/** Computes the three body angle interaction energy (see \ref tclcommand_inter, \ref tclcommand_analyze).
@param p_mid Pointer to first particle.
@param p_left Pointer to second/middle particle.
@param p_right Pointer to third particle.
@param iaparams bond type number of the angle interaction (see \ref tclcommand_inter).
@param _energy return energy pointer.
@return 0.
*/
inline int angle_harmonic_energy(Particle *p_mid, Particle *p_left, Particle *p_right,
Bonded_ia_parameters *iaparams, double *_energy)
{
double cosine, vec1[3], vec2[3], d1i, d2i, dist2;
int j;
cosine=0.0;
/* vector from p_mid to p_left */
get_mi_vector(vec1, p_mid->r.p, p_left->r.p);
dist2 = sqrlen(vec1);
d1i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec1[j] *= d1i;
/* vector from p_right to p_mid */
get_mi_vector(vec2, p_right->r.p, p_mid->r.p);
dist2 = sqrlen(vec2);
d2i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec2[j] *= d2i;
/* scalar produvt of vec1 and vec2 */
cosine = scalar(vec1, vec2);
if ( cosine > TINY_COS_VALUE) cosine = TINY_COS_VALUE;
if ( cosine < -TINY_COS_VALUE) cosine = -TINY_COS_VALUE;
/* bond angle energy */
{
double phi;
phi = acos(-cosine);
*_energy = 0.5*iaparams->p.angle_harmonic.bend*SQR(phi - iaparams->p.angle_harmonic.phi0);
}
return 0;
}
/** Computes the three body angle interaction force and adds this
force to the particle forces (see \ref tclcommand_inter).
@param p_mid Pointer to second/middle particle.
@param p_left Pointer to first/left particle.
@param p_right Pointer to third/right particle.
@param iaparams bond type number of the angle interaction (see \ref tclcommand_inter).
@param force1 returns force of particle 1
@param force2 returns force of particle 2
@return 0
*/
inline int calc_angle_cosine_force(Particle *p_mid, Particle *p_left, Particle *p_right,
Bonded_ia_parameters *iaparams, double force1[3], double force2[3])
{
double cosine, vec1[3], vec2[3], d1i, d2i, dist2, fac, f1=0.0, f2=0.0;
int j;
cosine=0.0;
/* vector from p_left to p_mid */
get_mi_vector(vec1, p_mid->r.p, p_left->r.p);
dist2 = sqrlen(vec1);
d1i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec1[j] *= d1i;
/* vector from p_mid to p_right */
get_mi_vector(vec2, p_right->r.p, p_mid->r.p);
dist2 = sqrlen(vec2);
d2i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec2[j] *= d2i;
/* scalar produvt of vec1 and vec2 */
cosine = scalar(vec1, vec2);
fac = iaparams->p.angle_cosine.bend;
if ( cosine > TINY_COS_VALUE ) cosine = TINY_COS_VALUE;
if ( cosine < -TINY_COS_VALUE) cosine = -TINY_COS_VALUE;
fac *= iaparams->p.angle_cosine.sin_phi0 * (cosine/sqrt(1-SQR(cosine))) + iaparams->p.angle_cosine.cos_phi0;
for(j=0;j<3;j++) {
f1 = fac * (cosine * vec1[j] - vec2[j]) * d1i;
f2 = fac * (cosine * vec2[j] - vec1[j]) * d2i;
force1[j] = (f1-f2);
force2[j] = -f1;
}
return 0;
}
/** Computes the three body angle interaction energy (see \ref tclcommand_inter, \ref tclcommand_analyze).
@param p_mid Pointer to first particle.
@param p_left Pointer to second/middle particle.
@param p_right Pointer to third particle.
@param iaparams bond type number of the angle interaction (see \ref tclcommand_inter).
@param _energy return energy pointer.
@return 0.
*/
inline int angle_cosine_energy(Particle *p_mid, Particle *p_left, Particle *p_right,
Bonded_ia_parameters *iaparams, double *_energy)
{
double cosine, vec1[3], vec2[3], d1i, d2i, dist2;
int j;
cosine=0.0;
/* vector from p_mid to p_left */
get_mi_vector(vec1, p_mid->r.p, p_left->r.p);
dist2 = sqrlen(vec1);
d1i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec1[j] *= d1i;
/* vector from p_right to p_mid */
get_mi_vector(vec2, p_right->r.p, p_mid->r.p);
dist2 = sqrlen(vec2);
d2i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec2[j] *= d2i;
/* scalar produvt of vec1 and vec2 */
cosine = scalar(vec1, vec2);
if ( cosine > TINY_COS_VALUE) cosine = TINY_COS_VALUE;
if ( cosine < -TINY_COS_VALUE) cosine = -TINY_COS_VALUE;
/* bond angle energy */
*_energy = iaparams->p.angle_cosine.bend*(cosine*iaparams->p.angle_cosine.cos_phi0 - sqrt(1-SQR(cosine))*iaparams->p.angle_cosine.sin_phi0+1);
return 0;
}
/** Computes the QUARTIC pair force and adds this
force to the particle forces (see \ref interaction_data.cpp).
@param p1 Pointer to first particle.
@param p2 Pointer to second/middle particle.
@param iaparams bond type number of the angle interaction (see \ref interaction_data.cpp).
@param dx particle distance vector
@param force returns force of particle 1
@return 0.
*/
inline int calc_quartic_pair_force(Particle *p1, Particle *p2, Bonded_ia_parameters *iaparams, double dx[3], double force[3])
{
int i;
double fac;
double dist2 = sqrlen(dx);
double dist = sqrt(dist2);
double dr;
if ((iaparams->p.quartic.r_cut > 0.0) &&
(dist > iaparams->p.quartic.r_cut))
return 1;
dr = dist - iaparams->p.quartic.r;
if (fabs(dr) > ROUND_ERROR_PREC) {
if(dist>ROUND_ERROR_PREC) { /* Regular case */
fac = dr / dist;
} else { /* dx[] == 0: the force is undefined. Let's use a random direction */
for(i=0;i<3;i++) dx[i] = d_random()-0.5;
fac = dr / sqrt(sqrlen(dx));
}
} else {
fac=0;
}
for(i=0;i<3;i++)
force[i] = -(iaparams->p.quartic.k0 + iaparams->p.quartic.k1 * dr * dr ) * fac*dx[i];
ONEPART_TRACE(if(p1->p.identity==check_id) fprintf(stderr,"%d: OPT: QUARTIC f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac %.3e\n",this_node,p1->f.f[0],p1->f.f[1],p1->f.f[2],p2->p.identity,dist2,fac));
ONEPART_TRACE(if(p2->p.identity==check_id) fprintf(stderr,"%d: OPT: QUARTIC f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac %.3e\n",this_node,p2->f.f[0],p2->f.f[1],p2->f.f[2],p1->p.identity,dist2,fac));
return 0;
}
/** Computes the FENE pair force and adds this
force to the particle forces (see \ref interaction_data.cpp).
