Ambertoppar Struct Reference

#include <parm.h>

Public Member Functions
	Ambertoppar ()
	~Ambertoppar ()
FILE *	genopen (const char *name)
void	genclose (FILE *)
char *	get (int)
void	preadln (FILE *, const char *, char *)
int	readparm (char *)
int	firstwat ()
int	read_fortran_12I6 (FILE *, int *, int)
int	moveto (FILE *, const char *)

Public Attributes
char	ititl [81]
int	IfBox
int	Nmxrs
int	IfCap
int	Natom
int	Ntypes
int	Nbonh
int	Mbona
int	Ntheth
int	Mtheta
int	Nphih
int	Mphia
int	Nhparm
int	Nparm
int	Nnb
int	Nres
int	Nbona
int	Ntheta
int	Nphia
int	Numbnd
int	Numang
int	Nptra
int	Natyp
int	Nphb
int	Nat3
int	Ntype2d
int	Nttyp
int	Nspm
int	Iptres
int	Nspsol
int	Ipatm
int	Natcap
char *	AtomNames
char *	ResNames
char *	AtomSym
char *	AtomTree
_REAL *	Charges
_REAL *	Masses
_REAL *	Rk
_REAL *	Req
_REAL *	Tk
_REAL *	Teq
_REAL *	Pk
_REAL *	Pn
_REAL *	Phase
_REAL *	Solty
_REAL *	Cn1
_REAL *	Cn2
_REAL *	HB12
_REAL *	HB6
_REAL	Box [3]
_REAL	Cutcap
_REAL	Xcap
_REAL	Ycap
_REAL	Zcap
int *	Iac
int *	Iblo
int *	Cno
int *	Ipres
int *	ExclAt
int *	TreeJoin
int *	AtomRes
int *	BondHAt1
int *	BondHAt2
int *	BondHNum
int *	BondAt1
int *	BondAt2
int *	BondNum
int *	AngleHAt1
int *	AngleHAt2
int *	AngleHAt3
int *	AngleHNum
int *	AngleAt1
int *	AngleAt2
int *	AngleAt3
int *	AngleNum
int *	DihHAt1
int *	DihHAt2
int *	DihHAt3
int *	DihHAt4
int *	DihHNum
int *	DihAt1
int *	DihAt2
int *	DihAt3
int *	DihAt4
int *	DihNum
int *	Boundary
int	popn
int	data_read

Detailed Description

Definition at line 15 of file parm.h.

Constructor & Destructor Documentation

Ambertoppar()

Ambertoppar::Ambertoppar

(

)

Definition at line 1124 of file parm.C.

References AngleAt1, AngleAt2, AngleAt3, AngleHAt1, AngleHAt2, AngleHAt3, AngleHNum, AngleNum, AtomNames, AtomRes, AtomSym, AtomTree, BondAt1, BondAt2, BondHAt1, BondHAt2, BondHNum, BondNum, Boundary, Charges, Cn1, Cn2, Cno, data_read, DihAt1, DihAt2, DihAt3, DihAt4, DihHAt1, DihHAt2, DihHAt3, DihHAt4, DihHNum, DihNum, ExclAt, HB12, HB6, Iac, Iblo, Ipres, Masses, Phase, Pk, Pn, Req, ResNames, Rk, Solty, Teq, Tk, and TreeJoin.

{
  data_read = 0;        // No data are read yet
  AtomNames = ResNames = AtomSym = AtomTree = NULL;
  Charges = Masses = Rk = Req = Tk = Teq = Pk = Pn = Phase = NULL;
  Solty = Cn1 = Cn2 = HB12 = HB6 = NULL;
  Iac = Iblo = Cno = Ipres = ExclAt = TreeJoin = AtomRes = NULL;
  BondHAt1 = BondHAt2 = BondHNum = BondAt1 = BondAt2 = NULL;
  BondNum = AngleHAt1 = AngleHAt2 = AngleHAt3 = AngleHNum = NULL;
  AngleAt1 = AngleAt2 = AngleAt3 = AngleNum = DihHAt1 = NULL;
  DihHAt2 = DihHAt3 = DihHAt4 = DihHNum = DihAt1 = DihAt2 = NULL;
  DihAt3 = DihAt4 = DihNum = Boundary = NULL;
}

~Ambertoppar()

Ambertoppar::~Ambertoppar

(

)

Definition at line 1141 of file parm.C.

References AngleAt1, AngleAt2, AngleAt3, AngleHAt1, AngleHAt2, AngleHAt3, AngleHNum, AngleNum, AtomNames, AtomRes, AtomSym, AtomTree, BondAt1, BondAt2, BondHAt1, BondHAt2, BondHNum, BondNum, Charges, Cn1, Cn2, Cno, DihAt1, DihAt2, DihAt3, DihAt4, DihHAt1, DihHAt2, DihHAt3, DihHAt4, DihHNum, DihNum, ExclAt, HB12, HB6, Iac, Iblo, Ipres, Masses, Phase, Pk, Pn, Req, ResNames, Rk, Solty, Teq, Tk, and TreeJoin.

{
  free(AtomNames);
  free(Charges);
  free(Masses);
  free(Iac);
  free(Iblo);
  free(Cno);
  free(ResNames);
  free(Ipres);
  free(Rk);
  free(Req);
  free(Tk);
  free(Teq);
  free(Pk);
  free(Pn);
  free(Phase);
  free(Solty);
  free(Cn1);
  free(Cn2);
  free(BondHAt1);
  free(BondHAt2);
  free(BondHNum);
  free(BondAt1);
  free(BondAt2);
  free(BondNum);
  free(AngleHAt1);
  free(AngleHAt2);
  free(AngleHAt3);
  free(AngleHNum);
  free(AngleAt1);
  free(AngleAt2);
  free(AngleAt3);
  free(AngleNum);
  free(DihHAt1);
  free(DihHAt2);
  free(DihHAt3);
  free(DihHAt4);
  free(DihHNum);
  free(DihAt1);
  free(DihAt2);
  free(DihAt3);
  free(DihAt4);
  free(DihNum);
  free(ExclAt);
  free(HB12);
  free(HB6);
  free(AtomSym);
  free(AtomTree);
  free(TreeJoin);
  free(AtomRes);
}

Member Function Documentation

firstwat()

int Ambertoppar::firstwat

(

)

Definition at line 1096 of file parm.C.

