2009-12-15 09:21:23 +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/histo command
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</H3>
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<P><B>Syntax:</B>
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</P>
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2010-04-29 21:48:00 +08:00
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<PRE>fix ID group-ID ave/histo Nevery Nrepeat Nfreq lo hi Nbin value1 value2 ... keyword args ...
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2009-12-15 09:21:23 +08:00
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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/histo = style name of this fix command
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<LI>Nevery = use input values every this many timesteps
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<LI>Nrepeat = # of times to use input values for calculating histogram
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2011-02-22 06:32:31 +08:00
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<LI>Nfreq = calculate histogram every this many timesteps
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<LI>lo,hi = lo/hi bounds within which to histogram
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<LI>Nbin = # of histogram bins
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<LI>one or more input values can be listed
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2009-12-16 00:27:48 +08:00
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<LI>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
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2010-01-30 00:16:38 +08:00
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<PRE> x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
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c_ID = scalar or vector calculated by a compute with ID
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2009-12-15 09:21:23 +08:00
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c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID
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f_ID = scalar or vector calculated by a fix with ID
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f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID
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v_name = value(s) calculated by an equal-style or atom-style variable with name
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</PRE>
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<LI>zero or more keyword/arg pairs may be appended
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<LI>keyword = <I>mode</I> or <I>file</I> or <I>ave</I> or <I>start</I> or <I>beyond</I> or <I>title1</I> or <I>title2</I> or <I>title3</I>
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<PRE> <I>mode</I> arg = <I>scalar</I> or <I>vector</I>
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scalar = all input values are scalars
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vector = all input values are vectors
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<I>file</I> arg = filename
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filename = name of file to output histogram(s) to
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2009-12-16 00:47:17 +08:00
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<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window</I>
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2009-12-15 09:21:23 +08:00
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one = output a new average value every Nfreq steps
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running = output cumulative average of all previous Nfreq steps
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2009-12-16 00:47:17 +08:00
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window M = output average of M most recent Nfreq steps
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2009-12-15 09:21:23 +08:00
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<I>start</I> args = Nstart
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Nstart = start averaging on this timestep
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<I>beyond</I> arg = <I>ignore</I> or <I>end</I> or <I>extra</I>
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ignore = ignore values outside histogram lo/hi bounds
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end = count values outside histogram lo/hi bounds in end bins
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extra = create 2 extra bins for value outside histogram lo/hi bounds
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<I>title1</I> arg = string
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2009-12-22 01:51:05 +08:00
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string = text to print as 1st line of output file
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<I>title2</I> arg = string
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string = text to print as 2nd line of output file
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<I>title3</I> arg = string
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string = text to print as 3rd line of output file, only for vector mode
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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/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
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fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 "My output values"
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fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
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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 values as inputs every few timesteps, histogram them,
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and average the histogram over longer timescales. The resulting
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2011-08-26 01:01:01 +08:00
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histogram can be used by other <A HREF = "Section_howto.html#howto_15">output
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commands</A>, and can also be written to a
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file.
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2009-12-15 09:21:23 +08:00
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</P>
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<P>The group specified with this command is ignored for global and local
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input values. For per-atom input values, only atoms in the group
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contribute to the histogram. Note that regardless of the specified
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2010-08-13 07:10:38 +08:00
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group, specified values may represent calculations performed by
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computes and fixes which store their own "group" definition.
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2009-12-15 09:21:23 +08:00
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</P>
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<P>A histogram is simply a count of the number of values that fall within
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a histogram bin. <I>Nbins</I> are defined, with even spacing between <I>lo</I>
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and <I>hi</I>. Values that fall outside the lo/hi bounds can be treated in
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different ways; see the discussion of the <I>beyond</I> keyword below.
