//main function
void main()
{
int value;
char res;
//introduction
printf("Queue Library\n");
do
{// loop of push elements
printf("Please enter the number\n");
scanf("%d", &value);
//push each element one at a time
enqueue(value);
printf("Do you want continue?(y|n)\n");
scanf(" %c",&res);
} while (res == 'y' || res == 'Y');
printf("The elements of the linked list are\n");
display(); // display the result
printf("first = %d\n", getfirst());
printf("rear = %d\n",getrear());
printf("pop from the queue %d\n", dequeue());
printf("first = %d\n", getfirst());
printf("rear = %d\n",getrear());
printf("The elements of the linked list are\n");
display(); // display the result
printf("first = %d\n", getfirst());
printf("rear = %d\n",getrear());
printf("pop from the queue %d\n", dequeue());
printf("The elements of the linked list are\n");
display(); // display the result
printf("first = %d\n", getfirst());
printf("rear = %d\n",getrear());
}
void datendump(LIST *l)
{
register struct Robot *rp;
NODE *n;
printf("Name Spiele Züge Lebend Kills"
" Panzerung Munition\n");
for(n=getfirst(l);n;n=getnext(l))
{
rp=getdata(n);
printf("%-14.14s %4d %9d %7.0fø %4d %5.1f%% %4d %5.2fø %6d/%6d %5.1f%% %6d/%6d %5.1f%%\n",
rp->name,
rp->killed+rp->survived,
rp->ticks,
1.0*rp->ticks/(rp->killed+rp->survived),
rp->survived,
100.0*rp->survived/(rp->killed+rp->survived),
rp->kills,
1.0*rp->kills/(rp->killed+rp->survived),
rp->armour,
rp->startarmour,
100.0*rp->armour/rp->startarmour,
rp->mun,
rp->startmun,
100.0*rp->mun/rp->startmun
);
}
}
/*------------------------------------------------------------------------
* signal -- signal a semaphore, releasing one waiting process
*------------------------------------------------------------------------
*/
SYSCALL signal(int sem)
{
//changes for incrementing count on syscall
int start_time;
if(call_active == 1)
{
call_used[currpid] = 1;
call_frequency[currpid][3]++;//id for signal()=3
start_time = ctr1000;
}
STATWORD ps;
register struct sentry *sptr;
disable(ps);
if (isbadsem(sem) || (sptr= &semaph[sem])->sstate==SFREE) {
restore(ps);
return(SYSERR);
}
if ((sptr->semcnt++) < 0)
ready(getfirst(sptr->sqhead), RESCHYES);
restore(ps);
if(call_active == 1)
{
call_duration[currpid][3] += ctr1000 - start_time;
}
return(OK);
}
syscall semdelete(sid32 sem)
{
intmask mask;
struct semEntry *semptr;
mask = disable();
if(isbadsid(sem))
{
restore(mask);
return SYSERR;
}
semptr = &semtab[sem];
if(semptr->sestate == SE_FREE)
{
restore(mask);
return SYSERR;
}
semptr->sestate = SE_FREE;
while(semptr->secount++ < 0)
{
ready(getfirst(semptr->sequeue), RESCHED_NO);
}
resched();
restore(mask);
return OK;
}
syscall semreset(sid32 sem, int32 count)
{
intmask mask;
struct semEntry * semptr;
qid16 queue;
pid32 proc;
mask = disable();
if(isbadsid(sem) || count<0 || semtab[sem].sestate==SE_FREE)
{
restore(mask);
return SYSERR;
}
semptr = &semtab[sem];
queue = semptr->sequeue;
//NOTE 这里的循环条件和semdelete里的应该是一样的
while((proc = getfirst(queue)) != EMPTY)
{
ready(proc, RESCHED_NO);
}
semptr->secount = count;
resched();
restore(mask);
return OK;
}
/*------------------------------------------------------------------------
* semreset - Reset a semaphore's count and release waiting processes
*------------------------------------------------------------------------
*/
syscall semreset(
sid32 sem, /* ID of semaphore to reset */
int32 count /* New count (must be >= 0) */
)
{
intmask mask; /* Saved interrupt mask */
struct sentry *semptr; /* Ptr to semaphore table entry */
