apply clang-format

src/angle.h

@@ -52,12 +52,12 @@ class Angle : protected Pointers {
   virtual void compute(int, int) = 0;
   virtual void settings(int, char **);
   virtual void coeff(int, char **) = 0;
-  virtual void init_style(){};
+  virtual void init_style() {};
   virtual double equilibrium_angle(int) = 0;
   virtual void write_restart(FILE *) = 0;
   virtual void read_restart(FILE *) = 0;
-  virtual void write_restart_settings(FILE *){};
-  virtual void read_restart_settings(FILE *){};
+  virtual void write_restart_settings(FILE *) {};
+  virtual void read_restart_settings(FILE *) {};
   virtual void write_data(FILE *) {}
   virtual double single(int, int, int, int) = 0;
   virtual void born_matrix(int /*atype*/, int /*at1*/, int /*at2*/, int /*at3*/, double &du,

src/angle_write.h

@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
 
 class AngleWrite : public Command {
  public:
-  AngleWrite(class LAMMPS *lmp) : Command(lmp){};
+  AngleWrite(class LAMMPS *lmp) : Command(lmp) {};
   void command(int, char **) override;
 };
 }    // namespace LAMMPS_NS

src/bond.h

@@ -61,8 +61,8 @@ class Bond : protected Pointers {
   virtual double equilibrium_distance(int) = 0;
   virtual void write_restart(FILE *) = 0;
   virtual void read_restart(FILE *) = 0;
-  virtual void write_restart_settings(FILE *){};
-  virtual void read_restart_settings(FILE *){};
+  virtual void write_restart_settings(FILE *) {};
+  virtual void read_restart_settings(FILE *) {};
   virtual void write_data(FILE *) {}
   virtual double single(int, double, int, int, double &) = 0;
   virtual double memory_usage();

src/comm_brick.h

@@ -44,7 +44,7 @@ class CommBrick : public Comm {
   void forward_comm(class Dump *) override;                 // forward comm from a Dump
   void reverse_comm(class Dump *) override;                 // reverse comm from a Dump
 
-  void forward_comm_array(int, double **) override;            // forward comm of array
+  void forward_comm_array(int, double **) override;    // forward comm of array
   void *extract(const char *, int &) override;
   double memory_usage() override;
 

src/comm_tiled.h

@@ -44,7 +44,7 @@ class CommTiled : public Comm {
   void forward_comm(class Dump *) override;                 // forward comm from a Dump
   void reverse_comm(class Dump *) override;                 // reverse comm from a Dump
 
-  void forward_comm_array(int, double **) override;            // forward comm of array
+  void forward_comm_array(int, double **) override;    // forward comm of array
 
   void coord2proc_setup() override;
   int coord2proc(double *, int &, int &, int &) override;
@@ -146,12 +146,12 @@ class CommTiled : public Comm {
   int point_drop_tiled_recurse(double *, int, int);
   int closer_subbox_edge(int, double *);
 
-  virtual void grow_send(int, int);               // reallocate send buffer
-  virtual void grow_recv(int, int flag = 0);      // free/allocate recv buffer
-  virtual void grow_list(int, int, int);          // reallocate sendlist for one swap/proc
-  void allocate_swap(int);                // allocate swap arrays
-  virtual void grow_swap_send(int, int, int);     // grow swap arrays for send and recv
-  void grow_swap_send_multi(int, int);    // grow multi swap arrays for send and recv
+  virtual void grow_send(int, int);              // reallocate send buffer
+  virtual void grow_recv(int, int flag = 0);     // free/allocate recv buffer
+  virtual void grow_list(int, int, int);         // reallocate sendlist for one swap/proc
+  void allocate_swap(int);                       // allocate swap arrays
+  virtual void grow_swap_send(int, int, int);    // grow swap arrays for send and recv
+  void grow_swap_send_multi(int, int);           // grow multi swap arrays for send and recv
   void grow_swap_recv(int, int);
   void deallocate_swap(int);    // deallocate swap arrays
 };

src/command.h

@@ -20,7 +20,7 @@ namespace LAMMPS_NS {
 
 class Command : protected Pointers {
  public:
-  Command(class LAMMPS *lmp) : Pointers(lmp){};
+  Command(class LAMMPS *lmp) : Pointers(lmp) {};
   virtual void command(int, char **) = 0;
 };
 

src/compute.h

@@ -132,7 +132,7 @@ class Compute : protected Pointers {
   virtual int pack_reverse_comm(int, int, double *) { return 0; }
   virtual void unpack_reverse_comm(int, int *, double *) {}
 
