{
fprintf( pCNDOoutput , "%7.3f %7.3f %7.3f %5d\n" , atomcast[ iatom ].cx , atomcast[ iatom ].cy , atomcast[ iatom ].cz , atomcast[ iatom ].atomlabel );
}
}
else
{
for( iatom = 0 ; iatom < natomDump ; iatom ++ )
{
fprintf( pCNDOoutput , "%7.3f %7.3f %7.3f %5d\n" , atomcast[ iatom ].cx , atomcast[ iatom ].cy , atomcast[ iatom ].cz , atomcast[ iatom ].atomlabel );
}
}
//fprintf( pCNDOoutput , "\n\n\n" );
if( exx != 99 )
{
if( natomDump > natomselect && natomDump <= natom )
{
for( iatom = natomselect ; iatom < natomDump ; iatom ++ )
{
//printf("\nPrinting out No.%d atom which is in residue : %s into CNDO input file ... \n\n" , iatom + 1 , atomlist[ iatom ].resname );
fprintf( pCNDOoutput , "%7.3f %7.3f %7.3f %5d %10.6f\n" , atomcast[ iatom ].cx , atomcast[ iatom ].cy , atomcast[ iatom ].cz , -1*atomcast[ iatom ].atomlabel , atomcast[ iatom ].atomcharge );
}
}
}
fprintf( pCNDOoutput , "\n\n\n\n\n" ) ;
/*
*/
// -----------------> The End ... Really???
return(0);
}
static int
parse_aiff_header(FILE *sf)
{
int is_aiff = 0;
long chunkSize = 0, subSize = 0;
IFF_AIFF aiff_info;
memset(&aiff_info, 0, sizeof(aiff_info));
chunkSize = Read32BitsHighLow(sf);
if ( Read32BitsHighLow(sf) != IFF_ID_AIFF )
return 0;
while ( chunkSize > 0 )
{
u_int type = 0;
chunkSize -= 4;
type = Read32BitsHighLow(sf);
/* fprintf(stderr,
"found chunk type %08x '%4.4s'\n", type, (char*)&type); */
/* don't use a switch here to make it easier to use 'break' for SSND */
if (type == IFF_ID_COMM) {
subSize = Read32BitsHighLow(sf);
chunkSize -= subSize;
aiff_info.numChannels = Read16BitsHighLow(sf);
subSize -= 2;
aiff_info.numSampleFrames = Read32BitsHighLow(sf);
subSize -= 4;
aiff_info.sampleSize = Read16BitsHighLow(sf);
subSize -= 2;
aiff_info.sampleRate = ReadIeeeExtendedHighLow(sf);
subSize -= 10;
if (fskip(sf, (long) subSize, SEEK_CUR) != 0 )
return 0;
} else if (type == IFF_ID_SSND) {
subSize = Read32BitsHighLow(sf);
chunkSize -= subSize;
aiff_info.blkAlgn.offset = Read32BitsHighLow(sf);
subSize -= 4;
aiff_info.blkAlgn.blockSize = Read32BitsHighLow(sf);
subSize -= 4;
if (fskip(sf, aiff_info.blkAlgn.offset, SEEK_CUR) != 0 )
return 0;
aiff_info.sampleType = IFF_ID_SSND;
is_aiff = 1;
/* We've found the audio data. Read no further! */
break;
} else {
subSize = Read32BitsHighLow(sf);
chunkSize -= subSize;
if (fskip(sf, (long) subSize, SEEK_CUR) != 0 )
return 0;
}
}
/* fprintf(stderr, "Parsed AIFF %d\n", is_aiff); */
if (is_aiff) {
/* make sure the header is sane */
aiff_check2("name", &aiff_info);
num_channels = aiff_info.numChannels;
samp_freq = aiff_info.sampleRate;
num_samples = aiff_info.numSampleFrames;
}
return is_aiff;
}
static int
parse_wave_header(FILE *sf)
{
fmt_chunk_data wave_info;
int is_wav = 0;
long data_length = 0, file_length, subSize = 0;
int loop_sanity = 0;
memset(&wave_info, 0, sizeof(wave_info));
file_length = Read32BitsHighLow(sf);
if (Read32BitsHighLow(sf) != WAV_ID_WAVE)
return 0;
for (loop_sanity = 0; loop_sanity < 20; ++loop_sanity) {
u_int type = Read32BitsHighLow(sf);
if (type == WAV_ID_FMT) {
subSize = Read32BitsLowHigh(sf);
if (subSize < 16) {
/*fprintf(stderr,
"'fmt' chunk too short (only %ld bytes)!", subSize); */
return 0;
}
wave_info.format_tag = Read16BitsLowHigh(sf);
subSize -= 2;
wave_info.channels = Read16BitsLowHigh(sf);
subSize -= 2;
