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rLAMMPS lammps
atom.h
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/* -*- 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.
------------------------------------------------------------------------- */
#ifndef LMP_ATOM_H
#define LMP_ATOM_H
#include "pointers.h"
namespace
LAMMPS_NS
{
class
Atom
:
protected
Pointers
{
public:
char
*
atom_style
;
class
AtomVec
*
avec
;
// atom counts
bigint
natoms
;
// total # of atoms in system, could be 0
// natoms may not be current if atoms lost
int
nlocal
,
nghost
;
// # of owned and ghost atoms on this proc
int
nmax
;
// max # of owned+ghost in arrays on this proc
int
tag_enable
;
// 0/1 if atom ID tags are defined
int
molecular
;
// 0 = atomic, 1 = standard molecular system,
// 2 = molecule template system
bigint
nbonds
,
nangles
,
ndihedrals
,
nimpropers
;
int
ntypes
,
nbondtypes
,
nangletypes
,
ndihedraltypes
,
nimpropertypes
;
int
bond_per_atom
,
angle_per_atom
,
dihedral_per_atom
,
improper_per_atom
;
int
extra_bond_per_atom
,
extra_angle_per_atom
;
int
extra_dihedral_per_atom
,
extra_improper_per_atom
;
int
firstgroup
;
// store atoms in this group first, -1 if unset
int
nfirst
;
// # of atoms in first group on this proc
char
*
firstgroupname
;
// group-ID to store first, NULL if unset
// per-atom arrays
// customize by adding new array
tagint
*
tag
;
int
*
type
,
*
mask
;
imageint
*
image
;
double
**
x
,
**
v
,
**
f
;
tagint
*
molecule
;
int
*
molindex
,
*
molatom
;
double
*
q
,
**
mu
;
double
**
omega
,
**
angmom
,
**
torque
;
double
*
radius
,
*
rmass
,
*
vfrac
,
*
s0
;
double
**
x0
;
int
*
ellipsoid
,
*
line
,
*
tri
,
*
body
;
int
*
spin
;
double
*
eradius
,
*
ervel
,
*
erforce
,
*
ervelforce
;
double
*
cs
,
*
csforce
,
*
vforce
;
int
*
etag
;
double
*
rho
,
*
drho
;
double
*
e
,
*
de
;
double
**
vest
;
double
*
cv
;
int
**
nspecial
;
// 0,1,2 = cummulative # of 1-2,1-3,1-4 neighs
tagint
**
special
;
// IDs of 1-2,1-3,1-4 neighs of each atom
int
maxspecial
;
// special[nlocal][maxspecial]
int
*
num_bond
;
int
**
bond_type
;
tagint
**
bond_atom
;
int
*
num_angle
;
int
**
angle_type
;
tagint
**
angle_atom1
,
**
angle_atom2
,
**
angle_atom3
;
int
*
num_dihedral
;
int
**
dihedral_type
;
tagint
**
dihedral_atom1
,
**
dihedral_atom2
,
**
dihedral_atom3
,
**
dihedral_atom4
;
int
*
num_improper
;
int
**
improper_type
;
tagint
**
improper_atom1
,
**
improper_atom2
,
**
improper_atom3
,
**
improper_atom4
;
// custom arrays used by fix property/atom
int
**
ivector
;
double
**
dvector
;
char
**
iname
,
**
dname
;
int
nivector
,
ndvector
;
// used by USER-CUDA to flag used per-atom arrays
unsigned
int
datamask
;
unsigned
int
datamask_ext
;
// atom style and per-atom array existence flags
// customize by adding new flag
int
sphere_flag
,
ellipsoid_flag
,
line_flag
,
tri_flag
,
body_flag
;
int
peri_flag
,
electron_flag
;
int
ecp_flag
;
int
wavepacket_flag
,
sph_flag
;
int
molecule_flag
,
molindex_flag
,
molatom_flag
;
int
q_flag
,
mu_flag
;
int
rmass_flag
,
radius_flag
,
omega_flag
,
torque_flag
,
angmom_flag
;
int
vfrac_flag
,
spin_flag
,
eradius_flag
,
ervel_flag
,
erforce_flag
;
int
cs_flag
,
csforce_flag
,
vforce_flag
,
ervelforce_flag
,
etag_flag
;
int
rho_flag
,
e_flag
,
cv_flag
,
vest_flag
;
// Peridynamics scale factor, used by dump cfg
double
pdscale
;
// molecule templates
// each template can be a set of consecutive molecules
// each with same ID (stored in molecules)
// 1st molecule in template stores nset = # in set
int
nmolecule
;
class
Molecule
**
molecules
;
// extra peratom info in restart file destined for fix & diag
double
**
extra
;
// per-type arrays
double
*
mass
;
int
*
mass_setflag
;
// callback ptrs for atom arrays managed by fix classes
int
nextra_grow
,
nextra_restart
,
nextra_border
;
// # of callbacks of each type
int
*
extra_grow
,
*
extra_restart
,
*
extra_border
;
// index of fix to callback to
int
nextra_grow_max
,
nextra_restart_max
;
// size of callback lists
int
nextra_border_max
;
int
nextra_store
;
int
map_style
;
