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<title>change_box command — LAMMPS 15 May 2015 version documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<div class="section" id="change-box-command">
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<span id="index-0"></span><h1>change_box command<a class="headerlink" href="#change-box-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>change_box group-ID parameter args ... keyword args ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>group-ID = ID of group of atoms to (optionally) displace</li>
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<li>one or more parameter/arg pairs may be appended</li>
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</ul>
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<pre class="literal-block">
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parameter = <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>xz</em> or <em>yz</em> or <em>boundary</em> or <em>ortho</em> or <em>triclinic</em> or <em>set</em> or <em>remap</em>
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<em>x</em>, <em>y</em>, <em>z</em> args = style value(s)
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style = <em>final</em> or <em>delta</em> or <em>scale</em> or <em>volume</em>
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<em>final</em> values = lo hi
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lo hi = box boundaries after displacement (distance units)
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<em>delta</em> values = dlo dhi
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dlo dhi = change in box boundaries after displacement (distance units)
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<em>scale</em> values = factor
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factor = multiplicative factor for change in box length after displacement
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<em>volume</em> value = none = adjust this dim to preserve volume of system
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<em>xy</em>, <em>xz</em>, <em>yz</em> args = style value
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style = <em>final</em> or <em>delta</em>
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<em>final</em> value = tilt
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tilt = tilt factor after displacement (distance units)
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<em>delta</em> value = dtilt
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dtilt = change in tilt factor after displacement (distance units)
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<em>boundary</em> args = x y z
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x,y,z = <em>p</em> or <em>s</em> or <em>f</em> or <em>m</em>, one or two letters
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<em>p</em> is periodic
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<em>f</em> is non-periodic and fixed
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<em>s</em> is non-periodic and shrink-wrapped
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<em>m</em> is non-periodic and shrink-wrapped with a minimum value
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<em>ortho</em> args = none = change box to orthogonal
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<em>triclinic</em> args = none = change box to triclinic
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<em>set</em> args = none = store state of current box
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<em>remap</em> args = none = remap atom coords from last saved state to current box
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</pre>
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<ul class="simple">
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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>units</em></li>
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</ul>
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<pre class="literal-block">
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<em>units</em> value = <em>lattice</em> or <em>box</em>
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lattice = distances are defined in lattice units
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box = distances are defined in simulation box units
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
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change_box all x scale 1.1 y volume z volume remap
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Change the volume and/or shape and/or boundary conditions for the
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simulation box. Orthogonal simulation boxes have 3 adjustable size
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parameters (x,y,z). Triclinic (non-orthogonal) simulation boxes have
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6 adjustable size/shape parameters (x,y,z,xy,xz,yz). Any or all of
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them can be adjusted independently by this command. Thus it can be
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used to expand or contract a box, or to apply a shear strain to a
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non-orthogonal box. It can also be used to change the boundary
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conditions for the simulation box, similar to the
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<a class="reference internal" href="boundary.html"><em>boundary</em></a> command.</p>
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<p>The size and shape of the initial simulation box are specified by the
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<a class="reference internal" href="create_box.html"><em>create_box</em></a> or <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
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<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command used to setup the simulation.
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The size and shape may be altered by subsequent runs, e.g. by use of
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the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> or <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> commands.
