2007-02-21 08:18:41 +08:00
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<HTML>
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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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<HR>
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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 value1 value2 ... keyword args ...
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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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2007-09-28 07:25:52 +08:00
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<LI>Nrepeat = # of times to repeat the Nevery calculation before averaging
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2007-10-15 23:07:59 +08:00
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<LI>Nfreq = timestep frequency at which the average value is computed
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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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2008-01-03 03:25:15 +08:00
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<LI>one or more values can be listed
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<LI>value = x, y, z, vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[N], f_ID, f_ID[N], v_name
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<PRE> x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
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density/number, density/mass = number or mass density
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c_ID = per-atom scalar value calculated by a compute with ID
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c_ID[N] = Nth component of per-atom vector calculated by a compute with ID
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f_ID = per-atom scalar value calculated by a fix with ID
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f_ID[N] = Nth component of per-atom vector calculated by a fix with ID
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v_name = per-atom value calculated by an atom-style variable with name
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</PRE>
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2007-10-19 08:33:05 +08:00
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<LI>zero or more keyword/arg pairs may be appended
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<LI>keyword = <I>norm</I> or <I>units</I> or <I>file</I> or <I>ave</I>
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2007-10-19 08:33:05 +08:00
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<PRE> <I>units</I> arg = <I>box</I> or <I>lattice</I> or <I>reduced</I>
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<I>norm</I> arg = <I>all</I> or <I>sample</I>
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<I>file</I> arg = filename
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filename = file to write results to
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<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
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one = output new average value every Nfreq steps
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running = output cummulative average of all previous Nfreq steps
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window M = output average of M most recent Nfreq steps
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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 0.02 myCentro units reduced
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fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
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fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 density/mass ave running
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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 average
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the layer values over a longer timescale. The resulting averages can
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be used by other <A HREF = "Section_howto.html#4_15">output commands</A> such as
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<A HREF = "thermo_style.html">thermo_style custom</A>, and can also be written to a
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file.
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</P>
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<P>Each listed value is averaged independently. The group specified with
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the command means only atoms within the group contribute to the layer
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averages.
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</P>
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<P>Each listed value can be an atom attribute (position, velocity, force
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component), a mass or number density, or the result of a
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<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or the evaluation of an
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atom-style <A HREF = "variable.html">variable</A>. In the latter cases, the
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compute, fix, or variable must produce a per-atom quantity, not a
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global quantity. If you wish to time-average global quantities from a
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compute, fix, or variable, then see the <A HREF = "fix_ave_time.html">fix
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ave/time</A> command.
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</P>
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<P><A HREF = "compute.html">Computes</A> that produce per-atom quantities are those
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which have the word <I>atom</I> in their style name. See the doc pages for
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individual <A HREF = "fix.html">fixes</A> to determine which ones produce per-atom
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quantities. <A HREF = "variable.html">Variables</A> of style <I>atom</I> are the only
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ones that can be used with this fix since all other styles of variable
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produce global quantities.
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</P>
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<HR>
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2007-10-19 06:27:53 +08:00
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<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
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timesteps the layer values will be generated in order to contribute to
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the average. The final averaged quantities are generated every
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<I>Nfreq</I> timesteps. The average is over <I>Nrepeat</I> quantities, computed
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in the preceeding portion of the simulation every <I>Nevery</I> timesteps.
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<I>Nfreq</I> must be a multiple of <I>Nevery</I> and <I>Nevery</I> must be non-zero
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even if <I>Nrepeat</I> is 1.
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</P>
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<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
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timesteps 90,92,94,96,98,100 will be used to compute the final average
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on timestep 100. Similary for timesteps 190,192,194,196,198,200 on
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timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
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averaging is done; values are simply generated on timesteps
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100,200,etc.
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</P>
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<HR>
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<P>Each per-atom property is also averaged over atoms in each layer,
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where the layers are in a particular <I>dim</I> and have a thickness given
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by <I>delta</I>. Every Nfreq steps, when an averaging is being performed
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and the per-atom property is calculated for the first time, the number
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of layers and the layer boundaries are computed. Thus if the
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simlation box changes size during a simulation, the number of layers
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and their boundaries may also change. Layers are defined relative to
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a specified <I>origin</I>, which may be the lower/upper edge of the box (in
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<I>dim</I>) or its center point, or a specified coordinate value. Starting
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at the origin, sufficient layers are created in both directions to
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completely cover the box. On subsequent timesteps every atom is
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mapped to one of the layers. Atoms beyond the lowermost/uppermost
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layer are counted in the first/last layer.
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2007-02-21 08:18:41 +08:00
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</P>
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2007-06-27 05:53:15 +08:00
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<P>For orthogonal simulation boxes, the layers are "slices" aligned with
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2007-06-27 05:47:46 +08:00
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the xyz coordinate axes. For non-orthogonal (triclinic) simulation
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boxes, the layers are "tilted slices" that are parallel to the tilted
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faces of the box. See the <A HREF = "region.html">region prism</A> command for a
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2007-06-27 05:47:46 +08:00
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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> when using a non-orthogonal simulation
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box, as discussed below.
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</P>
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<HR>
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<P>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
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self-explanatory.
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</P>
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<P>The <I>density/number</I> value means the number density is computed in
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each layer, i.e. a weighting of 1 for each atom. The <I>density/mass</I>
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value means the mass density is computed in each layer, i.e. each atom
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is weighted by its mass. The resulting density is normalized by the
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volume of the layer so that units of number/volume or mass/volume are
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output.