qid16 semqueue; /* Semaphore's process queue ID */
pid32 pid; /* ID of a waiting process */
mask = disable();
if (count < 0 || isbadsem(sem) || semtab[sem].sstate==S_FREE) {
restore(mask);
return SYSERR;
}
semptr = &semtab[sem];
semqueue = semptr->squeue; /* Free any waiting processes */
resched_cntl(DEFER_START);
while ((pid=getfirst(semqueue)) != EMPTY)
ready(pid);
semptr->scount = count; /* Reset count as specified */
resched_cntl(DEFER_STOP);
restore(mask);
return OK;
}
/*------------------------------------------------------------------------
* sreset -- reset the count and queue of a semaphore
*------------------------------------------------------------------------
*/
SYSCALL sreset(int sem, int count)
{
int start;
if(activated == 1)
start = ctr1000;
STATWORD ps;
struct sentry *sptr;
int pid;
int slist;
disable(ps);
if (isbadsem(sem) || count<0 || semaph[sem].sstate==SFREE) {
restore(ps);
return(SYSERR);
}
sptr = &semaph[sem];
slist = sptr->sqhead;
while ((pid=getfirst(slist)) != EMPTY)
ready(pid,RESCHNO);
sptr->semcnt = count;
resched();
restore(ps);
if(activated == 1)
{
Info[currpid][SRESET].freq++;
Info[currpid][SRESET].time += (ctr1000 - start);
}
return(OK);
}
/**
* Remove and return the first thread on a list
* @param q target queue
* @return thread id of removed thread, or EMPTY
*/
tid_typ dequeue(qid_typ q)
{
int tid;
if (isbadqid(q))
{
kprintf("%s:%d: isbadqid(%d) = TRUE!\n", __FILE__, __LINE__, q );
kprintf(" quehead(x) < 0 -> %d\n", quehead(q) < 0 );
kprintf(" quehead(x) != quetail(x)-1 -> %d\n", quehead(q) != ( quetail(q) - 1 ) );
kprintf(" quetail(x) >= NQENT -> %d\n", quetail(q) >= NQENT );
return SYSERR;
}
if (isempty(q))
{
return EMPTY;
}
tid = getfirst(q);
if (!isbadtid(tid))
{
quetab[tid].prev = EMPTY;
quetab[tid].next = EMPTY;
}
return tid;
}
/**
* Function to get the size of the Linkd List
* @return size of the Linked List in number of data sets
*/
int getsize()
{
nodePtr_t n = getfirst();
int i = 0;
while(n != NULL)
{
n = getnext(n);
i++;
}
return i;
}
//-------------------------------------------
//removes element with number == n
bool derlist::delnum ( long d )
{
list* pel = getfirst( );
while ( ( pel != NULL ) && ( pel->num != d ) )
pel = pel->next;
if ( pel == NULL )
return 1;
if ( pel->num == d )
pel = del ( pel );
cout<<" Deleted! ";
return 0;
}
/*------------------------------------------------------------------------
* signal -- signal a semaphore, releasing one waiting process
*------------------------------------------------------------------------
*/
SYSCALL signal(register int sem)
{
register struct sentry *sptr;
sigset_t ps;
disable(ps);
if (isbadsem(sem) || (sptr= &semaph[sem])->sstate==SFREE) {
restore(ps);
return(SYSERR);
}
if ((sptr->semcnt++) < 0)
ready(getfirst(sptr->sqhead), RESCHYES);
restore(ps);
return(OK);
}
//-------------------------------------------
//delete all numbers greater than minimal * 3
void derlist::delmin( )
{
list *min = getlast( ), *pel, *temp;
pel = getfirst( );
while ( pel != NULL )
{
if( pel->num > 3*(min->num) ){
temp = pel;
pel = del( temp );
cout<<"Removing...";
}
else
pel = pel->next;
}
}
//------------------------------------------------------------------------
// signal -- signal a semaphore, releasing one waiting process
//------------------------------------------------------------------------
SYSCALL
signal(int sem)
{
struct sentry *sptr;
int ps;
ps = disable();
if (isbadsem(sem) || (sptr = &semaph[sem])->sstate == SFREE) {
restore(ps);
return SYSERR;
}
if ((sptr->semcnt++) < 0)
