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lammps/src/RIGID/fix_rigid_small.h
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fix_rigid_small.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(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 {
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);
double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int, int);
void set_arrays(int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
int pack_comm(int, int *, double *, int, int *);
void unpack_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 reset_dt();
protected:
int me,nprocs;
double dtv,dtf,dtq;
double *step_respa;
int triclinic;
double MINUSPI,TWOPI;
int firstflag; // 1 for first-time setup of rigid bodies
int commflag; // various modes of forward/reverse comm
int nbody; // total # of rigid bodies
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 on COM
double quat[4]; // quaternion for orientation of body
double inertia[3]; // 3 principal components of inertia
double itensor[6]; // 6 space-frame components of inertia tensor
double ex_space[3]; // principal axes in space coords
double ey_space[3];
double ez_space[3];
double angmom[3]; // angular momentum of body
double omega[3]; // omega of body
tagint 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
int *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
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;
int **counts;
// 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
// class data used by ring communication callbacks
std::map<int,int> *hash;
double **bbox;
double **ctr;
int *idclose;
double *rsqclose;
void set_xv();
void set_v();
void create_bodies();
void setup_bodies();
void grow_body();
void reset_atom2body();
// callback functions for ring communication
static void bbox_update(int, char *);
static void nearest_update(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 molecule requires atom attribute molecule
Self-explanatory.
E: Could not find fix rigid group ID
A group ID used in the fix rigid command does not exist.
E: One or more atoms belong to multiple rigid bodies
Two or more rigid bodies defined by the fix rigid command cannot
contain the same atom.
E: No rigid bodies defined
The fix specification did not end up defining any rigid bodies.
E: Fix rigid z force cannot be on for 2d simulation
Self-explanatory.
E: Fix rigid xy torque cannot be on for 2d simulation
Self-explanatory.
E: Fix rigid langevin period must be > 0.0
Self-explanatory.
E: One or zero atoms in rigid body
Any rigid body defined by the fix rigid command must contain 2 or more
atoms.
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: 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 atom has non-zero image flag in a non-periodic dimension
You cannot set image flags for non-periodic dimensions.
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 infile %s
UNDOCUMENTED
E: Unexpected end of fix rigid file
UNDOCUMENTED
E: Incorrect rigid body format in fix rigid file
UNDOCUMENTED
E: Invalid rigid body ID in fix rigid file
UNDOCUMENTED
*/
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