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compute reduce command

compute reduce/region command

Syntax

compute ID group-ID style arg mode input1 input2 ... keyword args ...

  • ID, group-ID are documented in compute command

  • style = reduce or reduce/region

    reduce arg = none
reduce/region arg = region-ID
  region-ID = ID of region to use for choosing atoms

  • mode = sum or min or minabs or max or maxabs or ave or sumsq or avesq or sumabs or aveabs

  • one or more inputs can be listed

  • input = x or y or z or vx or vy or vz or fx or fy or fz or c_ID or c_ID[N] or f_ID or f_ID[N] or v_name

    x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
c_ID = per-atom or local vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
f_ID = per-atom or local vector calculated by a fix with ID
f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below)
v_name = per-atom vector calculated by an atom-style variable with name

  • zero or more keyword/args pairs may be appended

  • keyword = replace or inputs

    replace args = vec1 vec2
  vec1 = reduced value from this input vector will be replaced
  vec2 = replace it with vec1[N] where N is index of max/min value from vec2
inputs arg = peratom or local
  peratom = all inputs are per-atom quantities (default)
  local = all input are local quantities

Examples

compute 1 all reduce sum c_force
compute 1 all reduce/region subbox sum c_force
compute 2 all reduce min c_press[2] f_ave v_myKE
compute 2 all reduce min c_press[*] f_ave v_myKE inputs peratom
compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
compute 4 all reduce max c_bond inputs local

Description

Define a calculation that “reduces” one or more vector inputs into scalar values, one per listed input. For the compute reduce command, the inputs can be either per-atom or local quantities and must all be of the same kind (per-atom or local); see discussion of the optional inputs keyword below. The compute reduce/region command can only be used with per-atom inputs.

Atom attributes are per-atom quantities, computes and fixes can generate either per-atom or local quantities, and atom-style variables generate per-atom quantities. See the variable command and its special functions which can perform the same reduction operations as the compute reduce command on global vectors.

The reduction operation is specified by the mode setting. The sum option adds the values in the vector into a global total. The min or max options find the minimum or maximum value across all vector values. The minabs or maxabs options find the minimum or maximum value across all absolute vector values. The ave setting adds the vector values into a global total, then divides by the number of values in the vector. The sumsq option sums the square of the values in the vector into a global total. The avesq setting does the same as sumsq, then divides the sum of squares by the number of values. The last two options can be useful for calculating the variance of some quantity (e.g., variance = sumsq \(-\) ave\(^2\)). The sumabs option sums the absolute values in the vector into a global total. The aveabs setting does the same as sumabs, then divides the sum of absolute values by the number of values.

Each listed input is operated on independently. For per-atom inputs, the group specified with this command means only atoms within the group contribute to the result. Likewise for per-atom inputs, if the compute reduce/region command is used, the atoms must also currently be within the region. Note that an input that produces per-atom quantities may define its own group which affects the quantities it returns. For example, if a compute is used as an input which generates a per-atom vector, it will generate values of 0.0 for atoms that are not in the group specified for that compute.

Each listed input can be an atom attribute (position, velocity, force component) or can be the result of a compute or fix or the evaluation of an atom-style variable.

Note that for values from a compute or fix, the bracketed index \(I\) can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form “*” or “*n” or “m*” or “m*n”. If \(N\) is the size of the vector (for mode = scalar) or the number of columns in the array (for mode = vector), then an asterisk with no numeric values means all indices from 1 to \(N\). A leading asterisk means all indices from 1 to n (inclusive). A trailing asterisk means all indices from m to \(N\) (inclusive). A middle asterisk means all indices from m to n (inclusive).

Using a wildcard is the same as if the individual columns of the array had been listed one by one. For example, the following two compute reduce commands are equivalent, since the compute stress/atom command creates a per-atom array with six columns:

compute myPress all stress/atom NULL
compute 2 all reduce min c_myPress[*]
compute 2 all reduce min c_myPress[1] c_myPress[2] c_myPress[3] &
                         c_myPress[4] c_myPress[5] c_myPress[6]

The atom attribute values (x, y, z, vx, vy, vz, fx, fy, and fz) are self-explanatory. Note that other atom attributes can be used as inputs to this fix by using the compute property/atom command and then specifying an input value from that compute.

If a value begins with “c_”, a compute ID must follow which has been previously defined in the input script. Valid computes can generate per-atom or local quantities. See the individual compute page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and add them to LAMMPS. See the discussion above for how \(I\) can be specified with a wildcard asterisk to effectively specify multiple values.

If a value begins with “f_”, a fix ID must follow which has been previously defined in the input script. Valid fixes can generate per-atom or local quantities. See the individual fix page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute reduce references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their own fix style and add them to LAMMPS. See the discussion above for how \(I\) can be specified with a wildcard asterisk to effectively specify multiple values.

If a value begins with “v_”, a variable name must follow which has been previously defined in the input script. It must be an atom-style variable. Atom-style variables can reference thermodynamic keywords and various per-atom attributes, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of generating per-atom quantities to reduce.

If the replace keyword is used, two indices vec1 and vec2 are specified, where each index ranges from 1 to the number of input values. The replace keyword can only be used if the mode is min or max. It works as follows. A min/max is computed as usual on the vec2 input vector. The index \(N\) of that value within vec2 is also stored. Then, instead of performing a min/max on the vec1 input vector, the stored index is used to select the \(N\)th element of the vec1 vector.

Thus, for example, if you wish to use this compute to find the bond with maximum stretch, you can do it as follows:

compute 1 all property/local batom1 batom2
compute 2 all bond/local dist
compute 3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
thermo_style custom step temp c_3[1] c_3[2] c_3[3]

The first two input values in the compute reduce command are vectors with the IDs of the two atoms in each bond, using the compute property/local command. The last input value is bond distance, using the compute bond/local command. Instead of taking the max of the two atom ID vectors, which does not yield useful information in this context, the replace keywords will extract the atom IDs for the two atoms in the bond of maximum stretch. These atom IDs and the bond stretch will be printed with thermodynamic output.

Added in version 21Nov2023.

The inputs keyword allows selection of whether all the inputs are per-atom or local quantities. As noted above, all the inputs must be the same kind (per-atom or local). Per-atom is the default setting. If a compute or fix is specified as an input, it must produce per-atom or local data to match this setting. If it produces both, like for example the compute voronoi/atom command, then this keyword selects between them. If a compute only produces local data, like for example the compute bond/local command, the setting “inputs local” is required.

If a single input is specified this compute produces a global scalar value. If multiple inputs are specified, this compute produces a global vector of values, the length of which is equal to the number of inputs specified.

As discussed below, for the sum, sumabs, and sumsq modes, the value(s) produced by this compute are all “extensive”, meaning their value scales linearly with the number of atoms involved. If normalized values are desired, this compute can be accessed by the thermo_style custom command with thermo_modify norm yes set as an option. Or it can be accessed by a variable that divides by the appropriate atom count.

Output info

This compute calculates a global scalar if a single input value is specified or a global vector of length \(N\), where \(N\) is the number of inputs, and which can be accessed by indices 1 to \(N\). These values can be used by any command that uses global scalar or vector values from a compute as input. See the Howto output doc page for an overview of LAMMPS output options.

All the scalar or vector values calculated by this compute are “intensive”, except when the sum, sumabs, or sumsq modes are used on per-atom or local vectors, in which case the calculated values are “extensive”.

The scalar or vector values will be in whatever units the quantities being reduced are in.

Restrictions

As noted above, the compute reduce/region command can only be used with per-atom inputs.

Default

The default value for the inputs keyword is peratom.