forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9360 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
332b6b6814
commit
2ed241a0cd
|
|
@ -22,11 +22,25 @@ different machines and different numbers of processors are included in
|
|||
the directories to compare your answers to. E.g. a log file like
|
||||
log.crack.foo.P means it ran on P processors of machine "foo".
|
||||
</P>
|
||||
<P>The dump files produced by the example runs can be animated using the
|
||||
xmovie tool described in the <A HREF = "Section_tools.html">Additional Tools</A>
|
||||
section of the LAMMPS documentation. Animations of many of these
|
||||
examples can be viewed on the Movies section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
|
||||
Site</A>.
|
||||
<P>For examples that use input data files, many of them were produced by
|
||||
<A HREF = "http://pizza.sandia.gov">Pizza.py</A> or setup tools described in the
|
||||
<A HREF = "Section_tools.html">Additional Tools</A> section of the LAMMPS
|
||||
documentation and provided with the LAMMPS distribution.
|
||||
</P>
|
||||
<P>If you uncomment the <A HREF = "dump.html">dump</A> command in the input script, a
|
||||
text dump file will be produced, which can be animated by various
|
||||
<A HREF = "http://lammps.sandia.gov/viz.html">visualization programs</A>. It can
|
||||
also be animated using the xmovie tool described in the <A HREF = "Section_tools.html">Additional
|
||||
Tools</A> section of the LAMMPS documentation.
|
||||
</P>
|
||||
<P>If you uncomment the <A HREF = "dump.html">dump image</A> command in the input
|
||||
script, and assuming you have built LAMMPS with a JPG library, JPG
|
||||
snapshot images will be produced when the simulation runs. They can
|
||||
be quickly post-processed into a movie using commands described on the
|
||||
<A HREF = "dump_image.html">dump image</A> doc page.
|
||||
</P>
|
||||
<P>Animations of many of these examples can be viewed on the Movies
|
||||
section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
|
||||
</P>
|
||||
<P>These are the sample problems in the examples sub-directories:
|
||||
</P>
|
||||
|
|
@ -77,8 +91,22 @@ lmp_linux < in.indent # run the problem
|
|||
</P>
|
||||
<PRE>../../tools/xmovie/xmovie -scale dump.indent
|
||||
</PRE>
|
||||
<P>If you uncomment the <A HREF = "dump_image.html">dump image</A> line(s) in the input
|
||||
script a series of JPG images will be produced by the run. These can
|
||||
be viewed individually or turned into a movie or animated by tools
|
||||
like ImageMagick or QuickTime or various Windows-based tools. See the
|
||||
<A HREF = "dump_image.html">dump image</A> doc page for more details. E.g. this
|
||||
Imagemagick command would create a GIF file suitable for viewing in a
|
||||
browser.
|
||||
</P>
|
||||
<PRE>% convert -loop 1 *.jpg foo.gif
|
||||
</PRE>
|
||||
<HR>
|
||||
|
||||
<P>There is also a COUPLE directory with examples of how to use LAMMPS as
|
||||
a library, either by itself or in tandem with another code or library.
|
||||
See the COUPLE/README file to get started.
|
||||
</P>
|
||||
<P>There is also an ELASTIC directory with an example script for
|
||||
computing elastic constants, using a zero temperature Si example. See
|
||||
the in.elastic file for more info.
|
||||
|
|
|
|||
|
|
@ -19,11 +19,25 @@ different machines and different numbers of processors are included in
|
|||
the directories to compare your answers to. E.g. a log file like
|
||||
log.crack.foo.P means it ran on P processors of machine "foo".
|
||||
|
||||
The dump files produced by the example runs can be animated using the
|
||||
xmovie tool described in the "Additional Tools"_Section_tools.html
|
||||
section of the LAMMPS documentation. Animations of many of these
|
||||
examples can be viewed on the Movies section of the "LAMMPS WWW
|
||||
Site"_lws.
|
||||
For examples that use input data files, many of them were produced by
|
||||
"Pizza.py"_http://pizza.sandia.gov or setup tools described in the
|
||||
"Additional Tools"_Section_tools.html section of the LAMMPS
|
||||
documentation and provided with the LAMMPS distribution.
