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whitespace cleanup

This commit is contained in:
Axel Kohlmeyer 2018-03-15 21:57:45 -04:00
parent d62534665f
commit 7d2ada9d80
16 changed files with 64 additions and 64 deletions
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12
src/USER-OMP/reaxc_bond_orders_omp.h
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@ -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*,

8
src/USER-OMP/reaxc_nonbonded_omp.h
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@ -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:

8
src/USER-OMP/reaxc_torsion_angles_omp.h
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@ -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:

4
src/atom.h
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@ -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);

4
src/atom_vec_body.h
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@ -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;

2
src/compute_centro_atom.h
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@ -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 *);
};

2
src/domain.h
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@ -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 **);

4
src/fix_nh.h
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@ -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

4
src/fix_nve_sphere.h
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@ -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.

6
src/library.h
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@ -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

28
src/math_extra.h
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@ -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];

4
src/molecule.h
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@ -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 *);

16
src/neigh_request.h
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@ -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

4
src/pair_ufm.h
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@ -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.
------------------------------------------------------------------------- */

20
src/rcb.h
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@ -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
};
}

2
src/set.h
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@ -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;