/** Calculate lj-cos2 force between particle p1 and p2 */
inline void add_ljcos2_pair_force(const Particle * const p1, const Particle * const p2, IA_parameters *ia_params,
double d[3], double dist, double force[3])
{
int j;
double r_off, frac2, frac6, fac=0.0;
if(CUTOFF_CHECK(dist < ia_params->LJCOS2_cut+ia_params->LJCOS2_offset)) {
r_off = dist - ia_params->LJCOS2_offset;
/* normal case: resulting force/energy smaller than capping. */
if(r_off > ia_params->LJCOS2_capradius) {
if(r_off < ia_params->LJCOS2_rchange) {
frac2 = SQR(ia_params->LJCOS2_sig/r_off);
frac6 = frac2*frac2*frac2;
fac = 48.0 * ia_params->LJCOS2_eps * frac6*(frac6 - 0.5) / (r_off*dist);
}
else if (r_off< ia_params->LJCOS2_rchange + ia_params->LJCOS2_w) {
fac = -ia_params->LJCOS2_eps*M_PI/2/ia_params->LJCOS2_w/dist * sin(M_PI*(r_off-ia_params->LJCOS2_rchange)/ia_params->LJCOS2_w);
}
for(j=0; j<3; j++)
force[j] += fac * d[j];
#ifdef LJ_WARN_WHEN_CLOSE
if(fac*dist > 1000) fprintf(stderr,"%d: LJ-Warning: Pair (%d-%d) force=%f dist=%f\n",
this_node,p1->p.identity,p2->p.identity,fac*dist,dist);
#endif
}
/* capped part of lj-cos2 potential. */
else if(dist > 0.0) {
frac2 = SQR(ia_params->LJCOS2_sig/ia_params->LJCOS2_capradius);
frac6 = frac2*frac2*frac2;
fac = 48.0 * ia_params->LJCOS2_eps * frac6*(frac6 - 0.5) / (ia_params->LJCOS2_capradius * dist);
for(j=0; j<3; j++)
/* vector d is rescaled to length LJCOS2_capradius */
force[j] += fac * d[j];
}
/* this should not happen! */
else {
LJ_TRACE(fprintf(stderr, "%d: Lennard-Jones warning: Particles id1=%d id2=%d exactly on top of each other\n",this_node,p1->p.identity,p2->p.identity));
frac2 = SQR(ia_params->LJCOS2_sig/ia_params->LJCOS2_capradius);
frac6 = frac2*frac2*frac2;
fac = 48.0 * ia_params->LJCOS2_eps * frac6*(frac6 - 0.5) / ia_params->LJCOS2_capradius;
force[0] += fac * ia_params->LJCOS2_capradius;
}
ONEPART_TRACE(if(p1->p.identity==check_id) fprintf(stderr,"%d: OPT: LJ 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,dist,fac));
ONEPART_TRACE(if(p2->p.identity==check_id) fprintf(stderr,"%d: OPT: LJ 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,dist,fac));
LJ_TRACE(fprintf(stderr,"%d: LJ: Pair (%d-%d) dist=%.3f: force+-: (%.3e,%.3e,%.3e)\n",
this_node,p1->p.identity,p2->p.identity,dist,fac*d[0],fac*d[1],fac*d[2]));
}
inline void add_ljcos_pair_force(const Particle * const p1, const Particle * const p2, IA_parameters *ia_params,
double d[3], double dist, double force[3])
{
int j;
double r_off, frac2, frac6, fac=0.0;
if(CUTOFF_CHECK(dist < ia_params->LJCOS_cut+ia_params->LJCOS_offset)) {
r_off = dist - ia_params->LJCOS_offset;
/* cos part of ljcos potential. */
if(dist > ia_params->LJCOS_rmin+ia_params->LJCOS_offset) {
fac = (r_off/dist) * ia_params->LJCOS_alfa * ia_params->LJCOS_eps * (sin(ia_params->LJCOS_alfa * SQR(r_off) + ia_params->LJCOS_beta));
for(j=0;j<3;j++)
force[j] += fac * d[j];