wave_info.samples_per_sec = Read32BitsLowHigh(sf);
subSize -= 4;
wave_info.avg_bytes_per_sec = Read32BitsLowHigh(sf);
subSize -= 4;
wave_info.block_align = Read16BitsLowHigh(sf);
subSize -= 2;
wave_info.bits_per_sample = Read16BitsLowHigh(sf);
subSize -= 2;
/* fprintf(stderr, " skipping %d bytes\n", subSize); */
if (subSize > 0) {
if (fskip(sf, (long)subSize, SEEK_CUR) != 0 )
return 0;
};
} else if (type == WAV_ID_DATA) {
subSize = Read32BitsLowHigh(sf);
data_length = subSize;
is_wav = 1;
/* We've found the audio data. Read no further! */
break;
} else {
subSize = Read32BitsLowHigh(sf);
if (fskip(sf, (long) subSize, SEEK_CUR) != 0 ) return 0;
}
}
if (is_wav) {
/* make sure the header is sane */
wave_check("name", &wave_info);
num_channels = wave_info.channels;
samp_freq = wave_info.samples_per_sec;
num_samples = data_length / (wave_info.channels * wave_info.bits_per_sample / 8);
}
return is_wav;
}
int preLoadGRO( FILE * pgroinput )
{
int groinfo ;
int iline = 0 ;
int iload = 0 ;
int natomgroline = 0 ;
int blank_signal , info ;
char buffer[ MAXCHARINLINE ] ;
//char cache[ MAXCHARINLINE ] ;
char tmp_char ;
rewind( pgroinput ) ;
fskip( pgroinput , 2 ) ;
while( ( groinfo = freadline( buffer , MAXCHARINLINE , pgroinput , ';' ) ) != 0 )
{
//printf("\n//--------------> WORKING ON NO. %d LINE ... <-------------//\n" , iline );
//info = freadline( buffer , MAXCHARINLINE , pinputfile , ';' );
//printf("\nNow we are at : %s\n" , buffer );
//printf("\n INFO is %d ...\n" , info );
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 );
iload ++ ;
}
//printf("\n%s\n" , buffer );
}
else
{
printf("\nSomething is wrong with the reading file part ...\n");
exit(1);
}
iline ++ ;
}//while( info != 0 );
natomgroline = iload - 1 ;
return( natomgroline ) ;
}
int preLoadEntry( FILE * pfile , char entryName[] , char commentSymbol )
{
int iline = 0 ;
int iload = 0 ;
int blank_signal , info ;
char buffer[ MAXCHARINLINE ] ;
//char cache[ MAXCHARINLINE ] ;
char tmp_char ;
rewind( pfile ) ;
info = fsearch( pfile , entryName ) ;
if( info == NO )
{
printf("\nNo Entry Name [ %s ] Found !\n\n" , entryName ) ;
exit( 179 ) ;
}
fskip( pfile , 1 ) ;
while( ( info = freadline( buffer , MAXCHARINLINE , pfile , commentSymbol ) ) != 0 )
{
//printf("\n//--------------> WORKING ON NO. %d LINE ... <-------------//\n" , iline );
//info = freadline( buffer , MAXCHARINLINE , pinputfile , ';' );
//printf("\nNow we are at : %s\n" , buffer );
//printf("\n INFO is %d ...\n" , info );
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 ) ) == commentSymbol )
{
//printf("\nThis is a comment line ... So nothing will be loaded ...\n");
//fskip( pinputfile , 1 );
continue ;
}
else
{
//printf("\nLine reads : %s ...\n" , buffer );
iload ++ ;
}
//printf("\n%s\n" , buffer );
}
else
{
printf("\nSomething is wrong with the reading file part ...\n");
exit(1);
}
iline ++ ;
}//while( info != 0 );
return( iload ) ;
}
int main( int argc, char * argv[] )
{
FILE * pDATinput , * pGJFoutput ;
char inpDATname[ 100 ] , outGJFname[ 100 ] ;
char method[ 200 ] ;
int multiplicity , charge ;
int natom , ncart , natomselect , natomPrint ;
int iatom ;
double dtmp ;
double dtmpArray[ 100 ] ;
char buffer[ MAXCHARINLINE ] ;
char cache[ MAXCHARINLINE ] ;
char tmpString[ 150 ] ;
char tmp_char ;
int itmp , itmp2 ;
// --------> Declaring utility functions ...
