cleanup, clarification and re-wrap of doc file sections
This commit is contained in:
Axel Kohlmeyer
@ -58,28 +58,30 @@ chunk ID for an individual atom can also be static (e.g. a molecule
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ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
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Note that this compute allows the per-atom output of other
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:doc:`computes <compute>`, :doc:`fixes <fix>`, and
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:doc:`variables <variable>` to be used to define chunk IDs for each
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atom. This means you can write your own compute or fix to output a
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per-atom quantity to use as chunk ID. See the :doc:`Modify <Modify>`
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doc pages for info on how to do this. You can also define a :doc:`per-atom variable <variable>` in the input script that uses a formula to
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generate a chunk ID for each atom.
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:doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`variables
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<variable>` to be used to define chunk IDs for each atom. This means
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you can write your own compute or fix to output a per-atom quantity to
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use as chunk ID. See the :doc:`Modify <Modify>` doc pages for info on
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how to do this. You can also define a :doc:`per-atom variable
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<variable>` in the input script that uses a formula to generate a chunk
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ID for each atom.
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Fix ave/chunk command:
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----------------------
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This fix takes the ID of a :doc:`compute chunk/atom <compute_chunk_atom>` command as input. For each chunk,
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it then sums one or more specified per-atom values over the atoms in
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each chunk. The per-atom values can be any atom property, such as
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velocity, force, charge, potential energy, kinetic energy, stress,
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etc. Additional keywords are defined for per-chunk properties like
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density and temperature. More generally any per-atom value generated
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by other :doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`per-atom variables <variable>`, can be summed over atoms in each chunk.
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This fix takes the ID of a :doc:`compute chunk/atom
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<compute_chunk_atom>` command as input. For each chunk, it then sums
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one or more specified per-atom values over the atoms in each chunk. The
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per-atom values can be any atom property, such as velocity, force,
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charge, potential energy, kinetic energy, stress, etc. Additional
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keywords are defined for per-chunk properties like density and
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temperature. More generally any per-atom value generated by other
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:doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`per-atom
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variables <variable>`, can be summed over atoms in each chunk.
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Similar to other averaging fixes, this fix allows the summed per-chunk
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values to be time-averaged in various ways, and output to a file. The
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fix produces a global array as output with one row of values per
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chunk.
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fix produces a global array as output with one row of values per chunk.
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Compute \*/chunk commands:
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--------------------------
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@ -97,17 +99,20 @@ category:
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* :doc:`compute torque/chunk <compute_vcm_chunk>`
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* :doc:`compute vcm/chunk <compute_vcm_chunk>`
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They each take the ID of a :doc:`compute chunk/atom <compute_chunk_atom>` command as input. As their names
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indicate, they calculate the center-of-mass, radius of gyration,
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moments of inertia, mean-squared displacement, temperature, torque,
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and velocity of center-of-mass for each chunk of atoms. The :doc:`compute property/chunk <compute_property_chunk>` command can tally the
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count of atoms in each chunk and extract other per-chunk properties.
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They each take the ID of a :doc:`compute chunk/atom
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<compute_chunk_atom>` command as input. As their names indicate, they
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calculate the center-of-mass, radius of gyration, moments of inertia,
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mean-squared displacement, temperature, torque, and velocity of
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center-of-mass for each chunk of atoms. The :doc:`compute
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property/chunk <compute_property_chunk>` command can tally the count of
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atoms in each chunk and extract other per-chunk properties.
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The reason these various calculations are not part of the :doc:`fix ave/chunk command <fix_ave_chunk>`, is that each requires a more
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The reason these various calculations are not part of the :doc:`fix
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ave/chunk command <fix_ave_chunk>`, is that each requires a more
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complicated operation than simply summing and averaging over per-atom
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values in each chunk. For example, many of them require calculation
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of a center of mass, which requires summing mass\*position over the
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atoms and then dividing by summed mass.
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values in each chunk. For example, many of them require calculation of
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a center of mass, which requires summing mass\*position over the atoms
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and then dividing by summed mass.
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All of these computes produce a global vector or global array as
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output, with one or more values per chunk. The output can be used in
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@ -118,9 +123,10 @@ various ways:
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* As input to the :doc:`fix ave/histo <fix_ave_histo>` command to
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histogram values across chunks. E.g. a histogram of cluster sizes or
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molecule diffusion rates.
