forked from lijiext/lammps
217 lines
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217 lines
11 KiB
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<H3>fix ave/spatial command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta file style args keyword value ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>ave/spatial = style name of this fix command
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<LI>Nevery = calculate property every this many timesteps
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<LI>Nrepeat = # of times to repeat the Nevery calculation before averaging
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<LI>Nfreq = timestep frequency at which the average value is written to file
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<LI>dim = <I>x</I> or <I>y</I> or <I>z</I>
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<LI>origin = <I>lower</I> or <I>center</I> or <I>upper</I> or coordinate value (distance units)
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<LI>delta = thickness of spatial layers in dim (distance units)
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<LI>file = filename to write results to
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<LI>style = <I>density</I> or <I>compute</I> or <I>fix</I>
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<PRE> <I>density</I> arg = <I>mass</I> or <I>number</I>
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<I>mass</I> = compute mass density
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<I>number</I> = compute number density
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<I>compute</I> arg = compute-ID that stores or calculates per-atom quantities
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<I>fix</I> arg = fix-ID that stores or calculates per-atom quantities
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</PRE>
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<PRE>
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</PRE>
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<LI>zero or more keyword/value pairs may be appended
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<PRE>keyword = <I>norm</I> or <I>units</I>
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<I>norm</I> value = <I>all</I> or <I>sample</I>
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<I>units</I> value = <I>box</I> or <I>lattice</I> or <I>reduced</I>
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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>fix 1 all ave/spatial 10000 1 10000 z lower 2.0 centro.profile compute myCentro
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fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vel.profile compute Vx norm sample
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fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 dens.profile density mass
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Calculate one or more instantaneous per-atom quantities every few
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timesteps, average them by layer in a chosen dimension and over a
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longer timescale, and print the results to a file. This can be used
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to spatially average per-atom properties (velocity, force) or per-atom
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quantities calculated by a <A HREF = "compute.html">compute</A> (energy, stress) or
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by another fix (see the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command) or
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by a variable via an equation you define (see the <A HREF = "compute_variable_atom.html">compute
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variable/atom</A> command).
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</P>
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<P>The <I>density</I> styles means to simply count the number of atoms in each
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layer, either by mass or number. The <I>compute</I> style allows
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specification of a <A HREF = "compute.html">compute</A> which will be invoked to
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calculate the desired property. The compute can be previously defined
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in the input script or it can be a compute defined by a <A HREF = "dump.html">dump
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custom</A> command.
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</P>
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<P>For the <I>compute</I> style, the fix ave/spatial command accesses the
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per-atom scalar or vector values stored by the compute. Thus it must
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be a "per-atom" compute with the word "atom" in its style name, rather
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than a "global" compute. See the <A HREF = "fix_ave_time.html">fix ave/time</A>
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command if you wish to time-average a global quantity calculated by a
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compute without the word atom in its style name, e.g. a compute that
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calculates a temperature or pressure.
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</P>
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<P>See the <A HREF = "compute.html">compute</A> command for a list of pre-defined
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per-atom computes. Two special computes are as follows. The <A HREF = "compute_attribute_atom.html">compute
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attribute/atom</A> command selects one or
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more atom attributes like vx or fz. The "compute variable/atom" style
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can calculate a value for an atom that can be specified by a <A HREF = "variable.html">variable
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atom</A> equation. Users can also write code for their own
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per-atom compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
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Note that the <A HREF = "dump.html">dump custom</A> command can also be used to
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directly output per-atom quantities calculated by a per-atom compute.
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</P>
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<P>For the <I>fix</I> style, the fix ave/spatial command accesses the per-atom
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scalar or vector values stored by another fix. The <A HREF = "fix_ave_atom.html">fix
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ave/atom</A> command is an example of such a fix.
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</P>
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<P>In all cases, the calculated property is averaged over atoms in each
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layer, where the layers are in a particular <I>dim</I> and have a thickness
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given by <I>delta</I>. Every Nfreq steps, when a property is calculated
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for the first time (after a previous write), the number of layers and
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the layer boundaries are computed. Thus if the simlation box changes
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size during a simulation, the number of layers and their boundaries
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may also change. Layers are defined relative to a specified <I>origin</I>,
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which may be the lower/upper edge of the box (in <I>dim</I>) or its center
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point, or a specified coordinate value. Starting at the origin,
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sufficient layers are created in both directions to completely cover
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the box. On subsequent timesteps every atom is mapped to one of the
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layers. Atoms beyond the lowermost/uppermost layer are counted in the
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first/last layer.