// --------> Some default values ...
multiplicity = 1 ;
charge = 0 ;
strcpy( method , "#P ZIndo( Singlets , NStates = 15 ) NoSymm Pop=Full Test" ) ;
// ==============> Handling the file names and Charge & Multiplicity ... <========= //
// -------> Parsing the Command Line Arguments ...
char ** pcmd ;
pcmd = argv ; //pcmd ++ ;
int icmd = 1 ;
//int exn = 10 ; int exr = 16 ; int exR = 18 ; int exH = 22 ; int exM = 28 ; int exL = 30 ;
int exf = 1 ; int exo = 3 ;
int exs = 18 ; int exmethod = 28 ;
char * flag ;
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 'f' : strcpy( inpDATname , *( ++ pcmd ) ) ;
printf("\nCommand-line argument indicates : Input File name : %s ...\n" , inpDATname );
exf = 7 ;
icmd = icmd + 2 ;
break ;
case 'o' : strcpy( outGJFname , *( ++ pcmd ) ) ;
printf("\nCommand-line argument indicates : Output File name : %s ...\n" , outGJFname );
exo = 9 ;
icmd = icmd + 2 ;
break ;
case 'L' : strcpy( method , *( ++ pcmd ) ) ;
printf("\nCommand-line argument indicates : G09 Method is : %s ...\n" , method );
exmethod = 29 ;
icmd = icmd + 2 ;
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 'h' : printf("\nUsage: %s [ -f 'input dat file name' ] [(optional) -o 'generated g09 input file name' ] [ -s # of atoms chosen as the solute ] [ -L Method for G09 Calculations ]\n\n" , * argv );
printf("\nNOTE : 1) [ -s all ] or [ -s All ] indicates all atoms chosen as solute;\n\n 2) Default for -s is all atoms when nresidue = 1 or natom in 1st residue when nresidue != 1 \n");
//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);
}
}
// --------> Setting DEFAULT value for important variables ...
char defGJFname[100] , defDATname[100] ;
int inputnamelength , outputnamelength ;
switch( exf * exo ) // File Names ... int exf = 1 / 7 ; int exo = 3 / 9;
{
case 1 * 3 : strcpy( inpDATname , "sys.dat" );
strcpy( outGJFname , "sys.inp" ) ;
break ;
case 1 * 9 : outputnamelength = strlen( outGJFname ) ;
strncpy( defDATname, outGJFname , outputnamelength - 4 ) ;
*( defDATname + outputnamelength - 4 ) = '\0' ;
strcat( defDATname, ".dat") ;
strcpy( inpDATname , defDATname );
break ;
case 7 * 3 : inputnamelength = strlen( inpDATname ) ;
strncpy( defGJFname, inpDATname , inputnamelength - 4 ) ;
*( defGJFname + inputnamelength - 4 ) = '\0' ;
strcat( defGJFname, ".inp") ;
strcpy( outGJFname , defGJFname ) ;
break ;
case 7 * 9 : printf("\n\nHoorayyyyyyyy ... All file names are specified !!!\n\n");
break ;
}
// --------------> Summarizing and File Access ...
printf("\n\nInput CNDO .dat file name is : %s ...\n" , inpDATname );
printf("\nOutput G09 inp file name is %s ...\n" , outGJFname );
if( ( pDATinput = fopen( inpDATname , "r" ) ) == NULL )
{
printf("\nUser defined .dat file %s does not exist ... \n" , inpDATname );
exit( 3 );
}
// pGJFoutput = fopen( outGJFname , "wb+" ) ;
// --------------> Reading information from CNDO .dat file ...
int iline = 0 , nRouteLines ;
int iload = 0 , nload ;
int blank_signal , info ;
int isoluteAtom = 0 , nsoluteAtom = 0 ;
int ipointCharge = 0 , npointCharge = 0 ;
double * molecularSpecification ;
if( fsearch( pDATinput , "CHARGE=" ) == 1 )
{
fscanf( pDATinput , "%s" , cache ) ;
charge = atoi( cache ) ;
}
rewind( pDATinput ) ;
if( fsearch( pDATinput , "MULT_CI=" ) == 1 )
{
fscanf( pDATinput , "%s" , cache ) ;
multiplicity = atoi( cache ) ;
}
printf("\nCharge is %d , Multiplicity is %d ...\n" , charge , multiplicity ) ;
rewind( pDATinput ) ;
while( ( info = freadline( buffer , MAXCHARINLINE , pDATinput , '$' ) ) != 0 )
{
blank_signal = stellblank( buffer ) ;
printf("\nLine reads : %s ...\n" , buffer );
if( blank_signal == 0 )
{
break ;
}
else
{
iline ++ ;
}
}
nRouteLines = iline ;
while( ( info = freadline( buffer , MAXCHARINLINE , pDATinput , '$' ) ) != 0 )