readysched(getfirst(sptr->sqhead));
restore(ps);
return OK;
}
/*------------------------------------------------------------------------
* dequeue - Remove and return the first process on a list
*------------------------------------------------------------------------
*/
pid32 dequeue(
qid16 q /* ID queue to use */
)
{
pid32 pid; /* ID of process removed */
if (isbadqid(q)) {
return SYSERR;
} else if (isempty(q)) {
return EMPTY;
}
pid = getfirst(q);
queuetab[pid].qprev = EMPTY;
queuetab[pid].qnext = EMPTY;
return pid;
}
/*------------------------------------------------------------------------
* ldelete -- delete a lock by releasing its table entry
*------------------------------------------------------------------------
*/
int ldelete (int lockdescriptor)
{
STATWORD ps;
int pid;
int temp,temp1;
struct lentry *lptr;
disable(ps);
if (isbadlock(lockdescriptor) || locks[lockdescriptor].lstate==DELETED || locks[lockdescriptor].lstate==LFREE) {
restore(ps);
return(SYSERR);
}
lptr = &locks[lockdescriptor];
lptr->lstate = DELETED;
lptr->ltype = NONE;
lptr->lreaders= 0;
if (nonempty(lptr->lqhead)) {
while( (pid=getfirst(lptr->lqhead)) != EMPTY)
{
proctab[pid].plockwaitret = DELETED;
proctab[pid].locktype[lockdescriptor] = DELETED;
dequeue(pid);
ready(pid,RESCHNO);
//kprintf("\n\t\t[LDELETE.C: 37] Proc '%s' deleted from waitqueue of Lock %d\n",proctab[pid].pname,lockdescriptor);
}
resched();
}
for(pid=1;pid<NPROC;pid++) {
if(locks[lockdescriptor].lprocs[pid] == READ || locks[lockdescriptor].lprocs[pid] == WRITE)
{
locks[lockdescriptor].lprocs[pid] = DELETED;
}
}
restore(ps);
return(OK);
}
/**
* Function to sort the Linked List
* This function sorts accorting to the getter function given
* @param n Pointer to the first element
* @param getter Function pointer to the function to get the field to sort for
*/
void sortaddress(nodePtr_t n, char* (*getter)(nodePtr_t n))
{
int s = getsize();
int i = 0;
int j = 0;
nodePtr_t t = getfirst();
nodePtr_t* a = (nodePtr_t) malloc(s * sizeof(nodePtr_t));
// Preparing array to sort
for(i = 0; i < s; i++)
{
a[i] = t;
t = getnext(t);
}
// Sorting the prepared array
for(i = 0; i < (s); i++)
{
for(j = 0; j < (s - i - 1); j++)
{
if(strcmp(getter(a[j]), getter(a[j+1])))
{
t = a[j];
a[j] = a[j + 1];
a[j + 1] = t;
}
}
}
// Order data according to sorted array
head = a[0];
tail = a[s-1];
a[0]->prev = NULL;
a[0]->next = a[1];
a[s-1]->next = NULL;
a[s-1]->prev = a[s-2];
for(i = 1; i < (s - 1); i++)
{
a[i]->next = a[i+1];
a[i]->prev = a[i-1];
}
return;
}
int ldelete(int lock_value)
{
STATWORD ps;
int pid, i;
struct lentry *lptr;
int lock_index;
int lock_version;
disable(ps);
lock_index = lock_value/MAXVERSION;
lock_version = lock_value%MAXVERSION;
lptr=&locks[lock_index];
if (locks[lock_index].lstate==LFREE)
{
restore(ps);
return(SYSERR);
}
if(locks[lock_index].version != lock_version)
{
restore(ps);
return(SYSERR);
}
locks[lock_index].lstate = LFREE;
if(nonempty(lptr->lqhead))
{
while( (pid=getfirst(lptr->lqhead)) != EMPTY)
{
proctab[pid].plwaitret = DELETED;
ready(pid,RESCHNO);
}
resched();
}
locks[lock_index].nreaders = 0;
locks[lock_index].nwriters = 0;
for(i = 0; i < NPROC; i++)
lockholdtab[i][lock_index] = 0;
restore(ps);
return(OK);
}
pid32 dequeue(qid16 qid)
{
if(isbadqid(qid))
{
return SYSERR;
}
else if (isqueue(qid))
{
return EMPTY;
}
pid32 pid;
pid = getfirst(qid);
queuetab[pid].qprev = EMPTY;
queuetab[pid].qnext = EMPTY;
return pid;
}
/*------------------------------------------------------------------------
* signal -- signal a semaphore, releasing one waiting process
