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polar.c
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/*
* polarization - use a -qa/r^3 term.
*/
/* polar.c
*
* collection of routines to service polared non-locaL nonbonded potentials
*
* POOP (Poor-mans Object Oriented Programming) using scope rules
*
* the routines for potential value, force and (eventually) second
* derivatives are here also
*
* force and 2nd derivative routines assume zero'd arrays for output
* this allows for parralellization if needed (on a PC?)
*
* forces are symmetric - so we don't have to fuck around with
* s matrices and the like.
*
* note that the non-bonded information is in the ATOM structures
*
*
*/
/*
* copyright 1992, 1993, 1994 Robert W. Harrison
*
* This notice may not be removed
* This program may be copied for scientific use
* It may not be sold for profit without explicit
* permission of the author(s) who retain any
* commercial rights including the right to modify
* this notice
*/
#define ANSI 1
/* misc includes - ANSI and some are just to be safe */
#include <stdio.h>
#include <ctype.h>
#include <math.h>
#ifdef ANSI
#include <stdlib.h>
#endif
#include "ammp.h"
/* ATOM structure contains a serial number for indexing into
* arrays and the like (a Hessian)
* but otherwise is self-contained. Note the hooks for Non-nonboned potentials
*/
#ifdef GRACELESS
#define exp(x) ((x) > -100.? exp(x): 0.)
#endif
/* f_polar()
*
* f_polar increments the forces in the atom structures by the force
* due to the polared-nonbonded components. NOTE THE WORD increment.
* the forces should first be zero'd.
* if not then this code will be invalid. THIS IS DELIBERATE.
* on bigger (and better?) machines the different potential terms
* may be updated at random or in parrellel, if we assume that this routine
* will initialize the forces then we can't do this.
*/
int f_polar(lambda)
float lambda;
/* returns 0 if error, 1 if OK */
{
float ux,uy,uz;
float k,r,r4,r0,xt,yt,zt;
float lcutoff,cutoff,get_f_variable();
int inbond,inangle,i,test;
ATOM *a1,*a2,*bonded[10],*angled[10];
ATOM *a_next( ); /* returns first ATOM when called with -1 */
int a_number(),inbuffer,imax;
float (*buffer)[];
int invector,atomsused,ii,jj;
float (*vector)[];
ATOM *(*atms)[],*(*atomall)[];
float dielectric;
float fx,fy,fz;
float xt2,xt3,xt4;
float yt2,yt3,yt4;
float zt2,zt3,zt4;
/* first update the lists
* this routine checks if any atom has
* broken the mxdq barrier and updates the
* forces, potentials and expansions thereof */
fv_update_polar( lambda);
dielectric = get_f_variable("dielec");
if( dielectric < 1.) dielectric = 1.;
dielectric = 332.17752/dielectric;
/* get the number of atoms and allocate the memory for the array space */
i = a_number();
atomall = malloc( i*sizeof(ATOM *) );
if( atomall == NULL)
{aaerror("cannot allocate memory in f_nonbon"); return 0;}
imax = a_number();
for( i=0; i< imax; i++)
{
(*atomall)[i] = a_next(i);
}
for( i= 0; i< imax; i++)
{
fx = 0.; fy = 0.; fz = 0.;
a1 = (*atomall)[i];
xt = a1->dx*lambda +a1->x - a1->px;
yt = a1->dy*lambda +a1->y - a1->py;
zt = a1->dz*lambda +a1->z - a1->pz;
fx = (a1->qxx*xt + a1->qxy*yt
+ a1->qxz*zt) ;
fy = (a1->qxy*xt + a1->qyy*yt
+ a1->qyz*zt) ;
fz = (a1->qxz*xt + a1->qyz*yt
+ a1->qzz*zt) ;
#ifdef CUBIC
xt2 = xt*xt; yt2 = yt*yt; zt2 = zt*zt;
fx += a1->qxxx*xt2/2. + a1->qxxy*xt*yt + a1->qxxz*xt*zt
+ a1->qxyy*yt/2. + a1->qxyz*yt*zt + a1->qxzz*zt2/2.;
fy += a1->qxxy*xt2/2. + a1->qxyy*xt*yt + a1->qxyz*xt*zt
+ a1->qyyy*yt/2. + a1->qyyz*yt*zt + a1->qyzz*zt2/2.;
fz += a1->qxxz*xt2/2. + a1->qxyz*xt*yt + a1->qxzz*xt*zt
+ a1->qyyz*yt/2. + a1->qyzz*yt*zt + a1->qzzz*zt2/2.;
#endif
#ifdef QUARTIC
xt3 = xt*xt2; yt3 = yt*yt2; zt3 = zt*zt2;
fx += a1->qxxxx*xt3/6. + a1->qxxxy*xt2*yt/2. + a1->qxxxz*xt2*zt/2.
+ a1->qxxyy*xt*yt/2. + a1->qxxyz*xt*yt*zt + a1->qxxzz*xt*zt2/2.
+ a1->qxyyy*yt3/6. + a1->qxyyz*yt2*zt/2. + a1->qxyzz*yt*zt2/2.
+ a1->qxzzz*zt3/6.;
fy += a1->qxxxy*xt3/6. + a1->qxxyy*xt2*yt/2. + a1->qxxyz*xt2*zt/2.
+ a1->qxyyy*xt*yt/2. + a1->qxyyz*xt*yt*zt + a1->qxyzz*xt*zt2/2.
+ a1->qyyyy*yt3/6. + a1->qyyyz*yt2*zt/2. + a1->qyyzz*yt*zt2/2.
