StaticModelLoader::StaticModelLoader(char* path, char *mpath)
{
m_infile.open(mpath);
if (!m_infile) {
cout << "Cannot open material file!\n";
throw 1;
}
infile.open(path); //"res/car.obj"
if (!infile) {
cout << "Cannot open file!\n";
throw 1;
}
mload();
vload();
infile.clear();
infile.seekg(0, ios::beg);
fload();
infile.close();
m_infile.close();
//debug models
std::cout << " verticies " << v_num
<< " textures " << vt_num
<< " normals " << vn_num
<< " polygones " << f_num
<< std::endl;
}
unint load_shader(const char *fname, GLenum type)
{
int size=0; void *data=NULL;
if(fload(fname,&size,&data))
{
const unint s=glCreateShader(type);
int val=0;
glShaderSource(s,1,(const char**)&data,&size);
free(data);
glCompileShader(s);
glGetShaderiv(s,GL_INFO_LOG_LENGTH,&val);
if(val>1)
{
char *log=(char*)malloc(val);
glGetShaderInfoLog(s,val,NULL,log);
info("Shader \"%s\" info:\n%s\n",fname,log);
free((void*)log);
}
glGetShaderiv(s,GL_COMPILE_STATUS,&val);
if(!val) info("Shader \"%s\" compiling failed\n",fname);
return s;
}
else return 0;
}
static int
i82563reset(Ctlr* ctlr)
{
int i, r;
detach(ctlr);
if(ctlr->type == i82566 || ctlr->type == i82567)
r = fload(ctlr);
else
r = eeload(ctlr);
if (r != 0 && r != 0xBABA){
print("%s: bad EEPROM checksum - 0x%4.4ux\n",
tname[ctlr->type], r);
return -1;
}
for(i = Ea; i < Eaddrlen/2; i++){
ctlr->ra[2*i] = ctlr->eeprom[i];
ctlr->ra[2*i+1] = ctlr->eeprom[i]>>8;
}
r = (csr32r(ctlr, Status) & Lanid) >> 2;
ctlr->ra[5] += r; /* ea ctlr[1] = ea ctlr[0]+1 */
r = ctlr->ra[3]<<24 | ctlr->ra[2]<<16 | ctlr->ra[1]<<8 | ctlr->ra[0];
csr32w(ctlr, Ral, r);
r = 0x80000000 | ctlr->ra[5]<<8 | ctlr->ra[4];
csr32w(ctlr, Rah, r);
for(i = 1; i < 16; i++){
csr32w(ctlr, Ral+i*8, 0);
csr32w(ctlr, Rah+i*8, 0);
}
for(i = 0; i < 128; i++)
csr32w(ctlr, Mta+i*4, 0);
csr32w(ctlr, Fcal, 0x00C28001);
csr32w(ctlr, Fcah, 0x00000100);
csr32w(ctlr, Fct, 0x00008808);
csr32w(ctlr, Fcttv, 0x00000100);
csr32w(ctlr, Fcrtl, ctlr->fcrtl);
csr32w(ctlr, Fcrth, ctlr->fcrth);
ilock(&ctlr->imlock);
csr32w(ctlr, Imc, ~0);
ctlr->im = 0; /* was = Lsc, which hangs some controllers */
csr32w(ctlr, Ims, ctlr->im);
iunlock(&ctlr->imlock);
return 0;
}
byte load_tex(unint t, const char *fname, unshort w, unshort h, GLenum fmt, tex_filter tf)
{
int size=0; void *data=NULL;
if(fload(fname,&size,&data))
{
use_tex(t);
glTexImage2D(GL_TEXTURE_2D,0,fmt,w,h,0,fmt,GL_UNSIGNED_BYTE,data);
free(data);
filter_tex(tf);
return 1;
}
else return 0;
}
void BytecodeAssembler::load(BasicType bt, u4 index) {
switch (bt) {
case T_BOOLEAN:
case T_CHAR:
case T_BYTE:
case T_SHORT:
case T_INT: iload(index); break;
case T_FLOAT: fload(index); break;
case T_DOUBLE: dload(index); break;
case T_LONG: lload(index); break;
case T_OBJECT:
case T_ARRAY: aload(index); break;
default:
ShouldNotReachHere();
}
}
void
rl_test(void)
{
uchar *in, *out;
size_t inlen;
size_t outlen;
while (1) {
char *line = readline(">> ");
in = (uchar*)fload(line, NULL, &inlen);
printf("inlen: %zd\n", inlen);
out = malloc(inlen);
