compute reduce/chunk command¶
compute ID group-ID reduce/chunk chunkID mode input1 input2 ...
ID, group-ID are documented in compute command
reduce/chunk = style name of this compute command
chunkID = ID of compute chunk/atom command
mode = sum or min or max
one or more inputs can be listed
input = c_ID, c_ID[N], f_ID, f_ID[N], v_ID
c_ID = per-atom vector calculated by a compute with ID c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) f_ID = per-atom vector calculated by a fix with ID f_ID[I] = Ith column of per-atom 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
compute 1 all reduce/chunk mychunk min c_cluster
Define a calculation that reduces one or more per-atom vectors into per-chunk values. This can be useful for diagnostic output. Or when used in conjunction with the compute chunk/spread/atom command it can be used to create per-atom values that induce a new set of chunks with a second compute chunk/atom command. An example is given below.
In LAMMPS, chunks are collections of atoms defined by a compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the compute chunk/atom and Howto chunk doc pages for details of how chunks can be defined and examples of how they can be used to measure properties of a system.
For each atom, this compute accesses its chunk ID from the specified chunkID compute. The per-atom value from an input contributes to a per-chunk value corresponding the the chunk ID.
The reduction operation is specified by the mode setting and is performed over all the per-atom values from the atoms in each chunk. The sum option adds the pre-atom values to a per-chunk total. The min or max options find the minimum or maximum value of the per-atom values for each chunk.
Note that only atoms in the specified group contribute to the reduction operation. If the chunkID compute returns a 0 for the chunk ID of an atom (i.e. the atom is not in a chunk defined by the compute chunk/atom command), that atom will also not contribute to the reduction operation. An input that is a compute or fix may define its own group which affects the quantities it returns. For example, a compute with return a zero value 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/chunk commands are equivalent, since the compute property/chunk command creates a per-atom array with 3 columns:
compute prop all property/atom vx vy vz compute 10 all reduce/chunk mychunk max c_prop[*] compute 10 all reduce/chunk mychunk max c_prop c_prop c_prop
Here is an example of using this compute, in conjunction with the compute chunk/spread/atom command to identify self-assembled micelles. The commands below can be added to the examples/in.micelle script.
Imagine a collection of polymer chains or small molecules with hydrophobic end groups. All the hydrophobic (HP) atoms are assigned to a group called “phobic”.
These commands will assign a unique cluster ID to all HP atoms within a specified distance of each other. A cluster will contain all HP atoms in a single molecule, but also the HP atoms in nearby molecules, e.g. molecules that have clumped to form a micelle due to the attraction induced by the hydrophobicity. The output of the chunk/reduce command will be a cluster ID per chunk (molecule). Molecules with the same cluster ID are in the same micelle.
group phobic type 4 # specific to in.micelle model compute cluster phobic cluster/atom 2.0 compute cmol all chunk/atom molecule compute reduce phobic reduce/chunk cmol min c_cluster
This per-chunk info could be output in at least two ways:
fix 10 all ave/time 1000 1 1000 c_reduce file tmp.phobic mode vector compute spread all chunk/spread/atom cmol c_reduce dump 1 all custom 1000 tmp.dump id type mol x y z c_cluster c_spread dump_modify 1 sort id
In the first case, each snapshot in the tmp.phobic file will contain one line per molecule. Molecules with the same value are in the same micelle. In the second case each dump snapshot contains all atoms, each with a final field with the cluster ID of the micelle that the HP atoms of that atom’s molecule belong to.
The result from compute chunk/spread/atom can be used to define a new set of chunks, where all the atoms in all the molecules in the same micelle are assigned to the same chunk, i.e. one chunk per micelle.
compute micelle all chunk/atom c_spread compress yes
Further analysis on a per-micelle basis can now be performed using any of the per-chunk computes listed on the Howto chunk doc page. E.g. count the number of atoms in each micelle, calculate its center or mass, shape (moments of inertia), radius of gyration, etc.
compute prop all property/chunk micelle count fix 20 all ave/time 1000 1 1000 c_prop file tmp.micelle mode vector
Each snapshot in the tmp.micelle file will have one line per micelle with its count of atoms, plus a first line for a chunk with all the solvent atoms. By the time 50000 steps have elapsed there are a handful of large micelles.
This compute calculates a global vector if a single input value is specified, otherwise a global array is output. The number of columns in the array is the number of inputs provided. The length of the vector or the number of vector elements or array rows = the number of chunks Nchunk as calculated by the specified compute chunk/atom command. The vector or array can be accessed by any command that uses global values from a compute as input. See the Howto output page for an overview of LAMMPS output options.
The per-atom values for the vector or each column of the array will be in whatever units the corresponding input value is in. The vector or array values are “intensive”.