References AtomNames, Ipres, Nres, and ResNames.

{
        char    *restr = ResNames; 
        char    *lastres = ResNames + Nres * 4 + 1;
        int     res = 0;

        /*
         *  find 1st water residue
         */

        for (; restr<lastres; restr+=4) {
                if (!strncmp(restr, "WAT ", 4)) {
                  printf("first water: res = %d, atom = %d (%.4s)\n", 
                                        res+1, Ipres[res],
                                        &AtomNames[Ipres[res]]);
#ifndef NAMD_NO_STDOUT_FLUSH
                  fflush(stdout);
#endif
                  return(Ipres[res]-1);
                }
                res++;
        }
        return(0);
}

genclose()

void Ambertoppar::genclose

(

FILE *

fileptr

)

Definition at line 86 of file parm.C.

References Fclose().

Referenced by readparm().

{
        Fclose(fileptr);
}

genopen()

FILE * Ambertoppar::genopen

(

const char *

name

)

Definition at line 72 of file parm.C.

References Fopen().

Referenced by readparm().

{
        return(Fopen(name,"r"));
}

get()

char * Ambertoppar::get

(

int

size

)

Definition at line 96 of file parm.C.

References NAMD_die().

{
        char    *ptr;

#ifdef DEBUG
        printf("malloc %d\n", size);
#ifndef NAMD_NO_STDOUT_FLUSH
        fflush(stdout);
#endif
#endif
        if (size ==0)
                return((char *) NULL);

        if ((ptr = (char *) malloc((unsigned)size)) == NULL) {
                printf("malloc %d", size);
#ifndef NAMD_NO_STDOUT_FLUSH
                fflush(stdout);
#endif
                NAMD_die("Memory allocation error in Ambertoppar::get()");
        }
        return(ptr);
}

moveto()

int Ambertoppar::moveto	(	FILE *	fp,
		const char *	label
	)

Definition at line 1226 of file parm.C.

References endi(), iout, iWARN(), and preadln().

Referenced by readparm().

{
  char s[76],buf[81];

 while ( 1 ) {
  // Find the string "%FLAG"
  do preadln(fp, "parm file", buf);
  while (strncmp(buf,"%FLAG",5));

  // See if the label is what we expected
  sscanf(buf+5,"%s",s);
  if (strcasecmp(s,label))
    iout << iWARN << "Skipping " << s << " in parm file while seeking " << label << ".\n" << endi;
  else
    break;
 }

  // The next line should begin with "%FORMAT"
  preadln(fp, "parm file", buf);
  if (strncmp(buf,"%FORMAT",7))
    return 0;

  return 1;
}

preadln()

void Ambertoppar::preadln	(	FILE *	file,
		const char *	name,
		char *	string
	)

Definition at line 123 of file parm.C.

References NAMD_die().

Referenced by moveto(), and readparm().

{
        int     i, j;

        for (i=0; i<81; i++) {
                if ((j = getc(file)) == EOF) {
                        NAMD_die("Unexpected EOF in Amber parm file");
                        printf("Error: unexpected EOF in %s\n", name);
                }
                string[i] = (char) j;
                if (string[i] == '\n') {
                        break;
                }
        }
        if (i == 80  &&  string[i] != '\n') {
                NAMD_die("Line too long in Amber parm file");
                printf("Error: line too long in %s:\n%.80s", name, string);
        }
}

read_fortran_12I6()

int Ambertoppar::read_fortran_12I6	(	FILE *	fp,
		int *	data,
		int	count
	)

Definition at line 1201 of file parm.C.

References readtoeoln().

Referenced by readparm().

{
  int i,j;
  char buf[7];
  
  for (i=0; i<count; ++i)
  { for (j=0; j<6; ++j)
    { buf[j]=getc(fp);
      if (buf[j]=='\n' || buf[j]=='\0' || buf[j]==EOF)
        return 0;
    }
    buf[6] = '\0';
    if (sscanf(buf,"%d",data+i) != 1)
      return 0;
    if (i%12==11 && i<count-1)
      readtoeoln(fp);
  }
  
  return 1;
}

readparm()

int Ambertoppar::readparm

(

char *

name

)

Definition at line 151 of file parm.C.

References _REAL, AngleAt1, AngleAt2, AngleAt3, AngleHAt1, AngleHAt2, AngleHAt3, AngleHNum, AngleNum, AtomNames, AtomRes, AtomSym, AtomTree, BondAt1, BondAt2, BondHAt1, BondHAt2, BondHNum, BondNum, Boundary, Charges, Cn1, Cn2, Cno, Cutcap, data_read, debug, DihAt1, DihAt2, DihAt3, DihAt4, DihHAt1, DihHAt2, DihHAt3, DihHAt4, DihHNum, DihNum, endi(), ExclAt, genclose(), genopen(), HB12, HB6, Iac, Iblo, IfBox, IfCap, iout, Ipatm, Ipres, Iptres, ititl, Masses, Mbona, moveto(), Mphia, Mtheta, Nat3, Natcap, Natom, Natyp, Nbona, Nbonh, Nhparm, Nmxrs, Nnb, Nparm, Nphb, Nphia, Nphih, Nptra, Nres, Nspm, Nspsol, Ntheta, Ntheth, Nttyp, Ntype2d, Ntypes, Numang, Numbnd, Phase, Pk, Pn, preadln(), read_fortran_12I6(), readtoeoln(), Req, ResNames, Rk, Solty, Teq, Tk, TreeJoin, Xcap, Ycap, and Zcap.

Referenced by NamdState::loadStructure().

