diff --git a/src/CG-DNA/bond_oxdna2_fene.cpp b/src/CG-DNA/bond_oxdna2_fene.cpp index 0fad5bfaae..54f2dab9d2 100644 --- a/src/CG-DNA/bond_oxdna2_fene.cpp +++ b/src/CG-DNA/bond_oxdna2_fene.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -19,30 +18,16 @@ using namespace LAMMPS_NS; -/* ---------------------------------------------------------------------- */ - -BondOxdna2Fene::BondOxdna2Fene(LAMMPS *lmp) : BondOxdnaFene(lmp) -{ - -} - -/* ---------------------------------------------------------------------- */ - -BondOxdna2Fene::~BondOxdna2Fene() -{ - -} - /* ---------------------------------------------------------------------- compute vector COM-sugar-phosphate backbone interaction site in oxDNA2 ------------------------------------------------------------------------- */ -void BondOxdna2Fene::compute_interaction_sites(double e1[3], double e2[3], - double /*e3*/[3], double r[3]) +void BondOxdna2Fene::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3], + double r[3]) const { - double d_cs_x=-0.34, d_cs_y=+0.3408; - - r[0] = d_cs_x*e1[0] + d_cs_y*e2[0]; - r[1] = d_cs_x*e1[1] + d_cs_y*e2[1]; - r[2] = d_cs_x*e1[2] + d_cs_y*e2[2]; + constexpr double d_cs_x = -0.34; + constexpr double d_cs_y = +0.3408; + r[0] = d_cs_x * e1[0] + d_cs_y * e2[0]; + r[1] = d_cs_x * e1[1] + d_cs_y * e2[1]; + r[2] = d_cs_x * e1[2] + d_cs_y * e2[2]; } diff --git a/src/CG-DNA/bond_oxdna2_fene.h b/src/CG-DNA/bond_oxdna2_fene.h index 98a74e3551..6c932f9421 100644 --- a/src/CG-DNA/bond_oxdna2_fene.h +++ b/src/CG-DNA/bond_oxdna2_fene.h @@ -26,9 +26,9 @@ namespace LAMMPS_NS { class BondOxdna2Fene : public BondOxdnaFene { public: - BondOxdna2Fene(class LAMMPS *); - virtual ~BondOxdna2Fene(); - virtual void compute_interaction_sites(double *, double *, double *, double *); + BondOxdna2Fene(class LAMMPS *lmp) : BondOxdnaFene(lmp) {} + virtual ~BondOxdna2Fene() {} + virtual void compute_interaction_sites(double *, double *, double *, double *) const; }; } // namespace LAMMPS_NS diff --git a/src/CG-DNA/bond_oxdna_fene.cpp b/src/CG-DNA/bond_oxdna_fene.cpp index 0075ec6bb0..5a332a0b8c 100644 --- a/src/CG-DNA/bond_oxdna_fene.cpp +++ b/src/CG-DNA/bond_oxdna_fene.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -18,31 +17,20 @@ #include "bond_oxdna_fene.h" #include "atom.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 "comm.h" #include "update.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +#include "atom_vec_ellipsoid.h" +#include "math_extra.h" #include using namespace LAMMPS_NS; -/* ---------------------------------------------------------------------- - 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]; -} - /* ---------------------------------------------------------------------- */ BondOxdnaFene::~BondOxdnaFene() @@ -56,6 +44,19 @@ BondOxdnaFene::~BondOxdnaFene() } +/* ---------------------------------------------------------------------- + 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]) const +{ + constexpr 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 ------------------------------------------------------------------------- */ @@ -187,8 +188,8 @@ 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,ra_cs); - compute_interaction_sites(bx,rb_cs); + compute_interaction_sites(ax,ay,az,ra_cs); + compute_interaction_sites(bx,by,bz,rb_cs); // vector backbone site b to a delr[0] = x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0]; diff --git a/src/CG-DNA/bond_oxdna_fene.h b/src/CG-DNA/bond_oxdna_fene.h index 6e2272d597..42b542a6fb 100644 --- a/src/CG-DNA/bond_oxdna_fene.h +++ b/src/CG-DNA/bond_oxdna_fene.h @@ -28,6 +28,7 @@ class BondOxdnaFene : public Bond { public: BondOxdnaFene(class LAMMPS *lmp) : Bond(lmp) {} virtual ~BondOxdnaFene(); + virtual void compute_interaction_sites(double *, double *, double *, double *) const; virtual void compute(int, int); void coeff(int, char **); void init_style(); diff --git a/src/CG-DNA/bond_oxrna2_fene.cpp b/src/CG-DNA/bond_oxrna2_fene.cpp index 71c5d9edf3..24de5f7714 100644 --- a/src/CG-DNA/bond_oxrna2_fene.cpp +++ b/src/CG-DNA/bond_oxrna2_fene.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -19,30 +18,17 @@ using namespace LAMMPS_NS; -/* ---------------------------------------------------------------------- */ - -BondOxrna2Fene::BondOxrna2Fene(LAMMPS *lmp) : BondOxdnaFene(lmp) -{ - -} - -/* ---------------------------------------------------------------------- */ - -BondOxrna2Fene::~BondOxrna2Fene() -{ - -} - /* ---------------------------------------------------------------------- compute vector COM-sugar-phosphate backbone interaction site in oxRNA2 ------------------------------------------------------------------------- */ -void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /*e2*/[3], - double e3[3], double r[3]) + +void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /*e2*/[3], double e3[3], + double r[3]) const { - double d_cs_x=-0.4, d_cs_z=+0.2; - - r[0] = d_cs_x*e1[0] + d_cs_z*e3[0]; - r[1] = d_cs_x*e1[1] + d_cs_z*e3[1]; - r[2] = d_cs_x*e1[2] + d_cs_z*e3[2]; + constexpr double d_cs_x = -0.4; + constexpr double d_cs_z = +0.2; + r[0] = d_cs_x * e1[0] + d_cs_z * e3[0]; + r[1] = d_cs_x * e1[1] + d_cs_z * e3[1]; + r[2] = d_cs_x * e1[2] + d_cs_z * e3[2]; } diff --git a/src/CG-DNA/bond_oxrna2_fene.h b/src/CG-DNA/bond_oxrna2_fene.h index 901daf2eb0..a805cd005f 100644 --- a/src/CG-DNA/bond_oxrna2_fene.h +++ b/src/CG-DNA/bond_oxrna2_fene.h @@ -26,9 +26,10 @@ namespace LAMMPS_NS { class BondOxrna2Fene : public BondOxdnaFene { public: - BondOxrna2Fene(class LAMMPS *); - virtual ~BondOxrna2Fene(); - virtual void compute_interaction_sites(double *, double *, double *, double *); + BondOxrna2Fene(class LAMMPS *lmp) : BondOxdnaFene(lmp) {} + virtual ~BondOxrna2Fene() {} + + virtual void compute_interaction_sites(double *, double *, double *, double *) const; }; } // namespace LAMMPS_NS