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/*******************************************************************************
* *
* Viewmol *
* *
* I N T E R N . C *
* *
* Copyright (c) Joerg-R. Hill, October 2003 *
* *
********************************************************************************
*
* $Id: intern.c,v 1.6 2003/11/07 11:05:17 jrh Exp $
* $Log: intern.c,v $
* Revision 1.6 2003/11/07 11:05:17 jrh
* Release 2.4
*
* Revision 1.5 2000/12/10 15:09:37 jrh
* Release 2.3
*
* Revision 1.4 1999/05/24 01:26:04 jrh
* Release 2.2.1
*
* Revision 1.3 1999/02/07 21:51:39 jrh
* Release 2.2
*
* Revision 1.2 1998/01/26 00:48:12 jrh
* Release 2.1
*
* Revision 1.1 1996/12/10 18:41:35 jrh
* Initial revision
*
*/
#include<math.h>
#include<stdio.h>
#include "viewmol.h"
double bondAverage(struct MOLECULE *, int);
double bondLength(struct ATOM *, int, int);
double bondAngle(struct ATOM *, int, int, int);
double torsionAngle(struct ATOM *, int, int, int, int);
double dist(double, double, double, double, double, double);
double angle(double, double, double, double, double, double, double,
double, double);
double torsion(double, double, double, double, double, double, double,
double, double, double, double, double);
extern struct MOLECULE *molecules;
extern double bndfac;
extern int debug;
int calcInternal(struct MOLECULE *mol, int n)
{
int uc;
register int i, j, k, l;
uc=0;
for (i=0; i<4; i++)
if (mol->internals[n].atoms[i] != -1 && (mol->internals[n].atoms[i] & 0x20000000)) uc++;
switch (mol->internals[n].type)
{
case BONDAVERAGE: if (uc == 0)
{
mol->internals[n].value=bndfac*bondAverage(mol,
mol->internals[n].atoms[0]);
i=mol->internals[n].atoms[0];
mol->internals[n].x=mol->atoms[i].x+0.05;
mol->internals[n].y=mol->atoms[i].y+0.05;
mol->internals[n].z=mol->atoms[i].z+0.05;
}
else
return(FALSE);
break;
case BONDLENGTH: i=mol->internals[n].atoms[0];
j=mol->internals[n].atoms[1];
switch (uc)
{
/* previous use: case 4 ??? */
case 2: i&=0x1fffffff;
j&=0x1fffffff;
mol->internals[n].value=bndfac*bondLength(mol->unitcell->corners, i, j);
mol->internals[n].x=(mol->unitcell->corners[i].x+mol->unitcell->corners[j].x)*0.5+0.05;
mol->internals[n].y=(mol->unitcell->corners[i].y+mol->unitcell->corners[j].y)*0.5+0.05;
mol->internals[n].z=(mol->unitcell->corners[i].z+mol->unitcell->corners[j].z)*0.5+0.05;
break;
case 0: mol->internals[n].value=bndfac*bondLength(mol->atoms, i, j);
mol->internals[n].x=(mol->atoms[i].x+mol->atoms[j].x)*0.5+0.05;
mol->internals[n].y=(mol->atoms[i].y+mol->atoms[j].y)*0.5+0.05;
mol->internals[n].z=(mol->atoms[i].z+mol->atoms[j].z)*0.5+0.05;
break;
default: return(FALSE);
}
break;
case ANGLE: i=mol->internals[n].atoms[0];
j=mol->internals[n].atoms[1];
k=mol->internals[n].atoms[2];
switch (uc)
{
/* previous use: case 4 ??? */
case 3: i&=0x1fffffff;
j&=0x1fffffff;
k&=0x1fffffff;
mol->internals[n].value=bondAngle(mol->unitcell->corners, i, j, k);
mol->internals[n].x=mol->unitcell->corners[j].x+0.05;
mol->internals[n].y=mol->unitcell->corners[j].y+0.05;
mol->internals[n].z=mol->unitcell->corners[j].z+0.05;
break;
case 0:
mol->internals[n].value=bondAngle(mol->atoms, i, j, k);
mol->internals[n].x=mol->atoms[j].x+0.05;
mol->internals[n].y=mol->atoms[j].y+0.05;
mol->internals[n].z=mol->atoms[j].z+0.05;
break;
default: return(FALSE);
}
break;
case TORSION: i=mol->internals[n].atoms[0];
j=mol->internals[n].atoms[1];
k=mol->internals[n].atoms[2];