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* As input to special functions of :doc:`equal-style variables <variable>`, like sum() and max() and ave(). E.g. to
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find the largest cluster or fastest diffusing molecule or average
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radius-of-gyration of a set of molecules (chunks).
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* As input to special functions of :doc:`equal-style variables
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<variable>`, like sum() and max() and ave(). E.g. to find the largest
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cluster or fastest diffusing molecule or average radius-of-gyration of
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a set of molecules (chunks).
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Other chunk commands:
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---------------------
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@ -138,9 +144,10 @@ spatially average per-chunk values calculated by a per-chunk compute.
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The :doc:`compute reduce/chunk <compute_reduce_chunk>` command reduces a
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peratom value across the atoms in each chunk to produce a value per
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chunk. When used with the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command it can
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create peratom values that induce a new set of chunks with a second
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:doc:`compute chunk/atom <compute_chunk_atom>` command.
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chunk. When used with the :doc:`compute chunk/spread/atom
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<compute_chunk_spread_atom>` command it can create peratom values that
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induce a new set of chunks with a second :doc:`compute chunk/atom
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<compute_chunk_atom>` command.
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Example calculations with chunks
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--------------------------------
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@ -206,11 +206,13 @@ IDs and the bond stretch will be printed with thermodynamic output.
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The *inputs* keyword allows selection of whether all the inputs are
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per-atom or local quantities. As noted above, all the inputs must be
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the same kind (per-atom or local). Per-atom is the default setting.
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If a compute or fix is specified as an input, it must produce per-atom
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or local data to match this setting. If it produces both, e.g. for
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the same kind (per-atom or local). Per-atom is the default setting. If
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a compute or fix is specified as an input, it must produce per-atom or
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local data to match this setting. If it produces both, like for example
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the :doc:`compute voronoi/atom <compute_voronoi_atom>` command, then
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this keyword selects between them.
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this keyword selects between them. If a compute *only* produces local
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data, like for example the :doc:`compute bond/local <compute_bond_local>
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command`, the setting "inputs local" is *required*.
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----------
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@ -37,55 +37,57 @@ Description
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Define a calculation that reduces one or more per-atom vectors into
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per-chunk values. This can be useful for diagnostic output. Or when
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used in conjunction with the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command it can be
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used to create per-atom values that induce a new set of chunks with a
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second :doc:`compute chunk/atom <compute_chunk_atom>` command. An
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example is given below.
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used in conjunction with the :doc:`compute chunk/spread/atom
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<compute_chunk_spread_atom>` command it can be used to create per-atom
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values that induce a new set of chunks with a second :doc:`compute
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chunk/atom <compute_chunk_atom>` command. An example is given below.
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In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` 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 :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
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doc pages for details of how chunks can be defined and examples of how
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they can be used to measure properties of a system.
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In LAMMPS, chunks are collections of atoms defined by a :doc:`compute
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chunk/atom <compute_chunk_atom>` command, which assigns each atom to a
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single chunk (or no chunk). The ID for this command is specified as
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chunkID. For example, a single chunk could be the atoms in a molecule
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or atoms in a spatial bin. See the :doc:`compute chunk/atom
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<compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>` doc pages for
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details of how chunks can be defined and examples of how they can be
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used to measure properties of a system.
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For each atom, this compute accesses its chunk ID from the specified
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*chunkID* compute. The per-atom value from an input contributes
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to a per-chunk value corresponding the the chunk ID.
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*chunkID* compute. The per-atom value from an input contributes to a
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per-chunk value corresponding the the chunk ID.
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The reduction operation is specified by the *mode* setting and is
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performed over all the per-atom values from the atoms in each chunk.
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The *sum* option adds the pre-atom values to a per-chunk total. The
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*min* or *max* options find the minimum or maximum value of the
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per-atom values for each chunk.
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*min* or *max* options find the minimum or maximum value of the per-atom
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values for each chunk.
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Note that only atoms in the specified group contribute to the
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reduction operation. If the *chunkID* compute returns a 0 for the
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chunk ID of an atom (i.e., the atom is not in a chunk defined by the
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:doc:`compute chunk/atom <compute_chunk_atom>` command), that atom will
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also not contribute to the reduction operation. An input that is a
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compute or fix may define its own group which affects the quantities
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it returns. For example, a compute with return a zero value for atoms
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that are not in the group specified for that compute.
