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@ -13,7 +13,7 @@
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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>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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@ -25,12 +25,12 @@
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<LI>Nfreq = calculate averages every this many timesteps
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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>dim, origin, delta can be repeated 1, 2, or 3 times for 1d, 2d, or 3d bins
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<PRE> dim = <I>x</I> or <I>y</I> or <I>z</I>
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origin = <I>lower</I> or <I>center</I> or <I>upper</I> or coordinate value (distance units)
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delta = thickness of spatial bins in dim (distance units)
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</PRE>
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<LI>one or more input 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[I], f_ID, f_ID[I], v_name
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@ -71,20 +71,21 @@
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<PRE>fix 1 all ave/spatial 10000 1 10000 z lower 0.02 c_myCentro units reduced &
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title1 "My output values"
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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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fix 1 flow ave/spatial 100 5 1000 z lower 1.0 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>Use one or more per-atom vectors as inputs every few timesteps, bin
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them spatially by layer in a dimension, and average the layer values
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over longer timescales. The resulting layer averages can be used by
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other <A HREF = "Section_howto.html#4_15">output commands</A> such as <A HREF = "thermo_style.html">thermo_style
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their values spatially into 1d, 2d, or 3d bins based on current atom
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coordinates, and average the bin values over longer timescales. The
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resulting bin averages can be used by other <A HREF = "Section_howto.html#4_15">output
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commands</A> such as <A HREF = "thermo_style.html">thermo_style
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custom</A>, and can also be written to a file.
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</P>
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<P>The group specified with the command means only atoms within the group
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contribute to layer averages. If the <I>region</I> keyword is used, the
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contribute to bin averages. If the <I>region</I> keyword is used, the
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atom must be in both the group and the specified geometric
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<A HREF = "region.html">region</A> in order to contribute to layer averages.
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<A HREF = "region.html">region</A> in order to contribute to bin 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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@ -105,17 +106,31 @@ produce global quantities.
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<P>The per-atom values of each input vector are binned and averaged
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independently of the per-atom values in other input vectors.
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</P>
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<P>The size and dimensionality of the bins (1d = layers or slabs, 2d =
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pencils, 3d = boxes) are determined by the <I>dim</I>, <I>origin</I>, and
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<I>delta</I> settings and how many times they are specified (1, 2, or 3).
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See details below.
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</P>
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<P>IMPORTANT NOTE: This fix works by creating an array of size Nbins by
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Nvalues on each processor. Nbins is the total number of bins; Nvalues
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is the number of input values specified. Each processor loops over
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its atoms, tallying its values to the appropriate bin. Then the
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entire array is summed across all processors. This means that using a
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large number of bins (easy to do for 2d or 3d bins) will incur an
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overhead in memory and computational cost (summing across processors),
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so be careful to use reasonable numbers of bins.
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</P>
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<HR>
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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 input values will be used to bin them into layers and
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contribute to the average. The final averaged quantities are
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generated every <I>Nfreq</I> timesteps. The average is over <I>Nrepeat</I>
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quantities, computed in the preceding portion of the simulation every
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<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
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<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
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contributing to the average value cannot overlap, i.e. Nfreq >
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(Nrepeat-1)*Nevery is required.
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timesteps the input values will be used to bin them and 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 preceding 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. Also, the timesteps contributing to the
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average value cannot overlap, i.e. Nfreq > (Nrepeat-1)*Nevery is
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required.
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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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@ -126,33 +141,38 @@ averaging is done; values are simply generated on timesteps
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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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simulation 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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<P>Each per-atom property is also averaged over atoms in each bin. Bins
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can be 1d layers or slabs, 2d pencils, or 3d boxes. This depends on
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how many times (1, 2, or 3) the <I>dim</I>, <I>origin</I>, and <I>delta</I> settings
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are specified in the fix ave/spatial command. For 2d or 3d bins,
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there is no restriction on specifying dim = x before dim = y, or dim =
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y before dim = z. Bins in a particular <I>dim</I> have a bin size in that
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dimension given by <I>delta</I>. Every Nfreq steps, when averaging is
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being performed and the per-atom property is calculated for the first
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time, the number of bins and the bin sizes and boundaries are
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computed. Thus if the simulation box changes size during a
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simulation, the number of bins and their boundaries may also change.