@param p1 Pointer to first particle.
@param p2 Pointer to second/middle particle.
@param iaparams bond type number of the angle interaction (see \ref interaction_data.cpp).
@param dx particle distance vector
@param force returns force of particle 1
@return true if the bond is broken
*/
inline int calc_fene_pair_force(Particle *p1, Particle *p2, Bonded_ia_parameters *iaparams, double dx[3], double force[3])
{
int i;
double fac, dr, len2, len;
len2 = sqrlen(dx);
len = sqrt(len2);
dr = len - iaparams->p.fene.r0;
if(dr >= iaparams->p.fene.drmax)
return 1;
fac = -iaparams->p.fene.k * dr / ((1.0 - dr*dr*iaparams->p.fene.drmax2i));
if (fabs(dr) > ROUND_ERROR_PREC) {
if(len > ROUND_ERROR_PREC) { /* Regular case */
fac /= len ;
} else { /* dx[] == 0: the force is undefined. Let's use a random direction */
for(i=0;i<3;i++) dx[i] = d_random()-0.5;
fac /= sqrt(sqrlen(dx));
}
} else {
fac = 0.0;
}
FENE_TRACE(if(fac > 50) fprintf(stderr,"WARNING: FENE force factor between Pair (%d,%d) large: %f at distance %f\n", p1->p.identity,p2->p.identity,fac,sqrt(len2)) );
for(i=0;i<3;i++)
force[i] = fac*dx[i];
ONEPART_TRACE(if(p1->p.identity==check_id) fprintf(stderr,"%d: OPT: FENE f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac %.3e\n",this_node,p1->f.f[0],p1->f.f[1],p1->f.f[2],p2->p.identity,sqrt(len2),fac));
ONEPART_TRACE(if(p2->p.identity==check_id) fprintf(stderr,"%d: OPT: FENE f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac %.3e\n",this_node,p2->f.f[0],p2->f.f[1],p2->f.f[2],p1->p.identity,sqrt(len2),fac));
return 0;
}
/* The force on each particle due to a three-body bonded potential
is computed. */
inline void calc_angle_cossquare_3body_forces(Particle *p_mid, Particle *p_left,
Particle *p_right, Bonded_ia_parameters *iaparams,
double force1[3], double force2[3], double force3[3]) {
int j;
double pot_dep;
double cos_phi;
double sin_phi;
double vec31[3];
double vec21[3];
double vec12[3]; // espresso convention
double vec21_sqr;
double vec31_sqr;
double vec21_magn;
double vec31_magn;
double fj[3];
double fk[3];
double fac;
get_mi_vector(vec12, p_mid->r.p, p_left->r.p);
for(j = 0; j < 3; j++)
vec21[j] = -vec12[j];
get_mi_vector(vec31, p_right->r.p, p_mid->r.p);
vec21_sqr = sqrlen(vec21);
vec21_magn = sqrt(vec21_sqr);
vec31_sqr = sqrlen(vec31);
vec31_magn = sqrt(vec31_sqr);
cos_phi = scalar(vec21, vec31) / (vec21_magn * vec31_magn);
sin_phi = sqrt(1.0 - SQR(cos_phi));
/* uncomment this block if interested in the angle
if(cos_phi < -1.0) cos_phi = -TINY_COS_VALUE;
if(cos_phi > 1.0) cos_phi = TINY_COS_VALUE;
phi = acos(cos_phi);
*/
{
double K, cos_phi0;
K = iaparams->p.angle_cossquare.bend;
cos_phi0 = iaparams->p.angle_cossquare.cos_phi0;
// potential dependent term [dU/dphi = K * (sin_phi * cos_phi0 - cos_phi * sin_phi)]
pot_dep = K * (sin_phi * cos_phi0 - cos_phi * sin_phi);
}
fac = pot_dep / sin_phi;
for(j = 0; j < 3; j++) {
fj[j] = vec31[j] / (vec21_magn * vec31_magn) - cos_phi * vec21[j] / vec21_sqr;
fk[j] = vec21[j] / (vec21_magn * vec31_magn) - cos_phi * vec31[j] / vec31_sqr;
}
// note that F1 = -(F2 + F3)
for(j = 0; j < 3; j++) {
force1[j] = force1[j] - fac * (fj[j] + fk[j]);
force2[j] = force2[j] + fac * fj[j];
force3[j] = force3[j] + fac * fk[j];
}
}
int calc_angledist_force(Particle *p_mid, Particle *p_left,
Particle *p_right,
Bonded_ia_parameters *iaparams,
double force1[3], double force2[3])
{
double cosine=0.0, vec1[3], vec2[3], d1i=0.0, d2i=0.0, dist2, fac=0.0, f1=0.0, f2=0.0;
int j;
/* vector from p_left to p_mid */
get_mi_vector(vec1, p_mid->r.p, p_left->r.p);
dist2 = sqrlen(vec1);
d1i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec1[j] *= d1i;
/* vector from p_mid to p_right */
get_mi_vector(vec2, p_right->r.p, p_mid->r.p);
dist2 = sqrlen(vec2);
d2i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec2[j] *= d2i;
/* scalar product of vec1 and vec2 */
cosine = scalar(vec1, vec2);
fac = iaparams->p.angledist.bend;
#ifdef BOND_ANGLEDIST_HARMONIC
{
double phi,sinphi;
/* NOTE: The angledist is ONLY implemented for the HARMONIC case */
double phi0 = calc_angledist_param(p_mid, p_left, p_right, iaparams);
if ( cosine > TINY_COS_VALUE) cosine = TINY_COS_VALUE;
if ( cosine < -TINY_COS_VALUE) cosine = -TINY_COS_VALUE;
phi = acos(-cosine);
sinphi = sin(phi);
if ( sinphi < TINY_SIN_VALUE ) sinphi = TINY_SIN_VALUE;
fac *= (phi - phi0)/sinphi;
// fprintf(stdout,"\n force: z_pmid=%f, phi0=%f phi=%f fac=%f",p_mid->r.p[2],phi0*180.0/PI,phi*180.0/PI,fac);
}
#endif
#ifdef BOND_ANGLEDIST_COSINE
#error angledist ONLY implemented for harmonic case!
#endif
#ifdef BOND_ANGLEDIST_COSSQUARE
#error angledist ONLY implemented for harmonic case!
#endif
for(j=0;j<3;j++) {
f1 = fac * (cosine * vec1[j] - vec2[j]) * d1i;
f2 = fac * (cosine * vec2[j] - vec1[j]) * d2i;
force1[j] = (f1-f2);
force2[j] = -f1;
}
return 0;
}
/** This function returns the angle btw the triangle p1,p2,p3 and p2,p3,p4.
* Be careful, the angle depends on the orientation of the trianlges!
