apply clang-format to all headers with some exceptions

src/ASPHERE/compute_erotate_asphere.h

@@ -37,7 +37,7 @@ class ComputeERotateAsphere : public Compute {
   class AtomVecTri *avec_tri;
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/ASPHERE/compute_temp_asphere.h

@@ -48,7 +48,7 @@ class ComputeTempAsphere : public Compute {
   void dof_compute();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/ASPHERE/fix_nh_asphere.h

@@ -33,7 +33,7 @@ class FixNHAsphere : public FixNH {
   void nh_v_temp();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 

src/ASPHERE/fix_nph_asphere.h

@@ -30,7 +30,7 @@ class FixNPHAsphere : public FixNHAsphere {
   ~FixNPHAsphere() {}
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/ASPHERE/fix_npt_asphere.h

@@ -30,7 +30,7 @@ class FixNPTAsphere : public FixNHAsphere {
   ~FixNPTAsphere() {}
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/ASPHERE/fix_nve_asphere.h

@@ -36,7 +36,7 @@ class FixNVEAsphere : public FixNVE {
   class AtomVecEllipsoid *avec;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/ASPHERE/fix_nve_asphere_noforce.h

@@ -35,7 +35,7 @@ class FixNVEAsphereNoforce : public FixNVENoforce {
   class AtomVecEllipsoid *avec;
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/ASPHERE/fix_nve_line.h

@@ -34,11 +34,11 @@ class FixNVELine : public FixNVE {
   void final_integrate();
 
  private:
-  double MINUSPI,TWOPI;
+  double MINUSPI, TWOPI;
   class AtomVecLine *avec;
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/ASPHERE/fix_nve_tri.h

@@ -38,7 +38,7 @@ class FixNVETri : public FixNVE {
   class AtomVecTri *avec;
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/ASPHERE/fix_nvt_asphere.h

@@ -30,7 +30,7 @@ class FixNVTAsphere : public FixNHAsphere {
   ~FixNVTAsphere() {}
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/ASPHERE/pair_gayberne.h

@@ -41,38 +41,35 @@ class PairGayBerne : public Pair {
   void write_data_all(FILE *);
 
  protected:
-  enum{SPHERE_SPHERE,SPHERE_ELLIPSE,ELLIPSE_SPHERE,ELLIPSE_ELLIPSE};
+  enum { SPHERE_SPHERE, SPHERE_ELLIPSE, ELLIPSE_SPHERE, ELLIPSE_ELLIPSE };
 
   double cut_global;
   double **cut;
 
-  double gamma,upsilon,mu;   // Gay-Berne parameters
+  double gamma, upsilon, mu;    // Gay-Berne parameters
   double **shape1;              // per-type radii in x, y and z
   double **shape2;              // per-type radii in x, y and z SQUARED
   double *lshape;               // precalculation based on the shape
   double **well;                // well depth scaling along each axis ^ -1.0/mu
-  double **epsilon,**sigma;  // epsilon and sigma values for atom-type pairs
+  double **epsilon, **sigma;    // epsilon and sigma values for atom-type pairs
 
   int **form;
-  double **lj1,**lj2,**lj3,**lj4;
+  double **lj1, **lj2, **lj3, **lj4;
   double **offset;
   int *setwell;
   class AtomVecEllipsoid *avec;
 
   void allocate();
-  double gayberne_analytic(const int i, const int j, double a1[3][3],
-                           double a2[3][3], double b1[3][3], double b2[3][3],
-                           double g1[3][3], double g2[3][3], double *r12,
-                           const double rsq, double *fforce, double *ttor,
+  double gayberne_analytic(const int i, const int j, double a1[3][3], double a2[3][3],
+                           double b1[3][3], double b2[3][3], double g1[3][3], double g2[3][3],
+                           double *r12, const double rsq, double *fforce, double *ttor,
                            double *rtor);
-  double gayberne_lj(const int i, const int j, double a1[3][3],
-                     double b1[3][3],double g1[3][3],double *r12,
-                     const double rsq, double *fforce, double *ttor);
-  void compute_eta_torque(double m[3][3], double m2[3][3],
-                          double *s, double ans[3][3]);
+  double gayberne_lj(const int i, const int j, double a1[3][3], double b1[3][3], double g1[3][3],
+                     double *r12, const double rsq, double *fforce, double *ttor);
+  void compute_eta_torque(double m[3][3], double m2[3][3], double *s, double ans[3][3]);
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/ASPHERE/pair_line_lj.h

@@ -37,15 +37,15 @@ class PairLineLJ : public Pair {
  protected:
   double cut_global;
   double *subsize;
-  double **epsilon,**sigma,**cutsub,**cutsubsq;
+  double **epsilon, **sigma, **cutsub, **cutsubsq;
   double **cut;
-  double **lj1,**lj2,**lj3,**lj4;     // for sphere/sphere interactions
+  double **lj1, **lj2, **lj3, **lj4;    // for sphere/sphere interactions
   class AtomVecLine *avec;
 
   double *size;    // per-type size of sub-particles to tile line segment
 
   struct Discrete {
-    double dx,dy;
+    double dx, dy;
   };
   Discrete *discrete;    // list of all discretes for all lines
   int ndiscrete;         // number of discretes in list
@@ -58,7 +58,7 @@ class PairLineLJ : public Pair {
   void discretize(int, double);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/ASPHERE/pair_resquared.h

@@ -39,7 +39,7 @@ class PairRESquared : public Pair {
   void read_restart_settings(FILE *);
 
  protected:
-  enum{SPHERE_SPHERE,SPHERE_ELLIPSE,ELLIPSE_SPHERE,ELLIPSE_ELLIPSE};
+  enum { SPHERE_SPHERE, SPHERE_ELLIPSE, ELLIPSE_SPHERE, ELLIPSE_ELLIPSE };
 
   double cut_global;
   double **cut;
@@ -48,10 +48,10 @@ class PairRESquared : public Pair {
   double **shape2;              // per-type radii in x, y and z SQUARED
   double *lshape;               // product of the radii
   double **well;                // well depth scaling along each axis
-  double **epsilon,**sigma;  // epsilon and sigma values for atom-type pairs
+  double **epsilon, **sigma;    // epsilon and sigma values for atom-type pairs
 
   int **form;
-  double **lj1,**lj2,**lj3,**lj4;
+  double **lj1, **lj2, **lj3, **lj4;
   double **offset;
   int *setwell;
   class AtomVecEllipsoid *avec;
@@ -75,16 +75,13 @@ class PairRESquared : public Pair {
 
   void allocate();
 
-  void precompute_i(const int i,RE2Vars &ws);
+  void precompute_i(const int i, RE2Vars &ws);
   double det_prime(const double m[3][3], const double m2[3][3]);
-  double resquared_analytic(const int i, const int j,
-                            const RE2Vars &wi, const RE2Vars &wj,
-                            const double *r, const double rsq,
-                            double *fforce, double *ttor,
+  double resquared_analytic(const int i, const int j, const RE2Vars &wi, const RE2Vars &wj,
+                            const double *r, const double rsq, double *fforce, double *ttor,
                             double *rtor);
-  double resquared_lj(const int i, const int j, const RE2Vars &wi,
-                      const double *r, const double rsq, double *fforce,
-                      double *ttor, bool calc_torque);
+  double resquared_lj(const int i, const int j, const RE2Vars &wi, const double *r,
+                      const double rsq, double *fforce, double *ttor, bool calc_torque);
 
   double cr60;        // 60^1/3
   double b_alpha;     // 45/56
@@ -92,7 +89,7 @@ class PairRESquared : public Pair {
   double solv_f_r;    // 3.0/(4.0*PI*2025)
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/ASPHERE/pair_tri_lj.h

