void integrate_vv(int n_steps)
{
int i;
#ifdef REACTIONS
int c, np, n;
Particle * p1, *p2, **pairs;
Cell * cell;
double dist2, vec21[3], rand;
if(reaction.rate > 0) {
int reactants = 0, products = 0;
int tot_reactants = 0, tot_products = 0;
double ratexp, back_ratexp;
ratexp = exp(-time_step*reaction.rate);
on_observable_calc();
for (c = 0; c < local_cells.n; c++) {
/* Loop cell neighbors */
for (n = 0; n < dd.cell_inter[c].n_neighbors; n++) {
pairs = dd.cell_inter[c].nList[n].vList.pair;
np = dd.cell_inter[c].nList[n].vList.n;
/* verlet list loop */
for(i = 0; i < 2 * np; i += 2) {
p1 = pairs[i]; //pointer to particle 1
p2 = pairs[i+1]; //pointer to particle 2
if( (p1->p.type == reaction.reactant_type && p2->p.type == reaction.catalyzer_type) || (p2->p.type == reaction.reactant_type && p1->p.type == reaction.catalyzer_type) ) {
get_mi_vector(vec21, p1->r.p, p2->r.p);
dist2 = sqrlen(vec21);
if(dist2 < reaction.range * reaction.range) {
rand =d_random();
if(rand > ratexp) {
if(p1->p.type==reaction.reactant_type) {
p1->p.type = reaction.product_type;
}
else {
p2->p.type = reaction.product_type;
}
}
}
}
}
}
}
if (reaction.back_rate < 0) { // we have to determine it dynamically
/* we count now how many reactants and products are in the sim box */
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p1 = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
if(p1[i].p.type == reaction.reactant_type)
reactants++;
else if(p1[i].p.type == reaction.product_type)
products++;
}
}
MPI_Allreduce(&reactants, &tot_reactants, 1, MPI_INT, MPI_SUM, comm_cart);
MPI_Allreduce(&products, &tot_products, 1, MPI_INT, MPI_SUM, comm_cart);
back_ratexp = ratexp * tot_reactants / tot_products ; //with this the asymptotic ratio reactant/product becomes 1/1 and the catalyzer volume only determines the time that it takes to reach this
}
else { //use the back reaction rate supplied by the user
back_ratexp = exp(-time_step*reaction.back_rate);
}
if(back_ratexp < 1 ) {
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p1 = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
if(p1[i].p.type == reaction.product_type) {
rand = d_random();
if(rand > back_ratexp) {
p1[i].p.type=reaction.reactant_type;
}
}
}
}
}
on_particle_change();
}
#endif /* ifdef REACTIONS */
/* Prepare the Integrator */
on_integration_start();
/* if any method vetoes (P3M not initialized), immediately bail out */
if (check_runtime_errors())
return;
/* Verlet list criterion */
skin2 = SQR(0.5 * skin);
INTEG_TRACE(fprintf(stderr,"%d: integrate_vv: integrating %d steps (recalc_forces=%d)\n",
this_node, n_steps, recalc_forces));
/* Integration Step: Preparation for first integration step:
Calculate forces f(t) as function of positions p(t) ( and velocities v(t) ) */
if (recalc_forces) {
thermo_heat_up();
#ifdef LB
transfer_momentum = 0;
#endif
#ifdef LB_GPU
transfer_momentum_gpu = 0;
#endif
//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);
if (check_runtime_errors()) return;
#ifdef ADRESS
// adress_update_weights();
if (check_runtime_errors()) return;
#endif
#endif
#ifdef COLLISION_DETECTION
prepare_collision_queue();
#endif
force_calc();
//VIRTUAL_SITES distribute forces
#ifdef VIRTUAL_SITES
ghost_communicator(&cell_structure.collect_ghost_force_comm);
init_forces_ghosts();
distribute_mol_force();
if (check_runtime_errors()) return;
#endif
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
calc_and_apply_mol_constraints();
#endif
rescale_forces();
recalc_forces = 0;
#ifdef COLLISION_DETECTION
handle_collisions();
#endif
}
if (check_runtime_errors())
return;
n_verlet_updates = 0;
/* Integration loop */
for(i=0;i<n_steps;i++) {
INTEG_TRACE(fprintf(stderr,"%d: STEP %d\n",this_node,i));
#ifdef BOND_CONSTRAINT
save_old_pos();
#endif
/* Integration Steps: Step 1 and 2 of Velocity Verlet scheme:
v(t+0.5*dt) = v(t) + 0.5*dt * f(t)
p(t + dt) = p(t) + dt * v(t+0.5*dt)
NOTE 1: Prefactors do not occur in formulas since we use
rescaled forces and velocities.
NOTE 2: Depending on the integration method Step 1 and Step 2
cannot be combined for the translation.