}
/* lennard-jones part of the potential. */
else if(dist > 0) {
frac2 = SQR(ia_params->LJCOS_sig/r_off);
frac6 = frac2*frac2*frac2;
fac = 48.0 * ia_params->LJCOS_eps * frac6*(frac6 - 0.5) / (r_off * dist);
for(j=0;j<3;j++)
force[j] += fac * d[j];
#ifdef LJ_WARN_WHEN_CLOSE
if(fac*dist > 1000) fprintf(stderr,"%d: LJCOS-Warning: Pair (%d-%d) force=%f dist=%f\n",
this_node,p1->p.identity,p2->p.identity,fac*dist,dist);
#endif
}
/* this should not happen! */
else {
LJ_TRACE(fprintf(stderr, "%d: Lennard-Jones warning: Particles id1=%d id2=%d exactly on top of each other\n",this_node,p1->p.identity,p2->p.identity));
frac2 = SQR(ia_params->LJ_sig/ia_params->LJ_capradius);
frac6 = frac2*frac2*frac2;
fac = 48.0 * ia_params->LJ_eps * frac6*(frac6 - 0.5) / ia_params->LJ_capradius;
force[0] += fac * ia_params->LJ_capradius;
}
ONEPART_TRACE(if(p1->p.identity==check_id) fprintf(stderr,"%d: OPT: LJ 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,dist,fac));
ONEPART_TRACE(if(p2->p.identity==check_id) fprintf(stderr,"%d: OPT: LJ 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,dist,fac));
LJ_TRACE(fprintf(stderr,"%d: LJ: Pair (%d-%d) dist=%.3f: force+-: (%.3e,%.3e,%.3e)\n",
this_node,p1->p.identity,p2->p.identity,dist,fac*d[0],fac*d[1],fac*d[2]));
}
/** Calculate lennard Jones force between particle p1 and p2 */
inline void add_ljgen_pair_force(Particle *p1, Particle *p2, IA_parameters *ia_params,
double d[3], double dist, double force[3])
{
if (CUTOFF_CHECK(dist < ia_params->LJGEN_cut+ia_params->LJGEN_offset)) {
int j;
double r_off, frac, fac=0.0;
r_off = dist - ia_params->LJGEN_offset;
#ifdef LJGEN_SOFTCORE
r_off *= r_off;
r_off += pow(ia_params->LJGEN_sig,2) * (1.0-ia_params->LJGEN_lambda)
* ia_params->LJGEN_softrad;
/* Taking a square root is not optimal, but we can't prevent the user from
using an odd m, n coefficient. */
r_off = sqrt(r_off);
#endif
/* normal case: resulting force/energy smaller than capping. */
if(r_off > ia_params->LJGEN_capradius) {
frac = ia_params->LJGEN_sig/r_off;
fac = ia_params->LJGEN_eps
#ifdef LJGEN_SOFTCORE
* ia_params->LJGEN_lambda
#endif
* (ia_params->LJGEN_b1 * ia_params->LJGEN_a1 * pow(frac, ia_params->LJGEN_a1)
- ia_params->LJGEN_b2 * ia_params->LJGEN_a2 * pow(frac, ia_params->LJGEN_a2))
/ (r_off * dist);
for(j=0;j<3;j++)
force[j] += fac * d[j];
#ifdef LJ_WARN_WHEN_CLOSE
if(fac*dist > 1000) fprintf(stderr,"%d: LJ-Gen-Warning: Pair (%d-%d) force=%f dist=%f\n",
this_node,p1->p.identity,p2->p.identity,fac*dist,dist);
#endif
}
/* capped part of lj potential. */
else if(dist > 0.0) {
frac = ia_params->LJGEN_sig/ia_params->LJGEN_capradius;
fac = ia_params->LJGEN_eps
* (ia_params->LJGEN_b1 * ia_params->LJGEN_a1 * pow(frac, ia_params->LJGEN_a1)
- ia_params->LJGEN_b2 * ia_params->LJGEN_a2 * pow(frac, ia_params->LJGEN_a2))
/ (ia_params->LJGEN_capradius * dist);
for(j=0;j<3;j++)