* You need to be sure that the orientation (direction of normal vector)
* of p1p2p3 is given by the cross product p2p1 x p2p3.
* The orientation of p2p3p4 must be given by p2p3 x p2p4.
*
* Example: p1 = (0,0,1), p2 = (0,0,0), p3=(1,0,0), p4=(0,1,0).
* The orientation of p1p2p3 should be in the direction (0,1,0)
* and indeed: p2p1 x p2p3 = (0,0,1)x(1,0,0) = (0,1,0)
* This function is called in the beginning of the simulation when creating
* bonds depending on the angle btw the triangles, the bending_force.
* Here, we determine the orientations by looping over the triangles
* and checking the correct orientation. So when defining the bonds by tcl command
* "part p2 bond xxxx p1 p3 p4", we correctly input the particle id's.
* So if you have the access to the order of particles, you are safe to call this
* function with exactly this order. Otherwise you need to check the orientations. */
inline double angle_btw_triangles(double *P1, double *P2, double *P3, double *P4) {
double phi;
double u[3],v[3],normal1[3],normal2[3]; //auxiliary variables
u[0] = P1[0] - P2[0]; // u = P2P1
u[1] = P1[1] - P2[1];
u[2] = P1[2] - P2[2];
v[0] = P3[0] - P2[0]; // v = P2P3
v[1] = P3[1] - P2[1];
v[2] = P3[2] - P2[2];
vector_product(u,v,normal1);
u[0] = P3[0] - P2[0]; // u = P2P3
u[1] = P3[1] - P2[1];
u[2] = P3[2] - P2[2];
v[0] = P4[0] - P2[0]; // v = P2P4
v[1] = P4[1] - P2[1];
v[2] = P4[2] - P2[2];
vector_product(u,v,normal2);
double tmp11,tmp22,tmp33;
// Now we compute the scalar product of n1 and n2 divided by the norms of n1 and n2
//tmp11 = dot(3,normal1,normal2); // tmp11 = n1.n2
tmp11 = scalar(normal1,normal2); // tmp11 = n1.n2
/*
tmp22 = normr(normal1);
tmp33 = normr(normal2);
tmp11 /= (tmp22*tmp33); // tmp11 = n1.n2/(|n1||n2|)
*/
tmp11 *= fabs(tmp11); // tmp11 = (n1.n2)^2
tmp22 = sqrlen(normal1); //tmp22 = |n1|^2
tmp33 = sqrlen(normal2); //tmp33 = |n1|^2
tmp11 /= (tmp22*tmp33); // tmp11 = (n1.n2/(|n1||n2|))^2
if (tmp11 > 0 ) {
tmp11 = sqrt(tmp11);
} else {
tmp11 = - sqrt(- tmp11);
}
if(tmp11>=1.) { tmp11=0.0;}
else if(tmp11<=-1.) { tmp11=M_PI;}
phi = M_PI - acos(tmp11); // The angle between the faces (not considering the orientation, always less or equal to Pi) is
// equal to Pi minus angle between the normals
// Now we need to determine, if the angle btw two triangles is less than Pi or more than Pi. To do this we check,
// if the point P4 lies in the halfspace given by trianlge P1P2P3 and the normal to this triangle. If yes, we have
// angle less than Pi, if not, we have angle more than Pi.
// General equation of the plane is n_x*x + n_y*y + n_z*z + d = 0 where (n_x,n_y,n_z) is the normal to the plane.
// Point P1 lies in the plane, therefore d = -(n_x*P1_x + n_y*P1_y + n_z*P1_z)
// Point P4 lies in the halfspace given by normal iff n_x*P4_x + n_y*P4_y + n_z*P4_z + d >= 0
tmp11 = - (normal1[0]*P1[0] + normal1[1]*P1[1] + normal1[2]*P1[2]);
if (normal1[0]*P4[0] + normal1[1]*P4[1] + normal1[2]*P4[2] + tmp11 < 0) phi = 2*M_PI - phi;
return phi;
}
/** Computes the three body overlapped angle interaction force.
Adds this force to the particle forces in forces.hpp (see \ref tclcommand_inter).
@param p_mid Pointer to second/middle particle.
@param p_left Pointer to first/left particle.
@param p_right Pointer to third/right particle.
@param iaparams bond type number of the angle interaction (see \ref tclcommand_inter).
@param force1 returns force of particle 1
@param force2 returns force of particle 2
@return 0
Needs feature OVERLAPPED compiled in (see \ref config.hpp).
*/
inline int calc_overlap_angle_force(Particle *p_mid, Particle *p_left,
Particle *p_right, Bonded_ia_parameters *iaparams,
double force1[3], double force2[3])
{
double cosine, vec1[3], vec2[3], d1i, d2i, dist2, fac, f1=0.0, f2=0.0;
int j;
int ig;
double ev;
double prob=0.;
double Apart=0.;
cosine=0.0;
/* vector from p_left to p_mid */
get_mi_vector(vec1, p_mid->r.p, p_left->r.p);
dist2 = sqrlen(vec1);
d1i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec1[j] *= d1i;
/* vector from p_mid to p_right */
get_mi_vector(vec2, p_right->r.p, p_mid->r.p);
dist2 = sqrlen(vec2);
d2i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec2[j] *= d2i;
/* scalar produvt of vec1 and vec2 */
/* Notice: cosine = - costheta */
cosine = scalar(vec1, vec2);
if ( cosine > TINY_COS_VALUE ) cosine = TINY_COS_VALUE;
if ( cosine < -TINY_COS_VALUE) cosine = -TINY_COS_VALUE;
/* compute fac = - dU/d(costheta) */
/* prob = sum_(i=1,N) [ a_i * exp(-(costheta -b_i)^2/c_i^2))] */
/* Apart = sum_(i=1,N) [ a_i * exp(-(costheta -b_i)^2/c_i^2)) * (costheta-b_i) / c_i^2] */
/* fac = -2.0 * ( Apart / prob ) */
for(ig=0; ig<iaparams->p.overlap.noverlaps; ig++) {
ev = (-cosine - iaparams->p.overlap.para_b[ig]) / iaparams->p.overlap.para_c[ig];
prob = prob + iaparams->p.overlap.para_a[ig] * exp (-1.0*ev*ev);
Apart = Apart + iaparams->p.overlap.para_a[ig] * exp (-1.0*ev*ev) * (-cosine-iaparams->p.overlap.para_b[ig]) / (iaparams->p.overlap.para_c[ig] * iaparams->p.overlap.para_c[ig]);
}
fac = -2. * ( Apart / prob);
/* compute force */
for(j=0;j<3;j++) {
f1 = fac * (cosine * vec1[j] - vec2[j]) * d1i;
f2 = fac * (cosine * vec2[j] - vec1[j]) * d2i;
force1[j] = (f1-f2);
force2[j] = -f1;
}
return 0;
}
/** Computes the three body angle interaction force and adds this
force to the particle forces (see \ref tclcommand_inter).
