int
forwsearch(int f, int n)
{
int status;
hst_init('/');
status = fsearch(f, n, FALSE, FALSE);
hst_flush();
return status;
}
/** Intersection of lists of occurrences **/
int svs (void *index, uint *idsIn, uint nids, uint **list, uint *len) {
//sorting ids ==> lists are sorted by frequency !!
uint i;
uint *ids = (uint *)malloc (sizeof(uint) * nids);
for (i=0;i<nids;i++) ids[i]=idsIn[i];
simplesort(ids,nids); // ==> change to sort by lenList !!
/**starting SVS ------------------------ */
//Creating the first list;
{ uint i,j,n;
uint *firstlist;
uint matches;
uncompressList (index, ids[0], list, len);
firstlist =*list;
n=*len;
uint result;
for (i=1; i<nids; i++) { //the nids-1 remaining lists
matches =0;
for (j=0;j<n;j++) {
result=fsearch (index, firstlist[j] , ids[i]);
//result=fsearchUNCOMPRESS (index, firstlist[j] , ids[i]);
if (result) {
//if (fsearch (index, firstlist[j] , ids[i])) {
//if (fsearchUNCOMPRESS (index, firstlist[j] , ids[i])) {
firstlist[matches++]= firstlist[j];
//printf("\nFSEARCH de posicion %d = acierto contra palabra ",firstlist[j]);
}
//else printf("\nFSEARCH de posicion %d = fallo contra palabra ",firstlist[j]);
}
n=matches;
if (n ==0) {
free(*list); *list=NULL;*len =0;
break;
}
}
*len =n;
free(ids);
}
return 0;
}
static int
make_alias_fname(mmv_t *mmv, REP *p)
{
char *fstart;
char *seqstart;
int seq;
fstart = mmv->pathbuf + strlen(mmv->pathbuf);
strcpy(fstart, TEMP);
seqstart = fstart + strlen(TEMP);
seq = 0;
while (true) {
sprintf(seqstart, "%03d", seq);
if (fsearch(fstart, p->r_hto->h_di) == NULL) {
break;
}
++seq;
}
return (seq);
}
//-------------------------------------------------------------------------
void reply_search(uint8_t * receivebuffer)
{
char filename[13];
uint8_t searchresults[20];
uint8_t numofsearch;
uint8_t i;
mystrncpy(filename, (char *)&receivebuffer[3], receivebuffer[0] - 3);
filename[receivebuffer[0] - 3] = '\0';
fsearch(searchresults, &numofsearch, filename);
for (i = 0; i < numofsearch; i++)
{
fdirnode((char *)&reply[3], 29, searchresults[i]);
reply[0] = mystrlen((char *)&reply[3]) + 3;
reply[1] = 221;
reply[2] = nodeid;
//printStringN(reply,32);
StandardSocketSend(0xefef, 0xffff, 32, reply);
}
}
int
scrforwsearch(int f, int n)
{
return fsearch(f, n, FALSE, TRUE);
}
/* ARGSUSED */
static int
rsearch(int f, int n, int dummy GCC_UNUSED, int fromscreen)
{
int status;
int wrapok;
MARK curpos;
int didwrap;
assert(curwp != 0);
if (f && n < 0) /* reverse direction */
return fsearch(f, -n, FALSE, fromscreen);
if (n == 0)
n = 1;
wrapok = window_b_val(curwp, MDWRAPSCAN);
last_srch_direc = REVERSE;
/* ask the user for the regular expression to search for, and
* find n'th occurrence.