+ a1->qyzzz*zt3/6.;
fz += a1->qxxxz*xt3/6. + a1->qxxyz*xt2*yt/2. + a1->qxxzz*xt2*zt/2.
+ a1->qxyyz*xt*yt/2. + a1->qxyzz*xt*yt*zt + a1->qxzzz*xt*zt2/2.
+ a1->qyyyz*yt3/6. + a1->qyyzz*yt2*zt/2. + a1->qyzzz*yt*zt2/2.
+ a1->qzzzz*zt3/6.;
#endif
#ifdef QUINTIC
xt4 = xt*xt3; yt4 = yt*yt3; zt4 = zt*zt3;
fx += a1->qxxxxx*xt4/24. + a1->qxxxxy*xt3*yt/6. + a1->qxxxxz*xt3*zt/6.
+ a1->qxxxyy*xt2*yt2/4. + a1->qxxxyz*xt2*yt*zt/2. + a1->qxxxzz*xt2*zt2/4.
+ a1->qxxyyy*xt*yt3/6. + a1->qxxyyz*xt*yt2*zt/2. + a1->qxxyzz*xt*yt*zt2/2.
+ a1->qxxzzz*xt*zt3/6. + a1->qxyyyy*yt4/24. + a1->qxyyyz*yt3*zt/6.
+ a1->qxyyzz*yt2*zt2/4. + a1->qxyzzz*yt*zt3/6. + a1->qxzzzz*zt4/24.;
fy += a1->qxxxxy*xt4/24. + a1->qxxxyy*xt3*yt/6. + a1->qxxxyz*xt3*zt/6.
+ a1->qxxyyy*xt2*yt2/4. + a1->qxxyyz*xt2*yt*zt/2. + a1->qxxyzz*xt2*zt2/4.
+ a1->qxyyyy*xt*yt3/6. + a1->qxyyyz*xt*yt2*zt/2. + a1->qxyyzz*xt*yt*zt2/2.
+ a1->qxyzzz*xt*zt3/6. + a1->qyyyyy*yt4/24. + a1->qyyyyz*yt3*zt/6.
+ a1->qyyyzz*yt2*zt2/4. + a1->qyyzzz*yt*zt3/6. + a1->qyzzzz*zt4/24.;
fz += a1->qxxxxz*xt4/24. + a1->qxxxyz*xt3*yt/6. + a1->qxxxzz*xt3*zt/6.
+ a1->qxxyyz*xt2*yt2/4. + a1->qxxyzz*xt2*yt*zt/2. + a1->qxxzzz*xt2*zt2/4.
+ a1->qxyyyz*xt*yt3/6. + a1->qxyyzz*xt*yt2*zt/2. + a1->qxyzzz*xt*yt*zt2/2.
+ a1->qxzzzz*xt*zt3/6. + a1->qyyyyz*yt4/24. + a1->qyyyzz*yt3*zt/6.
+ a1->qyyzzz*yt2*zt2/4. + a1->qyzzzz*yt*zt3/6. + a1->qzzzzz*zt4/24.;
#endif
a1->fx += fx + a1->dpx;
a1->fy += fy + a1->dpy;
a1->fz += fz + a1->dpz;
/* do the close atoms */
for( jj=0; jj< NCLOSE; jj++)
{ if( a1->close[jj] == NULL) break; }
for( ii=0; ii< jj;ii++)
{
a2 = a1->close[ii];
/* note ux is backwards from below */
ux = (a2->dx -a1->dx)*lambda +(a2->x -a1->x);
uy = (a2->dy -a1->dy)*lambda +(a2->y -a1->y);
uz = (a2->dz -a1->dz)*lambda +(a2->z -a1->z);
r = ux*ux + uy*uy + uz*uz; r0 = sqrt(r);
ux = ux/r0; uy = uy/r0; uz = uz/r0;
/* standard point atoms
k = -dielectric*a1->q*a2->q/r;
*/
k = -dielectric*a1->q*a2->q/r;
r4 = r*r;
k += 0.5*(a1->a*a2->q*a2->q + a2->a*a1->q*a1->q)/r4/r0*4;
r = r*r*r;
k += a1->a*a2->a/r/r0*6;
k -= a1->b*a2->b/r/r/r0*12;
a1->fx += ux*k;
a1->fy += uy*k;
a1->fz += uz*k;
a2->fx -= ux*k;
a2->fy -= uy*k;
a2->fz -= uz*k;
}
}
a_inactive_f_zero();
free( atomall); return 1;
}
/* v_polar()
* this function sums up the potentials
* for the atoms defined in the nonbon data structure.
