forked from lijiext/lammps
440 lines
22 KiB
Plaintext
440 lines
22 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/chunk command :h3
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[Syntax:]
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fix ID group-ID ave/chunk Nevery Nrepeat Nfreq chunkID 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/chunk = 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 averages :l
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Nfreq = calculate averages every this many timesteps :l
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chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l
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one or more input values can be listed :l
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value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name :l
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vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
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density/number, density/mass = number or mass density
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temp = temperature
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c_ID = per-atom vector calculated by a compute with ID
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c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID
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f_ID = per-atom vector calculated by a fix with ID
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f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID
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v_name = per-atom vector calculated by an 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 = {norm} or {ave} or {bias} or {adof} or {cdof} or {file} or {overwrite} or {title1} or {title2} or {title3} :l
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{norm} arg = {all} or {sample} or {none} = how output on {Nfreq} steps is normalized
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all = output is sum of atoms across all {Nrepeat} samples, divided by atom count
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sample = output is sum of {Nrepeat} sample averages, divided by {Nrepeat}
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none = output is sum of {Nrepeat} sums, divided by {Nrepeat}
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{ave} args = {one} or {running} or {window M}
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one = output 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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{bias} arg = bias-ID
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bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation
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{adof} value = dof_per_atom
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dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation
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{cdof} value = dof_per_chunk
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dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
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{file} arg = filename
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filename = file to write results to
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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 :pre
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:ule
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[Examples:]
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fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro ttle1 "My output values"
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fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
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fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
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fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running :pre
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[IMPORTANT NOTE:]
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If you are trying to replace an older fix ave/spatial command with the
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newer, more flexible fix ave/chunk and "compute
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chunk/atom"_compute_chunk_atom.html commands, you simply need to split
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the fix ave/spatial arguments across the two new commands. For
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example, this command:
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fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile :pre
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could be replaced by:
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compute cc1 flow chunk/atom bin/1d y 0.0 1.0
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fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile :pre
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[Description:]
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Use one or more per-atom vectors as inputs every few timesteps, sum
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their values for multiple chunks of atoms, and average the values for
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each chunk over longer timescales. The resulting chunk averages can
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be used by other "output commands"_Section_howto.html#howto_15 such as
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"thermo_style custom"_thermo_style.html, and can also be written to a
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file.
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In LAMMPS, chunks are collections of atoms defined by a "compute
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chunk/atom"_compute_chunk_atom.html command, which assigns each atom
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to a single chunk (or no chunk). The ID for this command is specified
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as chunkID. For example, a single chunk could be the atoms in a
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molecule or atoms in a spatial bin. See the "compute
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chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
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23"_Section_howto.html#howto_23 for details of how chunks can be
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defined and examples of how they can be used to measure properties of
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a system.
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Note that only atoms in the specified group contribute to the summing
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and averaging calculations. The "compute
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chunk/atom"_compute_chunk_atom.html command defines its own group as
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well as an optional region. Atoms will have a chunk ID = 0, meaning
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they belong to no chunk, if they are not in that group or region.
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Thus you can specify the "all" group for this command if you simply
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want to use the chunk definitions provided by chunkID.
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Each specified per-atom value can be an atom attribute (position,
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velocity, force component), a mass or number density, or the result of
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a "compute"_compute.html or "fix"_fix.html or the evaluation of an
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atom-style "variable"_variable.html. In the latter cases, the
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compute, fix, or variable must produce a per-atom quantity, not a
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global quantity. Note that the "compute
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property/atom"_compute_property_atom.html command provides access to
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any attribute defined and stored by atoms. If you wish to
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time-average global quantities from a compute, fix, or variable, then
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see the "fix ave/time"_fix_ave_time.html command.
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"Computes"_compute.html that produce per-atom quantities are those
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which have the word {atom} in their style name. See the doc pages for
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individual "fixes"_fix.html to determine which ones produce per-atom
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quantities. "Variables"_variable.html of style {atom} are the only
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ones that can be used with this fix since all other styles of variable
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produce global quantities.
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The per-atom values of each input vector are summed and averaged
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independently of the per-atom values in other input vectors.
