Updating to develop

src/.gitignore

@@ -1502,6 +1502,8 @@
 /pair_dpd_fdt.h
 /pair_dpd_fdt_energy.cpp
 /pair_dpd_fdt_energy.h
+/pair_harmonic_cut.cpp
+/pair_harmonic_cut.h
 /pair_lennard_mdf.cpp
 /pair_lennard_mdf.h
 /pair_lj_cut_coul_long_cs.cpp

src/ADIOS/dump_atom_adios.h

@@ -30,12 +30,12 @@ class DumpAtomADIOS : public DumpAtom {
 
  public:
   DumpAtomADIOS(class LAMMPS *, int, char **);
-  virtual ~DumpAtomADIOS();
+  ~DumpAtomADIOS() override;
 
  protected:
-  virtual void openfile();
-  virtual void write();
-  virtual void init_style();
+  void openfile() override;
+  void write() override;
+  void init_style() override;
 
  private:
   DumpAtomADIOSInternal *internal;

src/ADIOS/dump_custom_adios.h

@@ -29,12 +29,12 @@ class DumpCustomADIOSInternal;
 class DumpCustomADIOS : public DumpCustom {
  public:
   DumpCustomADIOS(class LAMMPS *, int, char **);
-  virtual ~DumpCustomADIOS();
+  ~DumpCustomADIOS() override;
 
  protected:
-  virtual void openfile();
-  virtual void write();
-  virtual void init_style();
+  void openfile() override;
+  void write() override;
+  void init_style() override;
 
  private:
   DumpCustomADIOSInternal *internal;

src/ADIOS/reader_adios.h

@@ -34,18 +34,18 @@ class ReadADIOSInternal;
 class ReaderADIOS : public Reader {
  public:
   ReaderADIOS(class LAMMPS *);
-  virtual ~ReaderADIOS();
+  ~ReaderADIOS() override;
 
-  virtual void settings(int, char **);
+  void settings(int, char **) override;
 
-  virtual int read_time(bigint &);
-  virtual void skip();
-  virtual bigint read_header(double[3][3], int &, int &, int, int, int *, char **, int, int, int &,
-                             int &, int &, int &);
-  virtual void read_atoms(int, int, double **);
+  int read_time(bigint &) override;
+  void skip() override;
+  bigint read_header(double[3][3], int &, int &, int, int, int *, char **, int, int, int &,
+                     int &, int &, int &) override;
+  void read_atoms(int, int, double **) override;
 
-  virtual void open_file(const char *);
-  virtual void close_file();
+  void open_file(const char *) override;
+  void close_file() override;
 
  private:
   int *fieldindex;         // mapping of input fields to dump

src/ASPHERE/compute_erotate_asphere.h

@@ -27,8 +27,8 @@ namespace LAMMPS_NS {
 class ComputeERotateAsphere : public Compute {
  public:
   ComputeERotateAsphere(class LAMMPS *, int, char **);
-  void init();
-  double compute_scalar();
+  void init() override;
+  double compute_scalar() override;
 
  private:
   double pfactor;

src/ASPHERE/compute_temp_asphere.h

@@ -27,16 +27,16 @@ namespace LAMMPS_NS {
 class ComputeTempAsphere : public Compute {
  public:
   ComputeTempAsphere(class LAMMPS *, int, char **);
-  ~ComputeTempAsphere();
-  void init();
-  void setup();
-  double compute_scalar();
-  void compute_vector();
+  ~ComputeTempAsphere() override;
+  void init() override;
+  void setup() override;
+  double compute_scalar() override;
+  void compute_vector() override;
 
-  void remove_bias(int, double *);
-  void restore_bias(int, double *);
-  void remove_bias_thr(int, double *, double *);
-  void restore_bias_thr(int, double *, double *);
+  void remove_bias(int, double *) override;
+  void restore_bias(int, double *) override;
+  void remove_bias_thr(int, double *, double *) override;
+  void restore_bias_thr(int, double *, double *) override;
 
  private:
   int mode;

src/ASPHERE/fix_nh_asphere.h

@@ -21,16 +21,15 @@ namespace LAMMPS_NS {
 class FixNHAsphere : public FixNH {
  public:
   FixNHAsphere(class LAMMPS *, int, char **);
-  virtual ~FixNHAsphere() {}
-  void init();
+  void init() override;
 
  protected:
   double dtq;
   class AtomVecEllipsoid *avec;
 
-  void nve_v();
-  void nve_x();
-  void nh_v_temp();
+  void nve_v() override;
+  void nve_x() override;
+  void nh_v_temp() override;
 };
 
 }    // namespace LAMMPS_NS

src/ASPHERE/fix_nph_asphere.h

@@ -27,7 +27,6 @@ namespace LAMMPS_NS {
 class FixNPHAsphere : public FixNHAsphere {
  public:
   FixNPHAsphere(class LAMMPS *, int, char **);
-  ~FixNPHAsphere() {}
 };
 
 }    // namespace LAMMPS_NS

src/ASPHERE/fix_npt_asphere.h

@@ -27,7 +27,6 @@ namespace LAMMPS_NS {
 class FixNPTAsphere : public FixNHAsphere {
  public:
   FixNPTAsphere(class LAMMPS *, int, char **);
-  ~FixNPTAsphere() {}
 };
 
 }    // namespace LAMMPS_NS

src/ASPHERE/fix_nve_asphere.h

@@ -27,9 +27,9 @@ namespace LAMMPS_NS {
 class FixNVEAsphere : public FixNVE {
  public:
   FixNVEAsphere(class LAMMPS *, int, char **);
-  void init();
-  void initial_integrate(int);
-  void final_integrate();
+  void init() override;
+  void initial_integrate(int) override;
+  void final_integrate() override;
 
  private:
   double dtq;

src/ASPHERE/fix_nve_asphere_noforce.h

@@ -27,8 +27,8 @@ namespace LAMMPS_NS {
 class FixNVEAsphereNoforce : public FixNVENoforce {
  public:
   FixNVEAsphereNoforce(class LAMMPS *, int, char **);
-  void initial_integrate(int);
-  void init();
+  void initial_integrate(int) override;
+  void init() override;
 
  private:
   double dtq;

src/ASPHERE/fix_nve_line.h

@@ -27,11 +27,10 @@ namespace LAMMPS_NS {
 class FixNVELine : public FixNVE {
  public:
   FixNVELine(class LAMMPS *, int, char **);
-  ~FixNVELine() {}
-  int setmask();
-  void init();
-  void initial_integrate(int);
-  void final_integrate();
+  int setmask() override;
+  void init() override;
+  void initial_integrate(int) override;
+  void final_integrate() override;
 
  private:
   double MINUSPI, TWOPI;

src/ASPHERE/fix_nve_tri.h

@@ -27,11 +27,10 @@ namespace LAMMPS_NS {
 class FixNVETri : public FixNVE {
  public:
   FixNVETri(class LAMMPS *, int, char **);
-  ~FixNVETri() {}
-  int setmask();
-  void init();
-  void initial_integrate(int);
-  void final_integrate();
+  int setmask() override;
+  void init() override;
+  void initial_integrate(int) override;
+  void final_integrate() override;
 
  private:
   double dtq;

src/ASPHERE/fix_nvt_asphere.h

@@ -27,7 +27,6 @@ namespace LAMMPS_NS {
 class FixNVTAsphere : public FixNHAsphere {
  public:
   FixNVTAsphere(class LAMMPS *, int, char **);
-  ~FixNVTAsphere() {}
 };
 
 }    // namespace LAMMPS_NS

src/ASPHERE/pair_gayberne.cpp

@@ -18,18 +18,18 @@
 
 #include "pair_gayberne.h"
 
-#include <cmath>
-#include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 #include "citeme.h"
-#include "memory.h"
+#include "comm.h"
 #include "error.h"
+#include "force.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neighbor.h"
 
+#include <cmath>
 
 using namespace LAMMPS_NS;
 

src/ASPHERE/pair_gayberne.h

@@ -27,18 +27,18 @@ namespace LAMMPS_NS {
 class PairGayBerne : public Pair {
  public:
   PairGayBerne(LAMMPS *lmp);
-  virtual ~PairGayBerne();
-  virtual void compute(int, int);
-  virtual void settings(int, char **);
-  void coeff(int, char **);
-  virtual void init_style();
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
+  ~PairGayBerne() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
 
  protected:
   enum { SPHERE_SPHERE, SPHERE_ELLIPSE, ELLIPSE_SPHERE, ELLIPSE_ELLIPSE };

src/ASPHERE/pair_line_lj.h

@@ -27,12 +27,12 @@ namespace LAMMPS_NS {
 class PairLineLJ : public Pair {
  public:
   PairLineLJ(class LAMMPS *);
-  virtual ~PairLineLJ();
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  virtual void init_style();
-  double init_one(int, int);
+  ~PairLineLJ() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double init_one(int, int) override;
 
  protected:
   double cut_global;

src/ASPHERE/pair_resquared.h

@@ -27,16 +27,16 @@ namespace LAMMPS_NS {
 class PairRESquared : public Pair {
  public:
   PairRESquared(LAMMPS *lmp);
-  virtual ~PairRESquared();
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  virtual void init_style();
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
+  ~PairRESquared() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
 
  protected:
   enum { SPHERE_SPHERE, SPHERE_ELLIPSE, ELLIPSE_SPHERE, ELLIPSE_ELLIPSE };

src/ASPHERE/pair_tri_lj.h

@@ -27,12 +27,12 @@ namespace LAMMPS_NS {
 class PairTriLJ : public Pair {
  public:
   PairTriLJ(class LAMMPS *);
-  virtual ~PairTriLJ();
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  virtual void init_style();
-  double init_one(int, int);
+  ~PairTriLJ() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double init_one(int, int) override;
 
  protected:
   double cut_global;

src/ATC/fix_atc.h

@@ -37,91 +37,91 @@ class FixATC : public Fix {
  public:
   /** constructor & destructor */
   FixATC(class LAMMPS *, int, char **);
-  ~FixATC();
+  ~FixATC() override;
 
   /** initialization functions */
-  void init();
-  void init_list(int id, NeighList *ptr);
-  void setup(int vflag);
-  void min_setup(int vflag);
+  void init() override;
+  void init_list(int id, NeighList *ptr) override;
+  void setup(int vflag) override;
+  void min_setup(int vflag) override;
 
   /** setmask: tell LAMMPS which fix methods to call */
-  int setmask();
+  int setmask() override;
 
   /** initial_integrate */
-  void initial_integrate(int vflag);
+  void initial_integrate(int vflag) override;
 
   /** after first integrate phase */
-  void post_integrate();
+  void post_integrate() override;
 
   /** final_integrate */
-  void final_integrate();
+  void final_integrate() override;
 
   /** end of step for run or minimize */
-  void end_of_step();
+  void end_of_step() override;
 
   /** pre_exchange is used to modify fix-specific data
        and is called before domain->pbc() and comm->exchange().  */
-  void setup_pre_exchange();
-  void pre_exchange();
-  void min_pre_exchange();
+  void setup_pre_exchange() override;
+  void pre_exchange() override;
+  void min_pre_exchange() override;
 
-  double memory_usage();
-  void grow_arrays(int);
-  void copy_arrays(int, int, int);
+  double memory_usage() override;
+  void grow_arrays(int) override;
+  void copy_arrays(int, int, int) override;
 
   /** pack_exchange called from atom_vec->pack_exchange()
        and packs fix-specific data for a given real (local)
        atom being sent to another processor.  */
-  int pack_exchange(int, double *);
+  int pack_exchange(int, double *) override;
 
   /** unpack_exchange called from atom_vec->unpack_exchange()
        and unpacks fix-specific data for a given real (local)
        atom received from another processor. */
-  int unpack_exchange(int, double *);
+  int unpack_exchange(int, double *) override;
 
   /** pack_comm called from comm->forward_comm_fix and
        packs fix-specific data for a given ghost atom
        from exchange with another proc */
-  int pack_forward_comm(int, int *, double *, int, int *);
+  int pack_forward_comm(int, int *, double *, int, int *) override;
 
   /** unpack_comm called from comm->forward_comm_fix and
        unpacks fix-specific data for a given ghost atom
        from exchange with another proc */
-  void unpack_forward_comm(int, int, double *);
+  void unpack_forward_comm(int, int, double *) override;
 
   /** pre_neighbor is used to modify fix-specific data
        and is called before neighbor list is built in
        neighbor->build().  */
-  void pre_neighbor();
-  void setup_pre_neighbor();
+  void pre_neighbor() override;
+  void setup_pre_neighbor() override;
 
   /** pre/post_force is used to modify fix-specific data
         and is before/after the various force computations. */
-  void pre_force(int vflag);
-  void post_force(int vflag);
+  void pre_force(int vflag) override;
+  void post_force(int vflag) override;
 
   /** post_run is called after a run completes */
-  void post_run();
+  void post_run() override;
 
   /** min_pre_force is called before forces are calculated in minimize */
-  void min_pre_force(int vflag);
+  void min_pre_force(int vflag) override;
 
   /** min_post_force is called after forces are calculated in minimize */
-  void min_post_force(int vflag);
+  void min_post_force(int vflag) override;
 
   /** modify atc parameters (parser) */
-  int modify_param(int narg, char **arg);
+  int modify_param(int narg, char **arg) override;
 
   /** calls ATC_Method to handle restarting/checkpointing */
   /** these four methods are for writing per-atom quantities */
-  int pack_restart(int, double *);
-  void unpack_restart(int, int);
-  int size_restart(int);
-  int maxsize_restart();
+  int pack_restart(int, double *) override;
+  void unpack_restart(int, int) override;
+  int size_restart(int) override;
+  int maxsize_restart() override;
   /** these two methods are for writing all other quantities */
-  void write_restart(FILE *);
-  void restart(char *);
+  void write_restart(FILE *) override;
+  void restart(char *) override;
 
   /** accessor function for ATC_Method class pointer */
   const ATC::ATC_Method *atc() { return atc_; }
@@ -130,9 +130,9 @@ class FixATC : public Fix {
   LAMMPS *lammps_;
 
   /** functions for "thermo" output */
-  virtual double compute_scalar();
-  virtual double compute_vector(int n);
-  virtual double compute_array(int irow, int icol);
+  double compute_scalar() override;
+  double compute_vector(int n) override;
+  double compute_array(int irow, int icol) override;
   double dtv, dtf;
   ATC::ATC_Method *atc_;
 };

src/AWPMD/atom_vec_wavepacket.h

@@ -28,12 +28,12 @@ class AtomVecWavepacket : public AtomVec {
  public:
   AtomVecWavepacket(class LAMMPS *);
 
-  void grow_pointers();
-  void force_clear(int, size_t);
-  void create_atom_post(int);
-  void data_atom_post(int);
-  int property_atom(char *);
-  void pack_property_atom(int, double *, int, int);
+  void grow_pointers() override;
+  void force_clear(int, size_t) override;
+  void create_atom_post(int) override;
+  void data_atom_post(int) override;
+  int property_atom(char *) override;
+  void pack_property_atom(int, double *, int, int) override;
 
  private:
   int *spin;

src/AWPMD/fix_nve_awpmd.h

@@ -31,13 +31,13 @@ namespace LAMMPS_NS {
 class FixNVEAwpmd : public Fix {
  public:
   FixNVEAwpmd(class LAMMPS *, int, char **);
-  int setmask();
-  virtual void init();
-  virtual void initial_integrate(int);
-  virtual void final_integrate();
-  void initial_integrate_respa(int, int, int);
-  void final_integrate_respa(int, int);
-  void reset_dt();
+  int setmask() override;
+  void init() override;
+  void initial_integrate(int) override;
+  void final_integrate() override;
+  void initial_integrate_respa(int, int, int) override;
+  void final_integrate_respa(int, int) override;
+  void reset_dt() override;
 
  protected:
   double dtv, dtf;

src/AWPMD/pair_awpmd_cut.h

@@ -34,22 +34,22 @@ class PairAWPMDCut : public Pair {
 
  public:
   PairAWPMDCut(class LAMMPS *);
-  virtual ~PairAWPMDCut();
-  virtual void compute(int, int);
-  virtual void settings(int, char **);
-  void coeff(int, char **);
-  void init_style();
+  ~PairAWPMDCut() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
   void min_pointers(double **, double **);
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  virtual void write_restart_settings(FILE *);
-  virtual void read_restart_settings(FILE *);
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
 
