lammps-sys 0.6.0

/* -*- 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"

namespace LAMMPS_NS {

class FixRigidSmall : public Fix {
  friend class ComputeRigidLocal;

 public:
  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();
  int modify_param(int, char **);
  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 *inpfile;             // file to read rigid body attributes from
  int setupflag;            // 1 if body properties are setup, else 0
  int earlyflag;            // 1 if forces/torques are computed at post_force()
  int commflag;             // various modes of forward/reverse comm
  int customflag;           // 1 if custom property/variable define bodies
  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 reinitflag;       // 1 if re-initialize rigid bodies between runs

  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

  double rsqfar;

  struct InRvous {
    int me,ilocal;
    tagint atomID,bodyID;
    double x[3];
  };

  struct OutRvous {
    int ilocal;
    tagint atomID;
  };

  // local methods

  void image_shift();
  void set_xv();
  void set_v();
  void create_bodies(tagint *);
  void setup_bodies_static();
  void setup_bodies_dynamic();
  void apply_langevin_thermostat();
  void compute_forces_and_torques();
  void readfile(int, double **, int *);
  void grow_body();
  void reset_atom2body();

  // callback function for rendezvous communication

  static int rendezvous_body(int, char *, int &, int *&, char *&, void *);

  // 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 custom requires previously defined property/atom

UNDOCUMENTED

E: Fix rigid/small custom requires integer-valued property/atom

UNDOCUMENTED

E: Variable name for fix rigid/small custom does not exist

UNDOCUMENTED

E: Fix rigid/small custom variable is no atom-style variable

UNDOCUMENTED

E: Unsupported fix rigid custom property

UNDOCUMENTED

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 inpfile %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.

*/