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fix_qeq_reax.h
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Wed, Jun 26, 11:30
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rLAMMPS lammps
fix_qeq_reax.h
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/* -*- c++ -*- ----------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Hasan Metin Aktulga, Purdue University
(now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov)
Please cite the related publication:
H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
"Parallel Reactive Molecular Dynamics: Numerical Methods and
Algorithmic Techniques", Parallel Computing, in press.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(qeq/reax,FixQEqReax)
#else
#ifndef LMP_FIX_QEQ_REAX_H
#define LMP_FIX_QEQ_REAX_H
#include "fix.h"
namespace LAMMPS_NS {
class FixQEqReax : public Fix {
public:
FixQEqReax(class LAMMPS *, int, char **);
~FixQEqReax();
int setmask();
void init();
void init_list(int,class NeighList *);
void init_storage();
void setup_pre_force(int);
void pre_force(int);
void setup_pre_force_respa(int, int);
void pre_force_respa(int, int, int);
void min_setup_pre_force(int);
void min_pre_force(int);
int matvecs;
double qeq_time;
private:
int nevery,reaxflag;
int n, N, m_fill;
int n_cap, nmax, m_cap;
int pack_flag;
int nlevels_respa;
class NeighList *list;
class PairReaxC *reaxc;
double swa, swb; // lower/upper Taper cutoff radius
double Tap[8]; // Taper function
double tolerance; // tolerance for the norm of the rel residual in CG
double *chi,*eta,*gamma; // qeq parameters
double **shld;
bigint ngroup;
// fictitious charges
double *s, *t;
double **s_hist, **t_hist;
int nprev;
typedef struct{
int n, m;
int *firstnbr;
int *numnbrs;
int *jlist;
double *val;
} sparse_matrix;
sparse_matrix H;
double *Hdia_inv;
double *b_s, *b_t;
double *b_prc, *b_prm;
//CG storage
double *p, *q, *r, *d;
//GMRES storage
//double *g,*y;
//double **v;
//double **h;
//double *hc, *hs;
void pertype_parameters(char*);
void init_shielding();
void init_taper();
void allocate_storage();
void deallocate_storage();
void reallocate_storage();
void allocate_matrix();
void deallocate_matrix();
void reallocate_matrix();
void init_matvec();
void init_H();
void compute_H();
double calculate_H(double,double);
void calculate_Q();
int CG(double*,double*);
//int GMRES(double*,double*);
void sparse_matvec(sparse_matrix*,double*,double*);
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
double parallel_norm( double*, int );
double parallel_dot( double*, double*, int );
double parallel_vector_acc( double*, int );
void vector_sum(double*,double,double*,double,double*,int);
void vector_add(double*, double, double*,int);
};
}
#endif
#endif
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