outlen = rl_encode1(out, in, inlen);
printf("outlen: %zd\n", outlen);
free(line);
free(in);
free(out);
}
}
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 ) ;
}
void system::read_binary(const char *filename, const int n_files)
{
#if 1
assert(n_files == 1);
vec3 rmin, rmax;
if (myproc == 0)
{
FILE *fin;
if (!(fin = fopen(filename, "r")))
{
std::cerr << "Cannot open file " << filename << std::endl;
exit(-1);
}
std::cerr << "proc= " << myproc << " read snapshot: " << filename << std::endl;
int ival;
float fval;
#define fload(x) { myfread(&fval, sizeof(float), 1, fin); x = fval; }
#define iload(x) { myfread(&ival, sizeof(int), 1, fin); x = ival;}
float ftmp;
int itmp, np0, npx, npy, npz;
iload(itmp); // 20*4
assert(itmp == 20*4);
iload(itmp); // myid
iload(np0);
iload(npx);
union
{
unsigned long long uint_long;
unsigned int uint[2];
} data;
iload(data.uint[0]);
iload(data.uint[1]);
scheduler.tsysU = data.uint_long;
float courant_No;
int nglob, nloc, ndim;
iload(nglob);
iload(nloc);
iload(ndim);
assert(ndim == 3);
fload(t_global);
fload(dt_global);
iload(iteration);
fload(courant_No);
fload(gamma_gas);
int periodic_on;
iload(periodic_on);
assert(periodic_on == -1);
fload(rmin.x);
fload(rmin.y);
fload(rmin.z);
fload(rmax.x);
fload(rmax.y);
fload(rmax.z);
iload(itmp); // 20*4
assert(itmp == 20*4);
ptcl_local.resize(nglob);
U_local.resize(nglob);
dU_local.resize(nglob);
fprintf(stderr, "np =%d nglob= %d \n", np0, nglob);
int pc = 0;
for (int pr = 0; pr < np0; pr++)
{
fprintf(stderr, " p= %d out of %d; nloc= %d\n", pr, np0, nloc);
for (int i = 0; i < nloc; i++)
{
Particle p;
p.tend = t_global;
p.rung = 0.0;
p.new_dt = 0.0;
p.local_id = i;
Fluid W(0.0);
iload(ival);
assert(ival == 26*4);
iload(ival); p.idx = ival;
fload(p.pos.x);
fload(p.pos.y);
fload(p.pos.z);
p.pos = periodic(p.pos);
assert(rmin.x <= p.pos.x);
assert(rmax.x >= p.pos.x);
assert(rmin.y <= p.pos.y);
assert(rmax.y >= p.pos.y);
assert(rmin.z <= p.pos.z);
assert(rmax.z >= p.pos.z);
p.orig_pos = p.pos;
p.pot = 0;
fload(p.vel.x);
fload(p.vel.y);
fload(p.vel.z);
p.orig_vel = p.vel;
fload(W[Fluid::DENS]);
fload(W[Fluid::ETHM]);
fload(ftmp); // compute_pressure(m.dens, m.ethm));
fload(p.rmax); //dump( (sqr(m.B.x ) + sqr(m.B.y ) + sqr(m.B.z ))*0.5f);
iload(p.boundary); // fload(ftmp); //dump(sqrt(sqr(m.vel.x) + sqr(m.vel.y) + sqr(m.vel.z)));
fload(W[Fluid::VELX]);
fload(W[Fluid::VELY]);
fload(W[Fluid::VELZ]);
fload(W[Fluid::BX]);
fload(W[Fluid::BY]);
fload(W[Fluid::BZ]);
float h;
fload(h);
fload(p.volume);
p.volume_new = p.volume;
fload(W[Fluid::PSI]);
fload(ftmp); //L*divB_i[i]);
fload(W[Fluid::ENTR]);
fload(ftmp); // Jx
fload(ftmp); // Jy
fload(ftmp); // Jz
iload(ival);
assert(ival == 26*4);
p.tlast = t_global;
ptcl_local[pc] = p;
U_local [pc] = W;
dU_local [pc] = 0.0;
dU_local [pc] = 0.0;
pc++;
}
fprintf(stderr, "p= %d np0= %d size= %d %d\n",
pr, np0, (int)U_local.size(), (int)ptcl_local.size());
if (!(pr < np0-1)) break;
iload(itmp); // 20*4
assert(itmp == 20*4);
