diff --git a/src/USER-OMP/reaxc_bond_orders_omp.h b/src/USER-OMP/reaxc_bond_orders_omp.h index 5fe0c4611c..cea31539a9 100644 --- a/src/USER-OMP/reaxc_bond_orders_omp.h +++ b/src/USER-OMP/reaxc_bond_orders_omp.h @@ -1,12 +1,12 @@ /*---------------------------------------------------------------------- PuReMD - Purdue ReaxFF Molecular Dynamics Program Website: https://www.cs.purdue.edu/puremd - + Copyright (2010) Purdue University - - Contributing authors: + + Contributing authors: H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: + Corresponding author: Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu Please cite the related publication: @@ -33,8 +33,8 @@ #include "reaxc_bond_orders.h" void Add_dBond_to_ForcesOMP( reax_system*, int, int, storage*, reax_list** ); -void Add_dBond_to_Forces_NPTOMP( reax_system *system, int, int, simulation_data*, - storage*, reax_list** ); +void Add_dBond_to_Forces_NPTOMP( reax_system *system, int, int, + simulation_data*, storage*, reax_list** ); int BOp_OMP(storage*, reax_list*, double, int, int, far_neighbor_data*, single_body_parameters*, single_body_parameters*, two_body_parameters*, diff --git a/src/USER-OMP/reaxc_nonbonded_omp.h b/src/USER-OMP/reaxc_nonbonded_omp.h index 66ecefa05b..f64e1abe48 100644 --- a/src/USER-OMP/reaxc_nonbonded_omp.h +++ b/src/USER-OMP/reaxc_nonbonded_omp.h @@ -1,12 +1,12 @@ /*---------------------------------------------------------------------- PuReMD - Purdue ReaxFF Molecular Dynamics Program Website: https://www.cs.purdue.edu/puremd - + Copyright (2010) Purdue University - - Contributing authors: + + Contributing authors: H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: + Corresponding author: Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu Please cite the related publication: diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.h b/src/USER-OMP/reaxc_torsion_angles_omp.h index 742de36eb7..39f8691877 100644 --- a/src/USER-OMP/reaxc_torsion_angles_omp.h +++ b/src/USER-OMP/reaxc_torsion_angles_omp.h @@ -1,12 +1,12 @@ /*---------------------------------------------------------------------- PuReMD - Purdue ReaxFF Molecular Dynamics Program Website: https://www.cs.purdue.edu/puremd - + Copyright (2010) Purdue University - - Contributing authors: + + Contributing authors: H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama - Corresponding author: + Corresponding author: Hasan Metin Aktulga, Michigan State University, hma@cse.msu.edu Please cite the related publication: diff --git a/src/atom.h b/src/atom.h index 62c2d64ca7..72c7aedc0d 100644 --- a/src/atom.h +++ b/src/atom.h @@ -98,7 +98,7 @@ class Atom : protected Pointers { double **cc, **cc_flux; // cc = chemical concentration double *edpd_temp,*edpd_flux; // temperature and heat flux - double *edpd_cv; // heat capacity + double *edpd_cv; // heat capacity int cc_species; // molecular info @@ -238,7 +238,7 @@ class Atom : protected Pointers { void data_bonus(int, char *, class AtomVec *, tagint); void data_bodies(int, char *, class AtomVecBody *, tagint); void data_fix_compute_variable(int, int); - + virtual void allocate_type_arrays(); void set_mass(const char *, int, const char *, int); void set_mass(const char *, int, int, double); diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h index 9ab935f91d..3244b0f64d 100644 --- a/src/atom_vec_body.h +++ b/src/atom_vec_body.h @@ -88,10 +88,10 @@ class AtomVecBody : public AtomVec { void data_body(int, int, int, int *, double *); // methods used by other classes to query/set body info - + double radius_body(int, int, int *, double *); void set_quat(int, double *); - + private: tagint *tag; int *type,*mask; diff --git a/src/compute_centro_atom.h b/src/compute_centro_atom.h index ef3128ee68..393d001f22 100644 --- a/src/compute_centro_atom.h +++ b/src/compute_centro_atom.h @@ -40,7 +40,7 @@ class ComputeCentroAtom : public Compute { class NeighList *list; double *centro; int axes_flag; - + void select(int, int, double *); void select2(int, int, double *, int *); }; diff --git a/src/domain.h b/src/domain.h index 0f47a3c2ca..5a651009b7 100644 --- a/src/domain.h +++ b/src/domain.h @@ -124,7 +124,7 @@ class Domain : protected Pointers { void unmap(const