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2023-09-07 17:21:15 -06:00
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156
doc/src/Howto_triclinic.rst
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@ -24,6 +24,9 @@ for info on how zlo and zhi are defined for 2d simulations.
----------
Triclinic simulation boxes
""""""""""""""""""""""""""
LAMMPS also allows simulations to be performed using triclinic
(non-orthogonal) simulation boxes shaped as a parallelepiped with
triclinic symmetry.
@ -46,55 +49,41 @@ this purpose. It allows dynamic control of the xy, xz, yz tilt
factors as a simulation runs. This is discussed in the next section
on non-equilibrium MD (NEMD) simulations.
Conceptually, the tricliic parallelepiped is defined with an "origin"
Conceptually, a triclinic parallelepiped is defined with an "origin"
at (xlo,ylo,zhi) and 3 edge vectors **A** = (ax,ay,az), **B** =
(bx,by,bz), **C** = (cx,cy,cz) which can now be arbitrary vectors, so
long as they are distinct and are not co-planar.
long as they are non-zero, distinct, and not co-planar. There is no
"right-hand rule" requirement that (**A** x **B**) point in the
direction of **C**.
The 4 commands listed above for defining orthogonal simulation boxes
have triclinic options which allow for specification of the origin and
edge vectors **A**, **B**, **C**. For each command, this can be done
in one of two ways, for what LAMMPS calls a *general* triclinic box,
or a *restricited* triclinic box. A *general* triclinic box is
specified by an origin and 9 parameters (ax,ay,az), (bx,by,bz),
(cx,cy,cz), or 12 parameters in total. A *restricted* triclinic box
also has an origin, but its edge vectors are of the following form:
**A** = (xhi-xlo,0,0), **B** = (xy,yhi-ylo,0), **C** =
(xz,yz,zhi-zlo). So 9 parameters in total.
in one of two ways, for what LAMMPS calls a *general* triclinic box or
a *restricted* triclinic box.
The restricted form of edge vectors means that **A** is along the
x-axis, **B** is in the x-y plane with a y-component in the +y
A *general* triclinic box is specified by an origin and 9 parameters
(ax,ay,az), (bx,by,bz), (cx,cy,cz), or 12 parameters in total. A
*restricted* triclinic box also has an origin, but its edge vectors
are of the following form: **A** = (xhi-xlo,0,0), **B** =
(xy,yhi-ylo,0), **C** = (xz,yz,zhi-zlo). So 9 parameters in total.
The restricted form of edge vectors requires that **A** is along the
x-axis, **B** is in the xy plane with a y-component in the +y
direction, and **C** has a z-component in the +z direction.
*Xy,xz,yz* can be 0.0 or positive or negative values and are called
*Xy,xz,yz* can be zero or positive or negative values and are called
"tilt factors" because they are the amount of displacement applied to
faces of an originally orthogonal box to transform it into a
restricted parallelepiped.
restricted triclinic parallelepiped.
.. note::
Any general triclinic box (i.e. any solid-state crystal basis
vectors) can be rotated/inverted in 3d around its origin to conform
to the definition of a restricted triclinic box. An inversion may
Any general triclinic box (i.e. solid-state crystal basis vectors)
can be rotated/inverted in 3d around its origin to conform to the
LAMMPS definition of a restricted triclinic box. An inversion may
need to be applied to the rotated **C** vector to ensure its final
z-component is in the +z direction.
.. note::
While LAMMPS allows specification of a triclinic simulation box in
either **general** or **restricted** form, internally LAMMPS only
uses restricted triclinic simulation boxes. This is for parallel
efficiency and to formulate partitioning of the simulation box
across processors, neighbor list building, and inter-processor
communication of per-atom data with methods similar to those used
for orthogonal boxes. This means 3 things. (1) Input of a general
triclinic is immediately converted to restricted form.
