void force_calc()
{
#ifdef LB_GPU
if (lattice_switch & LATTICE_LB_GPU) lb_calc_particle_lattice_ia_gpu();
#endif
init_forces();
switch (cell_structure.type) {
case CELL_STRUCTURE_LAYERED:
layered_calculate_ia();
break;
case CELL_STRUCTURE_DOMDEC:
if(dd.use_vList) {
if (rebuild_verletlist)
build_verlet_lists_and_calc_verlet_ia();
else
calculate_verlet_ia();
}
else
calc_link_cell();
break;
case CELL_STRUCTURE_NSQUARE:
nsq_calculate_ia();
}
calc_long_range_forces();
#ifdef LB
if (lattice_switch & LATTICE_LB) calc_particle_lattice_ia() ;
#endif
#ifdef COMFORCE
calc_comforce();
#endif
#ifdef METADYNAMICS
/* Metadynamics main function */
meta_perform();
#endif
#ifdef LB_GPU
if (lattice_switch & LATTICE_LB_GPU) lb_send_forces_gpu();
#endif
/* this must be the last force to be calculated (Mehmet)*/
#ifdef COMFIXED
calc_comfixed();
#endif
}
void force_calc()
{
// Communication step: distribute ghost positions
cells_update_ghosts();
// VIRTUAL_SITES pos (and vel for DPD) update for security reason !!!
#ifdef VIRTUAL_SITES
update_mol_vel_pos();
ghost_communicator(&cell_structure.update_ghost_pos_comm);
#endif
#if defined(VIRTUAL_SITES_RELATIVE) && defined(LB)
// This is on a workaround stage:
// When using virtual sites relative and LB at the same time, it is necessary
// to reassemble the cell lists after all position updates, also of virtual
// particles.
if ((lattice_switch & LATTICE_LB) && cell_structure.type == CELL_STRUCTURE_DOMDEC && (!dd.use_vList) )
cells_update_ghosts();
#endif
espressoSystemInterface.update();
#ifdef COLLISION_DETECTION
prepare_collision_queue();
#endif
#ifdef LB_GPU
#ifdef SHANCHEN
if (lattice_switch & LATTICE_LB_GPU && this_node == 0) lattice_boltzmann_calc_shanchen_gpu();
#endif // SHANCHEN
// transfer_momentum_gpu check makes sure the LB fluid doesn't get updated on integrate 0
// this_node==0 makes sure it is the master node where the gpu exists
if (lattice_switch & LATTICE_LB_GPU && transfer_momentum_gpu && (this_node == 0) ) lb_calc_particle_lattice_ia_gpu();
#endif // LB_GPU
#ifdef ELECTROSTATICS
if (iccp3m_initialized && iccp3m_cfg.set_flag)
iccp3m_iteration();
#endif
init_forces();
for (ActorList::iterator actor = forceActors.begin();
actor != forceActors.end(); ++actor)
{
(*actor)->computeForces(espressoSystemInterface);
#ifdef ROTATION
(*actor)->computeTorques(espressoSystemInterface);
#endif
}
calc_long_range_forces();
switch (cell_structure.type) {
case CELL_STRUCTURE_LAYERED:
layered_calculate_ia();
break;
case CELL_STRUCTURE_DOMDEC:
if(dd.use_vList) {
if (rebuild_verletlist)
build_verlet_lists_and_calc_verlet_ia();
else
calculate_verlet_ia();
}
else
calc_link_cell();
break;
case CELL_STRUCTURE_NSQUARE:
nsq_calculate_ia();
}
#ifdef OIF_GLOBAL_FORCES
double area_volume[2]; //There are two global quantities that need to be evaluated: object's surface and object's volume. One can add another quantity.
area_volume[0] = 0.0;
area_volume[1] = 0.0;
for (int i=0;i< MAX_OBJECTS_IN_FLUID;i++){
calc_oif_global(area_volume,i);
if (fabs(area_volume[0])<1e-100 && fabs(area_volume[1])<1e-100) break;
add_oif_global_forces(area_volume,i);
}
#endif
#ifdef IMMERSED_BOUNDARY
// Must be done here. Forces need to be ghost-communicated
IBM_VolumeConservation();
#endif
#ifdef LB
if (lattice_switch & LATTICE_LB) calc_particle_lattice_ia() ;
#endif
#ifdef COMFORCE
calc_comforce();
#endif
#ifdef METADYNAMICS
/* Metadynamics main function */
meta_perform();
#endif
#ifdef CUDA
copy_forces_from_GPU();
#endif
// VIRTUAL_SITES distribute forces
#ifdef VIRTUAL_SITES
ghost_communicator(&cell_structure.collect_ghost_force_comm);
init_forces_ghosts();
distribute_mol_force();
#endif
// Communication Step: ghost forces
ghost_communicator(&cell_structure.collect_ghost_force_comm);
// apply trap forces to trapped molecules
#ifdef MOLFORCES
calc_and_apply_mol_constraints();
#endif
// should be pretty late, since it needs to zero out the total force
#ifdef COMFIXED
calc_comfixed();
#endif
// mark that forces are now up-to-date
recalc_forces = 0;
}
void integrate_sd(int n_steps)
{
/* Prepare the Integrator */
on_integration_start();
/* if any method vetoes (P3M not initialized), immediately bail out */