-  void min_xf_pointers(int, double **, double **);
-  void min_xf_get(int);
-  void min_x_set(int);
-  double memory_usage();
+  void min_xf_pointers(int, double **, double **) override;
+  void min_xf_get(int) override;
+  void min_x_set(int) override;
+  double memory_usage() override;
 
  private:
   int flexible_pressure_flag;

src/BOCS/compute_pressure_bocs.cpp

@@ -233,23 +233,14 @@ double ComputePressureBocs::get_cg_p_corr(double ** grid, int basis_type,
                                           double vCG)
 {
   int i = find_index(grid[0],vCG);
-  double correction, deltax = vCG - grid[0][i];
+  double deltax = vCG - grid[0][i];
 
   if (basis_type == BASIS_LINEAR_SPLINE)
-  {
-    correction = grid[1][i] + (deltax) *
-          ( grid[1][i+1] - grid[1][i] ) / ( grid[0][i+1] - grid[0][i] );
-  }
+    return grid[1][i] + (deltax) * ( grid[1][i+1] - grid[1][i] ) / ( grid[0][i+1] - grid[0][i] );
   else if (basis_type == BASIS_CUBIC_SPLINE)
-  {
-    correction = grid[1][i] + (grid[2][i] * deltax) +
-            (grid[3][i] * pow(deltax,2)) + (grid[4][i] * pow(deltax,3));
-  }
-  else
-  {
-    error->all(FLERR,"bad spline type passed to get_cg_p_corr()\n");
-  }
-  return correction;
+    return grid[1][i] + (grid[2][i] * deltax) + (grid[3][i] * pow(deltax,2)) + (grid[4][i] * pow(deltax,3));
+  else error->all(FLERR,"bad spline type passed to get_cg_p_corr()\n");
+  return 0.0;
 }
 
 /* ----------------------------------------------------------------------
@@ -261,11 +252,8 @@ void ComputePressureBocs::send_cg_info(int basis_type, int sent_N_basis,
                                        double *sent_phi_coeff, int sent_N_mol,
                                        double sent_vavg)
 {
-  if (basis_type == BASIS_ANALYTIC) { p_basis_type = BASIS_ANALYTIC; }
-  else
-  {
-    error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n");
-  }
+  if (basis_type == BASIS_ANALYTIC) p_basis_type = BASIS_ANALYTIC;
+  else error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n");
 
   p_match_flag = 1;
 

src/BOCS/compute_pressure_bocs.h

@@ -38,11 +38,11 @@ const int NUM_CUBIC_SPLINE_COLUMNS = 5;     // cubic spline columns passed to co
 class ComputePressureBocs : public Compute {
  public:
   ComputePressureBocs(class LAMMPS *, int, char **);
-  virtual ~ComputePressureBocs();
-  virtual void init();
-  virtual double compute_scalar();
-  virtual void compute_vector();
-  void reset_extra_compute_fix(const char *);
+  ~ComputePressureBocs() override;
+  void init() override;
+  double compute_scalar() override;
+  void compute_vector() override;
+  void reset_extra_compute_fix(const char *) override;
 
   double compute_cg_scalar();
   double get_cg_p_corr(int, double *, int, double, double);

src/BOCS/fix_bocs.h

@@ -30,26 +30,26 @@ namespace LAMMPS_NS {
 class FixBocs : public Fix {
  public:
   FixBocs(class LAMMPS *, int, char **);    // MRD NJD
-  virtual ~FixBocs();                       // MRD NJD
-  int setmask();
-  virtual void init();
-  virtual void setup(int);
-  virtual void initial_integrate(int);
-  virtual void final_integrate();
-  void initial_integrate_respa(int, int, int);
-  void pre_force_respa(int, int, int);
-  void final_integrate_respa(int, int);
-  virtual void pre_exchange();
-  double compute_scalar();
-  virtual double compute_vector(int);
-  void write_restart(FILE *);
+  ~FixBocs() override;                       // MRD NJD
+  int setmask() override;
+  void init() override;
+  void setup(int) override;
+  void initial_integrate(int) override;
+  void final_integrate() override;
+  void initial_integrate_respa(int, int, int) override;
+  void pre_force_respa(int, int, int) override;
+  void final_integrate_respa(int, int) override;
+  void pre_exchange() override;
+  double compute_scalar() override;
+  double compute_vector(int) override;
+  void write_restart(FILE *) override;
   virtual int pack_restart_data(double *);    // pack restart data
-  virtual void restart(char *);
-  int modify_param(int, char **);
-  void reset_target(double);
-  void reset_dt();
-  virtual void *extract(const char *, int &);
-  double memory_usage();
+  void restart(char *) override;
+  int modify_param(int, char **) override;
+  void reset_target(double) override;
+  void reset_dt() override;
+  void *extract(const char *, int &) override;
+  double memory_usage() override;
 
  protected:
   int dimension, which;

src/BODY/body_nparticle.h

@@ -28,21 +28,21 @@ namespace LAMMPS_NS {
 class BodyNparticle : public Body {
  public:
   BodyNparticle(class LAMMPS *, int, char **);
-  ~BodyNparticle();
+  ~BodyNparticle() override;
   int nsub(struct AtomVecBody::Bonus *);
   double *coords(struct AtomVecBody::Bonus *);
 
-  int pack_border_body(struct AtomVecBody::Bonus *, double *);
-  int unpack_border_body(struct AtomVecBody::Bonus *, double *);
-  void data_body(int, int, int, int *, double *);
-  int pack_data_body(tagint, int, double *);
-  int write_data_body(FILE *, double *);
-  double radius_body(int, int, int *, double *);
+  int pack_border_body(struct AtomVecBody::Bonus *, double *) override;
+  int unpack_border_body(struct AtomVecBody::Bonus *, double *) override;
+  void data_body(int, int, int, int *, double *) override;
+  int pack_data_body(tagint, int, double *) override;
+  int write_data_body(FILE *, double *) override;
+  double radius_body(int, int, int *, double *) override;
 
-  int noutrow(int);
-  int noutcol();
-  void output(int, int, double *);
-  int image(int, double, double, int *&, double **&);
+  int noutrow(int) override;
+  int noutcol() override;
+  void output(int, int, double *) override;
+  int image(int, double, double, int *&, double **&) override;
 
  private:
   int *imflag;

src/BODY/body_rounded_polygon.h

@@ -28,7 +28,7 @@ namespace LAMMPS_NS {
 class BodyRoundedPolygon : public Body {
  public:
   BodyRoundedPolygon(class LAMMPS *, int, char **);
-  ~BodyRoundedPolygon();
+  ~BodyRoundedPolygon() override;
   int nsub(struct AtomVecBody::Bonus *);
   double *coords(struct AtomVecBody::Bonus *);
   int nedges(struct AtomVecBody::Bonus *);
@@ -36,17 +36,17 @@ class BodyRoundedPolygon : public Body {
   double enclosing_radius(struct AtomVecBody::Bonus *);
   double rounded_radius(struct AtomVecBody::Bonus *);
 
-  int pack_border_body(struct AtomVecBody::Bonus *, double *);
-  int unpack_border_body(struct AtomVecBody::Bonus *, double *);
-  void data_body(int, int, int, int *, double *);
-  int pack_data_body(tagint, int, double *);
-  int write_data_body(FILE *, double *);
-  double radius_body(int, int, int *, double *);
+  int pack_border_body(struct AtomVecBody::Bonus *, double *) override;
+  int unpack_border_body(struct AtomVecBody::Bonus *, double *) override;
+  void data_body(int, int, int, int *, double *) override;
+  int pack_data_body(tagint, int, double *) override;
+  int write_data_body(FILE *, double *) override;
+  double radius_body(int, int, int *, double *) override;
 
-  int noutrow(int);
-  int noutcol();
-  void output(int, int, double *);
-  int image(int, double, double, int *&, double **&);
+  int noutrow(int) override;
+  int noutcol() override;
+  void output(int, int, double *) override;
+  int image(int, double, double, int *&, double **&) override;
 
  private:
   int *imflag;

src/BODY/body_rounded_polyhedron.h

@@ -28,7 +28,7 @@ namespace LAMMPS_NS {
 class BodyRoundedPolyhedron : public Body {
  public:
   BodyRoundedPolyhedron(class LAMMPS *, int, char **);
-  ~BodyRoundedPolyhedron();
+  ~BodyRoundedPolyhedron() override;
   int nsub(struct AtomVecBody::Bonus *);
   double *coords(struct AtomVecBody::Bonus *);
   int nedges(struct AtomVecBody::Bonus *);
@@ -38,17 +38,17 @@ class BodyRoundedPolyhedron : public Body {
   double enclosing_radius(struct AtomVecBody::Bonus *);
   double rounded_radius(struct AtomVecBody::Bonus *);
 
-  int pack_border_body(struct AtomVecBody::Bonus *, double *);
-  int unpack_border_body(struct AtomVecBody::Bonus *, double *);
-  void data_body(int, int, int, int *, double *);
-  int pack_data_body(tagint, int, double *);
-  int write_data_body(FILE *, double *);
-  double radius_body(int, int, int *, double *);
+  int pack_border_body(struct AtomVecBody::Bonus *, double *) override;
+  int unpack_border_body(struct AtomVecBody::Bonus *, double *) override;
+  void data_body(int, int, int, int *, double *) override;
+  int pack_data_body(tagint, int, double *) override;
+  int write_data_body(FILE *, double *) override;
+  double radius_body(int, int, int *, double *) override;
 
-  int noutrow(int);
-  int noutcol();
-  void output(int, int, double *);
-  int image(int, double, double, int *&, double **&);
+  int noutrow(int) override;
+  int noutcol() override;
+  void output(int, int, double *) override;
+  int image(int, double, double, int *&, double **&) override;
 
  private:
   int *imflag;

src/BODY/compute_body_local.h

@@ -27,10 +27,10 @@ namespace LAMMPS_NS {
 class ComputeBodyLocal : public Compute {
  public:
   ComputeBodyLocal(class LAMMPS *, int, char **);
-  ~ComputeBodyLocal();
-  void init();
-  void compute_local();
-  double memory_usage();
+  ~ComputeBodyLocal() override;
+  void init() override;
+  void compute_local() override;
+  double memory_usage() override;
 
  private:
   int nvalues;

src/BODY/compute_temp_body.h

@@ -27,14 +27,14 @@ namespace LAMMPS_NS {
 class ComputeTempBody : public Compute {
  public:
   ComputeTempBody(class LAMMPS *, int, char **);
-  ~ComputeTempBody();
-  void init();
-  void setup();
-  double compute_scalar();
-  void compute_vector();
+  ~ComputeTempBody() override;
+  void init() override;
+  void setup() override;
+  double compute_scalar() override;
+  void compute_vector() override;
 
-  void remove_bias(int, double *);
-  void restore_bias(int, double *);
+  void remove_bias(int, double *) override;
+  void restore_bias(int, double *) override;
 
  private:
   int mode;

src/BODY/fix_nh_body.h

@@ -21,16 +21,15 @@ namespace LAMMPS_NS {
 class FixNHBody : public FixNH {
  public:
   FixNHBody(class LAMMPS *, int, char **);
-  virtual ~FixNHBody() {}
-  void init();
+  void init() override;
 
  protected:
   double dtq;
   class AtomVecBody *avec;
 
-  void nve_v();
-  void nve_x();
-  void nh_v_temp();
+  void nve_v() override;
+  void nve_x() override;
+  void nh_v_temp() override;
 };
 
 }    // namespace LAMMPS_NS

src/BODY/fix_nph_body.h

@@ -27,7 +27,6 @@ namespace LAMMPS_NS {
 class FixNPHBody : public FixNHBody {
  public:
   FixNPHBody(class LAMMPS *, int, char **);
-  ~FixNPHBody() {}
 };
 
 }    // namespace LAMMPS_NS

src/BODY/fix_npt_body.h

@@ -27,7 +27,6 @@ namespace LAMMPS_NS {
 class FixNPTBody : public FixNHBody {
  public:
   FixNPTBody(class LAMMPS *, int, char **);
-  ~FixNPTBody() {}
 };
 
 }    // namespace LAMMPS_NS

src/BODY/fix_nve_body.h

@@ -27,9 +27,9 @@ namespace LAMMPS_NS {
 class FixNVEBody : public FixNVE {
  public:
   FixNVEBody(class LAMMPS *, int, char **);
-  void init();
-  void initial_integrate(int);
-  void final_integrate();
+  void init() override;
+  void initial_integrate(int) override;
+  void final_integrate() override;
 
  private:
   double dtq;

src/BODY/fix_nvt_body.h

@@ -27,7 +27,6 @@ namespace LAMMPS_NS {
 class FixNVTBody : public FixNHBody {
  public:
   FixNVTBody(class LAMMPS *, int, char **);
-  ~FixNVTBody() {}
 };
 
 }    // namespace LAMMPS_NS

src/BODY/fix_wall_body_polygon.h

@@ -27,12 +27,12 @@ namespace LAMMPS_NS {
 class FixWallBodyPolygon : public Fix {
  public:
   FixWallBodyPolygon(class LAMMPS *, int, char **);
-  virtual ~FixWallBodyPolygon();
-  int setmask();
-  void init();
-  void setup(int);
-  virtual void post_force(int);
-  void reset_dt();
+  ~FixWallBodyPolygon() override;
+  int setmask() override;
+  void init() override;
+  void setup(int) override;
+  void post_force(int) override;
+  void reset_dt() override;
 
   struct Contact {
     int ibody, jbody;     // body (i.e. atom) indices (not tags)

src/BODY/fix_wall_body_polyhedron.h

@@ -27,12 +27,12 @@ namespace LAMMPS_NS {
 class FixWallBodyPolyhedron : public Fix {
  public:
   FixWallBodyPolyhedron(class LAMMPS *, int, char **);
-  virtual ~FixWallBodyPolyhedron();
-  int setmask();
-  void init();
-  void setup(int);
-  virtual void post_force(int);
-  void reset_dt();
+  ~FixWallBodyPolyhedron() override;
+  int setmask() override;
+  void init() override;
+  void setup(int) override;
+  void post_force(int) override;
+  void reset_dt() override;
 
   struct Contact {
     int ibody, jbody;     // body (i.e. atom) indices (not tags)

src/BODY/pair_body_nparticle.h

@@ -27,12 +27,12 @@ namespace LAMMPS_NS {
 class PairBodyNparticle : public Pair {
  public:
   PairBodyNparticle(class LAMMPS *);
-  ~PairBodyNparticle();
-  void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  void init_style();
-  double init_one(int, int);
+  ~PairBodyNparticle() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double init_one(int, int) override;
 
  protected:
   double cut_global;

src/BODY/pair_body_rounded_polygon.h

@@ -27,12 +27,12 @@ namespace LAMMPS_NS {
 class PairBodyRoundedPolygon : public Pair {
  public:
   PairBodyRoundedPolygon(class LAMMPS *);
-  ~PairBodyRoundedPolygon();
-  void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  void init_style();
-  double init_one(int, int);
+  ~PairBodyRoundedPolygon() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double init_one(int, int) override;
 
   struct Contact {
     int ibody, jbody;     // body (i.e. atom) indices (not tags)

src/BODY/pair_body_rounded_polyhedron.h

@@ -27,12 +27,12 @@ namespace LAMMPS_NS {
 class PairBodyRoundedPolyhedron : public Pair {
  public:
   PairBodyRoundedPolyhedron(class LAMMPS *);
-  ~PairBodyRoundedPolyhedron();
-  void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  void init_style();
-  double init_one(int, int);
+  ~PairBodyRoundedPolyhedron() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double init_one(int, int) override;
 
   virtual void kernel_force(double R, int itype, int jtype, double &energy, double &fpair);
 

src/BPM/atom_vec_sphere_bpm.h

@@ -27,17 +27,17 @@ namespace LAMMPS_NS {
 class AtomVecSphereBPM : public AtomVec {
  public:
   AtomVecSphereBPM(class LAMMPS *);
-  void process_args(int, char **);
-  void init();
+  void process_args(int, char **) override;
+  void init() override;
 