l=mol->internals[n].atoms[3];
switch (uc)
{
case 4: i&=0x1fffffff;
j&=0x1fffffff;
k&=0x1fffffff;
l&=0x1fffffff;
mol->internals[n].value=torsionAngle(mol->unitcell->corners, i, j, k, l);
mol->internals[n].x=(mol->unitcell->corners[j].x+mol->unitcell->corners[k].x)*0.5+0.05;
mol->internals[n].y=(mol->unitcell->corners[j].y+mol->unitcell->corners[k].y)*0.5+0.05;
mol->internals[n].z=(mol->unitcell->corners[j].z+mol->unitcell->corners[k].z)*0.5+0.05;
break;
case 0:
mol->internals[n].value=torsionAngle(mol->atoms, i, j, k, l);
mol->internals[n].x=(mol->atoms[j].x+mol->atoms[k].x)*0.5+0.05;
mol->internals[n].y=(mol->atoms[j].y+mol->atoms[k].y)*0.5+0.05;
mol->internals[n].z=(mol->atoms[j].z+mol->atoms[k].z)*0.5+0.05;
break;
default: return(FALSE);
}
if (mol->internals[n].value > 360.) return(FALSE);
break;
}
if (debug) printf("Internal coordinate %d: %d-%d-%d-%d, %f\n", n,
mol->internals[n].atoms[0], mol->internals[n].atoms[1],
mol->internals[n].atoms[2], mol->internals[n].atoms[3],
mol->internals[n].value);
return(TRUE);
}
double bondAverage(struct MOLECULE *mol, int i)
{
register double value=0.0;
register int j, k=0;
for (j=0; j<mol->nb; j++)
{
if (mol->bonds[j].first == i ||
mol->bonds[j].second == i)
{
value+=bondLength(mol->atoms, mol->bonds[j].first, mol->bonds[j].second);
k++;
}
}
if (k > 0)
value/=(double)k;
else
value=0.0;
return(value);
}
double bondLength(struct ATOM *atoms, int i, int j)
{
return(dist(atoms[i].x, atoms[i].y, atoms[i].z,
atoms[j].x, atoms[j].y, atoms[j].z));
}
double bondAngle(struct ATOM *atoms, int i, int j, int k)
{
return(angle(atoms[i].x, atoms[i].y, atoms[i].z,
atoms[j].x, atoms[j].y, atoms[j].z,
atoms[k].x, atoms[k].y, atoms[k].z));
}
double torsionAngle(struct ATOM *atoms, int i, int j, int k, int l)
{
return(torsion(atoms[i].x, atoms[i].y, atoms[i].z,
atoms[j].x, atoms[j].y, atoms[j].z,
atoms[k].x, atoms[k].y, atoms[k].z,
atoms[l].x, atoms[l].y, atoms[l].z));
}
double dist(double x1, double y1, double z1, double x2, double y2, double z2)
{
return(sqrt((x1-x2)*(x1-x2)+(y1-y2)*(y1-y2)+(z1-z2)*(z1-z2)));
}
double angle(double x1, double y1, double z1, double x2, double y2, double z2,
double x3, double y3, double z3)
{
double todeg=45.0/atan(1.0);
double xa, ya, za, xb, yb, zb, r;
xa=x1-x2;
ya=y1-y2;
za=z1-z2;
xb=x3-x2;
yb=y3-y2;
zb=z3-z2;
r=dist(x1, y1, z1, x2, y2, z2)*dist(x3, y3, z3, x2, y2, z2);
r=(xa*xb+ya*yb+za*zb)/r;
r=r > 1.0 ? 1.0 : r < -1.0 ? -1.0 : r;
return(todeg*acos(r));
}
double torsion(double x1, double y1, double z1, double x2, double y2, double z2,
double x3, double y3, double z3, double x4, double y4, double z4)
{
double todeg=45.0/atan(1.0);
double xa, ya, za, xb, yb, zb, xc, yc, zc, xd, yd, zd, xe, ye, ze, xf, yf, zf;
double sgn, r;
xa=x1-x2;
ya=y1-y2;
za=z1-z2;
xb=x3-x2;
yb=y3-y2;
zb=z3-z2;
xc=x4-x3;
yc=y4-y3;
zc=z4-z3;
xd=ya*zb-yb*za;
yd=xb*za-xa*zb;
zd=xa*yb-xb*ya;
xe=yc*zb-yb*zc;
ye=xb*zc-xc*zb;
ze=xc*yb-xb*yc;
xf=yd*ze-ye*zd;
yf=xe*zd-xd*ze;
zf=xd*ye-xe*yd;
sgn=xf*xb+yf*yb+zf*zb;
r=sqrt((xd*xd+yd*yd+zd*zd)*(xe*xe+ye*ye+ze*ze));
/* The torsion angle is undefined (linear arrangement of atoms),
return 400.0 as torsion angle which is outside the expected
range */
if (fabs(r) < 1.0e-6) return((double)400.);
r=(xd*xe+yd*ye+zd*ze)/r;
if (fabs(r) > 1.0) r/=fabs(r);
if (sgn < 0.0)
return(-todeg*acos(r));
else
return(todeg*acos(r));
}
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