(2) If output in general triclinic form is requested (e.g. for atom
coordinates in a dump file), then conversion from restricted
triclinic coordinates is done at the time of output. (3) Most
importantly, other LAMMPS commands such as the :doc:`region
<region>` command, that refer to the simulation box geometry,
operate on restricted triclinic boxes, even if a general triclinic
box was specified as input.
z-component is in the +z direction. See the discussion in the next
sub-section about general triclinic simulation boxes in LAMMPS.
Note that for 2d simulations a triclinic simulation box is effectively
a parallelogram; see the :doc:'Howto 2d <Howto_2d>` doc page for
@ -111,26 +100,68 @@ if the xz and/or yz tilt factors are non-zero, then particles which
exit the -z face of the box will be displaced in x by the xz tilt
factor and in y by the yz tilt factor.
For general and restricted triclinic boxes, their **A**, **B**, **C**
edge vector components can be output via
The :doc:`thermo_style custom <thermo_style>` command has keywords for
outputting the parameters that define restricted and general triclinic
simulation boxes. For restricted triclinic, this is (xlo,ylo,zlo),
(xhi,yhi,zhi), and the xy,xz,yz tilt factors. For general triclinic,
this is the (xlo,ylo,zhi) origin and the 9 components of the **A**,
**B**, **C** edge vectors. For both orthogonal and restricted
triclinic boxes, lx/ly/lz refer to the same box sizes, namely lx =
xhi - xlo, etc.
The :doc:`thermo_style custom <thermo_style>` command also has options
for outputting the parameters that define general and restricted
triclinic simulation boxes. For general triclinic, this is the
(xlo,ylo,zhi) origin and the 9 components of the **A**, **B**, **C**
edge vectors. For restricted triclinic, this is (xlo,ylo,zlo),
(xhi,yhi,zhi), and the xy,xz,yz tilt factors. For both orthogonal and
restricted triclinic boxes, lx/ly/lz refer to the same box sizes,
namely lx = xhi - xlo, etc.
The remainder of this doc page explains mathematical transformations
between different ways of representing general and restrictied
triclinic boxes, which may be useful when creating LAMMPS inputs for
triclinic simulations or interpreting outputs. How LAMMPS uses tilt
factors for restricted triclinic simulation boxes is also discussed.
The remainder of this doc page explains (a) how LAMMPS operates with
general triclinic simulation boxes, (b) mathematical transformations
between general and restricted triclinic boxes (which may be useful
when creating LAMMPS inputs or interpreting outputs for triclinic
simulations, and (c) how LAMMPS uses tilt factors for restricted
triclinic simulation boxes.
----------
General triclinic simulation boxes in LAMMPS
""""""""""""""""""""""""""""""""""""""""""""
LAMMPS allows specification of general triclinic simulation boxes as a
convenience for users who may be converting data from solid-state
crystallograhic representations for input to LAMMPS.
However, internally LAMMPS only uses restricted triclinic simulation
boxes. This is for parallel efficiency and to formulate partitioning
of the simulation box across processors, neighbor list building, and
inter-processor communication of per-atom data with methods similar to
those used for orthogonal boxes.
This means 3 things which it is important to understand:
* Input of a general triclinic system is immediately converted to a
restricted triclinic system.
* If output of general triclinic data is requested (e.g. for atom
coordinates in a dump file), then conversion from restricted
triclinic data is done at the time of output.
* Most importantly, other LAMMPS commands such as the :doc:`boundary
<boundary>` command or :doc:`region <region>` command, that refer to
the simulation box geometry, operate on restricted triclinic boxes,
even if a general triclinic box was defined initially.
