have compute_reduce require either peratom or local inputs
This commit is contained in:
Steve Plimpton
@ -37,13 +37,16 @@ Syntax
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v_name = per-atom vector calculated by an atom-style variable with name
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* zero or more keyword/args pairs may be appended
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* keyword = *replace*
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* keyword = *replace* or *inputs*
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.. parsed-literal::
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*replace* args = vec1 vec2
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vec1 = reduced value from this input vector will be replaced
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vec2 = replace it with vec1[N] where N is index of max/min value from vec2
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*inputs* arg = peratom or local
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peratom = all inputs are per-atom quantities (default)
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local = all input are local quantities
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Examples
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""""""""
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@ -61,26 +64,30 @@ Description
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Define a calculation that "reduces" one or more vector inputs into
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scalar values, one per listed input. The inputs can be per-atom or
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local quantities; they cannot be global quantities. Atom attributes
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are per-atom quantities, :doc:`computes <compute>` and :doc:`fixes <fix>`
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may generate any of the three kinds of quantities, and :doc:`atom-style variables <variable>` generate per-atom quantities. See the
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:doc:`variable <variable>` command and its special functions which can
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perform the same operations as the compute reduce command on global
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vectors.
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local quantities and must all be the same kind (per-atom or local);
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see discussion of the optional *inputs* keyword below.
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Atom attributes are per-atom quantities, :doc:`computes <compute>` and
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:doc:`fixes <fix>` can generate either per-atom or local quantities,
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and :doc:`atom-style variables <variable>` generate per-atom
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quantities. See the :doc:`variable <variable>` command and its
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special functions which can perform the same reduction operations as
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the compute reduce command on global vectors.
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The reduction operation is specified by the *mode* setting. The *sum*
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option adds the values in the vector into a global total. The *min*
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or *max* options find the minimum or maximum value across all vector
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values. The *minabs* or *maxabs* options find the minimum or maximum
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value across all absolute vector values. The *ave* setting adds the
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vector values into a global total, then divides by the number of values
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in the vector. The *sumsq* option sums the square of the values in the
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vector into a global total. The *avesq* setting does the same as *sumsq*,
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then divides the sum of squares by the number of values. The last two options
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can be useful for calculating the variance of some quantity (e.g., variance =
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sumsq :math:`-` ave\ :math:`^2`). The *sumabs* option sums the absolute
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values in the vector into a global total. The *aveabs* setting does the same
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as *sumabs*, then divides the sum of absolute values by the number of
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vector values into a global total, then divides by the number of
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values in the vector. The *sumsq* option sums the square of the
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values in the vector into a global total. The *avesq* setting does
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the same as *sumsq*, then divides the sum of squares by the number of
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values. The last two options can be useful for calculating the
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variance of some quantity (e.g., variance = sumsq :math:`-` ave\
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:math:`^2`). The *sumabs* option sums the absolute values in the
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vector into a global total. The *aveabs* setting does the same as
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*sumabs*, then divides the sum of absolute values by the number of
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values.
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Each listed input is operated on independently. For per-atom inputs,
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@ -123,52 +130,54 @@ array with six columns:
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----------
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The atom attribute values (*x*, *y*, *z*, *vx*, *vy*, *vz*, *fx*, *fy*, and
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*fz*) are self-explanatory. Note that other atom attributes can be used as
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inputs to this fix by using the
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:doc:`compute property/atom <compute_property_atom>` command and then specifying
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an input value from that compute.
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The atom attribute values (*x*, *y*, *z*, *vx*, *vy*, *vz*, *fx*,
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*fy*, and *fz*) are self-explanatory. Note that other atom attributes
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can be used as inputs to this fix by using the :doc:`compute
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property/atom <compute_property_atom>` command and then specifying an
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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. Computes can generate
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per-atom or local quantities. See the individual
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:doc:`compute <compute>` page for details. If no bracketed integer
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is appended, the vector calculated by the compute is used. If a
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bracketed integer is appended, the Ith column of the array calculated
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by the compute is used. Users can also write code for their own
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compute styles and :doc:`add them to LAMMPS <Modify>`. See the
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discussion above for how :math:`I` can be specified with a wildcard asterisk
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to effectively specify multiple values.
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previously defined in the input script. Valid computes can generate
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per-atom or local quantities. See the individual :doc:`compute
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<compute>` page for details. If no bracketed integer is appended, the
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vector calculated by the compute is used. If a bracketed integer is
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appended, the Ith column of the array calculated by the compute is
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used. Users can also write code for their own compute styles and
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:doc:`add them to LAMMPS <Modify>`. See the discussion above for how
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:math:`I` can be specified with a wildcard asterisk to effectively
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specify multiple values.
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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. Fixes can generate per-atom
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or local quantities. See the individual :doc:`fix <fix>` page for
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details. Note that some fixes only produce their values on certain
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timesteps, which must be compatible with when compute reduce
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previously defined in the input script. Valid fixes can generate
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per-atom or local quantities. See the individual :doc:`fix <fix>`
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page for details. Note that some fixes only produce their values on
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certain timesteps, which must be compatible with when compute reduce
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references the values, else an error results. If no bracketed integer
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is appended, the vector calculated by the fix is used. If a bracketed
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integer is appended, the Ith column of the array calculated by the fix
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is used. Users can also write code for their own fix style and
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:doc:`add them to LAMMPS <Modify>`. See the discussion above for how
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:math:`I` can be specified with a wildcard asterisk to effectively specify
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multiple values.