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Note that only atoms in the specified group contribute to the reduction
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operation. If the *chunkID* compute returns a 0 for the chunk ID of an
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atom (i.e., the atom is not in a chunk defined by the :doc:`compute
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chunk/atom <compute_chunk_atom>` command), that atom will also not
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contribute to the reduction operation. An input that is a compute or
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fix may define its own group which affects the quantities it returns.
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For example, a compute with return a zero value for atoms that are not
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in the group specified for that compute.
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Each listed input is operated on independently. Each input can be the
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result of a :doc:`compute <compute>` or :doc:`fix <fix>` or the evaluation
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of an atom-style :doc:`variable <variable>`.
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result of a :doc:`compute <compute>` or :doc:`fix <fix>` or the
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evaluation of an atom-style :doc:`variable <variable>`.
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Note that for values from a compute or fix, the bracketed index I can
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be specified using a wildcard asterisk with the index to effectively
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Note that for values from a compute or fix, the bracketed index I can be
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specified using a wildcard asterisk with the index to effectively
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specify multiple values. This takes the form "\*" or "\*n" or "m\*" or
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"m\*n". If :math:`N` is the size of the vector (for *mode* = scalar) or the
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number of columns in the array (for *mode* = vector), then an asterisk
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with no numeric values means all indices from 1 to :math:`N`. A leading
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asterisk means all indices from 1 to n (inclusive). A trailing
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asterisk means all indices from n to :math:`N` (inclusive). A middle asterisk
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means all indices from m to n (inclusive).
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"m\*n". If :math:`N` is the size of the vector (for *mode* = scalar) or
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the number of columns in the array (for *mode* = vector), then an
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asterisk with no numeric values means all indices from 1 to :math:`N`.
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A leading asterisk means all indices from 1 to n (inclusive). A
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trailing asterisk means all indices from n to :math:`N` (inclusive). A
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middle asterisk means all indices from m to n (inclusive).
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Using a wildcard is the same as if the individual columns of the array
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had been listed one by one. For example, the following two compute reduce/chunk
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commands are equivalent, since the
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:doc:`compute property/chunk <compute_property_chunk>` command creates a per-atom
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had been listed one by one. For example, the following two compute
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reduce/chunk commands are equivalent, since the :doc:`compute
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property/chunk <compute_property_chunk>` command creates a per-atom
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array with 3 columns:
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.. code-block:: LAMMPS
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@ -164,13 +166,14 @@ Output info
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"""""""""""
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This compute calculates a global vector if a single input value is
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specified, otherwise a global array is output. The number of columns
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in the array is the number of inputs provided. The length of the
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vector or the number of vector elements or array rows = the number of
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chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The vector or array can
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be accessed by any command that uses global values from a compute as
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input. See the :doc:`Howto output <Howto_output>` page for an
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overview of LAMMPS output options.
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specified, otherwise a global array is output. The number of columns in
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the array is the number of inputs provided. The length of the vector or
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the number of vector elements or array rows = the number of chunks
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*Nchunk* as calculated by the specified :doc:`compute chunk/atom
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<compute_chunk_atom>` command. The vector or array can be accessed by
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any command that uses global values from a compute as input. See the
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:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
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options.
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The per-atom values for the vector or each column of the array will be
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in whatever :doc:`units <units>` the corresponding input value is in.
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@ -183,7 +186,9 @@ Restrictions
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Related commands
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""""""""""""""""
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:doc:`compute chunk/atom <compute_chunk_atom>`, :doc:`compute reduce <compute_reduce>`, :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
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:doc:`compute chunk/atom <compute_chunk_atom>`,
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:doc:`compute reduce <compute_reduce>`,
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:doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
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Default
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"""""""
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@ -162,7 +162,7 @@ potential energy is above the threshold value :math:`-3.0`.
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compute 1 all pe/atom
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compute 2 all reduce sum c_1
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thermo_style custom step temp pe c_2
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run 0
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run 0 post no
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variable eatom atom "c_1 > -3.0"
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group hienergy variable eatom
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@ -173,7 +173,7 @@ Note that these lines
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compute 2 all reduce sum c_1
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thermo_style custom step temp pe c_2
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run 0
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run 0 post no
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are necessary to ensure that the "eatom" variable is current when the
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group command invokes it. Because the eatom variable computes the
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