forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@326 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
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commit
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@ -13,26 +13,45 @@
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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 Nfreq dim origin delta file keyword value ...
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<PRE>fix ID group-ID ave/spatial Nevery 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>Nfreq = write average property to file every this many steps
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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
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<LI>delta = thickness of spatial layers in dim
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<LI>file = filename to write results to
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<LI>keyword = <I>density</I> or <I>atom</I> or <I>compute</I>
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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>Nfreq = write average property to file every this many steps
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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>atom</I> or <I>compute</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>atom</I> arg = <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>fx</I> or <I>fy</I> or <I>fz</I>
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<I>compute</I> arg = compute-ID that calculates per-atom quantities
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</PRE>
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<LI>zero or more keyword/value pairs may be appended to the args
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<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>
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</PRE>
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</UL>
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<PRE> <I>density</I> value = none
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<I>atom</I> value = <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>fx</I> or <I>fy</I> or <I>fz</I>
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<I>compute value</I> = compute-ID that calculates per-atom quantities
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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all ave/time 10000 10000 z lower 2.0 centro.profile compute myCentro
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fix 1 flow ave/time 100 1000 y 0.0 1.0 vel.profile atom vx
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fix 1 flow ave/time 100 1000 y 0.0 1.0 vel.profile atom vx norm sample
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fix 1 flow ave/time 100 1000 y 0.0 1.0 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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@ -43,20 +62,20 @@ to spatially average per-atom properties such as velocity or energy or
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a quantity calculated by an equation you define; see the <A HREF = "variable.html">variable
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atom</A> command.
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</P>
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<P>The <I>density</I> keyword means to simply count the number of atoms in
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each layer. The <I>atom</I> keyword allows an atom property such as
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x-velocity to be specified. The <I>compute</I> keyword 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. Note that the "compute variable/atom" style
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allows you to calculate any quantity for an atom that can be specified
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by a <A HREF = "variable.html">variable atom</A> equation. Users can also write
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code for their own compute styles and <A HREF = "Section_modify.html">add them to
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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>atom</I> style allows an atom
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property such as x-velocity to be specified. The <I>compute</I> style
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allows specification of a <A HREF = "compute.html">compute</A> which will be invoked
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to calculate the desired property. The compute can be previously
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defined in the input script. Note that the "compute variable/atom"
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style allows you to calculate any quantity for an atom that can be
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specified by a <A HREF = "variable.html">variable atom</A> equation. Users can also
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write code for their own compute styles and <A HREF = "Section_modify.html">add them to
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LAMMPS</A>. Note that the <A HREF = "dump.html">dump custom</A>
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command can also be used to output per-atom quantities calculated by a
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compute.
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</P>
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<P>For the <I>compute</I> keyword, the fix ave/spatial style uses the per-atom
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<P>For the <I>compute</I> style, the fix ave/spatial style uses the per-atom
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scalar or vector calculated by the compute. See the <A HREF = "fix_ave_time.html">fix
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ave/time</A> command if you wish to time-average a
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global quantity, e.g. via a compute that temperature or pressure.
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@ -75,6 +94,14 @@ 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>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 <I>origin</I> if it is a coordinate
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value. A <I>box</I> value selects standard distance units as defined by
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the <A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or
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metal. A <I>lattice</I> value means the distance units are in lattice
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spacings. The <A HREF = "lattice.html">lattice</A> command must have been
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previously used to define the lattice spacing.
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</P>
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<P>The <I>Nevery</I> and <I>Nfreq</I> arguments specify how the property calculated
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for each layer is time-averaged. The property is calculated once each
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Nevery timesteps. It is averaged and output every Nfreq timesteps.
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@ -82,6 +109,18 @@ Nfreq must be a multiple of Nevery. In the 2nd example above, the
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property is calculated every 100 steps. After 10 calculations, the
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average result is written to the file, once every 1000 steps.