@param p_mid Pointer to second/middle particle.
@param p_left Pointer to first/left particle.
@param p_right Pointer to third/right particle.
@param iaparams bond type number of the angle interaction (see \ref tclcommand_inter).
@param force1 returns force of particle 1
@param force2 returns force of particle 2
@return 0
*/
inline int calc_angle_harmonic_force(Particle *p_mid, Particle *p_left, Particle *p_right,
Bonded_ia_parameters *iaparams, double force1[3], double force2[3])
{
double cosine, vec1[3], vec2[3], d1i, d2i, dist2, fac, f1=0.0, f2=0.0;
int j;
cosine=0.0;
/* vector from p_left to p_mid */
get_mi_vector(vec1, p_mid->r.p, p_left->r.p);
dist2 = sqrlen(vec1);
d1i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec1[j] *= d1i;
/* vector from p_mid to p_right */
get_mi_vector(vec2, p_right->r.p, p_mid->r.p);
dist2 = sqrlen(vec2);
d2i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec2[j] *= d2i;
/* scalar produvt of vec1 and vec2 */
cosine = scalar(vec1, vec2);
fac = iaparams->p.angle_harmonic.bend;
{
double phi,sinphi;
if ( cosine > TINY_COS_VALUE) cosine = TINY_COS_VALUE;
if ( cosine < -TINY_COS_VALUE) cosine = -TINY_COS_VALUE;
phi = acos(-cosine);
sinphi = sin(phi);
if ( sinphi < TINY_SIN_VALUE ) sinphi = TINY_SIN_VALUE;
fac *= (phi - iaparams->p.angle_harmonic.phi0)/sinphi;
#ifdef CONFIGTEMP
extern double configtemp[2];
if (p_left->p.configtemp) {
configtemp[0] += SQR(fac*sinphi*d1i);
configtemp[1] -= iaparams->p.angle_harmonic.bend*(1+cosine/sinphi*(phi - iaparams->p.angle_harmonic.phi0))*SQR(d1i);
}
if (p_mid->p.configtemp) {
configtemp[0] += SQR(fac*sinphi) * (1./sqrlen(vec1) + 1./sqrlen(vec2) - 2*cosine*d1i*d2i);
configtemp[1] -= iaparams->p.angle_harmonic.bend*((1/sqrlen(vec1)+1/sqrlen(vec2)-cosine*d1i*d2i)
+cosine/sinphi * (1./sqrlen(vec1)+1./sqrlen(vec2)-d1i*d2i/cosine) *(phi - iaparams->p.angle_harmonic.phi0));
}
if (p_right->p.configtemp) {
configtemp[0] += SQR(fac*sinphi*d2i);
configtemp[1] -= iaparams->p.angle_harmonic.bend*(1+cosine/sinphi*(phi - iaparams->p.angle_harmonic.phi0))*SQR(d2i);
}
#endif
}
for(j=0;j<3;j++) {
f1 = fac * (cosine * vec1[j] - vec2[j]) * d1i;
f2 = fac * (cosine * vec2[j] - vec1[j]) * d2i;
force1[j] = (f1-f2);
force2[j] = -f1;
}
return 0;
}
/** Computes the three body angle interaction force and adds this
force to the particle forces (see \ref tclcommand_inter).
@param p_mid Pointer to second/middle particle.
@param p_left Pointer to first/left particle.
@param p_right Pointer to third/right particle.
@param iaparams bond type number of the angle interaction (see \ref tclcommand_inter).
@param force1 returns force of particle 1
@param force2 returns force of particle 2
@return 0
*/
inline int calc_angle_force(Particle *p_mid, Particle *p_left, Particle *p_right,
Bonded_ia_parameters *iaparams, double force1[3], double force2[3])
{
double cosine, vec1[3], vec2[3], d1i, d2i, dist2, fac, f1=0.0, f2=0.0;
int j;
cosine=0.0;
/* vector from p_left to p_mid */
get_mi_vector(vec1, p_mid->r.p, p_left->r.p);
dist2 = sqrlen(vec1);
d1i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec1[j] *= d1i;
/* vector from p_mid to p_right */
get_mi_vector(vec2, p_right->r.p, p_mid->r.p);
dist2 = sqrlen(vec2);
d2i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec2[j] *= d2i;
/* scalar produvt of vec1 and vec2 */
cosine = scalar(vec1, vec2);
fac = iaparams->p.angle.bend;
#ifdef BOND_ANGLE_HARMONIC
{
double phi,sinphi;
if ( cosine > TINY_COS_VALUE) cosine = TINY_COS_VALUE;
if ( cosine < -TINY_COS_VALUE) cosine = -TINY_COS_VALUE;
phi = acos(-cosine);
sinphi = sin(phi);
if ( sinphi < TINY_SIN_VALUE ) sinphi = TINY_SIN_VALUE;
fac *= (phi - iaparams->p.angle.phi0)/sinphi;
}
#endif
#ifdef BOND_ANGLE_COSINE
if ( cosine > TINY_COS_VALUE ) cosine = TINY_COS_VALUE;
if ( cosine < -TINY_COS_VALUE) cosine = -TINY_COS_VALUE;
fac *= iaparams->p.angle.sin_phi0 * (cosine/sqrt(1-SQR(cosine))) + iaparams->p.angle.cos_phi0;
#endif
#ifdef BOND_ANGLE_COSSQUARE
fac *= iaparams->p.angle.cos_phi0 + cosine;
#endif
for(j=0;j<3;j++) {
f1 = fac * (cosine * vec1[j] - vec2[j]) * d1i;
f2 = fac * (cosine * vec2[j] - vec1[j]) * d2i;
force1[j] = (f1-f2);
force2[j] = -f1;
}
return 0;
}
void nsq_calculate_virials()
{
Particle *partl, *partg;
Particle *pt1, *pt2;
int p, p2, npl, npg, c;
double d[3], dist2, dist;
npl = local->n;
partl = local->part;
/* calculate bonded interactions and non bonded node-node */
for (p = 0; p < npl; p++) {
pt1 = &partl[p];
add_kinetic_virials(pt1,0);
add_bonded_virials(pt1);
#ifdef BOND_ANGLE
add_three_body_bonded_stress(pt1);
#endif
/* other particles, same node */
for (p2 = p + 1; p2 < npl; p2++) {
pt2 = &partl[p2];
get_mi_vector(d, pt1->r.p, pt2->r.p);
dist2 = sqrlen(d);
dist = sqrt(dist2);
#ifdef EXCLUSIONS
if (do_nonbonded(pt1, pt2))
#endif
add_non_bonded_pair_virials(pt1, pt2, d, dist, dist2);
}
/* calculate with my ghosts */
for (c = 0; c < me_do_ghosts.n; c++) {
npg = me_do_ghosts.cell[c]->n;
partg = me_do_ghosts.cell[c]->part;
for (p2 = 0; p2 < npg; p2++) {
pt2 = &partg[p2];
get_mi_vector(d, pt1->r.p, pt2->r.p);
dist2 = sqrlen(d);
dist = sqrt(dist2);
#ifdef EXCLUSIONS
if (do_nonbonded(pt1, pt2))
#endif
add_non_bonded_pair_virials(pt1, pt2, d, dist, dist2);
}
}
}
}
inline int bonded_coulomb_pair_energy(Particle *p1, Particle *p2, Bonded_ia_parameters *iaparams, double dx[3], double *_energy)
{
double dist = sqrt(sqrlen(dx));
*_energy = iaparams->p.bonded_coulomb.prefactor * p1->p.q * p2->p.q / dist;
return 0;
}
void print_bond_len()
{
int i, k, c, np;
Cell *cell;
Particle *p;
Bonded_ia_parameters *b_ia;
double r_ij[3];
printf("%d: ", this_node);
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
k=0;
while(k<p[i].bl.n)
{
b_ia = &bonded_ia_params[p[i].bl.e[k]];
if(b_ia->type == BONDED_IA_RIGID_BOND)
{
Particle *p2 = local_particles[p[i].bl.e[k++]];
if (!p2) {
runtimeErrorMsg() <<"rigid bond broken between particles " << p[i].p.identity << " and " << p[i].bl.e[k-1] << " (particles not stored on the same node)";
return;
}
get_mi_vector(r_ij, p[i].r.p , p2->r.p);
printf(" bl (%d %d): %f\t", p[i].p.identity, p2->p.identity,sqrlen(r_ij));
}
else
k += b_ia->num;
} //while k loop
} //for i loop
}// for c loop
printf("\n");
}
/** Computes the two body overlapped bonded force.