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</P>
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<P>If a value begins with "c_", a compute ID must follow which has been
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previously defined in the input script. If no bracketed term is
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appended, the per-atom scalar calculated by the compute is used. If a
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bracketed term is appended, the Nth vector per-atom value calculated
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by the compute is used. Users can also write code for their own
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compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
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</P>
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<P>If a value begins with "f_", a fix ID must follow which has been
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previously defined in the input script. If no bracketed term is
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appended, the per-atom scalar calculated by the fix is used. If a
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bracketed term is appended, the Nth vector per-atom value calculated
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by the fix is used. Note that some fixes only produce their values on
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certain timesteps, which must be compatible with <I>Nevery</I>, else an
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error results. Users can also write code for their own fix styles and
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<A HREF = "Section_modify.html">add them to LAMMPS</A>.
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</P>
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<P>If a value begins with "v_", a variable name must follow which has
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been previously defined in the input script. Variables of style
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<I>atom</I> can reference thermodynamic keywords, or invoke other computes,
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fixes, or variables when they are evaluated, so this is a very general
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means of generating per-atom quantities to spatially average.
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2007-10-19 06:27:53 +08:00
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</P>
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<HR>
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<P>Additional optional keywords also affect the operation of this fix.
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2007-06-27 05:47:46 +08:00
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</P>
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2007-02-21 08:49:36 +08:00
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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-orthogonal (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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2008-01-03 03:25:15 +08:00
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<P>The <I>norm</I> keyword affects how averaging is done for the output
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produced every <I>Nfreq</I> timesteps. For an <I>all</I> setting, a layer
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quantity is summed over all atoms in all <I>Nrepeat</I> samples, as is the
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count of atoms in the layer. The printed value for the layer is
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Total-quantity / Total-count. In other words it is an average over
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the entire <I>Nfreq</I> timescale.
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</P>
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<P>For a <I>sample</I> setting, the layer quantity is summed over atoms for
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only a 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 <I>Nrepeat</I> "average sample values", In
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other words it is an average of an average.
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2007-02-21 08:18:41 +08:00
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</P>
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2007-10-19 06:27:53 +08:00
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<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
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timesteps, layer info will be written to a text file in the following
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format. A line with the timestep and number of layers is written.
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Then one 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 values in
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each line corresponds to the number of values specified in the fix
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ave/spatial command. The number of atoms and the value(s) are average
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quantities. If the value of the <I>units</I> keyword is <I>box</I> or
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<I>lattice</I>, the "coord" is printed in box units. If the value of the
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<I>units</I> keyword is <I>reduced</I>, the "coord" is printed in reduced units
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(0-1).
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2007-10-19 06:27:53 +08:00
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</P>
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<P>The <I>ave</I> keyword determines how the layer values produced every
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<I>Nfreq</I> steps are averaged with layer values produced on previous
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steps that were multiples of <I>Nfreq</I>, before they are accessed by
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another output command or written to a file.
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</P>
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<P>If the <I>ave</I> setting is <I>one</I>, then the layuer values produced on
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timesteps that are multiples of <I>Nfreq</I> are independent of each other;
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they are output as-is without further averaging.
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</P>
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<P>If the <I>ave</I> setting is <I>running</I>, then the layer values produced on
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timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
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cummulative sense before being output. Each output layer value is
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thus the average of the layer value produced on that timestep with all
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preceeding values for the same layer. This running average begins
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when the fix is defined; it can only be restarted by deleting the fix
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via the <A HREF = "unfix.html">unfix</A> command, or re-defining the fix by
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re-specifying it.
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</P>
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<P>If the <I>ave</I> setting is <I>window</I>, then the layer values produced on
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timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
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a moving "window" of time, so that the last M values for the same
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layer are used to produce the output. E.g. if M = 3 and Nfreq = 1000,
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then the output on step 10000 will be the average of the individual
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layer values on steps 8000,9000,10000. Outputs on early steps will
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average over less than M values if they are not available.
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</P>
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<HR>
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2007-10-11 06:28:11 +08:00
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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2007-06-26 08:03:39 +08:00
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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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2007-10-15 23:07:59 +08:00
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are relevant to this fix.
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</P>
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2008-01-03 03:25:15 +08:00
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<P>This fix computes a global vector of quantities which can be accessed
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by various <A HREF = "Section_howto.html#4_15">output commands</A>. The values can
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2007-10-15 23:07:59 +08:00
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only be accessed on timesteps that are multiples of <I>Nfreq</I> since that
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2008-01-03 03:25:15 +08:00
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is when averaging is performed. The global vector is of length N =
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nlayers*nvalues where nlayers is the number of layers and nvalues is
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the number of values per layer that the fix is averaging. When
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accessed by another output command, a single index M is specified
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which is mapped into a layer I as I = M / nvalues + 1 and into value J
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as J = M % nvalues + 1. If I exceeds the current number of layers
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than a 0.0 is returned by the fix instead of an error, since the
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number of layers can vary as a simulation runs, depending on the
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simulation box size. The vector values calculated by this fix are
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"intensive", meaning they are independent of the number of atoms in
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the simulation, since they are already normalized by the count of
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atoms in each layer.
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2007-10-15 23:07:59 +08:00
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</P>
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<P>No 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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2007-06-26 08:03:39 +08:00
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</P>
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2007-10-19 08:33:05 +08:00
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<P><B>Restrictions:</B>
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</P>
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<P>When the <I>ave</I> keyword is set to <I>running</I> or <I>window</I> then the number
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of layers must remain the same during the simulation, so that the
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appropriate averaging can be done. This will be the case if the
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simulation box size doesn't change or if the <I>units</I> keyword is set to
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<I>reduced</I>.
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2007-02-21 08:18:41 +08:00
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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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2007-02-21 08:49:36 +08:00
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<P><B>Default:</B>
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</P>
|
2007-10-19 06:27:53 +08:00
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<P>The option defaults are units = lattice, norm = all, no file output,
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and ave = one.
|
2007-02-21 08:18:41 +08:00
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</P>
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</HTML>
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