*------------------------------------------------------------------------
*/
SYSCALL signal(int sem)
{
STATWORD ps;
register struct sentry *sptr;
int curridx = 3;
if(syscalltrace == 1) {
syscallused[currpid] = 1;
syscallcnt[currpid][curridx]++;}
disable(ps);
if (isbadsem(sem) || (sptr= &semaph[sem])->sstate==SFREE) {
restore(ps);
return(SYSERR);
}
if ((sptr->semcnt++) < 0)
ready(getfirst(sptr->sqhead), RESCHYES);
restore(ps);
return(OK);
}
/*------------------------------------------------------------------------
* signal -- signal a semaphore, releasing one waiting process
*------------------------------------------------------------------------
*/
SYSCALL signal(int sem)
{
STATWORD ps;
register struct sentry *sptr;
disable(ps);
if (isbadsem(sem) || (sptr= &semaph[sem])->sstate==SFREE) {
restore(ps);
return(SYSERR);
}
if ((sptr->semcnt++) < 0)
ready(getfirst(sptr->sqhead), RESCHYES);
restore(ps);
if( syscalls_trace )
{
signal_freq[currpid]++;
}
return(OK);
}
SYSCALL sreset(int sem, int count)
{
STATWORD ps;
struct sentry *sptr;
int pid;
int slist;
disable(ps);
if (isbadsem(sem) || count<0 || semaph[sem].sstate==SFREE) {
restore(ps);
return(SYSERR);
}
sptr = &semaph[sem];
slist = sptr->sqhead;
while ((pid=getfirst(slist)) != EMPTY)
ready(pid,RESCHNO);
sptr->semcnt = count;
resched();
restore(ps);
return(OK);
}
int ldelete (int lockdescriptor)
{
STATWORD ps;
int pid;
struct lentry *lptr;
disable(ps);
if (isbadlock(lockdescriptor%100) || lockarr[lockdescriptor%100].lstate==LFREE) {
restore(ps);
return(SYSERR);
}
lptr = &lockarr[lockdescriptor%100];
lptr->lstate = LFREE;
if (nonempty(lptr->lqhead)) {
while( (pid=getfirst(lptr->lqhead)) != EMPTY)
{
proctab[pid].pwaitret = DELETED;
ready(pid,RESCHNO);
}
resched();
}
restore(ps);
return(OK);
}
/*------------------------------------------------------------------------
* signal -- signal a semaphore, releasing one waiting process
*------------------------------------------------------------------------
*/
SYSCALL signal(int sem)
{
// added for PA0 tracing
int start_time;
int curridx = 16;
if(syscall_trace_on == 1) {
syscall_used[currpid] = 1;
syscall_cnt[currpid][curridx]++;
start_time = ctr1000;
}
STATWORD ps;
register struct sentry *sptr;
disable(ps);
if (isbadsem(sem) || (sptr= &semaph[sem])->sstate==SFREE) {
restore(ps);
// added for PA0 tracing
if(syscall_trace_on == 1) {
syscall_time[currpid][curridx] += ctr1000 - start_time;
}
return(SYSERR);
}
if ((sptr->semcnt++) < 0)
ready(getfirst(sptr->sqhead), RESCHYES);
restore(ps);
// added for PA0 tracing
if(syscall_trace_on == 1) {
syscall_time[currpid][curridx] += ctr1000 - start_time;
}
return(OK);
}
/*------------------------------------------------------------------------
* sdelete -- delete a semaphore by releasing its table entry
*------------------------------------------------------------------------
*/
SYSCALL sdelete(int sem)
{
STATWORD ps;
int pid;
struct sentry *sptr;
disable(ps);
if (isbadsem(sem) || semaph[sem].sstate==SFREE) {
restore(ps);
return(SYSERR);
}
sptr = &semaph[sem];
sptr->sstate = SFREE;
if (nonempty(sptr->sqhead)) {
while( (pid=getfirst(sptr->sqhead)) != EMPTY)
{
proctab[pid].pwaitret = DELETED;
ready(pid,RESCHNO);
}
resched();
}
restore(ps);
return(OK);
}
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 ) ;
}
/*-----------------------------------------------------------------------
* resched -- reschedule processor to highest priority ready process
*
* Notes: Upon entry, currpid gives current process id.