/* vector d is rescaled to length LJGEN_capradius */
force[j] += fac * d[j];
}
/* this should not happen! */
else {
LJ_TRACE(fprintf(stderr, "%d: Lennard-Jones-Generic warning: Particles id1=%d id2=%d exactly on top of each other\n",this_node,p1->p.identity,p2->p.identity));
frac = ia_params->LJGEN_sig/ia_params->LJGEN_capradius;
fac = ia_params->LJGEN_eps
#ifdef LJGEN_SOFTCORE
* ia_params->LJGEN_lambda
#endif
* (ia_params->LJGEN_b1 * ia_params->LJGEN_a1 * pow(frac, ia_params->LJGEN_a1)
- ia_params->LJGEN_b2 * ia_params->LJGEN_a2 * pow(frac, ia_params->LJGEN_a2))
/ ia_params->LJGEN_capradius;
force[0] += fac * ia_params->LJGEN_capradius;
}
ONEPART_TRACE(if(p1->p.identity==check_id) fprintf(stderr,"%d: OPT: LJGEN 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,dist,fac));
ONEPART_TRACE(if(p2->p.identity==check_id) fprintf(stderr,"%d: OPT: LJGEN 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,dist,fac));
LJ_TRACE(fprintf(stderr,"%d: LJGEN: Pair (%d-%d) dist=%.3f: force+-: (%.3e,%.3e,%.3e)\n",
this_node,p1->p.identity,p2->p.identity,dist,fac*d[0],fac*d[1],fac*d[2]));
}
/** Calculate lj-angle force between particle p1 and p2
Involves 6 particles total */
inline void add_ljangle_force(Particle *p1, Particle *p2, IA_parameters *ia_params,
double d[3], double dist)
{
if(!CUTOFF_CHECK(dist < ia_params->LJANGLE_cut))
return;
int j;
double frac2=0.0, frac10=0.0, rad=0.0, radprime=0.0;
double r31[3], r41[3], r52[3], r62[3], rij[3], rik[3], rkn[3];
double l_rij, l_rik, l_rkn, l_rij2, l_rik2, l_rkn2;
double cos_jik, cos_ikn;
double angular_jik, angular_ikn, angular_jik_prime, angular_ikn_prime;
/* Recreate angular dependence of potential by including 6 particles instead of 2. */
Particle *p3=NULL, *p4=NULL, *p5=NULL, *p6=NULL;
int part1p, part1n, part2p, part2n;
/* Optional 2nd environment */
double effective_eps=ia_params->LJANGLE_eps, z1, z2, z_middle, z_ref, z_ref5,
localz0=ia_params->LJANGLE_z0, localdz2=ia_params->LJANGLE_dz/2.,
localkappa6=pow(1/ia_params->LJANGLE_kappa,6);
/* Retrieve the bonded partners from parsing */
if (ia_params->LJANGLE_bonded1type == p1->p.type) {
part1p = p1->p.identity + ia_params->LJANGLE_bonded1pos;
part1n = p1->p.identity + ia_params->LJANGLE_bonded1neg;
part2p = p2->p.identity + ia_params->LJANGLE_bonded2pos;
part2n = p2->p.identity + ia_params->LJANGLE_bonded2neg;
} else {
part1p = p1->p.identity + ia_params->LJANGLE_bonded2pos;
part1n = p1->p.identity + ia_params->LJANGLE_bonded2neg;
part2p = p2->p.identity + ia_params->LJANGLE_bonded1pos;
part2n = p2->p.identity + ia_params->LJANGLE_bonded1neg;
}
if (part1p >= 0 && part1p < n_part &&
part1n >= 0 && part1n < n_part &&
part2p >= 0 && part2p < n_part &&
part2n >= 0 && part2n < n_part ) {
p3 = local_particles[part1p];
p4 = local_particles[part1n];
p5 = local_particles[part2p];
p6 = local_particles[part2n];
/* Check whether pointers have been allocated.
