forked from lijiext/lammps
321 lines
15 KiB
Plaintext
321 lines
15 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix ave/histo command :h3
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[Syntax:]
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fix ID group-ID ave/histo Nevery Nrepeat Nfreq lo hi Nbin value1 value2 ... keyword args ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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ave/histo = style name of this fix command :l
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Nevery = use input values every this many timesteps :l
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Nrepeat = # of times to use input values for calculating histogram :l
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Nfreq = calculate histogram every this many timesteps :l
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lo,hi = lo/hi bounds within which to histogram :l
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Nbin = # of histogram bins :l
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one or more input values can be listed :l
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value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
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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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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 :pre
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zero or more keyword/arg pairs may be appended :l
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keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {title1} or {title2} or {title3} :l
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{mode} arg = {scalar} or {vector}
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scalar = all input values are scalars
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vector = all input values are vectors
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{file} arg = filename
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filename = name of file to output histogram(s) to
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{ave} args = {one} or {running} or {window}
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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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window M = output average of M most recent Nfreq steps
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{start} args = Nstart
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Nstart = start averaging on this timestep
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{beyond} arg = {ignore} or {end} or {extra}
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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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{overwrite} arg = none = overwrite output file with only latest output
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{title1} arg = string
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string = text to print as 1st line of output file
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{title2} arg = string
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string = text to print as 2nd line of output file
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{title3} arg = string
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string = text to print as 3rd line of output file, only for vector mode :pre
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:ule
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[Examples:]
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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 :pre
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[Description:]
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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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histogram can be used by other "output
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commands"_Section_howto.html#howto_15, and can also be written to a
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file.
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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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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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A histogram is simply a count of the number of values that fall within
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a histogram bin. {Nbins} are defined, with even spacing between {lo}
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and {hi}. Values that fall outside the lo/hi bounds can be treated in
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different ways; see the discussion of the {beyond} keyword below.
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Each input value can be an atom attribute (position, velocity, force
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component) or can be the result of a "compute"_compute.html or
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"fix"_fix.html or the evaluation of an equal-style or atom-style
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"variable"_variable.html. 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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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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The input values must either be all scalars or all vectors (or
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arrays), depending on the setting of the {mode} keyword.
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If {mode} = 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 "compute
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com/molecule"_compute_com_molecule.html command creates a global array
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with 3 columns:
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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 :pre
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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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:line
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The {Nevery}, {Nrepeat}, and {Nfreq} 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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histogram. The final histogram is generated on timesteps that are
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multiple of {Nfreq}. It is averaged over {Nrepeat} histograms,
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computed in the preceding portion of the simulation every {Nevery}
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timesteps. {Nfreq} must be a multiple of {Nevery} and {Nevery} must
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be non-zero even if {Nrepeat} 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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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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:line
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The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
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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 "compute
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property/atom"_compute_property_atom.html command and then specifying
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an input value from that compute.
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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 {mode} = 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 {mode} =
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vector, then if no bracketed term is appended, the global or per-atom
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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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Note that there is a "compute reduce"_compute_reduce.html 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 "thermodynamic
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output"_thermo_style.html or other fixes such as "fix
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nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. 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 "add them
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to LAMMPS"_Section_modify.html.
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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 {mode} = 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 {mode} = vector, then
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if no bracketed term is appended, the global or per-atom or local
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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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Note that some fixes only produce their values on certain timesteps,
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which must be compatible with {Nevery}, else an error will result.
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Users can also write code for their own fix styles and "add them to
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LAMMPS"_Section_modify.html.
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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 {mode} = scalar, then
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only equal-style variables can be used, which produce a global value.
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If {mode} = vector, then only atom-style variables can be used, which
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produce a per-atom vector. See the "variable"_variable.html command
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for details. Note that variables of style {equal} and {atom} 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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:line
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Additional optional keywords also affect the operation of this fix.
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If the {mode} keyword is set to {scalar}, then all input values must
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be global scalars, or elements of global vectors. If the {mode}
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keyword is set to {vector}, 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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The {beyond} keyword determines how input values that fall outside the
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{lo} to {hi} bounds are treated. Values such that {lo} <= value <=
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{hi} are assigned to one bin. Values on a bin boundary are assigned
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to the lower of the 2 bins. If {beyond} is set to {ignore} then
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values < {lo} and values > {hi} are ignored, i.e. they are not binned.
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If {beyond} is set to {end} then values < {lo} are counted in the
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first bin and values > {hi} are counted in the last bin. If {beyond}
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is set to {extend} then two extra bins are created, so that there are
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Nbins+2 total bins. Values < {lo} are counted in the first bin and
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values > {hi} are counted in the last bin (Nbins+1). Values between
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{lo} and {hi} (inclusive) are counted in bins 2 thru Nbins+1. The
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"coordinate" stored and printed for these two extra bins is {lo} and
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{hi}.
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The {ave} keyword determines how the histogram produced every {Nfreq}
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steps are averaged with histograms produced on previous steps that
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were multiples of {Nfreq}, before they are accessed by another output
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command or written to a file.
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If the {ave} setting is {one}, then the histograms produced on
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timesteps that are multiples of {Nfreq} are independent of each other;
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they are output as-is without further averaging.
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If the {ave} setting is {running}, then the histograms produced on
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timesteps that are multiples of {Nfreq} 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 "unfix"_unfix.html command, or by re-defining the fix by
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re-specifying it.
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If the {ave} setting is {window}, then the histograms produced on
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timesteps that are multiples of {Nfreq} 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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The {start} 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 {start} to a larger value can avoid including a 0.0 in
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a running or windowed histogram.
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The {file} keyword allows a filename to be specified. Every {Nfreq}
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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 {beyond} 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 {lo} and
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{hi}), 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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The {overwrite} keyword will continuously overwrite the output file
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with the latest output, so that it only contains one timestep worth of
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output. This option can only be used with the {ave running} setting.
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The {title1} and {title2} and {title3} 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 {file} 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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By default, these header lines are as follows:
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# 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 :pre
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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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:line
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. None of the "fix_modify"_fix_modify.html options
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are relevant to this fix.
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This fix produces a global vector and global array which can be
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accessed by various "output commands"_Section_howto.html#howto_15.
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The values can only be accessed on timesteps that are multiples of
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{Nfreq} since that is when a histogram is generated. The global
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vector has 4 values:
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1 = total counts in the histogram
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2 = values that were not histogrammed (see {beyond} keyword)
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3 = min value of all input values, including ones not histogrammed
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4 = max value of all input values, including ones not histogrammed :ul
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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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The vector and array values calculated by this fix are all treated as
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"intensive". If this is not the case, e.g. due to histogramming
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per-atom input values, then you will need to account for that when
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interpreting the values produced by this fix.
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No parameter of this fix can be used with the {start/stop} keywords of
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the "run"_run.html command. This fix is not invoked during "energy
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minimization"_minimize.html.
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[Restrictions:] none
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[Related commands:]
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"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
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ave/spatial"_fix_ave_spatial.html, "fix ave/time"_fix_ave_time.html,
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"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html,
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[Default:] none
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The option defaults are mode = scalar, ave = one, start = 0, no file
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output, beyond = ignore, and title 1,2,3 = strings as described above.
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