{
        _REAL           *H;
        int             i, idum, res, ifpert;
        int             *buffer, amber7_format;
        FILE            *file;

        if (data_read)
        { iout << "Duplicate parm data in one object!\n" << endi;
          return(0);
        }

//      printf("Reading parm file (%s)\n", name);
        iout << "Reading parm file (" << name << ") ...\n" << endi;

//      if ((file = genopen(name, "parm")) == NULL) 
        if ((file = genopen(name)) == NULL)
                return(0);

        /* READ TITLE */

        preadln(file, name, ititl);
// "ititle" doesn't guarantee to have '\0' (as the end of a string),
// so the following is disabled in order to avoid strange output
//      printf("%s title:\n%s", name, ititl);

        // Check whether it's in AMBER 7 format or in old format
        
        if (strncmp(ititl,"%VERSION",8))
                amber7_format = 0;  // old format
        else
        {       amber7_format = 1;  // AMBER 7 format
                iout << "PARM file in AMBER 7 format\n" << endi;
                if (!moveto(file,"TITLE"))
                { genclose(file);
                  return 0;
                }
                preadln(file, name, ititl);
        }

        /* READ CONTROL INTEGERS */

        if (amber7_format)
        {       if (!moveto(file,"POINTERS"))
                { genclose(file);
                  return 0;
                }
//      fscanf(file, f9118, 
                fscanf(file, "%d%d%d%d%d%d%d%d%d%d%d%d",
                &Natom,  &Ntypes, &Nbonh, &Mbona, 
                &Ntheth, &Mtheta, &Nphih, &Mphia, 
                &Nhparm, &Nparm,  &Nnb,   &Nres);

//      fscanf(file, f9118, 
                fscanf(file, "%d%d%d%d%d%d%d%d%d%d%d%d",
                &Nbona,  &Ntheta, &Nphia, &Numbnd, 
                &Numang, &Nptra,  &Natyp, &Nphb, 
                &ifpert,      &idum,        &idum,       &idum);

                fscanf(file, " %d %d %d %d %d %d", 
                &idum, &idum,&idum,&IfBox,&Nmxrs,&IfCap);
        }
        else
        {       buffer = new int[30];
                if (!read_fortran_12I6(file,buffer,30))
                { genclose(file);
                  return 0;
                }
                Natom = buffer[0];
                Ntypes = buffer[1];
                Nbonh = buffer[2];
                Mbona = buffer[3];
                Ntheth = buffer[4];
                Mtheta = buffer[5];
                Nphih = buffer[6];
                Mphia = buffer[7];
                Nhparm = buffer[8];
                Nparm = buffer[9];
                Nnb = buffer[10];
                Nres = buffer[11];
                Nbona = buffer[12];
                Ntheta = buffer[13];
                Nphia = buffer[14];
                Numbnd = buffer[15];
                Numang = buffer[16];
                Nptra = buffer[17];
                Natyp = buffer[18];
                Nphb = buffer[19];
                ifpert = buffer[20];
                IfBox = buffer[27];
                Nmxrs = buffer[28];
                IfCap = buffer[29];
                delete [] buffer;
//      skipeoln(file);
                readtoeoln(file);
        }

        if (ifpert) {
                printf("not equipped to read perturbation prmtop\n");
                return(0);
        }

        /* ALLOCATE MEMORY */

        Nat3 = 3 * Natom;
        Ntype2d = Ntypes * Ntypes;
        Nttyp = Ntypes*(Ntypes+1)/2;

        /*
         * get most of the indirect stuff; some extra allowed for char arrays
         */

        AtomNames = (char *) get(4*Natom+81);
        Charges = (_REAL *) get(sizeof(_REAL)*Natom);
        Masses = (_REAL *) get(sizeof(_REAL)*Natom);
        Iac = (int *) get(sizeof(int)*Natom);
        Iblo = (int *) get(sizeof(int)*Natom);
        Cno = (int *) get(sizeof(int)* Ntype2d);
        ResNames = (char *) get(4* Nres+81);
        Ipres = (int *) get(sizeof(int)*( Nres+1));
        Rk = (_REAL *) get(sizeof(_REAL)* Numbnd);
        Req = (_REAL *) get(sizeof(_REAL)* Numbnd);
        Tk = (_REAL *) get(sizeof(_REAL)* Numang);
        Teq = (_REAL *) get(sizeof(_REAL)* Numang);
        Pk = (_REAL *) get(sizeof(_REAL)* Nptra);
        Pn = (_REAL *) get(sizeof(_REAL)* Nptra);
        Phase = (_REAL *) get(sizeof(_REAL)* Nptra);
        Solty = (_REAL *) get(sizeof(_REAL)* Natyp);
        Cn1 = (_REAL *) get(sizeof(_REAL)* Nttyp);
        Cn2 = (_REAL *) get(sizeof(_REAL)* Nttyp);
        BondHAt1 = (int *) get(sizeof(int)* Nbonh);
        BondHAt2 = (int *) get(sizeof(int)* Nbonh);
        BondHNum = (int *) get(sizeof(int)* Nbonh);
        BondAt1 = (int *) get(sizeof(int)* Nbona);
        BondAt2 = (int *) get(sizeof(int)* Nbona);
        BondNum = (int *) get(sizeof(int)* Nbona);
        AngleHAt1 = (int *) get(sizeof(int)* Ntheth);
        AngleHAt2 = (int *) get(sizeof(int)* Ntheth);
        AngleHAt3 = (int *) get(sizeof(int)* Ntheth);
        AngleHNum = (int *) get(sizeof(int)* Ntheth);
        AngleAt1 = (int *) get(sizeof(int)* Ntheta);
        AngleAt2 = (int *) get(sizeof(int)*Ntheta);
        AngleAt3 = (int *) get(sizeof(int)*Ntheta);
        AngleNum = (int *) get(sizeof(int)*Ntheta);
        DihHAt1 = (int *) get(sizeof(int)*Nphih);
        DihHAt2 = (int *) get(sizeof(int)*Nphih);
        DihHAt3 = (int *) get(sizeof(int)*Nphih);
        DihHAt4 = (int *) get(sizeof(int)*Nphih);
        DihHNum = (int *) get(sizeof(int)*Nphih);
        DihAt1 = (int *) get(sizeof(int)*Nphia);
        DihAt2 = (int *) get(sizeof(int)*Nphia);
        DihAt3 = (int *) get(sizeof(int)*Nphia);
        DihAt4 = (int *) get(sizeof(int)*Nphia);
        DihNum = (int *) get(sizeof(int)*Nphia);
        ExclAt = (int *) get(sizeof(int)*Nnb);
        HB12 = (_REAL *) get(sizeof(_REAL)*Nphb);
        HB6 = (_REAL *) get(sizeof(_REAL)*Nphb);
        AtomSym = (char *) get(4*Natom+81);
        AtomTree = (char *) get(4*Natom+81);
        TreeJoin = (int *) get(sizeof(int)*Natom);
        AtomRes = (int *) get(sizeof(int)*Natom);