{
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 ) ) == '$' )
{
//printf("\nThis is a comment line ... So nothing will be loaded ...\n");
//fskip( pinputfile , 1 );
continue ;
}
else
{
printf("\nLine reads : %s ...\n" , buffer );
itmp = inLineWC( buffer ) ;
if( itmp == 4 )
{
isoluteAtom ++ ;
}
else if( itmp == 5 )
{
ipointCharge ++ ;
}
else
{
continue ;
}
}
//printf("\n%s\n" , buffer );
}
else
{
printf("\nSomething is wrong with the reading file part ...\n");
exit(1);
}
iload ++ ;
}
nload = iload ; nsoluteAtom = isoluteAtom ; npointCharge = ipointCharge ;
printf("\n En TOTO %d coordinates and other specifications loaded ... %d are atoms and %d are point charges ... \n" , nload , isoluteAtom , ipointCharge ) ;
DAT atomlist[ nsoluteAtom + npointCharge ] ;
rewind( pDATinput ) ;
fskip( pDATinput , nRouteLines ) ;
iload = 0 ; isoluteAtom = 0 ; ipointCharge = 0 ;
while( ( info = freadline( buffer , MAXCHARINLINE , pDATinput , '$' ) ) != 0 )
{
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 );
itmp = inLineWC( buffer ) ;
if( itmp == 4 )
{
strpickword( buffer , 1 , cache ) ;
atomlist[ isoluteAtom ].cx = atof( cache ) ;
strpickword( buffer , 2 , cache ) ;
atomlist[ isoluteAtom ].cy = atof( cache ) ;
strpickword( buffer , 3 , cache ) ;
atomlist[ isoluteAtom ].cz = atof( cache ) ;
strpickword( buffer , 4 , cache ) ;
atomlist[ isoluteAtom ].atomlabel = atoi( cache ) ;
printf("\n No. %d atom ...\n" , isoluteAtom ) ;
isoluteAtom ++ ;
}
else if( itmp == 5 )
{
strpickword( buffer , 1 , cache ) ;
atomlist[ nsoluteAtom + ipointCharge ].cx = atof( cache ) ;
strpickword( buffer , 2 , cache ) ;
atomlist[ nsoluteAtom + ipointCharge ].cy = atof( cache ) ;
strpickword( buffer , 3 , cache ) ;
atomlist[ nsoluteAtom + ipointCharge ].cz = atof( cache ) ;
strpickword( buffer , 4 , cache ) ;
atomlist[ nsoluteAtom + ipointCharge ].atomlabel = -1 * atoi( cache ) ;
strpickword( buffer , 5 , cache ) ;
atomlist[ nsoluteAtom + ipointCharge ].atomcharge = atof( cache ) ;
printf("\n No. %d atom ...\n" , nsoluteAtom + ipointCharge ) ;
ipointCharge ++ ;
}
else
{
continue ;
}
}
//printf("\n%s\n" , buffer );
}
else
{
printf("\nSomething is wrong with the reading file part ...\n");
exit(1);
}
iload ++ ;
}
if( iload == nload && ipointCharge == npointCharge && isoluteAtom == nsoluteAtom )
{
printf("\n En TOTO %d coordinates and other specifications loaded ... %d are atoms and %d are point charges ... \n" , nload , nsoluteAtom , npointCharge ) ;
}
else
{
printf("\nEh...oh... Something is wrong during the loading ... \n");
printf("\n En TOTO %d coordinates and other specifications loaded ... %d are atoms and %d are point charges ... \n" , nload , nsoluteAtom , npointCharge ) ;
exit( 515 ) ;
}
natom = nsoluteAtom + npointCharge ;
switch ( exs )
{
case 19 : natomPrint = natomselect ; break ;
case 18 : natomPrint = nsoluteAtom ; break ;
case 20 : natomPrint = natom ; break ;
default : printf("\nSomething is wrong during the printing-out ...\n") ; exit( 538 ) ;
}
// --------------> Outputing ...
char chkname[ 100 ] , rwfname[ 100 ] ;
outputnamelength = strlen( outGJFname ) ;
strncpy( chkname , outGJFname , outputnamelength - 4 ) ;
*( chkname + outputnamelength - 4 ) = '\0' ;
strcat( chkname, ".chk") ;
strncpy( rwfname , outGJFname , outputnamelength - 4 ) ;
*( rwfname + outputnamelength - 4 ) = '\0' ;
strcat( rwfname, ".rwf") ;
if( exmethod == 28 )
{
printf("\nNo QC method specified in command-line , go with ===> %s <===\n" , method );
}
pGJFoutput = fopen( outGJFname , "wb+" );
fprintf( pGJFoutput , "%%chk=%s\n%%rwf=%s\n%%mem=4GB\n%%nprocshared=2\n\n" , chkname , rwfname );
fprintf( pGJFoutput , "%s\n\n" , method );
fprintf( pGJFoutput , "%s corresponding QC\n\n" , inpDATname );
fprintf( pGJFoutput , "%d\t%d\t\n" , charge , multiplicity );