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</P>
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<P>For orthogonal simulation boxes, the layers are "slices" aligned with
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the xyz coordinate axes. For non-orthogonal (triclinic) simulation
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boxes, the layers are "tilted slices" that align with the tilted faces
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of the box. See the <A HREF = "region.html">region prism</A> command for a
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discussion of the geometry of tilted boxes in LAMMPS. As described
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there, a tilted simulation box has edge vectors a,b,c. In that
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nomenclature, layers in the x dimension have faces with normals in the
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"b" cross "c" direction. Layers in y have faces normal to the "a"
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cross "c" direction. And layers in z have faces normal to the "a"
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cross "b" direction. Note that in order to define the thickness and
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position of these tilted layers in an unambiguous fashion, the <I>units</I>
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option must be set to <I>reduced</I>.
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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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for the layer thickness <I>delta</I> and for <I>origin</I> if it is a coordinate
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value. For orthogonal simulation boxes, any of the 3 options may be
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used. For non-orthongal (triclinic) simulation boxes, only the
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<I>reduced</I> option may be used.
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</P>
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<P>A <I>box</I> value selects standard distance units as defined by the
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<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
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A <I>lattice</I> value means the distance units are in lattice spacings.
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The <A HREF = "lattice.html">lattice</A> command must have been previously used to
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define the lattice spacing. A <I>reduced</I> value means normalized
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unitless values between 0 and 1, which represent the lower and upper
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faces of the simulation box respectively. Thus an <I>origin</I> value of
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0.5 means the center of the box in any dimension. A <I>delta</I> value of
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0.1 means 10 layers span the box in any dimension.
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</P>
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<P>Consider a non-orthogonal box, with layers in the x dimension. No
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matter how the box is tilted, an <I>origin</I> of 0.0 means start layers at
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the lower "b" cross "c" plane of the simulation box and an <I>origin</I> of
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1.0 means to start layers at the upper "b" cross "c" face of the box.
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A <I>delta</I> value of 0.1 means there will be 10 layers from 0.0 to 1.0,
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regardless of the current size or shape of the simulation box.
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</P>
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<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify how the
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property will be time-averaged. The final averaged value(s) are
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computed every <I>Nfreq</I> timesteps. The average is over <I>Nrepeat</I>
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values, computed in the preceeding portion of the simulation every
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<I>Nevery</I> timesteps. Thus if Nevery=2, Nrepeat=6, and Nfreq=100, then
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values on timesteps 90,92,94,96,98,100 will be used to compute the
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final average written to the file on timestep 100. Similary for
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timesteps 190,192,194,196,198,200 on timestep 200, etc.
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</P>
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<P>The <I>norm</I> keyword also affects how time-averaging is done. For an
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<I>all</I> setting, a layer quantity is summed over all atoms in all
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Nfreq/Nevery samples, as is the count of atoms in the layer. The
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printed value for the layer is Total-quantity / Total-count.
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In other words it is an average over the entire Nfreq timescale.
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</P>
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<P>For a <I>sample</I> setting, the quantity is summed over atoms for only a
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single sample, as is the count, and a "average sample value" is
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computed, i.e. Sample-quantity / Sample-count. The printed value for
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the layer is the average of the M "average sample values", where M =
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Nfreq/Nevery. In other words it is an average of an average.
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</P>
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<P>Each time info is written to the file, it is in the following format.
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A line with the timestep and number of layers is written. Then one
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line per layer is written, containing the layer ID (1-N), the
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coordinate of the center of the layer, the number of atoms in the
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layer, and one or more calculated values. The number of atoms and the
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value(s) are average quantities. If the value of the <I>units</I> keyword
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is <I>box</I> or <I>lattice</I>, the "coord" is printed in box units. If the
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value of the <I>units</I> keyword is <I>reduced</I>, the "coord" is printed in
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reduced units (0-1).
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</P>
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<P>If the <I>density</I> keyword is used, or the <I>compute</I> or <I>fix</I> keyword
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with a compute/fix that calculates a single quantity per atom, then a
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single value will be printed for each layer. If the <I>compute</I> or
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<I>fix</I> keyword is used with a compute/fix that calculates N quantities
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per atom, then N values per line will be written, each of them
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averaged independently.
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</P>
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<P>For the <I>compute</I> and <I>fix</I> keywords, the calculation performed by the
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compute or fix is on the group defined by the that command. However,
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only atoms in the fix group are included in the layer averaging.
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</P>
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<P>Note that some computes perform costly calculations, involving use of
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or creation of neighbor lists. If the compute is invoked too often by
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fix ave/spatial, it can slow down a simulation.
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</P>
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<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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are relevant to this fix. No quantities calculated by this fix can be
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output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
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parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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<P><B>Restrictions:</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 = "compute.html">compute</A>, <A HREF = "fix_ave_time.html">fix ave/time</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 norm = all and units = lattice.
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</P>
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</HTML>
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