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The <a class="reference internal" href="create_box.html"><em>create_box</em></a>, <a class="reference internal" href="read_data.html"><em>read data</em></a>, and
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<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands also determine whether the
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simulation box is orthogonal or triclinic and their doc pages explain
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the meaning of the xy,xz,yz tilt factors.</p>
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<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,
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and how to transform these parameters to and from other commonly used
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triclinic representations.</p>
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<p>The keywords used in this command are applied sequentially to the
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simulation box and the atoms in it, in the order specified.</p>
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<p>Before the sequence of keywords are invoked, the current box
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size/shape is stored, in case a <em>remap</em> keyword is used to map the
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atom coordinates from a previously stored box size/shape to the
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current one.</p>
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<p>After all the keywords have been processed, any shrink-wrap boundary
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conditions are invoked (see the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command)
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which may change simulation box boundaries, and atoms are migrated to
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new owning processors.</p>
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<p>IMPORTANT_NOTE: This means that you cannot use the change_box command
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to enlarge a shrink-wrapped box, e.g. to make room to insert more
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atoms via the <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> command, because the
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simulation box will be re-shrink-wrapped before the change_box command
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completes. Instead you could do something like this, assuming the
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simulation box is non-periodic and atoms extend from 0 to 20 in all
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dimensions:</p>
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<div class="highlight-python"><div class="highlight"><pre>change_box all x final -10 20
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create_atoms 1 single -5 5 5 # this will fail to insert an atom
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>change_box all x final -10 20 boundary f s s
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create_atoms 1 single -5 5 5
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change_box boundary s s s # this will work
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</pre></div>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">Unlike the earlier “displace_box” version of this
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command, atom remapping is NOT performed by default. This command
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allows remapping to be done in a more general way, exactly when you
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specify it (zero or more times) in the sequence of transformations.
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Thus if you do not use the <em>remap</em> keyword, atom coordinates will not
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be changed even if the box size/shape changes. If a uniformly
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strained state is desired, the <em>remap</em> keyword should be specified.</p>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">It is possible to lose atoms with this command.
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E.g. by changing the box without remapping the atoms, and having atoms
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end up outside of non-periodic boundaries. It is also possible to
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alter bonds between atoms straddling a boundary in bad ways. E.g. by
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converting a boundary from periodic to non-periodic. It is also
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possible when remapping atoms to put them (nearly) on top of each
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other. E.g. by converting a boundary from non-periodic to periodic.
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All of these will typically lead to bad dynamics and/or generate error
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messages.</p>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">The simulation box size/shape can be changed by
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arbitrarily large amounts by this command. This is not a problem,
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except that the mapping of processors to the simulation box is not
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changed from its initial 3d configuration; see the
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<a class="reference internal" href="processors.html"><em>processors</em></a> command. Thus, if the box size/shape
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changes dramatically, the mapping of processors to the simulation box
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may not end up as optimal as the initial mapping attempted to be.</p>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">Because the keywords used in this command are applied
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one at a time to the simulation box and the atoms in it, care must be
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taken with triclinic cells to avoid exceeding the limits on skew after
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each transformation in the sequence. If skew is exceeded before the
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final transformation this can be avoided by changing the order of the
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sequence, or breaking the transformation into two or more smaller
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transformations. For more information on the allowed limits for box
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skew see the discussion on triclinic boxes on <a class="reference internal" href="Section_howto.html#howto-12"><span>this page</span></a>.</p>
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</div>
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<hr class="docutils" />
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<p>For the <em>x</em>, <em>y</em>, and <em>z</em> parameters, this is the meaning of their
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styles and values.</p>
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<p>For style <em>final</em>, the final lo and hi box boundaries of a dimension
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are specified. The values can be in lattice or box distance units.