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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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is used with a compute that calculates N quantities per atom, then N
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values per line will be written, each of them averaged independently.
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</P>
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<P>Note that for the <I>density</I> keyword, the printed count of atoms in the
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layer is actually what you should use to infer a density. The
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calculated value is always 1.0, since it is normalized by the number
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of atoms in the layer.
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</P>
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<P>For the <I>compute</I> keyword, the calculation performed by the compute in
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on the group defined by the compute. However, only atoms in the fix
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group are included in the layer averaging. LAMMPS prints a warning if
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@ -115,6 +149,8 @@ fix ave/spatial, it can slow down a simulation.
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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> none
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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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@ -10,25 +10,35 @@ fix ave/spatial command :h3
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[Syntax:]
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fix ID group-ID ave/spatial Nevery Nfreq dim origin delta file keyword value ... :pre
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fix ID group-ID ave/spatial Nevery Nfreq dim origin delta file style args keyword value ... :pre
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ID, group-ID are documented in "fix"_fix.html command
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ave/spatial = style name of this fix command
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Nevery = calculate property every this many timesteps
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Nfreq = write average property to file every this many steps
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dim = {x} or {y} or {z}
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origin = {lower} or {center} or {upper} or coordinate value
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delta = thickness of spatial layers in dim
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file = filename to write results to
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keyword = {density} or {atom} or {compute} :ul
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{density} value = none
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{atom} value = {vx} or {vy} or {vz} or {fx} or {fy} or {fz}
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{compute value} = compute-ID that calculates per-atom quantities :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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ave/spatial = style name of this fix command :l
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Nevery = calculate property every this many timesteps :l
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Nfreq = write average property to file every this many steps :l
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dim = {x} or {y} or {z} :l
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origin = {lower} or {center} or {upper} or coordinate value (distance units) :l
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delta = thickness of spatial layers in dim (distance units) :l
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file = filename to write results to :l
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style = {density} or {atom} or {compute} :l
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{density} arg = {mass} or {number}
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{mass} = compute mass density
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{number} = compute number density
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{atom} arg = {vx} or {vy} or {vz} or {fx} or {fy} or {fz}
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{compute} arg = compute-ID that calculates per-atom quantities :pre
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zero or more keyword/value pairs may be appended to the args :l
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keyword = {norm} or {units}
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{norm} value = {all} or {sample}
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{units} value = {box} or {lattice} :pre
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:ule
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[Examples:]
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fix 1 all ave/time 10000 10000 z lower 2.0 centro.profile compute myCentro
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fix 1 flow ave/time 100 1000 y 0.0 1.0 vel.profile atom vx :pre
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fix 1 flow ave/time 100 1000 y 0.0 1.0 vel.profile atom vx norm sample
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fix 1 flow ave/time 100 1000 y 0.0 1.0 dens.profile density mass :pre
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[Description:]
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@ -39,20 +49,20 @@ to spatially average per-atom properties such as velocity or energy or
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a quantity calculated by an equation you define; see the "variable
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atom"_variable.html command.
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The {density} keyword means to simply count the number of atoms in
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each layer. The {atom} keyword allows an atom property such as
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x-velocity to be specified. The {compute} keyword allows
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specification of a "compute"_compute.html 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. Note that the "compute variable/atom" style
|
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allows you to calculate any quantity for an atom that can be specified
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by a "variable atom"_variable.html equation. Users can also write
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code for their own compute styles and "add them to
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The {density} styles means to simply count the number of atoms in each
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layer, either by mass or number. The {atom} style allows an atom
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property such as x-velocity to be specified. The {compute} style
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allows specification of a "compute"_compute.html which will be invoked
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to calculate the desired property. The compute can be previously
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defined in the input script. Note that the "compute variable/atom"
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style allows you to calculate any quantity for an atom that can be
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specified by a "variable atom"_variable.html equation. Users can also
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write code for their own compute styles and "add them to
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LAMMPS"_Section_modify.html. Note that the "dump custom"_dump.html
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command can also be used to output per-atom quantities calculated by a
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compute.