* Proctab[currpid].pstate gives correct NEXT state for
* current process if other than PRREADY.
*------------------------------------------------------------------------
*/
int resched()
{
register struct pentry *optr; /* pointer to old process entry */
register struct pentry *nptr; /* pointer to new process entry */
int itemA, itemB, itemC,proc;
int num, i;
//STATWORD ps;
optr = &proctab[currpid];
if(sched_type==RANDOMSCHED)
{
/*if(count_random==0)
{
count_random++;
enqueue(dequeue(0),queueC_tail);
}*/
if((!nonempty(queueC_head)) && (!nonempty(queueC_head)) && (!nonempty(queueC_head)))
{
return OK;
}
proctab[currpid].quantumLeft = preempt; //quantum used in last execution
if(switched_to_randomsched==1)
{
switched_to_randomsched=0;
proctab[currpid].procCpuTicks += (proctab[currpid].assignedQuantum - preempt);
}
else
{
proctab[currpid].procCpuTicks += (QUANTUM - preempt);
}
//proctab[currpid].procCpuTicks += (QUANTUM - preempt);
/*Make current process as ready*/
if (optr->pstate == PRCURR)
{
//kprintf("\nen inside ");
optr->pstate = PRREADY;
if(((optr->pprio)>=66) && ((optr->pprio)<=99))
{
//kprintf("\nReady Queue A, %s", optr->pname);
enqueue(currpid, queueA_tail);
}
else if(optr->pprio>=33 && optr->pprio<=65)
{
//kprintf("\nReady Queue b, %s", optr->pname);
enqueue(currpid, queueB_tail);
}
else if(optr->pprio>=0 && optr->pprio<=32)
{
//kprintf("\nReady Queue c, %s", optr->pname);
enqueue(currpid, queueC_tail);
//enqueue(0,queueC_tail);
}
}
//srand(1);
generate_random:
num = rand();
//kprintf("\n rand 1: %d", num);
num = (num%97);
//kprintf("\n normalized rand 1: %d", num);
if(num>=50)
{
if(nonempty(queueA_head))
{
itemA = getfirst(queueA_head);
//kprintf("\nresched Queue A, %d",itemA);
nptr = &proctab[ (currpid = itemA)];//getfirst(queueA_head)) ];
nptr->pstate = PRCURR; /* mark it currently running */
#ifdef RTCLOCK
preempt = QUANTUM; /* reset preemption counter */
#endif
ctxsw((int)&optr->pesp, (int)optr->pirmask, (int)&nptr->pesp, (int)nptr->pirmask);
/* The OLD process returns here when resumed. */
return OK;
}
else
goto generate_random;//resched();
}
else if(num>20 && num <50)
{
if(nonempty(queueB_head))
{
itemB = getfirst(queueB_head);
//kprintf("\nresched Queue B, %d, %s",itemB, proctab[itemB].pname);
nptr = &proctab[ (currpid = itemB)];//getfirst(queueB_head)) ];
nptr->pstate = PRCURR; /* mark it currently running */
#ifdef RTCLOCK
preempt = QUANTUM; /* reset preemption counter */
#endif
ctxsw((int)&optr->pesp, (int)optr->pirmask, (int)&nptr->pesp, (int)nptr->pirmask);
/* The OLD process returns here when resumed. */
return OK;
}
else
goto generate_random;//resched();
}
else if(num<=20)
{
if(nonempty(queueC_head))
{
itemC = getfirst(queueC_head);
//kprintf("\nresched Queue C, %d, %s",itemC, proctab[itemC].pname);
nptr = &proctab[ (currpid = itemC)];//getfirst(queueC_head)) ];
nptr->pstate = PRCURR; /* mark it currently running */
#ifdef RTCLOCK
preempt = QUANTUM; /* reset preemption counter */
#endif
ctxsw((int)&optr->pesp, (int)optr->pirmask, (int)&nptr->pesp, (int)nptr->pirmask);
/* The OLD process returns here when resumed. */
return OK;
}
else
goto generate_random;//resched();
}
}
