int set_particle_torque_lab(int part, double torque_lab[3])
{
int pnode;
if (!particle_node)
build_particle_node();
if (part < 0 || part > max_seen_particle)
return ES_ERROR;
pnode = particle_node[part];
if (pnode == -1)
return ES_ERROR;
/* Internal functions require the body coordinates
so we need to convert to these from the lab frame */
double A[9];
double torque[3];
Particle particle;
get_particle_data(part, &particle);
define_rotation_matrix(&particle, A);
torque[0] = A[0 + 3*0]*torque_lab[0] + A[0 + 3*1]*torque_lab[1] + A[0 + 3*2]*torque_lab[2];
torque[1] = A[1 + 3*0]*torque_lab[0] + A[1 + 3*1]*torque_lab[1] + A[1 + 3*2]*torque_lab[2];
torque[2] = A[2 + 3*0]*torque_lab[0] + A[2 + 3*1]*torque_lab[1] + A[2 + 3*2]*torque_lab[2];
mpi_send_torque(pnode, part, torque);
return ES_OK;
}
void convert_vec_space_to_body(Particle *p, double *v,double* res)
{
double A[9];
define_rotation_matrix(p, A);
res[0] = A[0 + 3*0]*v[0] + A[0 + 3*1]*v[1] + A[0 + 3*2]*v[2];
res[1] = A[1 + 3*0]*v[0] + A[1 + 3*1]*v[1] + A[1 + 3*2]*v[2];
res[2] = A[2 + 3*0]*v[0] + A[2 + 3*1]*v[1] + A[2 + 3*2]*v[2];
}
void convert_vel_space_to_body(Particle *p, double *vel_body)
{
double A[9];
define_rotation_matrix(p, A);
vel_body[0] = A[0 + 3*0]*p->m.v[0] + A[0 + 3*1]*p->m.v[1] + A[0 + 3*2]*p->m.v[2];
vel_body[1] = A[1 + 3*0]*p->m.v[0] + A[1 + 3*1]*p->m.v[1] + A[1 + 3*2]*p->m.v[2];
vel_body[2] = A[2 + 3*0]*p->m.v[0] + A[2 + 3*1]*p->m.v[1] + A[2 + 3*2]*p->m.v[2];
}
void convert_torques_body_to_space(Particle *p, double *torque)
{
double A[9];
define_rotation_matrix(p, A);
torque[0] = A[0 + 3*0]*p->f.torque[0] + A[1 + 3*0]*p->f.torque[1] + A[2 + 3*0]*p->f.torque[2];
torque[1] = A[0 + 3*1]*p->f.torque[0] + A[1 + 3*1]*p->f.torque[1] + A[2 + 3*1]*p->f.torque[2];
torque[2] = A[0 + 3*2]*p->f.torque[0] + A[1 + 3*2]*p->f.torque[1] + A[2 + 3*2]*p->f.torque[2];
}
void convert_omega_body_to_space(Particle *p, double *omega)
{
double A[9];
define_rotation_matrix(p, A);
omega[0] = A[0 + 3*0]*p->m.omega[0] + A[1 + 3*0]*p->m.omega[1] + A[2 + 3*0]*p->m.omega[2];
omega[1] = A[0 + 3*1]*p->m.omega[0] + A[1 + 3*1]*p->m.omega[1] + A[2 + 3*1]*p->m.omega[2];
omega[2] = A[0 + 3*2]*p->m.omega[0] + A[1 + 3*2]*p->m.omega[1] + A[2 + 3*2]*p->m.omega[2];
}
/** convert the torques to the body-fixed frames before the integration loop */
void convert_initial_torques()
{
Particle *p;
Cell *cell;
int c,i, np;
double tx, ty, tz;
INTEG_TRACE(fprintf(stderr,"%d: convert_initial_torques:\n",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++) {
#ifdef ROTATION_PER_PARTICLE
if (!p[i].p.rotation)
continue;
#endif
double A[9];
define_rotation_matrix(&p[i], A);
tx = A[0 + 3*0]*p[i].f.torque[0] + A[0 + 3*1]*p[i].f.torque[1] + A[0 + 3*2]*p[i].f.torque[2];
ty = A[1 + 3*0]*p[i].f.torque[0] + A[1 + 3*1]*p[i].f.torque[1] + A[1 + 3*2]*p[i].f.torque[2];
tz = A[2 + 3*0]*p[i].f.torque[0] + A[2 + 3*1]*p[i].f.torque[1] + A[2 + 3*2]*p[i].f.torque[2];
if ( thermo_switch & THERMO_LANGEVIN ) {
friction_thermo_langevin_rotation(&p[i]);
p[i].f.torque[0]+= tx;
p[i].f.torque[1]+= ty;
p[i].f.torque[2]+= tz;
} else {
p[i].f.torque[0] = tx;
