8.4.2. Use chunks to calculate system properties
In LAMMS, “chunks” are collections of atoms, as defined by the compute chunk/atom command, which assigns each atom to a chunk ID (or to no chunk at all). The number of chunks and the assignment of chunk IDs to atoms can be static or change over time. Examples of “chunks” are molecules or spatial bins or atoms with similar values (e.g. coordination number or potential energy).
The per-atom chunk IDs can be used as input to two other kinds of commands, to calculate various properties of a system:
Here a brief overview for each of the 4 kinds of chunk-related commands is provided. Then some examples are given of how to compute different properties with chunk commands.
Compute chunk/atom command:
This compute can assign atoms to chunks of various styles. Only atoms in the specified group and optional specified region are assigned to a chunk. Here are some possible chunk definitions:
|atoms in same molecule||chunk ID = molecule ID|
|atoms of same atom type||chunk ID = atom type|
|all atoms with same atom property (charge, radius, etc)||chunk ID = output of compute property/atom|
|atoms in same cluster||chunk ID = output of compute cluster/atom command|
|atoms in same spatial bin||chunk ID = bin ID|
|atoms in same rigid body||chunk ID = molecule ID used to define rigid bodies|
|atoms with similar potential energy||chunk ID = output of compute pe/atom|
|atoms with same local defect structure||chunk ID = output of compute centro/atom or compute coord/atom command|
Note that chunk IDs are integer values, so for atom properties or computes that produce a floating point value, they will be truncated to an integer. You could also use the compute in a variable that scales the floating point value to spread it across multiple integers.
Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins = pencils, 3d bins = boxes, spherical bins, cylindrical bins.
This compute also calculates the number of chunks Nchunk, which is used by other commands to tally per-chunk data. Nchunk can be a static value or change over time (e.g. the number of clusters). The chunk ID for an individual atom can also be static (e.g. a molecule ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
Note that this compute allows the per-atom output of other computes, fixes, and variables to be used to define chunk IDs for each atom. This means you can write your own compute or fix to output a per-atom quantity to use as chunk ID. See the Modify doc pages for info on how to do this. You can also define a per-atom variable in the input script that uses a formula to generate a chunk ID for each atom.
Fix ave/chunk command:
This fix takes the ID of a compute chunk/atom command as input. For each chunk, it then sums one or more specified per-atom values over the atoms in each chunk. The per-atom values can be any atom property, such as velocity, force, charge, potential energy, kinetic energy, stress, etc. Additional keywords are defined for per-chunk properties like density and temperature. More generally any per-atom value generated by other computes, fixes, and per-atom variables, can be summed over atoms in each chunk.
Similar to other averaging fixes, this fix allows the summed per-chunk values to be time-averaged in various ways, and output to a file. The fix produces a global array as output with one row of values per chunk.
Compute */chunk commands:
The following computes operate on chunks of atoms to produce per-chunk values. Any compute whose style name ends in “/chunk” is in this category:
- compute com/chunk
- compute gyration/chunk
- compute inertia/chunk
- compute msd/chunk
- compute property/chunk
- compute temp/chunk
- compute torque/chunk
- compute vcm/chunk
They each take the ID of a compute chunk/atom command as input. As their names indicate, they calculate the center-of-mass, radius of gyration, moments of inertia, mean-squared displacement, temperature, torque, and velocity of center-of-mass for each chunk of atoms. The compute property/chunk command can tally the count of atoms in each chunk and extract other per-chunk properties.
The reason these various calculations are not part of the fix ave/chunk command, is that each requires a more complicated operation than simply summing and averaging over per-atom values in each chunk. For example, many of them require calculation of a center of mass, which requires summing mass*position over the atoms and then dividing by summed mass.
All of these computes produce a global vector or global array as output, wih one or more values per chunk. The output can be used in various ways:
- As input to the fix ave/time command, which can write the values to a file and optionally time average them.
- As input to the fix ave/histo command to histogram values across chunks. E.g. a histogram of cluster sizes or molecule diffusion rates.
- As input to special functions of equal-style variables, like sum() and max() and ave(). E.g. to find the largest cluster or fastest diffusing molecule or average radius-of-gyration of a set of molecules (chunks).
Other chunk commands:
The compute chunk/spread/atom command spreads per-chunk values to each atom in the chunk, producing per-atom values as its output. This can be useful for outputting per-chunk values to a per-atom dump file. Or for using an atom’s associated chunk value in an atom-style variable.
The compute reduce/chunk command reduces a peratom value across the atoms in each chunk to produce a value per chunk. When used with the compute chunk/spread/atom command it can create peratom values that induce a new set of chunks with a second compute chunk/atom command.
Example calculations with chunks
Here are examples using chunk commands to calculate various properties:
- Average velocity in each of 1000 2d spatial bins:
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
(2) Temperature in each spatial bin, after subtracting a flow velocity:
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced compute vbias all temp/profile 1 0 0 y 10 fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out
- Center of mass of each molecule:
compute cc1 all chunk/atom molecule compute myChunk all com/chunk cc1 fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
- Total force on each molecule and ave/max across all molecules:
compute cc1 all chunk/atom molecule fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out variable xave equal ave(f_1) variable xmax equal max(f_1) thermo 1000 thermo_style custom step temp v_xave v_xmax
- Histogram of cluster sizes:
compute cluster all cluster/atom 1.0 compute cc1 all chunk/atom c_cluster compress yes compute size all property/chunk cc1 count fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
(6) An example of using a per-chunk value to apply per-atom forces to compress individual polymer chains (molecules) in a mixture, is explained on the compute chunk/spread/atom command doc page.
(7) An example of using one set of per-chunk values for molecule chunks, to create a 2nd set of micelle-scale chunks (clustered molecules, due to hydrophobicity), is explained on the compute chunk/reduce command doc page.