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In each dimension, bins are defined relative to a specified <I>origin</I>,
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which may be the lower/upper edge of the simulation box (in <I>dim</I>) or
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its center point, or a specified coordinate value. Starting at the
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origin, sufficient bins are created in both directions to completely
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cover the box. On subsequent timesteps every atom is mapped to one of
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the bins. Atoms beyond the lowermost/uppermost bin in a dimension are
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counted in the first/last bin in that dimension.
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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 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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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>For orthogonal simulation boxes, the bins are also layers, pencils, or
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boxes aligned with the xyz coordinate axes. For triclinic
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(non-orthogonal) simulation boxes, the bins are so that they are
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parallel to the tilted faces of the simulation box. See <A HREF = "Section_howto.html#4_12">this
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section</A> of the manual for a discussion of the
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geometry of triclinic boxes in LAMMPS. As described there, a tilted
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simulation box has edge vectors a,b,c. In that nomenclature, bins in
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the x dimension have faces with normals in the "b" cross "c"
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direction. Bins in y have faces normal to the "a" cross "c"
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direction. And bins in z have faces normal to the "a" cross "b"
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direction. Note that in order to define the size and position of
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these bins in an unambiguous fashion, the <I>units</I> option must be set
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to <I>reduced</I> when using a triclinic simulation box, as noted below.
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</P>
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<HR>
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@ -163,10 +183,10 @@ property/atom</A> command and then specifying
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an input value from that compute.
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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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each bin, 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 bind, 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 density are
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volume of the bin so that units of number/volume or density are
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output. See the <A HREF = "units.html">units</A> command doc page for the
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definition of density for each choice of units, e.g. gram/cm^3.
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</P>
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@ -198,7 +218,7 @@ quantities to spatially average.
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<P>Additional optional keywords also affect the operation of this fix.
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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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for the bin size <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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@ -211,63 +231,64 @@ 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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0.1 means 10 bins span the box in that 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>Consider a non-orthogonal box, with bins that are 1d layers or slabs
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in the x dimension. No matter how the box is tilted, an <I>origin</I> of
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0.0 means start layers at the lower "b" cross "c" plane of the
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simulation box and an <I>origin</I> of 1.0 means to start layers at the
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upper "b" cross "c" face of the box. A <I>delta</I> value of 0.1 means
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there will be 10 layers from 0.0 to 1.0, regardless of the current
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size or shape of the simulation box.
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</P>
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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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produced every <I>Nfreq</I> timesteps. For an <I>all</I> setting, a bin
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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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count of atoms in the bin. The printed value for the bin 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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<P>For a <I>sample</I> setting, the bin quantity is summed over atoms for only
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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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the bin 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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</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>The <I>ave</I> keyword determines how the bin values produced every <I>Nfreq</I>
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steps are averaged with bin values produced on previous steps that
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were multiples of <I>Nfreq</I>, before they are accessed by another output
|
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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 layer values produced on
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<P>If the <I>ave</I> setting is <I>one</I>, then the bin 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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<P>If the <I>ave</I> setting is <I>running</I>, then the bin 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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cumulative sense before being output. Each output layer value is
|
||||
thus the average of the layer value produced on that timestep with all
|
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preceding values for the same layer. This running average begins
|
||||
when the fix is defined; it can only be restarted by deleting the fix
|
||||
via the <A HREF = "unfix.html">unfix</A> command, or re-defining the fix by
|
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cumulative sense before being output. Each output bin value is thus
|
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the average of the bin value produced on that timestep with all
|
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preceding values for the same bin. This running average begins when
|
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the fix is defined; it can only be restarted by deleting the fix via
|
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the <A HREF = "unfix.html">unfix</A> command, or re-defining the fix by
|
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re-specifying it.
|
||||
</P>
|
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<P>If the <I>ave</I> setting is <I>window</I>, then the layer values produced on
|
||||
<P>If the <I>ave</I> setting is <I>window</I>, then the bin values produced on
|
||||
timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
|
||||
a moving "window" of time, so that the last M values for the same
|
||||
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
|
||||
average over less than M values if they are not available.