|
||||
|
||||
If you uncomment the "dump"_dump.html command in the input script, a
|
||||
text dump file will be produced, which can be animated by various
|
||||
"visualization programs"_http://lammps.sandia.gov/viz.html. It can
|
||||
also be animated using the xmovie tool described in the "Additional
|
||||
Tools"_Section_tools.html section of the LAMMPS documentation.
|
||||
|
||||
If you uncomment the "dump image"_dump.html command in the input
|
||||
script, and assuming you have built LAMMPS with a JPG library, JPG
|
||||
snapshot images will be produced when the simulation runs. They can
|
||||
be quickly post-processed into a movie using commands described on the
|
||||
"dump image"_dump_image.html doc page.
|
||||
|
||||
Animations of many of these examples can be viewed on the Movies
|
||||
section of the "LAMMPS WWW Site"_lws.
|
||||
|
||||
These are the sample problems in the examples sub-directories:
|
||||
|
||||
|
|
@ -72,8 +86,22 @@ Running the simulation produces the files {dump.indent} and
|
|||
|
||||
../../tools/xmovie/xmovie -scale dump.indent :pre
|
||||
|
||||
If you uncomment the "dump image"_dump_image.html line(s) in the input
|
||||
script a series of JPG images will be produced by the run. These can
|
||||
be viewed individually or turned into a movie or animated by tools
|
||||
like ImageMagick or QuickTime or various Windows-based tools. See the
|
||||
"dump image"_dump_image.html doc page for more details. E.g. this
|
||||
Imagemagick command would create a GIF file suitable for viewing in a
|
||||
browser.
|
||||
|
||||
% convert -loop 1 *.jpg foo.gif :pre
|
||||
|
||||
:line
|
||||
|
||||
There is also a COUPLE directory with examples of how to use LAMMPS as
|
||||
a library, either by itself or in tandem with another code or library.
|
||||
See the COUPLE/README file to get started.
|
||||
|
||||
There is also an ELASTIC directory with an example script for
|
||||
computing elastic constants, using a zero temperature Si example. See
|
||||
the in.elastic file for more info.
|
||||
|
|
|
|||
|
|
@ -18,8 +18,10 @@
|
|||
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>body</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>line</I> or <I>meso</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>tri</I> or <I>hybrid</I>
|
||||
</UL>
|
||||
<PRE> args = none for any style except <I>body</I> and <I>hybrid</I>
|
||||
<I>body</I> args = bstyle
|
||||
<I>body</I> args = bstyle Nmin Nmax
|
||||
bstyle = style of body particles
|
||||
Nmin = minimum # of sub-particles in any body
|
||||
Nmax = maximum # of sub-particles in any body
|
||||
<I>hybrid</I> args = list of one or more sub-styles, each with their args
|
||||
</PRE>
|
||||
<P><B>Examples:</B>
|
||||
|
|
@ -126,7 +128,7 @@ points of the triangle).
|
|||
attributes defined by the "style" of the bodies, which is specified by
|
||||
the <I>bstyle</I> argument. Body particles can represent complex entities,
|
||||
such as surface meshes of discrete points, collections of
|
||||
sub-particles, deformable objects, etc.
|
||||
sub-particles, deformable objects, etc.
|
||||
</P>
|
||||
<P>The <A HREF = "body.html">body</A> doc page descibes the body styles LAMMPS
|
||||
currently supports, and provides more details as to the kind of body
|
||||
|
|
@ -134,6 +136,10 @@ particles they represent. For all styles, each body particle stores
|
|||
moments of inertia and a quaternion 4-vector, so that its orientation
|
||||
and position can be time integrated due to forces and torques.
|
||||
</P>
|
||||
<P>Note that there may be additional arguments required along with the
|
||||
<I>bstyle</I> specification, in the atom_style body command. These
|
||||
arguments are described in the <A HREF = "body.html">body</A> doc page.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>Typically, simulations require only a single (non-hybrid) atom style.
