correct/improve formatting
This commit is contained in:
Axel Kohlmeyer
@ -155,18 +155,18 @@ compute huge energies and forces, leading to bad dynamics. There are
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several strategies to avoid this problem:
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* Use the :doc:`delete_atoms overlap <delete_atoms>` command after
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create_atoms. For example, this strategy can be used to overlay and
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surround a large protein molecule with a volume of water molecules,
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then delete water molecules that overlap with the protein atoms.
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create_atoms. For example, this strategy can be used to overlay and
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surround a large protein molecule with a volume of water molecules,
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then delete water molecules that overlap with the protein atoms.
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* For the *random* style, use the optional *overlap* keyword to avoid
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overlaps when each new particle is created.
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overlaps when each new particle is created.
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* Before running dynamics on an overlapped system, perform an
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:doc:`energy minimization <minimize>`. Or run initial dynamics with
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:doc:`pair_style soft <pair_soft>` or with :doc:`fix nve/limit
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<fix_nve_limit>` to un-overlap the particles, before running normal
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dynamics.
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:doc:`energy minimization <minimize>`. Or run initial dynamics with
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:doc:`pair_style soft <pair_soft>` or with :doc:`fix nve/limit
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<fix_nve_limit>` to un-overlap the particles, before running normal
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dynamics.
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.. note::
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@ -268,6 +268,11 @@ directly. The *set* keyword is used to identify the names of these
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other variables, one variable for the x-coordinate of a created atom,
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one for y, and one for z.
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.. figure:: img/sinusoid.jpg
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:figwidth: 50%
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:align: right
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:target: _images/sinusoid.jpg
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When an atom is created, its x,y,z coordinates become the values for
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any *set* variable that is defined. The *var* variable is then
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evaluated. If the returned value is 0.0, the atom is not created. If
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@ -281,28 +286,26 @@ the sinusoid would appear to be "smoother". Also note the use of the
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"xlat" and "ylat" :doc:`thermo_style <thermo_style>` keywords which
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converts lattice spacings to distance.
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.. only:: html
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(Click on the image for a larger version)
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.. code-block:: LAMMPS
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dimension 2
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variable x equal 100
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variable y equal 25
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lattice hex 0.8442
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region box block 0 $x 0 $y -0.5 0.5
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create_box 1 box
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dimension 2
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variable x equal 100
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variable y equal 25
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lattice hex 0.8442
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region box block 0 $x 0 $y -0.5 0.5
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create_box 1 box
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variable xx internal 0.0
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variable yy internal 0.0
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variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
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create_atoms 1 box var v set x xx set y yy
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write_dump all atom sinusoid.lammpstrj
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variable xx internal 0.0
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variable yy internal 0.0
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variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
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create_atoms 1 box var v set x xx set y yy
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write_dump all atom sinusoid.lammpstrj
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.. image:: img/sinusoid.jpg
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:scale: 50%
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:align: center
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.. raw:: html
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Click on the image for a larger version.
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-----
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The *rotate* keyword allows specification of the orientation
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at which molecules are inserted. The axis of rotation is
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@ -345,17 +348,22 @@ new particles into a dense system using the *overlap* keyword),
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setting the *maxtry* keyword to a large value may result in this
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command running for a long time.
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.. figure:: img/overlap.png
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:figwidth: 30%
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:align: right
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:target: _images/overlap.png
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Here is an example for the *random* style using these commands
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.. code-block:: LAMMPS
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units lj
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dimension 2
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region box block 0 50 0 50 -0.5 0.5
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create_box 1 box
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create_atoms 1 random 2000 13487 NULL overlap 1.0 maxtry 50
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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units lj
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dimension 2
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region box block 0 50 0 50 -0.5 0.5
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create_box 1 box
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create_atoms 1 random 2000 13487 NULL overlap 1.0 maxtry 50
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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to produce a system as shown in the image with 1520 particles (out of
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2000 requested) that are moderately dense and which have no overlaps
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@ -363,13 +371,11 @@ sufficient to prevent the LJ pair_style from running properly (because
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the overlap criterion = 1.0). The create_atoms command ran for 0.3 s
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on a single CPU core.
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.. image:: img/overlap.png
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:scale: 50%
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:align: center
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.. only:: html
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.. raw:: html
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(Click on the image for a larger version)
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Click on the image for a larger version.
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-----
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The *units* keyword determines the meaning of the distance units used
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to specify the coordinates of the one particle created by the *single*
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