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fixed rcut for unbonded pair #93

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merged 1 commit into from
Mar 14, 2024
Merged

fixed rcut for unbonded pair #93

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15 changes: 10 additions & 5 deletions contrib/tostiguerra/src/CGNucleicAcidsInteraction.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -80,8 +80,9 @@ void CGNucleicAcidsInteraction::get_settings(input_file &inp) {
void CGNucleicAcidsInteraction::init() {
_sqr_rfene = SQR(_rfene);
_PS_sqr_rep_rcut = pow(2. * _WCA_sigma, 2. / _PS_n);
// _WCA_sigma_unbonded = _WCA_sigma * (6.0 / _bead_size - _3b_sigma) / 2.0; // disabled for now
_WCA_sigma_unbonded = _WCA_sigma;
_WCA_sigma_unbonded = _WCA_sigma * (6.0 / _bead_size - _3b_sigma) / 2.0; // not disabled
_PS_sqr_rep_rcut_unbonded = pow(2. * _WCA_sigma_unbonded, 2. / _PS_n);
// _WCA_sigma_unbonded = _WCA_sigma; // disabled

OX_LOG(Logger::LOG_INFO, "CGNA: WCA sigma = %lf, WCA sigma unbonded = %lf", _WCA_sigma, _WCA_sigma_unbonded);

Expand Down Expand Up @@ -215,18 +216,22 @@ number CGNucleicAcidsInteraction::_fene(BaseParticle *p, BaseParticle *q, bool u

number CGNucleicAcidsInteraction::_WCA(BaseParticle *p, BaseParticle *q, bool update_forces) {
number sqr_r = _computed_r.norm();
if(sqr_r > _PS_sqr_rep_rcut) {

number sigma = p->is_bonded(q) ? _WCA_sigma : _WCA_sigma_unbonded;
number sqr_rcut = p->is_bonded(q) ? _PS_sqr_rep_rcut : _PS_sqr_rep_rcut_unbonded;

if(sqr_r > sqr_rcut) {
return (number) 0.;
}

number energy = 0;
// this number is the module of the force over r, so we don't have to divide the distance vector for its module
number force_mod = 0;

number sigma = p->is_bonded(q) ? _WCA_sigma : _WCA_sigma_unbonded;


// cut-off for all the repulsive interactions
if(sqr_r < _PS_sqr_rep_rcut) {
if(sqr_r < sqr_rcut) {
number part = 1.;
number ir2_scaled = SQR(sigma) / sqr_r;
for(int i = 0; i < _PS_n / 2; i++) {
Expand Down
2 changes: 1 addition & 1 deletion contrib/tostiguerra/src/CGNucleicAcidsInteraction.h
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ class CGNucleicAcidsInteraction: public BaseInteraction {
number _rfene = 1.5;
number _sqr_rfene;
number _WCA_sigma = 1.0, _WCA_sigma_unbonded;
number _PS_sqr_rep_rcut;
number _PS_sqr_rep_rcut, _PS_sqr_rep_rcut_unbonded;
number _tC = 37.0;
number dS_mod = 1.0;
number alpha_mod = 1.0;
Expand Down
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