double *, imageint, double *); void image_flip(int, int, int); int ownatom(int, double *, imageint *, int); - + void set_lattice(int, char **); void add_region(int, char **); void delete_region(int, char **); diff --git a/src/fix_nh.h b/src/fix_nh.h index c65014724a..8176c3ebb7 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -221,9 +221,9 @@ Self-explanatory. E: Using update dipole flag requires atom attribute mu Self-explanatory. - + E: The dlm flag must be used with update dipole - + Self-explanatory. E: Fix nvt/npt/nph damping parameters must be > 0.0 diff --git a/src/fix_nve_sphere.h b/src/fix_nve_sphere.h index 1e739f4aae..9a95f4db5f 100644 --- a/src/fix_nve_sphere.h +++ b/src/fix_nve_sphere.h @@ -62,9 +62,9 @@ An atom style with this attribute is needed. E: Fix nve/sphere requires extended particles This fix can only be used for particles of a finite size. - + E: Fix nve/sphere dlm must be used with update dipole - + The DLM algorithm can only be used in conjunction with update dipole. diff --git a/src/library.h b/src/library.h index e4f9accaa6..1cb3f9cbf3 100644 --- a/src/library.h +++ b/src/library.h @@ -36,7 +36,7 @@ void lammps_free(void *); int lammps_extract_setting(void *, char *); void *lammps_extract_global(void *, char *); -void lammps_extract_box(void *, double *, double *, +void lammps_extract_box(void *, double *, double *, double *, double *, double *, int *, int *); void *lammps_extract_atom(void *, char *); void *lammps_extract_compute(void *, char *, int, int); @@ -56,10 +56,10 @@ void lammps_scatter_atoms(void *, char *, int, int, void *); // caller must match to how LAMMPS library is built #ifdef LAMMPS_BIGBIG -void lammps_create_atoms(void *, int, int64_t *, int *, +void lammps_create_atoms(void *, int, int64_t *, int *, double *, double *, int64_t *, int); #else -void lammps_create_atoms(void *, int, int *, int *, +void lammps_create_atoms(void *, int, int *, int *, double *, double *, int *, int); #endif diff --git a/src/math_extra.h b/src/math_extra.h index a67acce3c6..eec9855b80 100644 --- a/src/math_extra.h +++ b/src/math_extra.h @@ -35,7 +35,7 @@ namespace MathExtra { inline void negate3(double *v); inline void scale3(double s, double *v); inline void add3(const double *v1, const double *v2, double *ans); - inline void scaleadd3(double s, const double *v1, const double *v2, + inline void scaleadd3(double s, const double *v1, const double *v2, double *ans); inline void sub3(const double *v1, const double *v2, double *ans); inline double len3(const double *v); @@ -81,7 +81,7 @@ namespace MathExtra { void rotate(double matrix[3][3], int i, int j, int k, int l, double s, double tau); void richardson(double *q, double *m, double *w, double *moments, double dtq); - void no_squish_rotate(int k, double *p, double *q, double *inertia, + void no_squish_rotate(int k, double *p, double *q, double *inertia, double dt); // shape matrix operations @@ -116,7 +116,7 @@ namespace MathExtra { inline void rotation_generator_x(const double m[3][3], double ans[3][3]); inline void rotation_generator_y(const double m[3][3], double ans[3][3]); inline void rotation_generator_z(const double m[3][3], double ans[3][3]); - + void BuildRxMatrix(double R[3][3], const double angle); void BuildRyMatrix(double R[3][3], const double angle); void BuildRzMatrix(double R[3][3], const double angle); @@ -183,7 +183,7 @@ inline void MathExtra::normalize3(const double *v, double *ans) scale a vector to length ------------------------------------------------------------------------- */ -inline void MathExtra::snormalize3(const double length, const double *v, +inline void MathExtra::snormalize3(const double length, const double *v, double *ans) { double scale = length/sqrt(v[0]*v[0]+v[1]*v[1]+v[2]*v[2]); @@ -229,7 +229,7 @@ inline void MathExtra::add3(const double *v1, const double *v2, double *ans) ans = s*v1 + v2 ------------------------------------------------------------------------- */ -inline void MathExtra::scaleadd3(double s, const double *v1, +inline void MathExtra::scaleadd3(double s, const double *v1, const double *v2, double *ans) { ans[0] = s*v1[0] + v2[0]; @@ -404,7 +404,7 @@ inline void MathExtra::times3(const double m[3][3], const