else if(sched_type == LINUXSCHED)
{
//int usedPreempt = preempt;
int highProc;
int oldPriority = proctab[currpid].pprio; //save the current process' priority so that the effect of chprio() or change in priority to the quantum
// or goodness is reflected in new epoch
//int procGoodness = 0;
int startNewEpoch = 1;
//disable(ps);
proctab[currpid].quantumLeft = preempt;
if(switched_to_linuxsched==1)
{
proctab[currpid].runnableProc = 1;
switched_to_linuxsched=0;
proctab[currpid].procCpuTicks += (QUANTUM - preempt);
proctab[currpid].assignedQuantum = proctab[currpid].assignedQuantum -(QUANTUM - preempt);
}
else
{
proctab[currpid].procCpuTicks += (proctab[currpid].assignedQuantum - preempt);
proctab[currpid].assignedQuantum = proctab[currpid].quantumLeft;
}
if(optr->pstate == PRCURR)
{
optr->pstate = PRREADY;
insert(currpid, rdyhead, proctab[currpid].procGoodness);
}
highProc = rdytail;
while(q[highProc].qprev!=rdyhead && q[highProc].qprev>=0 && q[highProc].qprev<NPROC) //q[temp].qnext!=rdytail && q[temp].qnext>=0 && q[temp].qnext<NPROC
{
//kprintf("\t pbdsf%s",proctab[q[highProc].qprev].pname);
if((proctab[q[highProc].qprev].runnableProc == 1) && (proctab[q[highProc].qprev].assignedQuantum > 0 ) ) //q[highProc].qnext!=0 &&
{
//kprintf("\n bacha hai : %d, %s",q[highProc].qprev, proctab[q[highProc].qprev].pname);
startNewEpoch = 0;
break;
}
highProc = q[highProc].qprev;
}
if(startNewEpoch == 1)
{
//kprintf("\nNew Epoch started---*******");
for(i=0; i<NPROC; i++)
{
if(proctab[i].pstate != PRFREE)
{
oldPriority = proctab[i].pprio; //prevent priority change effect in calculation of quantum
//proctab[i].runnableProc = 1;
//calculate quantum of each process either sleeping/waiting or ready
if(proctab[i].runnableProc == 1)
{
if(proctab[i].assignedQuantum > 0)
{
proctab[i].assignedQuantum = (oldPriority + (proctab[i].assignedQuantum /2));
proctab[i].procGoodness = (oldPriority + proctab[i].quantumLeft);
//kprintf("\nNew quantum and goodness %d, %d, %s",proctab[i].assignedQuantum, proctab[i].procGoodness, proctab[i].pname);
}
else
{
proctab[i].assignedQuantum = oldPriority;
proctab[i].procGoodness = 0;//(oldPriority);
//kprintf("\nused up quantum %d, %d, %s",proctab[i].assignedQuantum, proctab[i].procGoodness, proctab[i].pname);
}
}
proctab[i].runnableProc = 1;
//kprintf("\nFinal values of quantum and goodness %d, %d, %s",proctab[i].assignedQuantum, proctab[i].procGoodness, proctab[i].pname);
dequeue(i);
insert(i, rdyhead, proctab[i].procGoodness);
}
}
}
//goodness is to be calculated for process in same epoch also ? -> no
highProc = rdytail;
while(q[highProc].qprev!=rdyhead && q[highProc].qprev>=0 && q[highProc].qprev<NPROC)
{
/*kprintf("\n Highest proc based on goodness %d, %d, %d", q[highProc].qprev, proctab[q[highProc].qprev].procGoodness, proctab[q[highProc].qprev].assignedQuantum);
if(proctab[q[highProc].qprev].pstate == PRREADY)
{
kprintf("\nstate: PRREADY, %d", proctab[q[highProc].qprev].runnableProc);
}*/
if( (proctab[q[highProc].qprev].runnableProc == 1) && (proctab[q[highProc].qprev].assignedQuantum > 0 ) )//&& (proctab[q[highProc].qprev].pstate==PRREADY) && q[highProc].qprev!=0 )
{
//kprintf(" \ninside----------- %d", currpid);