p[i].f.torque[1] = ty;
p[i].f.torque[2] = tz;
}
#ifdef ROTATION_PER_PARTICLE
if (!(p[i].p.rotation & 2))
p[i].f.torque[0]=0;
if (!(p[i].p.rotation & 4))
p[i].f.torque[1]=0;
if (!(p[i].p.rotation & 8))
p[i].f.torque[2]=0;
#endif
ONEPART_TRACE(if(p[i].p.identity==check_id) fprintf(stderr,"%d: OPT: SCAL f = (%.3e,%.3e,%.3e) v_old = (%.3e,%.3e,%.3e)\n",this_node,p[i].f.f[0],p[i].f.f[1],p[i].f.f[2],p[i].m.v[0],p[i].m.v[1],p[i].m.v[2]));
}
}
}
int observable_calc_particle_angular_momentum(observable* self) {
double* A = self->last_value;
IntList* ids;
if (!sortPartCfg()) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{094 could not sort partCfg} ");
return -1;
}
ids=(IntList*) self->container;
for ( int i = 0; i<ids->n; i++ ) {
if (ids->e[i] >= n_part)
return 1;
#ifdef ROTATION
double RMat[9];
double omega[3];
define_rotation_matrix(&partCfg[ids->e[i]], RMat);
omega[0] = RMat[0 + 3*0]*partCfg[ids->e[i]].m.omega[0] + RMat[1 + 3*0]*partCfg[ids->e[i]].m.omega[1] + RMat[2 + 3*0]*partCfg[ids->e[i]].m.omega[2];
omega[1] = RMat[0 + 3*1]*partCfg[ids->e[i]].m.omega[0] + RMat[1 + 3*1]*partCfg[ids->e[i]].m.omega[1] + RMat[2 + 3*1]*partCfg[ids->e[i]].m.omega[2];
omega[2] = RMat[0 + 3*2]*partCfg[ids->e[i]].m.omega[0] + RMat[1 + 3*2]*partCfg[ids->e[i]].m.omega[1] + RMat[2 + 3*2]*partCfg[ids->e[i]].m.omega[2];
A[3*i + 0] = omega[0];
A[3*i + 1] = omega[1];
A[3*i + 2] = omega[2];
#else
A[3*i + 0] = 0.0;
A[3*i + 1] = 0.0;
A[3*i + 2] = 0.0;
#endif
}
return 0;
}
/** convert the torques to the body-fixed frames and propagate angular velocities */
void convert_torques_propagate_omega()
{
Particle *p;
Cell *cell;
int c,i, np, times;
double dt2, tx, ty, tz;
dt2 = time_step*0.5;
INTEG_TRACE(fprintf(stderr,"%d: convert_torques_propagate_omega:\n",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++) {
double A[9];
define_rotation_matrix(&p[i], A);
tx = A[0 + 3*0]*p[i].f.torque[0] + A[0 + 3*1]*p[i].f.torque[1] + A[0 + 3*2]*p[i].f.torque[2];
ty = A[1 + 3*0]*p[i].f.torque[0] + A[1 + 3*1]*p[i].f.torque[1] + A[1 + 3*2]*p[i].f.torque[2];
tz = A[2 + 3*0]*p[i].f.torque[0] + A[2 + 3*1]*p[i].f.torque[1] + A[2 + 3*2]*p[i].f.torque[2];
if ( thermo_switch & THERMO_LANGEVIN ) {
#ifdef THERMOSTAT_IGNORE_NON_VIRTUAL
if (!ifParticleIsVirtual(&p[i]))
#endif
{
friction_thermo_langevin_rotation(&p[i]);
p[i].f.torque[0]+= tx;
p[i].f.torque[1]+= ty;
p[i].f.torque[2]+= tz;
}
} else {
p[i].f.torque[0] = tx;
p[i].f.torque[1] = ty;
p[i].f.torque[2] = tz;
}
ONEPART_TRACE(if(p[i].p.identity==check_id) fprintf(stderr,"%d: OPT: SCAL f = (%.3e,%.3e,%.3e) v_old = (%.3e,%.3e,%.3e)\n",this_node,p[i].f.f[0],p[i].f.f[1],p[i].f.f[2],p[i].m.v[0],p[i].m.v[1],p[i].m.v[2]));
#ifdef ROTATIONAL_INERTIA
p[i].m.omega[0]+= dt2*p[i].f.torque[0]/p[i].p.rinertia[0]/I[0];
p[i].m.omega[1]+= dt2*p[i].f.torque[1]/p[i].p.rinertia[1]/I[1];
p[i].m.omega[2]+= dt2*p[i].f.torque[2]/p[i].p.rinertia[2]/I[2];
#else
p[i].m.omega[0]+= dt2*p[i].f.torque[0]/I[0];
p[i].m.omega[1]+= dt2*p[i].f.torque[1]/I[1];
p[i].m.omega[2]+= dt2*p[i].f.torque[2]/I[2];
#endif
/* if the tensor of inertia is isotrpic, the following refinement is not needed.
