// 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);
}
}
// Distribute forces that have accumulated on virtual particles to the
// associated real particles
void distribute_mol_force()
{
// Iterate over all the particles in the local cells
Particle *p;
int i, np, c;
Cell *cell;
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++) {
// We only care about virtual particles
if (ifParticleIsVirtual(&p[i])) {
update_mol_pos_particle(&p[i]);
// First obtain the real particle responsible for this virtual particle:
Particle *p_real = vs_relative_get_real_particle(&p[i]);
// Get distance vector pointing from real to virtual particle, respecting periodic boundary i
// conditions
double d[3];
get_mi_vector(d,p[i].r.p,p_real->r.p);
// The rules for transfering forces are:
// F_realParticle +=F_virtualParticle
// T_realParticle +=f_realParticle \times (r_virtualParticle-r_realParticle)
// Calculate torque to be added on real particle
double tmp[3];
vector_product(d,p[i].f.f,tmp);
// Add forces and torques
int j;
// printf("Particle %d gets torque from %f %f %f of particle %d\n",p_real->p.identity, p[i].f.f[0], p[i].f.f[1],p[i].f.f[2], p[i].p.identity);
for (j=0;j<3;j++) {
p_real->f.torque[j]+=tmp[j];
// printf("%f ",tmp[j]);
p_real->f.f[j]+=p[i].f.f[j];
// Clear forces on virtual particle
p[i].f.f[j]=0;
}
}
}
}
}
// Update the vel of the given virtual particle as defined by the real
// particles in the same molecule
void update_mol_vel_particle(Particle *p)
{
// NOT TESTED!
// First obtain the real particle responsible for this virtual particle:
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
// Get omega of real particle in space-fixed frame
double omega_space_frame[3];
convert_omega_body_to_space(p_real,omega_space_frame);
// Obtain velocity from v=v_real particle + omega_real_particle \times director
vector_product(omega_space_frame,director,p->m.v);
int i;
// Add prefactors and add velocity of real particle
for (i=0;i<3;i++)
{
// Scale the velocity by the distance of virtual particle from the real particle
// Also, espresso stores not velocity but velocity * time_step
p->m.v[i] *= time_step * p->p.vs_relative_distance/l;
// Add velocity of real particle
p->m.v[i] += p_real->m.v[i];
}
}
// Rigid body conribution to scalar pressure and stress tensor
void vs_relative_pressure_and_stress_tensor(double* pressure, double* stress_tensor)
{
// Division by 3 volume is somewhere else. (pressure.cpp after all presure calculations)
// Iterate over all the particles in the local cells
Particle *p;
int i, np, c;
Cell *cell;
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++) {
// We only care about virtual particles
if (!ifParticleIsVirtual(&p[i]))
continue;
update_mol_pos_particle(&p[i]);
// First obtain the real particle responsible for this virtual particle:
Particle *p_real = vs_relative_get_real_particle(&p[i]);
// Get distance vector pointing from real to virtual particle, respecting periodic boundary i
// conditions
double d[3];
get_mi_vector(d,p_real->r.p,p[i].r.p);
// Stress tensor conribution
for (int k =0; k<3;k++)
for (int l =0;l<3;l++)
stress_tensor[k*3+l] +=p[i].f.f[k] *d[l];
// Pressure = 1/3 trace of stress tensor
// but the 1/3 is applied somewhere else.
*pressure +=(p[i].f.f[0] *d[0] +p[i].f.f[1] *d[1] +p[i].f.f[2] *d[2]);
}
}
*pressure/=0.5*time_step*time_step;
for (i=0;i<9;i++)
stress_tensor[i]/=0.5*time_step*time_step;
}