@@ -37,12 +37,12 @@ class PairTriLJ : public Pair {
  protected:
   double cut_global;
   double **cut;
-  double **epsilon,**sigma;
-  double **lj1,**lj2,**lj3,**lj4;
+  double **epsilon, **sigma;
+  double **lj1, **lj2, **lj3, **lj4;
   class AtomVecTri *avec;
 
   struct Discrete {
-    double dx,dy,dz;
+    double dx, dy, dz;
     double sigma;
   };
   Discrete *discrete;    // list of all discretes for all lines
@@ -56,7 +56,7 @@ class PairTriLJ : public Pair {
   void discretize(int, double, double *, double *, double *);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/BODY/body_nparticle.h

@@ -20,8 +20,8 @@ BodyStyle(nparticle,BodyNparticle);
 #ifndef LMP_BODY_NPARTICLE_H
 #define LMP_BODY_NPARTICLE_H
 
-#include "body.h"
 #include "atom_vec_body.h"
+#include "body.h"
 
 namespace LAMMPS_NS {
 
@@ -49,7 +49,7 @@ class BodyNparticle : public Body {
   double **imdata;
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/BODY/body_rounded_polygon.h

@@ -20,8 +20,8 @@ BodyStyle(rounded/polygon,BodyRoundedPolygon);
 #ifndef LMP_BODY_ROUNDED_POLYGON_H
 #define LMP_BODY_ROUNDED_POLYGON_H
 
-#include "body.h"
 #include "atom_vec_body.h"
+#include "body.h"
 
 namespace LAMMPS_NS {
 
@@ -53,7 +53,7 @@ class BodyRoundedPolygon : public Body {
   double **imdata;
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/BODY/body_rounded_polyhedron.h

@@ -20,8 +20,8 @@ BodyStyle(rounded/polyhedron,BodyRoundedPolyhedron);
 #ifndef LMP_BODY_ROUNDED_POLYHEDRON_H
 #define LMP_BODY_ROUNDED_POLYHEDRON_H
 
-#include "body.h"
 #include "atom_vec_body.h"
+#include "body.h"
 
 namespace LAMMPS_NS {
 
@@ -55,7 +55,7 @@ class BodyRoundedPolyhedron : public Body {
   double **imdata;
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/BODY/compute_body_local.h

@@ -34,7 +34,7 @@ class ComputeBodyLocal : public Compute {
 
  private:
   int nvalues;
-  int *which,*index;
+  int *which, *index;
 
   int nmax;
 
@@ -45,7 +45,7 @@ class ComputeBodyLocal : public Compute {
   void reallocate(int);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/BODY/compute_temp_body.h

@@ -46,7 +46,7 @@ class ComputeTempBody : public Compute {
   void dof_compute();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/BODY/fix_nh_body.h

@@ -33,7 +33,7 @@ class FixNHBody : public FixNH {
   void nh_v_temp();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 

src/BODY/fix_nph_body.h

@@ -30,7 +30,7 @@ class FixNPHBody : public FixNHBody {
   ~FixNPHBody() {}
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/BODY/fix_npt_body.h

@@ -30,7 +30,7 @@ class FixNPTBody : public FixNHBody {
   ~FixNPTBody() {}
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/BODY/fix_nve_body.h

@@ -36,7 +36,7 @@ class FixNVEBody : public FixNVE {
   class AtomVecBody *avec;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/BODY/fix_nvt_body.h

@@ -30,7 +30,7 @@ class FixNVTBody : public FixNHBody {
   ~FixNVTBody() {}
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/BODY/fix_wall_body_polygon.h

@@ -40,16 +40,16 @@ class FixWallBodyPolygon : public Fix {
     int edge;             // edge of the second polygon
     double xv[3];         // coordinates of the vertex
     double xe[3];         // coordinates of the projection of the vertex on the edge
-    double separation;// separation at contact
+    double separation;    // separation at contact
   };
 
  protected:
-  int wallstyle,pairstyle,wiggle,axis;
+  int wallstyle, pairstyle, wiggle, axis;
   double kn;     // normal repulsion strength
   double c_n;    // normal damping coefficient
   double c_t;    // tangential damping coefficient
-  double lo,hi,cylradius;
-  double amplitude,period,omega;
+  double lo, hi, cylradius;
+  double amplitude, period, omega;
   double dt;
   int time_origin;
 
@@ -75,26 +75,21 @@ class FixWallBodyPolygon : public Fix {
 
   void body2space(int);
 
-  int vertex_against_wall(int ibody, double wall_pos, double** x,
-                          double** f, double** torque, int side,
-                          Contact* contact_list, int &num_contacts,
-                          double* facc);
-
-  int compute_distance_to_wall(double* x0, double rradi, double wall_pos,
-                               int side, double &d, double hi[3], int &contact);
-  double contact_separation(const Contact& c1, const Contact& c2);
-  void contact_forces(Contact& contact, double j_a, double** x,
-                      double** v, double** angmom, double** f, double** torque,
-                      double* vwall, double* facc);
-  void sum_torque(double* xm, double *x, double fx,
-                  double fy, double fz, double* torque);
-  void total_velocity(double* p, double *xcm, double* vcm, double *angmom,
-                      double *inertia, double *quat, double* vi);
-  void distance(const double* x2, const double* x1, double& r);
+  int vertex_against_wall(int ibody, double wall_pos, double **x, double **f, double **torque,
+                          int side, Contact *contact_list, int &num_contacts, double *facc);
 
+  int compute_distance_to_wall(double *x0, double rradi, double wall_pos, int side, double &d,
+                               double hi[3], int &contact);
+  double contact_separation(const Contact &c1, const Contact &c2);
+  void contact_forces(Contact &contact, double j_a, double **x, double **v, double **angmom,
+                      double **f, double **torque, double *vwall, double *facc);
+  void sum_torque(double *xm, double *x, double fx, double fy, double fz, double *torque);
+  void total_velocity(double *p, double *xcm, double *vcm, double *angmom, double *inertia,
+                      double *quat, double *vi);
+  void distance(const double *x2, const double *x1, double &r);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/BODY/fix_wall_body_polyhedron.h

@@ -40,14 +40,14 @@ class FixWallBodyPolyhedron : public Fix {
     int edge;             // edge of the second polygon
     double xv[3];         // coordinates of the vertex
     double xe[3];         // coordinates of the projection of the vertex on the edge
-    double separation;// separation at contact
+    double separation;    // separation at contact
   };
 
  protected:
-  int wallstyle,pairstyle,wiggle,axis;
-  double kn,c_n,c_t;
-  double lo,hi,cylradius;
-  double amplitude,period,omega;
+  int wallstyle, pairstyle, wiggle, axis;
+  double kn, c_n, c_t;
+  double lo, hi, cylradius;
+  double amplitude, period, omega;
   double dt;
   int time_origin;
 