        /* 
         * READ ATOM NAMES -IH(M04)
         */

        if (amber7_format)
                if (!moveto(file,"ATOM_NAME"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i<(Natom/20 + (Natom%20 ? 1 : 0)); i++)
                preadln(file, "", &AtomNames[i*80]);

        /* 
         * READ ATOM CHARGES -X(L15)
         *      (pre-multiplied by an energy factor of 18.2223 == sqrt(332)
         *       for faster force field calculations)
         */

        if (amber7_format)
                if (!moveto(file,"CHARGE"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i<Natom; i++)
#ifdef DOUBLE
                fscanf(file, " %lf", &Charges[i]);
#else
                fscanf(file, " %f", &Charges[i]);
#endif
//      skipeoln(file);
        readtoeoln(file);

        /* 
         * READ ATOM MASSES -X(L20)
         */

        if (amber7_format)
                if (!moveto(file,"MASS"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i<Natom; i++)
#ifdef DOUBLE
                fscanf(file, " %le", &Masses[i]);
#else
                fscanf(file, " %e", &Masses[i]);
#endif
//      skipeoln(file);
        readtoeoln(file);

        /* 
         * READ ATOM L-J TYPES -IX(I04)
         */

        if (amber7_format)
        {       if (!moveto(file,"ATOM_TYPE_INDEX"))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Natom; i++)
                        fscanf(file, " %d", &Iac[i]);
        }
        else
        {       if (!read_fortran_12I6(file,Iac,Natom))
                { genclose(file);
                  return 0;
                }
//      skipeoln(file);
                readtoeoln(file);
        }

        /* 
         * READ ATOM INDEX TO 1st IN EXCLUDED ATOM LIST "NATEX" -IX(I08)
         */

        if (amber7_format)
        {       if (!moveto(file,"NUMBER_EXCLUDED_ATOMS"))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Natom; i++)
                        fscanf(file, " %d", &Iblo[i]);
        }
        else
        {       if (!read_fortran_12I6(file,Iblo,Natom))
                { genclose(file);
                  return 0;
                }
//      skipeoln(file);
                readtoeoln(file);
        }

        /* 
         * READ TYPE INDEX TO N-B TYPE -IX(I06)
         */

        if (amber7_format)
        {       if (!moveto(file,"NONBONDED_PARM_INDEX"))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Ntype2d; i++)
                        fscanf(file, " %d", &Cno[i]);
        }
        else
        {       if (!read_fortran_12I6(file,Cno,Ntype2d))
                { genclose(file);
                  return 0;
                }
//      skipeoln(file);
                readtoeoln(file);
        }

        /* 
         * READ RES NAMES (4 chars each, 4th blank) -IH(M02)
         */

        if (amber7_format)
                if (!moveto(file,"RESIDUE_LABEL"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i<(Nres/20 + (Nres%20 ? 1 : 0)); i++)
                preadln(file, "", &ResNames[i*80]);

        /* 
         * READ RES POINTERS TO 1st ATOM                -IX(I02)
         */

        if (amber7_format)
        {       if (!moveto(file,"RESIDUE_POINTER"))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Nres; i++) 
                        fscanf(file, " %d", &Ipres[i]);
        }
        else
        {       if (!read_fortran_12I6(file,Ipres,Nres))
                { genclose(file);
                  return 0;
                }
//      skipeoln(file);
                readtoeoln(file);
        }
        Ipres[Nres] = Natom + 1;

        /* 
         * READ BOND FORCE CONSTANTS                    -RK()
         */

        if (amber7_format)
                if (!moveto(file,"BOND_FORCE_CONSTANT"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i< Numbnd; i++) 
#ifdef DOUBLE
                fscanf(file, " %lf", &Rk[i]);
#else
                fscanf(file, " %f", &Rk[i]);
#endif
//      skipeoln(file);
        readtoeoln(file);

        /* 
         * READ BOND LENGTH OF MINIMUM ENERGY           -REQ()
         */

        if (amber7_format)
                if (!moveto(file,"BOND_EQUIL_VALUE"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i< Numbnd; i++) 
#ifdef DOUBLE
                fscanf(file, " %lf", &Req[i]);
#else
                fscanf(file, " %f", &Req[i]);
#endif
//      skipeoln(file);
        readtoeoln(file);

        /* 
         * READ BOND ANGLE FORCE CONSTANTS (following Rk nomen) -TK()
         */

        if (amber7_format)
                if (!moveto(file,"ANGLE_FORCE_CONSTANT"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i< Numang; i++) 
#ifdef DOUBLE
                fscanf(file, " %lf", &Tk[i]);
#else
                fscanf(file, " %f", &Tk[i]);
#endif
//      skipeoln(file);
        readtoeoln(file);

        /* 
         * READ BOND ANGLE OF MINIMUM ENERGY (following Req nomen) -TEQ()
         */

        if (amber7_format)
                if (!moveto(file,"ANGLE_EQUIL_VALUE"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i< Numang; i++) 
#ifdef DOUBLE
                fscanf(file, " %lf", &Teq[i]);
#else
                fscanf(file, " %f", &Teq[i]);
#endif
//      skipeoln(file);
        readtoeoln(file);

        /* 
         * READ DIHEDRAL PEAK MAGNITUDE                 -PK()
         */

        if (amber7_format)
                if (!moveto(file,"DIHEDRAL_FORCE_CONSTANT"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i< Nptra; i++) 
#ifdef DOUBLE
                fscanf(file, " %lf", &Pk[i]);
#else
                fscanf(file, " %f", &Pk[i]);
#endif
//      skipeoln(file);
        readtoeoln(file);

        /* 
         * READ DIHEDRAL PERIODICITY                    -PN()
         */

        if (amber7_format)
                if (!moveto(file,"DIHEDRAL_PERIODICITY"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i< Nptra; i++) 
#ifdef DOUBLE
                fscanf(file, " %lf", &Pn[i]);
#else
                fscanf(file, " %f", &Pn[i]);
#endif
//      skipeoln(file);
        readtoeoln(file);