*/
status = readpattern("Reverse search: ", &searchpat, &gregexp,
EOS, fromscreen);
if (status != TRUE)
return status;
ignorecase = window_b_val(curwp, MDIGNCASE);
if (curwp == 0)
return FALSE;
curpos = DOT;
scanboundry(wrapok, DOT, REVERSE);
didwrap = FALSE;
while (n--) {
movenext(&(DOT), REVERSE);
status = scanner(gregexp, REVERSE, wrapok, &didwrap);
if (didwrap) {
mlwrite(
"[Search wrapped past start of buffer]");
didwrap = FALSE;
}
if (status != TRUE)
break;
}
if (status == TRUE) {
savematch(DOT, gregexp->mlen);
if (samepoint(DOT, curpos)) {
mlwrite(onlyonemsg);
}
} else if (status == FALSE) {
movenext(&(DOT), FORWARD);
not_found_msg(wrapok, REVERSE);
} else if (status == ABORT) {
mlwarn("[Aborted]");
DOT = curpos;
return status;
}
attrib_matches();
return status;
}
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);
}
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 );
}
int main( int argc , char * argv[ ] )
{
FILE * pndx , * pdxdr , * pfreq , * patomlist , * passgn ;
FILE * debug ;
char dxdrname [ 50 ] , ndxname [ 50 ] , atomlistname [ 50 ] , freqname [ 50 ], outassgnname [ 50 ] ;
char ** pcmd ; pcmd = argv ;
int icmd , itmp ;
int ncart , natom , nmode , nfreqprovide;
int icart , iatom , imode , ifreq ;
int exfreq , exatomlist ;
int fakeOrNot = 0 ;
time_t current_time;
time( ¤t_time );
char now[ 300 ] ;
strcpy( now , ctime( ¤t_time ) );
int lennow = strlen( now ) ;
*( now + lennow - 1 ) = ' ';
// ========> Recording Command-Line Arguments ...
printf("\n**********************************************************************\n");
printf("* G_NMASSGN_D : Listing the localization of all vibrational modes. *\n");
printf("* *\n");
printf("* ");
for( icmd = 0 ; icmd < argc ; icmd ++ )
{
printf("%s " , *( pcmd + icmd ) );
}
printf("\n");
printf("* *\n");
printf("* *\n");
printf("* Current Time : %s *\n" , now );
printf("* *\n");
printf("* *\n");
printf("**********************************************************************\n");
// =====> Setting up default file names ...
strcpy( dxdrname , "dxdr.deb" );
strcpy( ndxname , "system.index" );
strcpy( freqname , "vibfrequency.deb" );
strcpy( outassgnname , "system.assgn" );
strcpy( atomlistname , "atom.list" );
// =====> Parsing command line input arguments ...
if( argc == 1 )
{
printf("\n\nNo command-line arguments provided ... Mission aborting ...\n\n");
printf("\nPlease refer to the usage by typing ' %s -h '\n\n" , * argv );
exit(1);
}
char * flag ;
icmd = 1 ;
while( icmd < argc )
{
pcmd ++ ;
flag = * pcmd ;
printf("\nNo.%d argument , Currently @ flag = %s ...\n\n" , icmd , flag );
if( ( * flag == '-' ) && ( strlen( flag ) == 2 ) )
{
switch ( *( flag + 1 ) )
{
case 'f' : strcpy( dxdrname , *( ++ pcmd ) ) ;
printf("\nCommand-line argument indicates : Input dxdr File name : %s ...\n" , dxdrname );
icmd = icmd + 2 ;
break ;
case 'o' : strcpy( outassgnname , *( ++ pcmd ) );
printf("\nCommand-line argument indicates : Output File name : %s ...\n" , outassgnname );
icmd = icmd + 2 ;
break ;
case 'w' : strcpy( freqname , *( ++ pcmd ) );
printf("\nCommand-line argument indicates : Input frequency File name : %s ...\n" , freqname );
icmd = icmd + 2 ;
break ;
case 'n' : strcpy( ndxname , *( ++ pcmd ) );
printf("\nCommand-line argument indicates : Input index File name : %s ...\n" , ndxname );
icmd = icmd + 2 ;
break ;
case 'l' : strcpy( atomlistname , *( ++ pcmd ) );
if( ( strcmp( atomlistname , "none" ) ) == 0 )
{
printf("\nCommand-line argument indicates : No AtomList needed ... Will not produce fake frequency file ...\n" );
fakeOrNot = 0 ;
}
else
{
printf("\nCommand-line argument indicates : Input atom list File name : %s ...\n" , atomlistname );
fakeOrNot = 1 ;
}
icmd = icmd + 2 ;
break ;
case 'h' : printf("\nUsage: %s [ -f 'input dxdr file name' ] [ -n 'input index file name (in GROMACS .ndx format)' ] [(optional) -o 'output NM assignment file name' ] [ -l atom list file (listing the atomic number of all atoms in system ; \"none\" if no frequency file desired)][ -w 'input vibrational frequency file ; best case length = nmode' ]\n\n" , * argv );
printf("\n\n==> NOTE : In order to be fool-proof , if there is mis-match on the NAtom between dxdr file and any other file , this code will set NAtom to be the number from dxdr automatically ...\n\n");
//printf("\nUsage: %s [ -t G09 calculation type : 1=ONIOM ; 2=Point Charge ] [ -f 'input gro file name' ] [(optional) -o 'output g09 file name' ] [ -n # of layers (integer) ] [ (optional) -r radius of middle layer (real) ] [-R radius of lower layer (real) ] [ -H method for Highest layer (string) ] [ (optional) -M method for Middle layer (string) ] [ -L method for Lower layer (string) ] [ -x input GMX .itp file ]\n\n" , * argv );
//exh = 9 ;
icmd = icmd + 1 ;
exit(1) ;
default : printf("\n\nInvalid option ' %s ' ... Please refer to the usage by typing ' %s -h '\n\n" , flag , * argv );
icmd = argc ;
exit(1);
}
}
else
{
printf("\n\nInvalid option ' %s ' ... Please refer to the usage by typing ' %s -h '\n\n" , flag , * argv );
exit(1);
}
}
// =====> Open the files ...