iload(itmp); // myid
iload(np0);
iload(npx);
iload(npy);
iload(npz);
int nglob1;
iload(nglob1);
if (nglob != nglob1) {
fprintf(stderr, "np; npx, npy, npz = %d; %d %d %d \n",
np0, npx, npy, npz);
fprintf(stderr, "nglob= %d nglob1= %d\n", nglob, nglob1);
}
assert(nglob == nglob1);
iload(nloc);
iload(ndim);
fload(t_global);
fload(dt_global);
iload(iteration);
fload(courant_No);
fload(gamma_gas);
iload(periodic_on);
fload(rmin.x);
fload(rmin.y);
fload(rmin.z);
fload(rmax.x);
fload(rmax.y);
fload(rmax.z);
iload(itmp); // 20*4
}
assert(pc == nglob);
assert(nglob == (int)U_local.size());
fclose(fin);
local_n = U_local.size();
}
global_n = U_local.size();
local_n = global_n;
MPI_Bcast(&global_n, 1, MPI_UNSIGNED_LONG_LONG, 0, MPI_COMM_WORLD);
MPI_Bcast(&iteration, 1, MPI_INT, 0, MPI_COMM_WORLD);
double dt_glob = dt_global;
double t_glob = t_global;
MPI_Bcast(& t_glob, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
MPI_Bcast(&dt_glob, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
MPI_Bcast(&scheduler.tsysU, 1, MPI_UNSIGNED_LONG_LONG, 0, MPI_COMM_WORLD);
dt_global = dt_glob;
t_global = t_glob;
scheduler.set_tsys(t_global);
assert(t_global == scheduler.get_tsys());
// scheduler.tsysU = (unsigned long long)(t_global / scheduler.dt_tick);
scheduler.min_rung = 0;
dt_global = 0.0f;
distribute_data(true, false, true);
#if 1
fit_vec(ptcl_local);
fit_vec(U_local);
fit_vec(dU_local);
fit_vec(Wrec_local);
#endif
all_active = true;
MPI_Barrier(MPI_COMM_WORLD);
for (int i = 0; i < (int)local_n; i++)
{
ptcl_local[i].tlast = t_global;
// ptcl_local[i].volume = cell_local[i].Volume;
Wrec_local[i] = Fluid_rec(U_local[i]);
U_local[i] = U_local[i].to_conservative(ptcl_local[i].volume);
dU_local[i] = 0.0;
}
MPI_Barrier(MPI_COMM_WORLD);
if (myproc == 0)
fprintf(stderr , " pvel ... \n");
get_active_ptcl(true);
MPI_Barrier(MPI_COMM_WORLD);
if (myproc == 0)
fprintf(stderr , " pvel ... \n");
cell_list.swap(cell_local);
ptcl_import.swap(ptcl_local);
U_import.swap(U_local);
site_active_list.swap(active_ptcl);
compute_pvel();
compute_timesteps(true);
cell_list.swap(cell_local);
ptcl_import.swap(ptcl_local);
U_import.swap(U_local);
site_active_list.swap(active_ptcl);
for (int i = 0; i < (int)local_n; i++)
{
ptcl_local[i].rung += 1;
ptcl_local[i].tend = ptcl_local[i].tlast + scheduler.get_dt(ptcl_local[i].rung);
ptcl_local[i].orig_vel = ptcl_local[i].vel;
ptcl_local[i].unset_active();
}
all_active = true;
scheduler.flush_list();
boundary_n = 0;
for (int i = 0; i < (int)local_n; i++)
{
scheduler.push_particle(i, (int)ptcl_local[i].rung);
if (ptcl_local[i].is_boundary())
boundary_n++;
}
unsigned long long boundary_glb;
MPI_Allreduce(&boundary_n, &boundary_glb, 1, MPI_UNSIGNED_LONG_LONG, MPI_SUM, MPI_COMM_WORLD);
if (myproc == 0)
fprintf(stderr, "boundary_glb= %lld\n", boundary_glb);
clear_mesh(true);
MPI_Barrier(MPI_COMM_WORLD);
if (myproc == 0) fprintf(stderr, " proc= %d: complete read_binary \n", myproc);
#endif
}
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 ...