|
||||
a moving "window" of time, so that the last M values for the same bin
|
||||
are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then
|
||||
the output on step 10000 will be the average of the individual bin
|
||||
values on steps 8000,9000,10000. Outputs on early steps will average
|
||||
over less than M values if they are not available.
|
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</P>
|
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<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
|
||||
timesteps, a section of layer info will be written to a text file in
|
||||
the following format. A line with the timestep and number of layers
|
||||
is written. Then one line per layer is written, containing the layer
|
||||
ID (1-N), the coordinate of the center of the layer, the number of
|
||||
atoms in the layer, and one or more calculated values. The number of
|
||||
values in each line corresponds to the number of values specified in
|
||||
the fix ave/spatial command. The number of atoms and the value(s) are
|
||||
average quantities. If the value of the <I>units</I> keyword is <I>box</I> or
|
||||
timesteps, a section of bin info will be written to a text file in the
|
||||
following format. A line with the timestep and number of bin is
|
||||
written. Then one line per bin is written, containing the bin ID
|
||||
(1-N), the coordinate of the center of the bin, the number of atoms
|
||||
in the bin, and one or more calculated values. The number of values
|
||||
in each line corresponds to the number of values specified in the fix
|
||||
ave/spatial command. The number of atoms and the value(s) are average
|
||||
quantities. If the value of the <I>units</I> keyword is <I>box</I> or
|
||||
<I>lattice</I>, the "coord" is printed in box units. If the value of the
|
||||
<I>units</I> keyword is <I>reduced</I>, the "coord" is printed in reduced units
|
||||
(0-1).
|
||||
|
|
@ -280,13 +301,16 @@ values for each of these, so they do not need to be specified.
|
|||
<P>By default, these header lines are as follows:
|
||||
</P>
|
||||
<PRE># Spatial-averaged data for fix ID and group name
|
||||
# Timestep Number-of-layers
|
||||
# Layer Coord Count value1 value2 ...
|
||||
# Timestep Number-of-bins
|
||||
# Bin Coord1 Coord2 Coord3 Count value1 value2 ...
|
||||
</PRE>
|
||||
<P>In the first line, ID and name are replaced with the fix-ID and group
|
||||
name. The second line describes the two values that are printed at
|
||||
the first of each section of output. In the third line the values are
|
||||
replaced with the appropriate fields from the fix ave/spatial command.
|
||||
The Coord2 and Coord3 entries in the third line only appear for 2d and
|
||||
3d bins respectively. For 1d bins, the word Coord1 is replaced by
|
||||
just Coord.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
|
@ -300,15 +324,17 @@ are relevant to this fix.
|
|||
various <A HREF = "Section_howto.html#4_15">output commands</A>. The values can
|
||||
only be accessed on timesteps that are multiples of <I>Nfreq</I> since that
|
||||
is when averaging is performed. The global array has # of rows =
|
||||
Nlayers and # of columns = Nvalues+2. The first column has the layer
|
||||
coordinate (center of the layer), the 2nd column has the count of
|
||||
atoms in that layer, and the remaining columns are the Nvalue
|
||||
quantities. When the array is accessed with an I that exceeds the
|
||||
current number of layers, than a 0.0 is returned by the fix instead of
|
||||
an error, since the number of layers can vary as a simulation runs,
|
||||
depending on the simulation box size. The array values calculated by
|
||||
this fix are "intensive", since they are already normalized by the
|
||||
count of atoms in each layer.
|
||||
Nbins and # of columns = Ndim+1+Nvalues, where Ndim = 1,2,3 for
|
||||
1d,2d,3d bins. The first 1 or 2 or 3 columns have the bin coordinates
|
||||
(center of the bin) in the appropriate dimensions, the next column has
|
||||
the count of atoms in that bin, and the remaining columns are the
|
||||
Nvalue quantities. When the array is accessed with an I that exceeds
|
||||
the current number of bins, than a 0.0 is returned by the fix instead
|
||||
of an error, since the number of bins can vary as a simulation runs,
|
||||
depending on the simulation box size. 2d or 3d bins are ordered so
|
||||
that the last dimension(s) vary fastest. The array values calculated
|
||||
by this fix are "intensive", since they are already normalized by the
|
||||
count of atoms in each bin.
