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@ -86,16 +86,22 @@ Description
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"""""""""""
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This command creates atoms (or molecules) within the simulation box,
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either on a lattice, or at a single specified location, or randomly,
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or on a surface defined by a triangulated mesh. It is an alternative
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to reading in atom coordinates explicitly via a :doc:`read_data
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<read_data>` or :doc:`read_restart <read_restart>` command. A
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simulation box must already exist, which is typically created via the
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:doc:`create_box <create_box>` command. Before using this command, a
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lattice must typically also be defined using the :doc:`lattice
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<lattice>` command, unless you specify the *single* style with units =
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box or the *random* style. For the remainder of this doc page, a
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created atom or molecule is referred to as a "particle".
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either on a lattice, or at random points, or on a surface defined by a
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triangulated mesh. Or it creates a single atom (or molecule) at a
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specified point. It is an alternative to reading in atom coordinates
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explicitly via a :doc:`read_data <read_data>` or :doc:`read_restart
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<read_restart>` command.
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To use this command a simulation box must already exist, which is
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typically created via the :doc:`create_box <create_box>` command.
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Before using this command, a lattice must typically also be defined
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using the :doc:`lattice <lattice>` command, unless you specify the
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*single* or *mesh* style with units = box or the *random* style. To
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create atoms on a lattice for general triclinic boxes, see the
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disucssion below.
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For the remainder of this doc page, a created atom or molecule is
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referred to as a "particle".
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If created particles are individual atoms, they are assigned the
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specified atom *type*, though this can be altered via the *basis*
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@ -126,46 +132,21 @@ periodic boundaries. If this is desired, you should either use the
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*box* style, or tweak the region size to get precisely the particles
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you want.
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----------
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------------------
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WORK on this
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If a general triclinic simulation box is defined ...
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As noted above, general triclinic boxes in LAMMPS allow for arbitrary
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edge vectors **A**, **B**, **C**. The only restrictions are that the
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three vectors be distinct, non-zero, and not co-planar. They must
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also define a right-handed system such that (**A** x **B**) points in
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the direction of **C**. Note that a left-handed system can be
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converted to a right-handed system by simply swapping the order of any
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pair of the **A**, **B**, **C** vectors.
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To create a general triclinic boxes, the region is specified as NULL
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and the next 6 parameters (alo,ahi,blo,bhi,clo,chi) define the three
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edge vectors **A**, **B**, **C** using additional information
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previously defind by the :doc:`lattice <lattice>` command.
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The lattice must be of style *custom* and use its *triclinic/general*
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option. This insures the lattice satisfies the restrictions listed
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above. The *a1, *a2*, *a3* settings of the :doc:`lattice <lattice>`
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If the simulation box is formulated as a general triclinic box defined
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by arbitary edge vectors **A**, **B**, **C**, then the *box* and
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*region* styles will create atoms on a lattice commensurate with those
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edge vectors. See the :doc:`Howto_triclinic <Howto_triclinic>` doc
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page for a detailed explanation of orthogonal, restricted triclinic,
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and general triclinic simulation boxes. As with the :doc:`create_box
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<create_box>` command, the :doc:`lattice <lattice>` command used by
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this command must be of style *custom* and use its *triclinic/general*
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option. The *a1, *a2*, *a3* settings of the :doc:`lattice <lattice>`
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command define the edge vectors of a unit cell of the general
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triclinic lattice. This command uses them to define the three edge
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vectors and origin of the general triclinic box as:
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explain region is applied after conversion to restricted triclinic atom coords
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explain general tri for box and region styles
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must use lattice triclinic/general
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paragraph about DFT motivation
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doc that single, random, mesh operate on restricted triclinic box
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------------------
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triclinic lattice. The :doc:`create_box <create_box>` command creates
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a simulation box which replicates that unit cell along each of the
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**A**, **B**, **C** edge vectors.
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.. note::
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@ -175,19 +156,28 @@ doc that single, random, mesh operate on restricted triclinic box
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input to LAMMPS. However, as explained on the
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:doc:`Howto_triclinic <Howto_triclinic>` doc page, internally,
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LAMMPS only uses restricted triclinic simulation boxes. This means
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the box defined by this command and per-atom information
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(e.g. coordinates, velocities) defined by the :doc:`create_atoms
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<create_atoms>` command are converted from general to restricted
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triclinic form when the two commands are invoked. The
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<Howto_triclinic>` doc page also discusses other LAMMPS commands
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which can input/output general triclinic representations of the
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simulation box and per-atom data.
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the box created by the :doc:`create_box <create_box>` command and
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the atoms with their per-atom information (e.g. coordinates,
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velocities) created by this command are converted (rotated) from
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general to restricted triclinic form when the two commands are
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invoked. The <Howto_triclinic>` doc page also discusses other
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LAMMPS commands which can input/output general triclinic
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representations of the simulation box and per-atom data.
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The *box* style will fill the entire general triclinic box with
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particles on the lattice, as explained above. The *region* style also
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operates as explained above, but the check for particles inside the
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region is performed *after* the particle coordinates have been
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converted to the restricted triclinic box. This means the region must
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also be defined with respect to the restricted triclinic box, not the
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general triclinic box.
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If the simulation box is general triclinic, the *single*, *random*,
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and *mesh* styles described next operate on the box after it has been
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converted to restricted triclinic. So all the settings for those
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styles should be made in that context.
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----------
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For the *single* style, a single particle is added to the system at
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the specified coordinates. This can be useful for debugging purposes
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Steve Plimpton