Adds this force to the particle forces in forces.hpp (see \ref tclcommand_inter).
@param p1 Pointer to first particle.
@param p2 Pointer to second/middle particle.
@param iaparams bond type number of the angle interaction (see \ref tclcommand_inter).
@param dx particle distance vector
@param force returns force of particle 1
@return 0.
Needs feature OVERLAPPED compiled in (see \ref config.hpp).
*/
inline int calc_overlap_bond_force(Particle *p1, Particle *p2, Bonded_ia_parameters *iaparams, double dx[3], double force[3])
{
int i;
double fac;
int ig;
double ev;
double prob=0.;
double Apart=0.;
double dist2 = sqrlen(dx);
double dist = sqrt(dist2);
/* compute fac = - 1/r * dU/dr */
/* prob = sum_(i=1,N) [ a_i * exp(-(r -b_i)^2/c_i^2))] */
/* Apart = sum_(i=1,N) [ a_i * exp(-(r -b_i)^2/c_i^2)) * (x-b_i) / c_i^2] */
/* fac = - 2.0 * ( 1/r + Apart / prob ) */
for(ig=0; ig<iaparams->p.overlap.noverlaps; ig++) {
ev = (dist - iaparams->p.overlap.para_b[ig]) / iaparams->p.overlap.para_c[ig];
prob = prob + iaparams->p.overlap.para_a[ig] * exp (-1.0*ev*ev);
Apart = Apart + iaparams->p.overlap.para_a[ig] * exp (-1.0*ev*ev) * (dist-iaparams->p.overlap.para_b[ig]) / (iaparams->p.overlap.para_c[ig] * iaparams->p.overlap.para_c[ig]);
}
fac = -2. * ( 1 / dist + Apart / prob);
fac /= dist;
/* compute force */
for(i=0;i<3;i++)
force[i] = fac*dx[i];
ONEPART_TRACE(if(p1->p.identity==check_id) fprintf(stderr,"%d: OPT: HARMONIC f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac %.3e\n",this_node,p1->f.f[0],p1->f.f[1],p1->f.f[2],p2->p.identity,dist2,fac));
ONEPART_TRACE(if(p2->p.identity==check_id) fprintf(stderr,"%d: OPT: HARMONIC f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac %.3e\n",this_node,p2->f.f[0],p2->f.f[1],p2->f.f[2],p1->p.identity,dist2,fac));
return 0;
}
/* Rectify an image point
* input and output in normalized coordinates
*/
Vec2d Intrinsic::rectify (Vec2d xd)
{
double r2 = len(xd);
if (dist_model == POLYNOMIAL_DISTORTION) {
double rd4 = r2*r2;
double rd6 = rd4*r2;
double rd8 = rd4*rd4;
double beta = getKC0()*r2+getKC1()*rd4+getKC0()*getKC0()*rd4+getKC1()*getKC1()*rd8+\
2*getKC0()*getKC1()*rd6;
double alpha = 1 + 4*getKC0()*r2 + 6*getKC1()*rd4;
return xd * (1 - beta/alpha);
} else if (dist_model == SPHERICAL_DISTORTION) {
Vec2d x = xd-cc;
r2 = sqrlen(x);
double r_new = value*value / sqrt(fabs(1 - value*value*value*value*r2));
x = x * r_new+cc; //
return x;
}
printf("undefined distortion model!\n");
assert(false);
return Vec2d (0,0);
}
inline int subt_lj_pair_energy(Particle *p1, Particle *p2, Bonded_ia_parameters *iaparams, double dx[3], double *_energy)
{
double energy=0.0;
IA_parameters *ia_params;
double r_off, frac2, frac6;
double dist2 = sqrlen(dx);
double dist = sqrt(dist2);
if(dist >= iaparams->p.subt_lj.r)
return 1;
ia_params = get_ia_param(p1->p.type,p2->p.type);
if(dist < ia_params->LJ_cut+ia_params->LJ_offset) {
r_off = dist - ia_params->LJ_offset;
if(r_off > ia_params->LJ_capradius) {
/* normal case: resulting force/energy smaller than capping. */
frac2 = SQR(ia_params->LJ_sig/r_off);
frac6 = frac2*frac2*frac2;
energy = 4.0*ia_params->LJ_eps*(SQR(frac6)-frac6+ia_params->LJ_shift);
}
else if(dist > 0.0) {
/* capped part of lj potential. */
frac2 = SQR(ia_params->LJ_sig/ia_params->LJ_capradius);
frac6 = frac2*frac2*frac2;
energy = 4.0*ia_params->LJ_eps*(SQR(frac6)-frac6+ia_params->LJ_shift);
}
}
*_energy = -energy;
return 0;
}
void nbhood(double pt[3], double r, IntList *il, int planedims[3] )
{
double d[3];
int i,j;
double r2;
r2 = r*r;
init_intlist(il);
updatePartCfg(WITHOUT_BONDS);
for (i = 0; i<n_part; i++) {
if ( (planedims[0] + planedims[1] + planedims[2]) == 3 ) {
get_mi_vector(d, pt, partCfg[i].r.p);
} else {
/* Calculate the in plane distance */
for ( j= 0 ; j < 3 ; j++ ) {
d[j] = planedims[j]*(partCfg[i].r.p[j]-pt[j]);
}
}
if (sqrlen(d) < r2) {
realloc_intlist(il, il->n + 1);
il->e[il->n] = partCfg[i].p.identity;
il->n++;
}
}
}
// Update the pos of the given virtual particle as defined by the real
// particles in the same molecule
void update_mol_pos_particle(Particle *p)
{
// First obtain the real particle responsible for this virtual particle:
// Find the 1st real particle in the topology for the virtual particle's mol_id
Particle *p_real = vs_relative_get_real_particle(p);
// Check, if a real particle was found
if (!p_real)
{
char *errtxt = runtime_error(128 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"virtual_sites_relative.cpp - update_mol_pos_particle(): No real particle associated with virtual site.\n");
return;
}
// Calculate the quaternion defining the orientation of the vecotr connectinhg
// the virtual site and the real particle
// This is obtained, by multiplying the quaternion representing the director
// of the real particle with the quaternion of the virtual particle, which
// specifies the relative orientation.
