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 angledist_set_params(int bond_type, double bend, double phimin, double distmin, double phimax, double distmax)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.angledist.bend = bend;
bonded_ia_params[bond_type].p.angledist.phimin = phimin;
bonded_ia_params[bond_type].p.angledist.distmin = distmin;
bonded_ia_params[bond_type].p.angledist.phimax = phimax;
bonded_ia_params[bond_type].p.angledist.distmax = distmax;
#ifdef BOND_ANGLEDIST_COSINE
#error angledist not implemented for BOND_ANGLEDIST_COSINE
#endif
#ifdef BOND_ANGLEDIST_COSSQUARE
#error angledist not implemented for BOND_ANGLEDIST_COSSQUARE
#endif
bonded_ia_params[bond_type].type = BONDED_IA_ANGLEDIST;
bonded_ia_params[bond_type].num = 2;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int ljcos2_set_params(int part_type_a, int part_type_b,
double eps, double sig, double offset,
double w)
{
IA_parameters *data = get_ia_param_safe(part_type_a, part_type_b);
if (!data) return ES_ERROR;
data->LJCOS2_eps = eps;
data->LJCOS2_sig = sig;
data->LJCOS2_offset = offset;
data->LJCOS2_w = w;
/* calculate dependent parameters */
data->LJCOS2_rchange = pow(2,1/6.)*sig;
data->LJCOS2_cut = w + data->LJCOS2_rchange;
/* broadcast interaction parameters */
mpi_bcast_ia_params(part_type_a, part_type_b);
if (lj_force_cap != -1.0)
mpi_lj_cap_forces(lj_force_cap);
return ES_OK;
}
int BMHTF_set_params(int part_type_a, int part_type_b,
double A, double B, double C,
double D, double sig, double cut)
{
double shift, dist2, pw6;
IA_parameters *data = get_ia_param_safe(part_type_a, part_type_b);
if (!data) return ES_ERROR;
dist2 = cut*cut;
pw6 = dist2*dist2*dist2;
shift = -(A*exp(B*(sig - cut)) - C/pw6 - D/pw6/dist2);
data->BMHTF_A = A;
data->BMHTF_B = B;
data->BMHTF_C = C;
data->BMHTF_D = D;
data->BMHTF_sig = sig;
data->BMHTF_cut = cut;
data->BMHTF_computed_shift = shift;
/* broadcast interaction parameters */
mpi_bcast_ia_params(part_type_a, part_type_b);
return ES_OK;
}
int IBM_VolumeConservation_SetParams(const int bond_type, const int softID, const double kappaV)
{
// Create bond
make_bond_type_exist(bond_type);
// General bond parameters
bonded_ia_params[bond_type].type = BONDED_IA_IBM_VOLUME_CONSERVATION;
bonded_ia_params[bond_type].num = 1; // This means that Espresso requires one bond partner. Here we simply ignore it, but Espresso cannot handle 0.
// Specific stuff
if ( softID > MaxNumIBM) { printf("Error: softID (%d) is larger than MaxNumIBM (%d)\n", softID, MaxNumIBM); return ES_ERROR; }
if ( softID < 0) { printf("Error: softID (%d) must be non-negative\n", softID); return ES_ERROR; }
bonded_ia_params[bond_type].p.ibmVolConsParameters.softID = softID;
bonded_ia_params[bond_type].p.ibmVolConsParameters.kappaV = kappaV;
bonded_ia_params[bond_type].p.ibmVolConsParameters.volRef = 0;
// NOTE: We cannot compute the reference volume here because not all interactions are setup
// and thus we do not know which triangles belong to this softID
// Calculate it later in the init function
//Communicate this to whoever is interested
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int lj_cos_set_params(int part_type_a, int part_type_b,
double eps, double sig, double cut,
double offset)
{
double facsq;
IA_parameters *data = get_ia_param_safe(part_type_a, part_type_b);
if (!data) return ES_ERROR;
data->LJCOS_eps = eps;
data->LJCOS_sig = sig;
data->LJCOS_cut = cut;
data->LJCOS_offset = offset;
/* Calculate dependent parameters */
facsq = driwu2*SQR(sig);
data->LJCOS_rmin = sqrt(driwu2)*sig;
data->LJCOS_alfa = PI/(SQR(data->LJCOS_cut)-facsq);
data->LJCOS_beta = PI*(1.-(1./(SQR(data->LJCOS_cut)/facsq-1.)));
/* broadcast interaction parameters */
mpi_bcast_ia_params(part_type_a, part_type_b);
return ES_OK;
}
int hydrogen_bond_set_params(int bond_type, DoubleList *params) {
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.hydrogen_bond.r0 = params->e[0];
bonded_ia_params[bond_type].p.hydrogen_bond.alpha = params->e[1];