*/
/* standard returns 0 if error (any) 1 if ok
* V is the potential */
int v_polar( V, lambda )
float *V,lambda;
{
float r,r4,r0,xt,yt,zt;
float get_f_variable();
float k;
int inbond,inangle,i;
ATOM *a1,*a2,*bonded[10],*angled[10];
ATOM *a_next( ); /* returns first ATOM when called with -1 */
int a_number(),inbuffer;
int invector,atomsused,ii,jj,imax;
float (*vector)[];
float vx;
float k2;
ATOM *(*atomall)[];
float dielectric;
float xt2,xt3,xt4,xt5;
float yt2,yt3,yt4,yt5;
float zt2,zt3,zt4,zt5;
fv_update_polar( lambda);
dielectric = get_f_variable("dielec");
if( dielectric < 1.) dielectric = 1.;
dielectric = 332.17752/dielectric;
/* get the number of atoms and allocate the memory for the array space */
i = a_number();
atomall = malloc( i*sizeof(ATOM *) );
if( atomall == NULL)
{aaerror("cannot allocate memory in v_nonbon"); return 0;}
imax = a_number();
for( i=0; i< imax; i++)
{
(*atomall)[i] = a_next(i);
}
for( i= 0; i< imax; i++)
{
a1 = (*atomall)[i];
vx = a1->VP;
xt = a1->dx*lambda +a1->x - a1->px;
yt = a1->dy*lambda +a1->y - a1->py;
zt = a1->dz*lambda +a1->z - a1->pz;
vx -= (a1->dpx*xt + a1->dpy*yt
+ a1->dpz*zt) ;
vx -= ( (xt*(.5*a1->qxx*xt + a1->qxy*yt + a1->qxz*zt)
+ yt*(.5*a1->qyy*yt + a1->qyz*zt) + .5*zt*a1->qzz*zt));
#ifdef CUBIC
xt2 = xt*xt; yt2 = yt*yt; zt2 = zt*zt;
xt3 = xt2*xt; yt3 = yt2*yt; zt3 = zt2*zt;
vx -= a1->qxxx*xt3/6. + a1->qxxy*xt2*yt/2 + a1->qxxz*xt2*zt/2
+ a1->qxyy*xt*yt2/2 + a1->qxyz*xt*yt*zt + a1->qxzz*xt*zt2/2
+ a1->qyyy*yt3/6 + a1->qyyz*yt2*zt/2 + a1->qyzz*yt*zt2/2
+ a1->qzzz*zt3/6.;
#endif
#ifdef QUARTIC
xt4 = xt3*xt; yt4 = yt3*yt; zt4 = zt3*zt;
vx -= a1->qxxxx*xt4/24. + a1->qxxxy*xt3*yt/6. + a1->qxxxz*xt3*yt/6. + a1->qxxyy*xt2*yt2/4.
+ a1->qxxyz*xt2*yt*zt/2. + a1->qxxzz*xt2*zt2/4. + a1->qxyyy*xt*yt3/6.
+ a1->qxyyz*xt*yt2*zt/2. + a1->qxyzz*xt*yt*zt2/2. + a1->qxzzz*xt*zt3/6.
+ a1->qyyyy*yt4/24. + a1->qyyyz*yt3*zt/6. + a1->qyyzz*yt2*zt2/4. + a1->qyzzz*yt*zt3/6.
+ a1->qzzzz*zt4/24.;
#endif
#ifdef QUINTIC
xt5 = xt4*xt; yt5 = yt4*yt; zt5 = zt4*zt;
vx -= a1->qxxxxx*xt5/120. + a1->qxxxxy*xt4*yt/24. + a1->qxxxxz*xt4*zt/24.
+ a1->qxxxyy*xt3*yt2/12. + a1->qxxxyz*xt3*yt*zt/6. + a1->qxxxzz*xt3*zt2/12.
+ a1->qxxyyy*xt2*yt3/12. + a1->qxxyyz*xt2*yt2*zt/4. + a1->qxxyzz*xt2*yt*zt2/4.
+ a1->qxxzzz*xt2*zt3/12. + a1->qxyyyy*xt*yt4/24. + a1->qxyyyz*xt*yt3*zt/6.
+ a1->qxyyzz*xt*yt2*zt2/4. + a1->qxyzzz*xt*yt*zt3/6. + a1->qxzzzz*xt*zt4/24.
+ a1->qyyyyy*yt5/120. + a1->qyyyyz*yt4*zt/24 + a1->qyyyzz*yt3*zt2/12.
+ a1->qyyzzz*yt2*zt3/12. + a1->qyzzzz*yt*zt4/24. + a1->qzzzzz*zt5/120.;
#endif
/* do the close atoms */
for( jj=0; jj< NCLOSE; jj++)
{ if( a1->close[jj] == NULL) break; }
for( ii=0; ii< jj;ii++)
{
a2 = a1->close[ii];
xt = (a2->dx -a1->dx)*lambda +(a2->x -a1->x);
yt = (a2->dy -a1->dy)*lambda +(a2->y -a1->y);
zt = (a2->dz -a1->dz)*lambda +(a2->z -a1->z);
r = xt*xt + yt*yt + zt*zt; r0 = sqrt(r);
/* xt = xt/r0; yt = yt/r0; zt = zt/r0;
*/
/* standard point atom
k = dielectric*a1->q*a2->q/r0;
*/
/* 1s 1s polared atoms */
k = dielectric*a1->q*a2->q/r0;
r4 = r*r;
k -= 0.5*(a1->a*a2->q*a2->q + a2->a*a1->q*a1->q)/r4;
r = r*r*r;
k -= a1->a*a2->a/r;
k += a1->b*a2->b/r/r;
vx += k;
}
*V += vx;
}
a_inactive_f_zero();
free( atomall); return 1;
}
/*zone_polar()
* this function sums up the potentials
* for the atoms defined in the nonbon data structure.