This is the list of commands that have specific general triclinic
options:
create_box
create_atoms
lattice
read_data
write_data
dump atoms, dump custom
dump_modify
thermo_style
thermo_modify
read_restart, write_restart
----------
Transformation from general to restricted triclinic boxes
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Let **A**,\ **B**,\ **C** be the edge vectors of a general triclinic
simulation box. Assume that **A** x **B** . **C** > 0. The
equivalent LAMMPS **a**,\ **b**,\ **c** for a restricted triclinic box
@ -163,12 +194,12 @@ inversion. This can be achieved by interchanging two of the **A**,
**B**, **C** vectors or by changing the sign of one of them.
For consistency, the same rotation/inversion applied to the triclinic
box edge vectors also typically needs to be applied to atom positions,
velocities, and other vector quantities. This can be conveniently
achieved by first converting to fractional coordinates in the general
triclinic coordinates and then converting to coordinates in the
resetricted triclinic basis. The transformation is given by the
following equation:
box edge vectors can also be applied to atom positions, velocities,
and other vector quantities. This can be conveniently achieved by
first converting to fractional coordinates in the general triclinic
coordinates and then converting to coordinates in the resetricted
triclinic basis. The transformation is given by the following
equation:
.. math::
@ -185,6 +216,9 @@ resulting vector in the restricted triclinic basis.
----------
Crystallographic general triclinic representation of a simulation box
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
General triclinic crystal structures are often defined using three
lattice constants *a*, *b*, and *c*, and three angles :math:`\alpha`,
:math:`\beta`, and :math:`\gamma`. Note that in this nomenclature, the
@ -222,6 +256,9 @@ The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and
----------
Output of restricted and general triclinic boxes in a dump file
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
As discussed on the :doc:`dump <dump>` command doc page, when the BOX
BOUNDS for a snapshot is written to a dump file for a resticted
triclinic box, an orthogonal bounding box which encloses the triclinic
@ -254,6 +291,9 @@ xlo_bound - MIN(0.0,xy,xz,xy+xz).
----------
Periodicity and tilt factors for triclinic simulation boxes
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
There is no requirement that a triclinic box be periodic in any
dimension, though as explained above it typically should be in y or z
if you wish enforce a shift in coordinates due to periodic boundary
@ -288,7 +328,7 @@ Similarly, both xz and yz should be between -(xhi-xlo)/2 and
+(yhi-ylo)/2. Note that these are not limitations, since if the
maximum tilt factor is 5 (as in this example), then simulations boxes
and atom configurations with tilt = ..., -15, -5, 5, 15, 25, ... are
geometrically all equivalent.
all geometrically equivalent.
If the box tilt exceeds this limit during a dynamics run (e.g. due to
the :doc:`fix deform <fix_deform>` command), then by default the box

293
doc/src/read_data.rst
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@ -122,16 +122,16 @@ keyword must be used.
.. note::
The simulation box size (xlo to xhi, ylo to yhi, zlo to zhi) in
the new data file will be merged with the existing simulation box to
create a large enough box in each dimension to contain both the
existing and new atoms. Each box dimension never shrinks due to this
merge operation, it only stays the same or grows. Care must be used if
you are growing the existing simulation box in a periodic dimension.
If there are existing atoms with bonds that straddle that periodic
boundary, then the atoms may become far apart if the box size grows.
This will separate the atoms in the bond, which can lead to "lost"
bond atoms or bad dynamics.
The simulation box size in the new data file will be merged with
the existing simulation box to create a large enough box in each
dimension to contain both the existing and new atoms. Each box
dimension never shrinks due to this merge operation, it only stays
the same or grows. Care must be used if you are growing the
existing simulation box in a periodic dimension. If there are
existing atoms with bonds that straddle that periodic boundary,
then the atoms may become far apart if the box size grows. This
will separate the atoms in the bond, which can lead to "lost" bond
atoms or bad dynamics.
The three choices for the *add* argument affect how the atom IDs and
molecule IDs of atoms in the data file are treated. If *append* is
@ -288,13 +288,16 @@ Format of the header of a data file
"""""""""""""""""""""""""""""""""""
These are the recognized header keywords. Header lines can come in
any order. The value(s) are read from the beginning of the line.
any order. Each keyword takes a single value unless noted in this
list. The value(s) are read from the beginning of the line.