void init(void)
{
if(init_mblur() && init_vig() && init_quad())
{
int size=0; void *data=NULL;
/*glClearColor(1.0f,1.0f,1.0f,1.0f);*/
glClearColor(0.04f,0.0f,0.04f,1.0f);
use_mblur();
send_mblur_samples(16.0f); /* adjust motion blur samples here */
use_vig();
send_vig_size((float)sw(),(float)sh());
vigmode(0);
use_basic();
persp(proj,75.0f,asp(),0.1f,24.0f);
if(fload("data/area-model.bin",&size,&data))
{
add_to_vbo(&area_mod,data,size);
free(data);
update_vbo();
gen_texs(1,&area_tex);
//if(load_tex_compressed(area_tex,"data/area-ao-texture.bin",tf_mipmap))
if(load_tex_compressed(area_tex,"data/area-texture.bin",tf_mipmap))
{
const int downsample=1; /* adjust fb down-sizing here */
texmode(1);
nsw=sw()/downsample;
nsh=sh()/downsample;
gen_texs(4,texs);
gen_rbs(3,rbs);
gen_fbs(4,fbos);
use_fb(fbos[0]);
add_fb_rb(0,rbs[0],nsw,nsh,GL_RGB8,4); /* adjust renderbuffer samples here */
add_fb_rb(0,rbs[1],nsw,nsh,GL_DEPTH_COMPONENT24,4); /* adjust renderbuffer samples here */
use_fb(fbos[1]);
add_fb_tex(0,texs[0],nsw,nsh,GL_RGB8,tf_linear);
add_fb_rb(0,rbs[2],nsw,nsh,GL_DEPTH_COMPONENT24,0);
use_fb(fbos[2]);
add_fb_tex(0,texs[1],nsw,nsh,GL_RGB8,tf_linear);
add_fb_tex(1,texs[2],nsw,nsh,GL_RGBA32F,tf_linear);
add_fb_rb(0,rbs[2],nsw,nsh,GL_DEPTH_COMPONENT24,0);
use_fb(fbos[3]);
add_fb_tex(0,texs[3],nsw,nsh,GL_RGB8,tf_linear);
use_fb(0);
use_rb(0);
use_tex(0);
}
else quit();
}
else quit();
}
else quit();
}
void vsmcreate(int argc, char *argv[])
{
TVSMHeader head; // VSM file header
TVSMResource res; // resource
char *fdir = NULL; // working directory
char *fn = NULL; // target file name
TCRC csum; // checksum
int i;
FILE *f;
char *tmp, *tmp2;
char ch;
// command line parameters
int vendor_id = -1;
bool dont_load_header = false;
bool dont_incl_footer = false;
int ins_version = 0;
unsigned short int version[4];
// process arguments passed by command line
for (i=2; i<argc; i++)
{
// -vid
if (strcasecmp(argv[i], "-vid") == 0)
{
// there is no argument after -vid
if (i+1 >= argc) errexit("Wrong parameter format '-vid'");
sscanf(argv[++i], "%u", &vendor_id);
}
// -dh
else if (strcasecmp(argv[i], "-dh") == 0)
dont_load_header = true;
// -df
else if (strcasecmp(argv[i], "-df") == 0)
dont_incl_footer = true;
// -v
else if (strcasecmp(argv[i], "-v") == 0)
{
if (i+1 >= argc) errexit("Wrong parameter format '-v'");
ins_version = 1;
if (sscanf(argv[++i], "%hd.%hd.%hd.%hd", &version[3], &version[2],
&version[1], &version[0]) != 4)
errexit("Wrong parameter format '-v'\nShould be '-v a.b.c.d'");
}
// File or directory name
else if (i+2 >= argc)
{
if (fdir == NULL) fdir = argv[i];
else fn = argv[i];
}
// Incorrect parameter
else
{
printf("Unknown argument: %s\n", argv[i]);
errexit("Wrong parameter format");
}
}
// Directory not specified
if (fdir == NULL) errexit("Input folder not specified");
// Target file not specified - generating filename from input folder
if (fn == NULL)
{
fn = new char[strlen(fdir) + 5];
strcpy(fn, fdir);
if (isSlash(fn)) fn[strlen(fn) -1] = '\0';
strcat(fn, ".vsm");
}
// End directory path by '\' char:
if (isSlash(fdir) == 0)
{
tmp = new char[strlen(fdir) + 2];
strcpy(tmp, fdir);
strcat(tmp, "\\");
fdir = tmp;
}
// File information
printf("Input folder: %s\n", fdir);
printf("Output file: %s\n", fn);
// Load header
if (dont_load_header == false)
{
// open file
tmp = new char[strlen(fdir) + 12];
strcpy(tmp, fdir);
strcat(tmp, "header.bin");
i = fload(tmp, &head, sizeof(head));
delete [] tmp;
// file doesn't exists
if (i < 0)
errexit("\nCan't open file 'header.bin'.\n"
"Use '-dh' switch to generate default header");
else if (i != sizeof(head))
errexit("\nIncorrect file 'header.bin'.\n"
"Use '-dh' switch to generate default header");
}
// generate header
else
{
memset(&head, 0, sizeof(head));