|
||||
|
|
|
|||
|
|
@ -16,8 +16,10 @@ style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
|
|||
{electron} or {ellipsoid} or {full} or {line} or {meso} or \
|
||||
{molecular} or {peri} or {sphere} or {tri} or {hybrid} :ul
|
||||
args = none for any style except {body} and {hybrid}
|
||||
{body} args = bstyle
|
||||
{body} args = bstyle Nmin Nmax
|
||||
bstyle = style of body particles
|
||||
Nmin = minimum # of sub-particles in any body
|
||||
Nmax = maximum # of sub-particles in any body
|
||||
{hybrid} args = list of one or more sub-styles, each with their args :pre
|
||||
|
||||
[Examples:]
|
||||
|
|
@ -122,7 +124,7 @@ For the {body} style, the particles are arbitrary bodies with internal
|
|||
attributes defined by the "style" of the bodies, which is specified by
|
||||
the {bstyle} argument. Body particles can represent complex entities,
|
||||
such as surface meshes of discrete points, collections of
|
||||
sub-particles, deformable objects, etc.
|
||||
sub-particles, deformable objects, etc.
|
||||
|
||||
The "body"_body.html doc page descibes the body styles LAMMPS
|
||||
currently supports, and provides more details as to the kind of body
|
||||
|
|
@ -130,6 +132,10 @@ particles they represent. For all styles, each body particle stores
|
|||
moments of inertia and a quaternion 4-vector, so that its orientation
|
||||
and position can be time integrated due to forces and torques.
|
||||
|
||||
Note that there may be additional arguments required along with the
|
||||
{bstyle} specification, in the atom_style body command. These
|
||||
arguments are described in the "body"_body.html doc page.
|
||||
|
||||
:line
|
||||
|
||||
Typically, simulations require only a single (non-hybrid) atom style.
|
||||
|
|
|
|||
166
doc/body.html
166
doc/body.html
|
|
@ -9,8 +9,16 @@
|
|||
|
||||
<HR>
|
||||
|
||||
<H3>atom_style command
|
||||
<H3>body particles
|
||||
</H3>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>This doc page is not about a specific LAMMPS input script command, but
|
||||
about body particles,
|
||||
</P>
|
||||
<P>which are a specific kind of
|
||||
<A HREF = "atom_style.html">atom_style</A> supported by LAMMPS
|
||||
</P>
|
||||
<P>These are the body styles that LAMMPS currently supports. The name in
|
||||
the first column is used as the <I>bstyle</I> argument for atom_style body:
|
||||
</P>
|
||||
|
|
@ -26,6 +34,15 @@ style.
|
|||
such as surface meshes of discrete points, collections of
|
||||
sub-particles, deformable objects, etc.
|
||||
</P>
|
||||
<P>By contrast, the <A HREF = "fix_rigid.html">fix rigid</A> command constructs rigid
|
||||
bodies out of multiple particles. The particles can be point
|
||||
particles or finite-size particles (spheres, ellipsoids, line
|
||||
segments, triangles). The particles in each rigid body interact with
|
||||
each other in the usual pairwise fashion via whatever pair style is
|
||||
defined. The sum of these interactions determine the total force and
|
||||
torque on each rigid body, which the <A HREF = "fix_rigid.html">fix rigid</A>
|
||||
command then time integrates.
|
||||
</P>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>atom_style style args
|
||||
|
|
@ -46,151 +63,4 @@ atom_style body nparticle 2 10
|
|||
atom_style hybrid charge bond
|
||||
atom_style hybrid charge body nparticle 2 5
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define what style of atoms to use in a simulation. This determines
|
||||
what attributes are associated with the atoms. This command must be
|
||||
used before a simulation is setup via a <A HREF = "read_data.html">read_data</A>,
|
||||
<A HREF = "read_restart.html">read_restart</A>, or <A HREF = "create_box.html">create_box</A>
|
||||
command.
|
||||
</P>
|
||||
<P>Once a style is assigned, it cannot be changed, so use a style general
|
||||
enough to encompass all attributes. E.g. with style <I>bond</I>, angular
|
||||
terms cannot be used or added later to the model. It is OK to use a
|
||||
style more general than needed, though it may be slightly inefficient.
|
||||
</P>
|
||||
<P>The choice of style affects what quantities are stored by each atom,
|
||||
what quantities are communicated between processors to enable forces
|
||||
to be computed, and what quantities are listed in the data file read
|
||||
by the <A HREF = "read_data.html">read_data</A> command.