if( ( pndx = fopen( ndxname , "r" ) ) == NULL )
{
printf("\nUser-defined index file %s does not exist ...\n\n" , ndxname );
exit( 1 );
}
if( ( pdxdr = fopen( dxdrname , "r" ) ) == NULL )
{
printf("\nUser-defined dxdr file %s does not exist ...\n\n" , dxdrname );
exit( 1 );
}
double * freq ;
if( ( pfreq = fopen( freqname , "r" ) ) == NULL )
{
printf("\nUser-defined frequency file %s does not exist ...\n\n" , freqname );
printf("\nBut it's OK , we will procede without frequency information ... \n");
exfreq = 0 ;
}
else
{
nfreqprovide = flength( pfreq );
rewind( pfreq ) ;
freq = ( double * ) calloc( nfreqprovide , sizeof( double ) ) ;
fload( pfreq , freq );
rewind( pfreq );
exfreq = 1 ;
}
int * atomlist , natomlistprovide ;
if( fakeOrNot == 1 )
{
if( ( patomlist = fopen( atomlistname , "r" ) ) == NULL )
{
printf("\nUser-defined atom list file %s does not exist ...\n\n" , atomlistname );
printf("\nMeaning ... All of your atoms will be carbon ...\n");
exatomlist = 0 ;
}
else
{
natomlistprovide = flength( patomlist );
rewind( patomlist );
atomlist = ( int * ) calloc( natomlistprovide , sizeof( int ) ) ;
int_fload( patomlist , atomlist );
exatomlist = 1 ;
}
}
// =====> Read the index file (*****.ndx) ...
int countlrb , countrrb ;
int ngroup ;
int ilrb , irrb , igroup ;
char c ;
char ** groupnames ;
char tmpstring[ 100 ] ;
char tmpchar ;
// -----> Finding out how many groups are defined in index file ...
ilrb = 0 ; irrb = 0 ;
//fsearch( pndx , "begin" );
//fscanf( pndx , "%s" , tmpstring );
//if( strcmp( tmpstring , "]" ) != 0 )
//{
// printf("\nSomething is wrong with the ndx file format at the beginning ... Mission Aborting ... \n") ;
//
// exit(3);
//
//}
//fskip( pndx , 1 ) ;
rewind( pndx ) ;
while( ( c = fgetc( pndx ) ) != EOF )
{
if( c == '[' )
{
ilrb ++ ;
}
else if( c == ']')
{
irrb ++ ;
}
else
{
continue ;
}
}
if( ilrb == irrb )
{
ngroup = ilrb ;
printf("\nThere are %d defined groups in the index file ...\n" , ngroup );
}
else
{
printf("\nSomething is wrong in the index file ... There are unmatched brackets or broken entries ...\n");
exit( 2 );
}
if( ngroup == 0 )
{
printf("\nThis index file is an empty file ... Mission Aborting ...\n");
exit(4);
}
// -----> Finding out how many atoms are in each group
int * natom_in_each_group = calloc( ngroup , sizeof( int ) ) ;
int current_atom_index , next_atom_index ;
int info ;
rewind( pndx ) ;
//fsearch( pndx , "begin" );
//fskip( pndx , 1 ) ;
for( igroup = 0 ; igroup < ngroup ; igroup ++ )
{
printf("\n--------------------------> GROUP #%d <----------------------------" , igroup + 1 );
//itmp = 0 ;
fsearch( pndx , "]" ) ;
//fskip( pndx , 1 ) ;
//printf("\nHere we are ... : %c " , fgetc( pndx ) );
fscanf( pndx , "%s" , tmpstring );
//printf("\nFor this group , the 1st grabbed tmpstring is %s ... \n" , tmpstring );
//while( strcmp( tmpstring , "[") != 0 )
for( itmp = 0 ; strcmp( tmpstring , "[" ) != 0 && info != EOF ; )
{
//printf("\nGrabbed tmpstring is %s ... \n" , tmpstring ) ;
if( strcmp( tmpstring , "-" ) == 0 )
{
//printf("\nThe '-' situation happened ... before '-' we are at No.%d atom ... \n" , current_atom_index );