head.signature = VSMSignature;
}
// change vendor id
if (vendor_id >= 0) head.vendor_id = vendor_id;
// change version number
if (ins_version)
{
for (i=0; i<4; i++)
head.version[i] = version[i];
}
// Show header info
printf("Vendor ID: %d\n\n", head.vendor_id);
// Check if output file already exists
if (FileExist(fn))
{
printf("File %s already exist. Overwrite? (y/N)\n\n", fn);
ch = getch();
if ((ch != 'y') && (ch != 'Y')) exit(0);
}
// Open output file
f = fopen(fn, "wb");
if (f == NULL) errexit("Can't create output file!");
// Write header
puts("writing header");
if (fwrite(&head, sizeof(head), 1, f) <= 0)
{
fclose(f);
errexit("Write error!");
}
// Prepare to listing files
tmp = new char[8192];
strcpy(tmp, fdir);
tmp2 = tmp + strlen(tmp);
strcat(tmp, "res*");
TFileList fl;
char *fname = FLFindFirst(&fl, tmp);
res.data = new char[VSMMaxResSize+1];
csum.newCRC32();
head.ressize = 0;
// Write file
while (fname)
{
i = ParseResName(fname);
// given file is not a resource file - skip
if (i < 0) continue;
res.id = i;
printf("writing resource 0x%04x from %s\n", res.id, fname);
// read resource file
strcpy(tmp2, fname);
i = fload(tmp, res.data, VSMMaxResSize+1);
if (i < 0) errexit("Can't read resource file!");
res.size = i;
if (i >= VSMMaxResSize+1) errexit("Resource file is too big!");
// write to output file
if (fwrite(&res, RHSIZE, 1, f) <= 0) errexit("Write error!");
if (fwrite(res.data, res.size, 1, f) <= 0) errexit("Write error!");
csum.add(&res, RHSIZE);
csum.add(res.data, res.size);
head.ressize += RHSIZE + res.size;
// make sure that file end up with even address
if (head.ressize & 1)
{
if (fwrite("\0", 1, 1, f) <= 0) errexit("Write error!");
head.ressize++;
csum.add(0);
}
fname = FLFind(&fl);
}
// Writing footer
if (dont_incl_footer == false)
{
// footer address (divided by 4)
i = head.ressize & 3;
if (i)
{
i = 4 - i;
if (fwrite("\0\0\0", i, 1, f) <= 0) errexit("Write error!");
}
// load footer
strcpy(tmp2, "footer.bin");
i = fload(tmp, res.data, VSMMaxResSize);
// if footer exists
if (i != -1)
{
puts("writing footer");
// can't read footer.bin
if (i < 0) errexit("\nCan't open file 'footer.bin'.\n"
"Use '-df' switch if you don't need footer");
// footer.bin length is 0
if (i == 0) printf("\nFile 'footer.bin' is empty.");
// write footer and check for errors
else if (fwrite(res.data, i, 1, f) <= 0) errexit("Write error!");
}
}
// Update header checksum
head.checksum = csum.getCRC32() ^ 0xffffffff;
puts("updating header (checksum and resources size)\n");
fseek(f, 0, SEEK_SET);
if (fwrite(&head, sizeof(head), 1, f) <= 0) errexit("Write error!");
fclose(f);
fileinfo(&head, head.checksum);
delete [] tmp;
delete [] res.data;
} // void vsmcreate(int argc, char *argv[])
int main( int argc , char * argv[ ] )
{
FILE * pdxdr , * pfreq , * patomlist , * pfakefreq ;
FILE * debug ;
char dxdrname [ 50 ] , atomlistname [ 50 ] , freqname [ 50 ], outfreqname [ 50 ] ;
char ** pcmd ; pcmd = argv ;
int icmd , itmp ;
int natom , ncart , nmode , nfreqprovide;
int natomSelect , ncartSelect , nmodeSelect ;
int icart , iatom , imode , ifreq ;
int exfreq , exatomlist , exselect ;
char buffer[ MAXCHARINLINE ] ;
int lenBuff ;
char cache[ MAXCHARINLINE ] ;
char stmp[ 150 ] , stmp2[ 150 ] , tmpString[ 150 ];
time_t current_time;
time( ¤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_FAKEFREQ_D : Organize (DX/DR) into G09 Format for visualization. *\n");
printf("* *\n");
printf("* ");
for( icmd = 0 ; icmd < argc ; icmd ++ )
{
printf("%s " , *( pcmd + icmd ) );
}
printf("\n");
printf("* *\n");
printf("* *\n");
printf("* Current Time : %s *\n" , now );
printf("* *\n");
printf("* *\n");
printf("**********************************************************************\n");
// =====> Setting up default file names ...