// style of atom map: 0=none, 1=array, 2=hash
int
map_user
;
// user selected style = same 0,1,2
tagint
map_tag_max
;
// max atom ID that map() is setup for
// spatial sorting of atoms
int
sortfreq
;
// sort atoms every this many steps, 0 = off
bigint
nextsort
;
// next timestep to sort on
// indices of atoms with same ID
int
*
sametag
;
// sametag[I] = next atom with same ID, -1 if no more
// functions
Atom
(
class
LAMMPS
*
);
~
Atom
();
void
settings
(
class
Atom
*
);
void
create_avec
(
const
char
*
,
int
,
char
**
,
char
*
suffix
=
NULL
);
class
AtomVec
*
new_avec
(
const
char
*
,
char
*
,
int
&
);
void
init
();
void
setup
();
class
AtomVec
*
style_match
(
const
char
*
);
void
modify_params
(
int
,
char
**
);
void
tag_check
();
void
tag_extend
();
int
tag_consecutive
();
int
parse_data
(
const
char
*
);
int
count_words
(
const
char
*
);
void
deallocate_topology
();
void
data_atoms
(
int
,
char
*
);
void
data_vels
(
int
,
char
*
);
void
data_bonds
(
int
,
char
*
,
int
*
);
void
data_angles
(
int
,
char
*
,
int
*
);
void
data_dihedrals
(
int
,
char
*
,
int
*
);
void
data_impropers
(
int
,
char
*
,
int
*
);
void
data_bonus
(
int
,
char
*
,
class
AtomVec
*
);
void
data_bodies
(
int
,
char
*
,
class
AtomVecBody
*
);
virtual
void
allocate_type_arrays
();
void
set_mass
(
const
char
*
);
void
set_mass
(
int
,
double
);
void
set_mass
(
int
,
char
**
);
void
set_mass
(
double
*
);
void
check_mass
();
int
radius_consistency
(
int
,
double
&
);
int
shape_consistency
(
int
,
double
&
,
double
&
,
double
&
);
void
add_molecule
(
int
,
char
**
);
int
find_molecule
(
char
*
);
void
add_molecule_atom
(
class
Molecule
*
,
int
,
int
,
tagint
);
void
first_reorder
();
virtual
void
sort
();
void
add_callback
(
int
);
void
delete_callback
(
const
char
*
,
int
);
void
update_callback
(
int
);
int
find_custom
(
char
*
,
int
&
);
int
add_custom
(
char
*
,
int
);
void
remove_custom
(
int
,
int
);
void
*
extract
(
char
*
);
inline
int
*
get_map_array
()
{
return
map_array
;};
inline
int
get_map_size
()
{
return
map_tag_max
+
1
;};
bigint
memory_usage
();
int
memcheck
(
const
char
*
);
// functions for global to local ID mapping
// map lookup function inlined for efficiency
// return -1 if no map defined
inline
int
map
(
tagint
global
)
{
if
(
map_style
==
1
)
return
map_array
[
global
];
else
if
(
map_style
==
2
)
return
map_find_hash
(
global
);
else
return
-
1
;
};
void
map_init
(
int
check
=
1
);
void
map_clear
();
void
map_set
();
void
map_one
(
tagint
,
int
);
int
map_style_set
();
void
map_delete
();
int
map_find_hash
(
tagint
);
protected:
// global to local ID mapping
int
*
map_array
;
// direct map via array that holds map_tag_max
int
map_maxarray
;
// allocated size of map_array (1 larger than this)
struct
HashElem
{
// hashed map
tagint
global
;
// key to search on = global ID
int
local
;
// value associated with key = local index
int
next
;
// next entry in this bucket, -1 if last
};
int
map_nhash
;
// # of entries hash table can hold
int
map_nused
;
// # of actual entries in hash table
int
map_free
;
// ptr to 1st unused entry in hash table
int
map_nbucket
;
// # of hash buckets
int
*
map_bucket
;
// ptr to 1st entry in each bucket
HashElem
*
map_hash
;
// hash table
int
max_same
;
// allocated size of sametag
// spatial sorting of atoms
int
nbins
;
// # of sorting bins
int
nbinx
,
nbiny
,
nbinz
;
// bins in each dimension
int
maxbin
;
// max # of bins
int
maxnext
;
// max size of next,permute
int
*
binhead
;
// 1st atom in each bin
int
*
next
;
// next atom in bin
int
*
permute
;
// permutation vector
double
userbinsize
;
// requested sort bin size
double
bininvx
,
bininvy
,
bininvz
;
// inverse actual bin sizes
double
bboxlo
[
3
],
bboxhi
[
3
];
// bounding box of my sub-domain
int
memlength
;
// allocated size of memstr
char
*
memstr
;
// string of array names already counted
void
setup_sort_bins
();
int
next_prime
(
int
);
};
}
#endif
/* ERROR/WARNING messages:
E: Atom IDs must be used for molecular systems
Atom IDs are used to identify and find partner atoms in bonds.