        /* 
         * READ DIHEDRAL PHASE                          -PHASE()
         */

        if (amber7_format)
                if (!moveto(file,"DIHEDRAL_PHASE"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i< Nptra; i++) 
#ifdef DOUBLE
                fscanf(file, " %lf", &Phase[i]);
#else
                fscanf(file, " %f", &Phase[i]);
#endif
//      skipeoln(file);
        readtoeoln(file);

        /* 
         * ?? "RESERVED"                                -SOLTY()
         */

        if (amber7_format)
                if (!moveto(file,"SOLTY"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i< Natyp; i++) 
#ifdef DOUBLE
                fscanf(file, " %lf", &Solty[i]);
#else
                fscanf(file, " %f", &Solty[i]);
#endif
//      skipeoln(file);
        readtoeoln(file);

        /* 
         * READ L-J R**12 FOR ALL PAIRS OF ATOM TYPES   -CN1()
         *      (SHOULD BE 0 WHERE H-BONDS)
         */

        if (amber7_format)
                if (!moveto(file,"LENNARD_JONES_ACOEF"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i< Nttyp; i++) 
#ifdef DOUBLE
                fscanf(file, " %lf", &Cn1[i]);
#else
                fscanf(file, " %f", &Cn1[i]);
#endif
//      skipeoln(file);
        readtoeoln(file);

        /* 
         * READ L-J R**6 FOR ALL PAIRS OF ATOM TYPES    -CN2()
         *      (SHOULD BE 0 WHERE H-BONDS)
         */

        if (amber7_format)
                if (!moveto(file,"LENNARD_JONES_BCOEF"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i< Nttyp; i++) 
#ifdef DOUBLE
                fscanf(file, " %lf", &Cn2[i]);
#else
                fscanf(file, " %f", &Cn2[i]);
#endif
//      skipeoln(file);
        readtoeoln(file);

        /* 
         * READ COVALENT BOND W/ HYDROGEN (3*(atnum-1)): 
         *      IBH = ATOM1             -IX(I12)
         *      JBH = ATOM2             -IX(I14)
         *      ICBH = BOND ARRAY PTR   -IX(I16)
         */

        if (amber7_format)
        {       if (!moveto(file,"BONDS_INC_HYDROGEN"))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Nbonh; i++)
                        fscanf(file, " %d %d %d", 
                            &BondHAt1[i], &BondHAt2[i], &BondHNum[i]);
        }
        else
        {       buffer = new int[3*Nbonh];
                if (!read_fortran_12I6(file,buffer,3*Nbonh))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Nbonh; i++) 
                { BondHAt1[i] = buffer[3*i];
                  BondHAt2[i] = buffer[3*i+1];
                  BondHNum[i] = buffer[3*i+2];
                }
                delete [] buffer;
//      skipeoln(file);
                readtoeoln(file);
        }

        /* 
         * READ COVALENT BOND W/OUT HYDROGEN (3*(atnum-1)):
         *      IB = ATOM1              -IX(I18)
         *      JB = ATOM2              -IX(I20)
         *      ICB = BOND ARRAY PTR    -IX(I22)
         */

        if (amber7_format)
        {       if (!moveto(file,"BONDS_WITHOUT_HYDROGEN"))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Nbona; i++)
                        fscanf(file, " %d %d %d", 
                                &BondAt1[i], &BondAt2[i], &BondNum[i]);
        }
        else
        {       buffer = new int[3*Nbona];
                if (!read_fortran_12I6(file,buffer,3*Nbona))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Nbona; i++)
                { BondAt1[i] = buffer[3*i];
                  BondAt2[i] = buffer[3*i+1];
                  BondNum[i] = buffer[3*i+2];
                }
                delete [] buffer;
//      skipeoln(file);
                readtoeoln(file);
        }

        /* 
         * READ ANGLE W/ HYDROGEN: 
         *      ITH = ATOM1                     -IX(I24)
         *      JTH = ATOM2                     -IX(I26)
         *      KTH = ATOM3                     -IX(I28)
         *      ICTH = ANGLE ARRAY PTR          -IX(I30)
         */

        if (amber7_format)
        {       if (!moveto(file,"ANGLES_INC_HYDROGEN"))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Ntheth; i++)
                        fscanf(file, " %d %d %d %d", 
                                &AngleHAt1[i], &AngleHAt2[i], 
                                &AngleHAt3[i], &AngleHNum[i]);
        }
        else
        {       buffer = new int[4*Ntheth];
                if (!read_fortran_12I6(file,buffer,4*Ntheth))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Ntheth; i++)
                { AngleHAt1[i] = buffer[4*i];
                  AngleHAt2[i] = buffer[4*i+1];
                  AngleHAt3[i] = buffer[4*i+2];
                  AngleHNum[i] = buffer[4*i+3];
                }
                delete [] buffer;
//      skipeoln(file);
                readtoeoln(file);
        }

        /* 
         * READ ANGLE W/OUT HYDROGEN: 
         *      IT = ATOM1                      -IX(I32)
         *      JT = ATOM2                      -IX(I34)
         *      KT = ATOM3                      -IX(I36)
         *      ICT = ANGLE ARRAY PTR           -IX(I38)
         */

        if (amber7_format)
        {       if (!moveto(file,"ANGLES_WITHOUT_HYDROGEN"))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Ntheta; i++)
                        fscanf(file, " %d %d %d %d", 
                                &AngleAt1[i], &AngleAt2[i], 
                                &AngleAt3[i], &AngleNum[i]);
        }
        else
        {       buffer = new int[4*Ntheta];
                if (!read_fortran_12I6(file,buffer,4*Ntheta))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Ntheta; i++)
                { AngleAt1[i] = buffer[4*i];
                  AngleAt2[i] = buffer[4*i+1];
                  AngleAt3[i] = buffer[4*i+2];
                  AngleNum[i] = buffer[4*i+3];
                }
                delete [] buffer;
//      skipeoln(file);
                readtoeoln(file);
        }

