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fix_rigid_small.h
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rLAMMPS lammps
fix_rigid_small.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.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(rigid/small,FixRigidSmall)
#else
#ifndef LMP_FIX_RIGID_SMALL_H
#define LMP_FIX_RIGID_SMALL_H
#include "fix.h"
// replace this later
#include <map>
namespace LAMMPS_NS {
class FixRigidSmall : public Fix {
friend class ComputeRigidLocal;
public:
// static variable for ring communication callback to access class data
static FixRigidSmall *frsptr;
FixRigidSmall(class LAMMPS *, int, char **);
virtual ~FixRigidSmall();
virtual int setmask();
virtual void init();
virtual void setup(int);
virtual void initial_integrate(int);
void post_force(int);
virtual void final_integrate();
void initial_integrate_respa(int, int, int);
void final_integrate_respa(int, int);
void write_restart_file(char *);
void grow_arrays(int);
void copy_arrays(int, int, int);
void set_arrays(int);
void set_molecule(int, tagint, int, double *, double *, double *);
int pack_exchange(int, double *);
int unpack_exchange(int, 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 *);
void setup_pre_neighbor();
void pre_neighbor();
int dof(int);
void deform(int);
void enforce2d();
void reset_dt();
void zero_momentum();
void zero_rotation();
void *extract(const char*, int &);
double extract_ke();
double extract_erotational();
double compute_scalar();
double memory_usage();
protected:
int me,nprocs;
double dtv,dtf,dtq;
double *step_respa;
int triclinic;
double MINUSPI,TWOPI;
char *infile; // file to read rigid body attributes from
int setupflag; // 1 if body properties are setup, else 0
int commflag; // various modes of forward/reverse comm
int nbody; // total # of rigid bodies
int nlinear; // total # of linear rigid bodies
tagint maxmol; // max mol-ID
double maxextent; // furthest distance from body owner to body atom
struct Body {
double mass; // total mass of body
double xcm[3]; // COM position
double vcm[3]; // COM velocity
double fcm[3]; // force on COM
double torque[3]; // torque around COM
double quat[4]; // quaternion for orientation of body
double inertia[3]; // 3 principal components of inertia
double ex_space[3]; // principal axes in space coords
double ey_space[3];
double ez_space[3];
double angmom[3]; // space-frame angular momentum of body
double omega[3]; // space-frame omega of body
double conjqm[4]; // conjugate quaternion momentum
imageint image; // image flags of xcm
int remapflag[4]; // PBC remap flags
int ilocal; // index of owning atom
};
Body *body; // list of rigid bodies, owned and ghost
int nlocal_body; // # of owned rigid bodies
int nghost_body; // # of ghost rigid bodies
int nmax_body; // max # of bodies that body can hold
int bodysize; // sizeof(Body) in doubles
// per-atom quantities
// only defined for owned atoms, except bodyown for own+ghost
int *bodyown; // index of body if atom owns a body, -1 if not
tagint *bodytag; // ID of body this atom is in, 0 if none
// ID = tag of atom that owns body
int *atom2body; // index of owned/ghost body this atom is in, -1 if not
// can point to original or any image of the body
imageint *xcmimage; // internal image flags for atoms in rigid bodies
// set relative to in-box xcm of each body
double **displace; // displacement of each atom in body coords
int *eflags; // flags for extended particles
double **orient; // orientation vector of particle wrt rigid body
double **dorient; // orientation of dipole mu wrt rigid body
int extended; // 1 if any particles have extended attributes
int orientflag; // 1 if particles store spatial orientation
int dorientflag; // 1 if particles store dipole orientation
int POINT,SPHERE,ELLIPSOID,LINE,TRIANGLE,DIPOLE; // bitmasks for eflags
int OMEGA,ANGMOM,TORQUE;
class AtomVecEllipsoid *avec_ellipsoid;
class AtomVecLine *avec_line;
class AtomVecTri *avec_tri;
// temporary per-body storage
int **counts; // counts of atom types in bodies
double **itensor; // 6 space-frame components of inertia tensor
// mass per body, accessed by granular pair styles
double *mass_body;
int nmax_mass;
// Langevin thermostatting
