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fix_poems.h
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Fri, Jun 21, 09:49

fix_poems.h
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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(poems,FixPOEMS)
#else
#ifndef LMP_FIX_POEMS_H
#define LMP_FIX_POEMS_H
#include "fix.h"
namespace LAMMPS_NS {
class FixPOEMS : public Fix {
public:
FixPOEMS(class LAMMPS *, int narg, char **arg);
~FixPOEMS();
int setmask();
void init();
void setup(int);
void initial_integrate(int);
void post_force(int);
void final_integrate();
void initial_integrate_respa(int, int, int);
void post_force_respa(int, int, int);
void final_integrate_respa(int, int);
void grow_arrays(int);
void copy_arrays(int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
double memory_usage();
void pre_neighbor();
int dof(int);
void deform(int);
void reset_dt();
private:
int me;
double dtv,dtf,dthalf;
double *step_respa;
int nlevels_respa;
double total_ke;
// atom assignment to rigid bodies
// double count joint atoms as being in multiple bodies
int *natom2body; // # of bodies each atom is part of
int **atom2body; // list of bodies each atom is part of
double **displace; // atom displace in body coords for 1st body it's in
// rigid body properties
// only nrigid double counts joint atoms as being in multiple bodies
// other quantities only count a joint atom as being in 1st body
int nbody; // # of rigid bodies
int *nrigid; // # of atoms in each rigid body
double *masstotal; // total mass of each rigid body
double **xcm; // coords of center-of-mass of each rigid body
double **vcm; // velocity of center-of-mass of each
double **fcm; // force on center-of-mass of each
double **inertia; // 6 inertia components of each (xx,yy,zz,xy,yz,xz)
double **ex_space,**ey_space,**ez_space;
// orientation of each body in space coords
double **angmom; // angular momentum of each in space coords
double **omega; // angular velocity of each in space coords
double **torque; // torque on each rigid body in space coords
double **sum,**all; // work vectors
// joint attributes between pairs of rigid bodies
int ncluster; // # of independent clusters of coupled bodies
int njoint; // # of interbody joints
int **jointbody; // indices of 2 rigid bodies in each joint (1-N)
double **xjoint; // coords of each joint point
int nfree; // # of isolated unconnected bodies
int *freelist; // indices of isolated bodies (1-N)
// POEMS object
class Workspace *poems;
// internal class functions
void readfile(char *);
int readline(FILE *, char **, int *);
void jointbuild();
void sortlist(int, int **);
int loopcheck(int, int, int **);
int jacobi(double **, double *, double **);
void rotate(double **, int, int, int, int, double, double);
void omega_from_mq(double *, double *, double *, double *,
double *, double *);
void set_v();
void set_xv();
};
}
#endif
#endif

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