|
||||
</P>
|
||||
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
|
||||
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
|
||||
|
|
@ -317,7 +343,7 @@ minimization</A>.
|
|||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>When the <I>ave</I> keyword is set to <I>running</I> or <I>window</I> then the number
|
||||
of layers must remain the same during the simulation, so that the
|
||||
of bins must remain the same during the simulation, so that the
|
||||
appropriate averaging can be done. This will be the case if the
|
||||
simulation box size doesn't change or if the <I>units</I> keyword is set to
|
||||
<I>reduced</I>.
|
||||
|
|
|
|||
|
|
@ -10,16 +10,17 @@ fix ave/spatial command :h3
|
|||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta value1 value2 ... keyword args ... :pre
|
||||
fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta ... value1 value2 ... keyword args ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
ave/spatial = style name of this fix command :l
|
||||
Nevery = use input values every this many timesteps :l
|
||||
Nrepeat = # of times to use input values for calculating averages :l
|
||||
Nfreq = calculate averages every this many timesteps :l
|
||||
dim = {x} or {y} or {z} :l
|
||||
origin = {lower} or {center} or {upper} or coordinate value (distance units) :l
|
||||
delta = thickness of spatial layers in dim (distance units) :l
|
||||
dim, origin, delta can be repeated 1, 2, or 3 times for 1d, 2d, or 3d bins :l
|
||||
dim = {x} or {y} or {z}
|
||||
origin = {lower} or {center} or {upper} or coordinate value (distance units)
|
||||
delta = thickness of spatial bins in dim (distance units) :pre
|
||||
one or more input values can be listed :l
|
||||
value = x, y, z, vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name :l
|
||||
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
|
||||
|
|
@ -55,20 +56,21 @@ keyword = {norm} or {units} or {file} or {ave} or {title1} or {title2} or {title
|
|||
fix 1 all ave/spatial 10000 1 10000 z lower 0.02 c_myCentro units reduced &
|
||||
title1 "My output values"
|
||||
fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
|
||||
fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 density/mass ave running :pre
|
||||
fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass ave running :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Use one or more per-atom vectors as inputs every few timesteps, bin
|
||||
them spatially by layer in a dimension, and average the layer values
|
||||
over longer timescales. The resulting layer averages can be used by
|
||||
other "output commands"_Section_howto.html#4_15 such as "thermo_style
|
||||
their values spatially into 1d, 2d, or 3d bins based on current atom
|
||||
coordinates, and average the bin values over longer timescales. The
|
||||
resulting bin averages can be used by other "output
|
||||
commands"_Section_howto.html#4_15 such as "thermo_style
|
||||
custom"_thermo_style.html, and can also be written to a file.
|
||||
|
||||
The group specified with the command means only atoms within the group
|
||||
contribute to layer averages. If the {region} keyword is used, the
|
||||
contribute to bin averages. If the {region} keyword is used, the
|
||||
atom must be in both the group and the specified geometric
|
||||
"region"_region.html in order to contribute to layer averages.
|
||||
"region"_region.html in order to contribute to bin averages.
|
||||
|
||||
Each listed value can be an atom attribute (position, velocity, force
|
||||
component), a mass or number density, or the result of a
|
||||
|
|
@ -89,17 +91,31 @@ produce global quantities.
|
|||
The per-atom values of each input vector are binned and averaged
|
||||
independently of the per-atom values in other input vectors.
|
||||
|
||||
The size and dimensionality of the bins (1d = layers or slabs, 2d =
|
||||
pencils, 3d = boxes) are determined by the {dim}, {origin}, and
|
||||
{delta} settings and how many times they are specified (1, 2, or 3).
|
||||
See details below.
|
||||
|
||||
IMPORTANT NOTE: This fix works by creating an array of size Nbins by
|
||||
Nvalues on each processor. Nbins is the total number of bins; Nvalues
|
||||
is the number of input values specified. Each processor loops over
|
||||
its atoms, tallying its values to the appropriate bin. Then the
|
||||
entire array is summed across all processors. This means that using a
|
||||
large number of bins (easy to do for 2d or 3d bins) will incur an
|
||||
overhead in memory and computational cost (summing across processors),
|
||||
so be careful to use reasonable numbers of bins.