-  virtual void reset_grid(){};
+  virtual void reset_grid() {};
 
   virtual int get_grid_by_name(const std::string &, int &) { return -1; };
   virtual void *get_grid_by_index(int) { return nullptr; };

src/compute_chunk.h

@@ -43,7 +43,7 @@ class ComputeChunk : public Compute {
   int firstflag, massneed;
   ComputeChunkAtom *cchunk;
 
-  virtual void allocate(){};
+  virtual void allocate() {};
 };
 }    // namespace LAMMPS_NS
 #endif

src/compute_dipole.h

@@ -28,7 +28,7 @@ class ComputeDipole : public Compute {
  public:
   ComputeDipole(class LAMMPS *, int, char **);
   ~ComputeDipole() override;
-  void init() override{};
+  void init() override {};
   void compute_vector() override;
   double compute_scalar() override;
 

src/compute_global_atom.h

@@ -33,7 +33,7 @@ class ComputeGlobalAtom : public Compute {
   double memory_usage() override;
 
  protected:
-    struct value_t {
+  struct value_t {
     int which;
     int argindex;
     std::string id;

src/deprecated.h

@@ -37,7 +37,7 @@ namespace LAMMPS_NS {
 
 class Deprecated : public Command {
  public:
-  Deprecated(class LAMMPS *lmp) : Command(lmp){};
+  Deprecated(class LAMMPS *lmp) : Command(lmp) {};
   void command(int, char **) override;
 };
 

src/dihedral.h

@@ -52,8 +52,8 @@ class Dihedral : protected Pointers {
   virtual void coeff(int, char **) = 0;
   virtual void write_restart(FILE *) = 0;
   virtual void read_restart(FILE *) = 0;
-  virtual void write_restart_settings(FILE *){};
-  virtual void read_restart_settings(FILE *){};
+  virtual void write_restart_settings(FILE *) {};
+  virtual void read_restart_settings(FILE *) {};
   virtual void write_data(FILE *) {}
   virtual double memory_usage();
   virtual void born_matrix(int /*dtype*/, int /*at1*/, int /*at2*/, int /*at3*/, int /*at4*/,

src/dihedral_write.h

@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
 
 class DihedralWrite : public Command {
  public:
-  DihedralWrite(class LAMMPS *lmp) : Command(lmp){};
+  DihedralWrite(class LAMMPS *lmp) : Command(lmp) {};
   void command(int, char **) override;
 };
 }    // namespace LAMMPS_NS

src/domain.h

@@ -39,8 +39,8 @@ class Domain : protected Pointers {
                          // 2 = shrink-wrap non-periodic
                          // 3 = shrink-wrap non-per w/ min
 
-  int triclinic;          // 0 = orthog box, 1 = triclinic (restricted or general)
-  int triclinic_general;  // 1 if general <-> restricted tri mapping is stored, 0 if not
+  int triclinic;            // 0 = orthog box, 1 = triclinic (restricted or general)
+  int triclinic_general;    // 1 if general <-> restricted tri mapping is stored, 0 if not
 
   // orthogonal box
 
@@ -91,9 +91,9 @@ class Domain : protected Pointers {
   // general triclinic box
   // boxlo = lower left corner
 
-  double avec[3], bvec[3], cvec[3];  // ABC edge vectors of general triclinic box
-  double rotate_g2r[3][3];           // rotation matrix from general --> restricted tri
-  double rotate_r2g[3][3];           // rotation matrix from restricted --> general tri
+  double avec[3], bvec[3], cvec[3];    // ABC edge vectors of general triclinic box
+  double rotate_g2r[3][3];             // rotation matrix from general --> restricted tri
+  double rotate_r2g[3][3];             // rotation matrix from restricted --> general tri
 
   // box flags
 
@@ -145,9 +145,8 @@ class Domain : protected Pointers {
   int ownatom(int, double *, imageint *, int);
 
   void define_general_triclinic(double *, double *, double *, double *);
-  void general_to_restricted_rotation(double *, double *, double *,
-                                      double [3][3],
-                                      double *, double *, double *);
+  void general_to_restricted_rotation(double *, double *, double *, double[3][3], double *,
+                                      double *, double *);
   void general_to_restricted_coords(double *);
   void restricted_to_general_coords(double *);
   void restricted_to_general_coords(double *, double *);

src/dump_atom.h

@@ -33,9 +33,9 @@ class DumpAtom : public Dump {
   const int ENDIAN = 0x0001;
 
  protected:
-  int scale_flag;        // 1 if atom coords are scaled, 0 if no
-  int image_flag;        // 1 if append box count to atom coords, 0 if no
-  int triclinic_general; // 1 if output box & coords for general triclinic, 0 if no
+  int scale_flag;           // 1 if atom coords are scaled, 0 if no
+  int image_flag;           // 1 if append box count to atom coords, 0 if no
+  int triclinic_general;    // 1 if output box & coords for general triclinic, 0 if no
 
