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fix_rigid_small.h
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rLAMMPS lammps
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
);
void
write_restart_file
(
char
*
);
void
grow_arrays
(
int
);
void
copy_arrays
(
int
,
int
,
int
);
void
set_arrays
(
int
);
void
set_molecule
(
int
,
tagint
,
double
*
,
double
*
,
double
*
);
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
();
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
firstflag
;
// 1 for first-time setup of rigid bodies
int
commflag
;
// various modes of forward/reverse comm
int
nbody
;
// total # of 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
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
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
// molecules added on-the-fly as rigid bodies
class
Molecule
*
onemol
;
// class data used by ring communication callbacks
std
::
map
<
tagint
,
int
>
*
hash
;
double
**
bbox
;
double
**
ctr
;
tagint
*
idclose
;
double
*
rsqclose
;
double
rsqfar
;
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.
W: Molecule template for fix rigid/small has multiple molecules
The fix rigid/small command will only recoginze molecules of a single
type, i.e. the first molecule in the template.
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: 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: Fix rigid file has no lines
Self-explanatory.
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 %ld %ld 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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