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@ -9,183 +9,52 @@
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<HR>
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<H3>displace_box command
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<H3>change_box command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>displace_box group-ID parameter args ... keyword value ...
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<PRE>change_box style
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</PRE>
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<UL><LI>group-ID = ID of group of atoms to displace
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<LI>style = <I>ortho</I> or <I>triclinic</I>
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<LI>one or more parameter/arg pairs may be appended
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<PRE>parameter = <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>xz</I> or <I>yz</I>
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<I>x</I>, <I>y</I>, <I>z</I> args = style value(s)
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style = <I>final</I> or <I>delta</I> or <I>scale</I> or <I>volume</I>
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<I>final</I> values = lo hi
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lo hi = box boundaries at end of run (distance units)
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<I>delta</I> values = dlo dhi
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dlo dhi = change in box boundaries at end of run (distance units)
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<I>scale</I> values = factor
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factor = multiplicative factor for change in box length at end of run
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<I>volume</I> value = none = adjust this dim to preserve volume of system
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<I>xy</I>, <I>xz</I>, <I>yz</I> args = style value
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style = <I>final</I> or <I>delta</I>
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<I>final</I> value = tilt
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tilt = tilt factor at end of run (distance units)
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<I>delta</I> value = dtilt
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dtilt = change in tilt factor at end of run (distance units)
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<PRE> <I>ortho</I> = convert simulation box from non-orthogonal (triclinic) to orthogonal
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<I>triclinic</I> = convert simulation box from orthogonal to non-orthogonal (triclinic)
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</PRE>
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<LI>zero or more keyword/value pairs may be appended to the args
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<LI>keyword = <I>remap</I> or <I>units</I>
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<PRE> <I>remap</I> value = <I>x</I> or <I>none</I>
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x = remap coords of atoms in group into deforming box
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none = no remapping of coords
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<I>units</I> value = <I>lattice</I> or <I>box</I>
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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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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>displace_box all xy final -2.0 z final 0.0 5.0 units box
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displace_box all x scale 1.1 y volume z volume
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<PRE>change_box ortho
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change_box triclinic
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Change the volume and/or shape of the simulation box. Orthogonal
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simulation boxes have 3 adjustable parameters (x,y,z). Triclinic
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(non-orthogonal) simulation boxes have 6 adjustable parameters
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(x,y,z,xy,xz,yz). Any or all of them can be adjusted independently
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and simultaneously by this command. This fix can be used to expand or
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contract a box, or to apply a shear strain to a non-orthogonal box.
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<P>By default LAMMPS runs a simulation in an orthogonal, axis-aligned
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simulation box. LAMMPS can also run simulations in <A HREF = "Section_howto.html#4_12">non-orthogonal
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(triclinic) simulation boxes</A>. A box is
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defined as either orthogonal or non-orthogonal when it is created via
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the <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read_data</A>, or
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<A HREF = "read_restart.html">read_restart</A> commands.
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</P>
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<P>Any parameter varied by this command must refer to a periodic
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dimension - see the <A HREF = "boundary.html">boundary</A> command. For parameters
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"xy", "xz", and "yz" this means both affected dimensions must be
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periodic, e.g. x and y for "xy". Dimensions not varied by this
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command can be periodic or non-periodic.
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<P>This command allows you to toggle the existing simulation box from
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orthogonal to non-orthogonal and vice versa. For example, an initial
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equilibration simulation can be run in an orthogonal box, the box can
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be toggled to non-orthogonal, and then a <A HREF = "Section_howto.html#4_13">non-equilibrium MD (NEMD)
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simulation</A> can be run with deformation via
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the <A HREF = "fix_deform.html">fix deform</A> command.
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</P>
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<P>The size and shape of the initial simulation box are specified by the
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<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> or
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<A HREF = "read_restart.html">read_restart</A> command used to setup the simulation,
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or they are the values from the end of the previous run. The
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<A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read data</A>, and
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<A HREF = "read_restart.html">read_restart</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. If the displace_box command
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changes the xy,xz,yz tilt factors, then the simulation box must be
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triclinic, even if its initial tilt factors are 0.0.
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</P>
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<HR>
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<P>For the <I>x</I>, <I>y</I>, and <I>z</I> parameters, this is the meaning of their
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styles and values.
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</P>
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<P>For style <I>final</I>, 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 discsussion of the units keyword below.
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</P>
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<P>For style <I>delta</I>, 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.