|
||||
</P>
|
||||
<P>These are the additional attributes of each style and the typical
|
||||
kinds of physical systems they are used to model. All styles store
|
||||
coordinates, velocities, atom IDs and types. See the
|
||||
<A HREF = "read_data.html">read_data</A>, <A HREF = "create_atoms.html">create_atoms</A>, and
|
||||
<A HREF = "set.html">set</A> commands for info on how to set these various
|
||||
quantities.
|
||||
</P>
|
||||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<TR><TD ><I>angle</I> </TD><TD > bonds and angles </TD><TD > bead-spring polymers with stiffness </TD></TR>
|
||||
<TR><TD ><I>atomic</I> </TD><TD > only the default values </TD><TD > coarse-grain liquids, solids, metals </TD></TR>
|
||||
<TR><TD ><I>body</I> </TD><TD > mass, inertia moments, quaternion, angular momentum </TD><TD > arbitrary bodies </TD></TR>
|
||||
<TR><TD ><I>bond</I> </TD><TD > bonds </TD><TD > bead-spring polymers </TD></TR>
|
||||
<TR><TD ><I>charge</I> </TD><TD > charge </TD><TD > atomic system with charges </TD></TR>
|
||||
<TR><TD ><I>dipole</I> </TD><TD > charge and dipole moment </TD><TD > system with dipolar particles </TD></TR>
|
||||
<TR><TD ><I>electron</I> </TD><TD > charge and spin and eradius </TD><TD > electronic force field </TD></TR>
|
||||
<TR><TD ><I>ellipsoid</I> </TD><TD > shape, quaternion, angular momentum </TD><TD > extended aspherical particles </TD></TR>
|
||||
<TR><TD ><I>full</I> </TD><TD > molecular + charge </TD><TD > bio-molecules </TD></TR>
|
||||
<TR><TD ><I>line</I> </TD><TD > end points, angular velocity </TD><TD > rigid bodies </TD></TR>
|
||||
<TR><TD ><I>meso</I> </TD><TD > rho, e, cv </TD><TD > SPH particles </TD></TR>
|
||||
<TR><TD ><I>molecular</I> </TD><TD > bonds, angles, dihedrals, impropers </TD><TD > uncharged molecules </TD></TR>
|
||||
<TR><TD ><I>peri</I> </TD><TD > mass, volume </TD><TD > mesocopic Peridynamic models </TD></TR>
|
||||
<TR><TD ><I>sphere</I> </TD><TD > diameter, mass, angular velocity </TD><TD > granular models </TD></TR>
|
||||
<TR><TD ><I>tri</I> </TD><TD > corner points, angular momentum </TD><TD > rigid bodies </TD></TR>
|
||||
<TR><TD ><I>wavepacket</I> </TD><TD > charge, spin, eradius, etag, cs_re, cs_im </TD><TD > AWPMD
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<P>All of the styles define point particles, except the <I>sphere</I>,
|
||||
<I>ellipsoid</I>, <I>electron</I>, <I>peri</I>, <I>wavepacket</I>, <I>line</I>, <I>tri</I>, and
|
||||
<I>body</I> styles, which define finite-size particles.
|
||||
</P>
|
||||
<P>All of the styles assign mass to particles on a per-type basis, using
|
||||
the <A HREF = "mass.html">mass</A> command, except for the finite-size particle
|
||||
styles. They assign mass to individual particles on a per-particle
|
||||
basis.
|
||||
</P>
|
||||
<P>For the <I>sphere</I> style, the particles are spheres and each stores a
|
||||
per-particle diameter and mass. If the diameter > 0.0, the particle
|
||||
is a finite-size sphere. If the diameter = 0.0, it is a point
|
||||
particle.
|
||||
</P>
|
||||
<P>For the <I>ellipsoid</I> style, the particles are ellipsoids and each
|
||||
stores a flag which indicates whether it is a finite-size ellipsoid or
|
||||
a point particle. If it is an ellipsoid, it also stores a shape
|
||||
vector with the 3 diamters of the ellipsoid and a quaternion 4-vector
|
||||
with its orientation.
|
||||
</P>
|
||||
<P>For the <I>electron</I> style, the particles representing electrons are 3d
|
||||
Gaussians with a specified position and bandwidth or uncertainty in
|
||||
position, which is represented by the eradius = electron size.
|
||||
</P>
|
||||
<P>For the <I>peri</I> style, the particles are spherical and each stores a
|
||||
per-particle mass and volume.