-  void grow_pointers();
-  void create_atom_post(int);
-  void pack_restart_pre(int);
-  void pack_restart_post(int);
-  void unpack_restart_init(int);
-  void data_atom_post(int);
-  void pack_data_pre(int);
-  void pack_data_post(int);
+  void grow_pointers() override;
+  void create_atom_post(int) override;
+  void pack_restart_pre(int) override;
+  void pack_restart_post(int) override;
+  void unpack_restart_init(int) override;
+  void data_atom_post(int) override;
+  void pack_data_pre(int) override;
+  void pack_data_post(int) override;
 
 
  private:

src/BPM/bond_bpm.h

@@ -23,16 +23,16 @@ namespace LAMMPS_NS {
 class BondBPM : public Bond {
  public:
   BondBPM(class LAMMPS *);
-  virtual ~BondBPM();
-  virtual void compute(int, int) = 0;
-  virtual void coeff(int, char **) = 0;
-  virtual void init_style();
-  void settings(int, char **);
-  double equilibrium_distance(int);
-  void write_restart(FILE *){};
-  void read_restart(FILE *){};
-  void write_data(FILE *) {};
-  double single(int, double, int, int, double &) = 0;
+  virtual ~BondBPM() override;
+  virtual void compute(int, int) override = 0;
+  virtual void coeff(int, char **) override = 0;
+  virtual void init_style() override;
+  void settings(int, char **) override;
+  double equilibrium_distance(int) override;
+  void write_restart(FILE *) override {};
+  void read_restart(FILE *) override {};
+  void write_data(FILE *) override {};
+  double single(int, double, int, int, double &) override = 0;
 
  protected:
   double r0_max_estimate;

src/BPM/bond_bpm_rotational.h

@@ -27,15 +27,15 @@ namespace LAMMPS_NS {
 class BondBPMRotational : public BondBPM {
  public:
   BondBPMRotational(class LAMMPS *);
-  virtual ~BondBPMRotational();
-  virtual void compute(int, int);
-  void coeff(int, char **);
-  void init_style();
-  void settings(int, char **);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_data(FILE *);
-  double single(int, double, int, int, double &);
+  virtual ~BondBPMRotational() override;
+  virtual void compute(int, int) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  void settings(int, char **) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_data(FILE *) override;
+  double single(int, double, int, int, double &) override;
 
  protected:
   double *Kr, *Ks, *Kt, *Kb, *gnorm, *gslide, *groll, *gtwist;

src/BPM/bond_bpm_spring.h

@@ -27,15 +27,15 @@ namespace LAMMPS_NS {
 class BondBPMSpring : public BondBPM {
  public:
   BondBPMSpring(class LAMMPS *);
-  virtual ~BondBPMSpring();
-  virtual void compute(int, int);
-  void coeff(int, char **);
-  void init_style();
-  void settings(int, char **);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_data(FILE *);
-  double single(int, double, int, int, double &);
+  virtual ~BondBPMSpring() override;
+  virtual void compute(int, int) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  void settings(int, char **) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_data(FILE *) override;
+  double single(int, double, int, int, double &) override;
 
  protected:
   double *k, *ecrit, *gamma;

src/BPM/compute_nbond_atom.h

@@ -27,12 +27,12 @@ namespace LAMMPS_NS {
 class ComputeNBondAtom : public Compute {
  public:
   ComputeNBondAtom(class LAMMPS *, int, char **);
-  ~ComputeNBondAtom();
-  void init() {}
-  void compute_peratom();
-  int pack_reverse_comm(int, int, double *);
-  void unpack_reverse_comm(int, int *, double *);
-  double memory_usage();
+  ~ComputeNBondAtom() override;
+  void init() override {}
+  void compute_peratom() override;
+  int pack_reverse_comm(int, int, double *) override;
+  void unpack_reverse_comm(int, int *, double *) override;
+  double memory_usage() override;
 
  private:
   int nmax;

src/BPM/fix_nve_sphere_bpm.h

@@ -27,10 +27,10 @@ namespace LAMMPS_NS {
 class FixNVESphereBPM : public FixNVE {
  public:
   FixNVESphereBPM(class LAMMPS *, int, char **);
-  virtual ~FixNVESphereBPM() {}
-  void init();
-  virtual void initial_integrate(int);
-  virtual void final_integrate();
+
+  void init() override;
+  void initial_integrate(int) override;
+  void final_integrate() override;
 
  protected:
   double inertia, inv_inertia;

src/BPM/pair_bpm_spring.h

@@ -27,16 +27,16 @@ namespace LAMMPS_NS {
 class PairBPMSpring : public Pair {
  public:
   PairBPMSpring(class LAMMPS *);
-  virtual ~PairBPMSpring();
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  double single(int, int, int, int, double, double, double, double &);
+  virtual ~PairBPMSpring() override;
+  virtual void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  double single(int, int, int, int, double, double, double, double &) override;
 
  protected:
   double **k,**cut,**gamma;

src/BROWNIAN/fix_brownian.h

@@ -27,9 +27,9 @@ namespace LAMMPS_NS {
 class FixBrownian : public FixBrownianBase {
  public:
   FixBrownian(class LAMMPS *, int, char **);
-  virtual ~FixBrownian(){};
-  void init();
-  void initial_integrate(int);
+
+  void init() override;
+  void initial_integrate(int) override;
 
  private:
   template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D> void initial_integrate_templated();

src/BROWNIAN/fix_brownian_asphere.h

@@ -27,9 +27,9 @@ namespace LAMMPS_NS {
 class FixBrownianAsphere : public FixBrownianBase {
  public:
   FixBrownianAsphere(class LAMMPS *, int, char **);
-  virtual ~FixBrownianAsphere(){};
-  void initial_integrate(int);
-  void init();
+
+  void initial_integrate(int) override;
+  void init() override;
 
  protected:
   class AtomVecEllipsoid *avec;

src/BROWNIAN/fix_brownian_base.h

@@ -21,10 +21,10 @@ namespace LAMMPS_NS {
 class FixBrownianBase : public Fix {
  public:
   FixBrownianBase(class LAMMPS *, int, char **);
-  virtual ~FixBrownianBase();
-  void init();
-  int setmask();
-  void reset_dt();
+  ~FixBrownianBase() override;
+  void init() override;
+  int setmask() override;
+  void reset_dt() override;
 
  protected:
   int seed;                  // RNG seed

src/BROWNIAN/fix_brownian_sphere.h

@@ -27,9 +27,9 @@ namespace LAMMPS_NS {
 class FixBrownianSphere : public FixBrownianBase {
  public:
   FixBrownianSphere(class LAMMPS *, int, char **);
-  virtual ~FixBrownianSphere(){};
-  void init();
-  void initial_integrate(int);
+
+  void init() override;
+  void initial_integrate(int) override;
 
  private:
   template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D> void initial_integrate_templated();

src/BROWNIAN/fix_propel_self.h

@@ -26,11 +26,11 @@ namespace LAMMPS_NS {
 class FixPropelSelf : public Fix {
  public:
   FixPropelSelf(class LAMMPS *, int, char **);
-  virtual ~FixPropelSelf(){};
-  void init();
-  void post_force(int);
-  void setup(int);
-  int setmask();
+
+  void init() override;
+  void post_force(int) override;
+  void setup(int) override;
+  int setmask() override;
 
  private:
   double magnitude;

src/CG-DNA/atom_vec_oxdna.h

@@ -27,11 +27,10 @@ namespace LAMMPS_NS {
 class AtomVecOxdna : public AtomVec {
  public:
   AtomVecOxdna(class LAMMPS *);
-  ~AtomVecOxdna() = default;
 
-  void grow_pointers();
-  void data_atom_post(int);
-  void data_bonds_post(int, int, tagint, tagint, tagint);
+  void grow_pointers() override;
+  void data_atom_post(int) override;
+  void data_bonds_post(int, int, tagint, tagint, tagint) override;
 
  private:
   tagint *id5p;

src/CG-DNA/bond_oxdna2_fene.h

@@ -27,8 +27,7 @@ namespace LAMMPS_NS {
 class BondOxdna2Fene : public BondOxdnaFene {
  public:
   BondOxdna2Fene(class LAMMPS *lmp) : BondOxdnaFene(lmp) {}
-  virtual ~BondOxdna2Fene() {}
-  virtual void compute_interaction_sites(double *, double *, double *, double *) const;
+  void compute_interaction_sites(double *, double *, double *, double *) const override;
 };
 
 }    // namespace LAMMPS_NS

src/CG-DNA/bond_oxdna_fene.cpp

@@ -24,8 +24,8 @@
 #include "neighbor.h"
 #include "update.h"
 
-#include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
+#include "pair.h"
 
 #include <cmath>
 
@@ -145,25 +145,21 @@ void BondOxdnaFene::ev_tally_xyz(int i, int j, int nlocal, int newton_bond, doub
 ------------------------------------------------------------------------- */
 void BondOxdnaFene::compute(int eflag, int vflag)
 {
-  int a, b, in, type;
-  double delf[3], delta[3], deltb[3];    // force, torque increment;;
-  double delr[3], ebond, fbond;
-  double rsq, Deltasq, rlogarg;
-  double r, rr0, rr0sq;
+  int a,b,in,type;
+  double delf[3],delta[3],deltb[3];    // force, torque increment;;
+  double delr[3],ebond,fbond;
+  double rsq,Deltasq,rlogarg;
+  double r,rr0,rr0sq;
   // vectors COM-backbone site in lab frame
-  double ra_cs[3], rb_cs[3];
-
-  double *qa, ax[3], ay[3], az[3];
-  double *qb, bx[3], by[3], bz[3];
+  double ra_cs[3],rb_cs[3];
+  // Cartesian unit vectors in lab frame
+  double ax[3],ay[3],az[3];
+  double bx[3],by[3],bz[3];
 
   double **x = atom->x;
   double **f = atom->f;
   double **torque = atom->torque;
 
-  AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
-  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
-  int *ellipsoid = atom->ellipsoid;
-
   int **bondlist = neighbor->bondlist;
   int nbondlist = neighbor->nbondlist;
   int nlocal = atom->nlocal;
@@ -172,6 +168,12 @@ void BondOxdnaFene::compute(int eflag, int vflag)
   ebond = 0.0;
   ev_init(eflag, vflag);
 
+  // n(x/y/z)_xtrct = extracted local unit vectors in lab frame from oxdna_excv
+  int dim;
+  nx_xtrct = (double **) force->pair->extract("nx",dim);
+  ny_xtrct = (double **) force->pair->extract("ny",dim);
+  nz_xtrct = (double **) force->pair->extract("nz",dim);
+
   // loop over FENE bonds
 
   for (in = 0; in < nbondlist; in++) {
@@ -180,10 +182,24 @@ void BondOxdnaFene::compute(int eflag, int vflag)
     b = bondlist[in][0];
     type = bondlist[in][2];
 
-    qa = bonus[ellipsoid[a]].quat;
-    MathExtra::q_to_exyz(qa, ax, ay, az);
-    qb = bonus[ellipsoid[b]].quat;
-    MathExtra::q_to_exyz(qb, bx, by, bz);
+    ax[0] = nx_xtrct[a][0];
+    ax[1] = nx_xtrct[a][1];
+    ax[2] = nx_xtrct[a][2];
+    ay[0] = ny_xtrct[a][0];
+    ay[1] = ny_xtrct[a][1];
+    ay[2] = ny_xtrct[a][2];
+    az[0] = nz_xtrct[a][0];
+    az[1] = nz_xtrct[a][1];
+    az[2] = nz_xtrct[a][2];
+    bx[0] = nx_xtrct[b][0];
+    bx[1] = nx_xtrct[b][1];
+    bx[2] = nx_xtrct[b][2];
+    by[0] = ny_xtrct[b][0];
+    by[1] = ny_xtrct[b][1];
+    by[2] = ny_xtrct[b][2];
+    bz[0] = nz_xtrct[b][0];
+    bz[1] = nz_xtrct[b][1];
+    bz[2] = nz_xtrct[b][2];
 
     // vector COM-backbone site a and b
     compute_interaction_sites(ax, ay, az, ra_cs);

src/CG-DNA/bond_oxdna_fene.h

@@ -27,19 +27,20 @@ namespace LAMMPS_NS {
 class BondOxdnaFene : public Bond {
  public:
   BondOxdnaFene(class LAMMPS *lmp) : Bond(lmp) {}
-  virtual ~BondOxdnaFene();
+  ~BondOxdnaFene() override;
   virtual void compute_interaction_sites(double *, double *, double *, double *) const;
-  virtual void compute(int, int);
-  void coeff(int, char **);
-  void init_style();
-  double equilibrium_distance(int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_data(FILE *);
-  double single(int, double, int, int, double &);
+  void compute(int, int) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double equilibrium_distance(int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_data(FILE *) override;
+  double single(int, double, int, int, double &) override;
 
  protected:
   double *k, *Delta, *r0;    // FENE
+  double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for local unit vectors
 
   void allocate();
   void ev_tally_xyz(int, int, int, int, double, double, double, double, double, double, double);

src/CG-DNA/bond_oxrna2_fene.h

@@ -27,9 +27,8 @@ namespace LAMMPS_NS {
 class BondOxrna2Fene : public BondOxdnaFene {
  public:
   BondOxrna2Fene(class LAMMPS *lmp) : BondOxdnaFene(lmp) {}
-  virtual ~BondOxrna2Fene() {}
 
-  virtual void compute_interaction_sites(double *, double *, double *, double *) const;
+  void compute_interaction_sites(double *, double *, double *, double *) const override;
 };
 