for( iatom = 0 ; iatom < natomPrint ; iatom ++ )
{
fprintf( pGJFoutput , "%d\t% 16.12f\t% 16.12f\t% 16.12f\n" , atomlist[ iatom ].atomlabel , atomlist[ iatom ].cx , atomlist[ iatom ].cy , atomlist[ iatom ].cz );
}
int nwords , signal ;
nwords = inLineWC( method ) ;
signal = 0 ;
for( itmp = 0 ; itmp < nwords ; itmp ++ )
{
strpickword( method , itmp + 1 , buffer ) ;
if( strcmp( buffer , "dftba") == 0 || strcmp( buffer , "DFTBA") == 0 )
{
signal = 1 ;
break ;
}
}
if( signal == 1 )
{
fprintf( pGJFoutput , "\n@GAUSS_EXEDIR:dftba.prm\n\n" );
}
fprintf( pGJFoutput , "\n" ) ;
fclose( pGJFoutput );
}
/*-------------------------------------------------------------------
* CTReadRAS - read a slice from a sun raster file
*-------------------------------------------------------------------
*/
static int CTReadRAS(FILE *fp, CTSlice slice, int x1, int y1, int x2, int y2)
{
int linesize,lsize,csize,isize,flipit,i,j,w,h,d,rv;
unsigned char *line, r[256], g[256], b[256];
struct rasterfile sunheader;
rv = 0;
/* read in the Sun Rasterfile picture */
flipit = 0;
fread(&sunheader, sizeof(struct rasterfile), 1, fp);
if (sunheader.ras_magic != RAS_MAGIC)
{
flipl( (unsigned char *) &sunheader.ras_magic);
if (sunheader.ras_magic == RAS_MAGIC)
flipit = 1;
else
flipl( (unsigned char *) &sunheader.ras_magic);
}
if (sunheader.ras_magic != RAS_MAGIC)
return( SunRasError("not a Sun rasterfile") );
if (flipit) {
flipl((unsigned char *) &sunheader.ras_width);
flipl((unsigned char *) &sunheader.ras_height);
flipl((unsigned char *) &sunheader.ras_depth);
flipl((unsigned char *) &sunheader.ras_length);
flipl((unsigned char *) &sunheader.ras_type);
flipl((unsigned char *) &sunheader.ras_maptype);
flipl((unsigned char *) &sunheader.ras_maplength);
}
/* make sure that the input picture can be dealt with */
if (sunheader.ras_depth != 8)
{
fprintf (stderr, "Sun rasterfile image has depth %d\n",
sunheader.ras_depth);
fprintf (stderr, "Depths supported are 8\n");
return 1;
}
if (sunheader.ras_type != RT_OLD && sunheader.ras_type != RT_STANDARD &&
sunheader.ras_type != RT_BYTE_ENCODED &&
sunheader.ras_type != RT_FORMAT_RGB)
{
fprintf (stderr, "Sun rasterfile of unsupported type %d\n",
sunheader.ras_type);
return 1;
}
if (sunheader.ras_maptype != RMT_RAW && sunheader.ras_maptype != RMT_NONE &&
sunheader.ras_maptype != RMT_EQUAL_RGB)
{
fprintf (stderr, "Sun rasterfile colormap of unsupported type %d\n",
sunheader.ras_maptype);
return 1;
}
w = sunheader.ras_width;
h = sunheader.ras_height;
d = sunheader.ras_depth;
isize = sunheader.ras_length ?
sunheader.ras_length :
(w * h * d) / 8;
csize = (sunheader.ras_maptype == RMT_NONE) ? 0 : sunheader.ras_maplength;
lsize = w * h * ( d == 1 ? d : d/8);
linesize = w * d;
/* if ((linesize % 48) && d == 24) linesize += (48 - (linesize % 48)); */
if (linesize % 16) linesize += (16 - (linesize % 16));
linesize /= 8;
#ifdef DEBUG
fprintf(stderr,"%s: LoadSunRas() - loading a %dx%d pic, %d planes\n",
cmd, w, h, d);
fprintf(stderr,
"type %d, maptype %d, isize %d, csize %d, lsize %d, linesize %d\n",
sunheader.ras_type, sunheader.ras_maptype,
isize, csize, lsize, linesize);
#endif
/* read in the colormap, if any */
if (sunheader.ras_maptype == RMT_EQUAL_RGB && csize)
{
fread (r, sizeof(unsigned char), sunheader.ras_maplength/3, fp);
fread (g, sizeof(unsigned char), sunheader.ras_maplength/3, fp);
fread (b, sizeof(unsigned char), sunheader.ras_maplength/3, fp);
}
else if (sunheader.ras_maptype == RMT_RAW && csize)
{
/* we don't know how to handle raw colormap, ignore */
fskip(fp, csize);
}
else
{
/* no colormap, make one up */
if (sunheader.ras_depth == 1)
{
r[0] = g[0] = b[0] = 0;
r[1] = g[1] = b[1] = 255;
}
else if (sunheader.ras_depth == 8)
{
for (i = 0; i < 256; i++)