        /* 
         * READ DIHEDRAL W/ HYDROGEN: 
         *      ITH = ATOM1                     -IX(40)
         *      JTH = ATOM2                     -IX(42)
         *      KTH = ATOM3                     -IX(44)
         *      LTH = ATOM4                     -IX(46)
         *      ICTH = DIHEDRAL ARRAY PTR       -IX(48)
         */

        if (amber7_format)
        {       if (!moveto(file,"DIHEDRALS_INC_HYDROGEN"))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Nphih; i++)
                        fscanf(file, " %d %d %d %d %d", 
                                &DihHAt1[i], &DihHAt2[i], &DihHAt3[i], 
                                &DihHAt4[i], &DihHNum[i]);
        }
        else
        {       buffer = new int[5*Nphih];
                if (!read_fortran_12I6(file,buffer,5*Nphih))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Nphih; i++)
                { DihHAt1[i] = buffer[5*i];
                  DihHAt2[i] = buffer[5*i+1];
                  DihHAt3[i] = buffer[5*i+2];
                  DihHAt4[i] = buffer[5*i+3];
                  DihHNum[i] = buffer[5*i+4];
                }
                delete [] buffer;
//      skipeoln(file);
                readtoeoln(file);
        }

        /* 
         * READ DIHEDRAL W/OUT HYDROGEN: 
         *      IT = ATOM1
         *      JT = ATOM2
         *      KT = ATOM3
         *      LT = ATOM4
         *      ICT = DIHEDRAL ARRAY PTR
         */

        if (amber7_format)
        {       if (!moveto(file,"DIHEDRALS_WITHOUT_HYDROGEN"))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Nphia; i++)
                        fscanf(file, " %d %d %d %d %d", 
                                &DihAt1[i], &DihAt2[i], &DihAt3[i], 
                                &DihAt4[i], &DihNum[i]);
        }
        else
        {       buffer = new int[5*Nphia];
                if (!read_fortran_12I6(file,buffer,5*Nphia))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Nphia; i++) {
                  DihAt1[i] = buffer[5*i];
                  DihAt2[i] = buffer[5*i+1];
                  DihAt3[i] = buffer[5*i+2];
                  DihAt4[i] = buffer[5*i+3];
                  DihNum[i] = buffer[5*i+4];
                }
                delete [] buffer;
//      skipeoln(file);
                readtoeoln(file);
        }

        /*
         * READ EXCLUDED ATOM LIST      -IX(I10)
         */

        if (amber7_format)
        {       if (!moveto(file,"EXCLUDED_ATOMS_LIST"))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Nnb; i++)
                        fscanf(file, " %d", &ExclAt[i]);
        }
        else
        {       if (!read_fortran_12I6(file,ExclAt,Nnb))
                { genclose(file);
                  return 0;
                }
//      skipeoln(file);
                readtoeoln(file);
        }

        /*
         * READ H-BOND R**12 TERM FOR ALL N-B TYPES     -ASOL()
         */

        if (amber7_format)
                if (!moveto(file,"HBOND_ACOEF"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i<Nphb; i++) 
#ifdef DOUBLE
                fscanf(file, " %lf", &HB12[i]);
#else
                fscanf(file, " %f", &HB12[i]);
#endif
//      skipeoln(file);
        readtoeoln(file);

        /*
         * READ H-BOND R**6 TERM FOR ALL N-B TYPES      -BSOL()
         */

        if (amber7_format)
                if (!moveto(file,"HBOND_BCOEF"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i<Nphb; i++) 
#ifdef DOUBLE
                fscanf(file, " %lf", &HB6[i]);
#else
                fscanf(file, " %f", &HB6[i]);
#endif
//      skipeoln(file);
        readtoeoln(file);

        /*
         * READ H-BOND CUTOFF (NOT USED) ??             -HBCUT()
         */

        if (amber7_format)
                if (!moveto(file,"HBCUT"))
                { genclose(file);
                  return 0;
                }
        H = (_REAL *) get(Nphb * sizeof(_REAL));
        for (i=0; i<Nphb; i++) 
#ifdef DOUBLE
                fscanf(file, " %lf", &H[i]);
#else
                fscanf(file, " %f", &H[i]);
#endif
        free((char *)H);
        
//      skipeoln(file);
        readtoeoln(file);

        /*
         * READ ATOM SYMBOLS (FOR ANALYSIS PROGS)       -IH(M06)
         */

        if (amber7_format)
                if (!moveto(file,"AMBER_ATOM_TYPE"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i<(Natom/20 + (Natom%20 ? 1 : 0)); i++)
                preadln(file, "", &AtomSym[i*80]);

        /*
         * READ TREE SYMBOLS (FOR ANALYSIS PROGS)       -IH(M08)
         */

        if (amber7_format)
                if (!moveto(file,"TREE_CHAIN_CLASSIFICATION"))
                { genclose(file);
                  return 0;
                }
        for (i=0; i<(Natom/20 + (Natom%20 ? 1 : 0)); i++)
                preadln(file, "", &AtomTree[i*80]);

        /*
         * READ TREE JOIN INFO (FOR ANALYSIS PROGS)     -IX(I64)
         */

        if (amber7_format)
        {       if (!moveto(file,"JOIN_ARRAY"))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Natom; i++)
                        fscanf(file, " %d", &TreeJoin[i]);
        }
        else
        {       if (!read_fortran_12I6(file,TreeJoin,Natom))
                { genclose(file);
                  return 0;
                }
//      skipeoln(file);
                readtoeoln(file);
        }

        /*
         * READ PER-ATOM RES NUMBER                     -IX(I66)
         *      NOTE: this appears to be something entirely different
         *      NOTE: overwriting this with correct PER-ATOM RES NUMBERs
         */

        if (amber7_format)
        {       if (!moveto(file,"IROTAT"))
                { genclose(file);
                  return 0;
                }
                for (i=0; i<Natom; i++)
                        fscanf(file, " %d", &AtomRes[i]);
        }
        else
                if (!read_fortran_12I6(file,AtomRes,Natom))
                { genclose(file);
                  return 0;
                }
        res = 0;
        for (i=0; i<Natom; i++) {
                if (i+1 == Ipres[res+1])        /* atom is 1st of next res */
                        res++;
                AtomRes[i] = res;
        }
      