   std::string columns;    // column labels
 

src/dump_custom.h

@@ -34,9 +34,9 @@ class DumpCustom : public Dump {
   const int ENDIAN = 0x0001;
 
  protected:
-  int nevery;        // dump frequency for output
-  char *idregion;    // region ID, nullptr if no region
-  int triclinic_general;  // 1 if output box & per-atom info for general triclinic
+  int nevery;               // dump frequency for output
+  char *idregion;           // region ID, nullptr if no region
+  int triclinic_general;    // 1 if output box & per-atom info for general triclinic
 
   int nthresh;                        // # of defined thresholds
   int nthreshlast;                    // # of defined thresholds with value = LAST

src/dump_image.h

@@ -79,17 +79,17 @@ class DumpImage : public DumpCustom {
   double *diamtype, *diamelement, *bdiamtype;          // per-type diameters
   double **colortype, **colorelement, **bcolortype;    // per-type colors
 
-  int gridflag;         // 0/1 for draw grid cells
+  int gridflag;    // 0/1 for draw grid cells
   class Grid2d *grid2d;
   class Grid3d *grid3d;
-  char *id_grid_compute,*id_grid_fix;
+  char *id_grid_compute, *id_grid_fix;
   class Compute *grid_compute;
   class Fix *grid_fix;
-  int grid_igrid,grid_idata,grid_index;
-  int nxgrid,nygrid,nzgrid;
-  int nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in;
+  int grid_igrid, grid_idata, grid_index;
+  int nxgrid, nygrid, nzgrid;
+  int nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in;
   double *gbuf;
-  int ngrid,maxgrid;
+  int ngrid, maxgrid;
   double gcorners[8][3];
 
   class AtomVecLine *avec_line;    // ptrs to atom style (sub)classes
@@ -98,10 +98,10 @@ class DumpImage : public DumpCustom {
 
   class Fix *fixptr;    // ptr to Fix that provides image data
 
-  class Image *image;   // class that renders each image
+  class Image *image;    // class that renders each image
 
-  int *chooseghost;     // extended choose array for comm
-  double **bufcopy;     // buffer for communicating bond/atom info
+  int *chooseghost;    // extended choose array for comm
+  double **bufcopy;    // buffer for communicating bond/atom info
   int maxbufcopy;
 
   void init_style() override;

src/fix_indent.h

@@ -61,10 +61,10 @@ class FixIndent : public Fix {
   // methods for conical indenter
 
   bool PointInsideCone(int, double *, double, double, double, double, double *);
-  void DistanceExteriorPoint(int, double *, double, double, double, double,
-                             double &, double &, double &);
-  void DistanceInteriorPoint(int, double *, double, double, double, double,
-                             double &, double &, double &);
+  void DistanceExteriorPoint(int, double *, double, double, double, double, double &, double &,
+                             double &);
+  void DistanceInteriorPoint(int, double *, double, double, double, double, double &, double &,
+                             double &);
   void point_on_line_segment(double *, double *, double *, double *);
   double closest(double *, double *, double *, double);
 };

src/imbalance.h

@@ -26,7 +26,7 @@ class Imbalance : protected Pointers {
   // parse options. return number of arguments consumed (required)
   virtual int options(int, char **) = 0;
   // reinitialize internal data (needed for fix balance) (optional)
-  virtual void init(int){};
+  virtual void init(int) {};
   // compute and apply weight factors to local atom array (required)
   virtual void compute(double *) = 0;
   // print information about the state of this imbalance compute (required)

src/improper.h

@@ -37,10 +37,10 @@ class Improper : protected Pointers {
                              // CENTROID_AVAIL = different and implemented
                              // CENTROID_NOTAVAIL = different, not yet implemented
 
-  int symmatoms[4];          // symmetry atom(s) of improper style
-                             // value of 0: interchangable atoms
-                             // value of 1: central atom
-                             // values >1: additional atoms of symmetry
+  int symmatoms[4];    // symmetry atom(s) of improper style
+                       // value of 0: interchangable atoms
+                       // value of 1: central atom
+                       // values >1: additional atoms of symmetry
 