bonded_ia_params[bond_type].p.hydrogen_bond.E0 = params->e[2];
bonded_ia_params[bond_type].p.hydrogen_bond.kd = params->e[3];
bonded_ia_params[bond_type].p.hydrogen_bond.sigma1 = params->e[4];
bonded_ia_params[bond_type].p.hydrogen_bond.sigma2 = params->e[5];
bonded_ia_params[bond_type].p.hydrogen_bond.psi10 = params->e[6];
bonded_ia_params[bond_type].p.hydrogen_bond.psi20 = params->e[7];
bonded_ia_params[bond_type].p.hydrogen_bond.E0sb = params->e[8];
bonded_ia_params[bond_type].p.hydrogen_bond.r0sb = params->e[9];
bonded_ia_params[bond_type].p.hydrogen_bond.alphasb = params->e[10];
bonded_ia_params[bond_type].p.hydrogen_bond.f2 = params->e[11];
bonded_ia_params[bond_type].p.hydrogen_bond.f3 = params->e[12];
bonded_ia_params[bond_type].type = BONDED_IA_CG_DNA_BASEPAIR;
bonded_ia_params[bond_type].num = 3;
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int lennard_jones_set_params(int part_type_a, int part_type_b,
double eps, double sig, double cut,
double shift, double offset,
double cap_radius, double min)
{
IA_parameters *data = get_ia_param_safe(part_type_a, part_type_b);
if (!data) return ES_ERROR;
data->LJ_eps = eps;
data->LJ_sig = sig;
data->LJ_cut = cut;
data->LJ_shift = shift;
data->LJ_offset = offset;
if (cap_radius > 0) {
data->LJ_capradius = cap_radius;
}
if (min > 0) {
data->LJ_min = min;
}
/* broadcast interaction parameters */
mpi_bcast_ia_params(part_type_a, part_type_b);
mpi_cap_forces(force_cap);
return ES_OK;
}
int inter_dpd_set_params(int part_type_a, int part_type_b,
double gamma, double r_c, int wf,
double tgamma, double tr_c,
int twf)
{
extern double temperature;
IA_parameters *data = get_ia_param_safe(part_type_a, part_type_b);
if (!data) return ES_ERROR;
data->dpd_gamma = gamma;
data->dpd_r_cut = r_c;
data->dpd_wf = wf;
data->dpd_pref1 = gamma/time_step;
data->dpd_pref2 = sqrt(24.0*temperature*gamma/time_step);
data->dpd_tgamma = tgamma;
data->dpd_tr_cut = tr_c;
data->dpd_twf = twf;
data->dpd_pref3 = tgamma/time_step;
data->dpd_pref4 = sqrt(24.0*temperature*tgamma/time_step);
/* broadcast interaction parameters */
mpi_bcast_ia_params(part_type_a, part_type_b);
return ES_OK;
}
int comfixed_set_params(int part_type_a, int part_type_b, int flag)
{
Particle *p;
int i, j, np, c;
Cell *cell;
IA_parameters *data = get_ia_param_safe(part_type_a, part_type_b);
if (!data)
return 1;
if (n_nodes > 1)
return 2;
data->COMFIXED_flag = flag;
/* broadcast interaction parameters */
mpi_bcast_ia_params(part_type_a, part_type_b);
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++) {
if(p[i].p.type==part_type_a) {
for(j = 0; j < 3; j++) {
p[i].m.v[j] = 0.;
p[i].f.f[j] = 0.;
}
}
}
}
return ES_OK;
}
int morse_set_params(int part_type_a, int part_type_b,
double eps, double alpha,
double rmin, double cut, double cap_radius)
{
double add1, add2;
IA_parameters *data = get_ia_param_safe(part_type_a, part_type_b);
if (!data) return ES_ERROR;
data->MORSE_eps = eps;
data->MORSE_alpha = alpha;
data->MORSE_rmin = rmin;
data->MORSE_cut = cut;
/* calculate dependent parameter */
add1 = exp(-2.0*data->MORSE_alpha*(data->MORSE_cut - data->MORSE_rmin));
add2 = 2.0*exp(-data->MORSE_alpha*(data->MORSE_cut - data->MORSE_rmin));
data->MORSE_rest = data->MORSE_eps * (add1 - add2);
if (cap_radius > 0) {
data->MORSE_capradius = cap_radius;
}
/* broadcast interaction parameters */
mpi_bcast_ia_params(part_type_a, part_type_b);
mpi_cap_forces(force_cap);
return ES_OK;
}
void IBM_InitVolumeConservation()
{
// Check since this function is called at the start of every integrate loop
// Also check if volume has been set due to reading of a checkpoint
if ( !VolumeInitDone /*&& VolumesCurrent[0] == 0 */)
{
// Calculate volumes
CalcVolumes();
//numWriteCOM = 0;
// Loop through all bonded interactions and check if we need to set the reference volume
for (int i=0; i < n_bonded_ia; i++)
{
if ( bonded_ia_params[i].type == BONDED_IA_IBM_VOLUME_CONSERVATION )
{
// This check is important because InitVolumeConservation may be called accidentally