* Otherwise, there's a communication error (verlet skin too small).
*/
if (p3==NULL ||p4==NULL ||p5==NULL ||p6==NULL)
fprintf(stderr, "LJANGLE - Communication error, all particles cannot be reached locally.\n");
get_mi_vector(r31, p1->r.p, p3->r.p);
get_mi_vector(r41, p1->r.p, p4->r.p);
get_mi_vector(r52, p2->r.p, p5->r.p);
get_mi_vector(r62, p2->r.p, p6->r.p);
/* Bead i represents the central particle of monomer 1.
* Bead j is the virtual particle that gives the orientation of monomer 1.
* Bead k represents the central particle of monomer 2.
* Bead n is the virtual particle that gives the orientation of monomer 2.
*/
for(j=0; j<3; ++j) {
rij[j] = r31[j] + r41[j];
rik[j] = -d[j]; /* At this point, rik[3] has length dist */
rkn[j] = r52[j] + r62[j];
}
l_rij2 = sqrlen(rij);
l_rik2 = dist*dist;
l_rkn2 = sqrlen(rkn);
l_rij = sqrt(l_rij2);
l_rik = dist;
l_rkn = sqrt(l_rkn2);
cos_jik = scalar(rij,rik)/(l_rij*l_rik);
cos_ikn = -scalar(rik,rkn)/(l_rik*l_rkn);
if(cos_jik>0. && cos_ikn>0.) {
angular_jik = pow(cos_jik,2);
angular_ikn = pow(cos_ikn,2);
angular_jik_prime = -2*cos_jik;
angular_ikn_prime = -2*cos_ikn;
/* Optional 2nd environment */
if (localdz2 > 0.) {
/* calculate center position of the interaction (calculate minimal distance) */
z1 = p1->r.p[2];
z2 = p2->r.p[2];
z_middle = z1 + z2;
z_middle /= 2.;
if (PERIODIC(2))
if (z_middle > box_l[2] || z_middle < 0.)
z_middle -= dround(z_middle *box_l_i[2])*box_l[2];
/* If we're in the environment #2 region, calculate the new interaction strength */
if (z_middle > localz0 - localdz2 && z_middle <= localz0) {
z_ref = z_middle - localz0 + localdz2;
z_ref5 = pow(z_ref,5);
effective_eps += (ia_params->LJANGLE_epsprime - ia_params->LJANGLE_eps) *
localkappa6*z_ref5*fabs(z_ref) /
(1 + localkappa6*z_ref5*z_ref);
} else if (z_middle > localz0 && z_middle < localz0 + localdz2) {
z_ref = z_middle - localz0 - localdz2;
z_ref5 = pow(z_ref,5);
effective_eps -= (ia_params->LJANGLE_epsprime - ia_params->LJANGLE_eps) *
localkappa6*z_ref5*fabs(z_ref) /
(1 + localkappa6*z_ref5*z_ref);
}
}
/* normal case: resulting force/energy smaller than capping. */
if(dist > ia_params->LJANGLE_capradius) {
frac2 = SQR(ia_params->LJANGLE_sig/dist);
frac10 = frac2*frac2*frac2*frac2*frac2;
rad = effective_eps * frac10*(5.0 * frac2 - 6.0);
radprime = 60.0 * effective_eps * frac10*(1.0 - frac2) / dist;
#ifdef LJ_WARN_WHEN_CLOSE
if(radprime > 1000) fprintf(stderr,"%d: LJANGLE-Warning: Pair (%d-%d) force=%f dist=%f\n",
this_node,p1->p.identity,p2->p.identity,radprime,dist);
#endif
}