@@ -80,33 +80,27 @@ class FixWallBodyPolyhedron : public Fix {
 
   void body2space(int);
 
-  int edge_against_wall(int ibody, double wall_pos, int side, double* vwall,
-     double** x, double** f, double** torque, Contact* contact_list,
-     int &num_contacts, double* facc);
-  int sphere_against_wall(int i, double wall_pos, int side, double* vwall,
-     double** x, double** v, double** f, double** angmom, double** torque);
+  int edge_against_wall(int ibody, double wall_pos, int side, double *vwall, double **x, double **f,
+                        double **torque, Contact *contact_list, int &num_contacts, double *facc);
+  int sphere_against_wall(int i, double wall_pos, int side, double *vwall, double **x, double **v,
+                          double **f, double **angmom, double **torque);
 
-  int compute_distance_to_wall(int ibody, int edge_index, double *xmi,
-                               double rounded_radius_i, double wall_pos, int side,
-                               double* vwall, int &contact);
-  double contact_separation(const Contact& c1, const Contact& c2);
-  void contact_forces(int ibody, double j_a, double *xi, double *xj,
-                      double delx, double dely, double delz,
-                      double fx, double fy, double fz, double** x, double** v,
-                      double** angmom, double** f, double** torque, double* vwall);
-
-  void contact_forces(Contact& contact, double j_a, double** x,
-                      double** v, double** angmom, double** f, double** torque,
-                      double* vwall, double* facc);
-  void sum_torque(double* xm, double *x, double fx,
-                  double fy, double fz, double* torque);
-  void total_velocity(double* p, double *xcm, double* vcm, double *angmom,
-                      double *inertia, double *quat, double* vi);
-  void distance(const double* x2, const double* x1, double& r);
+  int compute_distance_to_wall(int ibody, int edge_index, double *xmi, double rounded_radius_i,
+                               double wall_pos, int side, double *vwall, int &contact);
+  double contact_separation(const Contact &c1, const Contact &c2);
+  void contact_forces(int ibody, double j_a, double *xi, double *xj, double delx, double dely,
+                      double delz, double fx, double fy, double fz, double **x, double **v,
+                      double **angmom, double **f, double **torque, double *vwall);
 
+  void contact_forces(Contact &contact, double j_a, double **x, double **v, double **angmom,
+                      double **f, double **torque, double *vwall, double *facc);
+  void sum_torque(double *xm, double *x, double fx, double fy, double fz, double *torque);
+  void total_velocity(double *p, double *xcm, double *vcm, double *angmom, double *inertia,
+                      double *quat, double *vi);
+  void distance(const double *x2, const double *x1, double &r);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/BODY/pair_body_nparticle.h

@@ -37,8 +37,8 @@ class PairBodyNparticle : public Pair {
  protected:
   double cut_global;
   double **cut;
-  double **epsilon,**sigma;
-  double **lj1,**lj2,**lj3,**lj4;
+  double **epsilon, **sigma;
+  double **lj1, **lj2, **lj3, **lj4;
 
   class AtomVecBody *avec;
   class BodyNparticle *bptr;
@@ -54,7 +54,7 @@ class PairBodyNparticle : public Pair {
   void body2space(int);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/BODY/pair_body_rounded_polygon.h

@@ -40,7 +40,7 @@ class PairBodyRoundedPolygon : public Pair {
     int edge;             // edge of the second polygon
     double xv[3];         // coordinates of the vertex
     double xe[3];         // coordinates of the projection of the vertex on the edge
-    double separation;// separation at contact
+    double separation;    // separation at contact
   };
 
  protected:
@@ -77,39 +77,34 @@ class PairBodyRoundedPolygon : public Pair {
   void body2space(int);
 
   // sphere-sphere interaction
-  void sphere_against_sphere(int i, int j, double delx, double dely, double delz,
-                             double rsq, double k_n, double k_na,
-                             double** x, double** v, double** f, int evflag);
+  void sphere_against_sphere(int i, int j, double delx, double dely, double delz, double rsq,
+                             double k_n, double k_na, double **x, double **v, double **f,
+                             int evflag);
   // vertex-edge interaction
-  int vertex_against_edge(int i, int j, double k_n, double k_na,
-                          double** x, double** f, double** torque,
-                          tagint* tag, Contact* contact_list,
-                          int &num_contacts, double &evdwl, double* facc);
+  int vertex_against_edge(int i, int j, double k_n, double k_na, double **x, double **f,
+                          double **torque, tagint *tag, Contact *contact_list, int &num_contacts,
+                          double &evdwl, double *facc);
   // compute distance between a point and an edge from another body
-  int compute_distance_to_vertex(int ibody, int edge_index, double* xmi,
-                                 double rounded_radius, double* x0,
-                                 double x0_rounded_radius, double cut_inner,
-                                 double &d, double hi[3], double &t,
-                                 int &contact);
+  int compute_distance_to_vertex(int ibody, int edge_index, double *xmi, double rounded_radius,
+                                 double *x0, double x0_rounded_radius, double cut_inner, double &d,
+                                 double hi[3], double &t, int &contact);
   // compute contact forces if contact points are detected
-  void contact_forces(Contact& contact, double j_a,
-                      double** x, double** v, double** angmom, double** f,
-                      double** torque, double &evdwl, double* facc);
+  void contact_forces(Contact &contact, double j_a, double **x, double **v, double **angmom,
+                      double **f, double **torque, double &evdwl, double *facc);
 
   // compute the separation between two contacts
-  double contact_separation(const Contact& c1, const Contact& c2);
+  double contact_separation(const Contact &c1, const Contact &c2);
 
   // accumulate torque to a body given a force at a given point
-  void sum_torque(double* xm, double *x, double fx,
-                  double fy, double fz, double* torque);
+  void sum_torque(double *xm, double *x, double fx, double fy, double fz, double *torque);
   // helper functions
-  int opposite_sides(double* x1, double* x2, double* a, double* b);
-  void total_velocity(double* p, double *xcm, double* vcm, double *angmom,
-                      double *inertia, double *quat, double* vi);
-  inline void distance(const double* x2, const double* x1, double& r);
+  int opposite_sides(double *x1, double *x2, double *a, double *b);
+  void total_velocity(double *p, double *xcm, double *vcm, double *angmom, double *inertia,
+                      double *quat, double *vi);
+  inline void distance(const double *x2, const double *x1, double &r);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/BODY/pair_body_rounded_polyhedron.h

@@ -34,13 +34,12 @@ class PairBodyRoundedPolyhedron : public Pair {
   void init_style();
   double init_one(int, int);
 
-  virtual void kernel_force(double R, int itype, int jtype,
-    double& energy, double& fpair);
+  virtual void kernel_force(double R, int itype, int jtype, double &energy, double &fpair);
 
   struct Contact {
     int ibody, jbody;     // body (i.e. atom) indices (not tags)
     int type;             // 0 = VERTEX-FACE; 1 = EDGE-EDGE
-    double fx,fy,fz;   // unscaled cohesive forces at contact
+    double fx, fy, fz;    // unscaled cohesive forces at contact
     double xi[3];         // coordinates of the contact point on ibody
     double xj[3];         // coordinates of the contact point on jbody
     double separation;    // contact surface separation
@@ -88,91 +87,78 @@ class PairBodyRoundedPolyhedron : public Pair {
   void body2space(int);
 