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</P>
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<P>For style <I>scale</I>, 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.
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</P>
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<P>The <I>volume</I> style changes the specified dimension in such a way that
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the box volume remains constant while other box dimensions are changed
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explicitly via the styles discussed above. For example, "x scale 1.1
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y scale 1.1 z volume" will shrink the z box length as the x,y box
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lengths increase, to keep the volume constant (product of x,y,z
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lengths). If "x scale 1.1 z volume" is specified and parameter <I>y</I> is
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unspecified, then the z box length will shrink as x increases to keep
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the product of x,z lengths constant. If "x scale 1.1 y volume z
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volume" is specified, then both the y,z box lengths will shrink as x
|
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increases to keep the volume constant (product of x,y,z lengths). In
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this case, the y,z box lengths shrink so as to keep their relative
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aspect ratio constant.
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</P>
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<P>For solids or liquids, note that when one dimension of the box is
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expanded by this command, it may be physically undesirable to hold the
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other 2 box lengths constant (unspecified by this command) since that
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implies a density change. Using the <I>volume</I> style for those 2
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dimensions to keep the box volume constant may make more physical
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sense, but may also not be correct for materials and potentials whose
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Poisson ratio is not 0.5.
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</P>
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<P>For the <I>scale</I> and <I>volume</I> styles, the box length is expanded or
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compressed around its mid point.
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</P>
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<HR>
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<P>For the <I>xy</I>, <I>xz</I>, and <I>yz</I> 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.
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</P>
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<P>For style <I>final</I>, 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.
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</P>
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<P>For style <I>delta</I>, 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 discsussion of the units keyword below.
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</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 always bounded by 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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equivalent. Any tilt factor specified by this command must be within
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these limits.
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</P>
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<HR>
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<P>The <I>remap</I> keyword determines whether atom positions are re-mapped to
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the new box. If <I>remap</I> is set to <I>x</I> (the default), atoms in the fix
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group are re-mapped; otherwise they are not. If <I>remap</I> is set to
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<I>none</I>, then this remapping does not take place.
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</P>
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<P>The <I>units</I> keyword determines the meaning of the distance units used
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to define various arguments. A <I>box</I> value selects standard distance
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units as defined by the <A HREF = "units.html">units</A> command, e.g. Angstroms for
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units = real or metal. A <I>lattice</I> value means the distance units are
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in lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have
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been previously used to define the lattice spacing.
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</P>
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<HR>
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<P>The simulation box size or shape can be changed by arbitrarily large
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amounts by this command. This is not a problem, except that the
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mapping of processors to the simulation box is not changed by this
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command from its initial 3d configuration; see the
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<A HREF = "processors.html">processors</A> command. Thus, if the box size or shape
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changes dramatically, the simulation may not be as well load-balanced
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(atoms per processor) as the initial mapping tried to achieve.
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<P>Note that if the simulation box is currently non-orthogonal and has
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non-zero tilt in xy, yz, or xz, then it cannot be converted to an
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orthogonal box.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>Any box dimension varied by this fix must be periodic.
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<P>When this command is used, no <A HREF = "dump.html">dumps</A> can be defined, nor
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can <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> or <A HREF = "fix_deform.html">fix
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deform</A> be defined. This is because these commands
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test whether the simulation box is orthogonal or not when they are
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first issued.
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</P>
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<P>This command requires inter-processor communication to migrate atoms
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once they have moved. This means that your system must be ready to
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perform a simulation before using this command (force fields are
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setup, atom masses are set, etc).
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<P><B>Related commands:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_deform.html">fix deform</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are remap = x and units = lattice.