Thus the keyword *atoms* should be in a line like "1000 atoms"; the
keyword *ylo yhi* should be in a line like "-10.0 10.0 ylo yhi"; the
keyword *xy xz yz* should be in a line like "0.0 5.0 6.0 xy xz yz".
All these settings have a default value of 0, except the lo/hi box
size defaults are -0.5 and 0.5. A line need only appear if the value
is different than the default.
All these settings have a default value of 0, except for the
simulation box size settings; their defaults are explained below. A
keyword line need only appear if its value is different than the
default.
* *atoms* = # of atoms in system
* *bonds* = # of bonds in system
@ -315,73 +318,150 @@ is different than the default.
* *lines* = # of line segments in system
* *triangles* = # of triangles in system
* *bodies* = # of bodies in system
* *xlo xhi* = simulation box boundaries in x dimension
* *ylo yhi* = simulation box boundaries in y dimension
* *zlo zhi* = simulation box boundaries in z dimension
* *xy xz yz* = simulation box tilt factors for triclinic system
* *xlo xhi* = simulation box boundaries in x dimension (2 values)
* *ylo yhi* = simulation box boundaries in y dimension (2 values)
* *zlo zhi* = simulation box boundaries in z dimension (2 values)
* *xy xz yz* = simulation box tilt factors for triclinic system (3 values)
* *avec* = first edge vector of a general triclinic simulation box (3 values)
* *bvec* = second edge vector of a general triclinic simulation box (3 values)
* *cvec* = third edge vector of a general triclinic simulation box (3 values)
* *abc origin* = origin on a general triclinic simulation box (3 values)
The initial simulation box size is determined by the lo/hi settings.
In any dimension, the system may be periodic or non-periodic; see the
:doc:`boundary <boundary>` command. When the simulation box is created
it is also partitioned into a regular 3d grid of rectangular bricks,
one per processor, based on the number of processors being used and
the settings of the :doc:`processors <processors>` command. The
partitioning can later be changed by the :doc:`balance <balance>` or
:doc:`fix balance <fix_balance>` commands.
----------
If the *xy xz yz* line does not appear, LAMMPS will set up an
axis-aligned (orthogonal) simulation box. If the line does appear,
LAMMPS creates a non-orthogonal simulation domain shaped as a
parallelepiped with triclinic symmetry. The parallelepiped has its
"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
(xz,yz,zhi-zlo). *Xy,xz,yz* can be 0.0 or positive or negative values
and are called "tilt factors" because they are the amount of
displacement applied to faces of an originally orthogonal box to
transform it into the parallelepiped.
Header specification of the simulation box size and shape
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The tilt factors (xy,xz,yz) should not skew the box more than half the
distance of the corresponding parallel box length. For example, if
:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x`
box length is 10 and the :math:`xy` tilt factor must be between
:math:`-5` and :math:`5`. Similarly, both :math:`xz` and :math:`yz`
must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and
:math:`+(y_\text{hi}-y_\text{lo})/2`. Note that this is not a
limitation, since if the maximum tilt factor is 5 (as in this example),
then configurations with tilt :math:`= \dots, -15`, :math:`-5`,
:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically
equivalent. Simulations with large tilt factors will run inefficiently,
since they require more ghost atoms and thus more communication. With
very large tilt factors, LAMMPS will eventually produce incorrect
trajectories and stop with errors due to lost atoms or similar.
The final 8 keywords in the list of header keywords are for simulation
boxes of 3 kinds which LAMMPS supports:
See the :doc:`Howto triclinic <Howto_triclinic>` page for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
triclinic representations.
* orthogonal box = faces are perpendicular to the xyz coordinate axes
* restricted triclinic box = a parallelepiped defined by 3 edge vectors oriented in a constrained manner
* general triclinic box = a parallelepiped defined by 3 arbitrary edge vectors
When a triclinic system is used, the simulation domain should normally
be periodic in the dimension that the tilt is applied to, which is
given by the second dimension of the tilt factor (e.g. y for xy tilt).
