forked from lijiext/lammps
168 lines
6.9 KiB
Plaintext
168 lines
6.9 KiB
Plaintext
.. index:: create_box
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create_box command
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==================
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Syntax
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""""""
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.. parsed-literal::
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create_box N region-ID keyword value ...
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* N = # of atom types to use in this simulation
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* region-ID = ID of region to use as simulation domain
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* zero or more keyword/value pairs may be appended
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* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom*
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.. parsed-literal::
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*bond/types* value = # of bond types
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*angle/types* value = # of angle types
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*dihedral/types* value = # of dihedral types
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*improper/types* value = # of improper types
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*extra/bond/per/atom* value = # of bonds per atom
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*extra/angle/per/atom* value = # of angles per atom
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*extra/dihedral/per/atom* value = # of dihedrals per atom
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*extra/improper/per/atom* value = # of impropers per atom
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*extra/special/per/atom* value = # of special neighbors per atom
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Examples
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""""""""
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.. parsed-literal::
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create_box 2 mybox
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create_box 2 mybox bond/types 2 extra/bond/per/atom 1
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Description
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"""""""""""
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This command creates a simulation box based on the specified region.
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Thus a :doc:`region <region>` command must first be used to define a
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geometric domain. It also partitions the simulation box into a
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regular 3d grid of rectangular bricks, one per processor, based on the
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number of processors being used and the settings of the
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:doc:`processors <processors>` command. The partitioning can later be
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changed by the :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
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The argument N is the number of atom types that will be used in the
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simulation.
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If the region is not of style *prism*\ , 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.
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If the region is of style *prism*\ , 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 :doc:`region prism <region>` command, the
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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). *Xy,xz,yz* can be 0.0 or
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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.
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By default, a *prism* 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
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the distance of the parallel box length. For example, if xlo = 2 and
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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
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-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
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since if the maximum tilt factor is 5 (as in this example), then
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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 :doc:`box tilt <box>`
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command, with a setting of *large*\ ; a setting of *small* is the
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default.
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See :ref:`Section_howto 12 <howto_12>` of the doc pages
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for a geometric description of triclinic boxes, as defined by LAMMPS,
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and how to transform these parameters to and from other commonly used
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triclinic representations.
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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
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by the second dimension of the tilt factor (e.g. y for xy tilt). This
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is so that pairs of atoms interacting across that boundary will have
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one of them shifted by the tilt factor. Periodicity is set by the
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:doc:`boundary <boundary>` command. For example, if the xy tilt factor
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is non-zero, then the y dimension should be periodic. Similarly, the
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z dimension should be periodic if xz or yz is non-zero. LAMMPS does
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not require this periodicity, but you may lose atoms if this is not
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the case.
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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
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be triclinic, even if the tilt factors are initially 0.0. You can
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also change an orthogonal box to a triclinic box or vice versa by
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using the :doc:`change box <change_box>` command with its *ortho* and
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*triclinic* options.
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.. note::
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If the system is non-periodic (in a dimension), then you should
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not make the lo/hi box dimensions (as defined in your
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:doc:`region <region>` 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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:doc:`create_atoms <create_atoms>` 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
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specified box size to layout the 3d grid of processors. A huge
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(mostly empty) box will be sub-optimal for performance when using
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"fixed" boundary conditions (see the :doc:`boundary <boundary>`
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command). When using "shrink-wrap" boundary conditions (see the
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:doc:`boundary <boundary>` 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.
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----------
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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
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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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:doc:`read_data <read_data>` command when it sets up a system.
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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 :doc:`bond potential <bond_style>` 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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:doc:`create_atoms mol <create_atoms>`, :doc:`fix deposit <fix_deposit>`
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or :doc:`fix pour <fix_pour>`.
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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 :doc:`fix deposit <fix_deposit>` command. The create_box command in the
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script uses the bond/types and extra/bond/per/atom keywords to allow
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this. If the added molecule contained more than 1 special bond
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(allowed by default), an extra/special/per/atom keyword would also
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need to be specified.
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----------
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Restrictions
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""""""""""""
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An :doc:`atom_style <atom_style>` and :doc:`region <region>` must have
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been previously defined to use this command.
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Related commands
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""""""""""""""""
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:doc:`read_data <read_data>`, :doc:`create_atoms <create_atoms>`,
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:doc:`region <region>`
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**Default:** none
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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