r[i] = g[i] = b[i] = i;
}
}
/*
CTSliceXSize(slice) = w;
CTSliceYSize(slice) = h;
*/
if (x1==-1)
{
slice->x1=slice->y1=x1=y1=0;
slice->x2=x2=w-1;
slice->y2=y2=h-1;
slice->cdata = (unsigned char *)malloc(sizeof(unsigned char)*(x2-x1+1)*
(y2-y1+1));
memset(slice->cdata, '\0', sizeof(char)*(x2-x1+1)*(y2-y1+1));
CTSliceWidth(slice) = w;
CTSliceHeight(slice) = h;
}
/* allocate memory for picture and read it in */
/* note we may slightly overallocate here (if image is padded) */
line = (unsigned char *) malloc (linesize);
if (line == NULL)
{
fprintf(stderr, "Can't allocate memory for image\n");
exit(1);
}
for (i = 0; i < h; i++)
{
if (sunheader.ras_type == RT_BYTE_ENCODED)
{
if (rle_read (line, 1, linesize, fp, (i==0)) != linesize) break;
}
else
{
if (fread (line, 1, linesize, fp) != (unsigned int)linesize)
return (SunRasError ("file read error"));
}
if (slice->y1 <= i && i <= slice->y2)
{
for (j=slice->x1; j<=slice->x2; j++)
CTSliceCharData(slice, i, j) = line[j];
}
/*
switch (d) {
case 1: SunRas1to8 (image + w * i, line, w); break;
case 8: memcpy (image + w * i, line, w); break;
case 24: memcpy (image + w * i * 3, line, w * 3); break;
}
*/
}
#ifdef DEBUG
fprintf(stderr,"Sun ras: image loaded!\n");
#endif
/*
if (d == 24) {
if (sunheader.ras_type != RT_FORMAT_RGB) fixBGR(image,w,h);
rv = Conv24to8 (image, w, h, nc);
free (image);
return (rv);
}
else {
pic = image;
pWIDE = w;
pHIGH = h;
return (0);
}
*/
CTSliceCompMinMaxD(slice);
return(0);
}
/*-------------------------------------------------------------------
* CTReadSLC - read a slice from an SLC file
*-------------------------------------------------------------------
*/
static int CTReadSLC(FILE *fp, CTSlice slice, int num, int x1, int y1,
int x2, int y2)
{
int i, remaining, current_value;
unsigned int size;
// unsigned int xsize, ysize, zsize, bits, magic;
// float xunit, yunit, zunit;
unsigned char *data_ptr;
C_CompressionType compression;
// C_UnitType unit;
// C_DataOrigin data;
// C_DataModification datamod;
if (x1==-1)
{
slice->x1=slice->y1=x1=y1=0;
slice->x2=x2=CTSliceXSize(slice)-1;
slice->y2=y2=CTSliceYSize(slice)-1;
slice->cdata=(unsigned char *)malloc(sizeof(char)*(x2-x1+1)*(y2-y1+1));
memset(slice->cdata, '\0', sizeof(char)*(x2-x1+1)*(y2-y1+1));
}
CTSliceWidth(slice) = x2-x1+1;
CTSliceHeight(slice) = y2-y1+1;
/* skip header */
fskip(fp, sizeof(int)*5 + sizeof(float)*3 + sizeof(C_UnitType) +
sizeof(C_DataOrigin) + sizeof(C_DataModification));
/* get compression type */
fread(&compression, sizeof(C_CompressionType), 1, fp);
/* skip (num-1) slices */
if (compression == C_NO_COMPRESSION)
{
fskip(fp, CTVolXSize(slice->vol)*CTVolYSize(slice->vol)*(num-1));
}
else
{
for (i=0; i<num-1; i++)
{
fread(&size, sizeof(int), 1, fp);
fskip(fp, size);
}
}
/* read slice */
switch (compression)
{
case C_NO_COMPRESSION:
fread(slice->cdata, sizeof(char),
CTVolXSize(slice->vol)*CTVolYSize(slice->vol), fp);
break;
case C_RUN_LENGTH_ENCODE:
fread(&size, sizeof(int), 1, fp);
data_ptr = slice->cdata;
while (1)
{
current_value = getc(fp);
if ( !(remaining = (current_value & 0x7f)) )
break;
if ( current_value & 0x80 )
while (remaining--)
*(data_ptr++) = getc(fp);
else
{
current_value = getc(fp);
while (remaining--)
*(data_ptr++) = current_value;
}
}
break;
default:
fprintf(stderr, "Error in compression type of SLC file\n");
return(-1);
}
CTSliceCompMinMaxD(slice);
return(0);
}
/**
* ti9x_file_read_flash:
* @filename: name of flash file to open.
* @content: where to store the file content.
*
* Load the flash file into a #FlashContent structure.
*
* Structure content must be freed with #tifiles_content_delete_flash when
* no longer used. If error occurs, the structure content is released for you.
*
* Return value: an error code, 0 otherwise.