This is so that pairs of atoms interacting across that boundary will
have one of them shifted by the tilt factor. Periodicity is set by
the :doc:`boundary <boundary>` command. For example, if the xy tilt
factor is non-zero, then the y dimension should be periodic.
Similarly, the z dimension should be periodic if xz or yz is non-zero.
LAMMPS does not require this periodicity, but you may lose atoms if
this is not the case.
For restricted and general triclinic boxes, see the
:doc:`Howto_triclinic <Howto_triclinic>` doc page for a fuller
description than is given here.
Also note that if your simulation will tilt the box, e.g. via the
:doc:`fix deform <fix_deform>` command, the simulation box must be setup
to be triclinic, even if the tilt factors are initially 0.0. You can
also change an orthogonal box to a triclinic box or vice versa by using
the :doc:`change box <change_box>` command with its *ortho* and
*triclinic* options.
The units of the values for all 8 keywords in in distance units; see
the :doc:`units <units>` command for details.
For 2d simulations, the *zlo zhi* values should be set to bound the z
coords for atoms that appear in the file; the default of -0.5 0.5 is
valid if all z coords are 0.0. For 2d triclinic simulations, the xz
and yz tilt factors must be 0.0.
For all 3 kinds of simulation boxes, the system may be periodic or
non-periodic in any dimension; see the :doc:`boundary <boundary>`
command. When the simulation box is created by the read_data command,
it is also partitioned into a regular 3d grid of subdomains, one per
processor, based on the number of processors being used and the
settings of the :doc:`processors <processors>` command. For each kind
of simulatino box the subdomains have the same shape as the simulation
box, i.e. smaller orthogonal bricks for orthogonal boxes, smaller
tilted bricks for triclinic boxes. The partitioning can later be
changed by the :doc:`balance <balance>` or :doc:`fix balance
<fix_balance>` commands.
For an orthogonal box, only the *xlo xhi*, *ylo yhi*, *zlo zhi*
keywords are used. They define the extent of the simulation box in
each dimension. The origin (lower left corner) of the orthogonal box
is at (xlo,ylo,zlo). The default values for these 3 keywords are -0.5
and 0.5 for each lo/hi pair. For a 2d simulation, the zlo and zhi
values must straddle zero. The default zlo/zhi values do this, so
that keyword is not needed in 2d.
For a restricted triclinic box, the *xy xz yz* keyword is used in
addition to the *xlo xhi*, *ylo yhi*, *zlo zhi* keywords. The three
*xy,xz,yz* values can be 0.0 or positive or negative, and are called
"tilt factors" because they are the amount of displacement applied to
faces of an orthogonal box to transform it into a restricted triclinic
parallelepiped.
The :doc:`Howto_triclinic <Howto_triclinic>` doc page discusses the
tilt factors in detail and explains that the resulting edge vectors of
the restricted triclinic box are:
* **A** = (xhi-xlo,0,0)
* **B** = (xy,yhi-ylo,0)
* **C** = (xz,yz,zhi-zlo)
This restricted form of edge vectors means that **A** is along the
x-axis, **B** is in the xy plane with a y-component in the +y
direction, and **C** has a z-component in the +z direction. The
origin (lower left corner) of the restricted triclinic box is at
(xlo,ylo,zlo).
For a 2d simulation, the zlo and zhi values must straddle zero. The
default zlo/zhi values do this, so that keyword is not needed in 2d.
The xz and yz values must also be zero in 2d. The shape of the 2d
restricted triclinic simulation box is effectively a parallelogram.
.. note::
When a restricted triclinic box is used, the simulation domain
should normally be periodic in any dimensions that tilt is applied
to, which is given by the second dimension of the tilt factor
(e.g. y for xy tilt). This is so that pairs of atoms interacting
across that boundary will have one of them shifted by the tilt
factor. Periodicity is set by the :doc:`boundary <boundary>`
command. For example, if the xy tilt factor is non-zero, then the
y dimension should be periodic. Similarly, the z dimension should
be periodic if xz or yz is non-zero. LAMMPS does not require this
periodicity, but you may lose atoms if this is not the case.