double q[4];
multiply_quaternions(p_real->r.quat,p->r.quat,q);
// Calculate the director resulting from the quaternions
double director[3];
convert_quat_to_quatu(q,director);
// normalize
double l =sqrt(sqrlen(director));
// Division comes in the loop below
// Calculate the new position of the virtual sites from
// position of real particle + director
int i;
double new_pos[3];
double tmp;
for (i=0;i<3;i++)
{
new_pos[i] =p_real->r.p[i] +director[i]/l*p->p.vs_relative_distance;
// Handle the case that one of the particles had gone over the periodic
// boundary and its coordinate has been folded
#ifdef PARTIAL_PERIODIC
if (PERIODIC(i))
#endif
{
tmp =p->r.p[i] -new_pos[i];
//printf("%f\n",tmp);
if (tmp > box_l[i]/2.) {
//printf("greater than box_l/2 %f\n",tmp);
p->r.p[i] =new_pos[i] + box_l[i];
}
else if (tmp < -box_l[i]/2.) {
//printf("smaller than box_l/2 %f\n",tmp);
p->r.p[i] =new_pos[i] - box_l[i];
}
else p->r.p[i] =new_pos[i];
}
#ifdef PARTIAL_PERIODIC
else p->r.p[i] =new_pos[i];
#endif
// fold_coordinate(p->r.p,p->l.i,i);
}
}
/// Calculate angle that p1--p2 makes with wall constraint
static double calc_pwangle(Particle *p1, Particle *p2, Bonded_ia_parameters *iaparams, int *constr)
{
int j;
double dist,di,cosine,phi;
double vec[3];
/* vector from p1 to p2 */
get_mi_vector(vec, p2->r.p, p1->r.p);
dist = sqrlen(vec);
di = 1.0/sqrt(dist);
for(j=0;j<3;j++) vec[j] *= di;
/*
fprintf(stdout,"Normalised: p1= %9.6f %9.6f %9.6f p1= %9.6f %9.6f %9.6f vec= %9.6f %9.6f %9.6f\n",p1->r.p[0],p1->r.p[1],p1->r.p[2],p2->r.p[0],p2->r.p[1],p2->r.p[2],vec[0],vec[1],vec[2]);
*/
/* vectors are normalised so cosine is just cos(angle_between_vec1_and_vec2)
* Wall is closest wall to particle
*/
cosine = scalar(vec, constraints[*constr].c.wal.n);
if ( cosine > TINY_COS_VALUE) cosine = TINY_COS_VALUE;
if ( cosine < -TINY_COS_VALUE) cosine = -TINY_COS_VALUE;
phi=acos(cosine);
/*
fprintf(stdout,"Angle with wall 0=%f ",(acos(scalar(vec, constraints[0].c.wal.n)))*180.0/PI);
fprintf(stdout,"Angle with wall 1=%f ",(acos(scalar(vec, constraints[1].c.wal.n)))*180.0/PI);
fprintf(stdout,"dxy=%f dz=%f angle=%f\n",sqrt(vec[0]*vec[0]+vec[1]*vec[1]),vec[2],atan(sqrt(vec[0]*vec[0]+vec[1]*vec[1])/vec[2])*180.0/PI);
fprintf(stdout,"Angle with closest wall %d=%f ",*constr,(acos(scalar(vec, constraints[*constr].c.wal.n)))*180.0/PI);
*/
return phi;
}
int angledist_energy(Particle *p_mid, Particle *p_left, Particle *p_right,
Bonded_ia_parameters *iaparams, double *_energy)
{
int j;
double cosine=0.0, d1i, d2i, dist1, dist2;
double vec1[3], vec2[3];
// if (phi0 < PI) {
// fprintf(stdout,"\nIn angledist_energy: z_p_mid=%f, phi0=%f\n",p_mid->r.p[2],phi0*180.0/PI);
// }
/* vector from p_mid to p_left */
get_mi_vector(vec1, p_mid->r.p, p_left->r.p);
dist1 = sqrlen(vec1);
d1i = 1.0 / sqrt(dist1);
for(j=0;j<3;j++) vec1[j] *= d1i;
/* vector from p_right to p_mid */
get_mi_vector(vec2, p_right->r.p, p_mid->r.p);
dist2 = sqrlen(vec2);
d2i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec2[j] *= d2i;
/* scalar produvt of vec1 and vec2 */
cosine = scalar(vec1, vec2);
if ( cosine > TINY_COS_VALUE) cosine = TINY_COS_VALUE;
if ( cosine < -TINY_COS_VALUE) cosine = -TINY_COS_VALUE;
#ifdef BOND_ANGLEDIST_HARMONIC
{
double phi;
double phi0=calc_angledist_param(p_mid, p_left, p_right, iaparams);
phi = acos(-cosine);
*_energy = 0.5*iaparams->p.angledist.bend*SQR(phi - phi0);
// fprintf(stdout,"\n energy: z_pmid=%f bend=%f phi0=%f phi=%f energy=%f",p_mid->r.p[2],iaparams->p.angledist.bend,phi0*180.0/PI,phi*180.0/PI,0.5*iaparams->p.angledist.bend*SQR(phi - phi0));
}
#endif
#ifdef BOND_ANGLEDIST_COSINE
#error angledist ONLY implemented for harmonic case!
#endif
#ifdef BOND_ANGLEDIST_COSSQUARE
#error angledist ONLY implemented for harmonic case!