**/
int ti9x_file_read_flash(const char *filename, Ti9xFlash *head)
{
FILE *f;
Ti9xFlash *content = head;
long cur_pos = 0;
int tib = 0;
char signature[9];
int ret = ERR_FILE_IO;
if (head == NULL)
{
tifiles_critical("%s: an argument is NULL", __FUNCTION__);
return ERR_INVALID_FILE;
}
if (!tifiles_file_is_flash(filename) && !tifiles_file_is_tib(filename))
{
ret = ERR_INVALID_FILE;
goto tfrf2;
}
// detect file type (old or new format)
tib = tifiles_file_is_tib(filename);
f = g_fopen(filename, "rb");
if (f == NULL)
{
tifiles_info("Unable to open this file: %s", filename);
ret = ERR_FILE_OPEN;
goto tfrf2;
}
if (fseek(f, 0, SEEK_END)) goto tfrf;
cur_pos = ftell(f);
if (cur_pos < 0) goto tfrf;
if (fseek(f, 0, SEEK_SET)) goto tfrf;
// The TI-68k series' members have at best 4 MB of Flash.
// TIB files larger than that size are insane.
if (cur_pos >= (4L << 20))
{
ret = ERR_INVALID_FILE;
goto tfrf;
}
if (tib)
{
// tib is an old format but mainly used by developers
memset(content, 0, sizeof(Ti9xFlash));
content->data_length = (uint32_t)cur_pos;
strncpy(content->name, "basecode", sizeof(content->name) - 1);
content->name[sizeof(content->name) - 1] = 0;
content->data_type = 0x23; // FLASH os
content->data_part = (uint8_t *)g_malloc0(content->data_length);
if (content->data_part == NULL)
{
ret = ERR_MALLOC;
goto tfrf;
}
if (fread(content->data_part, 1, content->data_length, f) < content->data_length) goto tfrf;
switch(content->data_part[8])
{
case 1: content->device_type = DEVICE_TYPE_92P; break; // TI92+
case 3: content->device_type = DEVICE_TYPE_89; break; // TI89
// value added by the TI community according to HWID parameter
// doesn't have any 'legal' existence.
case 8: content->device_type = DEVICE_TYPE_92P; break; // V200PLT
case 9: content->device_type = DEVICE_TYPE_89; break; // Titanium
}
content->next = NULL;
}
else
{
for (content = head;; content = content->next)
{
if (fread_8_chars(f, signature) < 0) goto tfrf;
content->model = tifiles_file_get_model(filename);
if (fread_byte(f, &(content->revision_major)) < 0) goto tfrf;
if (fread_byte(f, &(content->revision_minor)) < 0) goto tfrf;
if (fread_byte(f, &(content->flags)) < 0) goto tfrf;
if (fread_byte(f, &(content->object_type)) < 0) goto tfrf;
if (fread_byte(f, &(content->revision_day)) < 0) goto tfrf;
if (fread_byte(f, &(content->revision_month)) < 0) goto tfrf;
if (fread_word(f, &(content->revision_year)) < 0) goto tfrf;
if (fskip(f, 1) < 0) goto tfrf;
if (fread_8_chars(f, content->name) < 0) goto tfrf;
if (fskip(f, 23) < 0) goto tfrf;
if (fread_byte(f, &(content->device_type)) < 0) goto tfrf;
if (fread_byte(f, &(content->data_type)) < 0) goto tfrf;
if (fskip(f, 23) < 0) goto tfrf;
if (fread_byte(f, &(content->hw_id)) < 0) goto tfrf;
if (fread_long(f, &(content->data_length)) < 0) goto tfrf;
if (content->data_type != TI89_LICENSE && !check_device_type(content->device_type))
{
ret = ERR_INVALID_FILE;
goto tfrf;
}
if (!check_data_type(content->data_type))
{
ret = ERR_INVALID_FILE;
goto tfrf;
}
// TODO: modify this code if TI ever makes a TI-eZ80 model with more than 4 MB of Flash memory...
if (content->data_length > 4U * 1024 * 1024 - 65536U)
{
// Data length larger than Flash memory size - boot code sector size doesn't look right.
ret = ERR_INVALID_FILE;
goto tfrf;
}
content->data_part = (uint8_t *)g_malloc0(content->data_length);
if (content->data_part == NULL)
{
ret = ERR_MALLOC;
goto tfrf;
}
if (fread(content->data_part, 1, content->data_length, f) < content->data_length) goto tfrf;
if ( (content->data_type == TI83p_AMS && content->data_part[0] != 0x80)
|| (content->data_type == TI83p_APPL && content->data_part[0] != 0x81))
{
ret = ERR_INVALID_FILE;
goto tfrf;
}
content->next = NULL;
// check for end of file
if (fread_8_chars(f, signature) < 0)
{
break;
}
if (strcmp(signature, "**TIFL**") || feof(f))
{
break;
}
if (fseek(f, -8, SEEK_CUR)) goto tfrf;
content->next = (Ti9xFlash *)g_malloc0(sizeof(Ti9xFlash));
if (content->next == NULL)
{
ret = ERR_MALLOC;
goto tfrf;
}
}
}
fclose(f);
return 0;
tfrf: // release on exit
tifiles_critical("%s: error reading / understanding file %s", __FUNCTION__, filename);
fclose(f);
tfrf2:
tifiles_content_delete_flash(content);
return ret;
}
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( ¤t_time );
char now[ 300 ] ;
strcpy( now , ctime( ¤t_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 ) ;
}
/**
* ti9x_file_read_flash:
* @filename: name of flash file to open.