*/
/* standard returns 0 if error (any) 1 if ok
* V is the potential */
int zone_polar( V, lambda ,alist, inalist )
float *V,lambda;
ATOM *( *alist)[] ;
int inalist;
{
float r,r0,xt,yt,zt;
float lcutoff,cutoff,get_f_variable();
int inbond,inangle,i,ii;
ATOM *a1,*a2;
ATOM *a_next( ); /* returns first ATOM when called with -1 */
float dielectric,ve,va,vh;
ATOM *a_m_serial();
/* nonbonded potentials
* do a double loop starting from the first atom to the
* last
* then from the second to the last
* etc
*
* also check to avoid bonded and 1-3 bonded atoms
*/
if( inalist <= 0 ) return 1;
dielectric = get_f_variable("dielec");
if( dielectric < 1.) dielectric = 1.;
dielectric = 332.17752/dielectric;
cutoff = get_f_variable("cutoff");
if( cutoff < 1.) cutoff = 1.e10;
lcutoff = -cutoff;
for( ii=0; ii< inalist; ii++)
{
a1 = (*alist)[ii];
if( a1 == NULL ) goto NOTANATOM;
ve = 0.; va = 0.; vh = 0.;
a2 = a_next(-1);
/*
* for(i = 0; i< a1->dontuse; i++)
* printf("%d ",a1->excluded[i]->serial);
* printf("\n");
*/
/*
while( (a2->next != a2) && (a2->next != NULL))
*/
while( (a2 != NULL) && (a2->next != NULL) && a2->next != a2)
{
/* goto SKIP is used because this is one case where it makes sense */
/* if( a2 == a1) break; */
if( a2 == a1) goto SKIP;
for(i = 0; i< a1->dontuse; i++)
if( a2 == a1->excluded[i]) goto SKIP;
/* non - bonded are only used when the atoms arent bonded */
xt = (a1->x -a2->x) + lambda*(a1->dx - a2->dx);
if( (xt > cutoff) || (xt < lcutoff) ) goto SKIP;
yt = (a1->y -a2->y) + lambda*(a1->dy - a2->dy);
if( (yt > cutoff) || (yt < lcutoff) ) goto SKIP;
zt = (a1->z -a2->z) + lambda*(a1->dz - a2->dz);
if( (zt > cutoff) || (zt < lcutoff) ) goto SKIP;
r = xt*xt+yt*yt+zt*zt;
if( r < 1.) r = 1.;
r0 = sqrt(r); r = r*r*r ;
/* debugging
printf(" %d %d %f %f %f \n", a1->serial,a2->serial,a1->q,a2->q,
332.17752*a1->q*a2->q/r0);
*/
ve += dielectric*a1->q*a2->q/r0;
va -= a1->a*a2->a/r;
vh += a1->b*a2->b/r/r;
SKIP:
/* if( a2->next == a1) break; */
if( a2->next == a2) break;
a2 = a2->next;
}
*V += ve + va + vh;
NOTANATOM:
i = i;
}
return 1;
}
/* a_polar()
* this function sums up the potentials
* for the atoms defined in the nonbon data structure.
*/
/* standard returns 0 if error (any) 1 if ok
* V is the potential */
int a_polar( V, lambda,ilow,ihigh,op )
float *V,lambda;
int ilow,ihigh;
FILE *op;
{
float r,r0,r4,xt,yt,zt;
float lcutoff,cutoff,get_f_variable();
int inbond,inangle,i,ii;
ATOM *a1,*a2;
ATOM *a_next( ); /* returns first ATOM when called with -1 */
float dielectric,ve,va,vh,vp;
float vel,val,vhl,vpl;
float vtint,vtout, vtt;
ATOM *a_m_serial();
float k;
/* nonbonded potentials
* do a double loop starting from the first atom to the
* last
* then from the second to the last
* etc
*
* also check to avoid bonded and 1-3 bonded atoms
*/
dielectric = get_f_variable("dielec");
if( dielectric < 1.) dielectric = 1.;
dielectric = 332.17752/dielectric;
cutoff = get_f_variable("cutoff");
if( cutoff < 1.) cutoff = 1.e10;
lcutoff = -cutoff;
vtint = 0.; vtout = 0.; vtt = 0.;
for( ii=ilow; ii<=ihigh; ii++)
{
a1 = a_m_serial(ii);
if( a1 == NULL ) goto NOTANATOM;
ve = 0.; va = 0.; vh = 0.; vp = 0.;
vel = 0.; val = 0.; vhl = 0.;vpl = 0.;
a2 = a_next(-1);
/*
* for(i = 0; i< a1->dontuse; i++)
* printf("%d ",a1->excluded[i]->serial);
* printf("\n");
*/
/*
while( (a2->next != a2) && (a2->next != NULL))
*/
while( (a2->next != NULL))
{
/* goto SKIP is used because this is one case where it makes sense */
/* if( a2 == a1) break; */
/* if( a2 == a1) goto SKIP; */
for(i = 0; i< a1->dontuse; i++)
if( a2 == a1->excluded[i]) goto SKIP;
/* non - bonded are only used when the atoms arent bonded */
if( lambda == 0.)