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<P><B>Default:</B> none
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</P>
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</HTML>
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@ -6,176 +6,49 @@
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:line
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displace_box command :h3
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change_box command :h3
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[Syntax:]
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displace_box group-ID parameter args ... keyword value ... :pre
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change_box style :pre
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group-ID = ID of group of atoms to displace :ulb,l
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one or more parameter/arg pairs may be appended :l
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parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
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{x}, {y}, {z} args = style value(s)
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style = {final} or {delta} or {scale} or {volume}
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{final} values = lo hi
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lo hi = box boundaries at end of run (distance units)
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{delta} values = dlo dhi
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dlo dhi = change in box boundaries at end of run (distance units)
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{scale} values = factor
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factor = multiplicative factor for change in box length at end of run
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{volume} value = none = adjust this dim to preserve volume of system
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{xy}, {xz}, {yz} args = style value
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style = {final} or {delta}
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{final} value = tilt
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tilt = tilt factor at end of run (distance units)
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{delta} value = dtilt
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dtilt = change in tilt factor at end of run (distance units) :pre
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zero or more keyword/value pairs may be appended to the args :l
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keyword = {remap} or {units} :l
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{remap} value = {x} or {none}
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x = remap coords of atoms in group into deforming box
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none = no remapping of coords
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{units} value = {lattice} or {box}
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lattice = distances are defined in lattice units
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box = distances are defined in simulation box units :pre
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:ule
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style = {ortho} or {triclinic} :l
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{ortho} = convert simulation box from non-orthogonal (triclinic) to orthogonal
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{triclinic} = convert simulation box from orthogonal to non-orthogonal (triclinic) :pre
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[Examples:]
|
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|
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displace_box all xy final -2.0 z final 0.0 5.0 units box
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displace_box all x scale 1.1 y volume z volume :pre
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change_box ortho
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change_box triclinic :pre
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|
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[Description:]
|
||||
|
||||
Change the volume and/or shape of the simulation box. Orthogonal
|
||||
simulation boxes have 3 adjustable parameters (x,y,z). Triclinic
|
||||
(non-orthogonal) simulation boxes have 6 adjustable parameters
|
||||
(x,y,z,xy,xz,yz). Any or all of them can be adjusted independently
|
||||
and simultaneously by this command. This fix can be used to expand or
|
||||
contract a box, or to apply a shear strain to a non-orthogonal box.
|
||||
By default LAMMPS runs a simulation in an orthogonal, axis-aligned
|
||||
simulation box. LAMMPS can also run simulations in "non-orthogonal
|
||||
(triclinic) simulation boxes"_Section_howto.html#4_12. A box is
|
||||
defined as either orthogonal or non-orthogonal when it is created via
|
||||
the "create_box"_create_box.html, "read_data"_read_data.html, or
|
||||
"read_restart"_read_restart.html commands.
|
||||
|
||||
Any parameter varied by this command must refer to a periodic
|
||||
dimension - see the "boundary"_boundary.html command. For parameters
|
||||
"xy", "xz", and "yz" this means both affected dimensions must be
|
||||
periodic, e.g. x and y for "xy". Dimensions not varied by this
|
||||
command can be periodic or non-periodic.
|
||||
This command allows you to toggle the existing simulation box from
|
||||
orthogonal to non-orthogonal and vice versa. For example, an initial
|
||||
equilibration simulation can be run in an orthogonal box, the box can
|
||||
be toggled to non-orthogonal, and then a "non-equilibrium MD (NEMD)
|
||||
simulation"_Section_howto.html#4_13 can be run with deformation via
|
||||
the "fix deform"_fix_deform.html command.
|
||||
|
||||
The size and shape of the initial simulation box are specified by the
|
||||
"create_box"_create_box.html or "read_data"_read_data.html or
|
||||
"read_restart"_read_restart.html command used to setup the simulation,
|
||||
or they are the values from the end of the previous run. The
|
||||
"create_box"_create_box.html, "read data"_read_data.html, and
|
||||
"read_restart"_read_restart.html commands also determine whether the
|
||||
simulation box is orthogonal or triclinic and their doc pages explain
|
||||
the meaning of the xy,xz,yz tilt factors. If the displace_box command
|
||||
changes the xy,xz,yz tilt factors, then the simulation box must be
|
||||
triclinic, even if its initial tilt factors are 0.0.
|
||||
|
||||
:line
|
||||
|
||||
For the {x}, {y}, and {z} parameters, this is the meaning of their
|
||||
styles and values.
|
||||
|
||||
For style {final}, the final lo and hi box boundaries of a dimension
|
||||
are specified. The values can be in lattice or box distance units.
|
||||
See the discsussion of the units keyword below.
|
||||
|
||||
For style {delta}, plus or minus changes in the lo/hi box boundaries
|
||||
of a dimension are specified. The values can be in lattice or box
|
||||
distance units. See the discussion of the units keyword below.
|
||||
|
||||
For style {scale}, a multiplicative factor to apply to the box length
|
||||
of a dimension is specified. For example, if the initial box length
|
||||
is 10, and the factor is 1.1, then the final box length will be 11. A
|
||||
factor less than 1.0 means compression.