int langflag; // 0/1 = no/yes Langevin thermostat
double t_start,t_stop,t_period; // thermostat params
double **langextra; // Langevin thermostat forces and torques
int maxlang; // max size of langextra
class RanMars *random; // RNG
int tstat_flag,pstat_flag; // 0/1 = no/yes thermostat/barostat
int t_chain,t_iter,t_order;
double p_start[3],p_stop[3];
double p_period[3],p_freq[3];
int p_flag[3];
int pcouple,pstyle;
int p_chain;
int allremap; // remap all atoms
int dilate_group_bit; // mask for dilation group
char *id_dilate; // group name to dilate
double p_current[3],p_target[3];
// molecules added on-the-fly as rigid bodies
class Molecule **onemols;
int nmol;
// class data used by ring communication callbacks
std::map<tagint,int> *hash;
double **bbox;
double **ctr;
tagint *idclose;
double *rsqclose;
double rsqfar;
void image_shift();
void set_xv();
void set_v();
void create_bodies();
void setup_bodies_static();
void setup_bodies_dynamic();
void readfile(int, double **, int *);
void grow_body();
void reset_atom2body();
// callback functions for ring communication
static void ring_bbox(int, char *);
static void ring_nearest(int, char *);
static void ring_farthest(int, char *);
// debug
//void check(int);
};
}
#endif
#endif
/* ERROR/WARNING messages:
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: Fix rigid/small requires atom attribute molecule
Self-explanatory.
E: Fix rigid/small requires an atom map, see atom_modify
Self-explanatory.
E: Fix rigid/small langevin period must be > 0.0
Self-explanatory.
E: Molecule template ID for fix rigid/small does not exist
Self-explanatory.
E: Fix rigid/small nvt/npt/nph dilate group ID does not exist
Self-explanatory.
E: Fix rigid/small molecule must have coordinates
The defined molecule does not specify coordinates.
E: Fix rigid/small molecule must have atom types
The defined molecule does not specify atom types.
W: More than one fix rigid
It is not efficient to use fix rigid more than once.
E: Rigid fix must come before NPT/NPH fix
NPT/NPH fix must be defined in input script after all rigid fixes,
else the rigid fix contribution to the pressure virial is
incorrect.
W: Cannot count rigid body degrees-of-freedom before bodies are fully initialized
This means the temperature associated with the rigid bodies may be
incorrect on this timestep.
W: Computing temperature of portions of rigid bodies
The group defined by the temperature compute does not encompass all
the atoms in one or more rigid bodies, so the change in
degrees-of-freedom for the atoms in those partial rigid bodies will
not be accounted for.
E: Fix rigid/small atom has non-zero image flag in a non-periodic dimension
Image flags for non-periodic dimensions should not be set.
E: One or more rigid bodies are a single particle
Self-explanatory.
E: Inconsistent use of finite-size particles by molecule template molecules
Not all of the molecules define a radius for their constituent
particles.
E: Insufficient Jacobi rotations for rigid body
Eigensolve for rigid body was not sufficiently accurate.
E: Fix rigid: Bad principal moments
The principal moments of inertia computed for a rigid body
are not within the required tolerances.
E: Cannot open fix rigid/small infile %s
The specified file cannot be opened. Check that the path and name are
correct.
E: Unexpected end of fix rigid/small file
A read operation from the file failed.
E: Incorrect rigid body format in fix rigid/small file
The number of fields per line is not what expected.
E: Invalid rigid body ID in fix rigid/small file
The ID does not match the number of an existing ID of rigid bodies
that are defined by the fix rigid/small command.
E: Cannot open fix rigid restart file %s
The specified file cannot be opened. Check that the path and name are
correct.
E: Rigid body atoms %d %d missing on proc %d at step %ld
This means that an atom cannot find the atom that owns the rigid body
it is part of, or vice versa. The solution is to use the communicate
cutoff command to insure ghost atoms are acquired from far enough away
to encompass the max distance printed when the fix rigid/small command
was invoked.
*/
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