forked from lijiext/lammps
152 lines
6.8 KiB
HTML
152 lines
6.8 KiB
HTML
<HTML>
|
|
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
<H3>create_box command
|
|
</H3>
|
|
<P><B>Syntax:</B>
|
|
</P>
|
|
<PRE>create_box N region-ID keyword value ...
|
|
</PRE>
|
|
<UL><LI>N = # of atom types to use in this simulation
|
|
|
|
<LI>region-ID = ID of region to use as simulation domain
|
|
|
|
<LI>zero or more keyword/value pairs may be appended
|
|
|
|
<LI>keyword = <I>bond/types</I> or <I>angle/types</I> or <I>dihedral/types</I> or <I>improper/types</I> or <I>extra/bond/per/atom</I> or <I>extra/angle/per/atom</I> or <I>extra/dihedral/per/atom</I> or <I>extra/improper/per/atom</I>
|
|
|
|
<PRE> <I>bond/types</I> value = # of bond types
|
|
<I>angle/types</I> value = # of angle types
|
|
<I>dihedral/types</I> value = # of dihedral types
|
|
<I>improper/types</I> value = # of improper types
|
|
<I>extra/bond/per/atom</I> value = # of bonds per atom
|
|
<I>extra/angle/per/atom</I> value = # of angles per atom
|
|
<I>extra/dihedral/per/atom</I> value = # of dihedrals per atom
|
|
<I>extra/improper/per/atom</I> value = # of impropers per atom
|
|
<I>extra/special/per/atom</I> value = # of special neighbors per atom
|
|
</PRE>
|
|
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>create_box 2 mybox
|
|
create_box 2 mybox bond/types 2 extra/bond/per/atom 1
|
|
</PRE>
|
|
<P><B>Description:</B>
|
|
</P>
|
|
<P>This command creates a simulation box based on the specified region.
|
|
Thus a <A HREF = "region.html">region</A> command must first be used to define a
|
|
geometric domain. It also partitions the simulation box into a
|
|
regular 3d grid of rectangular bricks, one per processor, based on the
|
|
number of processors being used and the settings of the
|
|
<A HREF = "processors.html">processors</A> command. The partitioning can later be
|
|
changed by the <A HREF = "balance.html">balance</A> or <A HREF = "fix_balance.html">fix
|
|
balance</A> commands.
|
|
</P>
|
|
<P>The argument N is the number of atom types that will be used in the
|
|
simulation.
|
|
</P>
|
|
<P>If the region is not of style <I>prism</I>, then LAMMPS encloses the region
|
|
(block, sphere, etc) with an axis-aligned orthogonal bounding box
|
|
which becomes the simulation domain.
|
|
</P>
|
|
<P>If the region is of style <I>prism</I>, LAMMPS creates a non-orthogonal
|
|
simulation domain shaped as a parallelepiped with triclinic symmetry.
|
|
As defined by the <A HREF = "region.html">region prism</A> command, 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). <I>Xy,xz,yz</I> 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 parallelipiped.
|
|
</P>
|
|
<P>A <I>prism</I> region used with the create_box command must have tilt
|
|
factors (xy,xz,yz) that do not skew the box more than half the
|
|
distance of the parallel box length. For example, if xlo = 2 and xhi
|
|
= 12, then the x box length is 10 and the xy tilt factor must be
|
|
between -5 and 5. Similarly, both xz and yz must be between
|
|
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
|
|
since if the maximum tilt factor is 5 (as in this example), then
|
|
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
|
|
geometrically equivalent.
|
|
</P>
|
|
<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
|
|
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.
|
|
</P>
|
|
<P>When a prism region is used, the simulation domain must be periodic in
|
|
any dimensions with a non-zero tilt factor, as defined by the
|
|
<A HREF = "boundary.html">boundary</A> command. I.e. if the xy tilt factor is
|
|
non-zero, then both the x and y dimensions must be periodic.
|
|
Similarly, x and z must be periodic if xz is non-zero and y and z must
|
|
be periodic if yz is non-zero. Also note that if your simulation will
|
|
tilt the box, e.g. via the <A HREF = "fix_deform.html">fix deform</A> command, the
|
|
simulation box must be defined as triclinic, even if the tilt factors
|
|
are initially 0.0.
|
|
</P>
|
|
<P>IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
|
|
you should not make the lo/hi box dimensions (as defined in your
|
|
<A HREF = "region.html">region</A> command) radically smaller/larger than the extent
|
|
of the atoms you eventually plan to create, e.g. via the
|
|
<A HREF = "create_atoms.html">create_atoms</A> command. For example, if your atoms
|
|
extend from 0 to 50, you should not specify the box bounds as -10000
|
|
and 10000. This is because as described above, LAMMPS uses the
|
|
specified box size to layout the 3d grid of processors. A huge
|
|
(mostly empty) box will be sub-optimal for performance when using
|
|
"fixed" boundary conditions (see the <A HREF = "boundary.html">boundary</A>
|
|
command). When using "shrink-wrap" boundary conditions (see the
|
|
<A HREF = "boundary.html">boundary</A> command), a huge (mostly empty) box may cause
|
|
a parallel simulation to lose atoms the first time that LAMMPS
|
|
shrink-wraps the box around the atoms.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The optional keywords can be used to create a system that allows for
|
|
bond (angle, dihedral, improper) interactions, or for molecules with
|
|
special 1-2,1-3,1-4 neighbors to be added later. These optional
|
|
keywords serve the same purpose as the analagous keywords that can be
|
|
used in a data file which are recognized by the
|
|
<A HREF = "read_data.html">read_data</A> command when it sets up a system.
|
|
</P>
|
|
<P>Note that if these keywords are not used, then the create_box command
|
|
creates an atomic (non-molecular) simulation that does not allow bonds
|
|
between pairs of atoms to be defined, or a <A HREF = "bond_style.html">bond
|
|
potential</A> to be specified, or for molecules with
|
|
special neighbors to be added to the system by commands such as
|
|
<A HREF = "create_atoms.html">create_atoms mol</A>, <A HREF = "fix_deposit.html">fix deposit</A>
|
|
or <A HREF = "fix_pour.html">fix pour</A>.
|
|
</P>
|
|
<P>As an example, see the examples/deposit/in.deposit.molecule script,
|
|
which deposits molecules onto a substrate. Initially there are no
|
|
molecules in the system, but they are added later by the <A HREF = "fix_deposit.html">fix
|
|
deposit</A> command. The create_box command in the
|
|
script uses the bond/types and extra/bond/per/atom keywords to allow
|
|
this. If the added molecule contained more than 1 special bond
|
|
(allowed by default), an extra/special/per/atom keyword would also
|
|
need to be specified.
|
|
</P>
|
|
<HR>
|
|
|
|
<P><B>Restrictions:</B>
|
|
</P>
|
|
<P>An <A HREF = "atom_style.html">atom_style</A> and <A HREF = "region.html">region</A> must have
|
|
been previously defined to use this command.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "read_data.html">read_data</A>, <A HREF = "create_atoms.html">create_atoms</A>,
|
|
<A HREF = "region.html">region</A>
|
|
</P>
|
|
<P><B>Default:</B> none
|
|
</P>
|
|
</HTML>
|