   // sphere-sphere interaction
-  void sphere_against_sphere(int ibody, int jbody, int itype, int jtype,
-                             double delx, double dely, double delz, double rsq,
-                             double** v, double** f, int evflag);
+  void sphere_against_sphere(int ibody, int jbody, int itype, int jtype, double delx, double dely,
+                             double delz, double rsq, double **v, double **f, int evflag);
   // sphere-edge interaction
-  void sphere_against_edge(int ibody, int jbody, int itype, int jtype,
-                           double** x, double** v, double** f, double** torque,
-                           double** angmom, int evflag);
+  void sphere_against_edge(int ibody, int jbody, int itype, int jtype, double **x, double **v,
+                           double **f, double **torque, double **angmom, int evflag);
   // sphere-face interaction
-  void sphere_against_face(int ibody, int jbody, int itype, int jtype,
-                           double** x, double** v, double** f, double** torque,
-                           double** angmom, int evflag);
+  void sphere_against_face(int ibody, int jbody, int itype, int jtype, double **x, double **v,
+                           double **f, double **torque, double **angmom, int evflag);
   // edge-edge interactions
-  int edge_against_edge(int ibody, int jbody, int itype, int jtype,
-                        double** x,Contact* contact_list, int &num_contacts,
-                        double &evdwl, double* facc);
+  int edge_against_edge(int ibody, int jbody, int itype, int jtype, double **x,
+                        Contact *contact_list, int &num_contacts, double &evdwl, double *facc);
   // edge-face interactions
-  int edge_against_face(int ibody, int jbody, int itype, int jtype,
-                        double** x, Contact* contact_list, int &num_contacts,
-                        double &evdwl, double* facc);
+  int edge_against_face(int ibody, int jbody, int itype, int jtype, double **x,
+                        Contact *contact_list, int &num_contacts, double &evdwl, double *facc);
 
   // a face vs. a single edge
-  int interaction_face_to_edge(int ibody, int face_index, double* xmi,
-                               double rounded_radius_i, int jbody, int edge_index,
-                               double* xmj, double rounded_radius_j,
-                               int itype, int jtype, double cut_inner,
-                               Contact* contact_list, int &num_contacts,
-                               double& energy, double* facc);
+  int interaction_face_to_edge(int ibody, int face_index, double *xmi, double rounded_radius_i,
+                               int jbody, int edge_index, double *xmj, double rounded_radius_j,
+                               int itype, int jtype, double cut_inner, Contact *contact_list,
+                               int &num_contacts, double &energy, double *facc);
   // an edge vs. an edge from another body
-  int interaction_edge_to_edge(int ibody, int edge_index_i, double* xmi,
-                               double rounded_radius_i, int jbody, int edge_index_j,
-                               double* xmj, double rounded_radius_j,
-                               int itype, int jtype, double cut_inner,
-                               Contact* contact_list, int &num_contacts,
-                               double& energy, double* facc);
+  int interaction_edge_to_edge(int ibody, int edge_index_i, double *xmi, double rounded_radius_i,
+                               int jbody, int edge_index_j, double *xmj, double rounded_radius_j,
+                               int itype, int jtype, double cut_inner, Contact *contact_list,
+                               int &num_contacts, double &energy, double *facc);
 
   // compute contact forces if contact points are detected
-  void contact_forces(int ibody, int jbody, double *xi, double *xj,
-    double delx, double dely, double delz, double fx, double fy, double fz,
-    double** x, double** v, double** angmom, double** f, double** torque,
-    double* facc);
+  void contact_forces(int ibody, int jbody, double *xi, double *xj, double delx, double dely,
+                      double delz, double fx, double fy, double fz, double **x, double **v,
+                      double **angmom, double **f, double **torque, double *facc);
 
   // compute force and torque between two bodies given a pair of interacting points
-  void pair_force_and_torque(int ibody, int jbody, double* pi, double* pj,
-                             double r, double contact_dist, int itype, int jtype,
-                             double** x, double** v, double** f, double** torque,
-                             double** angmom, int jflag, double& energy, double* facc);
+  void pair_force_and_torque(int ibody, int jbody, double *pi, double *pj, double r,
+                             double contact_dist, int itype, int jtype, double **x, double **v,
+                             double **f, double **torque, double **angmom, int jflag,
+                             double &energy, double *facc);
 
   // rescale the cohesive forces if a contact area is detected
-  void rescale_cohesive_forces(double** x, double** f, double** torque,
-                               Contact* contact_list, int &num_contacts,
-                               int itype, int jtype, double* facc);
+  void rescale_cohesive_forces(double **x, double **f, double **torque, Contact *contact_list,
+                               int &num_contacts, int itype, int jtype, double *facc);
 
   // compute the separation between two contacts
-  double contact_separation(const Contact& c1, const Contact& c2);
+  double contact_separation(const Contact &c1, const Contact &c2);
 
   // detect the unique contact points (as there may be double counts)
-  void find_unique_contacts(Contact* contact_list, int& num_contacts);
+  void find_unique_contacts(Contact *contact_list, int &num_contacts);
 
   // accumulate torque to a body given a force at a given point
-  void sum_torque(double* xm, double *x, double fx, double fy, double fz, double* torque);
+  void sum_torque(double *xm, double *x, double fx, double fy, double fz, double *torque);
 
   // find the intersection point (if any) between an edge and a face
-  int edge_face_intersect(double* x1, double* x2, double* x3, double* a, double* b,
-                          double* hi1, double* hi2, double& d1, double& d2,
-                          int& inside_a, int& inside_b);
+  int edge_face_intersect(double *x1, double *x2, double *x3, double *a, double *b, double *hi1,
+                          double *hi2, double &d1, double &d2, int &inside_a, int &inside_b);
   // helper functions
-  int opposite_sides(double* n, double* x0, double* a, double* b);
-  void project_pt_plane(const double* q, const double* p,
-                        const double* n, double* q_proj, double &d);
-  void project_pt_plane(const double* q, const double* x1, const double* x2,
-                        const double* x3, double* q_proj, double &d, int& inside);
-  void project_pt_line(const double* q, const double* xi1, const double* xi2,
-                          double* h, double& d, double& t);
-  void inside_polygon(int ibody, int face_index, double* xmi,
-                     const double* q1, const double* q2, int& inside1, int& inside2);
+  int opposite_sides(double *n, double *x0, double *a, double *b);
+  void project_pt_plane(const double *q, const double *p, const double *n, double *q_proj,
+                        double &d);
+  void project_pt_plane(const double *q, const double *x1, const double *x2, const double *x3,
+                        double *q_proj, double &d, int &inside);
+  void project_pt_line(const double *q, const double *xi1, const double *xi2, double *h, double &d,
+                       double &t);
+  void inside_polygon(int ibody, int face_index, double *xmi, const double *q1, const double *q2,
+                      int &inside1, int &inside2);
 
-  void distance_bt_edges(const double* x1, const double* x2,
-                      const double* x3, const double* x4,
-                      double* h1, double* h2, double& t1, double& t2, double& r);
-  void total_velocity(double* p, double *xcm, double* vcm, double *angmom,
-                      double *inertia, double *quat, double* vi);
+  void distance_bt_edges(const double *x1, const double *x2, const double *x3, const double *x4,
+                         double *h1, double *h2, double &t1, double &t2, double &r);
+  void total_velocity(double *p, double *xcm, double *vcm, double *angmom, double *inertia,
+                      double *quat, double *vi);
   void sanity_check();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CLASS2/angle_class2.h