        /*
         * BOUNDARY CONDITION STUFF
         */

        if (!IfBox) {
                Nspm = 1;
                Boundary = (int *) get(sizeof(int)*Nspm);
                Boundary[0] = Natom;
        } else {
                if (amber7_format)
                {       if (!moveto(file,"SOLVENT_POINTERS"))
                        { genclose(file);
                          return 0;
                        }
                        fscanf(file, " %d %d %d", &Iptres, &Nspm, 
                                                        &Nspsol);
                }
                else
                {
//              skipeoln(file);
                        readtoeoln(file);
                        buffer = new int[3];
                        if (!read_fortran_12I6(file,buffer,3))
                        { genclose(file);
                          return 0;
                        }
                        Iptres = buffer[0];
                        Nspm = buffer[1];
                        Nspsol = buffer[2];
                        delete [] buffer;
//              skipeoln(file);
                        readtoeoln(file);
                }
                Boundary = (int *) get(sizeof(int)*Nspm);
                if (amber7_format)
                {       if (!moveto(file,"ATOMS_PER_MOLECULE"))
                        { genclose(file);
                          return 0;
                        }
                        for (i=0; i<Nspm; i++)
                                fscanf(file, " %d", &Boundary[i]);
                }
                else
                {       if (!read_fortran_12I6(file,Boundary,Nspm))
                        { genclose(file);
                          return 0;
                        }
//              skipeoln(file);
                        readtoeoln(file);
                }
                if (amber7_format)
                        if (!moveto(file,"BOX_DIMENSIONS"))
                        { genclose(file);
                          return 0;
                        }
#ifdef DOUBLE
                fscanf(file, " %lf %lf %lf", 
#else
                fscanf(file, " %f %f %f", 
#endif
                                &Box[0], &Box[1], &Box[2]);
//              skipeoln(file);
                readtoeoln(file);
                if (Iptres)
                        Ipatm = Ipres[Iptres] - 1; 
                /* IF(IPTRES.GT.0) IPTATM = IX(I02+IPTRES-1+1)-1 */
        }

        /*
         * ----- LOAD THE CAP INFORMATION IF NEEDED -----
         */

        // I don't know the label for it, so I don't read it if
        // it's AMBER 7 format. It's not used in NAMD anyway.
//      if (IfCap) {
        if (IfCap && !amber7_format) {
                /* if (IfBox) 
                        skipeoln(file); */
#ifdef DOUBLE
                fscanf(file, " %d %lf %lf %lf %lf", 
#else
                fscanf(file, " %d %f %f %f %f", 
#endif
                                &Natcap, &Cutcap, 
                                &Xcap, &Ycap, &Zcap);
        }
        genclose(file);
        if (debug) {
                printf("rdprm done\n");
#ifndef NAMD_NO_STDOUT_FLUSH
                fflush(stdout);
#endif
        }
        data_read = 1;
        return(1);
}

Member Data Documentation

AngleAt1

int * Ambertoppar::AngleAt1

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

AngleAt2

int * Ambertoppar::AngleAt2

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

AngleAt3

int * Ambertoppar::AngleAt3

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

AngleHAt1

int * Ambertoppar::AngleHAt1

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

AngleHAt2

int * Ambertoppar::AngleHAt2

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

AngleHAt3

int * Ambertoppar::AngleHAt3

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

AngleHNum

int * Ambertoppar::AngleHNum

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

AngleNum

int * Ambertoppar::AngleNum

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

AtomNames

char* Ambertoppar::AtomNames

Definition at line 23 of file parm.h.

Referenced by Ambertoppar(), firstwat(), PDB::PDB(), readparm(), and ~Ambertoppar().

AtomRes

int * Ambertoppar::AtomRes

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), PDB::PDB(), readparm(), and ~Ambertoppar().

AtomSym

char * Ambertoppar::AtomSym

Definition at line 23 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

AtomTree

char * Ambertoppar::AtomTree

Definition at line 23 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

BondAt1

int * Ambertoppar::BondAt1

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

BondAt2

int * Ambertoppar::BondAt2

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

BondHAt1

int * Ambertoppar::BondHAt1

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

BondHAt2

int * Ambertoppar::BondHAt2

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

BondHNum

int * Ambertoppar::BondHNum

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

BondNum

int * Ambertoppar::BondNum

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

Boundary

int * Ambertoppar::Boundary

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), and readparm().

Box

_REAL Ambertoppar::Box[3]

Definition at line 26 of file parm.h.

Charges

_REAL* Ambertoppar::Charges

Definition at line 24 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

Cn1

_REAL * Ambertoppar::Cn1

Definition at line 24 of file parm.h.

Referenced by Ambertoppar(), Parameters::read_parm(), readparm(), and ~Ambertoppar().

Cn2

_REAL * Ambertoppar::Cn2

Definition at line 24 of file parm.h.

Referenced by Ambertoppar(), Parameters::read_parm(), readparm(), and ~Ambertoppar().

Cno

int * Ambertoppar::Cno

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), Parameters::read_parm(), readparm(), and ~Ambertoppar().

Cutcap

_REAL Ambertoppar::Cutcap

Definition at line 26 of file parm.h.

Referenced by readparm().

data_read

int Ambertoppar::data_read

Definition at line 34 of file parm.h.

Referenced by Ambertoppar(), Parameters::read_parm(), and readparm().

DihAt1

int * Ambertoppar::DihAt1

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

DihAt2

int * Ambertoppar::DihAt2

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

DihAt3

int * Ambertoppar::DihAt3

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

DihAt4

int * Ambertoppar::DihAt4

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

DihHAt1

int * Ambertoppar::DihHAt1

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

DihHAt2

int * Ambertoppar::DihHAt2

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

DihHAt3

int * Ambertoppar::DihHAt3

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

DihHAt4

int * Ambertoppar::DihHAt4

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

DihHNum

int * Ambertoppar::DihHNum

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

DihNum

int * Ambertoppar::DihNum

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

ExclAt

int * Ambertoppar::ExclAt

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

HB12

_REAL * Ambertoppar::HB12

Definition at line 24 of file parm.h.

Referenced by Ambertoppar(), Parameters::read_parm(), readparm(), and ~Ambertoppar().

HB6

_REAL * Ambertoppar::HB6

Definition at line 24 of file parm.h.

Referenced by Ambertoppar(), Parameters::read_parm(), readparm(), and ~Ambertoppar().

Iac

int* Ambertoppar::Iac

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

Iblo

int * Ambertoppar::Iblo

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

IfBox

int Ambertoppar::IfBox

Definition at line 17 of file parm.h.

Referenced by readparm().