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IMPORTANT NOTE: This fix works by creating an array of size {Nchunk}
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by Nvalues on each processor. {Nchunk} is the number of chunks which
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is defined by the "compute chunk/atom"_doc/compute_chunk_atom.html
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command. Nvalues is the number of input values specified. Each
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processor loops over its atoms, tallying its values to the appropriate
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chunk. Then the entire array is summed across all processors. This
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means that using a large number of chunks will incur an overhead in
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memory and computational cost (summing across processors), so be
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careful to define a reasonable number of chunks.
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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 accessed and contribute to the
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average. The final averaged quantities are generated on timesteps
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that are a multiples of {Nfreq}. The average is over {Nrepeat}
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quantities, computed in the preceding portion of the simulation every
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{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and
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{Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps
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contributing to the average value cannot overlap, i.e. Nfreq >
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(Nrepeat-1)*Nevery is required.
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For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
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timesteps 90,92,94,96,98,100 will be used to compute the final average
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on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
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timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
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averaging is done; values are simply generated on timesteps
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100,200,etc.
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Each input value can also be averaged over the atoms in each chunk.
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The way the averaging is done across the {Nrepeat} timesteps to
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produce output on the {Nfreq} timesteps, and across multiple {Nfreq}
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outputs, is determined by the {norm} and {ave} keyword settings, as
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discussed below.
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IMPORTANT NOTE: To perform per-chunk averaging within a {Nfreq} time
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window, the number of chunks {Nchunk} defined by the "compute
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chunk/atom"_compute_chunk_atom.html command must remain constant. If
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the {ave} keyword is set to {running} or {window} then {Nchunk} must
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remain constant for the duration of the simulation. This fix forces
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the chunk/atom compute specified by chunkID to hold {Nchunk} constant
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for the appropriate time windows, by not allowing it to re-calcualte
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{Nchunk}, which can also affect how it assigns chunk IDs to atoms.
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More details are given on the "compute
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chunk/atom"_compute_chunk_atom.html doc page.
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:line
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The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
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As noted above, any other atom attributes can be used as input values
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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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The {density/number} value means the number density is computed for
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each chunk, i.e. a weighting of 1 for each atom. The {density/mass}
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value means the mass density is computed for each , i.e. each atom is
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weighted by its mass. The resulting density is normalized by the
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volume of the chunk so that units of number/volume or density are
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output. See the "units"_units.html command doc page for the
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definition of density for each choice of units, e.g. gram/cm^3. If
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the chunks defined by the "compute chunk/atom"_compute_chunk_atom.html
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command are spatial bins, the volume is the bin volume. Otherwise it
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is the volume of the entire simulation box.
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The {temp} value means the temperature is computed for each chunk, by
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the formula KE = DOF/2 k T, where KE = total kinetic energy of the
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chunk of atoms (sum of 1/2 m v^2), DOF = the total number of degrees
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of freedom for all atoms in the chunk, k = Boltzmann constant, and T =
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temperature.
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The DOF is calculated as N*adof + cdof, where N = number of atoms in
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the chunk, adof = degrees of freedom per atom, and cdof = degrees of
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freedom per chunk. By default adof = 2 or 3 = dimensionality of
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system, as set via the "dimension"_dimension.html command, and cdof =
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0.0. This gives the usual formula for temperature.
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Note that currently this temperature only includes translational
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degrees of freedom for each atom. No rotational degrees of freedom
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are included for finite-size particles. Also no degrees of freedom
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are subtracted for any velocity bias or constraints that are applied,
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such as "compute temp/partial"_compute_temp_partial.html, or "fix
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shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is because
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those degrees of freedom (e.g. a constrained bond) could apply to sets
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of atoms that are both included and excluded from a specific chunk,
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and hence the concept is somewhat ill-defined. In some cases, you can
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use the {adof} and {cdof} keywords to adjust the calculated degress of
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freedom appropriately, as explained below.
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Also note that a bias can be subtracted from atom velocities before
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they are used in the above formula for KE, by using the {bias}
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keyword. This allows, for example, a thermal temperature to be
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computed after removal of a flow velocity profile.
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Note that this fix and the "compute
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temp/chunk"_compute_temp_chunk.html command can calculate different
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things. The compute calculates the temperature for each chunk for a
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single snapshot. This fix can do that but can time average those
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values over many snapshots, or it can compute a temperature as if the
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atoms in the chunk on different timesteps were collected together as
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one set of atoms to calculate their temperature. The compute allows
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the center-of-mass velocity of each chunk to be subtracted before
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calculating the temperature; this fix does not.
