diff --git a/src/CG-DNA/bond_oxdna_fene.cpp b/src/CG-DNA/bond_oxdna_fene.cpp index 483e54e809..0075ec6bb0 100644 --- a/src/CG-DNA/bond_oxdna_fene.cpp +++ b/src/CG-DNA/bond_oxdna_fene.cpp @@ -17,25 +17,30 @@ #include "bond_oxdna_fene.h" -#include #include "atom.h" -#include "neighbor.h" -#include "comm.h" -#include "update.h" -#include "force.h" -#include "memory.h" -#include "error.h" - #include "atom_vec_ellipsoid.h" +#include "comm.h" +#include "error.h" +#include "force.h" #include "math_extra.h" +#include "memory.h" +#include "neighbor.h" +#include "update.h" + +#include using namespace LAMMPS_NS; -/* ---------------------------------------------------------------------- */ - -BondOxdnaFene::BondOxdnaFene(LAMMPS *lmp) : Bond(lmp) +/* ---------------------------------------------------------------------- + compute vector COM-sugar-phosphate backbone interaction site in oxDNA +------------------------------------------------------------------------- */ +static void compute_interaction_sites(const double e1[3], double r[3]) { + constexpr double d_cs=-0.4; + r[0] = d_cs*e1[0]; + r[1] = d_cs*e1[1]; + r[2] = d_cs*e1[2]; } /* ---------------------------------------------------------------------- */ @@ -43,30 +48,14 @@ BondOxdnaFene::BondOxdnaFene(LAMMPS *lmp) : Bond(lmp) BondOxdnaFene::~BondOxdnaFene() { if (allocated) { - memory->destroy(setflag); memory->destroy(k); memory->destroy(Delta); memory->destroy(r0); - } } -/* ---------------------------------------------------------------------- - compute vector COM-sugar-phosphate backbone interaction site in oxDNA -------------------------------------------------------------------------- */ -void BondOxdnaFene::compute_interaction_sites(double e1[3], double /*e2*/[3], - double /*e3*/[3], double r[3]) -{ - double d_cs=-0.4; - - r[0] = d_cs*e1[0]; - r[1] = d_cs*e1[1]; - r[2] = d_cs*e1[2]; - -} - /* ---------------------------------------------------------------------- tally energy and virial into global and per-atom accumulators ------------------------------------------------------------------------- */ @@ -198,8 +187,8 @@ void BondOxdnaFene::compute(int eflag, int vflag) MathExtra::q_to_exyz(qb,bx,by,bz); // vector COM-backbone site a and b - compute_interaction_sites(ax,ay,az,ra_cs); - compute_interaction_sites(bx,by,bz,rb_cs); + compute_interaction_sites(ax,ra_cs); + compute_interaction_sites(bx,rb_cs); // vector backbone site b to a delr[0] = x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0]; @@ -218,11 +207,8 @@ void BondOxdnaFene::compute(int eflag, int vflag) // if r > 2*Delta something serious is wrong, abort if (rlogarg < 0.1) { - char str[128]; - sprintf(str,"FENE bond too long: " BIGINT_FORMAT " " - TAGINT_FORMAT " " TAGINT_FORMAT " %g", - update->ntimestep,atom->tag[a],atom->tag[b],r); - error->warning(FLERR,str); + error->warning(FLERR,"FENE bond too long: {} {} {} {}", + update->ntimestep,atom->tag[a],atom->tag[b],r); rlogarg = 0.1; } @@ -398,10 +384,8 @@ double BondOxdnaFene::single(int type, double rsq, int /*i*/, int /*j*/, // if r > 2*Delta something serious is wrong, abort if (rlogarg < 0.1) { - char str[128]; - sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %g", - update->ntimestep,sqrt(rsq)); - error->warning(FLERR,str); + error->warning(FLERR,"FENE bond too long: {} {:.8}", + update->ntimestep,sqrt(rsq)); rlogarg = 0.1; } diff --git a/src/CG-DNA/bond_oxdna_fene.h b/src/CG-DNA/bond_oxdna_fene.h index d0151da4af..6e2272d597 100644 --- a/src/CG-DNA/bond_oxdna_fene.h +++ b/src/CG-DNA/bond_oxdna_fene.h @@ -26,9 +26,8 @@ namespace LAMMPS_NS { class BondOxdnaFene : public Bond { public: - BondOxdnaFene(class LAMMPS *); + BondOxdnaFene(class LAMMPS *lmp) : Bond(lmp) {} virtual ~BondOxdnaFene(); - virtual void compute_interaction_sites(double *, double *, double *, double *); virtual void compute(int, int); void coeff(int, char **); void init_style();