/* capped part of lj-angle potential. */
else if(dist > 0.0) {
/* set the length of rik to capradius */
for (j=0; j<3; ++j)
rik[j] *= ia_params->LJANGLE_capradius/dist;
l_rik = ia_params->LJANGLE_capradius;
frac2 = SQR(ia_params->LJANGLE_sig/ia_params->LJANGLE_capradius);
frac10 = frac2*frac2*frac2*frac2*frac2;
rad = effective_eps * frac10*(5.0 * frac2 - 6.0);
radprime = 60.0 * effective_eps * frac10*(1.0 - frac2) / (ia_params->LJANGLE_capradius);
}
/* Regroup the last two cases in one */
/* Propagate all forces in this function rather than in the forces.hpp file */
if (dist > 0.0) {
for(j=0; j<3; ++j) {
p1->f.f[j] += angular_jik * angular_ikn * rik[j]/l_rik *radprime
+ angular_ikn * rad * angular_jik_prime
* ( ( 2*rik[j]-rij[j] )/( l_rij*l_rik )
- cos_jik*( 2*rij[j]/l_rij2 - rik[j]/l_rik2 ) )
+ angular_jik * rad * angular_ikn_prime
* ( rkn[j]/( l_rik*l_rkn )
+ cos_ikn*rik[j]/l_rik2 );
p2->f.f[j] += -angular_jik * angular_ikn * rik[j]/l_rik *radprime
+ angular_ikn * rad * angular_jik_prime
* ( rij[j]/( l_rij*l_rik )
- cos_jik*rik[j]/l_rik2 )
+ angular_jik * rad * angular_ikn_prime
* ( -(2*rik[j]+rkn[j])/(l_rik*l_rkn)
- cos_ikn*( 2*rkn[j]/l_rkn2 + rik[j]/l_rik2 ) );
p3->f.f[j] += angular_ikn * rad * angular_jik_prime
* ( -rik[j]/(l_rij*l_rik)
+ cos_jik*rij[j]/l_rij2 );
p4->f.f[j] += angular_ikn * rad * angular_jik_prime
* ( -rik[j]/(l_rij*l_rik)
+ cos_jik*rij[j]/l_rij2 );
p5->f.f[j] += angular_jik * rad * angular_ikn_prime
* ( rik[j]/(l_rik*l_rkn)
+ cos_ikn*rkn[j]/l_rkn2 );
p6->f.f[j] += angular_jik * rad * angular_ikn_prime
* ( rik[j]/(l_rik*l_rkn)
+ cos_ikn*rkn[j]/l_rkn2 );
}
}
/* this should not happen! In this case consider only radial potential*/
else {
LJ_TRACE(fprintf(stderr, "%d: LJ-angle warning: Particles id1=%d id2=%d exactly on top of each other\n",this_node,p1->p.identity,p2->p.identity));
frac2 = SQR(ia_params->LJANGLE_sig/ia_params->LJANGLE_capradius);
frac10 = frac2*frac2*frac2*frac2*frac2;
rad = effective_eps * frac10*(5.0 * frac2 - 6.0) / ia_params->LJANGLE_capradius;
p1->f.f[0] += rad * ia_params->LJANGLE_capradius;
}
ONEPART_TRACE(if(p1->p.identity==check_id) fprintf(stderr,"%d: OPT: LJANGLE 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,dist,radprime));
ONEPART_TRACE(if(p2->p.identity==check_id) fprintf(stderr,"%d: OPT: LJANGLE 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,dist,radprime));
LJ_TRACE(fprintf(stderr,"%d: LJANGLE: Pair (%d-%d) dist=%.3f: force+-: (%.3e,%.3e,%.3e)\n",
this_node,p1->p.identity,p2->p.identity,dist,rad*d[0],rad*d[1],rad*d[2]));
}