|
||||
|
||||
:line
|
||||
|
||||
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
|
||||
timesteps the input values will be used to bin them into layers and
|
||||
contribute to the average. The final averaged quantities are
|
||||
generated every {Nfreq} timesteps. The average is over {Nrepeat}
|
||||
quantities, computed in the preceding portion of the simulation every
|
||||
{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and
|
||||
{Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps
|
||||
contributing to the average value cannot overlap, i.e. Nfreq >
|
||||
(Nrepeat-1)*Nevery is required.
|
||||
timesteps the input values will be used to bin them and contribute to
|
||||
the average. The final averaged quantities are generated every
|
||||
{Nfreq} timesteps. The average is over {Nrepeat} quantities, computed
|
||||
in the preceding portion of the simulation every {Nevery} timesteps.
|
||||
{Nfreq} must be a multiple of {Nevery} and {Nevery} must be non-zero
|
||||
even if {Nrepeat} is 1. Also, the timesteps contributing to the
|
||||
average value cannot overlap, i.e. Nfreq > (Nrepeat-1)*Nevery is
|
||||
required.
|
||||
|
||||
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
|
||||
timesteps 90,92,94,96,98,100 will be used to compute the final average
|
||||
|
|
@ -110,33 +126,38 @@ averaging is done; values are simply generated on timesteps
|
|||
|
||||
:line
|
||||
|
||||
Each per-atom property is also averaged over atoms in each layer,
|
||||
where the layers are in a particular {dim} and have a thickness given
|
||||
by {delta}. Every Nfreq steps, when an averaging is being performed
|
||||
and the per-atom property is calculated for the first time, the number
|
||||
of layers and the layer boundaries are computed. Thus if the
|
||||
simulation box changes size during a simulation, the number of layers
|
||||
and their boundaries may also change. Layers are defined relative to
|
||||
a specified {origin}, which may be the lower/upper edge of the box (in
|
||||
{dim}) or its center point, or a specified coordinate value. Starting
|
||||
at the origin, sufficient layers are created in both directions to
|
||||
completely cover the box. On subsequent timesteps every atom is
|
||||
mapped to one of the layers. Atoms beyond the lowermost/uppermost
|
||||
layer are counted in the first/last layer.
|
||||
Each per-atom property is also averaged over atoms in each bin. Bins
|
||||
can be 1d layers or slabs, 2d pencils, or 3d boxes. This depends on
|
||||
how many times (1, 2, or 3) the {dim}, {origin}, and {delta} settings
|
||||
are specified in the fix ave/spatial command. For 2d or 3d bins,
|
||||
there is no restriction on specifying dim = x before dim = y, or dim =
|
||||
y before dim = z. Bins in a particular {dim} have a bin size in that
|
||||
dimension given by {delta}. Every Nfreq steps, when averaging is
|
||||
being performed and the per-atom property is calculated for the first
|
||||
time, the number of bins and the bin sizes and boundaries are
|
||||
computed. Thus if the simulation box changes size during a
|
||||
simulation, the number of bins and their boundaries may also change.
|
||||
In each dimension, bins are defined relative to a specified {origin},
|
||||
which may be the lower/upper edge of the simulation box (in {dim}) or
|
||||
its center point, or a specified coordinate value. Starting at the
|
||||
origin, sufficient bins are created in both directions to completely
|
||||
cover the box. On subsequent timesteps every atom is mapped to one of
|
||||
the bins. Atoms beyond the lowermost/uppermost bin in a dimension are
|
||||
counted in the first/last bin in that dimension.
