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Set rlogarg to intermediate value, force capped at 35 LJU

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This commit is contained in:
Oliver Henrich
2024-05-15 22:50:37 +01:00
parent 5f6f6ba0d6
commit 83cfa0bfdd
1 changed files with 4 additions and 4 deletions
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8
src/CG-DNA/bond_oxdna_fene.cpp
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@ -167,7 +167,7 @@ void BondOxdnaFene::compute(int eflag, int vflag)
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
int newton_bond = force->newton_bond; int newton_bond = force->newton_bond;
const double rlogarg_min = 0.1; const double rlogarg_min = 0.2;
ebond = 0.0; ebond = 0.0;
ev_init(eflag, vflag); ev_init(eflag, vflag);
@ -225,11 +225,11 @@ void BondOxdnaFene::compute(int eflag, int vflag)
ebond = -0.5 * k[type] * log(rlogarg); ebond = -0.5 * k[type] * log(rlogarg);
} }
// switching to capped force for r-r0 -> Delta, i.e. // switching to capped force for r-r0 -> Delta at
// r > r_max = r0 + Delta*sqrt(1-rlogarg) OR // r > r_max = r0 + Delta*sqrt(1-rlogarg) OR
// r < r_min = r0 - Delta*sqrt(1-rlogarg) // r < r_min = r0 - Delta*sqrt(1-rlogarg)
if (rlogarg < rlogarg_min) { if (rlogarg < rlogarg_min) {
// issue warning, reset rlogarg and rr0 to cap force to // issue warning, reset rlogarg and rr0 to cap force
error->warning(FLERR, "FENE bond too long: {} {} {} {}", update->ntimestep, atom->tag[a], error->warning(FLERR, "FENE bond too long: {} {} {} {}", update->ntimestep, atom->tag[a],
atom->tag[b], r); atom->tag[b], r);
rlogarg = rlogarg_min; rlogarg = rlogarg_min;
@ -243,7 +243,7 @@ void BondOxdnaFene::compute(int eflag, int vflag)
(r - r0[type] - Delta[type] * sqrt(1.0-rlogarg)); (r - r0[type] - Delta[type] * sqrt(1.0-rlogarg));
} }
} }
// if overcompressed F(r)=F(r_min)=F_max, E(r)=E(r_min)+F_max*(r-r_min) // if overcompressed F(r)=F(r_min)=F_max, E(r)=E(r_min)+F_max*(r_min-r)
else if (r < r0[type]) { else if (r < r0[type]) {
rr0 = -Delta[type]*sqrt(1.0-rlogarg); rr0 = -Delta[type]*sqrt(1.0-rlogarg);
// energy // energy