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fix_rigid.h
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rLAMMPS lammps
fix_rigid.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,FixRigid)
#else
#ifndef LMP_FIX_RIGID_H
#define LMP_FIX_RIGID_H
#include "fix.h"
namespace LAMMPS_NS {
class FixRigid : public Fix {
public:
FixRigid(class LAMMPS *, int, char **);
virtual ~FixRigid();
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 *);
virtual double compute_scalar();
virtual int modify_param(int, char **) {return 0;}
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 *);
void pre_neighbor();
int dof(int);
void deform(int);
void reset_dt();
void zero_momentum();
void zero_rotation();
virtual void *extract(const char*, int &);
double extract_ke();
double extract_erotational();
double compute_array(int, int);
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 rstyle; // SINGLE,MOLECULE,GROUP
int firstflag; // 1 for first-time setup of rigid bodies
int dimension; // # of dimensions
int nbody; // # of rigid bodies
int *nrigid; // # of atoms in each rigid body
int *mol2body; // convert mol-ID to rigid body index
int *body2mol; // convert rigid body index to mol-ID
int maxmol; // size of mol2body = max mol-ID
int *body; // which body each atom is part of (-1 if none)
double **displace; // displacement of each atom in body coords
double *masstotal; // total mass of each rigid body
double **xcm; // coords of center-of-mass of each rigid body
double **vcm; // velocity of center-of-mass of each
double **fcm; // force on center-of-mass of each
double **inertia; // 3 principal components of inertia of each
double **ex_space,**ey_space,**ez_space;
// principal axes of each in space coords
double **angmom; // angular momentum of each in space coords
double **omega; // angular velocity of each in space coords
double **torque; // torque on each rigid body in space coords
double **quat; // quaternion of each rigid body
imageint *imagebody; // image flags of xcm of each rigid body
double **fflag; // flag for on/off of center-of-mass force
double **tflag; // flag for on/off of center-of-mass torque
double **langextra; // Langevin thermostat forces and torques
double **sum,**all; // work vectors for each rigid body
int **remapflag; // PBC remap flags for each 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 *eflags; // flags for extended particles
double **orient; // orientation vector of particle wrt rigid body
double **dorient; // orientation of dipole mu wrt rigid body
double tfactor; // scale factor on temperature of rigid bodies
int langflag; // 0/1 = no/yes Langevin thermostat
int tstat_flag; // NVT settings
double t_start,t_stop,t_target;
double t_period,t_freq;
int t_chain,t_iter,t_order;
int pstat_flag; // NPT settings
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
class RanMars *random;
class AtomVecEllipsoid *avec_ellipsoid;
class AtomVecLine *avec_line;
class AtomVecTri *avec_tri;
int POINT,SPHERE,ELLIPSOID,LINE,TRIANGLE,DIPOLE; // bitmasks for eflags
int OMEGA,ANGMOM,TORQUE;
void no_squish_rotate(int, double *, double *, double *, double) const;
void set_xv();
void set_v();
void setup_bodies_static();
void setup_bodies_dynamic();
void readfile(int, double *, double **, 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: Fix rigid npt/nph dilate group ID does not exist
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: Cannot count rigid body degrees-of-freedom before bodies are fully initialized
UNDOCUMENTED
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
Image flags for non-periodic dimensions should not be set.
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
The specified file cannot be opened. Check that the path and name are
correct.
E: Unexpected end of fix rigid file
A read operation from the file failed.
E: Incorrect rigid body format in fix rigid file
The number of fields per line is not what expected.
E: Invalid rigid body ID in fix rigid file
The ID does not match the number or an existing ID of rigid bodies
that are defined by the fix rigid command.
*/
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