|
||||
|
||||
For orthogonal simulation boxes, the layers are "slices" aligned with
|
||||
the xyz coordinate axes. For non-orthogonal (triclinic) simulation
|
||||
boxes, the layers are "tilted slices" that are parallel to the tilted
|
||||
faces of the box. See the "region prism"_region.html command for a
|
||||
discussion of the geometry of tilted boxes in LAMMPS. As described
|
||||
there, a tilted simulation box has edge vectors a,b,c. In that
|
||||
nomenclature, layers in the x dimension have faces with normals in the
|
||||
"b" cross "c" direction. Layers in y have faces normal to the "a"
|
||||
cross "c" direction. And layers in z have faces normal to the "a"
|
||||
cross "b" direction. Note that in order to define the thickness and
|
||||
position of these tilted layers in an unambiguous fashion, the {units}
|
||||
option must be set to {reduced} when using a non-orthogonal simulation
|
||||
box, as discussed below.
|
||||
For orthogonal simulation boxes, the bins are also layers, pencils, or
|
||||
boxes aligned with the xyz coordinate axes. For triclinic
|
||||
(non-orthogonal) simulation boxes, the bins are so that they are
|
||||
parallel to the tilted faces of the simulation box. See "this
|
||||
section"_Section_howto.html#4_12 of the manual for a discussion of the
|
||||
geometry of triclinic boxes in LAMMPS. As described there, a tilted
|
||||
simulation box has edge vectors a,b,c. In that nomenclature, bins in
|
||||
the x dimension have faces with normals in the "b" cross "c"
|
||||
direction. Bins in y have faces normal to the "a" cross "c"
|
||||
direction. And bins in z have faces normal to the "a" cross "b"
|
||||
direction. Note that in order to define the size and position of
|
||||
these bins in an unambiguous fashion, the {units} option must be set
|
||||
to {reduced} when using a triclinic simulation box, as noted below.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -147,10 +168,10 @@ property/atom"_compute_property_atom.html command and then specifying
|
|||
an input value from that compute.
|
||||
|
||||
The {density/number} value means the number density is computed in
|
||||
each layer, i.e. a weighting of 1 for each atom. The {density/mass}
|
||||
value means the mass density is computed in each layer, i.e. each atom
|
||||
each bin, i.e. a weighting of 1 for each atom. The {density/mass}
|
||||
value means the mass density is computed in each bind, i.e. each atom
|
||||
is weighted by its mass. The resulting density is normalized by the
|
||||
volume of the layer so that units of number/volume or density are
|
||||
volume of the bin so that units of number/volume or density are
|
||||
output. See the "units"_units.html command doc page for the
|
||||
definition of density for each choice of units, e.g. gram/cm^3.
|
||||
|
||||
|
|
@ -182,7 +203,7 @@ quantities to spatially average.
|
|||
Additional optional keywords also affect the operation of this fix.
|
||||
|
||||
The {units} keyword determines the meaning of the distance units used
|
||||
for the layer thickness {delta} and for {origin} if it is a coordinate
|
||||
for the bin size {delta} and for {origin} if it is a coordinate
|
||||
value. For orthogonal simulation boxes, any of the 3 options may be
|
||||
used. For non-orthogonal (triclinic) simulation boxes, only the
|
||||
{reduced} option may be used.
|
||||
|
|
@ -195,63 +216,64 @@ define the lattice spacing. A {reduced} value means normalized
|
|||
unitless values between 0 and 1, which represent the lower and upper
|
||||
faces of the simulation box respectively. Thus an {origin} value of
|
||||
0.5 means the center of the box in any dimension. A {delta} value of
|
||||
0.1 means 10 layers span the box in any dimension.
|
||||
0.1 means 10 bins span the box in that dimension.
|
||||
|
||||
Consider a non-orthogonal box, with layers in the x dimension. No
|
||||
matter how the box is tilted, an {origin} of 0.0 means start layers at
|
||||
the lower "b" cross "c" plane of the simulation box and an {origin} of
|
||||
1.0 means to start layers at the upper "b" cross "c" face of the box.
|
||||
A {delta} value of 0.1 means there will be 10 layers from 0.0 to 1.0,
|
||||
regardless of the current size or shape of the simulation box.
|
||||
Consider a non-orthogonal box, with bins that are 1d layers or slabs
|
||||
in the x dimension. No matter how the box is tilted, an {origin} of
|
||||
0.0 means start layers at the lower "b" cross "c" plane of the
|
||||
simulation box and an {origin} of 1.0 means to start layers at the
|
||||
upper "b" cross "c" face of the box. A {delta} value of 0.1 means
|
||||
there will be 10 layers from 0.0 to 1.0, regardless of the current
|
||||
size or shape of the simulation box.