{
xt = (a1->x - a2->x);
if( (xt > cutoff) || (xt < lcutoff) ) goto SKIP;
yt = (a1->y - a2->y);
if( (yt > cutoff) || (yt < lcutoff) ) goto SKIP;
zt = (a1->z - a2->z);
if( (zt > cutoff) || (zt < lcutoff) ) goto SKIP;
} else
{
xt = (a1->x - a2->x +lambda*(a1->dx - a2->dx));
if( (xt > cutoff) || (xt < lcutoff) ) goto SKIP;
yt = (a1->y - a2->y +lambda*(a1->dy - a2->dy));
if( (yt > cutoff) || (yt < lcutoff) ) goto SKIP;
zt = (a1->z - a2->z +lambda*(a1->dz - a2->dz));
if( (zt > cutoff) || (zt < lcutoff) ) goto SKIP;
}
r = xt*xt+yt*yt+zt*zt;
if( r < .01) r = .01;
r0 = sqrt(r); r4 = r*r; r = r*r*r ;
/* debugging
* printf(" %d %d %f %f %f \n", a1->serial,a2->serial,a1->q,a2->q,
* 332.17752*a1->q*a2->q/r0);
*/
/*
* ve += dielectric*a1->q*a2->q/r0;
*/
/* 1s 1s polared atoms */
k = dielectric*a1->q*a2->q/r0;
/*
*/
ve += k;
va -= a1->a*a2->a/r;
vh += a1->b*a2->b/r/r;
vp -= 0.5*( a1->q*a1->q*a2->a + a1->a*a2->q*a2->q)/r4;
if( a2->serial < ilow || a2->serial > ihigh)
{
/*
vel += dielectric*a1->q*a2->q/r0;
*/
vel += k;
val -= a1->a*a2->a/r;
vhl += a1->b*a2->b/r/r;
vpl -= 0.5*( a1->q*a1->q*a2->a + a1->a*a2->q*a2->q)/r4;
}
SKIP:
/* if( a2->next == a1) break; */
if( a2->next == a2) break;
a2 = a2->next;
}
fprintf(op,"Vpolar internal %d Eq %f Ep %f E6 %f E12 %f\n",
ii,ve-vel,vp-vpl,va-val,vh-vhl);
fprintf(op,"Vpolar external %d Eq %f Ep %f E6 %f E12 %f\n",ii,vel,vpl,val,vhl);
fprintf(op,"Vpolar total %d Eq %f Ep %f E6 %f E12 %f\n",ii,ve,vp,va,vh);
*V += ve + va + vh+ vp;
vtint += ve -vel+ va -val + vh -vhl + vp - vpl;
vtout += vel + val + vhl + vpl;
vtt += ve + va + vh +vp;
NOTANATOM:
i = i;
}
fprintf(op," Vpolar total internal %f \n",vtint);
fprintf(op," Vpolar total external %f \n",vtout);
fprintf(op," Vpolar total %f \n",vtt);
return 1;
}
int fv_update_polar( lambda )
float lambda;
{
float r,r4,r0,xt,yt,zt,pt;
float k,k1,k2,k3,k4,k5;
float ka3,ka2;
float kb3,kb2;
float kp3,kp2;
float get_f_variable();
int inbond,inangle,i;
ATOM *a1,*a2,*bonded[10],*angled[10];
ATOM *a_next( ); /* returns first ATOM when called with -1 */
int (*indexes)[],inindex,in;
int a_number();
int ii,j,jj,imax,inclose;
float (*vector)[];
/* float (*vecold)[];
*/
ATOM *close[NCLOSE],*(*atomall)[];
float mxdq,dielectric,mxcut;
static float dielecold = -1.;
mxdq = get_f_variable("mxdq");
/* if( mxdq < 0.) mxdq = 0.;
*/
mxcut = get_f_variable("mxcut");
if( mxcut < 0.) mxcut= 5.;
if( mxdq > 0.) mxdq = mxdq*mxdq;
dielectric = get_f_variable("dielec");
if( dielectric < 1.) dielectric = 1.;
if( dielecold != dielectric)
{
dielecold = dielectric;
mxdq = -1.;
}
dielectric = 332.17752/dielectric;
/* get the number of atoms and allocate the memory for the array space */
i = a_number();
vector = malloc( 4*i*sizeof(float) );
if( vector == NULL)
{ aaerror("cannot allocate memory in v_nonbon\n"); return 0;}
/*
vecold = malloc( 4*i*sizeof(float) );
if( vecold == NULL)
{ aaerror("cannot allocate memory in v_nonbon\n"); return 0;}
*/
atomall = malloc( i*sizeof(ATOM *) );
if( atomall == NULL)
{aaerror("cannot allocate memory in v_nonbon\n"); return 0;}
imax = a_number();
for( i=0; i< imax; i++)
{
(*atomall)[i] = a_next(i);
}
/* first check if anyone's moved and update the lists */
/* note that this must be a look-ahead rather than
* look back search because
* we cannot update ->px until we've used that atom !!! */
for( ii=0; ii< imax; ii++)
{
a1 = (*atomall)[ii];
xt = a1->dx*lambda +a1->x - a1->px;
yt = a1->dy*lambda +a1->y - a1->py;
zt = a1->dz*lambda +a1->z - a1->pz;
r = xt*xt + yt*yt + zt*zt;
if( r > mxdq ) goto DOIT;
}
free( vector);
/* free( vecold);
*/
free (atomall);
return 1;
DOIT:
xt = get_f_variable("mmbox");
if( xt > 0.)
{ free(vector); free(atomall); mm_fv_update_polar(lambda); return 1;}
indexes = malloc( imax* sizeof(int) );
if( indexes == NULL ){
aaerror(" cannot allocate memory in fv_update\n");
return 0;}
for( ii=0; ii< imax; ii++)
{
a1 = (*atomall)[ii];
a1 -> VP = 0.;
a1 -> dpx = 0.;
a1 -> dpy = 0.;
a1 -> dpz = 0.;
a1 -> qxx = 0.;
a1 -> qxy = 0.;
a1 -> qxz = 0.;
a1 -> qyy = 0.;
a1 -> qyz = 0.;
a1 -> qzz = 0.;
#ifdef CUBIC
a1 -> qxxx = 0.;
a1 -> qxxy = 0.;
a1 -> qxxz = 0.;
a1 -> qxyy = 0.;
a1 -> qxyz = 0.;
a1 -> qxzz = 0.;
a1 -> qyyy = 0.;
a1 -> qyyz = 0.;
a1 -> qyzz = 0.;
a1 -> qzzz = 0.;
#endif
for( j=0; j< NCLOSE; j++)
a1->close[j] = NULL;
}
for( ii=0; ii< imax; ii++)
{ /* if this is met we update the expansion for this atom */
a1 = (*atomall)[ii];
inclose = 0;
if( lambda != 0.)
