correct bug in derived CG-DNA FENE bond classes and optimize code

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],
+void BondOxdna2Fene::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3],
-  double /*e3*/[3], double r[3])
+                                               double r[3]) const
 {
-  double d_cs_x=-0.34, d_cs_y=+0.3408;
+  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];
 
+  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];
 }

src/CG-DNA/bond_oxdna2_fene.h

@@ -26,9 +26,9 @@ namespace LAMMPS_NS {
 
 class BondOxdna2Fene : public BondOxdnaFene {
  public:
-  BondOxdna2Fene(class LAMMPS *);
+  BondOxdna2Fene(class LAMMPS *lmp) : BondOxdnaFene(lmp) {}
-  virtual ~BondOxdna2Fene();
+  virtual ~BondOxdna2Fene() {}
-  virtual void compute_interaction_sites(double *, double *, double *, double *);
+  virtual void compute_interaction_sites(double *, double *, double *, double *) const;
 };
 
 }    // namespace LAMMPS_NS

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 <cmath>
 
 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(ax,ay,az,ra_cs);
-    compute_interaction_sites(bx,rb_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];

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();

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;
+  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];
 
+  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];
 }

src/CG-DNA/bond_oxrna2_fene.h

@@ -26,9 +26,10 @@ namespace LAMMPS_NS {
 
 class BondOxrna2Fene : public BondOxdnaFene {
  public:
-  BondOxrna2Fene(class LAMMPS *);
+  BondOxrna2Fene(class LAMMPS *lmp) : BondOxdnaFene(lmp) {}
-  virtual ~BondOxrna2Fene();
+  virtual ~BondOxrna2Fene() {}
-  virtual void compute_interaction_sites(double *, double *, double *, double *);
+
+  virtual void compute_interaction_sites(double *, double *, double *, double *) const;
 };
 
 }    // namespace LAMMPS_NS