Otherwise repeat this loop 2-3 times depending on the required accuracy */
for(times=0;times<=5;times++) {
double Wd[3];
#ifdef ROTATIONAL_INERTIA
Wd[0] = (p[i].m.omega[1]*p[i].m.omega[2]*(I[1]-I[2]))/I[0]/p[i].p.rinertia[0];
Wd[1] = (p[i].m.omega[2]*p[i].m.omega[0]*(I[2]-I[0]))/I[1]/p[i].p.rinertia[1];
Wd[2] = (p[i].m.omega[0]*p[i].m.omega[1]*(I[0]-I[1]))/I[2]/p[i].p.rinertia[2];
#else
Wd[0] = (p[i].m.omega[1]*p[i].m.omega[2]*(I[1]-I[2]))/I[0];
Wd[1] = (p[i].m.omega[2]*p[i].m.omega[0]*(I[2]-I[0]))/I[1];
Wd[2] = (p[i].m.omega[0]*p[i].m.omega[1]*(I[0]-I[1]))/I[2];
#endif
p[i].m.omega[0]+= dt2*Wd[0];
p[i].m.omega[1]+= dt2*Wd[1];
p[i].m.omega[2]+= dt2*Wd[2];
}
ONEPART_TRACE(if(p[i].p.identity==check_id) fprintf(stderr,"%d: OPT: PV_2 v_new = (%.3e,%.3e,%.3e)\n",this_node,p[i].m.v[0],p[i].m.v[1],p[i].m.v[2]));
}
}
}
/** convert the torques to the body-fixed frames and propagate angular velocities */
void convert_torques_propagate_omega()
{
Particle *p;
Cell *cell;
int np;
double tx, ty, tz;
INTEG_TRACE(fprintf(stderr,"%d: convert_torques_propagate_omega:\n",this_node));
#if defined(LB_GPU) && defined(ENGINE)
if (lattice_switch & LATTICE_LB_GPU) {
copy_v_cs_from_GPU();
}
#endif
for (int c = 0; c < local_cells.n; c++)
{
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
for(int i = 0; i < np; i++)
{
#ifdef ROTATION_PER_PARTICLE
if (!p[i].p.rotation)
continue;
#endif
double A[9];
define_rotation_matrix(&p[i], A);
tx = A[0 + 3*0]*p[i].f.torque[0] + A[0 + 3*1]*p[i].f.torque[1] + A[0 + 3*2]*p[i].f.torque[2];
ty = A[1 + 3*0]*p[i].f.torque[0] + A[1 + 3*1]*p[i].f.torque[1] + A[1 + 3*2]*p[i].f.torque[2];
tz = A[2 + 3*0]*p[i].f.torque[0] + A[2 + 3*1]*p[i].f.torque[1] + A[2 + 3*2]*p[i].f.torque[2];
if ( thermo_switch & THERMO_LANGEVIN )
{
#if defined (VIRTUAL_SITES) && defined(THERMOSTAT_IGNORE_NON_VIRTUAL)
if (!ifParticleIsVirtual(&p[i]))
#endif
{
friction_thermo_langevin_rotation(&p[i]);
p[i].f.torque[0]+= tx;
p[i].f.torque[1]+= ty;
p[i].f.torque[2]+= tz;
}
}
else
{
p[i].f.torque[0] = tx;
p[i].f.torque[1] = ty;
p[i].f.torque[2] = tz;
}
#ifdef ROTATION_PER_PARTICLE
if (!(p[i].p.rotation & 2))
p[i].f.torque[0]=0;
if (!(p[i].p.rotation & 4))
p[i].f.torque[1]=0;
if (!(p[i].p.rotation & 8))
p[i].f.torque[2]=0;
#endif
#if defined(ENGINE) && (defined(LB) || defined(LB_GPU))
double omega_swim[3] = {0, 0, 0};
double omega_swim_body[3] = {0, 0, 0};
if ( p[i].swim.swimming && lattice_switch != 0 )
{
double dip[3];
double diff[3];
double cross[3];
double l_diff, l_cross;
dip[0] = p[i].swim.dipole_length * p[i].r.quatu[0];
dip[1] = p[i].swim.dipole_length * p[i].r.quatu[1];
dip[2] = p[i].swim.dipole_length * p[i].r.quatu[2];
diff[0] = ( p[i].swim.v_center[0] - p[i].swim.v_source[0] );
diff[1] = ( p[i].swim.v_center[1] - p[i].swim.v_source[1] );