fscanf( pndx , "%d" , &next_atom_index );
//printf("\nAnd after '-' we are at No.%d atom ... \n" , next_atom_index );
itmp = itmp + ( next_atom_index - current_atom_index );
*( natom_in_each_group + igroup ) = itmp ;
current_atom_index = next_atom_index ;
info = fscanf( pndx , "%s" , tmpstring ) ;
}
else
{
itmp ++ ;
*( natom_in_each_group + igroup ) = itmp ;
current_atom_index = atoi( tmpstring );
//printf("\nNormal situation ... current_atom_index is %d ... \n" , current_atom_index );
info = fscanf( pndx , "%s" , tmpstring );
}
}
if( info == EOF )
{
printf("\nHit the bottom of file ...\n\n") ;
break ;
}
printf("\nDone with #%d group ... \n" , igroup + 1 );
}
printf("\n--------------------------> Done checking up groups <----------------------------");
/* Debugging output for this part ... */
printf("\n== Group Information Summary ==\n");
for( igroup = 0 ; igroup < ngroup ; igroup ++ )
{
printf("\nNo.%d Group Has %d atoms ...\n" , igroup + 1 , *( natom_in_each_group + igroup ) );
}
// -----> Recording the name of each group ...
groupnames = ( char ** ) calloc( ngroup , sizeof( char * ) ) ;
int tmp_groupname_length ;
rewind( pndx ) ;
//fsearch( pndx , "begin" );
//fskip( pndx , 1 );
for( igroup = 0 ; igroup < ngroup ; igroup ++ )
{
fsearch( pndx , "[" ) ;
fscanf( pndx , "%s" , tmpstring );
tmp_groupname_length = strlen( tmpstring ) ;
*( groupnames + igroup ) = ( char * ) calloc( tmp_groupname_length + 3 , sizeof( char ) ) ;
strcpy( *( groupnames + igroup ) , tmpstring ) ;
printf("\nName of %d group is %s ...\n" , igroup + 1 , *( groupnames + igroup ) );
}
// =====> Loading the eigenvectors ( dxdr file ) ...
printf("\n--------------------------> Begin reading dxdr file ... <----------------------------" );
int len_dxdr = flength( pdxdr ) ;
printf("\nThere are %d numbers in eigenvectors file ... \n" , len_dxdr );
ncart = sqrt( len_dxdr );
natom = ncart / 3 ;
double * dxdr = calloc( len_dxdr , sizeof( double ) ) ;
rewind( pdxdr );
fload( pdxdr , dxdr ) ;
rewind( pdxdr ) ;
printf("\nDone with loading dxdr file ... \n");
switch( natom )
{
case 1 : printf("\nSeriously? Only ONE atom? ...\n") ; exit( 9 ) ; break ;
case 2 : nmode = 6 ; break ;
default : nmode = ncart - 0 ; break ;
}
if( exfreq == 0 )
{
freq = ( double * ) calloc( nmode , sizeof( double ) ) ;
dzeros( nmode , 1 , freq ) ;
}
else
{
if( nfreqprovide > nmode )
{
printf("\nOkay ... The number of vibrational frequency you provided is more than the normal mode we have from eigenvectors ...\n");
printf("\nSo I will take only the first #_of_eigenvectors frequencies from the file you provided ...\n");
}
else if( nfreqprovide < nmode )
{
printf("\nOkay ... The number of vibrational frequency you provided is less than the normal mode we have from eigenvectors ...\n");
printf("\nThe rest will be padded with zeros ... Sorry, I really don't want to do the diagonalization ...\n");
free( freq ) ;
freq = ( double * ) calloc( nmode , sizeof( double ) ) ;
rewind( pfreq );
fload( pfreq , freq ) ;
dzeros( nmode - nfreqprovide , 1 , freq + nfreqprovide ) ;
}
}
if( exatomlist == 0 )
{
if( fakeOrNot == 1 )
{
for( iatom = 0 ; iatom < natom ; iatom ++ )