if (check_runtime_errors())
return;
INTEG_TRACE(fprintf(stderr,"%d: integrate_vv: integrating %d steps (recalc_forces=%d)\n",
this_node, n_steps, recalc_forces));
/* Integration Step:
Calculate forces f(t) as function of positions p(t) ( and velocities v(t) ) */
//if (recalc_forces) {
//thermo_heat_up();
ghost_communicator(&cell_structure.collect_ghost_force_comm);
#ifdef ROTATION
convert_initial_torques();
#endif
//thermo_cool_down();
/* Communication Step: ghost forces */
/*apply trap forces to trapped molecules*/
#ifdef MOLFORCES
// prob. works only with harmonic bounds
calc_and_apply_mol_constraints();
#endif
/* should be pretty late, since it needs to zero out the total force */
#ifdef COMFIXED
calc_comfixed();
#endif
//rescale_forces();
#ifdef COLLISION_DETECTION
//should not be neccessery, as integrator avoids collision
handle_collisions();
#endif
// end of force calculation
#ifdef GHMC
if(thermo_switch & THERMO_GHMC)
ghmc_init();
#endif
if (check_runtime_errors())
return;
n_verlet_updates = 0;
/* Integration loop */
for(int step=0;step<n_steps;step++) {
INTEG_TRACE(fprintf(stderr,"%d: STEP %d\n",this_node,step));
//sd_set_particles_apart();
#ifdef BOND_CONSTRAINT
save_old_pos();
#endif
#ifdef GHMC
if(thermo_switch & THERMO_GHMC) {
if (step % ghmc_nmd == 0)
ghmc_momentum_update();
}
#endif
if(thermo_switch & ~(THERMO_SD|THERMO_BD) ){
static bool warned_thermo_sd_other=false;
if (!warned_thermo_sd_other){
fprintf (stderr, "Warning, using another thermo than the one provided by StokesDynamics breaks (most likely) StokesDynamics.\n");
warned_thermo_sd_other=true;
}
}
if (thermo_switch & THERMO_SD && thermo_switch &THERMO_BD) {
fprintf (stderr, "Warning: cannot use BD and SD. Disabeling BD!\n");
thermo_switch &= ~THERMO_BD;
}
/* Integration Step: Step 3 of Velocity Verlet scheme:
Calculate f(t) as function of positions p(t) ( and ``velocities'' v(t) ) */
#ifdef LB
transfer_momentum = 1;
#endif
#ifdef LB_GPU
transfer_momentum_gpu = 1;
#endif
force_calc();
#ifdef CATALYTIC_REACTIONS
integrate_reaction();
#endif
if (check_runtime_errors())
break;
#ifdef LB
if (lattice_switch & LATTICE_LB)
lattice_boltzmann_update();
if (check_runtime_errors())
break;
#endif
#ifdef LB_GPU
if(this_node == 0){
#ifdef ELECTROKINETICS
if (ek_initialized) {
ek_integrate();
}
else {
#endif
if (lattice_switch & LATTICE_LB_GPU)
lattice_boltzmann_update_gpu();
#ifdef ELECTROKINETICS
}
#endif
}
#endif //LB_GPU
#ifdef ELECTROSTATICS
if(coulomb.method == COULOMB_MAGGS) {
maggs_propagate_B_field(0.5*time_step);
}
#endif
#ifdef NPT
if((this_node==0) && (integ_switch == INTEG_METHOD_NPT_ISO))
nptiso.p_inst_av += nptiso.p_inst;
#endif
#ifdef GHMC
if(thermo_switch & THERMO_GHMC) {
if (step % ghmc_nmd == ghmc_nmd-1)
ghmc_mc();
}
#endif
/** Integration Steps: Update the Positions
\[ p_i(t + dt) = p_i(t) + dt * \mu_{ij} * f_j(t) + dt * \mu_{ij} * f^B_j \]
*/
propagate_pos_sd(); // we dont have velocities
#ifdef BOND_CONSTRAINT
static bool bond_constraint_with_sd_warned=false;
if (!bond_constraint_with_sd_warned){ // warn only once
fprintf (stderr, "Warning, using BOND_CONSTRAINT with StokesDynamics might not work as expected!.\n");
bond_constraint_with_sd_warned=true;
}
/**Correct those particle positions that participate in a rigid/constrained bond */
cells_update_ghosts();
correct_pos_shake();
#endif
#ifdef ELECTROSTATICS
if(coulomb.method == COULOMB_MAGGS) {
maggs_propagate_B_field(0.5*time_step);
}
#endif
#ifdef NPT
if (check_runtime_errors())
break;
#endif
/* Propagate time: t = t+dt */
sim_time += time_step;
}
/* verlet list statistics */
if(n_verlet_updates>0) verlet_reuse = n_steps/(double) n_verlet_updates;
else verlet_reuse = 0;
#ifdef NPT
if(integ_switch == INTEG_METHOD_NPT_ISO) {
nptiso.invalidate_p_vel = 0;
MPI_Bcast(&nptiso.p_inst, 1, MPI_DOUBLE, 0, comm_cart);
MPI_Bcast(&nptiso.p_diff, 1, MPI_DOUBLE, 0, comm_cart);
MPI_Bcast(&nptiso.volume, 1, MPI_DOUBLE, 0, comm_cart);
if(this_node==0) nptiso.p_inst_av /= 1.0*n_steps;
MPI_Bcast(&nptiso.p_inst_av, 1, MPI_DOUBLE, 0, comm_cart);
}
#endif
#ifdef GHMC
if(thermo_switch & THERMO_GHMC)
ghmc_close();
#endif
}