*/
if(integ_switch == INTEG_METHOD_NPT_ISO || nemd_method != NEMD_METHOD_OFF) {
propagate_vel(); propagate_pos(); }
else
propagate_vel_pos();
#ifdef BOND_CONSTRAINT
/**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
cells_update_ghosts();
//VIRTUAL_SITES update pos and vel (for DPD)
#ifdef VIRTUAL_SITES
update_mol_vel_pos();
ghost_communicator(&cell_structure.update_ghost_pos_comm);
if (check_runtime_errors()) break;
#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 (cell_structure.type == CELL_STRUCTURE_DOMDEC && (!dd.use_vList) )
cells_update_ghosts();
#endif
#ifdef ADRESS
//adress_update_weights();
if (check_runtime_errors()) break;
#endif
#endif
/* Integration Step: Step 3 of Velocity Verlet scheme:
Calculate f(t+dt) as function of positions p(t+dt) ( and velocities v(t+0.5*dt) ) */
#ifdef LB
transfer_momentum = 1;
#endif
#ifdef LB_GPU
transfer_momentum_gpu = 1;
#endif
#ifdef COLLISION_DETECTION
prepare_collision_queue();
#endif
force_calc();
//VIRTUAL_SITES distribute forces
#ifdef VIRTUAL_SITES
ghost_communicator(&cell_structure.collect_ghost_force_comm);
init_forces_ghosts();
distribute_mol_force();
if (check_runtime_errors()) break;
#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
if (check_runtime_errors())
break;
/* Integration Step: Step 4 of Velocity Verlet scheme:
v(t+dt) = v(t+0.5*dt) + 0.5*dt * f(t+dt) */
rescale_forces_propagate_vel();
recalc_forces = 0;
#ifdef LB
if (lattice_switch & LATTICE_LB) lattice_boltzmann_update();
if (check_runtime_errors()) break;
#endif
#ifdef LB_GPU
if(this_node == 0){
if (lattice_switch & LATTICE_LB_GPU) lattice_boltzmann_update_gpu();
}
#endif
#ifdef BOND_CONSTRAINT
ghost_communicator(&cell_structure.update_ghost_pos_comm);
correct_vel_shake();
#endif
#ifdef ROTATION
convert_torques_propagate_omega();
#endif
//VIRTUAL_SITES update vel
#ifdef VIRTUAL_SITES
ghost_communicator(&cell_structure.update_ghost_pos_comm);
update_mol_vel();
if (check_runtime_errors()) break;
#endif
#ifdef ELECTROSTATICS
if(coulomb.method == COULOMB_MAGGS) {
maggs_propagate_B_field(0.5*time_step);
}
#endif
#ifdef COLLISION_DETECTION
handle_collisions();
#endif
#ifdef NPT
if((this_node==0) && (integ_switch == INTEG_METHOD_NPT_ISO))
nptiso.p_inst_av += nptiso.p_inst;
#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
}
void integrate_reaction() {
int c, np, n, i;
Particle * p1, *p2, **pairs;
Cell * cell;
double dist2, vec21[3], rand;
if(reaction.rate > 0) {
int reactants = 0, products = 0;
int tot_reactants = 0, tot_products = 0;
double ratexp, back_ratexp;
ratexp = exp(-time_step*reaction.rate);
on_observable_calc();
for (c = 0; c < local_cells.n; c++) {
/* Loop cell neighbors */
for (n = 0; n < dd.cell_inter[c].n_neighbors; n++) {
pairs = dd.cell_inter[c].nList[n].vList.pair;
np = dd.cell_inter[c].nList[n].vList.n;
/* verlet list loop */
for(i = 0; i < 2 * np; i += 2) {
p1 = pairs[i]; //pointer to particle 1
p2 = pairs[i+1]; //pointer to particle 2
if( (p1->p.type == reaction.reactant_type && p2->p.type == reaction.catalyzer_type) || (p2->p.type == reaction.reactant_type && p1->p.type == reaction.catalyzer_type) ) {
get_mi_vector(vec21, p1->r.p, p2->r.p);
dist2 = sqrlen(vec21);
if(dist2 < reaction.range * reaction.range) {
rand = d_random();
if(rand > ratexp) {
if(p1->p.type == reaction.reactant_type) {
p1->p.type = reaction.product_type;
}
else {
p2->p.type = reaction.product_type;
}
}
}
}
}
}
}
if (reaction.back_rate < 0) { // we have to determine it dynamically
/* we count now how many reactants and products are in the sim box */
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p1 = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
if(p1[i].p.type == reaction.reactant_type)
reactants++;
else if(p1[i].p.type == reaction.product_type)
products++;
}
}
MPI_Allreduce(&reactants, &tot_reactants, 1, MPI_INT, MPI_SUM, comm_cart);
MPI_Allreduce(&products, &tot_products, 1, MPI_INT, MPI_SUM, comm_cart);
back_ratexp = ratexp * tot_reactants / tot_products ; //with this the asymptotic ratio reactant/product becomes 1/1 and the catalyzer volume only determines the time that it takes to reach this
}
else { //use the back reaction rate supplied by the user
back_ratexp = exp(-time_step*reaction.back_rate);
}
if(back_ratexp < 1 ) {
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p1 = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
if(p1[i].p.type == reaction.product_type) {
rand = d_random();
if(rand > back_ratexp) {
printf("DEBUG: integrate_reaction; back_react\n"); //TODO delete
p1[i].p.type=reaction.reactant_type;
}
}
}
}
}
on_particle_change();
}
}