{
*( atomlist + iatom ) = 6 ;
}
}
}
else
{
if( natomlistprovide > natom )
{
printf("\nOkay ... The number of atom you provided is more than the NAtom we have from eigenvectors ...\n");
printf("\nSo I will take only the first #_of_atoms from the file you provided ...\n");
}
else if( natomlistprovide < natom )
{
printf("\nOkay ... The number of atom you provided is less than the NAtom we have from eigenvectors ...\n");
printf("\nSo all the rest will be automatically set as Carbon ... \n");
free( atomlist );
atomlist = ( int * ) calloc( natom , sizeof( int ) ) ;
rewind( patomlist );
int_fload( patomlist , atomlist );
for( iatom = natom - natomlistprovide ; iatom < natom ; iatom ++ )
{
*( atomlist + iatom ) = 6 ;
}
}
}
// =====> Loading the eigenvectors ( dxdr file ) ...
// -----> Based on group information, prepare the recording structures (array) ...
printf("\n=================================> _ <=====================================\n");
printf("\nStarting from here, we will actually read index file and give the assignment ... \n");
double * assgninfo = calloc( ngroup * nmode , sizeof( double ) ) ;
rewind( pndx ) ;
//fsearch( pndx , "begin" );
//fskip( pndx , 1 ) ;
double tmp_xcomponent , tmp_ycomponent , tmp_zcomponent , tmp_magnitude ;
//printf("\nDebugging ... Debugging ... % 12.8E\t% 12.8E\t% 12.8E\n\n" , *( dxdr + 3 ) , *( dxdr + 4 ) , *( dxdr + 5 ) );
info = 9 ;
for( igroup = 0 ; igroup < ngroup ; igroup ++ )
{
printf("\n--------------------------> GROUP #%d : %s <----------------------------" , igroup + 1 , *( groupnames + igroup ) );
fsearch( pndx , "]" ) ;
fscanf( pndx , "%s" , tmpstring );
//printf("\nFor this group , the 1st grabbed tmpstring is %s ... \n" , tmpstring );
for( itmp = 0 ; strcmp( tmpstring , "[" ) != 0 && info != EOF ; )
{
//printf("\nGrabbed tmpstring is %s ... \n" , tmpstring ) ;
if( strcmp( tmpstring , "-" ) == 0 )
{
//printf("\nThe '-' situation happened ... before '-' we are at No.%d atom ... \n" , current_atom_index );
fscanf( pndx , "%d" , &next_atom_index );
//printf("\nAnd after '-' we are at No.%d atom ... \n" , next_atom_index );
itmp = itmp + ( next_atom_index - current_atom_index );
for( iatom = current_atom_index ; iatom < next_atom_index ; iatom ++ )
{
//tmp_xcomponent = 0.0000 ; tmp_ycomponent = 0.0000 ; tmp_zcomponent = 0.0000 ;
//tmp_magnitude = tmp_xcomponent * tmp_xcomponent + tmp_ycomponent * tmp_ycomponent + tmp_zcomponent * tmp_zcomponent ;
printf("\nWorking on No.%d atom ... in No.%d group ...\n" , iatom + 1 , igroup + 1 );
for( imode = 0 ; imode < nmode ; imode ++ )
{
tmp_xcomponent = *( dxdr + ( 3 * ( iatom - 0 ) + 0 ) * nmode + imode ) ;
//printf("\nNO.%d mode has % 12.8E on #%d atom X ... \n" , imode + 1 , tmp_xcomponent , iatom + 1 );
tmp_ycomponent = *( dxdr + ( 3 * ( iatom - 0 ) + 1 ) * nmode + imode ) ;
//printf("\nNO.%d mode has % 12.8E on #%d atom Y ... \n" , imode + 1 , tmp_ycomponent , iatom + 1 );
tmp_zcomponent = *( dxdr + ( 3 * ( iatom - 0 ) + 2 ) * nmode + imode ) ;
//printf("\nNO.%d mode has % 12.8E on #%d atom Z ... \n" , imode + 1 , tmp_zcomponent , iatom + 1 );
