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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
);
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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