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</P>
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2009-12-16 00:27:48 +08:00
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<P>Each input value can be an atom attribute (position, velocity, force
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component) or can be the result of a <A HREF = "compute.html">compute</A> or
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2009-12-15 09:21:23 +08:00
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<A HREF = "fix.html">fix</A> or the evaluation of an equal-style or atom-style
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<A HREF = "variable.html">variable</A>. The set of input values can be either all
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global, all per-atom, or all local quantities. Inputs of different
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2010-05-25 01:03:24 +08:00
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kinds (e.g. global and per-atom) cannot be mixed. Atom attributes are
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per-atom vector values. See the doc page for individual "compute" and
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"fix" commands to see what kinds of quantities they generate.
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</P>
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<P>The input values must either be all scalars or all vectors (or
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arrays), depending on the setting of the <I>mode</I> keyword.
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</P>
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<P>If <I>mode</I> = vector, then the input values may either be vectors or
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arrays. If a global array is listed, then it is the same as if the
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individual columns of the array had been listed one by one.
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E.g. these 2 fix ave/histo commands are equivalent, since the <A HREF = "compute_com_molecule.html">compute
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com/molecule</A> command creates a global array
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with 3 columns:
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</P>
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<PRE>compute myCOM all com/molecule
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fix 1 all ave/histo 100 1 100 c_myCOM file tmp1.com mode vector
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fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
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</PRE>
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2009-12-15 09:21:23 +08:00
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<P>The output of this command is a single histogram for all input values
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combined together, not one histogram per input value. See below for
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details on the format of the output of this fix.
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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 in order to contribute to the
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2010-11-23 23:13:14 +08:00
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histogram. The final histogram is generated on timesteps that are
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multiple of <I>Nfreq</I>. It is averaged over <I>Nrepeat</I> histograms,
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computed in the preceding portion of the simulation every <I>Nevery</I>
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timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and <I>Nevery</I> must
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be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps contributing
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to the histogram cannot overlap, i.e. Nfreq > (Nrepeat-1)*Nevery is
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required.
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2009-12-15 09:21:23 +08:00
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</P>
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<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values
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on timesteps 90,92,94,96,98,100 will be used to compute the final
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histogram on timestep 100. Similarly for timesteps
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190,192,194,196,198,200 on timestep 200, etc. If Nrepeat=1 and Nfreq
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= 100, then no time averaging of the histogram is done; a histogram is
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simply generated on timesteps 100,200,etc.
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</P>
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<HR>
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2009-12-16 00:27:48 +08:00
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<P>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
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2009-12-17 01:12:09 +08:00
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self-explanatory. Note that other atom attributes can be used as
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inputs to this fix by using the <A HREF = "compute_property_atom.html">compute
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property/atom</A> command and then specifying
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an input value from that compute.
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2009-12-16 00:27:48 +08:00
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</P>
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2009-12-15 09:21:23 +08:00
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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 <I>mode</I> = scalar, then if
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no bracketed term is appended, the global scalar calculated by the
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compute is used. If a bracketed term is appended, the Ith element of
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the global vector calculated by the compute is used. If <I>mode</I> =
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vector, then if no bracketed term is appended, the global or per-atom
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2010-05-25 01:03:24 +08:00
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or local vector calculated by the compute is used. Or if the compute
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calculates an array, all of the columns of the array are used as if
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they had been specified as individual vectors (see description above).
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If a bracketed term is appended, the Ith column of the global or
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per-atom or local array calculated by the compute is used.
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2009-12-15 09:21:23 +08:00
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</P>
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<P>Note that there is a <A HREF = "compute_reduce.html">compute reduce</A> command
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which can sum per-atom quantities into a global scalar or vector which
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can thus be accessed by fix ave/histo. Or it can be a compute defined
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not in your input script, but by <A HREF = "thermo_style.html">thermodynamic
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2010-04-03 00:51:06 +08:00
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output</A> or other fixes such as <A HREF = "fix_nh.html">fix
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2009-12-15 09:21:23 +08:00
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nvt</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. See
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the doc pages for these commands which give the IDs of these computes.