   // KOKKOS host/device flag and data masks
 
@@ -57,8 +57,8 @@ class Improper : protected Pointers {
   virtual void coeff(int, char **) = 0;
   virtual void write_restart(FILE *) = 0;
   virtual void read_restart(FILE *) = 0;
-  virtual void write_restart_settings(FILE *){};
-  virtual void read_restart_settings(FILE *){};
+  virtual void write_restart_settings(FILE *) {};
+  virtual void read_restart_settings(FILE *) {};
   virtual void write_data(FILE *) {}
   virtual double memory_usage();
   virtual void born_matrix(int /*dtype*/, int /*at1*/, int /*at2*/, int /*at3*/, int /*at4*/,

src/kspace.h

@@ -112,17 +112,17 @@ class KSpace : protected Pointers {
 
   // general child-class methods
 
-  virtual void settings(int, char **){};
+  virtual void settings(int, char **) {};
   virtual void init() = 0;
   virtual void setup() = 0;
-  virtual void reset_grid(){};
+  virtual void reset_grid() {};
   virtual void compute(int, int) = 0;
-  virtual void compute_group_group(int, int, int){};
+  virtual void compute_group_group(int, int, int) {};
 
-  virtual void pack_forward_grid(int, void *, int, int *){};
-  virtual void unpack_forward_grid(int, void *, int, int *){};
-  virtual void pack_reverse_grid(int, void *, int, int *){};
-  virtual void unpack_reverse_grid(int, void *, int, int *){};
+  virtual void pack_forward_grid(int, void *, int, int *) {};
+  virtual void unpack_forward_grid(int, void *, int, int *) {};
+  virtual void pack_reverse_grid(int, void *, int, int *) {};
+  virtual void unpack_reverse_grid(int, void *, int, int *) {};
 
   virtual int timing(int, double &, double &) { return 0; }
   virtual int timing_1d(int, double &) { return 0; }

src/lammps.h

@@ -66,7 +66,7 @@ class LAMMPS {
   int suffix_enable;         // 1 if suffixes are enabled, 0 if disabled
   int pair_only_flag;        // 1 if only force field pair styles are accelerated, 0 if all
   const char *non_pair_suffix() const;
-  char *exename;             // pointer to argv[0]
+  char *exename;    // pointer to argv[0]
 
   char ***packargs;    // arguments for cmdline package commands
   int num_package;     // number of cmdline package commands
@@ -103,9 +103,9 @@ class LAMMPS {
   void init_pkg_lists();
   void help();
   /// Default constructor. Declared private to prohibit its use
-  LAMMPS(){};
+  LAMMPS() {};
   /// Copy constructor. Declared private to prohibit its use
-  LAMMPS(const LAMMPS &){};
+  LAMMPS(const LAMMPS &) {};
 };
 
 }    // namespace LAMMPS_NS

src/region_plane.h

@@ -44,7 +44,6 @@ class RegPlane : public Region {
   char *xstr, *ystr, *zstr;
 
   void variable_check();
-
 };
 
 }    // namespace LAMMPS_NS

src/set.h

@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
 
 class Set : public Command {
  public:
-  Set(class LAMMPS *lmp) : Command(lmp){};
+  Set(class LAMMPS *lmp) : Command(lmp) {};
   void command(int, char **) override;
 
  private:

src/utils.h

@@ -409,7 +409,8 @@ This functions adds the following case to :cpp:func:`utils::bounds() <LAMMPS_NS:
    *
    *  This function has the same arguments as expand_type() but returns an integer value */
 
-  int expand_type_int(const char *file, int line, const std::string &str, int mode, LAMMPS *lmp, bool verify = false);
+  int expand_type_int(const char *file, int line, const std::string &str, int mode, LAMMPS *lmp,
+                      bool verify = false);
 
   /*! Check grid reference for valid Compute or Fix which produces per-grid data
    *

src/variable.h

@@ -144,8 +144,8 @@ class Variable : protected Pointers {
   int math_function(char *, char *, Tree **, Tree **, int &, double *, int &, int);
   int group_function(char *, char *, Tree **, Tree **, int &, double *, int &, int);
   Region *region_function(char *, int);
-  int special_function(const std::string &, char *, Tree **, Tree **, int &, double *, int &,
-                       int, char *, int &, char *&);
+  int special_function(const std::string &, char *, Tree **, Tree **, int &, double *, int &, int,
+                       char *, int &, char *&);
   int feature_function(char *, char *, Tree **, Tree **, int &, double *, int &, int);
   void peratom2global(int, char *, double *, int, tagint, Tree **, Tree **, int &, double *, int &);
   void custom2global(int *, double *, int, tagint, Tree **, Tree **, int &, double *, int &);

src/write_coeff.h

@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
 
 class WriteCoeff : public Command {
  public:
-  WriteCoeff(class LAMMPS *lmp) : Command(lmp){};
+  WriteCoeff(class LAMMPS *lmp) : Command(lmp) {};
   void command(int, char **) override;
 };
 

src/write_dump.h

@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
 
 class WriteDump : public Command {
  public:
-  WriteDump(class LAMMPS *lmp) : Command(lmp){};
+  WriteDump(class LAMMPS *lmp) : Command(lmp) {};
   void command(int, char **) override;
 };