|
||||
|
||||
The {volume} style changes the specified dimension in such a way that
|
||||
the box volume remains constant while other box dimensions are changed
|
||||
explicitly via the styles discussed above. For example, "x scale 1.1
|
||||
y scale 1.1 z volume" will shrink the z box length as the x,y box
|
||||
lengths increase, to keep the volume constant (product of x,y,z
|
||||
lengths). If "x scale 1.1 z volume" is specified and parameter {y} is
|
||||
unspecified, then the z box length will shrink as x increases to keep
|
||||
the product of x,z lengths constant. If "x scale 1.1 y volume z
|
||||
volume" is specified, then both the y,z box lengths will shrink as x
|
||||
increases to keep the volume constant (product of x,y,z lengths). In
|
||||
this case, the y,z box lengths shrink so as to keep their relative
|
||||
aspect ratio constant.
|
||||
|
||||
For solids or liquids, note that when one dimension of the box is
|
||||
expanded by this command, it may be physically undesirable to hold the
|
||||
other 2 box lengths constant (unspecified by this command) since that
|
||||
implies a density change. Using the {volume} style for those 2
|
||||
dimensions to keep the box volume constant may make more physical
|
||||
sense, but may also not be correct for materials and potentials whose
|
||||
Poisson ratio is not 0.5.
|
||||
|
||||
For the {scale} and {volume} styles, the box length is expanded or
|
||||
compressed around its mid point.
|
||||
|
||||
:line
|
||||
|
||||
For the {xy}, {xz}, and {yz} parameters, this is the meaning of their
|
||||
styles and values. Note that changing the tilt factors of a triclinic
|
||||
box does not change its volume.
|
||||
|
||||
For style {final}, the final tilt factor is specified. The value
|
||||
can be in lattice or box distance units. See the discussion of the
|
||||
units keyword below.
|
||||
|
||||
For style {delta}, a plus or minus change in the tilt factor is
|
||||
specified. The value can be in lattice or box distance units. See
|
||||
the discsussion of the units keyword below.
|
||||
|
||||
All of these styles change the xy, xz, yz tilt factors. In LAMMPS,
|
||||
tilt factors (xy,xz,yz) for triclinic boxes are always bounded by 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
|
||||
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
|
||||
equivalent. Any tilt factor specified by this command must be within
|
||||
these limits.
|
||||
|
||||
:line
|
||||
|
||||
The {remap} keyword determines whether atom positions are re-mapped to
|
||||
the new box. If {remap} is set to {x} (the default), atoms in the fix
|
||||
group are re-mapped; otherwise they are not. If {remap} is set to
|
||||
{none}, then this remapping does not take place.
|
||||
|
||||
The {units} keyword determines the meaning of the distance units used
|
||||
to define various arguments. A {box} value selects standard distance
|
||||
units as defined by the "units"_units.html command, e.g. Angstroms for
|
||||
units = real or metal. A {lattice} value means the distance units are
|
||||
in lattice spacings. The "lattice"_lattice.html command must have
|
||||
been previously used to define the lattice spacing.
|
||||
|
||||
:line
|
||||
|
||||
The simulation box size or shape can be changed by arbitrarily large
|
||||
amounts by this command. This is not a problem, except that the
|
||||
mapping of processors to the simulation box is not changed by this
|
||||
command from its initial 3d configuration; see the
|
||||
"processors"_processors.html command. Thus, if the box size or shape
|
||||
changes dramatically, the simulation may not be as well load-balanced
|
||||
(atoms per processor) as the initial mapping tried to achieve.
|
||||
Note that if the simulation box is currently non-orthogonal and has
|
||||
non-zero tilt in xy, yz, or xz, then it cannot be converted to an
|
||||
orthogonal box.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Any box dimension varied by this fix must be periodic.
|
||||
When this command is used, no "dumps"_dump.html can be defined, nor
|
||||
can "fix ave/spatial"_fix_ave_spatial.html or "fix
|
||||
deform"_fix_deform.html be defined. This is because these commands
|
||||
test whether the simulation box is orthogonal or not when they are
|
||||
first issued.
|
||||
|
||||
This command requires inter-processor communication to migrate atoms
|
||||
once they have moved. This means that your system must be ready to
|
||||
perform a simulation before using this command (force fields are
|
||||
setup, atom masses are set, etc).
|
||||
[Related commands:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix deform"_fix_deform.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are remap = x and units = lattice.
|
||||
[Default:] none
|
||||
|
|
|
|||
Loading…
Reference in New Issue