virtual void setup_potential(){
auto compot = new pele::CombinedPotential();
compot->add_potential(std::make_shared<pele::LJCutAtomList>(c6, c12, rcut, atomsA));
compot->add_potential(std::make_shared<pele::LJCutAtomList>(c6, c12, rcut, atomsA, atomsB));
compot->add_potential(std::make_shared<pele::LJCutAtomList>(c6, c12, rcut, atomsB));
pot = std::shared_ptr<pele::BasePotential> (compot);
}
void apot_init(void)
{
int i;
add_pot(lj, 2);
add_pot(eopp, 6);
add_pot(morse, 3);
#ifdef COULOMB
add_potential("ms", 3, &ms_shift);
add_potential("buck", 3, &buck_shift);
#else
add_potential("ms", 3, &ms_value);
add_potential("buck", 3, &buck_value);
#endif /* COULOMB */
add_pot(softshell, 2);
add_pot(eopp_exp, 6);
add_pot(meopp, 7);
add_pot(power, 2);
add_pot(power_decay, 2);
add_pot(exp_decay, 2);
add_pot(bjs, 3);
add_pot(parabola, 3);
add_pot(csw, 4);
add_pot(universal, 4);
add_pot(const, 1);
add_pot(sqrt, 2);
add_pot(mexp_decay, 3);
add_pot(strmm, 5);
add_pot(double_morse, 7);
add_pot(double_exp, 5);
add_pot(poly_5, 5);
add_pot(kawamura, 9);
add_pot(kawamura_mix, 12);
add_pot(exp_plus, 3);
add_pot(mishin, 6);
add_pot(gen_lj, 5);
add_pot(gljm, 12);
add_pot(vas, 2);
add_pot(vpair, 7);
add_pot(csw2, 4);
add_pot(sheng_phi1, 5);
add_pot(sheng_phi2, 4);
add_pot(sheng_rho, 5);
add_pot(sheng_F, 4);
#ifdef STIWEB
add_pot(stiweb_2, 6);
add_pot(stiweb_3, 2);
add_pot(lambda, (int)(0.5 * ntypes * ntypes * (ntypes + 1)));
#endif /* STIWEB */
#ifdef TERSOFF
add_pot(tersoff_pot, 11);
add_pot(tersoff_mix, 2);
#endif /* TERSOFF */
reg_for_free(function_table.name, "function_table.name");
reg_for_free(function_table.n_par, "function_table.n_par");
reg_for_free(function_table.fvalue, "function_table.fvalue");
for (i = 0; i < n_functions; i++)
reg_for_free(function_table.name[i], "function_table.name[i]");
return;
}
std::shared_ptr<Model> Deserno2005ModelFactory::create() const {
auto model = std::make_shared<Model>(num_lipid * 3);
std::shared_ptr<FENEBondPotential> head_tail_bond(
new FENEBondPotential(
/* r0= */1.5*sigma,
/* k = */30*epsilon/sigma/sigma,
/* b = */0.95*sigma,
/* e = */epsilon));
for (std::size_t i(0); i < num_lipid; ++i)
head_tail_bond->add_bond(std::make_pair(i*3, i*3+1));
model->add_potential(head_tail_bond);
std::shared_ptr<FENEBondPotential> tail_tail_bond(
new FENEBondPotential(
/* r0= */1.5*sigma,
/* k = */30*epsilon/sigma/sigma,
/* b = */sigma,
/* e = */epsilon));
for (std::size_t i(0); i < num_lipid; ++i)
tail_tail_bond->add_bond(std::make_pair(i*3+1, i*3+2));
model->add_potential(tail_tail_bond);
std::shared_ptr<LowestOrderHarmonicBendPotential> bend(
new LowestOrderHarmonicBendPotential(
/* r0= */4*sigma,
/* k = */10*epsilon/sigma/sigma));
for (std::size_t i(0); i < num_lipid; ++i)
bend->add_pair(std::make_pair(i*3, i*3+2));
model->add_potential(bend);
std::shared_ptr<WeeksChandlerAndersonPotential> head_head_replusion(
new WeeksChandlerAndersonPotential(
/* s= */0.95*sigma,
/* e= */epsilon));
head_head_replusion->set_pair("LH", "LH");
model->add_potential(head_head_replusion);
std::shared_ptr<WeeksChandlerAndersonPotential> head_tail_replusion(
new WeeksChandlerAndersonPotential(
/* s= */0.95*sigma,
/* e= */epsilon));
head_tail_replusion->set_pair("LH", "LT");
model->add_potential(head_tail_replusion);
std::shared_ptr<WeeksChandlerAndersonPotential> tail_tail_replusion(
new WeeksChandlerAndersonPotential(
/* s= */sigma,
/* e= */epsilon));
tail_tail_replusion->set_pair("LT", "LT");
model->add_potential(tail_tail_replusion);
std::shared_ptr<TailsAttractionPotential> tails_attraction(
new TailsAttractionPotential(
/* r_c= */pow(2,1.0/6.0)*sigma,
/* w_c= */w_c,
/* e = */epsilon));
tails_attraction->set_pair("LT", "LT");
model->add_potential(tails_attraction);
return model;
}