#endif
return 0;
}
/** calculates unit vector */
inline void unit_vector(double v[3],double y[3]) {
double d = 0.0;
int i;
d=sqrt( sqrlen(v) );
for(i=0;i<3;i++)
y[i] = v[i]/d;
return;
}
/**Compute positional corrections*/
void compute_pos_corr_vec(int *repeat_)
{
Bonded_ia_parameters *ia_params;
int i, j, k, c, np, cnt=-1;
Cell *cell;
Particle *p, *p1, *p2;
double r_ij_t[3], r_ij[3], r_ij_dot, G, pos_corr, r_ij2;
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
p1 = &p[i];
k=0;
while(k<p1->bl.n) {
ia_params = &bonded_ia_params[p1->bl.e[k++]];
if( ia_params->type == BONDED_IA_RIGID_BOND ) {
cnt++;
p2 = local_particles[p1->bl.e[k++]];
if (!p2) {
char *errtxt = runtime_error(128 + 2*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"{051 rigid bond broken between particles %d and %d (particles not stored on the same node)} ",
p1->p.identity, p1->bl.e[k-1]);
return;
}
get_mi_vector(r_ij , p1->r.p , p2->r.p );
r_ij2 = sqrlen(r_ij);
if(fabs(1.0 - r_ij2/ia_params->p.rigid_bond.d2) > ia_params->p.rigid_bond.p_tol) {
get_mi_vector(r_ij_t, p1->r.p_old, p2->r.p_old);
r_ij_dot = scalar(r_ij_t, r_ij);
G = 0.50*(ia_params->p.rigid_bond.d2 - r_ij2 )/r_ij_dot;
#ifdef MASS
G /= (PMASS(*p1)+PMASS(*p2));
#else
G /= 2;
#endif
for (j=0;j<3;j++) {
pos_corr = G*r_ij_t[j];
p1->f.f[j] += pos_corr*PMASS(*p2);
p2->f.f[j] -= pos_corr*PMASS(*p1);
}
/*Increase the 'repeat' flag by one */
*repeat_ = *repeat_ + 1;
}
}
else
/* skip bond partners of nonrigid bond */
k+=ia_params->num;
} //while loop
} //for i loop
} //for c loop
}
/** Computes the HARMONIC pair force and adds this
force to the particle forces (see \ref interaction_data.cpp).
@param p1 Pointer to first particle.
@param p2 Pointer to second/middle particle.
@param iaparams bond type number of the angle interaction (see \ref interaction_data.cpp).
@param dx particle distance vector
@param force returns force of particle 1
@return 0.
*/
inline int calc_harmonic_pair_force(Particle *p1, Particle *p2, Bonded_ia_parameters *iaparams, double dx[3], double force[3])
{
int i;
double fac;
double dist2 = sqrlen(dx);
double dist = sqrt(dist2);
double dr;
if ((iaparams->p.harmonic.r_cut > 0.0) &&
(dist > iaparams->p.harmonic.r_cut))
return 1;
dr = dist - iaparams->p.harmonic.r;
fac = -iaparams->p.harmonic.k * dr;
if (fabs(dr) > ROUND_ERROR_PREC) {
if(dist>ROUND_ERROR_PREC) { /* Regular case */
fac /= dist;
} else { /* dx[] == 0: the force is undefined. Let's use a random direction */
for(i=0;i<3;i++) dx[i] = d_random()-0.5;
fac /= sqrt(sqrlen(dx));
}
} else {
fac=0;
}
for(i=0;i<3;i++)
force[i] = fac*dx[i];
ONEPART_TRACE(if(p1->p.identity==check_id) fprintf(stderr,"%d: OPT: HARMONIC f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac %.3e\n",this_node,p1->f.f[0],p1->f.f[1],p1->f.f[2],p2->p.identity,dist2,fac));
ONEPART_TRACE(if(p2->p.identity==check_id) fprintf(stderr,"%d: OPT: HARMONIC f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac %.3e\n",this_node,p2->f.f[0],p2->f.f[1],p2->f.f[2],p1->p.identity,dist2,fac));
#ifdef CONFIGTEMP
extern double configtemp[2];
int numfac = 0;
if (p1->p.configtemp) numfac+=1;
if (p2->p.configtemp) numfac+=1;
configtemp[0] += numfac*SQR(iaparams->p.harmonic.k * dr);
configtemp[1] -= numfac*iaparams->p.harmonic.k*(3-2.*iaparams->p.harmonic.r/dist);
#endif
return 0;
}
/** Computes the three body overlapped angle interaction energy (see \ref tclcommand_inter, \ref tclcommand_analyze).
@param p_mid Pointer to first particle.
@param p_left Pointer to second/middle particle.
@param p_right Pointer to third particle.
@param iaparams bond type number of the angle interaction (see \ref tclcommand_inter).
@param _energy return energy pointer.
@return 0.
Needs feature OVERLAPPED compiled in (see \ref config.hpp).
*/
inline int overlap_angle_energy(Particle *p_mid, Particle *p_left,
Particle *p_right, Bonded_ia_parameters *iaparams,
double *_energy)
{
double cosine, vec1[3], vec2[3], d1i, d2i, dist2;
int j;
int ig;
double ev;
double prob=0.;
cosine=0.0;
/* vector from p_mid to p_left */
get_mi_vector(vec1, p_mid->r.p, p_left->r.p);
dist2 = sqrlen(vec1);
d1i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec1[j] *= d1i;
/* vector from p_right to p_mid */
get_mi_vector(vec2, p_right->r.p, p_mid->r.p);
dist2 = sqrlen(vec2);
d2i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec2[j] *= d2i;
/* scalar produvt of vec1 and vec2 */
/* Notice: cosine = - costheta */
cosine = scalar(vec1, vec2);
if ( cosine > TINY_COS_VALUE) cosine = TINY_COS_VALUE;
if ( cosine < -TINY_COS_VALUE) cosine = -TINY_COS_VALUE;
/* compute overlapped cosangl energy */
/*prob = sum_(i=1,N) [ a_i * exp(-(costheta -b_i)^2/c_i^2))] */
/*pot = -1.0 * Log { prob } */
for(ig=0; ig<iaparams->p.overlap.noverlaps; ig++) {
ev = (-cosine - iaparams->p.overlap.para_b[ig]) / iaparams->p.overlap.para_c[ig];
prob = prob + iaparams->p.overlap.para_a[ig] * exp (-1.0*ev*ev);
}
*_energy = - log (prob);
return 0;
}
inline int harmonic_pair_energy(Particle *p1, Particle *p2, Bonded_ia_parameters *iaparams, double dx[3], double *_energy)
{
double dist2 = sqrlen(dx);
double dist = sqrt(dist2);
if ((iaparams->p.harmonic.r_cut > 0.0) &&
(dist > iaparams->p.harmonic.r_cut))
return 1;
*_energy = 0.5*iaparams->p.harmonic.k*SQR(dist - iaparams->p.harmonic.r);
return 0;
}
/** Computes the negative of the LENNARD-JONES pair forces
and adds this force to the particle forces (see \ref tclcommand_inter).
@param p1 Pointer to first particle.
@param p2 Pointer to second/middle particle.
