gsl_matrix *
dTcovariance(gsl_matrix *A, gsl_matrix *B, gsl_matrix *Cov) {
gsl_matrix *AA = NULL, *BB = NULL;
AA = dtranspose(A, AA);
BB = dtranspose(B, BB);
Cov = dcovariance(AA, BB, Cov);
gsl_matrix_free(AA);
gsl_matrix_free(BB);
return Cov;
}
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 ) ;
}