 }    // namespace LAMMPS_NS

src/CG-DNA/fix_nve_dot.h

@@ -27,9 +27,9 @@ namespace LAMMPS_NS {
 class FixNVEDot : public FixNVE {
  public:
   FixNVEDot(class LAMMPS *, int, char **);
-  void init();
-  void initial_integrate(int);
-  void final_integrate();
+  void init() override;
+  void initial_integrate(int) override;
+  void final_integrate() override;
 
  private:
   double dt, dthlf, dthlfm;

src/CG-DNA/fix_nve_dotc_langevin.h

@@ -27,10 +27,10 @@ namespace LAMMPS_NS {
 class FixNVEDotcLangevin : public FixNVE {
  public:
   FixNVEDotcLangevin(class LAMMPS *, int, char **);
-  virtual ~FixNVEDotcLangevin();
-  void init();
-  void initial_integrate(int);
-  void final_integrate();
+  ~FixNVEDotcLangevin() override;
+  void init() override;
+  void initial_integrate(int) override;
+  void final_integrate() override;
 
  private:
   double dt, dthlf, dthlfm, dtqrt;

src/CG-DNA/pair_oxdna2_coaxstk.cpp

@@ -18,7 +18,6 @@
 #include "pair_oxdna2_coaxstk.h"
 
 #include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
@@ -102,7 +101,7 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
 {
 
   double delf[3],delta[3],deltb[3]; // force, torque increment;
-  double evdwl,fpair,finc,tpair,factor_lj;
+  double evdwl,finc,tpair,factor_lj;
   double v1tmp[3];
   double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss;
   double delr_st[3],delr_st_norm[3],rsq_st,r_st,rinv_st;
@@ -118,9 +117,9 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
   double ra_cs[3],ra_cst[3];
   double rb_cs[3],rb_cst[3];
 
-  // quaternions and Cartesian unit vectors in lab frame
-  double *qa,ax[3],ay[3],az[3];
-  double *qb,bx[3],by[3],bz[3];
+  // Cartesian unit vectors in lab frame
+  double ax[3],az[3];
+  double bx[3],bz[3];
 
   double **x = atom->x;
   double **f = atom->f;
@@ -132,10 +131,6 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
   int *alist,*blist,*numneigh,**firstneigh;
   double *special_lj = force->special_lj;
 
-  AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
-  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
-  int *ellipsoid = atom->ellipsoid;
-
   int a,b,ia,ib,anum,bnum,atype,btype;
 
   double f2,f4f6t1,f4t4,f4t5,f4t6;
@@ -149,6 +144,11 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
 
+  // n(x/z)_xtrct = extracted local unit vectors from oxdna_excv
+  int dim;
+  nx_xtrct = (double **) force->pair->extract("nx",dim);
+  nz_xtrct = (double **) force->pair->extract("nz",dim);
+
   // loop over pair interaction neighbors of my atoms
 
   for (ia = 0; ia < anum; ia++) {
@@ -156,8 +156,9 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
     a = alist[ia];
     atype = type[a];
 
-    qa=bonus[ellipsoid[a]].quat;
-    MathExtra::q_to_exyz(qa,ax,ay,az);
+    ax[0] = nx_xtrct[a][0];
+    ax[1] = nx_xtrct[a][1];
+    ax[2] = nx_xtrct[a][2];
 
     // vector COM a - stacking site a
     ra_cst[0] = d_cst*ax[0];
@@ -180,8 +181,9 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
 
       btype = type[b];
 
-      qb=bonus[ellipsoid[b]].quat;
-      MathExtra::q_to_exyz(qb,bx,by,bz);
+      bx[0] = nx_xtrct[b][0];
+      bx[1] = nx_xtrct[b][1];
+      bx[2] = nx_xtrct[b][2];
 
       // vector COM b - stacking site b
       rb_cst[0] = d_cst*bx[0];
@@ -232,6 +234,13 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
       // early rejection criterium
       if (f4f6t1) {
 
+      az[0] = nz_xtrct[a][0];
+      az[1] = nz_xtrct[a][1];
+      az[2] = nz_xtrct[a][2];
+      bz[0] = nz_xtrct[b][0];
+      bz[1] = nz_xtrct[b][1];
+      bz[2] = nz_xtrct[b][2];
+
       cost4 = MathExtra::dot3(az,bz);
       if (cost4 >  1.0) cost4 =  1.0;
       if (cost4 < -1.0) cost4 = -1.0;
@@ -306,9 +315,7 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
               DF4(theta6p, a_cxst6[atype][btype], theta_cxst6_0[atype][btype], dtheta_cxst6_ast[atype][btype],
               b_cxst6[atype][btype], dtheta_cxst6_c[atype][btype])*rsint;
 
-     // force, torque and virial contribution for forces between stacking sites
-
-      fpair = 0.0;
+      // force, torque and virial contribution for forces between stacking sites
 
       delf[0] = 0.0;
       delf[1] = 0.0;
@@ -324,7 +331,6 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
 
       // radial force
       finc  = -df2 * f4f6t1 * f4t4 * f4t5 * f4t6 * rinv_st * factor_lj;
-      fpair += finc;
 
       delf[0] += delr_st[0] * finc;
       delf[1] += delr_st[1] * finc;
@@ -334,7 +340,6 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
       if (theta5 && theta5p) {
 
         finc   = -f2 * f4f6t1 * f4t4 * df4t5 * f4t6 * rinv_st * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_st_norm[0]*cost5 - az[0]) * finc;
         delf[1] += (delr_st_norm[1]*cost5 - az[1]) * finc;
@@ -346,7 +351,6 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
       if (theta6 && theta6p) {
 
         finc   = -f2 * f4f6t1* f4t4 * f4t5 * df4t6 * rinv_st * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_st_norm[0]*cost6 - bz[0]) * finc;
         delf[1] += (delr_st_norm[1]*cost6 - bz[1]) * finc;

src/CG-DNA/pair_oxdna2_coaxstk.h

@@ -27,39 +27,35 @@ namespace LAMMPS_NS {
 class PairOxdna2Coaxstk : public Pair {
  public:
   PairOxdna2Coaxstk(class LAMMPS *);
-  virtual ~PairOxdna2Coaxstk();
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  void init_list(int, class NeighList *);
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  void *extract(const char *, int &);
+  ~PairOxdna2Coaxstk() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_list(int, class NeighList *) override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  void *extract(const char *, int &) override;
 
  protected:
   // coaxial stacking interaction
   double **k_cxst, **cut_cxst_0, **cut_cxst_c, **cut_cxst_lo, **cut_cxst_hi;
   double **cut_cxst_lc, **cut_cxst_hc, **b_cxst_lo, **b_cxst_hi;
   double **cutsq_cxst_hc;
-
   double **a_cxst1, **theta_cxst1_0, **dtheta_cxst1_ast;
   double **b_cxst1, **dtheta_cxst1_c;
-
   double **a_cxst4, **theta_cxst4_0, **dtheta_cxst4_ast;
   double **b_cxst4, **dtheta_cxst4_c;
-
   double **a_cxst5, **theta_cxst5_0, **dtheta_cxst5_ast;
   double **b_cxst5, **dtheta_cxst5_c;
-
   double **a_cxst6, **theta_cxst6_0, **dtheta_cxst6_ast;
   double **b_cxst6, **dtheta_cxst6_c;
-
   double **AA_cxst1, **BB_cxst1;
+  double **nx_xtrct, **nz_xtrct; // per-atom arrays for local unit vectors
 
   virtual void allocate();
 };

src/CG-DNA/pair_oxdna2_dh.cpp

@@ -18,7 +18,6 @@
 #include "pair_oxdna2_dh.h"
 
 #include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
@@ -87,10 +86,9 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
   // vectors COM-backbone sites in lab frame
   double ra_cs[3],rb_cs[3];
 
-  // quaternions and Cartesian unit vectors in lab frame
-  double *qa,ax[3],ay[3],az[3];
-  double *qb,bx[3],by[3],bz[3];
-  double *special_lj = force->special_lj;
+  // Cartesian unit vectors in lab frame
+  double ax[3],ay[3],az[3];
+  double bx[3],by[3],bz[3];
 
   double **x = atom->x;
   double **f = atom->f;
@@ -100,10 +98,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
   int nlocal = atom->nlocal;
   int newton_pair = force->newton_pair;
   int *alist,*blist,*numneigh,**firstneigh;
-
-  AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
-  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
-  int *ellipsoid = atom->ellipsoid;
+  double *special_lj = force->special_lj;
 
   int a,b,ia,ib,anum,bnum,atype,btype;
 
@@ -115,6 +110,12 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
 
+  // n(x/y/z)_xtrct = extracted local unit vectors from oxdna_excv
+  int dim;
+  nx_xtrct = (double **) force->pair->extract("nx",dim);
+  ny_xtrct = (double **) force->pair->extract("ny",dim);
+  nz_xtrct = (double **) force->pair->extract("nz",dim);
+
   // loop over pair interaction neighbors of my atoms
 
   for (ia = 0; ia < anum; ia++) {
@@ -122,8 +123,15 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
     a = alist[ia];
     atype = type[a];
 
-    qa=bonus[ellipsoid[a]].quat;
-    MathExtra::q_to_exyz(qa,ax,ay,az);
+    ax[0] = nx_xtrct[a][0];
+    ax[1] = nx_xtrct[a][1];
+    ax[2] = nx_xtrct[a][2];
+    ay[0] = ny_xtrct[a][0];
+    ay[1] = ny_xtrct[a][1];
+    ay[2] = ny_xtrct[a][2];
+    az[0] = nz_xtrct[a][0];
+    az[1] = nz_xtrct[a][1];
+    az[2] = nz_xtrct[a][2];
 
     // vector COM-backbone site a
     compute_interaction_sites(ax,ay,az,ra_cs);
@@ -142,8 +150,15 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
       b &= NEIGHMASK;
       btype = type[b];
 
-      qb=bonus[ellipsoid[b]].quat;
-      MathExtra::q_to_exyz(qb,bx,by,bz);
+      bx[0] = nx_xtrct[b][0];
+      bx[1] = nx_xtrct[b][1];
+      bx[2] = nx_xtrct[b][2];
+      by[0] = ny_xtrct[b][0];
+      by[1] = ny_xtrct[b][1];
+      by[2] = ny_xtrct[b][2];
+      bz[0] = nz_xtrct[b][0];
+      bz[1] = nz_xtrct[b][1];
+      bz[2] = nz_xtrct[b][2];
 
       // vector COM-backbone site b
       compute_interaction_sites(bx,by,bz,rb_cs);

src/CG-DNA/pair_oxdna2_dh.h

@@ -27,24 +27,25 @@ namespace LAMMPS_NS {
 class PairOxdna2Dh : public Pair {
  public:
   PairOxdna2Dh(class LAMMPS *);
-  virtual ~PairOxdna2Dh();
+  ~PairOxdna2Dh() override;
   virtual void compute_interaction_sites(double *, double *, double *, double *);
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  void init_list(int, class NeighList *);
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  void *extract(const char *, int &);
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_list(int, class NeighList *) override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  void *extract(const char *, int &) override;
 
  protected:
   double **qeff_dh_pf, **kappa_dh;
   double **b_dh, **cut_dh_ast, **cutsq_dh_ast, **cut_dh_c, **cutsq_dh_c;
+  double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for local unit vectors
 
   virtual void allocate();
 };

src/CG-DNA/pair_oxdna2_excv.h

@@ -27,8 +27,8 @@ namespace LAMMPS_NS {
 class PairOxdna2Excv : public PairOxdnaExcv {
  public:
   PairOxdna2Excv(class LAMMPS *lmp) : PairOxdnaExcv(lmp) {}
-  virtual ~PairOxdna2Excv() {}
-  virtual void compute_interaction_sites(double *, double *, double *, double *, double *);
+
+  void compute_interaction_sites(double *, double *, double *, double *, double *) override;
 };
 
 }    // namespace LAMMPS_NS

src/CG-DNA/pair_oxdna_coaxstk.cpp

@@ -18,7 +18,6 @@
 #include "pair_oxdna_coaxstk.h"
 
 #include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
@@ -106,9 +105,8 @@ PairOxdnaCoaxstk::~PairOxdnaCoaxstk()
 
 void PairOxdnaCoaxstk::compute(int eflag, int vflag)
 {
-
   double delf[3],delt[3],delta[3],deltb[3]; // force, torque increment;
-  double evdwl,fpair,finc,tpair,factor_lj;
+  double evdwl,finc,tpair,factor_lj;
   double v1tmp[3],v2tmp[3],v3tmp[3];
   double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss;
   double delr_st[3],delr_st_norm[3],rsq_st,r_st,rinv_st;
@@ -129,10 +127,9 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
   // vectors COM-backbone site, COM-stacking site in lab frame
   double ra_cs[3],ra_cst[3];
   double rb_cs[3],rb_cst[3];
-
-  // quaternions and Cartesian unit vectors in lab frame
-  double *qa,ax[3],ay[3],az[3];
-  double *qb,bx[3],by[3],bz[3];
+  // Cartesian unit vectors in lab frame
+  double ax[3],ay[3],az[3];
+  double bx[3],bz[3];
 
   double **x = atom->x;
   double **f = atom->f;
@@ -144,10 +141,6 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
   int *alist,*blist,*numneigh,**firstneigh;
   double *special_lj = force->special_lj;
 
-  AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
-  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
-  int *ellipsoid = atom->ellipsoid;
-
   int a,b,ia,ib,anum,bnum,atype,btype;
 
   double f2,f4t1,f4t4,f4t5,f4t6,f5c3;
@@ -161,6 +154,12 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
 
+  // n(x/y/z)_xtrct = extracted local unit vectors in lab frame from oxdna_excv
+  int dim;
+  nx_xtrct = (double **) force->pair->extract("nx",dim);
+  ny_xtrct = (double **) force->pair->extract("ny",dim);
+  nz_xtrct = (double **) force->pair->extract("nz",dim);
+
   // loop over pair interaction neighbors of my atoms
 
   for (ia = 0; ia < anum; ia++) {
@@ -168,8 +167,10 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
     a = alist[ia];
     atype = type[a];
 
-    qa=bonus[ellipsoid[a]].quat;
-    MathExtra::q_to_exyz(qa,ax,ay,az);
+    ax[0] = nx_xtrct[a][0];
+    ax[1] = nx_xtrct[a][1];
+    ax[2] = nx_xtrct[a][2];
+    // a(y/z) not needed here as oxDNA(1) co-linear
 
     // vector COM a - stacking site a
     ra_cst[0] = d_cst*ax[0];
@@ -192,8 +193,10 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
 
       btype = type[b];
 
-      qb=bonus[ellipsoid[b]].quat;
-      MathExtra::q_to_exyz(qb,bx,by,bz);
+      bx[0] = nx_xtrct[b][0];
+      bx[1] = nx_xtrct[b][1];
+      bx[2] = nx_xtrct[b][2];
+      // b(y/z) not needed here as oxDNA(1) co-linear
 
       // vector COM b - stacking site b
       rb_cst[0] = d_cst*bx[0];
@@ -245,6 +248,13 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
       // early rejection criterium
       if (f4t1) {
 
+      az[0] = nz_xtrct[a][0];
+      az[1] = nz_xtrct[a][1];
+      az[2] = nz_xtrct[a][2];
+      bz[0] = nz_xtrct[b][0];
+      bz[1] = nz_xtrct[b][1];
+      bz[2] = nz_xtrct[b][2];
+
       cost4 = MathExtra::dot3(az,bz);
       if (cost4 >  1.0) cost4 =  1.0;
       if (cost4 < -1.0) cost4 = -1.0;
@@ -330,8 +340,6 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
 
      // force, torque and virial contribution for forces between stacking sites
 
-      fpair = 0.0;
-
       delf[0] = 0.0;
       delf[1] = 0.0;
       delf[2] = 0.0;
@@ -346,7 +354,6 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
 
