int ljcos2_set_params(int part_type_a, int part_type_b,
double eps, double sig, double offset,
double w)
{
IA_parameters *data, *data_sym;
make_particle_type_exist(part_type_a);
make_particle_type_exist(part_type_b);
data = get_ia_param(part_type_a, part_type_b);
data_sym = get_ia_param(part_type_b, part_type_a);
if (!data || !data_sym) {
return TCL_ERROR;
}
/* lj-cos2 should be symmetrically */
data->LJCOS2_eps = data_sym->LJCOS2_eps = eps;
data->LJCOS2_sig = data_sym->LJCOS2_sig = sig;
data->LJCOS2_offset = data_sym->LJCOS2_offset = offset;
data->LJCOS2_w = data_sym->LJCOS2_w = w;
/* calculate dependent parameters */
data->LJCOS2_rchange = data_sym->LJCOS2_rchange = pow(2,1/6.)*sig;
data->LJCOS2_cut = data_sym->LJCOS2_cut = w + data_sym->LJCOS2_rchange;
/* broadcast interaction parameters */
mpi_bcast_ia_params(part_type_a, part_type_b);
mpi_bcast_ia_params(part_type_b, part_type_a);
if (lj_force_cap != -1.0)
mpi_lj_cap_forces(lj_force_cap);
return TCL_OK;
}
int ljangle_set_params(int part_type_a, int part_type_b,
double eps, double sig, double cut,
int b1p, int b1n, int b2p, int b2n,
double cap_radius, double z0, double dz,
double kappa, double epsprime)
{
IA_parameters *data, *data_sym;
make_particle_type_exist(part_type_a);
make_particle_type_exist(part_type_b);
data = get_ia_param(part_type_a, part_type_b);
data_sym = get_ia_param(part_type_b, part_type_a);
if (!data || !data_sym) {
return TCL_ERROR;
}
/* LJ_ANGLE should be symmetrically */
data->LJANGLE_eps = data_sym->LJANGLE_eps = eps;
data->LJANGLE_sig = data_sym->LJANGLE_sig = sig;
data->LJANGLE_cut = data_sym->LJANGLE_cut = cut;
data->LJANGLE_bonded1pos = data_sym->LJANGLE_bonded1pos = b1p;
data->LJANGLE_bonded1neg = data_sym->LJANGLE_bonded1neg = b1n;
data->LJANGLE_bonded2pos = data_sym->LJANGLE_bonded2pos = b2p;
data->LJANGLE_bonded2neg = data_sym->LJANGLE_bonded2neg = b2n;
data->LJANGLE_bonded1type = data_sym->LJANGLE_bonded1type = part_type_a;
if (cap_radius > 0) {
data->LJANGLE_capradius = cap_radius;
data_sym->LJANGLE_capradius = cap_radius;
}
if (dz > 0.) {
data->LJANGLE_z0 = data_sym->LJANGLE_z0 = z0;
data->LJANGLE_dz = data_sym->LJANGLE_dz = dz;
data->LJANGLE_kappa = data_sym->LJANGLE_kappa = kappa;
data->LJANGLE_epsprime = data_sym->LJANGLE_epsprime = epsprime;
}
/* broadcast interaction parameters */
mpi_bcast_ia_params(part_type_a, part_type_b);
mpi_bcast_ia_params(part_type_b, part_type_a);
if (ljangle_force_cap != -1.0)
mpi_ljangle_cap_forces(ljangle_force_cap);
return TCL_OK;
}
int collision_detection_set_params(int mode, double d, int bond_centers, int bond_vs,int t)
{
// If we don't have virtual sites relative feature, mode 2 isn't allowed.
#ifndef VIRTUAL_SITES_RELATIVE
if (mode==2)
return 1;
#endif
// Collision detection only works on a single cpu
if (mode!=0 && n_nodes !=1)
return 2;
// Check if bonded ia exist
if (((mode>0) && (bond_centers+1>n_bonded_ia)) || ((mode==2) && (bond_vs+1>n_bonded_ia)))
return 3;
if (bonded_ia_params[bond_centers].num != 1)
return 4;
if ((mode ==2) && (
bonded_ia_params[bond_vs].num != 1 &&
bonded_ia_params[bond_vs].num != 2))
return 5;
// Set params
collision_detection_mode=mode;
collision_detection_bond_centers=bond_centers;
collision_detection_bond_vs=bond_vs;
collision_distance=d;
collision_vs_particle_type=t;
make_particle_type_exist(t);
recalc_forces=1;
return 0;
}
/* TODO: This function is not used anywhere. To be removed? */
int tf_print(Tcl_Interp * interp, int part_type)
{
TF_parameters *data;
Tcl_ResetResult(interp);
make_particle_type_exist(part_type);
data = get_tf_param(part_type);
return tclprint_to_result_TF(interp, part_type);
}
int tclcommand_inter_print_non_bonded(Tcl_Interp * interp,
int part_type_a, int part_type_b)
{
IA_parameters *data, *data_sym;
Tcl_ResetResult(interp);
make_particle_type_exist(part_type_a);
make_particle_type_exist(part_type_b);
data = get_ia_param(part_type_a, part_type_b);
data_sym = get_ia_param(part_type_b, part_type_a);
if (!data || !data_sym) {
Tcl_AppendResult(interp, "particle types must be nonnegative",
(char *) NULL);
return TCL_ERROR;
}
return tclprint_to_result_NonbondedIA(interp, part_type_a, part_type_b);
}
int on_program_start(Tcl_Interp *interp)
{
EVENT_TRACE(fprintf(stderr, "%d: on_program_start\n", this_node));
/*
call the initialization of the modules here
*/
init_random();
init_bit_random();
setup_node_grid();
/* calculate initial minimimal number of cells (see tclcallback_min_num_cells) */
min_num_cells = calc_processor_min_num_cells();
cells_pre_init();
ghost_init();
/* Initialise force and energy tables */
force_and_energy_tables_init();
#ifdef ADRESS
#ifdef INTERFACE_CORRECTION
adress_force_and_energy_tables_init();
#endif
/** #ifdef THERMODYNAMIC_FORCE */
tf_tables_init();
/** #endif */
#endif
#ifdef ELP3M
fft_pre_init();
#endif
#ifdef LB_GPU
if(this_node == 0){
lb_pre_init_gpu();
}
#endif
#ifdef LB
lb_pre_init();
#endif
/*
call all initializations to do only on the master node here.