@@ -37,15 +37,15 @@ class AngleClass2 : public Angle {
   double single(int, int, int, int);
 
  protected:
-  double *theta0,*k2,*k3,*k4;
-  double *bb_k,*bb_r1,*bb_r2;
-  double *ba_k1,*ba_k2,*ba_r1,*ba_r2;
-  int *setflag_a,*setflag_bb,*setflag_ba;
+  double *theta0, *k2, *k3, *k4;
+  double *bb_k, *bb_r1, *bb_r2;
+  double *ba_k1, *ba_k2, *ba_r1, *ba_r2;
+  int *setflag_a, *setflag_bb, *setflag_ba;
 
   void allocate();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CLASS2/bond_class2.h

@@ -38,12 +38,12 @@ class BondClass2 : public Bond {
   virtual void *extract(const char *, int &);
 
  protected:
-  double *r0,*k2,*k3,*k4;
+  double *r0, *k2, *k3, *k4;
 
   void allocate();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CLASS2/dihedral_class2.h

@@ -35,22 +35,22 @@ class DihedralClass2 : public Dihedral {
   void write_data(FILE *);
 
  protected:
-  double *k1,*k2,*k3;
-  double *phi1,*phi2,*phi3;
-  double *mbt_f1,*mbt_f2,*mbt_f3,*mbt_r0;
-  double *ebt_f1_1,*ebt_f2_1,*ebt_f3_1,*ebt_r0_1;
-  double *ebt_f1_2,*ebt_f2_2,*ebt_f3_2,*ebt_r0_2;
-  double *at_f1_1,*at_f2_1,*at_f3_1,*at_theta0_1;
-  double *at_f1_2,*at_f2_2,*at_f3_2,*at_theta0_2;
-  double *aat_k,*aat_theta0_1,*aat_theta0_2;
-  double *bb13t_k,*bb13t_r10,*bb13t_r30;
-  int *setflag_d,*setflag_mbt,*setflag_ebt;
-  int *setflag_at,*setflag_aat,*setflag_bb13t;
+  double *k1, *k2, *k3;
+  double *phi1, *phi2, *phi3;
+  double *mbt_f1, *mbt_f2, *mbt_f3, *mbt_r0;
+  double *ebt_f1_1, *ebt_f2_1, *ebt_f3_1, *ebt_r0_1;
+  double *ebt_f1_2, *ebt_f2_2, *ebt_f3_2, *ebt_r0_2;
+  double *at_f1_1, *at_f2_1, *at_f3_1, *at_theta0_1;
+  double *at_f1_2, *at_f2_2, *at_f3_2, *at_theta0_2;
+  double *aat_k, *aat_theta0_1, *aat_theta0_2;
+  double *bb13t_k, *bb13t_r10, *bb13t_r30;
+  int *setflag_d, *setflag_mbt, *setflag_ebt;
+  int *setflag_at, *setflag_aat, *setflag_bb13t;
 
   void allocate();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CLASS2/improper_class2.h

@@ -35,9 +35,9 @@ class ImproperClass2 : public Improper {
   void write_data(FILE *);
 
  protected:
-  double *k0,*chi0;
-  double *aa_k1,*aa_k2,*aa_k3,*aa_theta0_1,*aa_theta0_2,*aa_theta0_3;
-  int *setflag_i,*setflag_aa;
+  double *k0, *chi0;
+  double *aa_k1, *aa_k2, *aa_k3, *aa_theta0_1, *aa_theta0_2, *aa_theta0_3;
+  int *setflag_i, *setflag_aa;
 
   void allocate();
   void angleangle(int, int);
@@ -45,7 +45,7 @@ class ImproperClass2 : public Improper {
   double dot(double *, double *);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CLASS2/pair_lj_class2.h

@@ -47,14 +47,14 @@ class PairLJClass2 : public Pair {
  protected:
   double cut_global;
   double **cut;
-  double **epsilon,**sigma;
-  double **lj1,**lj2,**lj3,**lj4,**offset;
+  double **epsilon, **sigma;
+  double **lj1, **lj2, **lj3, **lj4, **offset;
   double *cut_respa;
 
   virtual void allocate();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CLASS2/pair_lj_class2_coul_cut.h

@@ -43,16 +43,16 @@ class PairLJClass2CoulCut : public Pair {
   void *extract(const char *, int &);
 
  protected:
-  double cut_lj_global,cut_coul_global;
-  double **cut_lj,**cut_ljsq;
-  double **cut_coul,**cut_coulsq;
-  double **epsilon,**sigma;
-  double **lj1,**lj2,**lj3,**lj4,**offset;
+  double cut_lj_global, cut_coul_global;
+  double **cut_lj, **cut_ljsq;
+  double **cut_coul, **cut_coulsq;
+  double **epsilon, **sigma;
+  double **lj1, **lj2, **lj3, **lj4, **offset;
 
   virtual void allocate();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CLASS2/pair_lj_class2_coul_long.h

@@ -48,17 +48,17 @@ class PairLJClass2CoulLong : public Pair {
 
  protected:
   double cut_lj_global;
-  double **cut_lj,**cut_ljsq;
-  double cut_coul,cut_coulsq;
-  double **epsilon,**sigma;
-  double **lj1,**lj2,**lj3,**lj4,**offset;
+  double **cut_lj, **cut_ljsq;
+  double cut_coul, cut_coulsq;
+  double **epsilon, **sigma;
+  double **lj1, **lj2, **lj3, **lj4, **offset;
   double g_ewald;
   double *cut_respa;
 
   virtual void allocate();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COLLOID/fix_wall_colloid.h

@@ -32,10 +32,10 @@ class FixWallColloid : public FixWall {
   void wall_particle(int, int, double);
 
  private:
-  double coeff1[6],coeff2[6],coeff3[6],coeff4[6];
+  double coeff1[6], coeff2[6], coeff3[6], coeff4[6];
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COLLOID/pair_brownian.h

@@ -39,9 +39,9 @@ class PairBrownian : public Pair {
   void read_restart_settings(FILE *);
 
  protected:
-  double cut_inner_global,cut_global;
-  double t_target,mu;
-  int flaglog,flagfld;
+  double cut_inner_global, cut_global;
+  double t_target, mu;
+  int flaglog, flagfld;
   int flagHI, flagVF;
   int flagdeform, flagwall;
   double vol_P;
@@ -49,16 +49,16 @@ class PairBrownian : public Pair {
   class FixWall *wallfix;
 
   int seed;
-  double **cut_inner,**cut;
-  double R0,RT0;
+  double **cut_inner, **cut;
+  double R0, RT0;
 
   class RanMars *random;
 
-  void set_3_orthogonal_vectors(double*,double*,double*);
+  void set_3_orthogonal_vectors(double *, double *, double *);
   void allocate();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COLLOID/pair_brownian_poly.h

@@ -33,7 +33,7 @@ class PairBrownianPoly : public PairBrownian {
   void init_style();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COLLOID/pair_colloid.h