       // radial force
       finc  = -df2 * f4t1 * f4t4 * f4t5 * f4t6 * f5c3 * f5c3 * rinv_st * factor_lj;
-      fpair += finc;
 
       delf[0] += delr_st[0] * finc;
       delf[1] += delr_st[1] * finc;
@@ -356,7 +363,6 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
       if (theta5 && theta5p) {
 
         finc   = -f2 * f4t1 * f4t4 * df4t5 * f4t6 * f5c3 * f5c3 * rinv_st * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_st_norm[0]*cost5 - az[0]) * finc;
         delf[1] += (delr_st_norm[1]*cost5 - az[1]) * finc;
@@ -368,7 +374,6 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
       if (theta6 && theta6p) {
 
         finc   = -f2 * f4t1* f4t4 * f4t5 * df4t6 * f5c3 * f5c3 * rinv_st * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_st_norm[0]*cost6 - bz[0]) * finc;
         delf[1] += (delr_st_norm[1]*cost6 - bz[1]) * finc;
@@ -380,8 +385,11 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
       // cosphi3 and cosphi4 (=cosphi3) force and virial
       if (cosphi3) {
 
+        ay[0] = ny_xtrct[a][0];
+        ay[1] = ny_xtrct[a][1];
+        ay[2] = ny_xtrct[a][2];
+
         finc   = -f2 * f4t1* f4t4 * f4t5 * f4t6 * 2.0 * f5c3 * df5c3 * factor_lj;
-        fpair += finc;
 
         gamma = d_cs - d_cst;
         gammacub = gamma * gamma * gamma;

src/CG-DNA/pair_oxdna_coaxstk.h

@@ -28,40 +28,36 @@ namespace LAMMPS_NS {
 class PairOxdnaCoaxstk : public Pair {
  public:
   PairOxdnaCoaxstk(class LAMMPS *);
-  virtual ~PairOxdnaCoaxstk();
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  void init_list(int, class NeighList *);
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  void *extract(const char *, int &);
+  ~PairOxdnaCoaxstk() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_list(int, class NeighList *) override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  void *extract(const char *, int &) override;
 
  protected:
   // coaxial stacking interaction
   double **k_cxst, **cut_cxst_0, **cut_cxst_c, **cut_cxst_lo, **cut_cxst_hi;
   double **cut_cxst_lc, **cut_cxst_hc, **b_cxst_lo, **b_cxst_hi;
   double **cutsq_cxst_hc;
-
   double **a_cxst1, **theta_cxst1_0, **dtheta_cxst1_ast;
   double **b_cxst1, **dtheta_cxst1_c;
-
   double **a_cxst4, **theta_cxst4_0, **dtheta_cxst4_ast;
   double **b_cxst4, **dtheta_cxst4_c;
-
   double **a_cxst5, **theta_cxst5_0, **dtheta_cxst5_ast;
   double **b_cxst5, **dtheta_cxst5_c;
-
   double **a_cxst6, **theta_cxst6_0, **dtheta_cxst6_ast;
   double **b_cxst6, **dtheta_cxst6_c;
-
   double **a_cxst3p, **cosphi_cxst3p_ast, **b_cxst3p, **cosphi_cxst3p_c;
   double **a_cxst4p, **cosphi_cxst4p_ast, **b_cxst4p, **cosphi_cxst4p_c;
+  double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for local unit vectors
 
   virtual void allocate();
 };

src/CG-DNA/pair_oxdna_excv.cpp

@@ -39,6 +39,9 @@ PairOxdnaExcv::PairOxdnaExcv(LAMMPS *lmp) : Pair(lmp)
 {
   single_enable = 0;
   writedata = 1;
+
+  // set comm size needed by this Pair
+  comm_forward = 9;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -47,6 +50,10 @@ PairOxdnaExcv::~PairOxdnaExcv()
 {
   if (allocated) {
 
+    memory->destroy(nx);
+    memory->destroy(ny);
+    memory->destroy(nz);
+
     memory->destroy(setflag);
     memory->destroy(cutsq);
 
@@ -108,7 +115,6 @@ void PairOxdnaExcv::compute_interaction_sites(double e1[3], double /*e2*/[3],
 
 void PairOxdnaExcv::compute(int eflag, int vflag)
 {
-
   double delf[3],delta[3],deltb[3]; // force, torque increment;
   double evdwl,fpair,factor_lj;
   double rtmp_s[3],rtmp_b[3];
@@ -118,10 +124,10 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
   // vectors COM-backbone site, COM-base site in lab frame
   double ra_cs[3],ra_cb[3];
   double rb_cs[3],rb_cb[3];
+  // Cartesian unit vectors in lab frame
+  double ax[3],ay[3],az[3];
+  double bx[3],by[3],bz[3];
 
-  // quaternions and Cartesian unit vectors in lab frame
-  double *qa,ax[3],ay[3],az[3];
-  double *qb,bx[3],by[3],bz[3];
   double *special_lj = force->special_lj;
 
   double **x = atom->x;
@@ -137,7 +143,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
   AtomVecEllipsoid::Bonus *bonus = avec->bonus;
   int *ellipsoid = atom->ellipsoid;
 
-  int a,b,ia,ib,anum,bnum,atype,btype;
+  int a,b,in,ia,ib,anum,bnum,atype,btype;
 
   evdwl = 0.0;
   ev_init(eflag,vflag);
@@ -147,6 +153,29 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
 
+  // loop over all local atoms, calculation of local reference frame
+  for (in = 0; in < atom->nlocal; in++) {
+
+    int n = alist[in];
+    double *qn,nx_temp[3],ny_temp[3],nz_temp[3]; // quaternion and Cartesian unit vectors in lab frame
+
+    qn=bonus[ellipsoid[n]].quat;
+    MathExtra::q_to_exyz(qn,nx_temp,ny_temp,nz_temp);
+
+    nx[n][0] = nx_temp[0];
+    nx[n][1] = nx_temp[1];
+    nx[n][2] = nx_temp[2];
+    ny[n][0] = ny_temp[0];
+    ny[n][1] = ny_temp[1];
+    ny[n][2] = ny_temp[2];
+    nz[n][0] = nz_temp[0];
+    nz[n][1] = nz_temp[1];
+    nz[n][2] = nz_temp[2];
+
+  }
+
+  comm->forward_comm_pair(this);
+
   // loop over pair interaction neighbors of my atoms
 
   for (ia = 0; ia < anum; ia++) {
@@ -154,8 +183,15 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
     a = alist[ia];
     atype = type[a];
 
-    qa=bonus[ellipsoid[a]].quat;
-    MathExtra::q_to_exyz(qa,ax,ay,az);
+    ax[0] = nx[a][0];
+    ax[1] = nx[a][1];
+    ax[2] = nx[a][2];
+    ay[0] = ny[a][0];
+    ay[1] = ny[a][1];
+    ay[2] = ny[a][2];
+    az[0] = nz[a][0];
+    az[1] = nz[a][1];
+    az[2] = nz[a][2];
 
     // vector COM - backbone and base site a
     compute_interaction_sites(ax,ay,az,ra_cs,ra_cb);
@@ -179,8 +215,15 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
 
       btype = type[b];
 
-      qb=bonus[ellipsoid[b]].quat;
-      MathExtra::q_to_exyz(qb,bx,by,bz);
+      bx[0] = nx[b][0];
+      bx[1] = nx[b][1];
+      bx[2] = nx[b][2];
+      by[0] = ny[b][0];
+      by[1] = ny[b][1];
+      by[2] = ny[b][2];
+      bz[0] = nz[b][0];
+      bz[1] = nz[b][1];
+      bz[2] = nz[b][2];
 
       // vector COM - backbone and base site b
       compute_interaction_sites(bx,by,bz,rb_cs,rb_cb);
@@ -400,6 +443,10 @@ void PairOxdnaExcv::allocate()
     for (int j = i; j <= n; j++)
       setflag[i][j] = 0;
 
+  memory->create(nx,atom->nmax,3,"pair:nx");
+  memory->create(ny,atom->nmax,3,"pair:ny");
+  memory->create(nz,atom->nmax,3,"pair:nz");
+
   memory->create(cutsq,n+1,n+1,"pair:cutsq");
 
   memory->create(epsilon_ss,n+1,n+1,"pair:epsilon_ss");
@@ -806,10 +853,58 @@ void PairOxdnaExcv::write_data_all(FILE *fp)
 
 /* ---------------------------------------------------------------------- */
 
+int PairOxdnaExcv::pack_forward_comm(int n, int *list, double *buf,
+                               int /*pbc_flag*/, int * /*pbc*/)
+{
+  int i,j,m;
+
+  m = 0;
+  for (i = 0; i < n; i++) {
+    j = list[i];
+	buf[m++] = nx[j][0];
+	buf[m++] = nx[j][1];
+	buf[m++] = nx[j][2];
+	buf[m++] = ny[j][0];
+	buf[m++] = ny[j][1];
+	buf[m++] = ny[j][2];
+	buf[m++] = nz[j][0];
+	buf[m++] = nz[j][1];
+	buf[m++] = nz[j][2];
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairOxdnaExcv::unpack_forward_comm(int n, int first, double *buf)
+{
+  int i,m,last;
+
+  m = 0;
+  last = first + n;
+  for (i = first; i < last; i++) {
+	nx[i][0] = buf[m++];
+	nx[i][1] = buf[m++];
+	nx[i][2] = buf[m++];
+	ny[i][0] = buf[m++];
+	ny[i][1] = buf[m++];
+	ny[i][2] = buf[m++];
+	nz[i][0] = buf[m++];
+	nz[i][1] = buf[m++];
+	nz[i][2] = buf[m++];
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
 void *PairOxdnaExcv::extract(const char *str, int &dim)
 {
   dim = 2;
 
+  if (strcmp(str,"nx") == 0) return (void *) nx;
+  if (strcmp(str,"ny") == 0) return (void *) ny;
+  if (strcmp(str,"nz") == 0) return (void *) nz;
+
   if (strcmp(str,"epsilon_ss") == 0) return (void *) epsilon_ss;
   if (strcmp(str,"sigma_ss") == 0) return (void *) sigma_ss;
   if (strcmp(str,"cut_ss_ast") == 0) return (void *) cut_ss_ast;

src/CG-DNA/pair_oxdna_excv.h

@@ -27,20 +27,22 @@ namespace LAMMPS_NS {
 class PairOxdnaExcv : public Pair {
  public:
   PairOxdnaExcv(class LAMMPS *);
-  virtual ~PairOxdnaExcv();
+  ~PairOxdnaExcv() override;
   virtual void compute_interaction_sites(double *, double *, double *, double *, double *);
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  void init_list(int, class NeighList *);
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  void *extract(const char *, int &);
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_list(int, class NeighList *) override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  void *extract(const char *, int &) override;
+  int pack_forward_comm(int, int *, double *, int, int *) override;
+  void unpack_forward_comm(int, int, double *) override;
 
  protected:
   // s=sugar-phosphate backbone site, b=base site, st=stacking site
@@ -52,6 +54,7 @@ class PairOxdnaExcv : public Pair {
   double **lj1_sb, **lj2_sb, **b_sb, **cut_sb_c, **cutsq_sb_c;
   double **epsilon_bb, **sigma_bb, **cut_bb_ast, **cutsq_bb_ast;
   double **lj1_bb, **lj2_bb, **b_bb, **cut_bb_c, **cutsq_bb_c;
+  double **nx, **ny, **nz; // per-atom arrays for local unit vectors
 
   virtual void allocate();
 };

src/CG-DNA/pair_oxdna_hbond.cpp

@@ -18,7 +18,6 @@
 #include "pair_oxdna_hbond.h"
 
 #include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
@@ -135,7 +134,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
 {
 
   double delf[3],delta[3],deltb[3]; // force, torque increment;
-  double evdwl,fpair,finc,tpair,factor_lj;
+  double evdwl,finc,tpair,factor_lj;
   double delr_hb[3],delr_hb_norm[3],rsq_hb,r_hb,rinv_hb;
   double theta1,t1dir[3],cost1;
   double theta2,t2dir[3],cost2;
@@ -148,10 +147,9 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
   double d_chb=+0.4;
   // vectors COM-h-bonding site in lab frame
   double ra_chb[3],rb_chb[3];
-
-  // quaternions and Cartesian unit vectors in lab frame
-  double *qa,ax[3],ay[3],az[3];
-  double *qb,bx[3],by[3],bz[3];
+  // Cartesian unit vectors in lab frame
+  double ax[3],az[3];
+  double bx[3],bz[3];
 
   double **x = atom->x;
   double **f = atom->f;
@@ -163,10 +161,6 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
   int *alist,*blist,*numneigh,**firstneigh;
   double *special_lj = force->special_lj;
 
-  AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
-  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
-  int *ellipsoid = atom->ellipsoid;
-
   int a,b,ia,ib,anum,bnum,atype,btype;
 
   double f1,f4t1,f4t4,f4t2,f4t3,f4t7,f4t8;
@@ -180,6 +174,12 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
 
+  // n(x/y/z)_xtrct = extracted local unit vectors from oxdna_excv
+  int dim;
+  nx_xtrct = (double **) force->pair->extract("nx",dim);
+  ny_xtrct = (double **) force->pair->extract("ny",dim);
+  nz_xtrct = (double **) force->pair->extract("nz",dim);
+
   // loop over pair interaction neighbors of my atoms
 
   for (ia = 0; ia < anum; ia++) {
@@ -187,8 +187,9 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
     a = alist[ia];
     atype = type[a];
 
-    qa=bonus[ellipsoid[a]].quat;
-    MathExtra::q_to_exyz(qa,ax,ay,az);
+    ax[0] = nx_xtrct[a][0];
+    ax[1] = nx_xtrct[a][1];
+    ax[2] = nx_xtrct[a][2];
 
     ra_chb[0] = d_chb*ax[0];
     ra_chb[1] = d_chb*ax[1];
@@ -205,8 +206,9 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
 
       btype = type[b];
 
-      qb=bonus[ellipsoid[b]].quat;
-      MathExtra::q_to_exyz(qb,bx,by,bz);
+      bx[0] = nx_xtrct[b][0];
+      bx[1] = nx_xtrct[b][1];
+      bx[2] = nx_xtrct[b][2];
 
       rb_chb[0] = d_chb*bx[0];
       rb_chb[1] = d_chb*bx[1];
@@ -265,6 +267,13 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
       // early rejection criterium
       if (f4t3) {
 
+      az[0] = nz_xtrct[a][0];
+      az[1] = nz_xtrct[a][1];
+      az[2] = nz_xtrct[a][2];
+      bz[0] = nz_xtrct[b][0];
+      bz[1] = nz_xtrct[b][1];
+      bz[2] = nz_xtrct[b][2];
+
       cost4 = MathExtra::dot3(az,bz);
       if (cost4 >  1.0) cost4 =  1.0;
       if (cost4 < -1.0) cost4 = -1.0;
@@ -324,8 +333,6 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
 
       // force, torque and virial contribution for forces between h-bonding sites
 
-      fpair = 0.0;
-
       delf[0] = 0.0;
       delf[1] = 0.0;
       delf[2] = 0.0;
@@ -340,7 +347,6 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
 