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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 no bracketed integer is
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appended, the per-atom vector calculated by the compute is used. If a
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bracketed integer is appended, the Ith column of the per-atom array
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calculated by the compute is used. Users can also write code for
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their own compute styles and "add them 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 no bracketed integer is
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appended, the per-atom vector calculated by the fix is used. If a
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bracketed integer is appended, the Ith column of the per-atom array
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calculated by the fix is used. Note that some fixes only produce
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their values on certain timesteps, which must be compatible with
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{Nevery}, else an error results. Users can also write code for their
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own fix styles and "add them to 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. Variables of style
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{atom} can reference thermodynamic keywords and various per-atom
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attributes, or invoke other computes, fixes, or variables when they
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are evaluated, so this is a very general means of generating per-atom
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quantities to average within chunks.
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:line
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Additional optional keywords also affect the operation of this fix
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and its outputs.
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The {norm} keyword affects how averaging is done for the per-chunk
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values that are output every {Nfreq} timesteps.
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It the {norm} setting is {all}, which is the default, a chunk value is
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summed over all atoms in all {Nrepeat} samples, as is the count of
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atoms in the chunk. The averaged output value for the chunk on the
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{Nfreq} timesteps is Total-sum / Total-count. In other words it is an
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average over atoms across the entire {Nfreq} timescale.
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If the {norm} setting is {sample}, the chunk value is summed over atoms
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for each sample, as is the count, and an "average sample value" is
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computed for each sample, i.e. Sample-sum / Sample-count. The outuput
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value for the chunk on the {Nfreq} timesteps is the average of the
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{Nrepeat} "average sample values", i.e. the sum of {Nrepeat} "average
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sample values" divided by {Nrepeat}. In other words it is an average
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of an average.
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If the {norm} setting is {none}, a similar computation as for the
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{sample} seting is done, except the individual "average sample values"
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are "summed sample values". A summed sample value is simply the chunk
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value summed over atoms in the sample, without dividing by the number
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of atoms in the sample. The outuput value for the chunk on the
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{Nfreq} timesteps is the average of the {Nrepeat} "summed sample
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values", i.e. the sum of {Nrepeat} "summed sample values" divided by
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{Nrepeat}.
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The {ave} keyword determines how the per-chunk values produced every
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{Nfreq} steps are averaged with values 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}, which is the default, then the chunk
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values produced on timesteps that are multiples of {Nfreq} are
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independent of each other; they are output as-is without further
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averaging.
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If the {ave} setting is {running}, then the chunk values 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 output chunk value is thus
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the average of the chunk value produced on that timestep with all
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preceding values for the same chunk. This running average begins when
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the fix is defined; it can only be restarted by deleting the fix via
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the "unfix"_unfix.html command, or re-defining the fix by
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re-specifying it.
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If the {ave} setting is {window}, then the chunk values produced on
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timesteps that are multiples of {Nfreq} are summed and averaged within
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a moving "window" of time, so that the last M values for the same
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chunk are used to produce the output. E.g. if M = 3 and Nfreq = 1000,
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then the output on step 10000 will be the average of the individual
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chunk values on steps 8000,9000,10000. Outputs on early steps will
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average over less than M values if they are not available.
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The {bias} keyword specifies the ID of a temperature compute that
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removes a "bias" velocity from each atom, specified as {bias-ID}. It
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is only used when the {temp} value is calculated, to compute the
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thermal temperature of each chunk after the translational kinetic
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energy components have been altered in a prescribed way, e.g. to
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remove a flow velocity profile. See the doc pages for individual
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computes that calculate a temperature to see which ones implement a
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bias.
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The {adof} and {cdof} keywords define the values used in the degree of
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freedom (DOF) formula described above for for temperature calculation
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for each chunk. They are only used when the {temp} value is
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calculated. They can be used to calculate a more appropriate
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temperature for some kinds of chunks. Here are 3 examples.
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If spatially binned chunks contain some number of water molecules and
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"fix shake"_fix_shake.html is used to make each molecule rigid, then
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you could calculate a temperature with 6 degrees of freedom (DOF) (3
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translational, 3 rotational) per molecule by setting {adof} to 2.0.
