forked from lijiext/lammps
Merge branch 'filter_corotate' of https://github.com/lukin17/lammps into pull-416
This commit is contained in:
Axel Kohlmeyer
commit
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Lukas Fath (KIT)
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some subroutines are from fix_shake.cpp
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------------------------------------------------------------------------- */
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#ifdef FIX_CLASS
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FixStyle(filter/corotate,FixFilterCorotate)
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#else
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#ifndef LMP_FIX_FILTER_COROTATE_H
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#define LMP_FIX_FILTER_COROTATE_H
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#include "fix.h"
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namespace LAMMPS_NS
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{
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class FixFilterCorotate : public Fix
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{
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public:
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FixFilterCorotate(class LAMMPS *, int, char **);
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~FixFilterCorotate();
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void setup(int);
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void setup_pre_neighbor();
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void pre_neighbor();
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void setup_pre_force_respa(int,int);
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// void setup_post_force_respa(int,int);
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void pre_force_respa(int, int, int);
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void post_force_respa(int, int, int);
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void init();
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int setmask();
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double compute_array(int,int);
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int pack_forward_comm(int, int *, double *, int, int *);
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void unpack_forward_comm(int, int, double *);
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void grow_arrays(int );
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double memory_usage();
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void copy_arrays(int, int, int);
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void set_arrays(int);
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void update_arrays(int, int);
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int pack_exchange(int, double *);
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int unpack_exchange(int, double *);
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protected:
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int me,nprocs;
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int flevel; //filtered respa level
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double **help2; //temp derivative
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double **x_store; //temp for atom->x
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double *g; //temp for derivative
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double*n1,*n2,*n3, *del1, *del2,*del3;
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double**dn1dx,**dn2dx,**dn3dx;
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int *bond_flag,*angle_flag; // bond/angle types to constrain
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int *type_flag; // constrain bonds to these types
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double *mass_list; // constrain bonds to these masses
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int nmass; // # of masses in mass_list
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int molecular; // copy of atom->molecular
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double *bond_distance,*angle_distance; // constraint distances
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int nlevels_respa; // copies of needed rRESPA variables
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double **x,**v,**f; // local ptrs to atom class quantities
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double *mass,*rmass;
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int *type;
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int nlocal;
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// atom-based arrays
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int *shake_flag; // 0 if atom not in SHAKE cluster
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// 1 = size 3 angle cluster
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// 2,3,4 = size of bond-only cluster
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tagint **shake_atom; // global IDs of atoms in cluster
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// central atom is 1st
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// lowest global ID is 1st for size 2
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int **shake_type; // bondtype of each bond in cluster
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// for angle cluster, 3rd value
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// is angletype
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int *nshake; // count
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int *list; // list of clusters to SHAKE
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int nlist,maxlist; // size and max-size of list
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double ***clist_derv; //stores derivative
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double **clist_q0; //stores reference config
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int *clist_nselect1, *clist_nselect2; //stores length of each selec. list
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int **clist_select1, **clist_select2; //stores selection lists
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void find_clusters();
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int masscheck(double);
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void filter_inner();
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void filter_outer();
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void general_cluster(int,int);
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void stats();
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int bondtype_findset(int, tagint, tagint, int);
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int angletype_findset(int, tagint, tagint, int);
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// static variable for ring communication callback to access class data
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// callback functions for ring communication
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static FixFilterCorotate *fsptr;
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static void ring_bonds(int, char *);
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static void ring_nshake(int, char *);
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static void ring_shake(int, char *);
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int sgn(double val) {
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return (0 < val) - (val < 0);
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};
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};
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}
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#endif
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Lukas Fath (KIT)
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some subroutines are from fix_shake.cpp
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------------------------------------------------------------------------- */
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#ifdef FIX_CLASS
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FixStyle(filter/corotate,FixFilterCorotate)
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#else
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#ifndef LMP_FIX_FILTER_COROTATE_H
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#define LMP_FIX_FILTER_COROTATE_H
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#include "fix.h"
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namespace LAMMPS_NS
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{
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class FixFilterCorotate : public Fix
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{
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public:
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FixFilterCorotate(class LAMMPS *, int, char **);
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~FixFilterCorotate();
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void setup(int);
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void setup_pre_neighbor();
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void pre_neighbor();
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void setup_pre_force_respa(int,int);
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// void setup_post_force_respa(int,int);
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void pre_force_respa(int, int, int);
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void post_force_respa(int, int, int);
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void init();
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int setmask();
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double compute_array(int,int);
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int pack_forward_comm(int, int *, double *, int, int *);
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void unpack_forward_comm(int, int, double *);
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void grow_arrays(int );
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double memory_usage();
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void copy_arrays(int, int, int);
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void set_arrays(int);
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void update_arrays(int, int);
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int pack_exchange(int, double *);
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int unpack_exchange(int, double *);
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protected:
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int me,nprocs;
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int flevel; //filtered respa level
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double **help2; //temp derivative
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double **x_store; //temp for atom->x
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double *g; //temp for derivative
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double*n1,*n2,*n3, *del1, *del2,*del3;
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double**dn1dx,**dn2dx,**dn3dx;
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int *bond_flag,*angle_flag; // bond/angle types to constrain
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int *type_flag; // constrain bonds to these types
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double *mass_list; // constrain bonds to these masses
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int nmass; // # of masses in mass_list
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int molecular; // copy of atom->molecular
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double *bond_distance,*angle_distance; // constraint distances
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int nlevels_respa; // copies of needed rRESPA variables
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double **x,**v,**f; // local ptrs to atom class quantities
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double *mass,*rmass;
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int *type;
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int nlocal;
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// atom-based arrays
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int *shake_flag; // 0 if atom not in SHAKE cluster
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// 1 = size 3 angle cluster
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// 2,3,4 = size of bond-only cluster
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tagint **shake_atom; // global IDs of atoms in cluster
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// central atom is 1st
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// lowest global ID is 1st for size 2
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int **shake_type; // bondtype of each bond in cluster
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// for angle cluster, 3rd value
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// is angletype
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int *nshake; // count
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int *list; // list of clusters to SHAKE
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int nlist,maxlist; // size and max-size of list
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double ***clist_derv; //stores derivative
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double **clist_q0; //stores reference config
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int *clist_nselect1, *clist_nselect2; //stores length of each selec. list
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int **clist_select1, **clist_select2; //stores selection lists
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void find_clusters();
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int masscheck(double);
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void filter_inner();
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void filter_outer();
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void general_cluster(int,int);
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void stats();
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int bondtype_findset(int, tagint, tagint, int);
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int angletype_findset(int, tagint, tagint, int);
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// static variable for ring communication callback to access class data
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// callback functions for ring communication
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static FixFilterCorotate *fsptr;
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static void ring_bonds(int, char *);
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static void ring_nshake(int, char *);
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static void ring_shake(int, char *);
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int sgn(double val) {
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return (0 < val) - (val < 0);
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};
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};
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}
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#endif
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#endif
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