currpid = dequeue(q[highProc].qprev);
//kprintf(" \nnew pid----------- %d", currpid);
//if(currpid != 0)
//{
nptr = &proctab[currpid];
nptr->pstate = PRCURR; /* mark it currently running */
#ifdef RTCLOCK
preempt = nptr->assignedQuantum; /* reset preemption counter */
#endif
ctxsw((int)&optr->pesp, (int)optr->pirmask, (int)&nptr->pesp, (int)nptr->pirmask);
/* The OLD process returns here when resumed. */
return ;// OK;
break;
}
else if( (q[rdyhead].qnext == 0) && (q[rdytail].qprev== 0))
{
//proctab[currpid].assignedQuantum = QUANTUM;
// kprintf(" \ninside----------- %d", currpid);
nptr = &proctab[(currpid=0)];
nptr->pstate = PRCURR; /* mark it currently running */
#ifdef RTCLOCK
preempt = QUANTUM; /* reset preemption counter */
#endif
ctxsw((int)&optr->pesp, (int)optr->pirmask, (int)&nptr->pesp, (int)nptr->pirmask);
/* The OLD process returns here when resumed. */
return;// OK;
break;
}
highProc = q[highProc].qprev;
}
}
else if(sched_type!=RANDOMSCHED && sched_type!=LINUXSCHED)
{
/* no switch needed if current process priority higher than next*/
if ( ( optr->pstate == PRCURR) && (lastkey(rdytail)<optr->pprio))
{
return(OK);
}
/* force context switch */
if (optr->pstate == PRCURR) {
optr->pstate = PRREADY;
insert(currpid,rdyhead,optr->pprio);
}
proctab[currpid].quantumLeft = preempt;
proctab[currpid].procCpuTicks += (QUANTUM - preempt);
/* remove highest priority process at end of ready list */
nptr = &proctab[ (currpid = getlast(rdytail)) ];
nptr->pstate = PRCURR; /* mark it currently running */
#ifdef RTCLOCK
preempt = QUANTUM; /* reset preemption counter */
#endif
ctxsw((int)&optr->pesp, (int)optr->pirmask, (int)&nptr->pesp, (int)nptr->pirmask);
/* The OLD process returns here when resumed. */
return OK;
}
}
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 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 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 preLoadGRO( FILE * pgroinput )
{
int groinfo ;
int iline = 0 ;
int iload = 0 ;
int natomgroline = 0 ;
int blank_signal , info ;
char buffer[ MAXCHARINLINE ] ;
//char cache[ MAXCHARINLINE ] ;
char tmp_char ;
rewind( pgroinput ) ;
fskip( pgroinput , 2 ) ;
while( ( groinfo = freadline( buffer , MAXCHARINLINE , pgroinput , ';' ) ) != 0 )
{
//printf("\n//--------------> WORKING ON NO. %d LINE ... <-------------//\n" , iline );
//info = freadline( buffer , MAXCHARINLINE , pinputfile , ';' );
//printf("\nNow we are at : %s\n" , buffer );
//printf("\n INFO is %d ...\n" , info );
blank_signal = stellblank( buffer ) ;
if( blank_signal == 0 )
{
//printf("\nNo.%d line is a blank line ... Moving on ...\n" , iline ) ;
continue ;
}
else if( blank_signal == 1 )
{
//printf("\nNo.%d line is NOT a blank line ... loading ...\n" , iline );
if( ( tmp_char = getfirst( buffer ) ) == ';' )
{
//printf("\nThis is a comment line ... So nothing will be loaded ...\n");
//fskip( pinputfile , 1 );
continue ;
}
else
{
//printf("\nLine reads : %s ...\n" , buffer );
iload ++ ;
}
//printf("\n%s\n" , buffer );
}
else
{
printf("\nSomething is wrong with the reading file part ...\n");
exit(1);
}
iline ++ ;
}//while( info != 0 );
natomgroline = iload - 1 ;
return( natomgroline ) ;
}