|
||||
</P>
|
||||
<P>The <I>meso</I> style is for smoothed particle hydrodynamics (SPH)
|
||||
particles which store a density (rho), energy (e), and heat capacity
|
||||
(cv).
|
||||
</P>
|
||||
<P>The <I>wavepacket</I> style is similar to <I>electron</I>, but the electrons may
|
||||
consist of several Gaussian wave packets, summed up with coefficients
|
||||
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
|
||||
particle in LAMMPS, wave packets belonging to the same electron must
|
||||
have identical <I>etag</I> values.
|
||||
</P>
|
||||
<P>For the <I>line</I> style, the particles are idealized line segments and
|
||||
each stores a per-particle mass and length and orientation (i.e. the
|
||||
end points of the line segment).
|
||||
</P>
|
||||
<P>For the <I>tri</I> style, the particles are planar triangles and each
|
||||
stores a per-particle mass and size and orientation (i.e. the corner
|
||||
points of the triangle).
|
||||
</P>
|
||||
<P>For the <I>body</I> style, the particles are arbitrary bodies with internal
|
||||
attributes defined by the "style" of the bodies, which is specified by
|
||||
the <I>bstyle</I> argument. Each body particle stores moments of inertia
|
||||
and a quaternion 4-vector, so that its orientation and position can be
|
||||
time integrated due to forces and torques. This atom style enables
|
||||
LAMMPS to work with particles that represent complex entities, such as
|
||||
surface meshes of discrete points, collections of sub-particles,
|
||||
deformable objects, etc. Of course, the interactions between pairs of
|
||||
bodies will need to be encoded in an appropriate pair style.
|
||||
</P>
|
||||
<P>The <A HREF = "body.html">body</A> doc page descibes the body styles LAMMPS
|
||||
supports, and provides more details.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>Typically, simulations require only a single (non-hybrid) atom style.
|
||||
If some atoms in the simulation do not have all the properties defined
|
||||
by a particular style, use the simplest style that defines all the
|
||||
needed properties by any atom. For example, if some atoms in a
|
||||
simulation are charged, but others are not, use the <I>charge</I> style.
|
||||
If some atoms have bonds, but others do not, use the <I>bond</I> style.
|
||||
</P>
|
||||
<P>The only scenario where the <I>hybrid</I> style is needed is if there is no
|
||||
single style which defines all needed properties of all atoms. For
|
||||
example, if you want dipolar particles which will rotate due to
|
||||
torque, you would need to use "atom_style hybrid sphere dipole". When
|
||||
a hybrid style is used, atoms store and communicate the union of all
|
||||
quantities implied by the individual styles.
|
||||
</P>
|
||||
<P>LAMMPS can be extended with new atom styles as well as new body
|
||||
styles; see <A HREF = "Section_modify.html">this section</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This command cannot be used after the simulation box is defined by a
|
||||
<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
|
||||
</P>
|
||||
<P>The <I>angle</I>, <I>bond</I>, <I>full</I>, and <I>molecular</I> styles are part of the
|
||||
MOLECULAR package. The <I>line</I>, <I>tri</I>, and <I>body</I> styles are part of
|
||||
the ASPHERE pacakge. The <I>dipole</I> style is part of the DIPOLE
|
||||
package. The <I>peri</I> style is part of the PERI package for
|
||||
Peridynamics. The <I>electron</I> style is part of the USER-EFF package
|
||||
for <A HREF = "pair_eff.html">electronic force fields</A>. The <I>meso</I> style is part
|
||||
of the USER-SPH package for smoothed particle hydrodyanmics (SPH).
|
||||
See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
|
||||
LAMMPS. The <I>wavepacket</I> style is part of the USER-AWPMD package for
|
||||
the <A HREF = "pair_awpmd.html">antisymmetrized wave packet MD method</A>. They are
|
||||
only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "read_data.html">read_data</A>, <A HREF = "pair_style.html">pair_style</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>atom_style atomic
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
|
|||
165
doc/body.txt
165
doc/body.txt
|
|
@ -6,8 +6,16 @@
|
|||
|
||||
:line
|
||||
|
||||
atom_style command :h3
|
||||
body particles :h3
|
||||
|
||||
[Description:]
|
||||
|
||||
This doc page is not about a specific LAMMPS input script command, but
|
||||
about body particles,
|
||||
|
||||
|
||||
which are a specific kind of
|
||||
"atom_style"_atom_style.html supported by LAMMPS
|
||||
|
||||
|
||||
|
||||
|
|
@ -25,6 +33,17 @@ such as surface meshes of discrete points, collections of
|
|||
sub-particles, deformable objects, etc.