@@ -41,19 +41,19 @@ class PairColloid : public Pair {
   double single(int, int, int, int, double, double, double, double &);
 
  protected:
-  enum {SMALL_SMALL,SMALL_LARGE,LARGE_LARGE};
+  enum { SMALL_SMALL, SMALL_LARGE, LARGE_LARGE };
 
   double cut_global;
   double **cut;
-  double **a12,**d1,**d2,**diameter,**a1,**a2,**offset;
-  double **sigma,**sigma3,**sigma6;
-  double **lj1,**lj2,**lj3,**lj4;
+  double **a12, **d1, **d2, **diameter, **a1, **a2, **offset;
+  double **sigma, **sigma3, **sigma6;
+  double **lj1, **lj2, **lj3, **lj4;
   int **form;
 
   void allocate();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COLLOID/pair_lubricate.h

@@ -44,22 +44,22 @@ class PairLubricate : public Pair {
   void unpack_forward_comm(int, int, double *);
 
  protected:
-  double mu,cut_inner_global,cut_global;
+  double mu, cut_inner_global, cut_global;
   double rad;
-  int flaglog,flagfld,shearing;
+  int flaglog, flagfld, shearing;
   int flagdeform, flagwall;
   double vol_P;
   class FixWall *wallfix;
   int flagVF, flagHI;
 
   double Ef[3][3];
-  double R0,RT0,RS0;
-  double **cut_inner,**cut;
+  double R0, RT0, RS0;
+  double **cut_inner, **cut;
 
   void allocate();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COLLOID/pair_lubricateU.h

@@ -41,7 +41,7 @@ class PairLubricateU : public Pair {
   void unpack_forward_comm(int, int, double *);
 
  protected:
-  double cut_inner_global,cut_global;
+  double cut_inner_global, cut_global;
   double mu;
   double rad;
   int flaglog;
@@ -50,16 +50,16 @@ class PairLubricateU : public Pair {
   double vol_P;
   class FixWall *wallfix;
 
-  double gdot,Ef[3][3];
-  double **cut_inner,**cut;
+  double gdot, Ef[3][3];
+  double **cut_inner, **cut;
   void allocate();
-  double R0,RT0,RS0;
+  double R0, RT0, RS0;
 
   int nmax;
-  double **fl,**Tl,**xl;
+  double **fl, **Tl, **xl;
 
   int cgmax;
-  double *bcg,*xcg,*rcg,*rcg1,*pcg,*RU;
+  double *bcg, *xcg, *rcg, *rcg1, *pcg, *RU;
 
   void compute_RE();
   virtual void compute_RE(double **);
@@ -71,10 +71,10 @@ class PairLubricateU : public Pair {
   void stage_two(double **);
   void copy_vec_uo(int, double *, double **, double **);
   void copy_uo_vec(int, double **, double **, double *);
-  double dot_vec_vec(int , double *, double *);
+  double dot_vec_vec(int, double *, double *);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COLLOID/pair_lubricateU_poly.h

@@ -43,7 +43,7 @@ class PairLubricateUPoly : public PairLubricateU {
   void compute_Fh(double **);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COLLOID/pair_lubricate_poly.h

@@ -32,7 +32,7 @@ class PairLubricatePoly : public PairLubricate {
   void init_style();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COLLOID/pair_yukawa_colloid.h

@@ -34,7 +34,7 @@ class PairYukawaColloid : public PairYukawa {
   double single(int, int, int, int, double, double, double, double &);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COMPRESS/dump_atom_gz.h

@@ -41,7 +41,7 @@ class DumpAtomGZ : public DumpAtom {
   virtual int modify_param(int, char **);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COMPRESS/dump_atom_zstd.h

@@ -47,7 +47,7 @@ class DumpAtomZstd : public DumpAtom {
   virtual int modify_param(int, char **);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COMPRESS/dump_cfg_gz.h

@@ -41,7 +41,7 @@ class DumpCFGGZ : public DumpCFG {
   virtual int modify_param(int, char **);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COMPRESS/dump_cfg_zstd.h

@@ -46,7 +46,7 @@ class DumpCFGZstd : public DumpCFG {
   virtual int modify_param(int, char **);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COMPRESS/dump_custom_gz.h

@@ -41,7 +41,7 @@ class DumpCustomGZ : public DumpCustom {
   virtual int modify_param(int, char **);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COMPRESS/dump_custom_zstd.h

@@ -48,7 +48,7 @@ class DumpCustomZstd : public DumpCustom {
   virtual int modify_param(int, char **);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COMPRESS/dump_local_gz.h

@@ -41,7 +41,7 @@ class DumpLocalGZ : public DumpLocal {
   virtual int modify_param(int, char **);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COMPRESS/dump_local_zstd.h

@@ -47,7 +47,7 @@ class DumpLocalZstd : public DumpLocal {
   virtual int modify_param(int, char **);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COMPRESS/dump_xyz_gz.h

@@ -41,7 +41,7 @@ class DumpXYZGZ : public DumpXYZ {
   virtual int modify_param(int, char **);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COMPRESS/dump_xyz_zstd.h

@@ -47,7 +47,7 @@ class DumpXYZZstd : public DumpXYZ {
   virtual int modify_param(int, char **);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/COMPRESS/gz_file_writer.h

@@ -30,17 +30,17 @@ class GzFileWriter : public FileWriter {
   int compression_level;
 
   gzFile gzFp;    // file pointer for the compressed output stream
-public:
+ public:
   GzFileWriter();
   virtual ~GzFileWriter();
   virtual void open(const std::string &path, bool append = false) override;
   virtual void close() override;
   virtual void flush() override;
-    virtual size_t write(const void * buffer, size_t length) override;
+  virtual size_t write(const void *buffer, size_t length) override;
   virtual bool isopen() const override;
 
   void setCompressionLevel(int level);
 };
-}
+}    // namespace LAMMPS_NS
 
 #endif

src/COMPRESS/zstd_file_writer.h

@@ -31,23 +31,24 @@ class ZstdFileWriter : public FileWriter {
   int compression_level;
   int checksum_flag;
 
-  ZSTD_CCtx * cctx;
-  FILE * fp;
-  char * out_buffer;
+  ZSTD_CCtx *cctx;
+  FILE *fp;
+  char *out_buffer;
   size_t out_buffer_size;
-public:
+
+ public:
   ZstdFileWriter();
   virtual ~ZstdFileWriter();
   virtual void open(const std::string &path, bool append = false) override;
   virtual void close() override;
   virtual void flush() override;
-    virtual size_t write(const void * buffer, size_t length) override;
+  virtual size_t write(const void *buffer, size_t length) override;
   virtual bool isopen() const override;
 
   void setCompressionLevel(int level);
   void setChecksum(bool enabled);
 };
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CORESHELL/compute_temp_cs.h

@@ -44,11 +44,11 @@ class ComputeTempCS : public Compute {
   void unpack_reverse_comm(int, int *, double *);
 
  private:
-  int groupbit_c,groupbit_s;
+  int groupbit_c, groupbit_s;
   int nshells;
   int firstflag;
   int maxatom;
-  int cgroup,sgroup;
+  int cgroup, sgroup;
 
   double tfactor;
   double **vint;
@@ -60,7 +60,7 @@ class ComputeTempCS : public Compute {
   void vcm_pairs();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CORESHELL/pair_born_coul_dsf_cs.h