{
#pragma _CNX no_recurrence
for( i=ii+1; i< imax; i++)
{
a2 = (*atomall)[i];
j = i*4;
(*vector)[j ] = a2->x - a1->x + lambda*(a2->dx -a1->dx);
(*vector)[j+1] = a2->y - a1->y + lambda*(a2->dy -a1->dy);
(*vector)[j+2] = a2->z - a1->z + lambda*(a2->dz -a1->dz);
}
}else {
#pragma _CNX no_recurrence
for( i=ii+1; i< imax; i++)
{
a2 = (*atomall)[i];
j = i*4;
(*vector)[j ] = a2->x - a1->x ;
(*vector)[j+1] = a2->y - a1->y ;
(*vector)[j+2] = a2->z - a1->z ;
}
} /* end of difference position into vector loops */
#pragma _CNX no_recurrence
for( i=ii+1; i< imax; i++)
{
j = i*4;
(*vector)[j+3] = sqrt((*vector)[j]*(*vector)[j] +
(*vector)[j+1]*(*vector)[j+1] +
(*vector)[j+2]*(*vector)[j+2]);
}
/* add the new components */
/* first extract indexes */
inindex = 0;
for( i=ii+1; i< imax; i++)
{
a2 = (*atomall)[i];
for( j=0; j< a1->dontuse; j++)
{ if( a2 == a1->excluded[j]) goto SKIPNEW;}
j = i*4;
if( (*vector)[j+3] > mxcut || inclose > NCLOSE)
{
(*indexes)[inindex++] = i;
}else {
a1->close[inclose++] = (*atomall)[i];
}
if( inclose == NCLOSE)
{
aaerror(
" fv_update_nonbon> too many atoms increase NCLOSE or decrease mxcut");
}
SKIPNEW: i = i;
}
/* and then use them */
#pragma _CNX no_recurrence
for( in=0; in< inindex; in++)
{
i = (*indexes)[in];
a2 = (*atomall)[i];
j = i*4;
r0 = one/(*vector)[j+3];
r = r0*r0;
r4 = r*r;
r = r*r*r; /* r0^-6 */
xt = a1->q*a2->q*dielectric*r0;
pt = 0.5*(a1->a*a2->q*a2->q + a1->q*a1->q*a2->q)*r4;
yt = a1->a*a2->a*r;
zt = a1->b*a2->b*r*r;
k = xt - yt + zt -pt;
xt = xt*r0; yt = yt*r0; zt = zt*r0; pt = pt*r0;
k1 = xt - yt*six + zt*twelve -pt*4;
xt = xt*r0; yt = yt*r0; zt = zt*r0; pt = pt*r0;
/*
k2 = xt*three; ka2 = - yt*6*8; kb2 = zt*12*14; kp2 = -pt*4*6;
*/
k2 = xt*three; ka2 = - yt*48.; kb2 = zt*168.; kp2 = -pt*24;
#ifdef CUBIC
xt = xt*r0; yt = yt*r0; zt = zt*r0;
k3 = -xt*5*3; ka3 = yt*6*8*10 ; kb3 = -zt*12*14*16; kp3 = pt*4*6*8;
#endif
k1 = -k1;
xt = (*vector)[j]*r0 ;
yt = (*vector)[j+1]*r0 ;
zt = (*vector)[j+2] *r0;
/*
xt = (*vector)[j] ;
yt = (*vector)[j+1] ;
zt = (*vector)[j+2] ;
*/
a1->VP += k;
a2->dpx -= k1*xt;
a1->dpx += k1*xt;
a2->dpy -= k1*yt;
a1->dpy += k1*yt;
a2->dpz -= k1*zt;
a1->dpz += k1*zt;
/* note that xt has the 1/r in it so k2*xt*xt is 1/r^5 */
a2->qxx -= k2*(xt*xt - third) + ka2*(xt*xt - eightth) + kb2*(xt*xt-fourteenth) +kp2*(xt*xt - 0.166666666666666666666);
a1->qxx -= k2*(xt*xt - third) + ka2*(xt*xt - eightth) + kb2*(xt*xt-fourteenth) +kp2*(xt*xt -0.1666666666666666666666);
a2->qxy -= (k2+ka2+kb2 +kp2)*yt*xt;
a1->qxy -= (k2+ka2+kb2 +kp2)*yt*xt;
a2->qxz -= (k2+ka2+kb2 +kp2)*zt*xt;
a1->qxz -= (k2+ka2+kb2 +kp2)*zt*xt;
a2->qyy -= k2*(yt*yt - third) + ka2*(yt*yt - eightth) + kb2*(yt*yt-fourteenth) +kp2*(yt*yt-0.166666666666666666666);
a1->qyy -= k2*(yt*yt - third) + ka2*(yt*yt - eightth) + kb2*(yt*yt-fourteenth) +kp2*(yt*yt-0.16666666666666666666666);
a2->qyz -= (k2+ka2+kb2 +kp2)*yt*zt;
a1->qyz -= (k2+ka2+kb2 +kp2)*yt*zt;
a2->qzz -= k2*(zt*zt - third) + ka2*(zt*zt - eightth) + kb2*(zt*zt-fourteenth) +kp2*(zt*zt-0.1666666666666666666666);
a1->qzz -= k2*(zt*zt - third) + ka2*(zt*zt - eightth) + kb2*(zt*zt-fourteenth) +kp2*(zt*zt-0.16666666666666666666666);
#ifdef CUBIC
a2->qxxx -= k3*(xt*xt*xt - xt*( 9./15 )) ;