|
||||
|
||||
|
||||
|
||||
|
||||
By contrast, the "fix rigid"_fix_rigid.html command constructs rigid
|
||||
bodies out of multiple particles. The particles can be point
|
||||
particles or finite-size particles (spheres, ellipsoids, line
|
||||
segments, triangles). The particles in each rigid body interact with
|
||||
each other in the usual pairwise fashion via whatever pair style is
|
||||
defined. The sum of these interactions determine the total force and
|
||||
torque on each rigid body, which the "fix rigid"_fix_rigid.html
|
||||
command then time integrates.
|
||||
|
||||
[Syntax:]
|
||||
|
||||
atom_style style args :pre
|
||||
|
|
@ -46,147 +65,3 @@ atom_style body nparticle 2 10
|
|||
atom_style hybrid charge bond
|
||||
atom_style hybrid charge body nparticle 2 5 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define what style of atoms to use in a simulation. This determines
|
||||
what attributes are associated with the atoms. This command must be
|
||||
used before a simulation is setup via a "read_data"_read_data.html,
|
||||
"read_restart"_read_restart.html, or "create_box"_create_box.html
|
||||
command.
|
||||
|
||||
Once a style is assigned, it cannot be changed, so use a style general
|
||||
enough to encompass all attributes. E.g. with style {bond}, angular
|
||||
terms cannot be used or added later to the model. It is OK to use a
|
||||
style more general than needed, though it may be slightly inefficient.
|
||||
|
||||
The choice of style affects what quantities are stored by each atom,
|
||||
what quantities are communicated between processors to enable forces
|
||||
to be computed, and what quantities are listed in the data file read
|
||||
by the "read_data"_read_data.html command.
|
||||
|
||||
These are the additional attributes of each style and the typical
|
||||
kinds of physical systems they are used to model. All styles store
|
||||
coordinates, velocities, atom IDs and types. See the
|
||||
"read_data"_read_data.html, "create_atoms"_create_atoms.html, and
|
||||
"set"_set.html commands for info on how to set these various
|
||||
quantities.
|
||||
|
||||
{angle} | bonds and angles | bead-spring polymers with stiffness |
|
||||
{atomic} | only the default values | coarse-grain liquids, solids, metals |
|
||||
{body} | mass, inertia moments, quaternion, angular momentum | arbitrary bodies |
|
||||
{bond} | bonds | bead-spring polymers |
|
||||
{charge} | charge | atomic system with charges |
|
||||
{dipole} | charge and dipole moment | system with dipolar particles |
|
||||
{electron} | charge and spin and eradius | electronic force field |
|
||||
{ellipsoid} | shape, quaternion, angular momentum | extended aspherical particles |
|
||||
{full} | molecular + charge | bio-molecules |
|
||||
{line} | end points, angular velocity | rigid bodies |
|
||||
{meso} | rho, e, cv | SPH particles |
|
||||
{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
|
||||
{peri} | mass, volume | mesocopic Peridynamic models |
|
||||
{sphere} | diameter, mass, angular velocity | granular models |
|
||||
{tri} | corner points, angular momentum | rigid bodies |
|
||||
{wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
|
||||
|
||||
All of the styles define point particles, except the {sphere},
|
||||
{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and
|
||||
{body} styles, which define finite-size particles.
|
||||
|
||||
All of the styles assign mass to particles on a per-type basis, using
|
||||
the "mass"_mass.html command, except for the finite-size particle
|
||||
styles. They assign mass to individual particles on a per-particle
|
||||
basis.
|
||||
|
||||
For the {sphere} style, the particles are spheres and each stores a
|
||||
per-particle diameter and mass. If the diameter > 0.0, the particle
|
||||
is a finite-size sphere. If the diameter = 0.0, it is a point
|
||||
particle.