@@ -30,7 +30,7 @@ class PairBornCoulDSFCS : public PairBornCoulDSF {
   virtual void compute(int, int);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CORESHELL/pair_born_coul_long_cs.h

@@ -30,7 +30,7 @@ class PairBornCoulLongCS : public PairBornCoulLong {
   virtual void compute(int, int);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CORESHELL/pair_born_coul_wolf_cs.h

@@ -30,7 +30,7 @@ class PairBornCoulWolfCS : public PairBornCoulWolf {
   virtual void compute(int, int);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CORESHELL/pair_buck_coul_long_cs.h

@@ -30,7 +30,7 @@ class PairBuckCoulLongCS : public PairBuckCoulLong {
   virtual void compute(int, int);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CORESHELL/pair_coul_long_cs.h

@@ -30,7 +30,7 @@ class PairCoulLongCS : public PairCoulLong {
   virtual void compute(int, int);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CORESHELL/pair_coul_wolf_cs.h

@@ -26,11 +26,11 @@ namespace LAMMPS_NS {
 
 class PairCoulWolfCS : public PairCoulWolf {
  public:
-  PairCoulWolfCS( class LAMMPS *);
-  virtual void compute( int, int);
+  PairCoulWolfCS(class LAMMPS *);
+  virtual void compute(int, int);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif /* LMP_PAIR_COUL_WOLF_CS_H_ */

src/CORESHELL/pair_lj_class2_coul_long_cs.h

@@ -34,7 +34,7 @@ class PairLJClass2CoulLongCS : public PairLJClass2CoulLong {
   void compute_outer(int, int);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/CORESHELL/pair_lj_cut_coul_long_cs.h

@@ -34,7 +34,7 @@ class PairLJCutCoulLongCS : public PairLJCutCoulLong {
   virtual void compute_outer(int, int);
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/DIPOLE/atom_vec_dipole.h

@@ -35,7 +35,7 @@ class AtomVecDipole : public AtomVec {
   double **mu;
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/DIPOLE/pair_lj_cut_dipole_cut.h

@@ -39,16 +39,16 @@ class PairLJCutDipoleCut : public Pair {
   void read_restart_settings(FILE *);
 
  protected:
-  double cut_lj_global,cut_coul_global;
-  double **cut_lj,**cut_ljsq;
-  double **cut_coul,**cut_coulsq;
-  double **epsilon,**sigma;
-  double **lj1,**lj2,**lj3,**lj4,**offset;
+  double cut_lj_global, cut_coul_global;
+  double **cut_lj, **cut_ljsq;
+  double **cut_coul, **cut_coulsq;
+  double **epsilon, **sigma;
+  double **lj1, **lj2, **lj3, **lj4, **offset;
 
   void allocate();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/DIPOLE/pair_lj_cut_dipole_long.h

@@ -43,10 +43,10 @@ class PairLJCutDipoleLong : public Pair {
 
  protected:
   double cut_lj_global;
-  double **cut_lj,**cut_ljsq;
+  double **cut_lj, **cut_ljsq;
   double cut_coulsq;
   double **epsilon;
-  double **lj1,**lj2,**lj3,**lj4,**offset;
+  double **lj1, **lj2, **lj3, **lj4, **offset;
   double g_ewald;
   int ewald_order;
   virtual void *extract(const char *, int &);
@@ -54,7 +54,7 @@ class PairLJCutDipoleLong : public Pair {
   void allocate();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/DIPOLE/pair_lj_long_dipole_long.h

@@ -56,7 +56,7 @@ class PairLJLongDipoleLong : public Pair {
   void allocate();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/GPU/fix_gpu.h

@@ -37,8 +37,8 @@ class FixGPU : public Fix {
   void post_force_respa(int, int, int);
   double memory_usage();
 
-  double binsize(const double subx, const double suby,
-                 const double subz, const int nlocal, const double cut);
+  double binsize(const double subx, const double suby, const double subz, const int nlocal,
+                 const double cut);
 
  private:
   int _gpu_mode;
@@ -47,7 +47,7 @@ class FixGPU : public Fix {
   double _binsize;
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/GPU/fix_nh_gpu.h

@@ -42,7 +42,7 @@ class FixNHGPU : public FixNH {
   virtual void nh_v_temp();
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 

src/GPU/fix_npt_gpu.h

@@ -34,7 +34,7 @@ class FixNPTGPU : public FixNHGPU {
   ~FixNPTGPU() {}
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/GPU/fix_nve_asphere_gpu.h

@@ -46,7 +46,7 @@ class FixNVEAsphereGPU : public FixNVE {
   class AtomVecEllipsoid *avec;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/fix_nve_gpu.h

@@ -44,7 +44,7 @@ class FixNVEGPU : public FixNVE {
   int _nlocal_max, _respa_on;
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/GPU/fix_nvt_gpu.h

@@ -34,7 +34,7 @@ class FixNVTGPU : public FixNHGPU {
   ~FixNVTGPU() {}
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/GPU/gpu_extra.h

@@ -18,90 +18,79 @@
 #ifndef LMP_GPU_EXTRA_H
 #define LMP_GPU_EXTRA_H
 
-#include "modify.h"
 #include "error.h"
+#include "modify.h"
 
 // ---------------------- OPENMP PREPROCESSOR STUFF ------------------
 #if defined(_OPENMP)
-  #if !defined(LAL_USE_OMP)
-  #define LAL_USE_OMP 1
-  #endif
+#if !defined(LAL_USE_OMP)
+#define LAL_USE_OMP 1
+#endif
 
-  #if !defined(LAL_USE_OMP_SIMD)
-    #if (_OPENMP >= 201307)
-    #define LAL_USE_OMP_SIMD 1
-    #else
-    #define LAL_USE_OMP_SIMD 0
-    #endif
-  #endif
+#if !defined(LAL_USE_OMP_SIMD)
+#if (_OPENMP >= 201307)
+#define LAL_USE_OMP_SIMD 1
 #else
-  #if !defined(LAL_USE_OMP)
-  #define LAL_USE_OMP 0
-  #endif
+#define LAL_USE_OMP_SIMD 0
+#endif
+#endif
+#else
+#if !defined(LAL_USE_OMP)
+#define LAL_USE_OMP 0
+#endif
 