IfCap

int Ambertoppar::IfCap

Definition at line 17 of file parm.h.

Referenced by readparm().

Ipatm

int Ambertoppar::Ipatm

Definition at line 17 of file parm.h.

Referenced by readparm().

Ipres

int * Ambertoppar::Ipres

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), firstwat(), readparm(), and ~Ambertoppar().

Iptres

int Ambertoppar::Iptres

Definition at line 17 of file parm.h.

Referenced by readparm().

ititl

char Ambertoppar::ititl[81]

Definition at line 16 of file parm.h.

Referenced by readparm().

Masses

_REAL * Ambertoppar::Masses

Definition at line 24 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

Mbona

int Ambertoppar::Mbona

Definition at line 17 of file parm.h.

Referenced by readparm().

Mphia

int Ambertoppar::Mphia

Definition at line 17 of file parm.h.

Referenced by readparm().

Mtheta

int Ambertoppar::Mtheta

Definition at line 17 of file parm.h.

Referenced by readparm().

Nat3

int Ambertoppar::Nat3

Definition at line 17 of file parm.h.

Referenced by readparm().

Natcap

int Ambertoppar::Natcap

Definition at line 17 of file parm.h.

Referenced by readparm().

Natom

int Ambertoppar::Natom

Definition at line 17 of file parm.h.

Referenced by PDB::PDB(), and readparm().

Natyp

int Ambertoppar::Natyp

Definition at line 17 of file parm.h.

Referenced by readparm().

Nbona

int Ambertoppar::Nbona

Definition at line 17 of file parm.h.

Referenced by readparm().

Nbonh

int Ambertoppar::Nbonh

Definition at line 17 of file parm.h.

Referenced by readparm().

Nhparm

int Ambertoppar::Nhparm

Definition at line 17 of file parm.h.

Referenced by readparm().

Nmxrs

int Ambertoppar::Nmxrs

Definition at line 17 of file parm.h.

Referenced by readparm().

Nnb

int Ambertoppar::Nnb

Definition at line 17 of file parm.h.

Referenced by readparm().

Nparm

int Ambertoppar::Nparm

Definition at line 17 of file parm.h.

Referenced by readparm().

Nphb

int Ambertoppar::Nphb

Definition at line 17 of file parm.h.

Referenced by readparm().

Nphia

int Ambertoppar::Nphia

Definition at line 17 of file parm.h.

Referenced by readparm().

Nphih

int Ambertoppar::Nphih

Definition at line 17 of file parm.h.

Referenced by readparm().

Nptra

int Ambertoppar::Nptra

Definition at line 17 of file parm.h.

Referenced by Parameters::read_parm(), and readparm().

Nres

int Ambertoppar::Nres

Definition at line 17 of file parm.h.

Referenced by firstwat(), and readparm().

Nspm

int Ambertoppar::Nspm

Definition at line 17 of file parm.h.

Referenced by readparm().

Nspsol

int Ambertoppar::Nspsol

Definition at line 17 of file parm.h.

Referenced by readparm().

Ntheta

int Ambertoppar::Ntheta

Definition at line 17 of file parm.h.

Referenced by readparm().

Ntheth

int Ambertoppar::Ntheth

Definition at line 17 of file parm.h.

Referenced by readparm().

Nttyp

int Ambertoppar::Nttyp

Definition at line 17 of file parm.h.

Referenced by readparm().

Ntype2d

int Ambertoppar::Ntype2d

Definition at line 17 of file parm.h.

Referenced by readparm().

Ntypes

int Ambertoppar::Ntypes

Definition at line 17 of file parm.h.

Referenced by Parameters::read_parm(), and readparm().

Numang

int Ambertoppar::Numang

Definition at line 17 of file parm.h.

Referenced by Parameters::read_parm(), and readparm().

Numbnd

int Ambertoppar::Numbnd

Definition at line 17 of file parm.h.

Referenced by Parameters::read_parm(), and readparm().

Phase

_REAL * Ambertoppar::Phase

Definition at line 24 of file parm.h.

Referenced by Ambertoppar(), Parameters::read_parm(), readparm(), and ~Ambertoppar().

Pk

_REAL * Ambertoppar::Pk

Definition at line 24 of file parm.h.

Referenced by Ambertoppar(), Parameters::read_parm(), readparm(), and ~Ambertoppar().

Pn

_REAL * Ambertoppar::Pn

Definition at line 24 of file parm.h.

Referenced by Ambertoppar(), Parameters::read_parm(), readparm(), and ~Ambertoppar().

popn

int Ambertoppar::popn

Definition at line 33 of file parm.h.

Req

_REAL * Ambertoppar::Req

Definition at line 24 of file parm.h.

Referenced by Ambertoppar(), Parameters::read_parm(), readparm(), and ~Ambertoppar().

ResNames

char * Ambertoppar::ResNames

Definition at line 23 of file parm.h.

Referenced by Ambertoppar(), firstwat(), PDB::PDB(), readparm(), and ~Ambertoppar().

Rk

_REAL * Ambertoppar::Rk

Definition at line 24 of file parm.h.

Referenced by Ambertoppar(), Parameters::read_parm(), readparm(), and ~Ambertoppar().

Solty

_REAL * Ambertoppar::Solty

Definition at line 24 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

Teq

_REAL * Ambertoppar::Teq

Definition at line 24 of file parm.h.

Referenced by Ambertoppar(), Parameters::read_parm(), readparm(), and ~Ambertoppar().

Tk

_REAL * Ambertoppar::Tk

Definition at line 24 of file parm.h.

Referenced by Ambertoppar(), Parameters::read_parm(), readparm(), and ~Ambertoppar().

TreeJoin

int * Ambertoppar::TreeJoin

Definition at line 27 of file parm.h.

Referenced by Ambertoppar(), readparm(), and ~Ambertoppar().

Xcap

_REAL Ambertoppar::Xcap

Definition at line 26 of file parm.h.

Referenced by readparm().

Ycap

_REAL Ambertoppar::Ycap

Definition at line 26 of file parm.h.

Referenced by readparm().

Zcap

_REAL Ambertoppar::Zcap

Definition at line 26 of file parm.h.

Referenced by readparm().

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The documentation for this struct was generated from the following files:

• parm.h
• parm.C