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Users can also write code for their own compute styles and <A HREF = "Section_modify.html">add them
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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 <I>mode</I> = scalar, then if
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no bracketed term is appended, the global scalar calculated by the fix
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is used. If a bracketed term is appended, the Ith element of the
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global vector calculated by the fix is used. If <I>mode</I> = vector, then
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if no bracketed term is appended, the global or per-atom or local
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2010-05-25 01:03:24 +08:00
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vector calculated by the fix is used. Or if the fix calculates an
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array, all of the columns of the array are used as if they had been
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specified as individual vectors (see description above). If a
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bracketed term is appended, the Ith column of the global or per-atom
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or local array calculated by the fix is used.
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2009-12-15 09:21:23 +08:00
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</P>
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<P>Note that some fixes only produce their values on certain timesteps,
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which must be compatible with <I>Nevery</I>, else an error will result.
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Users can also write code for their own fix styles and <A HREF = "Section_modify.html">add them to
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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. If <I>mode</I> = scalar, then
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only equal-style variables can be used, which produce a global value.
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If <I>mode</I> = vector, then only atom-style variables can be used, which
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produce a per-atom vector. See the <A HREF = "variable.html">variable</A> command
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for details. Note that variables of style <I>equal</I> and <I>atom</I> define a
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formula which can reference individual atom properties or
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thermodynamic keywords, or they can invoke other computes, fixes, or
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variables when they are evaluated, so this is a very general means of
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specifying quantities to histogram.
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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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</P>
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<P>If the <I>mode</I> keyword is set to <I>scalar</I>, then all input values must
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be global scalars, or elements of global vectors. If the <I>mode</I>
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keyword is set to <I>vector</I>, then all input values must be global or
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per-atom or local vectors, or columns of global or per-atom or local
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arrays.
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</P>
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<P>The <I>beyond</I> keyword determines how input values that fall outside the
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<I>lo</I> to <I>hi</I> bounds are treated. Values such that <I>lo</I> <= value <=
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<I>hi</I> are assigned to one bin. Values on a bin boundary are assigned
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to the lower of the 2 bins. If <I>beyond</I> is set to <I>ignore</I> then
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values < <I>lo</I> and values > <I>hi</I> are ignored, i.e. they are not binned.
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If <I>beyond</I> is set to <I>end</I> then values < <I>lo</I> are counted in the
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first bin and values > <I>hi</I> are counted in the last bin. If <I>beyond</I>
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is set to <I>extend</I> then two extra bins are created, so that there are
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Nbins+2 total bins. Values < <I>lo</I> are counted in the first bin and
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values > <I>hi</I> are counted in the last bin (Nbins+1). Values between
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<I>lo</I> and <I>hi</I> (inclusive) are counted in bins 2 thru Nbins+1. The
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"coordinate" stored and printed for these two extra bins is <I>lo</I> and
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<I>hi</I>.
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</P>
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<P>The <I>ave</I> keyword determines how the histogram produced every <I>Nfreq</I>
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steps are averaged with histograms 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 histograms 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 histograms 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 bin value in the histogram
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is thus the average of the bin value produced on that timestep with
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all preceding values for the same bin. 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 by re-defining the fix by
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re-specifying it.
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</P>
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2009-12-16 00:47:17 +08:00
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<P>If the <I>ave</I> setting is <I>window</I>, then the histograms produced on
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timesteps that are multiples of <I>Nfreq</I> are summed within a moving
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"window" of time, so that the last M histograms are used to produce
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the output. E.g. if M = 3 and Nfreq = 1000, then the output on step
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10000 will be the combined histogram of the individual histograms on
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steps 8000,9000,10000. Outputs on early steps will be sums over less
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than M histograms if they are not available.
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</P>
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2009-12-15 09:21:23 +08:00
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<P>The <I>start</I> keyword specifies what timestep histogramming will begin
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on. The default is step 0. Often input values can be 0.0 at time 0,
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so setting <I>start</I> to a larger value can avoid including a 0.0 in
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2009-12-16 00:47:17 +08:00
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a running or windowed histogram.