strcpy( dxdrname , "dxdr.deb" );
strcpy( freqname , "vibfrequency.deb" );
strcpy( outfreqname , "fakeg09.freq" );
strcpy( atomlistname , "atom.list" );
// =====> Parsing command line input arguments ...
exselect = 20 ;
if( argc == 1 )
{
printf("\n\nNo command-line arguments provided ... Mission aborting ...\n\n");
printf("\nPlease refer to the usage by typing ' %s -h '\n\n" , * argv );
exit(1);
}
char * flag ;
icmd = 1 ;
while( icmd < argc )
{
pcmd ++ ;
flag = * pcmd ;
printf("\nNo.%d argument , Currently @ flag = %s ...\n\n" , icmd , flag );
if( ( * flag == '-' ) && ( strlen( flag ) == 2 ) )
{
switch ( *( flag + 1 ) )
{
case 'f' : strcpy( dxdrname , *( ++ pcmd ) ) ;
printf("\nCommand-line argument indicates : Input dxdr File name : %s ...\n" , dxdrname );
icmd = icmd + 2 ;
break ;
case 'o' : strcpy( outfreqname , *( ++ pcmd ) );
printf("\nCommand-line argument indicates : Output File name : %s ...\n" , outfreqname );
icmd = icmd + 2 ;
break ;
case 'w' : strcpy( freqname , *( ++ pcmd ) );
printf("\nCommand-line argument indicates : Input frequency File name : %s ...\n" , freqname );
icmd = icmd + 2 ;
break ;
case 'l' : strcpy( atomlistname , *( ++ pcmd ) );
printf("\nCommand-line argument indicates : Input atom list File name : %s ...\n" , atomlistname );
icmd = icmd + 2 ;
break ;
case 's' : strcpy( tmpString , *( ++ pcmd ) ) ;
if( strcmp( tmpString , "all" ) == 0 || strcmp( tmpString , "All" ) == 0 )
{
exselect = 22 ;
printf("\nCommand-line argument indicates : All atoms will be chosen as solute ...\n" );
}
else
{
printf("\nReceived information : %s ...\n" , tmpString ) ;
natomSelect = atoi( tmpString );
exselect = 21 ;
printf("\nCommand-line argument indicates : First %d atoms will be chosen as solute ...\n" , natomSelect );
}
icmd = icmd + 2 ;
break ;
case 'h' : printf("\nUsage: %s [ -f 'input dxdr file name' ] [(optional) -o 'output NM assignment file name' ] [ -l atom list file (listing the atomic number of all atoms in system)] [ -s # of atom selected to output ] [ -w 'input vibrational frequency file' ]\n\n" , * argv );
printf("\n\n==> NOTE : In order to be fool-proof , if there is mis-match on the NAtom between dxdr file and any other file , this code will set NAtom to be the number from dxdr automatically ...\n\n");
//printf("\nUsage: %s [ -t G09 calculation type : 1=ONIOM ; 2=Point Charge ] [ -f 'input gro file name' ] [(optional) -o 'output g09 file name' ] [ -n # of layers (integer) ] [ (optional) -r radius of middle layer (real) ] [-R radius of lower layer (real) ] [ -H method for Highest layer (string) ] [ (optional) -M method for Middle layer (string) ] [ -L method for Lower layer (string) ] [ -x input GMX .itp file ]\n\n" , * argv );
//exh = 9 ;
icmd = icmd + 1 ;
exit(1) ;
default : printf("\n\nInvalid option ' %s ' ... Please refer to the usage by typing ' %s -h '\n\n" , flag , * argv );
icmd = argc ;
exit(1);
}
}
else
{
printf("\n\nInvalid option ' %s ' ... Please refer to the usage by typing ' %s -h '\n\n" , flag , * argv );
exit(1);
}
}
// =====> Open the files ...