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See the discussion of the units keyword below.</p>
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<p>For style <em>delta</em>, plus or minus changes in the lo/hi box boundaries
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of a dimension are specified. The values can be in lattice or box
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distance units. See the discussion of the units keyword below.</p>
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<p>For style <em>scale</em>, a multiplicative factor to apply to the box length
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of a dimension is specified. For example, if the initial box length
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is 10, and the factor is 1.1, then the final box length will be 11. A
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factor less than 1.0 means compression.</p>
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<p>The <em>volume</em> style changes the specified dimension in such a way that
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the overall box volume remains constant with respect to the operation
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performed by the preceding keyword. The <em>volume</em> style can only be
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used following a keyword that changed the volume, which is any of the
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<em>x</em>, <em>y</em>, <em>z</em> keywords. If the preceding keyword “key” had a <em>volume</em>
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style, then both it and the current keyword apply to the keyword
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preceding “key”. I.e. this sequence of keywords is allowed:</p>
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<div class="highlight-python"><div class="highlight"><pre>change_box all x scale 1.1 y volume z volume
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</pre></div>
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</div>
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<p>The <em>volume</em> style changes the associated dimension so that the
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overall box volume is unchanged relative to its value before the
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preceding keyword was invoked.</p>
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<p>If the following command is used, then the z box length will shrink by
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the same 1.1 factor the x box length was increased by:</p>
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<div class="highlight-python"><div class="highlight"><pre>change_box all x scale 1.1 z volume
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</pre></div>
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</div>
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<p>If the following command is used, then the y,z box lengths will each
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shrink by sqrt(1.1) to keep the volume constant. In this case, the
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y,z box lengths shrink so as to keep their relative aspect ratio
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constant:</p>
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<div class="highlight-python"><div class="highlight"><pre>change_box all"x scale 1.1 y volume z volume
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</pre></div>
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</div>
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<p>If the following command is used, then the final box will be a factor
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of 10% larger in x and y, and a factor of 21% smaller in z, so as to
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keep the volume constant:</p>
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<div class="highlight-python"><div class="highlight"><pre>change_box all x scale 1.1 z volume y scale 1.1 z volume
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</pre></div>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">For solids or liquids, when one dimension of the box
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is expanded, it may be physically undesirable to hold the other 2 box
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lengths constant since that implies a density change. For solids,
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adjusting the other dimensions via the <em>volume</em> style may make
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physical sense (just as for a liquid), but may not be correct for
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materials and potentials whose Poisson ratio is not 0.5.</p>
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</div>
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<p>For the <em>scale</em> and <em>volume</em> styles, the box length is expanded or
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compressed around its mid point.</p>
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<hr class="docutils" />
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<p>For the <em>xy</em>, <em>xz</em>, and <em>yz</em> parameters, this is the meaning of their
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styles and values. Note that changing the tilt factors of a triclinic
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box does not change its volume.</p>
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<p>For style <em>final</em>, the final tilt factor is specified. The value
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can be in lattice or box distance units. See the discussion of the
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units keyword below.</p>
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<p>For style <em>delta</em>, a plus or minus change in the tilt factor is
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specified. The value can be in lattice or box distance units. See
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the discussion of the units keyword below.</p>
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<p>All of these styles change the xy, xz, yz tilt factors. In LAMMPS,
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tilt factors (xy,xz,yz) for triclinic boxes are required to be no more
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than half the distance of the parallel box length. For example, if
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xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
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factor must be between -5 and 5. Similarly, both xz and yz must be
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between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a
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limitation, since if the maximum tilt factor is 5 (as in this
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example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