|
||||
|
||||
The {norm} keyword affects how averaging is done for the output
|
||||
produced every {Nfreq} timesteps. For an {all} setting, a layer
|
||||
produced every {Nfreq} timesteps. For an {all} setting, a bin
|
||||
quantity is summed over all atoms in all {Nrepeat} samples, as is the
|
||||
count of atoms in the layer. The printed value for the layer is
|
||||
count of atoms in the bin. The printed value for the bin is
|
||||
Total-quantity / Total-count. In other words it is an average over
|
||||
the entire {Nfreq} timescale.
|
||||
|
||||
For a {sample} setting, the layer quantity is summed over atoms for
|
||||
only a single sample, as is the count, and a "average sample value" is
|
||||
For a {sample} setting, the bin quantity is summed over atoms for only
|
||||
a single sample, as is the count, and a "average sample value" is
|
||||
computed, i.e. Sample-quantity / Sample-count. The printed value for
|
||||
the layer is the average of the {Nrepeat} "average sample values", In
|
||||
the bin is the average of the {Nrepeat} "average sample values", In
|
||||
other words it is an average of an average.
|
||||
|
||||
The {ave} keyword determines how the layer values produced every
|
||||
{Nfreq} steps are averaged with layer values produced on previous
|
||||
steps that were multiples of {Nfreq}, before they are accessed by
|
||||
another output command or written to a file.
|
||||
The {ave} keyword determines how the bin values produced every {Nfreq}
|
||||
steps are averaged with bin values produced on previous steps that
|
||||
were multiples of {Nfreq}, before they are accessed by another output
|
||||
command or written to a file.
|
||||
|
||||
If the {ave} setting is {one}, then the layer values produced on
|
||||
If the {ave} setting is {one}, then the bin values produced on
|
||||
timesteps that are multiples of {Nfreq} are independent of each other;
|
||||
they are output as-is without further averaging.
|
||||
|
||||
If the {ave} setting is {running}, then the layer values produced on
|
||||
If the {ave} setting is {running}, then the bin values produced on
|
||||
timesteps that are multiples of {Nfreq} are summed and averaged in a
|
||||
cumulative sense before being output. Each output layer value is
|
||||
thus the average of the layer value produced on that timestep with all
|
||||
preceding values for the same layer. This running average begins
|
||||
when the fix is defined; it can only be restarted by deleting the fix
|
||||
via the "unfix"_unfix.html command, or re-defining the fix by
|
||||
cumulative sense before being output. Each output bin value is thus
|
||||
the average of the bin value produced on that timestep with all
|
||||
preceding values for the same bin. This running average begins when
|
||||
the fix is defined; it can only be restarted by deleting the fix via
|
||||
the "unfix"_unfix.html command, or re-defining the fix by
|
||||
re-specifying it.
|
||||
|
||||
If the {ave} setting is {window}, then the layer values produced on
|
||||
If the {ave} setting is {window}, then the bin values produced on
|
||||
timesteps that are multiples of {Nfreq} are summed and averaged within
|
||||
a moving "window" of time, so that the last M values for the same
|
||||
layer are used to produce the output. E.g. if M = 3 and Nfreq = 1000,
|
||||
then the output on step 10000 will be the average of the individual
|
||||
layer values on steps 8000,9000,10000. Outputs on early steps will
|
||||
average over less than M values if they are not available.
|
||||
a moving "window" of time, so that the last M values for the same bin
|
||||
are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then
|
||||
the output on step 10000 will be the average of the individual bin
|
||||
values on steps 8000,9000,10000. Outputs on early steps will average
|
||||
over less than M values if they are not available.
