compute reduce command¶
compute reduce/region command¶
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 max or ave or sumsq or avesq or sumabs or aveabs
one or more inputs can be listed
input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], 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
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
compute 1 all reduce sum c_force compute 1 all reduce/region subbox sum c_force compute 2 all reduce min c_press f_ave v_myKE compute 2 all reduce min c_press[*] f_ave v_myKE compute 3 fluid reduce max c_index c_index c_dist replace 1 3 replace 2 3
Define a calculation that “reduces” one or more vector inputs into scalar values, one per listed input. The inputs can be per-atom or local quantities; they cannot be global quantities. Atom attributes are per-atom quantities, computes and fixes may generate any of the three kinds of quantities, and atom-style variables generate per-atom quantities. See the variable command and its special functions which can perform the same 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 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. 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.
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 “n*” or “m*n”. If N = 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 n 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. E.g. these 2 compute reduce commands are equivalent, since the compute stress/atom command creates a per-atom array with 6 columns:
compute myPress all stress/atom NULL compute 2 all reduce min c_myPress[*] compute 2 all reduce min c_myPress c_myPress c_myPress & c_myPress c_myPress c_myPress
The atom attribute values (x,y,z,vx,vy,vz,fx,fy,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. 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. 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 # 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 Nth 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 c_1 c_2 replace 1 3 replace 2 3 thermo_style custom step temp c_3 c_3 c_3
The first two input values in the compute reduce command are vectors with the IDs of the 2 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.
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.
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.