Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/RIGID/fix_shake.h
503cd8206557lammm-master-deprecated

Last Change
Raw File

fix_shake.h
View Options

/* -*- 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.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(shake,FixShake)
#else
#ifndef LMP_FIX_SHAKE_H
#define LMP_FIX_SHAKE_H
#include "fix.h"
namespace LAMMPS_NS {
class FixShake : public Fix {
friend class FixEHEX;
public:
FixShake(class LAMMPS *, int, char **);
virtual ~FixShake();
virtual int setmask();
virtual void init();
void setup(int);
void pre_neighbor();
virtual void post_force(int);
virtual void post_force_respa(int, int, int);
virtual double memory_usage();
virtual void grow_arrays(int);
virtual void copy_arrays(int, int, int);
void set_arrays(int);
virtual void update_arrays(int, int);
void set_molecule(int, tagint, int, double *, double *, double *);
virtual int pack_exchange(int, double *);
virtual int unpack_exchange(int, double *);
virtual int pack_forward_comm(int, int *, double *, int, int *);
virtual void unpack_forward_comm(int, int, double *);
virtual void shake_end_of_step(int vflag);
virtual void correct_coordinates(int vflag);
virtual void correct_velocities();
int dof(int);
virtual void reset_dt();
void *extract(const char *, int &);
protected:
int vflag_post_force; // store the vflag of last post_force call
int respa; // 0 = vel. Verlet, 1 = respa
int me,nprocs;
int rattle; // 0 = SHAKE, 1 = RATTLE
double tolerance; // SHAKE tolerance
int max_iter; // max # of SHAKE iterations
int output_every; // SHAKE stat output every so often
bigint next_output; // timestep for next output
// settings from input command
int *bond_flag,*angle_flag; // bond/angle types to constrain
int *type_flag; // constrain bonds to these types
double *mass_list; // constrain bonds to these masses
int nmass; // # of masses in mass_list
int molecular; // copy of atom->molecular
double *bond_distance,*angle_distance; // constraint distances
int ifix_respa; // rRESPA fix needed by SHAKE
int nlevels_respa; // copies of needed rRESPA variables
int *loop_respa;
double *step_respa;
double **x,**v,**f; // local ptrs to atom class quantities
double **ftmp, **vtmp; // pointers to temporary arrays for forces and velocities
double *mass,*rmass;
int *type;
int nlocal;
// atom-based arrays
int *shake_flag; // 0 if atom not in SHAKE cluster
// 1 = size 3 angle cluster
// 2,3,4 = size of bond-only cluster
tagint **shake_atom; // global IDs of atoms in cluster
// central atom is 1st
// lowest global ID is 1st for size 2
int **shake_type; // bondtype of each bond in cluster
// for angle cluster, 3rd value
// is angletype
double **xshake; // unconstrained atom coords
int *nshake; // count
double dtv,dtfsq; // timesteps for trial move
double dtf_inner,dtf_innerhalf; // timesteps for rRESPA trial move
int *list; // list of clusters to SHAKE
int nlist,maxlist; // size and max-size of list
// stat quantities
int *b_count,*b_count_all; // counts for each bond type
double *b_ave,*b_max,*b_min; // ave/max/min dist for each bond type
double *b_ave_all,*b_max_all,*b_min_all; // MPI summing arrays
int *a_count,*a_count_all; // ditto for angle types
double *a_ave,*a_max,*a_min;
double *a_ave_all,*a_max_all,*a_min_all;
class Molecule **atommols; // atom style template pointer
class Molecule **onemols; // molecule added on-the-fly
int nmol;
void find_clusters();
int masscheck(double);
void unconstrained_update();
void unconstrained_update_respa(int);
void shake(int);
void shake3(int);
void shake4(int);
void shake3angle(int);
void stats();
int bondtype_findset(int, tagint, tagint, int);
int angletype_findset(int, tagint, tagint, int);
// static variable for ring communication callback to access class data
// callback functions for ring communication
static FixShake *fsptr;
static void ring_bonds(int, char *);
static void ring_nshake(int, char *);
static void ring_shake(int, char *);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Cannot use fix shake with non-molecular system
Your choice of atom style does not have bonds.
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Invalid bond type index for fix shake
Self-explanatory. Check the fix shake command in the input script.
E: Invalid angle type index for fix shake
Self-explanatory.
E: Invalid atom type index for fix shake
Atom types must range from 1 to Ntypes inclusive.
E: Invalid atom mass for fix shake
Mass specified in fix shake command must be > 0.0.
E: Too many masses for fix shake
The fix shake command cannot list more masses than there are atom
types.
E: Molecule template ID for fix shake does not exist
Self-explanatory.
W: Molecule template for fix shake has multiple molecules
The fix shake command will only recoginze molecules of a single
type, i.e. the first molecule in the template.
E: Fix shake molecule template must have shake info
The defined molecule does not specify SHAKE information.
E: More than one fix shake
Only one fix shake can be defined.
E: Fix shake cannot be used with minimization
Cannot use fix shake while doing an energy minimization since
it turns off bonds that should contribute to the energy.
E: Shake fix must come before NPT/NPH fix
NPT fix must be defined in input script after SHAKE fix, else the
SHAKE fix contribution to the pressure virial is incorrect.
E: Bond potential must be defined for SHAKE
Cannot use fix shake unless bond potential is defined.
E: Angle potential must be defined for SHAKE
When shaking angles, an angle_style potential must be used.
E: Shake angles have different bond types
All 3-atom angle-constrained SHAKE clusters specified by the fix shake
command that are the same angle type, must also have the same bond
types for the 2 bonds in the angle.
E: Shake atoms %d %d missing on proc %d at step %ld
The 2 atoms in a single shake cluster specified by the fix shake
command are not all accessible to a processor. This probably means
an atom has moved too far.
E: Shake atoms %d %d %d missing on proc %d at step %ld
The 3 atoms in a single shake cluster specified by the fix shake
command are not all accessible to a processor. This probably means
an atom has moved too far.
E: Shake atoms %d %d %d %d missing on proc %d at step %ld
The 4 atoms in a single shake cluster specified by the fix shake
command are not all accessible to a processor. This probably means
an atom has moved too far.
E: Did not find fix shake partner info
Could not find bond partners implied by fix shake command. This error
can be triggered if the delete_bonds command was used before fix
shake, and it removed bonds without resetting the 1-2, 1-3, 1-4
weighting list via the special keyword.
E: Shake cluster of more than 4 atoms
A single cluster specified by the fix shake command can have no more
than 4 atoms.
E: Shake clusters are connected
A single cluster specified by the fix shake command must have a single
central atom with up to 3 other atoms bonded to it.
W: Shake determinant < 0.0
The determinant of the quadratic equation being solved for a single
cluster specified by the fix shake command is numerically suspect. LAMMPS
will set it to 0.0 and continue.
E: Shake determinant = 0.0
The determinant of the matrix being solved for a single cluster
specified by the fix shake command is numerically invalid.
*/
c4science · Help