* @content: where to store the file content.
*
* Load the flash file into a #FlashContent structure.
*
* Structure content must be freed with #tifiles_content_delete_flash when
* no longer used. If error occurs, the structure content is released for you.
*
* Return value: an error code, 0 otherwise.
**/
int ti9x_file_read_flash(const char *filename, Ti9xFlash *head)
{
FILE *f;
Ti9xFlash *content = head;
int tib = 0;
char signature[9];
if (!tifiles_file_is_flash(filename) && !tifiles_file_is_tib(filename))
{
return ERR_INVALID_FILE;
}
if (head == NULL)
{
tifiles_critical("%s: an argument is NULL", __FUNCTION__);
return ERR_INVALID_FILE;
}
// detect file type (old or new format)
tib = tifiles_file_is_tib(filename);
f = g_fopen(filename, "rb");
if (f == NULL)
{
tifiles_info("Unable to open this file: %s\n", filename);
return ERR_FILE_OPEN;
}
if (tib)
{ // tib is an old format but mainly used by developers
memset(content, 0, sizeof(Ti9xFlash));
if(fseek(f, 0, SEEK_END)) goto tfrf;
content->data_length = (uint32_t) ftell(f);
if(fseek(f, 0, SEEK_SET)) goto tfrf;
strcpy(content->name, "basecode");
content->data_type = 0x23; // FLASH os
content->data_part = (uint8_t *)g_malloc0(content->data_length);
if (content->data_part == NULL)
{
fclose(f);
return ERR_MALLOC;
}
if(fread(content->data_part, 1, content->data_length, f) < content->data_length) goto tfrf;
switch(content->data_part[8])
{
case 1: content->device_type = DEVICE_TYPE_92P; break; // TI92+
case 3: content->device_type = DEVICE_TYPE_89; break; // TI89
// value added by the TI community according to HWID parameter
// doesn't have any 'legal' existence.
case 8: content->device_type = DEVICE_TYPE_92P; break; // V200PLT
case 9: content->device_type = DEVICE_TYPE_89; break; // Titanium
}
content->next = NULL;
}
else
{
for (content = head;; content = content->next)
{
if(fread_8_chars(f, signature) < 0) goto tfrf;
content->model = tifiles_file_get_model(filename);
if(fread_byte(f, &(content->revision_major)) < 0) goto tfrf;
if(fread_byte(f, &(content->revision_minor)) < 0) goto tfrf;
if(fread_byte(f, &(content->flags)) < 0) goto tfrf;
if(fread_byte(f, &(content->object_type)) < 0) goto tfrf;
if(fread_byte(f, &(content->revision_day)) < 0) goto tfrf;
if(fread_byte(f, &(content->revision_month)) < 0) goto tfrf;
if(fread_word(f, &(content->revision_year)) < 0) goto tfrf;
if(fskip(f, 1) < 0) goto tfrf;
if(fread_8_chars(f, content->name) < 0) goto tfrf;
if(fskip(f, 23) < 0) goto tfrf;
if(fread_byte(f, &(content->device_type)) < 0) goto tfrf;
if(fread_byte(f, &(content->data_type)) < 0) goto tfrf;
if(fskip(f, 23) < 0) goto tfrf;
if(fread_byte(f, &(content->hw_id)) < 0) goto tfrf;
if(fread_long(f, &(content->data_length)) < 0) goto tfrf;
if(content->data_type != TI89_LICENSE && !check_device_type(content->device_type))
{
return ERR_INVALID_FILE;
}
if(!check_data_type(content->data_type))
{
return ERR_INVALID_FILE;
}
content->data_part = (uint8_t *)g_malloc0(content->data_length);
if (content->data_part == NULL)
{
fclose(f);
tifiles_content_delete_flash(content);
return ERR_MALLOC;
}
if(fread(content->data_part, 1, content->data_length, f) < content->data_length) goto tfrf;
content->next = NULL;
// check for end of file
if(fread_8_chars(f, signature) < 0)
{
break;
}
if(strcmp(signature, "**TIFL**") || feof(f))
{
break;
}
if(fseek(f, -8, SEEK_CUR)) goto tfrf;
content->next = (Ti9xFlash *)g_malloc0(sizeof(Ti9xFlash));
if (content->next == NULL)
{
fclose(f);
tifiles_content_delete_flash(content);
return ERR_MALLOC;
}
}
}
fclose(f);
return 0;
tfrf: // release on exit
tifiles_critical("%s: error reading / understanding file %s", __FUNCTION__, filename);
fclose(f);
tifiles_content_delete_flash(content);
return ERR_FILE_IO;
}