tmp_magnitude = tmp_xcomponent * tmp_xcomponent + tmp_ycomponent * tmp_ycomponent + tmp_zcomponent * tmp_zcomponent ;
//printf("\nNO.%d mode has % 12.8E on #%d atom ... \n" , imode + 1 , tmp_magnitude , iatom + 1 ) ;
*( assgninfo + igroup * nmode + imode ) = *( assgninfo + igroup * nmode + imode ) + tmp_magnitude ;
printf("\nUp to No.%d atom , No.%d mode has % 12.8E on #%d group ...\n" , iatom + 1 , imode + 1 , *( assgninfo + igroup * nmode + imode ) , igroup + 1 );
}
}
current_atom_index = next_atom_index ;
info = fscanf( pndx , "%s" , tmpstring ) ;
}
else
{
itmp ++ ;
current_atom_index = atoi( tmpstring );
//printf("\nNormal situation ... current_atom_index is %d ... \n" , current_atom_index );
printf("\nWorking on No.%d atom ... in No.%d group ...\n" , current_atom_index , igroup + 1 );
for( imode = 0 ; imode < nmode ; imode ++ )
{
tmp_xcomponent = *( dxdr + ( 3 * ( current_atom_index - 1 ) + 0 ) * nmode + imode ) ;
//printf("\nNO.%d mode has % 12.8E on #%d atom X ... \n" , imode + 1 , tmp_xcomponent , current_atom_index );
tmp_ycomponent = *( dxdr + ( 3 * ( current_atom_index - 1 ) + 1 ) * nmode + imode ) ;
//printf("\nNO.%d mode has % 12.8E on #%d atom Y ... \n" , imode + 1 , tmp_ycomponent , current_atom_index );
tmp_zcomponent = *( dxdr + ( 3 * ( current_atom_index - 1 ) + 2 ) * nmode + imode ) ;
//printf("\nNO.%d mode has % 12.8E on #%d atom Z ... \n" , imode + 1 , tmp_zcomponent , current_atom_index );
tmp_magnitude = tmp_xcomponent * tmp_xcomponent + tmp_ycomponent * tmp_ycomponent + tmp_zcomponent * tmp_zcomponent ;
//printf("\nNO.%d mode has % 12.8E on #%d atom ... \n" , imode + 1 , tmp_magnitude , current_atom_index ) ;
*( assgninfo + igroup * nmode + imode ) = *( assgninfo + igroup * nmode + imode ) + tmp_magnitude ;
printf("\nUp to No.%d atom , No.%d mode has % 12.8E on #%d group ...\n" , current_atom_index , imode + 1 , *( assgninfo + igroup * nmode + imode ) , igroup + 1 );
}
info = fscanf( pndx , "%s" , tmpstring );
}
}
if( info == EOF )
{
printf("\nHit the bottom of file ...\n\n") ;
break ;
}
printf("\nDone Loading Information of [ % 5d ] group ... \n" , igroup + 1 );
}
/* Debugging output ... */
debug = fopen( "assgnfull.info" , "wb+" );
fprintf( debug , "Mode#\t" ) ;
for( igroup = 0 ; igroup < ngroup ; igroup ++ )
{
fprintf( debug , "% 12s\t" , *( groupnames + igroup ) ) ;
}
fprintf( debug , "vib-Frequencies" );
fprintf( debug , "\n\n" );
for( imode = 0 ; imode < nmode ; imode ++ )
{
fprintf( debug , "%d\t" , imode + 1 );
for( igroup = 0 ; igroup < ngroup ; igroup ++ )
{
fprintf( debug , "% 12.8E\t" , *( assgninfo + igroup * nmode + imode ) );
}
fprintf( debug , "% 12.8E\n\n" , *( freq + imode ) ) ;
}
// =====> Writing the output file ( MATLAB loadable pure number array file ) ...
passgn = fopen( outassgnname , "wb+" ) ;
fprintf( passgn , "\n\n" );
for( imode = 0 ; imode < nmode ; imode ++ )
{
fprintf( passgn , "%d\t" , imode + 1 );
for( igroup = 0 ; igroup < ngroup ; igroup ++ )
{
fprintf( passgn , "% 12.8E\t" , *( assgninfo + igroup * nmode + imode ) );
}
fprintf( passgn , "% 12.8E\n\n" , *( freq + imode ) ) ;
}
// =====> Writing the output file ( MATLAB loadable pure number array file ) ...