|
||||
|
||||
For the {ellipsoid} style, the particles are ellipsoids and each
|
||||
stores a flag which indicates whether it is a finite-size ellipsoid or
|
||||
a point particle. If it is an ellipsoid, it also stores a shape
|
||||
vector with the 3 diamters of the ellipsoid and a quaternion 4-vector
|
||||
with its orientation.
|
||||
|
||||
For the {electron} style, the particles representing electrons are 3d
|
||||
Gaussians with a specified position and bandwidth or uncertainty in
|
||||
position, which is represented by the eradius = electron size.
|
||||
|
||||
For the {peri} style, the particles are spherical and each stores a
|
||||
per-particle mass and volume.
|
||||
|
||||
The {meso} style is for smoothed particle hydrodynamics (SPH)
|
||||
particles which store a density (rho), energy (e), and heat capacity
|
||||
(cv).
|
||||
|
||||
The {wavepacket} style is similar to {electron}, but the electrons may
|
||||
consist of several Gaussian wave packets, summed up with coefficients
|
||||
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
|
||||
particle in LAMMPS, wave packets belonging to the same electron must
|
||||
have identical {etag} values.
|
||||
|
||||
For the {line} style, the particles are idealized line segments and
|
||||
each stores a per-particle mass and length and orientation (i.e. the
|
||||
end points of the line segment).
|
||||
|
||||
For the {tri} style, the particles are planar triangles and each
|
||||
stores a per-particle mass and size and orientation (i.e. the corner
|
||||
points of the triangle).
|
||||
|
||||
For the {body} style, the particles are arbitrary bodies with internal
|
||||
attributes defined by the "style" of the bodies, which is specified by
|
||||
the {bstyle} argument. Each body particle stores moments of inertia
|
||||
and a quaternion 4-vector, so that its orientation and position can be
|
||||
time integrated due to forces and torques. This atom style enables
|
||||
LAMMPS to work with particles that represent complex entities, such as
|
||||
surface meshes of discrete points, collections of sub-particles,
|
||||
deformable objects, etc. Of course, the interactions between pairs of
|
||||
bodies will need to be encoded in an appropriate pair style.
|
||||
|
||||
The "body"_body.html doc page descibes the body styles LAMMPS
|
||||
supports, and provides more details.
|
||||
|
||||
:line
|
||||
|
||||
Typically, simulations require only a single (non-hybrid) atom style.
|
||||
If some atoms in the simulation do not have all the properties defined
|
||||
by a particular style, use the simplest style that defines all the
|
||||
needed properties by any atom. For example, if some atoms in a
|
||||
simulation are charged, but others are not, use the {charge} style.
|
||||
If some atoms have bonds, but others do not, use the {bond} style.
|
||||
|
||||
The only scenario where the {hybrid} style is needed is if there is no
|
||||
single style which defines all needed properties of all atoms. For
|
||||
example, if you want dipolar particles which will rotate due to
|
||||
torque, you would need to use "atom_style hybrid sphere dipole". When
|
||||
a hybrid style is used, atoms store and communicate the union of all
|
||||
quantities implied by the individual styles.
|
||||
|
||||
LAMMPS can be extended with new atom styles as well as new body
|
||||
styles; see "this section"_Section_modify.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command cannot be used after the simulation box is defined by a
|
||||
"read_data"_read_data.html or "create_box"_create_box.html command.
|
||||
|
||||
The {angle}, {bond}, {full}, and {molecular} styles are part of the
|
||||
MOLECULAR package. The {line}, {tri}, and {body} styles are part of
|
||||
the ASPHERE pacakge. The {dipole} style is part of the DIPOLE
|
||||
package. The {peri} style is part of the PERI package for
|
||||
Peridynamics. The {electron} style is part of the USER-EFF package
|
||||
for "electronic force fields"_pair_eff.html. The {meso} style is part
|
||||
of the USER-SPH package for smoothed particle hydrodyanmics (SPH).
|
||||
See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
|
||||
LAMMPS. The {wavepacket} style is part of the USER-AWPMD package for
|
||||
the "antisymmetrized wave packet MD method"_pair_awpmd.html. They are
|
||||
only enabled if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"read_data"_read_data.html, "pair_style"_pair_style.html
|
||||
|
||||
[Default:]
|
||||
|
||||
atom_style atomic
|
||||
|
|
|
|||
Loading…
Reference in New Issue