double m2[3][3], multiply the transpose of mat1 times mat2 ------------------------------------------------------------------------- */ -inline void MathExtra::transpose_times3(const double m[3][3], +inline void MathExtra::transpose_times3(const double m[3][3], const double m2[3][3],double ans[3][3]) { ans[0][0] = m[0][0]*m2[0][0] + m[1][0]*m2[1][0] + m[2][0]*m2[2][0]; @@ -422,7 +422,7 @@ inline void MathExtra::transpose_times3(const double m[3][3], multiply mat1 times transpose of mat2 ------------------------------------------------------------------------- */ -inline void MathExtra::times3_transpose(const double m[3][3], +inline void MathExtra::times3_transpose(const double m[3][3], const double m2[3][3],double ans[3][3]) { ans[0][0] = m[0][0]*m2[0][0] + m[0][1]*m2[0][1] + m[0][2]*m2[0][2]; @@ -462,7 +462,7 @@ inline void MathExtra::invert3(const double m[3][3], double ans[3][3]) matrix times vector ------------------------------------------------------------------------- */ -inline void MathExtra::matvec(const double m[3][3], const double *v, +inline void MathExtra::matvec(const double m[3][3], const double *v, double *ans) { ans[0] = m[0][0]*v[0] + m[0][1]*v[1] + m[0][2]*v[2]; @@ -474,7 +474,7 @@ inline void MathExtra::matvec(const double m[3][3], const double *v, matrix times vector ------------------------------------------------------------------------- */ -inline void MathExtra::matvec(const double *ex, const double *ey, +inline void MathExtra::matvec(const double *ex, const double *ey, const double *ez, const double *v, double *ans) { ans[0] = ex[0]*v[0] + ey[0]*v[1] + ez[0]*v[2]; @@ -529,7 +529,7 @@ inline void MathExtra::transpose_diag3(const double m[3][3], const double *d, row vector times matrix ------------------------------------------------------------------------- */ -inline void MathExtra::vecmat(const double *v, const double m[3][3], +inline void MathExtra::vecmat(const double *v, const double m[3][3], double *ans) { ans[0] = v[0]*m[0][0] + v[1]*m[1][0] + v[2]*m[2][0]; @@ -553,7 +553,7 @@ inline void MathExtra::scalar_times3(const double f, double m[3][3]) upper-triangular 3x3, stored as 6-vector in Voigt notation ------------------------------------------------------------------------- */ -inline void MathExtra::multiply_shape_shape(const double *one, +inline void MathExtra::multiply_shape_shape(const double *one, const double *two, double *ans) { ans[0] = one[0]*two[0]; @@ -660,7 +660,7 @@ inline void MathExtra::axisangle_to_quat(const double *v, const double angle, Apply principal rotation generator about x to rotation matrix m ------------------------------------------------------------------------- */ -inline void MathExtra::rotation_generator_x(const double m[3][3], +inline void MathExtra::rotation_generator_x(const double m[3][3], double ans[3][3]) { ans[0][0] = 0; @@ -678,7 +678,7 @@ inline void MathExtra::rotation_generator_x(const double m[3][3], Apply principal rotation generator about y to rotation matrix m ------------------------------------------------------------------------- */ -inline void MathExtra::rotation_generator_y(const double m[3][3], +inline void MathExtra::rotation_generator_y(const double m[3][3], double ans[3][3]) { ans[0][0] = m[0][2]; @@ -696,7 +696,7 @@ inline void MathExtra::rotation_generator_y(const double m[3][3], Apply principal rotation generator about z to rotation matrix m ------------------------------------------------------------------------- */ -inline void MathExtra::rotation_generator_z(const double m[3][3], +inline void MathExtra::rotation_generator_z(const double m[3][3], double ans[3][3]) { ans[0][0] = -m[0][1]; diff --git a/src/molecule.h b/src/molecule.h index bfc9da1857..e6455609ab 100644 --- a/src/molecule.h +++ b/src/molecule.h @@ -111,7 +111,7 @@ class Molecule : protected Pointers { double *quat_external; // orientation imposed by external class // e.g. FixPour or CreateAtoms - + Molecule(class LAMMPS *, int, char **, int &); ~Molecule(); void compute_center(); @@ -127,7 +127,7 @@ class Molecule : protected Pointers { int toffset,boffset,aoffset,doffset,ioffset; int autospecial; double sizescale; - + void read(int); void coords(char *); void types(char *); diff --git a/src/neigh_request.h b/src/neigh_request.h index 16e6f1a8c0..55fb533171 100644 --- a/src/neigh_request.h +++ b/src/neigh_request.h @@ -26,10 +26,10 @@ class NeighRequest : protected Pointers { int id; // ID of request as stored by requestor // used to track multiple requests from one class - // ----------------------------- + // ----------------------------- // flags set by requesting class for attributes of neighor list they need // all must be set appropriately, all have defaults - // ----------------------------- + // ----------------------------- // which class style requests the list // one flag is 1, others are 0 @@ -56,11 +56,11 @@ class NeighRequest : protected Pointers { // 0 if use force::newton_pair setting // 1 if override with pair newton on // 2 if override with pair newton off - + int ghost; // 1 if includes ghost atom neighbors int size; // 1 if pair cutoff set by particle radius int history; // 1 if there is also neigh history info (FixNeighHist) - int granonesided; // 1 if one-sided granular list for + int granonesided; // 1 if one-sided granular list for // sphere/surf interactions int respainner; // 1 if need a rRESPA inner list int respamiddle; // 1 if need a rRESPA middle list @@ -85,9 +85,9 @@ class NeighRequest : protected Pointers { const char *command_style; - // ----------------------------- + // ----------------------------- // flags set by Neighbor class to morph original requests - // ----------------------------- + // ----------------------------- int skiplist; // index of list to skip from int off2on; // 1 if this is newton on list, but skips from off list @@ -101,9 +101,9 @@ class NeighRequest : protected Pointers { int unique; // 1 if this list requires its own // NStencil, Nbin class - because of requestor cutoff - // ----------------------------- + // ----------------------------- // internal settings made by Neighbor class - // ----------------------------- + // ----------------------------- int index_bin; // index of NBin class assigned to this request int index_stencil; // index of NStencil class assigned to this request diff --git a/src/pair_ufm.h b/src/pair_ufm.h index 2161c2acaf..e43cc7c6c3 100644 --- a/src/pair_ufm.h +++ b/src/pair_ufm.h @@ -2,12 +2,12 @@ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov - + Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. - + See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ diff --git a/src/rcb.h b/src/rcb.h index 90b82f5952..f65ee2388a 100644 --- a/src/rcb.h +++ b/src/rcb.h @@ -57,7 +57,7 @@ class RCB : protected Pointers { double valuelo,valuehi; // position of dot(s) nearest to cut double wtlo,wthi; // total weight of dot(s) at that position int countlo,counthi; // # of dots at that position - int proclo,prochi; // unique proc who owns a nearest dot + int proclo,prochi; // unique proc who owns a nearest dot }; struct BBox { @@ -79,8 +79,8 @@ class RCB : protected Pointers { // tree of RCB cuts struct Tree { - double cut; // position of cut - int dim; // dimension = 0/1/2 of cut + double cut; // position of cut + int dim; // dimension = 0/1/2 of cut }; // inversion message @@ -119,13 +119,13 @@ class RCB : protected Pointers { double bboxhi[3]; Tree *tree; // tree of RCB cuts, used by reuse() int counters[7]; // diagnostic counts - // 0 = # of median iterations - // 1 = # of points sent - // 2 = # of points received - // 3 = most points this proc ever owns - // 4 = most point memory this proc ever allocs - // 5 = # of times a previous cut is re-used - // 6 = # of reallocs of point vector + // 0 = # of median iterations + // 1 = # of points sent + // 2 = # of points received + // 3 = most points this proc ever owns + // 4 = most point memory this proc ever allocs + // 5 = # of times a previous cut is re-used + // 6 = # of reallocs of point vector }; } diff --git a/src/set.h b/src/set.h index 5584e228ba..1412fb9a0d 100644 --- a/src/set.h +++ b/src/set.h @@ -36,7 +36,7 @@ class Set : protected Pointers { int ximage,yimage,zimage,ximageflag,yimageflag,zimageflag; double dvalue,xvalue,yvalue,zvalue,wvalue,fraction; int cc_index; - + int varflag,varflag1,varflag2,varflag3,varflag4; int ivar1,ivar2,ivar3,ivar4; double *vec1,*vec2,*vec3,*vec4;