FILE * pfakefreq ;
int ibatch = 0 ;
int nbatch = nmode / 3 ;
if( fakeOrNot == 1 )
{
pfakefreq = fopen( "fakeg09.freq" , "wb+" );
if( natom == 1 )
{
printf("\nReally? Really?? Really???\n\n");
exit( 1 ) ;
}
else if( natom == 2 )
{
fprintf( pfakefreq , " 1\n A\nFrequencies -- %10.4f\n" , *( freq + 5 ) ) ;
fprintf( pfakefreq , "Red. masses -- %10.4f\nFrc consts -- %10.4f\nIR Inten -- %10.4f\n Atom AN X Y Z \n" , 1.00 , 1.00 , 1.00 );
for( iatom = 0 ; iatom < natom ; iatom ++ )
{
fprintf( pfakefreq , "%5d%4d % 8.4f % 8.4f %8.4f\n" , iatom + 1 , *( atomlist + iatom ) , *( dxdr + 3 * iatom + 0 ) , *( dxdr + 3 * iatom + 1 ) , *( dxdr + 3 * iatom + 2 ) );
}
}
else
{
for( ibatch = 2 ; ibatch < nbatch ; ibatch ++ )
{
fprintf( pfakefreq , " %5d %5d %5d\n" , 3 * ( ibatch - 2 ) + 1 , 3 * ( ibatch - 2 ) + 2 , 3 * ( ibatch - 2 ) + 3 );
fprintf( pfakefreq , " %5c %5c %5c\n" , 'A' , 'A', 'A' );
fprintf( pfakefreq , "%-12s -- %10.4f %10.4f %10.4f\n" , " Frequencies" , *( freq + 3 * ibatch + 0 ) , *( freq + 3 * ibatch + 1 ) , *( freq + 3 * ibatch + 2 ) );
fprintf( pfakefreq , "%-12s -- %10.4f %10.4f %10.4f\n" , " Red. masses" , 1.00 , 1.00 , 1.00 );
fprintf( pfakefreq , "%-12s -- %10.4f %10.4f %10.4f\n" , " Frc consts" , 10.00 , 10.00 , 10.00 );
fprintf( pfakefreq , "%-12s -- %10.4f %10.4f %10.4f\n" , " IR Inten" , 10.00 , 10.00 , 10.00 );
fprintf( pfakefreq , " Atom AN X Y Z X Y Z X Y Z\n");
for( iatom = 0 ; iatom < natom ; iatom ++ )
{
fprintf( pfakefreq , "%5d%4d" , iatom + 1 , *( atomlist + iatom ) ) ;
fprintf( pfakefreq , " % 8.4f % 8.4f %8.4f" , *( dxdr + nmode * ( 3 * iatom + 0 ) + ( 3 * ( ibatch + 0 ) + 0 ) ) , *( dxdr + nmode * ( 3 * iatom + 1 ) + ( 3 * ( ibatch + 0 ) + 0 ) ) , *( dxdr + nmode * ( 3 * iatom + 2 ) + ( 3 * ( ibatch + 0 ) + 0 ) ) ) ;
fprintf( pfakefreq , " % 8.4f % 8.4f %8.4f" , *( dxdr + nmode * ( 3 * iatom + 0 ) + ( 3 * ( ibatch + 0 ) + 1 ) ) , *( dxdr + nmode * ( 3 * iatom + 1 ) + ( 3 * ( ibatch + 0 ) + 1 ) ) , *( dxdr + nmode * ( 3 * iatom + 2 ) + ( 3 * ( ibatch + 0 ) + 1 ) ) ) ;
fprintf( pfakefreq , " % 8.4f % 8.4f %8.4f\n" , *( dxdr + nmode * ( 3 * iatom + 0 ) + ( 3 * ( ibatch + 0 ) + 2 ) ) , *( dxdr + nmode * ( 3 * iatom + 1 ) + ( 3 * ( ibatch + 0 ) + 2 ) ) , *( dxdr + nmode * ( 3 * iatom + 2 ) + ( 3 * ( ibatch + 0 ) + 2 ) ) ) ;
}
}
}
}
return( 0 );
} // The End ...