diff[2] = ( p[i].swim.v_center[2] - p[i].swim.v_source[2] );
cross[0] = diff[1]*dip[2] - diff[2]*dip[1];
cross[1] = diff[0]*dip[2] - diff[2]*dip[0];
cross[2] = diff[0]*dip[1] - diff[1]*dip[0];
l_diff = sqrt(diff[0]*diff[0] + diff[1]*diff[1] + diff[2]*diff[2]);
l_cross = sqrt(cross[0]*cross[0] + cross[1]*cross[1] + cross[2]*cross[2]);
if ( l_cross > 0 && p[i].swim.dipole_length > 0 )
{
omega_swim[0] = l_diff * cross[0] / ( l_cross * p[i].swim.dipole_length );
omega_swim[1] = l_diff * cross[1] / ( l_cross * p[i].swim.dipole_length );
omega_swim[2] = l_diff * cross[2] / ( l_cross * p[i].swim.dipole_length );
omega_swim_body[0] = A[0 + 3*0]*omega_swim[0] + A[0 + 3*1]*omega_swim[1] + A[0 + 3*2]*omega_swim[2];
omega_swim_body[1] = A[1 + 3*0]*omega_swim[0] + A[1 + 3*1]*omega_swim[1] + A[1 + 3*2]*omega_swim[2];
omega_swim_body[2] = A[2 + 3*0]*omega_swim[0] + A[2 + 3*1]*omega_swim[1] + A[2 + 3*2]*omega_swim[2];
p[i].f.torque[0] += p[i].swim.rotational_friction * ( omega_swim_body[0] - p[i].m.omega[0] );
p[i].f.torque[1] += p[i].swim.rotational_friction * ( omega_swim_body[1] - p[i].m.omega[1] );
p[i].f.torque[2] += p[i].swim.rotational_friction * ( omega_swim_body[2] - p[i].m.omega[2] );
}
}
#endif
ONEPART_TRACE(if(p[i].p.identity==check_id) fprintf(stderr,"%d: OPT: SCAL f = (%.3e,%.3e,%.3e) v_old = (%.3e,%.3e,%.3e)\n",this_node,p[i].f.f[0],p[i].f.f[1],p[i].f.f[2],p[i].m.v[0],p[i].m.v[1],p[i].m.v[2]));
#ifdef ROTATIONAL_INERTIA
p[i].m.omega[0]+= time_step_half*p[i].f.torque[0]/p[i].p.rinertia[0]/I[0];
p[i].m.omega[1]+= time_step_half*p[i].f.torque[1]/p[i].p.rinertia[1]/I[1];
p[i].m.omega[2]+= time_step_half*p[i].f.torque[2]/p[i].p.rinertia[2]/I[2];
#else
p[i].m.omega[0]+= time_step_half*p[i].f.torque[0]/I[0];
p[i].m.omega[1]+= time_step_half*p[i].f.torque[1]/I[1];
p[i].m.omega[2]+= time_step_half*p[i].f.torque[2]/I[2];
#endif
/* if the tensor of inertia is isotropic, the following refinement is not needed.
Otherwise repeat this loop 2-3 times depending on the required accuracy */
for(int times=0; times <= 5; times++)
{
double Wd[3];
#ifdef ROTATIONAL_INERTIA
Wd[0] = (p[i].m.omega[1]*p[i].m.omega[2]*(I[1]-I[2]))/I[0]/p[i].p.rinertia[0];
Wd[1] = (p[i].m.omega[2]*p[i].m.omega[0]*(I[2]-I[0]))/I[1]/p[i].p.rinertia[1];
Wd[2] = (p[i].m.omega[0]*p[i].m.omega[1]*(I[0]-I[1]))/I[2]/p[i].p.rinertia[2];
#else
Wd[0] = (p[i].m.omega[1]*p[i].m.omega[2]*(I[1]-I[2]))/I[0];
Wd[1] = (p[i].m.omega[2]*p[i].m.omega[0]*(I[2]-I[0]))/I[1];
Wd[2] = (p[i].m.omega[0]*p[i].m.omega[1]*(I[0]-I[1]))/I[2];
#endif
p[i].m.omega[0]+= time_step_half*Wd[0];
p[i].m.omega[1]+= time_step_half*Wd[1];
p[i].m.omega[2]+= time_step_half*Wd[2];
}
ONEPART_TRACE(if(p[i].p.identity==check_id) fprintf(stderr,"%d: OPT: PV_2 v_new = (%.3e,%.3e,%.3e)\n",this_node,p[i].m.v[0],p[i].m.v[1],p[i].m.v[2]));
}
}
}