if( ( pdxdr = fopen( dxdrname , "r" ) ) == NULL )
{
printf("\nUser-defined dxdr file %s does not exist ...\n\n" , dxdrname );
exit( 1 );
}
double * freq ;
if( ( pfreq = fopen( freqname , "r" ) ) == NULL )
{
printf("\nUser-defined frequency file %s does not exist ...\n\n" , freqname );
printf("\nBut it's OK , we will procede without frequency information ... \n");
exfreq = 0 ;
}
else
{
nfreqprovide = flength( pfreq );
rewind( pfreq ) ;
freq = ( double * ) calloc( nfreqprovide , sizeof( double ) ) ;
fload( pfreq , freq );
rewind( pfreq );
exfreq = 1 ;
}
int * atomlist , natomlistprovide ;
if( ( patomlist = fopen( atomlistname , "r" ) ) == NULL )
{
printf("\nUser-defined atom list file %s does not exist ...\n\n" , atomlistname );
printf("\nMeaning ... All of your atoms will be carbon ...\n");
exatomlist = 0 ;
}
else
{
natomlistprovide = flength( patomlist );
rewind( patomlist );
atomlist = ( int * ) calloc( natomlistprovide , sizeof( int ) ) ;
int_fload( patomlist , atomlist );
exatomlist = 1 ;
}
// =====> Loading the eigenvectors ( dxdr file ) ...
printf("\n--------------------------> Begin reading dxdr file ... <----------------------------" );
int len_dxdr = flength( pdxdr ) ;
printf("\nThere are %d numbers in eigenvectors file ... \n" , len_dxdr );
ncart = sqrt( len_dxdr );
natom = ncart / 3 ;
double * dxdr = calloc( len_dxdr , sizeof( double ) ) ;
rewind( pdxdr );
fload( pdxdr , dxdr ) ;
rewind( pdxdr ) ;
printf("\nDone with loading dxdr file ... \n");
switch( natom )
{
case 1 : printf("\nSeriously? Only ONE atom? ...\n") ; exit( 9 ) ; break ;
case 2 : nmode = 6 ; break ;
default : nmode = ncart - 0 ; break ;
}
if( exfreq == 0 )
{
freq = ( double * ) calloc( nmode , sizeof( double ) ) ;
dzeros( nmode , 1 , freq ) ;
}
else
{
if( nfreqprovide > nmode )
{
printf("\nOkay ... The number of vibrational frequency you provided is more than the normal mode we have from eigenvectors ...\n");
printf("\nSo I will take only the first #_of_eigenvectors frequencies from the file you provided ...\n");
}
else if( nfreqprovide < nmode )
{
printf("\nOkay ... The number of vibrational frequency you provided is less than the normal mode we have from eigenvectors ...\n");
printf("\nThe rest will be padded with zeros ... Sorry, I really don't want to do the diagonalization ...\n");
free( freq ) ;
freq = ( double * ) calloc( nmode , sizeof( double ) ) ;
rewind( pfreq );
fload( pfreq , freq ) ;
dzeros( nmode - nfreqprovide , 1 , freq + nfreqprovide ) ;
}
}
if( exatomlist == 0 )
{
for( iatom = 0 ; iatom < natom ; iatom ++ )
{
*( atomlist + iatom ) = 6 ;
}
}
else
{
if( natomlistprovide > natom )
{
printf("\nOkay ... The number of atom you provided is more than the NAtom we have from eigenvectors ...\n");
printf("\nSo I will take only the first #_of_atoms from the file you provided ...\n");
}
else if( natomlistprovide < natom )
{
printf("\nOkay ... The number of atom you provided is less than the NAtom we have from eigenvectors ...\n");
printf("\nSo all the rest will be automatically set as Carbon ... \n");
free( atomlist );
atomlist = ( int * ) calloc( natom , sizeof( int ) ) ;
rewind( patomlist );
int_fload( patomlist , atomlist );
for( iatom = natom - natomlistprovide ; iatom < natom ; iatom ++ )
{
*( atomlist + iatom ) = 6 ;
}
}
}
if( exselect == 20 )
{
printf("\nBy default , all %d atoms are selected as solute ... \n\n" , natom ) ;
natomSelect = natom ;
}
else if( exselect == 22 )
{
printf("\nPer user's request , all %d atoms are selected as solute ... \n\n" , natom ) ;
natomSelect = natom ;
}
else if( exselect == 21 )
{
if( natomSelect > natom )
{
printf("\nOops ... you requested %d atoms as solute but we only have %d atoms in G09 .inp file ... By default , all atoms are selected as solute ... \n\n" , natomSelect , natom ) ;
natomSelect = natom ;
}
else if( natomSelect <= natom && natomSelect > 0 )
{
printf("\nPer user's request , the first %d atoms are selected as solute ... \n\n" , natomSelect ) ;
}
else if( natomSelect <= 0 )
{
printf("\n# of solute atom must be a positive integer!!!\n\n") ;
exit( 52 ) ;
}
}
ncartSelect = natomSelect * 3 ;
switch( natomSelect )
{
case 1 : printf("\nSeriously? Only ONE atom selected ? ...\n") ; exit( 9 ) ; break ;
case 2 : nmodeSelect = 6 ; break ;
default : nmodeSelect = ncartSelect - 0 ; break ;
}
// =====> Writing the output file ( MATLAB loadable pure number array file ) ...
