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< title > create_box command — LAMMPS 15 May 2015 version documentation< / title >
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< li > create_box command< / li >
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< span id = "index-0" > < / span > < h1 > create_box command< a class = "headerlink" href = "#create-box-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > create_box N region-ID keyword value ...
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > N = # of atom types to use in this simulation< / li >
< li > region-ID = ID of region to use as simulation domain< / li >
< li > zero or more keyword/value pairs may be appended< / li >
< li > keyword = < em > bond/types< / em > or < em > angle/types< / em > or < em > dihedral/types< / em > or < em > improper/types< / em > or < em > extra/bond/per/atom< / em > or < em > extra/angle/per/atom< / em > or < em > extra/dihedral/per/atom< / em > or < em > extra/improper/per/atom< / em > < / li >
< / ul >
< pre class = "literal-block" >
< em > bond/types< / em > value = # of bond types
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< em > angle/types< / em > value = # of angle types
< em > dihedral/types< / em > value = # of dihedral types
< em > improper/types< / em > value = # of improper types
< em > extra/bond/per/atom< / em > value = # of bonds per atom
< em > extra/angle/per/atom< / em > value = # of angles per atom
< em > extra/dihedral/per/atom< / em > value = # of dihedrals per atom
< em > extra/improper/per/atom< / em > value = # of impropers per atom
< em > extra/special/per/atom< / em > value = # of special neighbors per atom
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< / pre >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > create_box 2 mybox
create_box 2 mybox bond/types 2 extra/bond/per/atom 1
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > This command creates a simulation box based on the specified region.
Thus a < a class = "reference internal" href = "region.html" > < em > region< / em > < / a > command must first be used to define a
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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
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< a class = "reference internal" href = "processors.html" > < em > processors< / em > < / a > command. The partitioning can later be
changed by the < a class = "reference internal" href = "balance.html" > < em > balance< / em > < / a > or < a class = "reference internal" href = "fix_balance.html" > < em > fix balance< / em > < / 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 < em > prism< / em > , then LAMMPS encloses the region
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(block, sphere, etc) with an axis-aligned orthogonal bounding box
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which becomes the simulation domain.< / p >
< p > If the region is of style < em > prism< / em > , LAMMPS creates a non-orthogonal
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simulation domain shaped as a parallelepiped with triclinic symmetry.
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As defined by the < a class = "reference internal" href = "region.html" > < em > region prism< / em > < / a > command, the
parallelepiped has its “ origin” at (xlo,ylo,zlo) and is defined by 3
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edge vectors starting from the origin given by A = (xhi-xlo,0,0); B =
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(xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). < em > Xy,xz,yz< / em > can be 0.0 or
positive or negative values and are called “ tilt factors” because they
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are the amount of displacement applied to faces of an originally
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orthogonal box to transform it into the parallelipiped.< / p >
< p > By default, a < em > prism< / em > region used with the create_box command must
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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
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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
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geometrically equivalent. If you wish to define a box with tilt
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factors that exceed these limits, you can use the < a class = "reference internal" href = "box.html" > < em > box tilt< / em > < / a >
command, with a setting of < em > large< / em > ; a setting of < em > small< / em > is the
default.< / p >
< p > See < a class = "reference internal" href = "Section_howto.html#howto-12" > < span > Section_howto 12< / span > < / a > of the doc pages
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for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
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triclinic representations.< / p >
< p > When a prism region is used, the simulation domain should normally be
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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
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< a class = "reference internal" href = "boundary.html" > < em > boundary< / em > < / a > command. For example, if the xy tilt factor
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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
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the case.< / p >
< p > Also note that if your simulation will tilt the box, e.g. via the < a class = "reference internal" href = "fix_deform.html" > < em > fix deform< / em > < / a > command, the simulation box must be setup to
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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
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using the < a class = "reference internal" href = "change_box.html" > < em > change box< / em > < / a > command with its < em > ortho< / em > and
< em > triclinic< / em > options.< / p >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > If the system is non-periodic (in a dimension), then
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you should not make the lo/hi box dimensions (as defined in your
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< a class = "reference internal" href = "region.html" > < em > region< / em > < / a > command) radically smaller/larger than the extent
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of the atoms you eventually plan to create, e.g. via the
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< a class = "reference internal" href = "create_atoms.html" > < em > create_atoms< / em > < / a > command. For example, if your atoms
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extend from 0 to 50, you should not specify the box bounds as -10000
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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
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“ fixed” boundary conditions (see the < a class = "reference internal" href = "boundary.html" > < em > boundary< / em > < / a >
command). When using “ shrink-wrap” boundary conditions (see the
< a class = "reference internal" href = "boundary.html" > < em > boundary< / em > < / a > command), a huge (mostly empty) box may cause
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a parallel simulation to lose atoms the first time that LAMMPS
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shrink-wraps the box around the atoms.< / p >
< / div >
< hr class = "docutils" / >
< p > The optional keywords can be used to create a system that allows for
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bond (angle, dihedral, improper) interactions, or for molecules with
special 1-2,1-3,1-4 neighbors to be added later. These optional
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keywords serve the same purpose as the analogous keywords that can be
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used in a data file which are recognized by the
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< a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > command when it sets up a system.< / p >
< p > Note that if these keywords are not used, then the create_box command
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creates an atomic (non-molecular) simulation that does not allow bonds
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between pairs of atoms to be defined, or a < a class = "reference internal" href = "bond_style.html" > < em > bond potential< / em > < / a > to be specified, or for molecules with
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special neighbors to be added to the system by commands such as
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< a class = "reference internal" href = "create_atoms.html" > < em > create_atoms mol< / em > < / a > , < a class = "reference internal" href = "fix_deposit.html" > < em > fix deposit< / em > < / a >
or < a class = "reference internal" href = "fix_pour.html" > < em > fix pour< / em > < / a > .< / p >
< p > As an example, see the examples/deposit/in.deposit.molecule script,
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which deposits molecules onto a substrate. Initially there are no
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molecules in the system, but they are added later by the < a class = "reference internal" href = "fix_deposit.html" > < em > fix deposit< / em > < / a > command. The create_box command in the
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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
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need to be specified.< / p >
< / div >
< hr class = "docutils" / >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > An < a class = "reference internal" href = "atom_style.html" > < em > atom_style< / em > < / a > and < a class = "reference internal" href = "region.html" > < em > region< / em > < / a > must have
been previously defined to use this command.< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > , < a class = "reference internal" href = "create_atoms.html" > < em > create_atoms< / em > < / a > ,
< a class = "reference internal" href = "region.html" > < em > region< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
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