       // radial force
       finc  = -df1 * f4t1 * f4t2 * f4t3 * f4t4 * f4t7 * f4t8 * factor_lj;
-      fpair += finc;
 
       delf[0] += delr_hb[0] * finc;
       delf[1] += delr_hb[1] * finc;
@@ -350,7 +356,6 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
       if (theta2) {
 
         finc  = -f1 * f4t1 * df4t2 * f4t3 * f4t4 * f4t7 * f4t8 * rinv_hb * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_hb_norm[0]*cost2 + ax[0]) * finc;
         delf[1] += (delr_hb_norm[1]*cost2 + ax[1]) * finc;
@@ -362,7 +367,6 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
       if (theta3) {
 
         finc  = -f1 * f4t1 * f4t2 * df4t3 * f4t4 * f4t7 * f4t8 * rinv_hb * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_hb_norm[0]*cost3 - bx[0]) * finc;
         delf[1] += (delr_hb_norm[1]*cost3 - bx[1]) * finc;
@@ -374,7 +378,6 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
       if (theta7) {
 
         finc  = -f1 * f4t1 * f4t2 * f4t3 * f4t4 * df4t7 * f4t8 * rinv_hb * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_hb_norm[0]*cost7 + az[0]) * finc;
         delf[1] += (delr_hb_norm[1]*cost7 + az[1]) * finc;
@@ -386,7 +389,6 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
       if (theta8) {
 
         finc  = -f1 * f4t1 * f4t2 * f4t3 * f4t4 * f4t7 * df4t8 * rinv_hb * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_hb_norm[0]*cost8 - bz[0]) * finc;
         delf[1] += (delr_hb_norm[1]*cost8 - bz[1]) * finc;

src/CG-DNA/pair_oxdna_hbond.h

@@ -28,19 +28,19 @@ namespace LAMMPS_NS {
 class PairOxdnaHbond : public Pair {
  public:
   PairOxdnaHbond(class LAMMPS *);
-  virtual ~PairOxdnaHbond();
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  void init_list(int, class NeighList *);
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  void *extract(const char *, int &);
+  ~PairOxdnaHbond() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_list(int, class NeighList *) override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  void *extract(const char *, int &) override;
 
  protected:
   // h-bonding interaction
@@ -48,25 +48,19 @@ class PairOxdnaHbond : public Pair {
   double **epsilon_hb, **a_hb, **cut_hb_0, **cut_hb_c, **cut_hb_lo, **cut_hb_hi;
   double **cut_hb_lc, **cut_hb_hc, **b_hb_lo, **b_hb_hi, **shift_hb;
   double **cutsq_hb_hc;
-
   double **a_hb1, **theta_hb1_0, **dtheta_hb1_ast;
   double **b_hb1, **dtheta_hb1_c;
-
   double **a_hb2, **theta_hb2_0, **dtheta_hb2_ast;
   double **b_hb2, **dtheta_hb2_c;
-
   double **a_hb3, **theta_hb3_0, **dtheta_hb3_ast;
   double **b_hb3, **dtheta_hb3_c;
-
   double **a_hb4, **theta_hb4_0, **dtheta_hb4_ast;
   double **b_hb4, **dtheta_hb4_c;
-
   double **a_hb7, **theta_hb7_0, **dtheta_hb7_ast;
   double **b_hb7, **dtheta_hb7_c;
-
   double **a_hb8, **theta_hb8_0, **dtheta_hb8_ast;
   double **b_hb8, **dtheta_hb8_c;
-
+  double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for local unit vectors
   int seqdepflag;
 
   virtual void allocate();

src/CG-DNA/pair_oxdna_stk.cpp

@@ -18,7 +18,6 @@
 #include "pair_oxdna_stk.h"
 
 #include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
@@ -212,9 +211,8 @@ void PairOxdnaStk::ev_tally_xyz(int i, int j, int nlocal, int newton_bond,
 
 void PairOxdnaStk::compute(int eflag, int vflag)
 {
-
   double delf[3],delta[3],deltb[3]; // force, torque increment;
-  double evdwl,fpair,finc,tpair;
+  double evdwl,finc,tpair;
   double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss;
   double delr_st[3],delr_st_norm[3],rsq_st,r_st,rinv_st;
   double theta4,t4dir[3],cost4;
@@ -227,10 +225,9 @@ void PairOxdnaStk::compute(int eflag, int vflag)
   // vectors COM-backbone site, COM-stacking site in lab frame
   double ra_cs[3],ra_cst[3];
   double rb_cs[3],rb_cst[3];
-
-  // quaternions and Cartesian unit vectors in lab frame
-  double *qa,ax[3],ay[3],az[3];
-  double *qb,bx[3],by[3],bz[3];
+  // Cartesian unit vectors in lab frame
+  double ax[3],ay[3],az[3];
+  double bx[3],by[3],bz[3];
 
   double **x = atom->x;
   double **f = atom->f;
@@ -245,10 +242,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
 
   tagint *id5p = atom->id5p;
 
-  AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
-  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
-  int *ellipsoid = atom->ellipsoid;
-
   int a,b,btemp,in,atype,btype;
 
   double f1,f4t4,f4t5,f4t6,f5c1,f5c2;
@@ -257,6 +250,12 @@ void PairOxdnaStk::compute(int eflag, int vflag)
   evdwl = 0.0;
   ev_init(eflag,vflag);
 
+  // n(x/y/z)_xtrct = extracted local unit vectors from oxdna_excv
+  int dim;
+  nx_xtrct = (double **) force->pair->extract("nx",dim);
+  ny_xtrct = (double **) force->pair->extract("ny",dim);
+  nz_xtrct = (double **) force->pair->extract("nz",dim);
+
   // loop over stacking interaction neighbors using bond topology
 
   for (in = 0; in < nbondlist; in++) {
@@ -275,10 +274,13 @@ void PairOxdnaStk::compute(int eflag, int vflag)
 
     // a now in 3' direction, b in 5' direction
 
-    qa=bonus[ellipsoid[a]].quat;
-    MathExtra::q_to_exyz(qa,ax,ay,az);
-    qb=bonus[ellipsoid[b]].quat;
-    MathExtra::q_to_exyz(qb,bx,by,bz);
+    ax[0] = nx_xtrct[a][0];
+    ax[1] = nx_xtrct[a][1];
+    ax[2] = nx_xtrct[a][2];
+    bx[0] = nx_xtrct[b][0];
+    bx[1] = nx_xtrct[b][1];
+    bx[2] = nx_xtrct[b][2];
+    // (a/b)y/z not needed here as oxDNA(1) co-linear
 
     // vector COM a - stacking site a
     ra_cst[0] = d_cst*ax[0];
@@ -336,6 +338,13 @@ void PairOxdnaStk::compute(int eflag, int vflag)
     // early rejection criterium
     if (f1) {
 
+    az[0] = nz_xtrct[a][0];
+    az[1] = nz_xtrct[a][1];
+    az[2] = nz_xtrct[a][2];
+    bz[0] = nz_xtrct[b][0];
+    bz[1] = nz_xtrct[b][1];
+    bz[2] = nz_xtrct[b][2];
+
     // theta4 angle and correction
     cost4 = MathExtra::dot3(bz,az);
     if (cost4 >  1.0) cost4 =  1.0;
@@ -360,6 +369,13 @@ void PairOxdnaStk::compute(int eflag, int vflag)
     // early rejection criterium
     if (f4t5) {
 
+    ay[0] = ny_xtrct[a][0];
+    ay[1] = ny_xtrct[a][1];
+    ay[2] = ny_xtrct[a][2];
+    by[0] = ny_xtrct[b][0];
+    by[1] = ny_xtrct[b][1];
+    by[2] = ny_xtrct[b][2];
+
     cost6p = MathExtra::dot3(delr_st_norm,az);
     if (cost6p >  1.0) cost6p =  1.0;
     if (cost6p < -1.0) cost6p = -1.0;
@@ -409,8 +425,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
 
     // force, torque and virial contribution for forces between stacking sites
 
-    fpair = 0.0;
-
     delf[0] = 0.0;
     delf[1] = 0.0;
     delf[2] = 0.0;
@@ -425,7 +439,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
 
     // radial force
     finc  = -df1 * f4t4 * f4t5 * f4t6 * f5c1 * f5c2;
-    fpair += finc;
 
     delf[0] += delr_st[0] * finc;
     delf[1] += delr_st[1] * finc;
@@ -435,7 +448,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
     if (theta5p) {
 
       finc   = -f1 * f4t4 * df4t5 * f4t6 * f5c1 * f5c2 * rinv_st;
-      fpair += finc;
 
       delf[0] += (delr_st_norm[0]*cost5p - bz[0]) * finc;
       delf[1] += (delr_st_norm[1]*cost5p - bz[1]) * finc;
@@ -447,7 +459,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
     if (theta6p) {
 
       finc   = -f1 * f4t4 * f4t5 * df4t6 * f5c1 * f5c2 * rinv_st;
-      fpair += finc;
 
       delf[0] += (delr_st_norm[0]*cost6p - az[0]) * finc;
       delf[1] += (delr_st_norm[1]*cost6p - az[1]) * finc;
@@ -499,8 +510,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
 
     // force, torque and virial contribution for forces between backbone sites
 
-    fpair = 0.0;
-
     delf[0] = 0.0;
     delf[1] = 0.0;
     delf[2] = 0.0;
@@ -517,7 +526,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
     if (cosphi1) {
 
       finc   = -f1 * f4t4 * f4t5 * f4t6 * df5c1 * f5c2 * rinv_ss;
-      fpair += finc;
 
       delf[0] += (delr_ss_norm[0]*cosphi1 - by[0]) * finc;
       delf[1] += (delr_ss_norm[1]*cosphi1 - by[1]) * finc;
@@ -529,7 +537,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
     if (cosphi2) {
 
       finc   = -f1 * f4t4 * f4t5 * f4t6 * f5c1 * df5c2 * rinv_ss;
-      fpair += finc;
 
       delf[0] += (delr_ss_norm[0]*cosphi2 - ay[0]) * finc;
       delf[1] += (delr_ss_norm[1]*cosphi2 - ay[1]) * finc;

src/CG-DNA/pair_oxdna_stk.h

@@ -28,20 +28,20 @@ namespace LAMMPS_NS {
 class PairOxdnaStk : public Pair {
  public:
   PairOxdnaStk(class LAMMPS *);
-  virtual ~PairOxdnaStk();
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  void init_style();
-  void init_list(int, class NeighList *);
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  void *extract(const char *, int &);
+  ~PairOxdnaStk() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  void init_list(int, class NeighList *) override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  void *extract(const char *, int &) override;
 
  protected:
   // stacking interaction
@@ -59,7 +59,7 @@ class PairOxdnaStk : public Pair {
   double **b_st6, **dtheta_st6_c;
   double **a_st1, **cosphi_st1_ast, **b_st1, **cosphi_st1_c;
   double **a_st2, **cosphi_st2_ast, **b_st2, **cosphi_st2_c;
-
+  double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for local unit vectors
   int seqdepflag;
 
   virtual void allocate();

src/CG-DNA/pair_oxdna_xstk.cpp

@@ -18,7 +18,6 @@
 #include "pair_oxdna_xstk.h"
 
 #include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
@@ -111,9 +110,8 @@ PairOxdnaXstk::~PairOxdnaXstk()
 
 void PairOxdnaXstk::compute(int eflag, int vflag)
 {
-
   double delf[3],delta[3],deltb[3]; // force, torque increment;
-  double evdwl,fpair,finc,tpair,factor_lj;
+  double evdwl,finc,tpair,factor_lj;
   double delr_hb[3],delr_hb_norm[3],rsq_hb,r_hb,rinv_hb;
   double theta1,t1dir[3],cost1;
   double theta2,t2dir[3],cost2;
@@ -126,10 +124,9 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
   double d_chb=+0.4;
   // vectors COM-h-bonding site in lab frame
   double ra_chb[3],rb_chb[3];
-
-  // quaternions and Cartesian unit vectors in lab frame
-  double *qa,ax[3],ay[3],az[3];
-  double *qb,bx[3],by[3],bz[3];
+  // Cartesian unit vectors in lab frame
+  double ax[3],az[3];
+  double bx[3],bz[3];
 
   double **x = atom->x;
   double **f = atom->f;
@@ -141,10 +138,6 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
   int *alist,*blist,*numneigh,**firstneigh;
   double *special_lj = force->special_lj;
 
-  AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
-  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
-  int *ellipsoid = atom->ellipsoid;
-
   int a,b,ia,ib,anum,bnum,atype,btype;
 
   double f2,f4t1,f4t4,f4t2,f4t3,f4t7,f4t8;
@@ -158,6 +151,12 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
 
+  // n(x/y/z)_xtrct = extracted local unit vectors from oxdna_excv
+  int dim;
+  nx_xtrct = (double **) force->pair->extract("nx",dim);
+  ny_xtrct = (double **) force->pair->extract("ny",dim);
+  nz_xtrct = (double **) force->pair->extract("nz",dim);
+
   // loop over pair interaction neighbors of my atoms
 
   for (ia = 0; ia < anum; ia++) {
@@ -165,8 +164,10 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
     a = alist[ia];
     atype = type[a];
 
-    qa=bonus[ellipsoid[a]].quat;
-    MathExtra::q_to_exyz(qa,ax,ay,az);
+    ax[0] = nx_xtrct[a][0];
+    ax[1] = nx_xtrct[a][1];
+    ax[2] = nx_xtrct[a][2];
+    // a(y/z) not needed here as oxDNA(1) co-linear
 
     ra_chb[0] = d_chb*ax[0];
     ra_chb[1] = d_chb*ax[1];
@@ -183,8 +184,10 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
 
       btype = type[b];
 
-      qb=bonus[ellipsoid[b]].quat;
-      MathExtra::q_to_exyz(qb,bx,by,bz);
+      bx[0] = nx_xtrct[b][0];
+      bx[1] = nx_xtrct[b][1];
+      bx[2] = nx_xtrct[b][2];
+      // b(y/z) not needed here as oxDNA(1) co-linear
 
       rb_chb[0] = d_chb*bx[0];
       rb_chb[1] = d_chb*bx[1];
@@ -243,6 +246,13 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
       // early rejection criterium
       if (f4t3) {
 
+      az[0] = nz_xtrct[a][0];
+      az[1] = nz_xtrct[a][1];
+      az[2] = nz_xtrct[a][2];
+      bz[0] = nz_xtrct[b][0];
+      bz[1] = nz_xtrct[b][1];
+      bz[2] = nz_xtrct[b][2];
+
       cost4 = MathExtra::dot3(az,bz);
       if (cost4 >  1.0) cost4 =  1.0;
       if (cost4 < -1.0) cost4 = -1.0;
@@ -322,8 +332,6 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
 
       // force, torque and virial contribution for forces between h-bonding sites
 
-      fpair = 0.0;
-
       delf[0] = 0.0;
       delf[1] = 0.0;
       delf[2] = 0.0;
@@ -338,7 +346,6 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
 