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... are all equivalent. Any tilt factor specified by this command
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must be within these limits.</p>
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<hr class="docutils" />
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<p>The <em>boundary</em> keyword takes arguments that have exactly the same
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meaning as they do for the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command. In each
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dimension, a single letter assigns the same style to both the lower
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and upper face of the box. Two letters assigns the first style to the
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lower face and the second style to the upper face.</p>
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<p>The style <em>p</em> means the box is periodic; the other styles mean
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non-periodic. For style <em>f</em>, the position of the face is fixed. For
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style <em>s</em>, the position of the face is set so as to encompass the
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atoms in that dimension (shrink-wrapping), no matter how far they
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move. For style <em>m</em>, shrink-wrapping occurs, but is bounded by the
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current box edge in that dimension, so that the box will become no
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smaller. See the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command for more
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explanation of these style options.</p>
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<p>Note that the “boundary” command itself can only be used before the
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simulation box is defined via a <a class="reference internal" href="read_data.html"><em>read_data</em></a> or
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<a class="reference internal" href="create_box.html"><em>create_box</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
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command. This command allows the boundary conditions to be changed
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later in your input script. Also note that the
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<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> will change boundary conditions to
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match what is stored in the restart file. So if you wish to change
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them, you should use the change_box command after the read_restart
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command.</p>
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<hr class="docutils" />
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<p>The <em>ortho</em> and <em>triclinic</em> keywords convert the simulation box to be
|
|
orthogonal or triclinic (non-orthongonal). See <a class="reference internal" href="Section_howto.html#howto-13"><span>this section</span></a> for a discussion of how non-orthongal
|
|
boxes are represented in LAMMPS.</p>
|
|
<p>The simulation box is defined as either orthogonal or triclinic when
|
|
it is created via the <a class="reference internal" href="create_box.html"><em>create_box</em></a>,
|
|
<a class="reference internal" href="read_data.html"><em>read_data</em></a>, or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
|
|
commands.</p>
|
|
<p>These keywords allow you to toggle the existing simulation box from
|
|
orthogonal to triclinic and vice versa. For example, an initial
|
|
equilibration simulation can be run in an orthogonal box, the box can
|
|
be toggled to triclinic, and then a <a class="reference internal" href="Section_howto.html#howto-13"><span>non-equilibrium MD (NEMD) simulation</span></a> can be run with deformation
|
|
via the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> command.</p>
|
|
<p>If the simulation box is currently triclinic and has non-zero tilt in
|
|
xy, yz, or xz, then it cannot be converted to an orthogonal box.</p>
|
|
<hr class="docutils" />
|
|
<p>The <em>set</em> keyword saves the current box size/shape. This can be
|
|
useful if you wish to use the <em>remap</em> keyword more than once or if you
|
|
wish it to be applied to an intermediate box size/shape in a sequence
|
|
of keyword operations. Note that the box size/shape is saved before
|
|
any of the keywords are processed, i.e. the box size/shape at the time
|
|
the create_box command is encountered in the input script.</p>
|
|
<p>The <em>remap</em> keyword remaps atom coordinates from the last saved box
|
|
size/shape to the current box state. For example, if you stretch the
|
|
box in the x dimension or tilt it in the xy plane via the <em>x</em> and <em>xy</em>
|
|
keywords, then the <em>remap</em> commmand will dilate or tilt the atoms to
|
|
conform to the new box size/shape, as if the atoms moved with the box
|
|
as it deformed.</p>
|
|
<p>Note that this operation is performed without regard to periodic
|
|
boundaries. Also, any shrink-wrapping of non-periodic boundaries (see
|
|
the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command) occurs after all keywords,
|
|
including this one, have been processed.</p>
|
|
<p>Only atoms in the specified group are remapped.</p>
|
|
<hr class="docutils" />
|
|
<p>The <em>units</em> keyword determines the meaning of the distance units used
|
|
to define various arguments. A <em>box</em> value selects standard distance
|
|
units as defined by the <a class="reference internal" href="units.html"><em>units</em></a> command, e.g. Angstroms for
|
|
units = real or metal. A <em>lattice</em> value means the distance units are
|
|
in lattice spacings. The <a class="reference internal" href="lattice.html"><em>lattice</em></a> command must have
|
|
been previously used to define the lattice spacing.</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>If you use the <em>ortho</em> or <em>triclinic</em> keywords, then at the point in
|
|
the input script when this command is issued, no <a class="reference internal" href="dump.html"><em>dumps</em></a> can
|
|
be active, nor can a <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a> or <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> be active. This is because these commands
|
|
test whether the simulation box is orthogonal when they are first
|
|
issued. Note that these commands can be used in your script before a
|
|
change_box command is issued, so long as an <a class="reference internal" href="undump.html"><em>undump</em></a> or
|
|
<a class="reference internal" href="unfix.html"><em>unfix</em></a> command is also used to turn them off.</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="fix_deform.html"><em>fix deform</em></a>, <a class="reference internal" href="boundary.html"><em>boundary</em></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
|
<p>The option default is units = lattice.</p>
|
|
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