// during the integration. Then we must not reset the reference
if ( bonded_ia_params[i].p.ibmVolConsParameters.volRef == 0 )
{
const int softID =bonded_ia_params[i].p.ibmVolConsParameters.softID;
bonded_ia_params[i].p.ibmVolConsParameters.volRef = VolumesCurrent[softID];
mpi_bcast_ia_params(i, -1);
}
}
}
}
VolumeInitDone = true;
}
// set out_direction parameters
int out_direction_set_params(int bond_type)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].type = BONDED_IA_OIF_OUT_DIRECTION;
bonded_ia_params[bond_type].num = 3;
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int hat_set_params(int part_type_a, int part_type_b,
double Fmax, double r)
{
IA_parameters *data = get_ia_param_safe(part_type_a, part_type_b);
if (!data) return ES_ERROR;
data->HAT_Fmax = Fmax;
data->HAT_r = r;
/* broadcast interaction parameters */
mpi_bcast_ia_params(part_type_a, part_type_b);
return ES_OK;
}
int IBM_Tribend_ResetParams(const int bond_type, const double kb)
{
// Check if bond exists and is of correct type
if ( bond_type >= n_bonded_ia ) { printf("bond does not exist while reading tribend checkpoint\n"); return ES_ERROR; }
if ( bonded_ia_params[bond_type].type != BONDED_IA_IBM_TRIBEND ) { printf("interaction type does not match while reading tribend checkpoint!\n"); return ES_ERROR; }
// Check if k is correct
if ( fabs( bonded_ia_params[bond_type].p.ibm_tribend.kb - kb) > 1e-6 ) { printf("kb does not match while reading tribend checkpoint. It is %.12e and read was %.12e\n", bonded_ia_params[bond_type].p.ibm_tribend.kb, kb); return ES_ERROR; }
//Communicate this to whoever is interested
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int virtual_set_params(int bond_type)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].type = BONDED_IA_VIRTUAL_BOND;
bonded_ia_params[bond_type].num = 1;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int bonded_coulomb_set_params(int bond_type, double prefactor)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.bonded_coulomb.prefactor = prefactor;
bonded_ia_params[bond_type].type = BONDED_IA_BONDED_COULOMB;
bonded_ia_params[bond_type].num = 1;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int IBM_VolumeConservation_ResetParams(const int bond_type, const double volRef)
{
// Check if bond exists and is of correct type
if ( bond_type >= n_bonded_ia ) return ES_ERROR;
if ( bonded_ia_params[bond_type].type != BONDED_IA_IBM_VOLUME_CONSERVATION ) return ES_ERROR;
// Specific stuff
// We need to set this here, since it is not re-calculated at the restarting of a sim as, e.g., triel
bonded_ia_params[bond_type].p.ibmVolConsParameters.volRef = volRef;
//Communicate this to whoever is interested
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int gaussian_set_params(int part_type_a, int part_type_b,
double eps, double sig, double cut)
{
IA_parameters *data = get_ia_param_safe(part_type_a, part_type_b);
if (!data) return ES_ERROR;
data->Gaussian_eps = eps;
data->Gaussian_sig = sig;
data->Gaussian_cut = cut;
/* broadcast interaction parameters */
mpi_bcast_ia_params(part_type_a, part_type_b);
return ES_OK;
}
int soft_sphere_set_params(int part_type_a, int part_type_b,
double a, double n, double cut, double offset)
{
IA_parameters *data = get_ia_param_safe(part_type_a, part_type_b);
if (!data) return ES_ERROR;
data->soft_a = a;
data->soft_n = n;
data->soft_cut = cut;
data->soft_offset = offset;
/* broadcast interaction parameters */
mpi_bcast_ia_params(part_type_a, part_type_b);
return ES_OK;
}
int subt_lj_set_params(int bond_type, double k, double r)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.subt_lj.k = k;
bonded_ia_params[bond_type].p.subt_lj.r = r;
bonded_ia_params[bond_type].type = BONDED_IA_SUBT_LJ;
bonded_ia_params[bond_type].p.subt_lj.r2 = SQR(bonded_ia_params[bond_type].p.subt_lj.r);
bonded_ia_params[bond_type].num = 1;
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
/// set dihedral parameters