a2->qxxx -= ka3*(xt*xt*xt - xt*( 24./80 )) ;
a2->qxxx -= kb3*(xt*xt*xt - xt*( 42./(14*16)));
a1->qxxx += k3*(xt*xt*xt - xt*( 9./15 )) ;
a1->qxxx += ka3*(xt*xt*xt - xt*( 24./80 )) ;
a1->qxxx += kb3*(xt*xt*xt - xt*( 42./(14*16)));
a2->qxxy -= k3*(yt*xt*xt - yt*( 6./ 15));
a2->qxxy -= ka3*(yt*xt*xt - yt*( 11./ 80));
a2->qxxy -= kb3*(yt*xt*xt - yt*( 17./ (14*16)));
a1->qxxy += k3*(yt*xt*xt - yt*( 6./ 15));
a1->qxxy += ka3*(yt*xt*xt - yt*( 11./ 80));
a1->qxxy += kb3*(yt*xt*xt - yt*( 17./ (14*16)));
a2->qxxz -= k3*(zt*xt*xt - zt*( 6./ 15));
a2->qxxz -= ka3*(zt*xt*xt - zt*( 11./ 80));
a2->qxxz -= kb3*(zt*xt*xt - zt*( 17./ (14*16)));
a1->qxxz += k3*(zt*xt*xt - zt*( 6./ 15));
a1->qxxz += ka3*(zt*xt*xt - zt*( 11./ 80));
a1->qxxz += kb3*(zt*xt*xt - zt*( 17./ (14*16)));
a2->qxyy -= k3*(yt*yt*xt - xt*( 6./ 15));
a2->qxyy -= ka3*(yt*yt*xt - xt*( 11./ 80));
a2->qxyy -= kb3*(yt*yt*xt - xt*( 17./ (14*16)));
a1->qxyy += k3*(yt*yt*xt - xt*( 6./ 15));
a1->qxyy += ka3*(yt*yt*xt - xt*( 11./ 80));
a1->qxyy += kb3*(yt*yt*xt - xt*( 17./ (14*16)));
a2->qxyz -= (k3+ka3+kb3)*yt*zt*xt;
a1->qxyz += (k3+ka3+kb3)*yt*zt*xt;
a2->qxzz -= k3*(zt*zt*xt - xt*( 6./ 15));
a2->qxzz -= ka3*(zt*zt*xt - xt*( 11./ 80));
a2->qxzz -= kb3*(zt*zt*xt - xt*( 17./ (14*16)));
a1->qxzz += k3*(zt*zt*xt - xt*( 6./ 15));
a1->qxzz += ka3*(zt*zt*xt - xt*( 11./ 80));
a1->qxzz += kb3*(zt*zt*xt - xt*( 17./ (14*16)));
a2->qyyy -= k3*(yt*yt*yt - yt*( 9./15 )) ;
a2->qyyy -= ka3*(yt*yt*yt - yt*( 24./80 )) ;
a2->qyyy -= kb3*(yt*yt*yt - yt*( 42./(14*16)));
a1->qyyy += k3*(yt*yt*yt - yt*( 9./15 )) ;
a1->qyyy += ka3*(yt*yt*yt - yt*( 24./80 )) ;
a1->qyyy += kb3*(yt*yt*yt - yt*( 42./(14*16)));
a2->qyyz -= k3*(yt*yt*zt - zt*( 6./ 15));
a2->qyyz -= ka3*(yt*yt*zt - zt*( 11./ 80));
a2->qyyz -= kb3*(yt*yt*zt - zt*( 17./ (14*16)));
a1->qyyz += k3*(yt*yt*zt - zt*( 6./ 15));
a1->qyyz += ka3*(yt*yt*zt - zt*( 11./ 80));
a1->qyyz += kb3*(yt*yt*zt - zt*( 17./ (14*16)));
a2->qyzz -= k3*(zt*zt*yt - yt*( 6./ 15));
a2->qyzz -= ka3*(zt*zt*yt - yt*( 11./ 80));
a2->qyzz -= kb3*(zt*zt*yt - yt*( 17./ (14*16)));
a1->qyzz += k3*(zt*zt*yt - yt*( 6./ 15));
a1->qyzz += ka3*(zt*zt*yt - yt*( 11./ 80));
a1->qyzz += kb3*(zt*zt*yt - yt*( 17./ (14*16)));
a2->qzzz -= k3*(zt*zt*zt - zt*( 9./15 )) ;
a2->qzzz -= ka3*(zt*zt*zt - zt*( 24./80 )) ;
a2->qzzz -= kb3*(zt*zt*zt - zt*( 42./(14*16)));
a1->qzzz += k3*(zt*zt*zt - zt*( 9./15 )) ;
a1->qzzz += ka3*(zt*zt*zt - zt*( 24./80 )) ;
a1->qzzz += kb3*(zt*zt*zt - zt*( 42./(14*16)));
#endif
/* debugging
j = i *4;
fprintf(stderr," mxcut %f %f inclose %d who %d \n",mxcut,(*vector)[j+3],inclose,(*atomall)[i]->serial);
fprintf(stderr," vector %f %f %f \n", (*vector)[j],(*vector)[j+1],(*vector)[j+2]);
*/
}/* end of loop i */
/* merge the non-bond mxcut lists */
/* a1->close[inclose] = NULL; */
/* set the position */
a1->px = a1->dx*lambda + a1->x;
a1->py = a1->dy*lambda + a1->y;
a1->pz = a1->dz*lambda + a1->z;
} /* end of ii loop */
a_inactive_f_zero();
free( indexes);
free( vector);
/* free( vecold);
*/
free (atomall);
return 1;
}
/*
* *
* polarmm.c multipole method with polarization
* *
* v 0.5 add the polarization to the neighbor terms (closest boxes
* since it is 1/r^3 this should converge.