|
||||
|
||||
The {file} keyword allows a filename to be specified. Every {Nfreq}
|
||||
timesteps, a section of layer info will be written to a text file in
|
||||
the following format. A line with the timestep and number of layers
|
||||
is written. Then one line per layer is written, containing the layer
|
||||
ID (1-N), the coordinate of the center of the layer, the number of
|
||||
atoms in the layer, and one or more calculated values. The number of
|
||||
values in each line corresponds to the number of values specified in
|
||||
the fix ave/spatial command. The number of atoms and the value(s) are
|
||||
average quantities. If the value of the {units} keyword is {box} or
|
||||
timesteps, a section of bin info will be written to a text file in the
|
||||
following format. A line with the timestep and number of bin is
|
||||
written. Then one line per bin is written, containing the bin ID
|
||||
(1-N), the coordinate of the center of the bin, the number of atoms
|
||||
in the bin, and one or more calculated values. The number of values
|
||||
in each line corresponds to the number of values specified in the fix
|
||||
ave/spatial command. The number of atoms and the value(s) are average
|
||||
quantities. If the value of the {units} keyword is {box} or
|
||||
{lattice}, the "coord" is printed in box units. If the value of the
|
||||
{units} keyword is {reduced}, the "coord" is printed in reduced units
|
||||
(0-1).
|
||||
|
|
@ -264,13 +286,16 @@ values for each of these, so they do not need to be specified.
|
|||
By default, these header lines are as follows:
|
||||
|
||||
# Spatial-averaged data for fix ID and group name
|
||||
# Timestep Number-of-layers
|
||||
# Layer Coord Count value1 value2 ... :pre
|
||||
# Timestep Number-of-bins
|
||||
# Bin Coord1 Coord2 Coord3 Count value1 value2 ... :pre
|
||||
|
||||
In the first line, ID and name are replaced with the fix-ID and group
|
||||
name. The second line describes the two values that are printed at
|
||||
the first of each section of output. In the third line the values are
|
||||
replaced with the appropriate fields from the fix ave/spatial command.
|
||||
The Coord2 and Coord3 entries in the third line only appear for 2d and
|
||||
3d bins respectively. For 1d bins, the word Coord1 is replaced by
|
||||
just Coord.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -284,15 +309,17 @@ This fix computes a global array of values which can be accessed by
|
|||
various "output commands"_Section_howto.html#4_15. The values can
|
||||
only be accessed on timesteps that are multiples of {Nfreq} since that
|
||||
is when averaging is performed. The global array has # of rows =
|
||||
Nlayers and # of columns = Nvalues+2. The first column has the layer
|
||||
coordinate (center of the layer), the 2nd column has the count of
|
||||
atoms in that layer, and the remaining columns are the Nvalue
|
||||
quantities. When the array is accessed with an I that exceeds the
|
||||
current number of layers, than a 0.0 is returned by the fix instead of
|
||||
an error, since the number of layers can vary as a simulation runs,
|
||||
depending on the simulation box size. The array values calculated by
|
||||
this fix are "intensive", since they are already normalized by the
|
||||
count of atoms in each layer.
|
||||
Nbins and # of columns = Ndim+1+Nvalues, where Ndim = 1,2,3 for
|
||||
1d,2d,3d bins. The first 1 or 2 or 3 columns have the bin coordinates
|
||||
(center of the bin) in the appropriate dimensions, the next column has
|
||||
the count of atoms in that bin, and the remaining columns are the
|
||||
Nvalue quantities. When the array is accessed with an I that exceeds
|
||||
the current number of bins, than a 0.0 is returned by the fix instead
|
||||
of an error, since the number of bins can vary as a simulation runs,
|
||||
depending on the simulation box size. 2d or 3d bins are ordered so
|
||||
that the last dimension(s) vary fastest. The array values calculated
|
||||
by this fix are "intensive", since they are already normalized by the
|
||||
count of atoms in each bin.
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command. This fix is not invoked during "energy
|
||||
|
|
@ -301,7 +328,7 @@ minimization"_minimize.html.
|
|||
[Restrictions:]
|
||||
|
||||
When the {ave} keyword is set to {running} or {window} then the number
|
||||
of layers must remain the same during the simulation, so that the
|
||||
of bins must remain the same during the simulation, so that the
|
||||
appropriate averaging can be done. This will be the case if the
|
||||
simulation box size doesn't change or if the {units} keyword is set to
|
||||
{reduced}.
|
||||
|
|
|
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Reference in New Issue