int dihedral_set_params(int bond_type, int mult, double bend, double phase)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].type = BONDED_IA_DIHEDRAL;
bonded_ia_params[bond_type].num = 3;
bonded_ia_params[bond_type].p.dihedral.mult = mult;
bonded_ia_params[bond_type].p.dihedral.bend = bend;
bonded_ia_params[bond_type].p.dihedral.phase = phase;
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
/*****************************************************************************
* setting parameters
*****************************************************************************/
int rigid_bond_set_params(int bond_type, double d, double p_tol, double v_tol)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.rigid_bond.d2 = d*d;
bonded_ia_params[bond_type].p.rigid_bond.p_tol = 2.0*p_tol;
bonded_ia_params[bond_type].p.rigid_bond.v_tol = v_tol*time_step;
bonded_ia_params[bond_type].type = BONDED_IA_RIGID_BOND;
bonded_ia_params[bond_type].num = 1;
n_rigidbonds += 1;
mpi_bcast_ia_params(bond_type, -1);
mpi_bcast_parameter(FIELD_RIGIDBONDS);
return ES_OK;
}
/** set parameters for the angle potential.
\todo The type of the angle potential
is chosen via config.hpp and cannot be changed at runtime.
*/
int angle_cossquare_set_params(int bond_type, double bend, double phi0)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.angle_cossquare.bend = bend;
bonded_ia_params[bond_type].p.angle_cossquare.phi0 = phi0;
bonded_ia_params[bond_type].p.angle_cossquare.cos_phi0 = cos(phi0);
bonded_ia_params[bond_type].type = BONDED_IA_ANGLE_COSSQUARE;
bonded_ia_params[bond_type].num = 2;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
/// set the parameters for the stretching_force potential
int stretching_force_set_params(int bond_type, double r0, double ks)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.stretching_force.ks = ks;
bonded_ia_params[bond_type].p.stretching_force.r0 = r0;
bonded_ia_params[bond_type].type = BONDED_IA_STRETCHING_FORCE;
bonded_ia_params[bond_type].num = 1;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
int harmonic_set_params(int bond_type, double k, double r,double r_cut)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.harmonic.k = k;
bonded_ia_params[bond_type].p.harmonic.r = r;
bonded_ia_params[bond_type].p.harmonic.r_cut = r_cut;
bonded_ia_params[bond_type].type = BONDED_IA_HARMONIC;
bonded_ia_params[bond_type].num = 1;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
/** set parameters for the AREA_FORCE_GLOBAL potential.
*/
int area_force_global_set_params(int bond_type, double A0_g, double ka_g)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.area_force_global.ka_g = ka_g;
bonded_ia_params[bond_type].p.area_force_global.A0_g = A0_g;
bonded_ia_params[bond_type].type = BONDED_IA_AREA_FORCE_GLOBAL;
bonded_ia_params[bond_type].num = 2;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
/** set parameters for the angle potential.
\todo The type of the angle potential
is chosen via config.hpp and cannot be changed at runtime.
*/
int angle_harmonic_set_params(int bond_type, double bend, double phi0)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.angle_harmonic.bend = bend;
bonded_ia_params[bond_type].p.angle_harmonic.phi0 = phi0;
bonded_ia_params[bond_type].type = BONDED_IA_ANGLE_HARMONIC;
bonded_ia_params[bond_type].num = 2;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
/** set parameters for the OIF_GLOBAL_FORCES potential.
*/
int oif_global_forces_set_params(int bond_type, double A0_g, double ka_g, double V0, double kv)
{
if(bond_type < 0)
return ES_ERROR;
make_bond_type_exist(bond_type);
bonded_ia_params[bond_type].p.oif_global_forces.ka_g = ka_g;
bonded_ia_params[bond_type].p.oif_global_forces.A0_g = A0_g;
bonded_ia_params[bond_type].p.oif_global_forces.V0 = V0;
bonded_ia_params[bond_type].p.oif_global_forces.kv = kv;
bonded_ia_params[bond_type].type = BONDED_IA_OIF_GLOBAL_FORCES;
bonded_ia_params[bond_type].num = 2;
/* broadcast interaction parameters */
mpi_bcast_ia_params(bond_type, -1);
return ES_OK;
}