E: Invalid atom style
The choice of atom style is unknown.
E: Could not find atom_modify first group ID
Self-explanatory.
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: Atom_modify id command after simulation box is defined
The atom_modify id command cannot be used after a read_data,
read_restart, or create_box command.
E: Atom_modify map command after simulation box is defined
The atom_modify map command cannot be used after a read_data,
read_restart, or create_box command.
E: Atom_modify sort and first options cannot be used together
Self-explanatory.
E: Atom ID is negative
Self-explanatory.
E: Atom ID is too big
The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
setting in your Makefile. See Section_start 2.2 of the manual for
more details.
E: Atom ID is zero
Either all atoms IDs must be zero or none of them.
E: Not all atom IDs are 0
Either all atoms IDs must be zero or none of them.
E: New atom IDs exceed maximum allowed ID
See the setting for tagint in the src/lmptype.h file.
E: Incorrect atom format in data file
Number of values per atom line in the data file is not consistent with
the atom style.
E: Incorrect velocity format in data file
Each atom style defines a format for the Velocity section
of the data file. The read-in lines do not match.
E: Invalid atom ID in Velocities section of data file
Atom IDs must be positive integers and within range of defined
atoms.
E: Invalid atom ID in Bonds section of data file
Atom IDs must be positive integers and within range of defined
atoms.
E: Invalid bond type in Bonds section of data file
Bond type must be positive integer and within range of specified bond
types.
E: Invalid atom ID in Angles section of data file
Atom IDs must be positive integers and within range of defined
atoms.
E: Invalid angle type in Angles section of data file
Angle type must be positive integer and within range of specified angle
types.
E: Invalid atom ID in Dihedrals section of data file
Atom IDs must be positive integers and within range of defined
atoms.
E: Invalid dihedral type in Dihedrals section of data file
Dihedral type must be positive integer and within range of specified
dihedral types.
E: Invalid atom ID in Impropers section of data file
Atom IDs must be positive integers and within range of defined
atoms.
E: Invalid improper type in Impropers section of data file
Improper type must be positive integer and within range of specified
improper types.
E: Incorrect bonus data format in data file
See the read_data doc page for a description of how various kinds of
bonus data must be formatted for certain atom styles.
E: Invalid atom ID in Bonus section of data file
Atom IDs must be positive integers and within range of defined
atoms.
E: Invalid atom ID in Bodies section of data file
Atom IDs must be positive integers and within range of defined
atoms.
E: Cannot set mass for this atom style
This atom style does not support mass settings for each atom type.
Instead they are defined on a per-atom basis in the data file.
E: Invalid mass line in data file
Self-explanatory.
E: Invalid type for mass set
Mass command must set a type from 1-N where N is the number of atom
types.
E: Invalid mass value
Self-explanatory.
E: All masses are not set
For atom styles that define masses for each atom type, all masses must
be set in the data file or by the mass command before running a
simulation. They must also be set before using the velocity
command.
E: Reuse of molecule template ID
The template IDs must be unique.
E: Atom sort did not operate correctly
This is an internal LAMMPS error. Please report it to the
developers.
E: Atom sorting has bin size = 0.0
The neighbor cutoff is being used as the bin size, but it is zero.
Thus you must explicitly list a bin size in the atom_modify sort
command or turn off sorting.
E: Too many atom sorting bins
This is likely due to an immense simulation box that has blown up
to a large size.
*/
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