@param iaparams Parameters of interaction
@param dx change in position
@param force force on particles
@return true if bond is broken
*/
inline int calc_subt_lj_pair_force(Particle *p1, Particle *p2, Bonded_ia_parameters *iaparams, double dx[3], double force[3])
{
int i;
double fac_lj=0.0;
IA_parameters *ia_params;
double r_off, frac2, frac6;
double dist2 = sqrlen(dx);
double dist = sqrt(dist2);
if(dist >= iaparams->p.subt_lj.r)
return 1;
ia_params = get_ia_param(p1->p.type,p2->p.type);
if(dist < ia_params->LJ_cut+ia_params->LJ_offset) {
r_off = dist - ia_params->LJ_offset;
if(r_off > ia_params->LJ_capradius) {
/* normal case: resulting force/energy smaller than capping. */
frac2 = SQR(ia_params->LJ_sig/r_off);
frac6 = frac2*frac2*frac2;
fac_lj = 48.0 * ia_params->LJ_eps * frac6*(frac6 - 0.5) / (r_off * dist);
}
else if(dist > 0.0) {
/* capped part of lj potential. */
frac2 = SQR(ia_params->LJ_sig/ia_params->LJ_capradius);
frac6 = frac2*frac2*frac2;
fac_lj = 48.0 * ia_params->LJ_eps * frac6*(frac6 - 0.5) / (ia_params->LJ_capradius * dist);
// #ifdef CONFIGTEMP
// extern double configtemp[2];
// int numfac = 0;
// if (p1->p.configtemp) numfac+=1;
// if (p2->p.configtemp) numfac+=1;
// configtemp[0] -= numfac*SQR(48.0 * ia_params->LJ_eps * frac6*(frac6 - 0.5) / r_off);
// configtemp[1] -= numfac*24.0 * ia_params->LJ_eps * frac6*(-22.0*frac6+5.0) / (SQR(r_off));
// #endif
}
}
for(i=0;i<3;i++)
force[i] = -fac_lj*dx[i];
ONEPART_TRACE(if(p1->p.identity==check_id) fprintf(stderr,"%d: OPT: SUBT_LJ f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac_lj %.3e\n",this_node,p1->f.f[0],p1->f.f[1],p1->f.f[2],p2->p.identity,sqrt(dist2),fac_lj));
ONEPART_TRACE(if(p2->p.identity==check_id) fprintf(stderr,"%d: OPT: SUBT_LJ f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac_lj %.3e\n",this_node,p2->f.f[0],p2->f.f[1],p2->f.f[2],p1->p.identity,sqrt(dist2),fac_lj));
return 0;
}
/** Computes the three body angle interaction energy (see \ref tclcommand_inter, \ref tclcommand_analyze).
@param p_mid Pointer to first particle.
@param p_left Pointer to second/middle particle.
@param p_right Pointer to third particle.
@param iaparams bond type number of the angle interaction (see \ref tclcommand_inter).
@param _energy return energy pointer.
@return 0.
*/
inline int angle_energy(Particle *p_mid, Particle *p_left, Particle *p_right,
Bonded_ia_parameters *iaparams, double *_energy)
{
double cosine, vec1[3], vec2[3], d1i, d2i, dist2;
int j;
cosine=0.0;
/* vector from p_mid to p_left */
get_mi_vector(vec1, p_mid->r.p, p_left->r.p);
dist2 = sqrlen(vec1);
d1i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec1[j] *= d1i;
/* vector from p_right to p_mid */
get_mi_vector(vec2, p_right->r.p, p_mid->r.p);
dist2 = sqrlen(vec2);
d2i = 1.0 / sqrt(dist2);
for(j=0;j<3;j++) vec2[j] *= d2i;
/* scalar produvt of vec1 and vec2 */
cosine = scalar(vec1, vec2);
if ( cosine > TINY_COS_VALUE) cosine = TINY_COS_VALUE;
if ( cosine < -TINY_COS_VALUE) cosine = -TINY_COS_VALUE;
/* bond angle energy */
#ifdef BOND_ANGLE_HARMONIC
{
double phi;
phi = acos(-cosine);
*_energy = 0.5*iaparams->p.angle.bend*SQR(phi - iaparams->p.angle.phi0);
}
#endif
#ifdef BOND_ANGLE_COSINE
*_energy = iaparams->p.angle.bend*(cosine*iaparams->p.angle.cos_phi0 - sqrt(1-SQR(cosine))*iaparams->p.angle.sin_phi0+1);
#endif
#ifdef BOND_ANGLE_COSSQUARE
*_energy = 0.5*iaparams->p.angle.bend*SQR(cosine + iaparams->p.angle.cos_phi0);
#endif
return 0;
}
/** Rotate the particle p around the NORMALIZED axis aSpaceFrame by amount phi */
void rotate_particle(Particle* p, double* aSpaceFrame, double phi)
{
// Convert rotation axis to body-fixed frame
double a[3];
convert_vec_space_to_body(p,aSpaceFrame,a);
// Apply restrictions from the rotation_per_particle feature
#ifdef ROTATION_PER_PARTICLE
// printf("%g %g %g - ",a[0],a[1],a[2]);
// Rotation turned off entirely?
if (p->p.rotation <2) return;
// Per coordinate fixing
if (!(p->p.rotation & 2)) a[0]=0;
if (!(p->p.rotation & 4)) a[1]=0;
if (!(p->p.rotation & 8)) a[2]=0;
// Re-normalize rotation axis
double l=sqrt(sqrlen(a));
// Check, if the rotation axis is nonzero
if (l<1E-10) return;
for (int i=0;i<3;i++)
a[i]/=l;
// printf("%g %g %g\n",a[0],a[1],a[2]);
#endif
double q[4];
q[0]=cos(phi/2);
double tmp=sin(phi/2);
q[1]=tmp*a[0];
q[2]=tmp*a[1];
q[3]=tmp*a[2];
// Normalize
normalize_quaternion(q);
// Rotate the particle
double qn[4]; // Resulting quaternion
multiply_quaternions(p->r.quat,q,qn);
for (int k=0; k<4; k++)
p->r.quat[k]=qn[k];
convert_quat_to_quatu(p->r.quat, p->r.quatu);
#ifdef DIPOLES
// When dipoles are enabled, update dipole moment
convert_quatu_to_dip(p->r.quatu, p->p.dipm, p->r.dip);
#endif
}
/* TODO: this function is not used anywhere. To be removed? */
double calc_mol_hydro_radius(Molecule mol)
{
int i, j, id1, id2;
double rh=0.0, diff_vec[3];
for(i=0; i<mol.part.n; i++) {
id1 = mol.part.e[i];
for(j=i+1; j<mol.part.n; j++) {
id2 = mol.part.e[i];
vecsub(partCfg[id1].r.p, partCfg[id2].r.p, diff_vec);
rh += 1.0/sqrt(sqrlen(diff_vec));
}
}
return 0.5*(mol.part.n*(mol.part.n-1))/rh;
}