-  #if !defined(LAL_USE_OMP_SIMD)
-  #define LAL_USE_OMP_SIMD 0
-  #endif
+#if !defined(LAL_USE_OMP_SIMD)
+#define LAL_USE_OMP_SIMD 0
+#endif
 #endif
 
 namespace GPU_EXTRA {
 
-  inline void check_flag(int error_flag, LAMMPS_NS::Error *error,
-                         MPI_Comm &world) {
+inline void check_flag(int error_flag, LAMMPS_NS::Error *error, MPI_Comm &world)
+{
   int all_success;
   MPI_Allreduce(&error_flag, &all_success, 1, MPI_INT, MPI_MIN, world);
   if (all_success != 0) {
     if (all_success == -1)
-        error->all(FLERR,
-                   "The package gpu command is required for gpu styles");
+      error->all(FLERR, "The package gpu command is required for gpu styles");
     else if (all_success == -2)
-        error->all(FLERR,
-                   "Could not find/initialize a specified accelerator device");
+      error->all(FLERR, "Could not find/initialize a specified accelerator device");
     else if (all_success == -3)
-        error->all(FLERR,"Insufficient memory on accelerator");
+      error->all(FLERR, "Insufficient memory on accelerator");
     else if (all_success == -4)
-        error->all(FLERR,"GPU library not compiled for this accelerator");
+      error->all(FLERR, "GPU library not compiled for this accelerator");
     else if (all_success == -5)
-        error->all(FLERR,
-                   "Double precision is not supported on this accelerator");
+      error->all(FLERR, "Double precision is not supported on this accelerator");
     else if (all_success == -6)
-        error->all(FLERR,"Unable to initialize accelerator for use");
+      error->all(FLERR, "Unable to initialize accelerator for use");
     else if (all_success == -7)
-        error->all(FLERR,
-                   "Accelerator sharing is not currently supported on system");
+      error->all(FLERR, "Accelerator sharing is not currently supported on system");
     else if (all_success == -8)
-        error->all(FLERR,
-                   "GPU particle split must be set to 1 for this pair style.");
+      error->all(FLERR, "GPU particle split must be set to 1 for this pair style.");
     else if (all_success == -9)
-        error->all(FLERR,
-                   "CPU neighbor lists must be used for ellipsoid/sphere mix.");
+      error->all(FLERR, "CPU neighbor lists must be used for ellipsoid/sphere mix.");
     else if (all_success == -10)
-        error->all(FLERR,
-                   "Invalid threads_per_atom specified.");
+      error->all(FLERR, "Invalid threads_per_atom specified.");
     else if (all_success == -11)
-        error->all(FLERR,
-                   "Invalid custom OpenCL parameter string.");
+      error->all(FLERR, "Invalid custom OpenCL parameter string.");
     else if (all_success == -12)
-        error->all(FLERR,
-                   "Invalid OpenCL platform ID.");
+      error->all(FLERR, "Invalid OpenCL platform ID.");
     else if (all_success == -13)
-        error->all(FLERR,
-                   "Invalid device configuration.");
+      error->all(FLERR, "Invalid device configuration.");
     else if (all_success == -15)
-        error->all(FLERR,
-                   "P3M built for FP64 and GPU device is FP32 only.");
+      error->all(FLERR, "P3M built for FP64 and GPU device is FP32 only.");
     else
-        error->all(FLERR,"Unknown error in GPU library");
-    }
-  }
-
-  inline void gpu_ready(LAMMPS_NS::Modify *modify, LAMMPS_NS::Error *error) {
-    int ifix = modify->find_fix("package_gpu");
-    if (ifix < 0)
-      error->all(FLERR,"The package gpu command is required for gpu styles");
+      error->all(FLERR, "Unknown error in GPU library");
   }
 }
 
+inline void gpu_ready(LAMMPS_NS::Modify *modify, LAMMPS_NS::Error *error)
+{
+  int ifix = modify->find_fix("package_gpu");
+  if (ifix < 0) error->all(FLERR, "The package gpu command is required for gpu styles");
+}
+}    // namespace GPU_EXTRA
+
 #endif
 
 /* ERROR/WARNING messages:

src/GPU/pair_beck_gpu.h

@@ -40,7 +40,7 @@ class PairBeckGPU : public PairBeck {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_born_coul_long_cs_gpu.h

@@ -40,7 +40,7 @@ class PairBornCoulLongCSGPU : public PairBornCoulLongCS {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_born_coul_long_gpu.h

@@ -40,7 +40,7 @@ class PairBornCoulLongGPU : public PairBornCoulLong {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_born_coul_wolf_cs_gpu.h

@@ -40,7 +40,7 @@ class PairBornCoulWolfCSGPU : public PairBornCoulWolfCS {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_born_coul_wolf_gpu.h

@@ -40,7 +40,7 @@ class PairBornCoulWolfGPU : public PairBornCoulWolf {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_born_gpu.h

@@ -41,7 +41,7 @@ class PairBornGPU : public PairBorn {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_buck_coul_cut_gpu.h

@@ -40,7 +40,7 @@ class PairBuckCoulCutGPU : public PairBuckCoulCut {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_buck_coul_long_gpu.h

@@ -40,7 +40,7 @@ class PairBuckCoulLongGPU : public PairBuckCoulLong {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_buck_gpu.h

@@ -41,7 +41,7 @@ class PairBuckGPU : public PairBuck {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_colloid_gpu.h

@@ -40,7 +40,7 @@ class PairColloidGPU : public PairColloid {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_coul_cut_gpu.h

@@ -41,7 +41,7 @@ class PairCoulCutGPU : public PairCoulCut {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_coul_debye_gpu.h

@@ -41,7 +41,7 @@ class PairCoulDebyeGPU : public PairCoulDebye {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_coul_dsf_gpu.h

@@ -40,7 +40,7 @@ class PairCoulDSFGPU : public PairCoulDSF {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_coul_long_cs_gpu.h

@@ -41,7 +41,7 @@ class PairCoulLongCSGPU : public PairCoulLongCS {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_coul_long_gpu.h

@@ -41,7 +41,7 @@ class PairCoulLongGPU : public PairCoulLong {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_dpd_gpu.h

@@ -40,7 +40,7 @@ class PairDPDGPU : public PairDPD {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_dpd_tstat_gpu.h

@@ -40,7 +40,7 @@ class PairDPDTstatGPU : public PairDPDTstat {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_eam_alloy_gpu.h

@@ -25,7 +25,7 @@ PairStyle(eam/alloy/gpu,PairEAMAlloyGPU);
 namespace LAMMPS_NS {
 
 class PairEAMAlloyGPU : public PairEAM {
-public:
+ public:
   PairEAMAlloyGPU(class LAMMPS *);
   virtual ~PairEAMAlloyGPU();
   void coeff(int, char **);
@@ -50,7 +50,7 @@ public:
   bool fp_single;
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/GPU/pair_eam_fs_gpu.h

@@ -25,7 +25,7 @@ PairStyle(eam/fs/gpu,PairEAMFSGPU);
 namespace LAMMPS_NS {
 
 class PairEAMFSGPU : public PairEAM {
-public:
+ public:
   PairEAMFSGPU(class LAMMPS *);
   virtual ~PairEAMFSGPU();
   void coeff(int, char **);
@@ -50,7 +50,7 @@ public:
   bool fp_single;
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/GPU/pair_eam_gpu.h

@@ -26,7 +26,6 @@ namespace LAMMPS_NS {
 
 class PairEAMGPU : public PairEAM {
  public:
-
   PairEAMGPU(class LAMMPS *);
   virtual ~PairEAMGPU();
   void compute(int, int);
@@ -47,7 +46,7 @@ class PairEAMGPU : public PairEAM {
   bool fp_single;
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif

src/GPU/pair_gauss_gpu.h

@@ -41,7 +41,7 @@ class PairGaussGPU : public PairGauss {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_gayberne_gpu.h

@@ -42,7 +42,7 @@ class PairGayBerneGPU : public PairGayBerne {
   double **quat;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif
 

src/GPU/pair_lj96_cut_gpu.h

@@ -40,7 +40,7 @@ class PairLJ96CutGPU : public PairLJ96Cut {
   double cpu_time;
 };
 
-}
+}    // namespace LAMMPS_NS
 #endif
 #endif