.. note::
Normally, the specified tilt factors (xy,xz,yz) should not skew the
simulation box by more than half the distance of the corresponding
parallel box length for computational efficiency. For example, if
:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the
:math:`x` box length is 10 and the :math:`xy` tilt factor should be
between :math:`-5` and :math:`5`. LAMMPS will issue a warning if
this is not the case. See the :doc:`Howto_triclinic
<Howto_triclinic>` doc page for more details.
.. note::
If a simulation box is initially orthogonal, but will tilt during a
simulation, e.g. via the :doc:`fix deform <fix_deform>` command,
then the box should be defined as restricted triclinic with all 3
tilt factors = 0.0. Alternatively, the :doc:`change box
<change_box>` command can be used to convert an orthogonal box to a
restricted triclinic box.
For a general triclinic box, the *avec*, *bvec*, *cvec*, and *abc
origin* keywords are used. The *xlo xhi*, *ylo yhi*, *zlo zhi*, and
*xy xz yz* keywords are not used. The first 3 keywords define the 3
edge vectors **A**, **B**, **C** of a general triclinic box. They can
be arbitrary vectors so long as they are distinct, non-zero, and not
co-planar. There is no "right-hand rule" requirement that (**A** x
**B**) point in the direction of **C**. The origin of the box (origin
of the 3 edge vectors) is set by the *abc origin* keyword.
The default values for these 4 keywords are as follows:
* avec = (1,0,0)
* bvec = (0,1,0)
* cvec = (0,0,1)
* *abc origin = (0,0,0) for 3d, (0,0,-0.5) for 2d
For 2d simulations, *cvec* = (0,0,1) is required, and the 3rd value of
*abc origin* must be -0.5. These are the default values, so the
*cvec* keyword is not needed in 2d.
.. note::
LAMMPS allows specification of general triclinic simulation boxes
as a convenience for users who may be converting data from
solid-state crystallograhic representations for input to LAMMPS.
However, as explained on the :doc:`Howto_triclinic
<Howto_triclinic>` doc page, internally LAMMPS only uses restricted
triclinic simulation boxes. This means the box and atom
information (coordinates, velocities) in the data file are
converted from general to restricted triclinic form as soon as the
file is read. The :doc:`Howto_triclinic <Howto_triclinic>` doc
page also discusses other LAMMPS commands which can input/output
general triclinic representations of the simulation box and
per-atom data.
The following explanations apply to all 3 kinds of simulation boxes:
orthogonal, restricted triclinic, and general triclinic.
If the system is periodic (in a dimension), then atom coordinates can
be outside the bounds (in that dimension); they will be remapped (in a
@ -406,7 +486,6 @@ individually back into the principal unit cell in that direction. This
operation is equivalent to the behavior of the :doc:`change_box command
<change_box>` when used to change periodicity.
If those atoms with non-zero image flags are involved in bonded
interactions, this reset can lead to undesired changes, when the image
flag values differ between the atoms, i.e. the bonded interaction
@ -440,25 +519,32 @@ needed, so that the image flag would be zero.
to lose atoms when LAMMPS shrink-wraps the box around the atoms. The
read_data command will generate an error in this case.
----------
Meaning of other header keywords
""""""""""""""""""""""""""""""""
The "extra bond per atom" setting (angle, dihedral, improper) is only
needed if new bonds (angles, dihedrals, impropers) will be added to
the system when a simulation runs, e.g. by using the :doc:`fix bond/create <fix_bond_create>` command. Using this header flag
is deprecated; please use the *extra/bond/per/atom* keyword (and
the system when a simulation runs, e.g. by using the :doc:`fix
bond/create <fix_bond_create>` command. Using this header flag is
deprecated; please use the *extra/bond/per/atom* keyword (and
correspondingly for angles, dihedrals and impropers) in the read_data
command instead. Either will pre-allocate space in LAMMPS data
structures for storing the new bonds (angles, dihedrals, impropers).