       // radial force
       finc  = -df2 * f4t1 * f4t2 * f4t3 * f4t4 * f4t7 * f4t8 * rinv_hb *factor_lj;
-      fpair += finc;
 
       delf[0] += delr_hb[0] * finc;
       delf[1] += delr_hb[1] * finc;
@@ -348,7 +355,6 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
       if (theta2) {
 
         finc  = -f2 * f4t1 * df4t2 * f4t3 * f4t4 * f4t7 * f4t8 * rinv_hb * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_hb_norm[0]*cost2 + ax[0]) * finc;
         delf[1] += (delr_hb_norm[1]*cost2 + ax[1]) * finc;
@@ -360,7 +366,6 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
       if (theta3) {
 
         finc  = -f2 * f4t1 * f4t2 * df4t3 * f4t4 * f4t7 * f4t8 * rinv_hb * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_hb_norm[0]*cost3 - bx[0]) * finc;
         delf[1] += (delr_hb_norm[1]*cost3 - bx[1]) * finc;
@@ -372,7 +377,6 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
       if (theta7) {
 
         finc  = -f2 * f4t1 * f4t2 * f4t3 * f4t4 * df4t7 * f4t8 * rinv_hb * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_hb_norm[0]*cost7 + az[0]) * finc;
         delf[1] += (delr_hb_norm[1]*cost7 + az[1]) * finc;
@@ -384,7 +388,6 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
       if (theta8) {
 
         finc  = -f2 * f4t1 * f4t2 * f4t3 * f4t4 * f4t7 * df4t8 * rinv_hb * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_hb_norm[0]*cost8 - bz[0]) * finc;
         delf[1] += (delr_hb_norm[1]*cost8 - bz[1]) * finc;

src/CG-DNA/pair_oxdna_xstk.h

@@ -28,43 +28,38 @@ namespace LAMMPS_NS {
 class PairOxdnaXstk : public Pair {
  public:
   PairOxdnaXstk(class LAMMPS *);
-  virtual ~PairOxdnaXstk();
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  void init_list(int, class NeighList *);
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  void *extract(const char *, int &);
+  ~PairOxdnaXstk() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_list(int, class NeighList *) override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  void *extract(const char *, int &) override;
 
  protected:
   // cross-stacking interaction
   double **k_xst, **cut_xst_0, **cut_xst_c, **cut_xst_lo, **cut_xst_hi;
   double **cut_xst_lc, **cut_xst_hc, **b_xst_lo, **b_xst_hi;
   double **cutsq_xst_hc;
-
   double **a_xst1, **theta_xst1_0, **dtheta_xst1_ast;
   double **b_xst1, **dtheta_xst1_c;
-
   double **a_xst2, **theta_xst2_0, **dtheta_xst2_ast;
   double **b_xst2, **dtheta_xst2_c;
-
   double **a_xst3, **theta_xst3_0, **dtheta_xst3_ast;
   double **b_xst3, **dtheta_xst3_c;
-
   double **a_xst4, **theta_xst4_0, **dtheta_xst4_ast;
   double **b_xst4, **dtheta_xst4_c;
-
   double **a_xst7, **theta_xst7_0, **dtheta_xst7_ast;
   double **b_xst7, **dtheta_xst7_c;
-
   double **a_xst8, **theta_xst8_0, **dtheta_xst8_ast;
   double **b_xst8, **dtheta_xst8_c;
+  double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for local unit vectors
 
   virtual void allocate();
 };

src/CG-DNA/pair_oxrna2_dh.h

@@ -27,8 +27,8 @@ namespace LAMMPS_NS {
 class PairOxrna2Dh : public PairOxdna2Dh {
  public:
   PairOxrna2Dh(class LAMMPS *lmp) : PairOxdna2Dh(lmp) {}
-  virtual ~PairOxrna2Dh() {}
-  virtual void compute_interaction_sites(double *, double *, double *, double *);
+
+  void compute_interaction_sites(double *, double *, double *, double *) override;
 };
 
 }    // namespace LAMMPS_NS

src/CG-DNA/pair_oxrna2_excv.h

@@ -27,8 +27,8 @@ namespace LAMMPS_NS {
 class PairOxrna2Excv : public PairOxdnaExcv {
  public:
   PairOxrna2Excv(class LAMMPS *lmp) : PairOxdnaExcv(lmp) {}
-  virtual ~PairOxrna2Excv() {}
-  virtual void compute_interaction_sites(double *, double *, double *, double *, double *);
+
+  void compute_interaction_sites(double *, double *, double *, double *, double *) override;
 };
 
 }    // namespace LAMMPS_NS

src/CG-DNA/pair_oxrna2_hbond.h

@@ -27,7 +27,6 @@ namespace LAMMPS_NS {
 class PairOxrna2Hbond : public PairOxdnaHbond {
  public:
   PairOxrna2Hbond(class LAMMPS *);
-  virtual ~PairOxrna2Hbond() {}
 };
 
 }    // namespace LAMMPS_NS

src/CG-DNA/pair_oxrna2_stk.cpp

@@ -18,7 +18,6 @@
 #include "pair_oxrna2_stk.h"
 
 #include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
@@ -222,7 +221,7 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
 {
 
   double delf[3],delta[3],deltb[3]; // force, torque increment;
-  double evdwl,fpair,finc,tpair;
+  double evdwl,finc,tpair;
   double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss;
   double delr_st[3],delr_st_norm[3],rsq_st,r_st,rinv_st;
   double theta5p,t5pdir[3],cost5p;
@@ -245,9 +244,9 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
   double ra_cs[3],ra_cst[3];
   double rb_cs[3],rb_cst[3];
 
-  // quaternions and Cartesian unit vectors in lab frame
-  double *qa,ax[3],ay[3],az[3];
-  double *qb,bx[3],by[3],bz[3];
+  // Cartesian unit vectors in lab frame
+  double ax[3],ay[3],az[3];
+  double bx[3],by[3],bz[3];
 
   double **x = atom->x;
   double **f = atom->f;
@@ -262,10 +261,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
 
   tagint *id5p = atom->id5p;
 
-  AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
-  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
-  int *ellipsoid = atom->ellipsoid;
-
   int a,b,btemp,in,atype,btype;
 
   double f1,f4t5,f4t6,f4t9,f4t10,f5c1,f5c2;
@@ -274,6 +269,12 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
   evdwl = 0.0;
   ev_init(eflag,vflag);
 
+  // n(x/y/z)_xtrct = extracted local unit vectors from oxdna_excv
+  int dim;
+  nx_xtrct = (double **) force->pair->extract("nx",dim);
+  ny_xtrct = (double **) force->pair->extract("ny",dim);
+  nz_xtrct = (double **) force->pair->extract("nz",dim);
+
   // loop over stacking interaction neighbors using bond topology
 
   for (in = 0; in < nbondlist; in++) {
@@ -290,12 +291,26 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
 
     }
 
-   // a now in 3' direction, b in 5' direction
+    // a now in 3' direction, b in 5' direction
 
-    qa=bonus[ellipsoid[a]].quat;
-    MathExtra::q_to_exyz(qa,ax,ay,az);
-    qb=bonus[ellipsoid[b]].quat;
-    MathExtra::q_to_exyz(qb,bx,by,bz);
+    ax[0] = nx_xtrct[a][0];
+    ax[1] = nx_xtrct[a][1];
+    ax[2] = nx_xtrct[a][2];
+    ay[0] = ny_xtrct[a][0];
+    ay[1] = ny_xtrct[a][1];
+    ay[2] = ny_xtrct[a][2];
+    az[0] = nz_xtrct[a][0];
+    az[1] = nz_xtrct[a][1];
+    az[2] = nz_xtrct[a][2];
+    bx[0] = nx_xtrct[b][0];
+    bx[1] = nx_xtrct[b][1];
+    bx[2] = nx_xtrct[b][2];
+    by[0] = ny_xtrct[b][0];
+    by[1] = ny_xtrct[b][1];
+    by[2] = ny_xtrct[b][2];
+    bz[0] = nz_xtrct[b][0];
+    bz[1] = nz_xtrct[b][1];
+    bz[2] = nz_xtrct[b][2];
 
     // vector COM a - 5'-stacking site a
     ra_cst[0] = d_cst_x_5p*ax[0] + d_cst_y_5p*ay[0];
@@ -442,8 +457,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
 
     // force, torque and virial contribution for forces between stacking sites
 
-    fpair = 0.0;
-
     delf[0] = 0.0;
     delf[1] = 0.0;
     delf[2] = 0.0;
@@ -458,7 +471,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
 
     // radial force
     finc  = -df1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2;
-    fpair += finc;
 
     delf[0] += delr_st[0] * finc;
     delf[1] += delr_st[1] * finc;
@@ -468,7 +480,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
     if (theta5p) {
 
       finc   = -f1 * df4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st;
-      fpair += finc;
 
       delf[0] += (delr_st_norm[0]*cost5p - bz[0]) * finc;
       delf[1] += (delr_st_norm[1]*cost5p - bz[1]) * finc;
@@ -480,7 +491,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
     if (theta6p) {
 
       finc   = -f1 * f4t5 * df4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st;
-      fpair += finc;
 
       delf[0] += (delr_st_norm[0]*cost6p - az[0]) * finc;
       delf[1] += (delr_st_norm[1]*cost6p - az[1]) * finc;
@@ -532,8 +542,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
 
     // force, torque and virial contribution for forces between backbone sites
 
-    fpair = 0.0;
-
     delf[0] = 0.0;
     delf[1] = 0.0;
     delf[2] = 0.0;
@@ -550,7 +558,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
     if (theta9) {
 
       finc   = -f1 * f4t5 * f4t6 * df4t9 * f4t10 * f5c1 * f5c2 * rinv_ss;
-      fpair += finc;
 
       delf[0] += (delr_ss_norm[0]*cost9 - aux3p[0]) * finc;
       delf[1] += (delr_ss_norm[1]*cost9 - aux3p[1]) * finc;
@@ -562,7 +569,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
     if (theta10) {
 
       finc   = -f1 * f4t5 * f4t6 * f4t9 * df4t10 * f5c1 * f5c2 * rinv_ss;
-      fpair += finc;
 
       delf[0] += (delr_ss_norm[0]*cost10 - aux5p[0]) * finc;
       delf[1] += (delr_ss_norm[1]*cost10 - aux5p[1]) * finc;
@@ -574,7 +580,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
     if (cosphi1) {
 
       finc   = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * df5c1 * f5c2 * rinv_ss;
-      fpair += finc;
 
       delf[0] += (delr_ss_norm[0]*cosphi1 - by[0]) * finc;
       delf[1] += (delr_ss_norm[1]*cosphi1 - by[1]) * finc;
@@ -586,7 +591,6 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
     if (cosphi2) {
 
       finc   = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * df5c2 * rinv_ss;
-      fpair += finc;
 
       delf[0] += (delr_ss_norm[0]*cosphi2 - ay[0]) * finc;
       delf[1] += (delr_ss_norm[1]*cosphi2 - ay[1]) * finc;

src/CG-DNA/pair_oxrna2_stk.h

@@ -27,20 +27,20 @@ namespace LAMMPS_NS {
 class PairOxrna2Stk : public Pair {
  public:
   PairOxrna2Stk(class LAMMPS *);
-  virtual ~PairOxrna2Stk();
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  void init_style();
-  void init_list(int, class NeighList *);
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  void *extract(const char *, int &);
+  ~PairOxrna2Stk() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  void init_list(int, class NeighList *) override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  void *extract(const char *, int &) override;
 
  protected:
   // stacking interaction
@@ -60,7 +60,7 @@ class PairOxrna2Stk : public Pair {
   double **b_st10, **dtheta_st10_c;
   double **a_st1, **cosphi_st1_ast, **b_st1, **cosphi_st1_c;
   double **a_st2, **cosphi_st2_ast, **b_st2, **cosphi_st2_c;
-
+  double **nx_xtrct, **ny_xtrct, **nz_xtrct; // per-atom arrays for local unit vectors
   int seqdepflag;
 
   virtual void allocate();

src/CG-DNA/pair_oxrna2_xstk.cpp

@@ -18,7 +18,6 @@
 #include "pair_oxrna2_xstk.h"
 
 #include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
@@ -107,7 +106,7 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
 {
 
   double delf[3],delta[3],deltb[3]; // force, torque increment;
-  double evdwl,fpair,finc,tpair,factor_lj;
+  double evdwl,finc,tpair,factor_lj;
   double delr_hb[3],delr_hb_norm[3],rsq_hb,r_hb,rinv_hb;
   double theta1,t1dir[3],cost1;
   double theta2,t2dir[3],cost2;
@@ -120,9 +119,9 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
   // vectors COM-h-bonding site in lab frame
   double ra_chb[3],rb_chb[3];
 
-  // quaternions and Cartesian unit vectors in lab frame
-  double *qa,ax[3],ay[3],az[3];
-  double *qb,bx[3],by[3],bz[3];
+  // Cartesian unit vectors in lab frame
+  double ax[3],az[3];
+  double bx[3],bz[3];
 
   double **x = atom->x;
   double **f = atom->f;
@@ -134,10 +133,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
   int *alist,*blist,*numneigh,**firstneigh;
   double *special_lj = force->special_lj;
 
-  AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
-  AtomVecEllipsoid::Bonus *bonus = avec->bonus;
-  int *ellipsoid = atom->ellipsoid;
-
   int a,b,ia,ib,anum,bnum,atype,btype;
 
   double f2,f4t1,f4t2,f4t3,f4t7,f4t8;
@@ -151,6 +146,11 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
 
+  // n(x/z)_xtrct = extracted local unit vectors from oxdna_excv
+  int dim;
+  nx_xtrct = (double **) force->pair->extract("nx",dim);
+  nz_xtrct = (double **) force->pair->extract("nz",dim);
+
   // loop over pair interaction neighbors of my atoms
 
   for (ia = 0; ia < anum; ia++) {
@@ -158,8 +158,9 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
     a = alist[ia];
     atype = type[a];
 
-    qa=bonus[ellipsoid[a]].quat;
-    MathExtra::q_to_exyz(qa,ax,ay,az);
+    ax[0] = nx_xtrct[a][0];
+    ax[1] = nx_xtrct[a][1];
+    ax[2] = nx_xtrct[a][2];
 
     ra_chb[0] = d_chb*ax[0];
     ra_chb[1] = d_chb*ax[1];
@@ -176,8 +177,9 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
 
       btype = type[b];
 
-      qb=bonus[ellipsoid[b]].quat;
-      MathExtra::q_to_exyz(qb,bx,by,bz);
+      bx[0] = nx_xtrct[b][0];
+      bx[1] = nx_xtrct[b][1];
+      bx[2] = nx_xtrct[b][2];
 
       rb_chb[0] = d_chb*bx[0];
       rb_chb[1] = d_chb*bx[1];
@@ -236,6 +238,10 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
       // early rejection criterium
       if (f4t3) {
 
+      az[0] = nz_xtrct[a][0];
+      az[1] = nz_xtrct[a][1];
+      az[2] = nz_xtrct[a][2];
+
       cost7 = -1.0*MathExtra::dot3(az,delr_hb_norm);
       if (cost7 >  1.0) cost7 =  1.0;
       if (cost7 < -1.0) cost7 = -1.0;
@@ -250,6 +256,10 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
       // early rejection criterium
       if (f4t7) {
 
+      bz[0] = nz_xtrct[b][0];
+      bz[1] = nz_xtrct[b][1];
+      bz[2] = nz_xtrct[b][2];
+
       cost8 = MathExtra::dot3(bz,delr_hb_norm);
       if (cost8 >  1.0) cost8 =  1.0;
       if (cost8 < -1.0) cost8 = -1.0;
@@ -295,8 +305,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
 
       // force, torque and virial contribution for forces between h-bonding sites
 
-      fpair = 0.0;
-
       delf[0] = 0.0;
       delf[1] = 0.0;
       delf[2] = 0.0;
@@ -311,7 +319,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
 
