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lammps
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10626 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-08-21 17:22:55 +00:00
parent 2cbcde563f
commit 7511965094
4 changed files with 55 additions and 9 deletions
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3
src/fix.cpp
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@ -46,8 +46,7 @@ Fix::Fix(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
style = new char[n];
strcpy(style,arg[2]);
restart_global = 0;
restart_peratom = 0;
restart_global = restart_peratom = restart_file = 0;
force_reneighbor = 0;
box_change_size = box_change_shape = box_change_domain = 0;
thermo_energy = 0;

2
src/fix.h
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@ -25,6 +25,7 @@ class Fix : protected Pointers {
int restart_global; // 1 if Fix saves global state, 0 if not
int restart_peratom; // 1 if Fix saves peratom state, 0 if not
int restart_file; // 1 if Fix writes own restart file, 0 if not
int force_reneighbor; // 1 if Fix forces reneighboring, 0 if not
int box_change_size; // 1 if Fix changes box size, 0 if not
@ -108,6 +109,7 @@ class Fix : protected Pointers {
virtual void end_of_step() {}
virtual void post_run() {}
virtual void write_restart(FILE *) {}
virtual void write_restart_file() {}
virtual void restart(char *) {}
virtual void grow_arrays(int) {}

52
src/math_extra.h
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@ -41,29 +41,31 @@ namespace MathExtra {
// 3x3 matrix operations
inline void col2mat(const double *ex, const double *ey, const double *ez,
double m[3][3]);
inline double det3(const double mat[3][3]);
inline void diag_times3(const double *diagonal, const double mat[3][3],
inline void diag_times3(const double *d, const double m[3][3],
double ans[3][3]);
inline void times3_diag(const double m[3][3], const double *d,
double ans[3][3]);
inline void plus3(const double m[3][3], const double m2[3][3],
double ans[3][3]);
inline void times3(const double m[3][3], const double m2[3][3],
double ans[3][3]);
inline void transpose_times3(const double mat1[3][3],
const double mat2[3][3],
inline void transpose_times3(const double m[3][3], const double m2[3][3],
double ans[3][3]);
inline void times3_transpose(const double mat1[3][3],
const double mat2[3][3],
inline void times3_transpose(const double m[3][3], const double m2[3][3],
double ans[3][3]);
inline void invert3(const double mat[3][3], double ans[3][3]);
inline void matvec(const double mat[3][3], const double *vec, double *ans);
inline void matvec(const double *ex, const double *ey, const double *ez,
const double *vec, double *ans);
inline void transpose_matvec(const double mat[3][3], const double*vec,
inline void transpose_matvec(const double mat[3][3], const double *vec,
double *ans);
inline void transpose_matvec(const double *ex, const double *ey,
const double *ez, const double *v,
double *ans);
inline void transpose_diag3(const double mat[3][3], const double*vec,
inline void transpose_diag3(const double m[3][3], const double *d,
double ans[3][3]);
inline void vecmat(const double *v, const double m[3][3], double *ans);
inline void scalar_times3(const double f, double m[3][3]);
@ -238,6 +240,24 @@ void MathExtra::cross3(const double *v1, const double *v2, double *ans)
ans[2] = v1[0]*v2[1] - v1[1]*v2[0];
}
/* ----------------------------------------------------------------------
construct matrix from 3 column vectors
------------------------------------------------------------------------- */
void MathExtra::col2mat(const double *ex, const double *ey, const double *ez,
double m[3][3])
{
m[0][0] = ex[0];
m[1][0] = ex[1];
m[2][0] = ex[2];
m[0][1] = ey[0];
m[1][1] = ey[1];
m[2][1] = ey[2];
m[0][2] = ez[0];
m[1][2] = ez[1];
m[2][2] = ez[2];
}
/* ----------------------------------------------------------------------
determinant of a matrix
------------------------------------------------------------------------- */
@ -268,6 +288,24 @@ void MathExtra::diag_times3(const double *d, const double m[3][3],
ans[2][2] = d[2]*m[2][2];
}
/* ----------------------------------------------------------------------
full matrix times a diagonal matrix
------------------------------------------------------------------------- */
void MathExtra::times3_diag(const double m[3][3], const double *d,
double ans[3][3])
{
ans[0][0] = m[0][0]*d[0];
ans[0][1] = m[0][1]*d[1];
ans[0][2] = m[0][2]*d[2];
ans[1][0] = m[1][0]*d[0];
ans[1][1] = m[1][1]*d[1];
ans[1][2] = m[1][2]*d[2];
ans[2][0] = m[2][0]*d[0];
ans[2][1] = m[2][1]*d[1];
ans[2][2] = m[2][2]*d[2];
}
/* ----------------------------------------------------------------------
add two matrices
------------------------------------------------------------------------- */

7
src/write_restart.cpp
View File

@ -29,6 +29,7 @@
#include "neighbor.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "universe.h"
#include "comm.h"
#include "output.h"
@ -292,6 +293,12 @@ void WriteRestart::write(char *file)
}
memory->destroy(buf);
// invoke any fixes that write their own restart file
for (int ifix = 0; ifix < modify->nfix; ifix++)
if (modify->fix[ifix]->restart_file)
modify->fix[ifix]->write_restart_file();
}
/* ----------------------------------------------------------------------