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For the {compute} keyword, the fix ave/spatial style uses the per-atom
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For the {compute} style, the fix ave/spatial style uses the per-atom
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scalar or vector calculated by the compute. See the "fix
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ave/time"_fix_ave_time.html command if you wish to time-average a
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global quantity, e.g. via a compute that temperature or pressure.
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@ -71,6 +81,14 @@ 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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The {units} keyword determines the meaning of the distance units used
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for the layer thickness {delta} and {origin} if it is a coordinate
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value. A {box} value selects standard distance units as defined by
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the "units"_units.html command, e.g. Angstroms for units = real or
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metal. A {lattice} value means the distance units are in lattice
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spacings. The "lattice"_lattice.html command must have been
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previously used to define the lattice spacing.
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The {Nevery} and {Nfreq} arguments specify how the property calculated
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for each layer is time-averaged. The property is calculated once each
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Nevery timesteps. It is averaged and output every Nfreq timesteps.
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@ -78,6 +96,18 @@ Nfreq must be a multiple of Nevery. In the 2nd example above, the
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property is calculated every 100 steps. After 10 calculations, the
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average result is written to the file, once every 1000 steps.
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The {norm} keyword also affects how time-averaging is done. For an
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{all} 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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For a {sample} 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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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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|
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@ -91,11 +121,6 @@ single value will be printed for each layer. If the {compute} keyword
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is used with a compute that calculates N quantities per atom, then N
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values per line will be written, each of them averaged independently.
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Note that for the {density} keyword, the printed count of atoms in the
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layer is actually what you should use to infer a density. The
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calculated value is always 1.0, since it is normalized by the number
|
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of atoms in the layer.
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For the {compute} keyword, the calculation performed by the compute in
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on the group defined by the compute. However, only atoms in the fix
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group are included in the layer averaging. LAMMPS prints a warning if
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@ -111,4 +136,7 @@ fix ave/spatial, it can slow down a simulation.
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"compute"_compute.html, "fix ave/time"_fix_ave_time.html
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[Default:] none
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[Default:]
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The option defaults are norm = all and units = lattice.
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|
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@ -24,14 +24,14 @@
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seed = random # seed (8 digits or less)
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<I>set</I> args = vx vy vz
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vx,vy,vz = velocity value or NULL (velocity units)
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<I>scale</I> args = temp
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<I>scale</I> arg = temp
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temp = temperature value (temperature units)
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<I>ramp</I> args = vdim vlo vhi dim clo chi
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vdim = <I>vx</I> or <I>vy</I> or <I>vz</I>
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vlo,vhi = lower and upper velocity value (velocity units)
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dim = <I>x</I> or <I>y</I> or <I>z</I>
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clo,chi = lower and upper coordinate bound (distance units)
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<I>zero</I> args = <I>linear</I> or <I>angular</I>
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<I>zero</I> arg = <I>linear</I> or <I>angular</I>
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<I>linear</I> = zero the linear momentum
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<I>angular</I> = zero the angular momentum
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</PRE>
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|
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@ -19,14 +19,14 @@ style = {create} or {set} or {scale} or {ramp} or {zero} :l
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seed = random # seed (8 digits or less)
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{set} args = vx vy vz
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vx,vy,vz = velocity value or NULL (velocity units)
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{scale} args = temp
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{scale} arg = temp
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temp = temperature value (temperature units)
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{ramp} args = vdim vlo vhi dim clo chi
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vdim = {vx} or {vy} or {vz}
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vlo,vhi = lower and upper velocity value (velocity units)
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dim = {x} or {y} or {z}
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clo,chi = lower and upper coordinate bound (distance units)
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{zero} args = {linear} or {angular}
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{zero} arg = {linear} or {angular}
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{linear} = zero the linear momentum
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{angular} = zero the angular momentum :pre
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Loading…
Reference in New Issue