*/
if (this_node == 0) {
/* interaction_data.c: make sure 0<->0 ia always exists */
make_particle_type_exist(0);
init_tcl(interp);
}
return TCL_OK;
}
void setup_reaction() {
MPI_Bcast(&reaction.reactant_type, 1, MPI_INT, 0, comm_cart);
MPI_Bcast(&reaction.product_type, 1, MPI_INT, 0, comm_cart);
MPI_Bcast(&reaction.catalyzer_type, 1, MPI_INT, 0, comm_cart);
MPI_Bcast(&reaction.range, 1, MPI_DOUBLE, 0, comm_cart);
MPI_Bcast(&reaction.rate, 1, MPI_DOUBLE, 0, comm_cart);
MPI_Bcast(&reaction.back_rate, 1, MPI_DOUBLE, 0, comm_cart);
make_particle_type_exist(reaction.catalyzer_type);
make_particle_type_exist(reaction.product_type);
make_particle_type_exist(reaction.reactant_type);
IA_parameters *data = get_ia_param_safe(reaction.reactant_type, reaction.catalyzer_type);
if(!data) {
char *error_msg = runtime_error(128);
ERROR_SPRINTF(error_msg, "{106 interaction parameters for reaction could not be set} ");
}
data->REACTION_range = reaction.range;
/* broadcast interaction parameters */
mpi_bcast_ia_params(reaction.reactant_type, reaction.catalyzer_type);
}
int set_particle_type(int part, int type)
{
int pnode;
make_particle_type_exist(type);
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;
// check if the particle exists already and the type is changed, then remove it from the list which contains it
Particle *cur_par = (Particle *) malloc( sizeof(Particle) );
if ( Type_array_init ) {
if ( cur_par != (Particle *) 0 ) {
if ( get_particle_data(part, cur_par) != ES_ERROR ) {
int prev_type = cur_par->p.type;
if ( prev_type != type ) {
// particle existed before so delete it from the list
remove_id_type_array(part, prev_type);
}
}
}
free(cur_par);
}
mpi_send_type(pnode, part, type);
#ifdef ADDITIONAL_CHECKS
if ( Type_array_init ) {
if ( add_particle_to_list(part, type) == ES_ERROR ){
//Tcl_AppendResult(interp, "gc particle add failed", (char *) NULL);
return ES_ERROR;
}
}
#endif
return ES_OK;
}
IA_parameters *get_ia_param_safe(int i, int j) {
make_particle_type_exist(std::max(i, j));
return get_ia_param(i, j);
}
void on_program_start()
{
EVENT_TRACE(fprintf(stderr, "%d: on_program_start\n", this_node));
/* tell Electric fence that we do realloc(0) on purpose. */
#ifdef EFENCE
extern int EF_ALLOW_MALLOC_0;
EF_ALLOW_MALLOC_0 = 1;
#endif
register_sigint_handler();
if (this_node == 0) {
/* master node */
#ifdef FORCE_CORE
/* core should be the last exit handler (process dies) */
atexit(core);
#endif
atexit(mpi_stop);
}
/*
call the initialization of the modules here
*/
init_random();
init_bit_random();
setup_node_grid();
/* calculate initial minimimal number of cells (see tclcallback_min_num_cells) */
min_num_cells = calc_processor_min_num_cells();
/* initially go for domain decomposition */
dd_topology_init(&local_cells);
ghost_init();
/* Initialise force and energy tables */
force_and_energy_tables_init();
#ifdef ADRESS
#ifdef INTERFACE_CORRECTION
adress_force_and_energy_tables_init();
#endif
/* #ifdef THERMODYNAMIC_FORCE */
tf_tables_init();
/* #endif */
#endif
#ifdef P3M
p3m_pre_init();
#endif
#ifdef DP3M
dp3m_pre_init();
#endif
#ifdef LB_GPU
if(this_node == 0) {
//lb_pre_init_gpu();
}
#endif
#ifdef LB
lb_pre_init();
#endif
#ifdef REACTIONS
reaction.back_rate=-1.0;
#endif
/*
call all initializations to do only on the master node here.
*/
if (this_node == 0) {
/* interaction_data.c: make sure 0<->0 ia always exists */
make_particle_type_exist(0);
}
}