The "extra special per atom" setting is typically only needed if new
bonds/angles/etc will be added to the system, e.g. by using the :doc:`fix bond/create <fix_bond_create>` command. Or if entire new molecules
will be added to the system, e.g. by using the
:doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>` commands,
which will have more special 1-2,1-3,1-4 neighbors than any other
molecules defined in the data file. Using this header flag is
deprecated; please use the *extra/special/per/atom* keyword instead.
Using this setting will pre-allocate space in the LAMMPS data
structures for storing these neighbors. See the
:doc:`special_bonds <special_bonds>` and :doc:`molecule <molecule>` doc
pages for more discussion of 1-2,1-3,1-4 neighbors.
bonds/angles/etc will be added to the system, e.g. by using the
:doc:`fix bond/create <fix_bond_create>` command. Or if entire new
molecules will be added to the system, e.g. by using the :doc:`fix
deposit <fix_deposit>` or :doc:`fix pour <fix_pour>` commands, which
will have more special 1-2,1-3,1-4 neighbors than any other molecules
defined in the data file. Using this header flag is deprecated;
please use the *extra/special/per/atom* keyword instead. Using this
setting will pre-allocate space in the LAMMPS data structures for
storing these neighbors. See the :doc:`special_bonds <special_bonds>`
and :doc:`molecule <molecule>` doc pages for more discussion of
1-2,1-3,1-4 neighbors.
.. note::
@ -470,13 +556,13 @@ pages for more discussion of 1-2,1-3,1-4 neighbors.
If they appear in later data files, they are ignored.
The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
only used with :doc:`atom_style ellipsoid or line or tri or body <atom_style>` and specify how many of the atoms are
finite-size ellipsoids or lines or triangles or bodies; the remainder
are point particles. See the discussion of ellipsoidflag and the
*Ellipsoids* section below. See the discussion of lineflag and the
*Lines* section below. See the discussion of triangleflag and the
*Triangles* section below. See the discussion of bodyflag and the
*Bodies* section below.
only used with :doc:`atom_style ellipsoid or line or tri or body
<atom_style>` and specify how many of the atoms are finite-size
ellipsoids or lines or triangles or bodies; the remainder are point
particles. See the discussion of ellipsoidflag and the *Ellipsoids*
section below. See the discussion of lineflag and the *Lines* section
below. See the discussion of triangleflag and the *Triangles* section
below. See the discussion of bodyflag and the *Bodies* section below.
.. note::
@ -680,6 +766,16 @@ appended to it, which indicate which image of a periodic simulation
box the atom is in. These may be important to include for some kinds
of analysis.
.. note::
For orthogonal and restricted and general triclinic simulation
boxes, the atom coordinates (x,y,z) listed in this section should
be inside the corresponding simulation box. For general triclinic
boxes that means the box defined by the 3 edge vectors specified by
the *avec*, *bvec*, *cvec* header keywords. See the discussion
above in the header section about how atom coordinates outside the
simulation box are (or are not) remapped to be inside the box.
.. list-table::
* - angle
@ -773,8 +869,9 @@ The per-atom values have these meanings and units, listed alphabetically:
The units for these quantities depend on the unit style; see the
:doc:`units <units>` command for details.
For 2d simulations specify z as 0.0, or a value within the *zlo zhi*
setting in the data file header.
For 2d simulations, z must be specified as 0.0. If the data file is
created by another program, then z values for a 2d simulation can be
within epsilon of 0.0, and LAMMPS will force them to zero.
The atom-ID is used to identify the atom throughout the simulation and
in dump files. Normally, it is a unique value from 1 to Natoms for
@ -1513,8 +1610,8 @@ fields:
atom-ID vx vy vz ervel wx wy wz
Translational velocities can also be set by the
:doc:`velocity <velocity>` command in the input script.
Translational velocities can also be (re)set by the :doc:`velocity
<velocity>` command in the input script.
----------