       // radial force
       finc  = -df2 * f4t1 * f4t2 * f4t3 * f4t7 * f4t8 * rinv_hb *factor_lj;
-      fpair += finc;
 
       delf[0] += delr_hb[0] * finc;
       delf[1] += delr_hb[1] * finc;
@@ -321,7 +328,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
       if (theta2) {
 
         finc  = -f2 * f4t1 * df4t2 * f4t3 * f4t7 * f4t8 * rinv_hb * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_hb_norm[0]*cost2 + ax[0]) * finc;
         delf[1] += (delr_hb_norm[1]*cost2 + ax[1]) * finc;
@@ -333,7 +339,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
       if (theta3) {
 
         finc  = -f2 * f4t1 * f4t2 * df4t3 * f4t7 * f4t8 * rinv_hb * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_hb_norm[0]*cost3 - bx[0]) * finc;
         delf[1] += (delr_hb_norm[1]*cost3 - bx[1]) * finc;
@@ -345,7 +350,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
       if (theta7) {
 
         finc  = -f2 * f4t1 * f4t2 * f4t3 * df4t7 * f4t8 * rinv_hb * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_hb_norm[0]*cost7 + az[0]) * finc;
         delf[1] += (delr_hb_norm[1]*cost7 + az[1]) * finc;
@@ -357,7 +361,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
       if (theta8) {
 
         finc  = -f2 * f4t1 * f4t2 * f4t3 * f4t7 * df4t8 * rinv_hb * factor_lj;
-        fpair += finc;
 
         delf[0] += (delr_hb_norm[0]*cost8 - bz[0]) * finc;
         delf[1] += (delr_hb_norm[1]*cost8 - bz[1]) * finc;

src/CG-DNA/pair_oxrna2_xstk.h

@@ -27,40 +27,36 @@ namespace LAMMPS_NS {
 class PairOxrna2Xstk : public Pair {
  public:
   PairOxrna2Xstk(class LAMMPS *);
-  virtual ~PairOxrna2Xstk();
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  void init_list(int, class NeighList *);
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  void *extract(const char *, int &);
+  ~PairOxrna2Xstk() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_list(int, class NeighList *) override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  void *extract(const char *, int &) override;
 
  protected:
   // cross-stacking interaction
   double **k_xst, **cut_xst_0, **cut_xst_c, **cut_xst_lo, **cut_xst_hi;
   double **cut_xst_lc, **cut_xst_hc, **b_xst_lo, **b_xst_hi;
   double **cutsq_xst_hc;
-
   double **a_xst1, **theta_xst1_0, **dtheta_xst1_ast;
   double **b_xst1, **dtheta_xst1_c;
-
   double **a_xst2, **theta_xst2_0, **dtheta_xst2_ast;
   double **b_xst2, **dtheta_xst2_c;
-
   double **a_xst3, **theta_xst3_0, **dtheta_xst3_ast;
   double **b_xst3, **dtheta_xst3_c;
-
   double **a_xst7, **theta_xst7_0, **dtheta_xst7_ast;
   double **b_xst7, **dtheta_xst7_c;
-
   double **a_xst8, **theta_xst8_0, **dtheta_xst8_ast;
   double **b_xst8, **dtheta_xst8_c;
+  double **nx_xtrct, **nz_xtrct; // per-atom arrays for local unit vectors
 
   virtual void allocate();
 };

src/CG-SDK/angle_sdk.h

@@ -27,15 +27,15 @@ namespace LAMMPS_NS {
 class AngleSDK : public Angle {
  public:
   AngleSDK(class LAMMPS *);
-  virtual ~AngleSDK();
-  virtual void compute(int, int);
-  void coeff(int, char **);
-  void init_style();
-  double equilibrium_angle(int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_data(FILE *);
-  double single(int, int, int, int);
+  ~AngleSDK() override;
+  void compute(int, int) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double equilibrium_angle(int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_data(FILE *) override;
+  double single(int, int, int, int) override;
 
  protected:
   double *k, *theta0;

src/CG-SDK/pair_lj_sdk.h

@@ -31,20 +31,20 @@ namespace LAMMPS_NS {
 class PairLJSDK : public Pair {
  public:
   PairLJSDK(LAMMPS *);
-  virtual ~PairLJSDK();
-  virtual void compute(int, int);
-  virtual void settings(int, char **);
-  virtual void coeff(int, char **);
-  virtual double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  double single(int, int, int, int, double, double, double, double &);
-  void *extract(const char *, int &);
-  virtual double memory_usage();
+  ~PairLJSDK() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  double single(int, int, int, int, double, double, double, double &) override;
+  void *extract(const char *, int &) override;
+  double memory_usage() override;
 
  protected:
   int **lj_type;    // type of lennard jones potential

src/CG-SDK/pair_lj_sdk_coul_long.h

@@ -31,21 +31,21 @@ namespace LAMMPS_NS {
 class PairLJSDKCoulLong : public Pair {
  public:
   PairLJSDKCoulLong(class LAMMPS *);
-  virtual ~PairLJSDKCoulLong();
-  virtual void compute(int, int);
-  virtual void settings(int, char **);
-  void coeff(int, char **);
-  void init_style();
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  virtual void write_restart_settings(FILE *);
-  virtual void read_restart_settings(FILE *);
-  virtual double single(int, int, int, int, double, double, double, double &);
-  virtual void *extract(const char *, int &);
-  virtual double memory_usage();
+  ~PairLJSDKCoulLong() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  double single(int, int, int, int, double, double, double, double &) override;
+  void *extract(const char *, int &) override;
+  double memory_usage() override;
 
  protected:
   double **cut_lj, **cut_ljsq;

src/CG-SDK/pair_lj_sdk_coul_msm.h

@@ -31,10 +31,9 @@ namespace LAMMPS_NS {
 class PairLJSDKCoulMSM : public PairLJSDKCoulLong {
  public:
   PairLJSDKCoulMSM(class LAMMPS *);
-  virtual ~PairLJSDKCoulMSM(){};
-  virtual void compute(int, int);
-  virtual double single(int, int, int, int, double, double, double, double &);
-  virtual void *extract(const char *, int &);
+  void compute(int, int) override;
+  double single(int, int, int, int, double, double, double, double &) override;
+  void *extract(const char *, int &) override;
 
  private:
   template <int EVFLAG, int EFLAG, int NEWTON_PAIR> void eval_msm();

src/CLASS2/angle_class2.h

@@ -27,14 +27,14 @@ namespace LAMMPS_NS {
 class AngleClass2 : public Angle {
  public:
   AngleClass2(class LAMMPS *);
-  virtual ~AngleClass2();
-  virtual void compute(int, int);
-  virtual void coeff(int, char **);
-  double equilibrium_angle(int);
-  virtual void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_data(FILE *);
-  double single(int, int, int, int);
+  ~AngleClass2() override;
+  void compute(int, int) override;
+  void coeff(int, char **) override;
+  double equilibrium_angle(int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_data(FILE *) override;
+  double single(int, int, int, int) override;
 
  protected:
   double *theta0, *k2, *k3, *k4;

src/CLASS2/bond_class2.h

@@ -27,15 +27,15 @@ namespace LAMMPS_NS {
 class BondClass2 : public Bond {
  public:
   BondClass2(class LAMMPS *);
-  virtual ~BondClass2();
-  virtual void compute(int, int);
-  virtual void coeff(int, char **);
-  double equilibrium_distance(int);
-  void write_restart(FILE *);
-  virtual void read_restart(FILE *);
-  void write_data(FILE *);
-  double single(int, double, int, int, double &);
-  virtual void *extract(const char *, int &);
+  ~BondClass2() override;
+  void compute(int, int) override;
+  void coeff(int, char **) override;
+  double equilibrium_distance(int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_data(FILE *) override;
+  double single(int, double, int, int, double &) override;
+  void *extract(const char *, int &) override;
 
  protected:
   double *r0, *k2, *k3, *k4;

src/CLASS2/dihedral_class2.h

@@ -27,12 +27,12 @@ namespace LAMMPS_NS {
 class DihedralClass2 : public Dihedral {
  public:
   DihedralClass2(class LAMMPS *);
-  virtual ~DihedralClass2();
-  virtual void compute(int, int);
-  virtual void coeff(int, char **);
-  void write_restart(FILE *);
-  virtual void read_restart(FILE *);
-  void write_data(FILE *);
+  ~DihedralClass2() override;
+  void compute(int, int) override;
+  void coeff(int, char **) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_data(FILE *) override;
 
  protected:
   double *k1, *k2, *k3;

src/CLASS2/improper_class2.h

@@ -27,12 +27,12 @@ namespace LAMMPS_NS {
 class ImproperClass2 : public Improper {
  public:
   ImproperClass2(class LAMMPS *);
-  virtual ~ImproperClass2();
-  virtual void compute(int, int);
-  virtual void coeff(int, char **);
-  void write_restart(FILE *);
-  virtual void read_restart(FILE *);
-  void write_data(FILE *);
+  ~ImproperClass2() override;
+  void compute(int, int) override;
+  void coeff(int, char **) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_data(FILE *) override;
 
  protected:
   double *k0, *chi0;

src/CLASS2/pair_lj_class2.h

@@ -25,24 +25,24 @@ namespace LAMMPS_NS {
 class PairLJClass2 : public Pair {
  public:
   PairLJClass2(class LAMMPS *);
-  virtual ~PairLJClass2();
-  virtual void compute(int, int);
-  virtual void settings(int, char **);
-  void coeff(int, char **);
-  void init_style();
-  virtual double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  double single(int, int, int, int, double, double, double, double &);
-  void *extract(const char *, int &);
+  ~PairLJClass2() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  double single(int, int, int, int, double, double, double, double &) override;
+  void *extract(const char *, int &) override;
 
-  void compute_inner();
-  void compute_middle();
-  void compute_outer(int, int);
+  void compute_inner() override;
+  void compute_middle() override;
+  void compute_outer(int, int) override;
 
  protected:
   double cut_global;

src/CLASS2/pair_lj_class2_coul_cut.h

@@ -27,20 +27,20 @@ namespace LAMMPS_NS {
 class PairLJClass2CoulCut : public Pair {
  public:
   PairLJClass2CoulCut(class LAMMPS *);
-  virtual ~PairLJClass2CoulCut();
-  virtual void compute(int, int);
-  virtual void settings(int, char **);
-  void coeff(int, char **);
-  virtual void init_style();
-  virtual double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  double single(int, int, int, int, double, double, double, double &);
-  void *extract(const char *, int &);
+  ~PairLJClass2CoulCut() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  double single(int, int, int, int, double, double, double, double &) override;
+  void *extract(const char *, int &) override;
 
  protected:
   double cut_lj_global, cut_coul_global;

src/CLASS2/pair_lj_class2_coul_long.h

@@ -27,24 +27,24 @@ namespace LAMMPS_NS {
 class PairLJClass2CoulLong : public Pair {
  public:
   PairLJClass2CoulLong(class LAMMPS *);
-  virtual ~PairLJClass2CoulLong();
-  virtual void compute(int, int);
-  virtual void settings(int, char **);
-  void coeff(int, char **);
-  virtual void init_style();
-  virtual double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  double single(int, int, int, int, double, double, double, double &);
+  ~PairLJClass2CoulLong() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  double single(int, int, int, int, double, double, double, double &) override;
 
-  void compute_inner();
-  void compute_middle();
-  void compute_outer(int, int);
-  void *extract(const char *, int &);
+  void compute_inner() override;
+  void compute_middle() override;
+  void compute_outer(int, int) override;
+  void *extract(const char *, int &) override;
 
  protected:
   double cut_lj_global;

src/COLLOID/fix_wall_colloid.h

@@ -27,9 +27,9 @@ namespace LAMMPS_NS {
 class FixWallColloid : public FixWall {
  public:
   FixWallColloid(class LAMMPS *, int, char **);
-  void init();
-  void precompute(int);
-  void wall_particle(int, int, double);
+  void init() override;
+  void precompute(int) override;
+  void wall_particle(int, int, double) override;
 
  private:
   double coeff1[6], coeff2[6], coeff3[6], coeff4[6];

src/COLLOID/pair_brownian.h

@@ -27,16 +27,16 @@ namespace LAMMPS_NS {
 class PairBrownian : public Pair {
  public:
   PairBrownian(class LAMMPS *);
-  virtual ~PairBrownian();
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  virtual double init_one(int, int);
-  virtual void init_style();
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
+  ~PairBrownian() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  double init_one(int, int) override;
+  void init_style() override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
 
  protected:
   double cut_inner_global, cut_global;

src/COLLOID/pair_brownian_poly.h

@@ -27,10 +27,10 @@ namespace LAMMPS_NS {
 class PairBrownianPoly : public PairBrownian {
  public:
   PairBrownianPoly(class LAMMPS *);
-  ~PairBrownianPoly() {}
-  void compute(int, int);
-  double init_one(int, int);
-  void init_style();
+
+  void compute(int, int) override;
+  double init_one(int, int) override;
+  void init_style() override;
 };
 
 }    // namespace LAMMPS_NS

src/COLLOID/pair_colloid.h

@@ -27,18 +27,18 @@ namespace LAMMPS_NS {
 class PairColloid : public Pair {
  public:
   PairColloid(class LAMMPS *);
-  virtual ~PairColloid();
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  double init_one(int, int);
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  void write_data(FILE *);
-  void write_data_all(FILE *);
-  double single(int, int, int, int, double, double, double, double &);
+  ~PairColloid() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  double single(int, int, int, int, double, double, double, double &) override;
 
  protected:
   enum { SMALL_SMALL, SMALL_LARGE, LARGE_LARGE };

src/COLLOID/pair_lubricate.h

@@ -27,21 +27,21 @@ namespace LAMMPS_NS {
 class PairLubricate : public Pair {
  public:
   PairLubricate(class LAMMPS *);
-  virtual ~PairLubricate();
-  virtual void compute(int, int);
-  void settings(int, char **);
-  void coeff(int, char **);
-  double init_one(int, int);
-  virtual void init_style();
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
+  ~PairLubricate() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  double init_one(int, int) override;
+  void init_style() override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
   int pre_adapt(char *, int, int, int, int);
   void adapt(int, int, int, int, int, double);
 
-  int pack_forward_comm(int, int *, double *, int, int *);
-  void unpack_forward_comm(int, int, double *);
+  int pack_forward_comm(int, int *, double *, int, int *) override;
+  void unpack_forward_comm(int, int, double *) override;
 
  protected:
   double mu, cut_inner_global, cut_global;

src/COLLOID/pair_lubricateU.h

@@ -27,18 +27,18 @@ namespace LAMMPS_NS {
 class PairLubricateU : public Pair {
  public:
   PairLubricateU(class LAMMPS *);
-  virtual ~PairLubricateU();
-  virtual void compute(int, int);
-  virtual void settings(int, char **);
-  void coeff(int, char **);
-  double init_one(int, int);
-  virtual void init_style();
-  void write_restart(FILE *);
-  void read_restart(FILE *);
-  void write_restart_settings(FILE *);
-  void read_restart_settings(FILE *);
-  int pack_forward_comm(int, int *, double *, int, int *);
-  void unpack_forward_comm(int, int, double *);
+  ~PairLubricateU() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  double init_one(int, int) override;
+  void init_style() override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  int pack_forward_comm(int, int *, double *, int, int *) override;
+  void unpack_forward_comm(int, int, double *) override;
 
  protected:
   double cut_inner_global, cut_global;

src/COLLOID/pair_lubricateU_poly.h

@@ -27,10 +27,10 @@ namespace LAMMPS_NS {
 class PairLubricateUPoly : public PairLubricateU {
  public:
   PairLubricateUPoly(class LAMMPS *);
-  ~PairLubricateUPoly() {}
-  void compute(int, int);
-  void settings(int, char **);
-  void init_style();
+
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void init_style() override;
 
  private:
   double vol_P;
@@ -38,9 +38,9 @@ class PairLubricateUPoly : public PairLubricateU {
   class FixWall *wallfix;
 
   void iterate(double **, int);
-  void compute_RE(double **);
-  void compute_RU(double **);
-  void compute_Fh(double **);
+  void compute_RE(double **) override;
+  void compute_RU(double **) override;
+  void compute_Fh(double **) override;
 };
 
 }    // namespace LAMMPS_NS