printf("\n--------------------------> Begin organizing dxdr file into G09 format... <----------------------------\n\n\n" );
pfakefreq = fopen( outfreqname , "wb+" );
int ibatch = 0 ;
int nbatch = nmodeSelect / 3 ;
if( natomSelect == 1 )
{
printf("\nReally? Really?? Really???\n\n");
exit( 1 ) ;
}
else if( natomSelect == 2 )
{
fprintf( pfakefreq , " 1\n A\nFrequencies -- %10.4f\n" , *( freq + 5 ) ) ;
fprintf( pfakefreq , "Red. masses -- %10.4f\nFrc consts -- %10.4f\nIR Inten -- %10.4f\n Atom AN X Y Z \n" , 1.00 , 1.00 , 1.00 );
for( iatom = 0 ; iatom < natomSelect ; iatom ++ )
{
fprintf( pfakefreq , "%5d%4d % 8.4f % 8.4f %8.4f\n" , iatom + 1 , *( atomlist + iatom ) , *( dxdr + 3 * iatom + 0 ) , *( dxdr + 3 * iatom + 1 ) , *( dxdr + 3 * iatom + 2 ) );
}
}
else
{
for( ibatch = 2 ; ibatch < nbatch ; ibatch ++ )
{
fprintf( pfakefreq , " %5d %5d %5d\n" , 3 * ( ibatch - 2 ) + 1 , 3 * ( ibatch - 2 ) + 2 , 3 * ( ibatch - 2 ) + 3 );
fprintf( pfakefreq , " %5c %5c %5c\n" , 'A' , 'A', 'A' );
fprintf( pfakefreq , "%-12s -- %10.4f %10.4f %10.4f\n" , " Frequencies" , *( freq + 3 * ibatch + 0 ) , *( freq + 3 * ibatch + 1 ) , *( freq + 3 * ibatch + 2 ) );
fprintf( pfakefreq , "%-12s -- %10.4f %10.4f %10.4f\n" , " Red. masses" , 1.00 , 1.00 , 1.00 );
fprintf( pfakefreq , "%-12s -- %10.4f %10.4f %10.4f\n" , " Frc consts" , 10.00 , 10.00 , 10.00 );
fprintf( pfakefreq , "%-12s -- %10.4f %10.4f %10.4f\n" , " IR Inten" , 10.00 , 10.00 , 10.00 );
fprintf( pfakefreq , " Atom AN X Y Z X Y Z X Y Z\n");
for( iatom = 0 ; iatom < natomSelect ; iatom ++ )
{
fprintf( pfakefreq , "%5d%4d" , iatom + 1 , *( atomlist + iatom ) ) ;
fprintf( pfakefreq , " % 8.4f % 8.4f %8.4f" , *( dxdr + nmode * ( 3 * iatom + 0 ) + ( 3 * ( ibatch + 0 ) + 0 ) ) , *( dxdr + nmode * ( 3 * iatom + 1 ) + ( 3 * ( ibatch + 0 ) + 0 ) ) , *( dxdr + nmode * ( 3 * iatom + 2 ) + ( 3 * ( ibatch + 0 ) + 0 ) ) ) ;
fprintf( pfakefreq , " % 8.4f % 8.4f %8.4f" , *( dxdr + nmode * ( 3 * iatom + 0 ) + ( 3 * ( ibatch + 0 ) + 1 ) ) , *( dxdr + nmode * ( 3 * iatom + 1 ) + ( 3 * ( ibatch + 0 ) + 1 ) ) , *( dxdr + nmode * ( 3 * iatom + 2 ) + ( 3 * ( ibatch + 0 ) + 1 ) ) ) ;
fprintf( pfakefreq , " % 8.4f % 8.4f %8.4f\n" , *( dxdr + nmode * ( 3 * iatom + 0 ) + ( 3 * ( ibatch + 0 ) + 2 ) ) , *( dxdr + nmode * ( 3 * iatom + 1 ) + ( 3 * ( ibatch + 0 ) + 2 ) ) , *( dxdr + nmode * ( 3 * iatom + 2 ) + ( 3 * ( ibatch + 0 ) + 2 ) ) ) ;
}
}
}
printf("\n==============> ALL DONE !!! ^-^ !!! <===============\n\n\n\n\n\n");
return( 0 );
} // The End ...