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:math:`I` can be specified with a wildcard asterisk to effectively
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specify multiple values.
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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. It must be an
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:doc:`atom-style variable <variable>`. Atom-style variables can
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reference thermodynamic keywords and various per-atom attributes, or
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invoke other computes, fixes, or variables when they are evaluated, so
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this is a very general means of generating per-atom quantities to reduce.
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this is a very general means of generating per-atom quantities to
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reduce.
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----------
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If the *replace* keyword is used, two indices *vec1* and *vec2* are
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specified, where each index ranges from 1 to the number of input values.
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The replace keyword can only be used if the *mode* is *min* or *max*\ .
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It works as follows. A min/max is computed as usual on the *vec2*
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input vector. The index :math:`N` of that value within *vec2* is also stored.
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Then, instead of performing a min/max on the *vec1* input vector, the
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stored index is used to select the :math:`N`\ th element of the *vec1* vector.
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specified, where each index ranges from 1 to the number of input
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values. The replace keyword can only be used if the *mode* is *min*
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or *max*\ . It works as follows. A min/max is computed as usual on
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the *vec2* input vector. The index :math:`N` of that value within
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*vec2* is also stored. Then, instead of performing a min/max on the
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*vec1* input vector, the stored index is used to select the :math:`N`\
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th element of the *vec1* vector.
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Thus, for example, if you wish to use this compute to find the bond
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with maximum stretch, you can do it as follows:
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@ -190,6 +199,14 @@ information in this context, the *replace* keywords will extract the
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atom IDs for the two atoms in the bond of maximum stretch. These atom
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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 :doc:`compute voronoi/atom <compute_voronoi_atom>` command, then
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this keyword selects between them.
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----------
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If a single input is specified this compute produces a global scalar
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@ -197,34 +214,35 @@ value. If multiple inputs are specified, this compute produces a
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global vector of values, the length of which is equal to the number of
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inputs specified.
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As discussed below, for the *sum*, *sumabs*, and *sumsq* modes, the value(s)
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produced by this compute are all "extensive", meaning their value
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scales linearly with the number of atoms involved. If normalized
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values are desired, this compute can be accessed by the
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As discussed below, for the *sum*, *sumabs*, and *sumsq* modes, the
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value(s) produced by this compute are all "extensive", meaning their
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value scales linearly with the number of atoms involved. If
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normalized values are desired, this compute can be accessed by the
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:doc:`thermo_style custom <thermo_style>` command with
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:doc:`thermo_modify norm yes <thermo_modify>` set as an option.
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Or it can be accessed by a
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:doc:`variable <variable>` that divides by the appropriate atom count.
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:doc:`thermo_modify norm yes <thermo_modify>` set as an option. Or it
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can be accessed by a :doc:`variable <variable>` that divides by the
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appropriate atom count.
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----------
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Output info
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"""""""""""
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This compute calculates a global scalar if a single input value is specified
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or a global vector of length :math:`N`, where :math:`N` is the number of
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inputs, and which can be accessed by indices 1 to :math:`N`. These values can
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be used by any command that uses global scalar or vector values from a
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compute as input. See the :doc:`Howto output <Howto_output>` doc page
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for an overview of LAMMPS output options.
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This compute calculates a global scalar if a single input value is
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specified or a global vector of length :math:`N`, where :math:`N` is
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the number of inputs, and which can be accessed by indices 1 to
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:math:`N`. These values can be used by any command that uses global
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scalar or vector values from a compute as input. See the :doc:`Howto
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output <Howto_output>` doc page for an overview of LAMMPS output
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options.
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All the scalar or vector values calculated by this compute are
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"intensive", except when the *sum*, *sumabs*, or *sumsq* modes are used on
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per-atom or local vectors, in which case the calculated values are
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"extensive".
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The scalar or vector values will be in whatever :doc:`units <units>` the
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quantities being reduced are in.
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The scalar or vector values will be in whatever :doc:`units <units>`
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the quantities being reduced are in.
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Restrictions
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""""""""""""
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@ -238,4 +256,4 @@ Related commands
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Default
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"""""""
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none
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The default value for the *inputs* keyword is peratom.
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@ -843,7 +843,7 @@ stress/atom <compute_stress_atom>` commands. The former can be
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accessed by :doc:`thermodynamic output <thermo_style>`. The default
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setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
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All of the *rigid* styles (not the *rigid/small* styles) compute a
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All of the *rigid* styles (but not the *rigid/small* styles) compute a
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global array of values which can be accessed by various :doc:`output
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commands <Howto_output>`. Similar information about the bodies
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defined by the *rigid/small* styles can be accessed via the
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@ -887,7 +887,8 @@ Restrictions
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""""""""""""
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These fixes are all part of the RIGID package. It is only enabled if
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LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
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LAMMPS was built with that package. See the :doc:`Build package
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<Build_package>` page for more info.
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Assigning a temperature via the :doc:`velocity create <velocity>`
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command to a system with :doc:`rigid bodies <fix_rigid>` may not have
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