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If "compute temp/partial"_compute_temp_partial.html is used with the
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{bias} keyword to only allow the x component of velocity to contribute
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to the temperature, then {adof} = 1.0 would be appropriate. If each
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chunk consists of a large molecule, with some number of its bonds
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constrained by "fix shake"_fix_shake.html or the entire molecule by
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"fix rigid/small"_fix_rigid.html, then {cdof} could be set to the
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remaining degrees of freedom for the entire molecule (entire chunk in
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this case).
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The {file} keyword allows a filename to be specified. Every {Nfreq}
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timesteps, a section of chunk info will be written to a text file in
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the following format. A line with the timestep and number of chunks
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is written. Then one line per chunk is written, containing the chunk
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ID (1-Nchunk), an optional original ID value, optional coordinate
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values for chunks that represent spatial bins, the number of atoms in
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the chunk, and one or more calculated values. More explanation of the
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optional values is given below. The number of values in each line
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corresponds to the number of values specified in the fix ave/chunk
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command. The number of atoms and the value(s) are summed or average
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quantities, as explained above.
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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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# Chunk-averaged data for fix ID and group name
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# Timestep Number-of-chunks
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# Chunk (OrigID) (Coord1) (Coord2) (Coord3) Ncount value1 value2 ... :pre
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In the first line, ID and name are replaced with the fix-ID and group
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name. The second line describes the two values that are printed at
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the first of each section of output. In the third line the values are
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replaced with the appropriate value names, e.g. fx or c_myCompute[2].
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The words in parenthesis only appear with corresponding columns if the
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chunk style specified for the "compute
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chunk/atom"_compute_chunk_atom.html command supports them. The OrigID
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column is only used if the {compress} keyword was set to {yes} for the
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"compute chunk/atom"_compute_chunk_atom.html command. This means that
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the original chunk IDs (e.g. molecule IDs) will have been compressed
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to remove chunk IDs with no atoms assigned to them. Thus a compresed
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chunk ID of 3 may correspond to an original chunk ID or molecule ID of
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415. The OrigID column will list 415 for the 3rd chunk.
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The CoordN columns only appear if a {binning} style was used in the
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"compute chunk/atom"_compute_chunk_atom.html command. For {bin/1d},
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{bin/2d}, and {bin/3d} styles the column values are the center point
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of the bin in the corresponding dimension. Just Coord1 is used for
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{bin/1d}, Coord2 is added for {bin/2d}, Coord3 is added for {bin/3d}.
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Note that if the value of the {units} keyword used in the "compute
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chunk/atom command"_compute_chunk_atom.html is {box} or {lattice}, the
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coordinate values will be in distance "units"_units.html. If the
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value of the {units} keyword is {reduced}, the coordinate values will
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be in unitless reduced units (0-1).
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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 computes a global array of values which can be accessed by
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various "output commands"_Section_howto.html#howto_15. The values can
|
|
only be accessed on timesteps that are multiples of {Nfreq} since that
|
|
is when averaging is performed. The global array has # of rows =
|
|
the number of chunks {Nchunk} as calculated by the specified "compute
|
|
chunk/atom"_compute_chunk_atom.html command. The # of columns =
|
|
M+1+Nvalues, where M = 1 to 4, depending on whether the optional
|
|
columns for OrigID and CoordN are used, as explained above.
|
|
Following the optional columns, the next column contains the count of
|
|
atoms in the chunk, and the remaining columns are the Nvalue
|
|
quantities. When the array is accessed with a row I that exceeds the
|
|
current number of chunks, than a 0.0 is returned by the fix instead of
|
|
an error, since the number of chunks can vary as a simulation runs
|
|
depending on how that value is computed by the compute chunk/atom
|
|
command.
|
|
|
|
The array values calculated by this fix are treated as "intensive",
|
|
since they are typically already normalized by the count of atoms in
|
|
each chunk.
|
|
|
|
No parameter of this fix can be used with the {start/stop} keywords of
|
|
the "run"_run.html command. This fix is not invoked during "energy
|
|
minimization"_minimize.html.
|
|
|
|
[Restrictions:] none
|
|
|
|
[Related commands:]
|
|
|
|
"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
|
|
ave/histo"_fix_ave_histo.html, "fix ave/time"_fix_ave_time.html,
|
|
"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html
|
|
|
|
[Default:]
|
|
|
|
The option defaults are norm = all, ave = one, bias = none, no file output, and
|
|
title 1,2,3 = strings as described above.
|