From 83cfa0bfdda6660b1af247b9f94bf33eb428876b Mon Sep 17 00:00:00 2001 From: Oliver Henrich Date: Wed, 15 May 2024 22:50:37 +0100 Subject: [PATCH] Set rlogarg to intermediate value, force capped at 35 LJU --- src/CG-DNA/bond_oxdna_fene.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/CG-DNA/bond_oxdna_fene.cpp b/src/CG-DNA/bond_oxdna_fene.cpp index 5509de786d..7a60ae3555 100644 --- a/src/CG-DNA/bond_oxdna_fene.cpp +++ b/src/CG-DNA/bond_oxdna_fene.cpp @@ -167,7 +167,7 @@ void BondOxdnaFene::compute(int eflag, int vflag) int nlocal = atom->nlocal; int newton_bond = force->newton_bond; - const double rlogarg_min = 0.1; + const double rlogarg_min = 0.2; ebond = 0.0; ev_init(eflag, vflag); @@ -225,11 +225,11 @@ void BondOxdnaFene::compute(int eflag, int vflag) 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_min = r0 - Delta*sqrt(1-rlogarg) 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], atom->tag[b], r); rlogarg = rlogarg_min; @@ -243,7 +243,7 @@ void BondOxdnaFene::compute(int eflag, int vflag) (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]) { rr0 = -Delta[type]*sqrt(1.0-rlogarg); // energy