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2009-12-15 09:21:23 +08:00
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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>
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steps, one histogram is written to the file. This includes a leading
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line that contains the timestep, number of bins, the total count of
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values contributing to the histogram, the count of values that were
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not histogrammed (see the <I>beyond</I> keyword), the minimum value
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encountered, and the maximum value encountered. The min/max values
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include values that were not histogrammed. Following the leading
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line, one line per bin is written into the file. Each line contains
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the bin #, the coordinate for the center of the bin (between <I>lo</I> and
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<I>hi</I>), the count of values in the bin, and the normalized count. The
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normalized count is the bin count divided by the total count (not
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including values not histogrammed), so that the normalized values sum
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to 1.0 across all bins.
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</P>
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<P>The <I>title1</I> and <I>title2</I> and <I>title3</I> keywords allow specification of
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the strings that will be printed as the first 3 lines of the output
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file, assuming the <I>file</I> keyword was used. LAMMPS uses default
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values for each of these, so they do not need to be specified.
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</P>
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<P>By default, these header lines are as follows:
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</P>
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<PRE># Histogram for fix ID
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# TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value
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# Bin Coord Count Count/Total
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</PRE>
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<P>In the first line, ID is replaced with the fix-ID. The second line
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describes the six values that are printed at the first of each section
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of output. The third describes the 4 values printed for each bin in
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the histogram.
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</P>
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<HR>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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|
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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|
are relevant to this fix.
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</P>
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|
<P>This fix produces a global vector and global array which can be
|
2011-08-26 01:01:01 +08:00
|
|
|
accessed by various <A HREF = "Section_howto.html#howto_15">output commands</A>.
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The values can only be accessed on timesteps that are multiples of
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<I>Nfreq</I> since that is when a histogram is generated. The global
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vector has 4 values:
|
2009-12-15 09:21:23 +08:00
|
|
|
</P>
|
2011-02-22 06:32:31 +08:00
|
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|
<UL><LI>1 = total counts in the histogram
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|
<LI>2 = values that were not histogrammed (see <I>beyond</I> keyword)
|
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<LI>3 = min value of all input values, including ones not histogrammed
|
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<LI>4 = max value of all input values, including ones not histogrammed
|
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|
</UL>
|
2009-12-15 09:21:23 +08:00
|
|
|
<P>The global array has # of rows = Nbins and # of columns = 3. The
|
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|
|
first column has the bin coordinate, the 2nd column has the count of
|
|
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|
|
values in that histogram bin, and the 3rd column has the bin count
|
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|
divided by the total count (not including missing counts), so that the
|
|
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|
|
values in the 3rd column sum to 1.0.
|
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|
|
|
</P>
|
|
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|
<P>The vector and array values calculated by this fix are all treated as
|
2010-03-03 05:59:33 +08:00
|
|
|
"intensive". If this is not the case, e.g. due to histogramming
|
2009-12-15 09:21:23 +08:00
|
|
|
per-atom input values, then you will need to account for that when
|
|
|
|
|
interpreting the values produced by this fix.
|
|
|
|
|
</P>
|
|
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|
<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
|
|
|
|
|
minimization</A>.
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Restrictions:</B> none
|
|
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|
|
</P>
|
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|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix
|
|
|
|
|
ave/spatial</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>,
|
2010-08-18 05:58:29 +08:00
|
|
|
<A HREF = "variable.html">variable</A>, <A HREF = "fix_ave_correlate.html">fix ave/correlate</A>,
|
2009-12-15 09:21:23 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B> none
|
|
|
|
|
</P>
|
|
|
|
|
<P>The option defaults are mode = scalar, ave = one, start = 0, no file
|
|
|
|
|
output, beyond = ignore, and title 1,2,3 = strings as described above.
|
|
|
|
|
</P>
|
|
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|
</HTML>
|