* if this doesn't work then we'll add it to the other boxes.
*
*/
/* rectmm.c
*
* integrated multipole method with the amortized
* standard nonbonded program.
* rectangular multipole expansion to the r^-6 order (5th order expansion)
*
* from Eyges "The Classical Electromagnetic Field"
* note that we use the oposite convention for sign of
* expansion so use + for all the cumulants, while he uses
* -1^n. This is solely due to choice of origin and for
* other applications (rxn feild ) the -1^n is correct.
*
*
* collection of routines to service nonbonded potentials
*
* POOP (Poor-mans Object Oriented Programming) using scope rules
*
* the routines for potential value, force and (eventually) second
* derivatives are here also
*
* force and 2nd derivative routines assume zero'd arrays for output
* this allows for parralellization if needed (on a PC?)
*
* forces are symmetric - so we don't have to fuck around with
* s matrices and the like.
*
* note that the non-bonded information is in the ATOM structures
*
*
* attempts at vectorization
*/
/*
* copyright 1992, 1993, 1994, 1995 Robert W. Harrison
*
* This notice may not be removed
* This program may be copied for scientific use
* It may not be sold for profit without explicit
* permission of the author(s) who retain any
* commercial rights including the right to modify
* this notice
*/
/*
#define FOURTH
#define FIFTH
#ifdef FIFTH
#define FOURTH
#endif
*/
typedef struct {
float xc,yc,zc;
float sqp;
/* dipole appx for r^-6 */
float sa,xa,ya,za;
float q100,q010,q001;
float q200,q020,q002,q110,q101,q011;
float q300,q030,q003,q210,q201,q120,q021,q102,q012,q111;
#ifdef FOURTH
float q400,q040,q004,q310,q301,q130,q031,q103,q013,q220,q202,q022,q211,q121,q112;
#endif
#ifdef FIFTH
float q500,q050,q005,q410,q401,q140,q041,q104,q014,q320,q230,q302,q203,q032,q023,q311,q131,q113,q221,q212,q122;
#endif
int first,last,innode; } MMNODE;
typedef struct {
ATOM *who;
int next,which; } MMATOM;
int mm_fv_update_polar( lambda )
float lambda;
{
float r,r0,xt,yt,zt;
/* polarization terms */
float r4, pt,kp2,kp3;
float xt2,xt3,xt4,yt2,yt3,yt4,zt2,zt3,zt4;
float k,k1,k2,k3,k4,k5;
float ka2,ka3;
float kb2,kb3;
float c1,c2,c3,c4,c5; /* constants for the mm expansion */
float get_f_variable();
int inbond,inangle,i;
ATOM *ap,*a1,*a2,*bonded[10],*angled[10];
ATOM *a_next( ); /* returns first ATOM when called with -1 */
int a_number();
int ii,j,jj,imax,inclose;
float (*vector)[];
/* */
ATOM *close[NCLOSE],*(*atomall)[];
float mxdq,dielectric,mxcut;
float mmbox;
float xmax,xmin,ymax,ymin,zmax,zmin;
int nx,ny,nz;
int ix,iy,iz,inode;
int naybor[27];
char line[80];
MMNODE (*nodelist)[];
MMATOM (*atomlist)[];
mmbox = get_f_variable("mmbox");
mxcut = get_f_variable("mxcut");
if( mxcut < 0.) mxcut= 5.;
dielectric = get_f_variable("dielec");
if( dielectric <= 0.) dielectric = 1.;
dielectric = 332.17752/dielectric;
/* get the number of atoms and allocate the memory for the array space */
i = a_number();
vector = malloc( 4*i*sizeof(float) );
if( vector == NULL)
{ aaerror("cannot allocate memory in mm_fv_update\n"); return 0;}
atomall = malloc( i*sizeof(ATOM *) );
if( atomall == NULL)
{aaerror("cannot allocate memory in mm_fv_update\n"); return 0;}
atomlist = malloc( i * sizeof( MMATOM ));
if( atomlist == NULL)
{ aaerror("cannot allocate memory in mm_fv_update\n"); return 0;}
imax = a_number();
jj = imax;
for( i=0; i< imax; i++)
{
(*atomall)[i] = a_next(i);
(*atomlist)[i].who = (*atomall)[i];
}
/* first check if anyone's moved and update the lists */
/* note that this must be a look-ahead rather than
* look back search because
* we cannot update ->px until we've used that atom !!! */
#pragma _CNX no_recurrence
for( ii=0; ii< imax; ii++)
{
a1 = (*atomall)[ii];
j = ii*4;
(*vector)[j] = a1->dx*lambda +a1->x ;
(*vector)[j+1] = a1->dy*lambda +a1->y;
(*vector)[j+2] = a1->dz*lambda +a1->z;
}
/* determine the bounds of box which surrounds all of the atoms */
xmax = -10e10;
ymax = -10e10;
zmax = -10e10;
xmin = 10e10;