compute command

Syntax

compute ID group-ID style args

  • ID = user-assigned name for the computation

  • group-ID = ID of the group of atoms to perform the computation on

  • style = one of a list of possible style names (see below)

  • args = arguments used by a particular style

Examples

compute 1 all temp
compute newtemp flow temp/partial 1 1 0
compute 3 all ke/atom

Description

Define a computation that will be performed on a group of atoms. Quantities calculated by a compute are instantaneous values, meaning they are calculated from information about atoms on the current timestep or iteration, though a compute may internally store some information about a previous state of the system. Defining a compute does not perform a computation. Instead computes are invoked by other LAMMPS commands as needed, e.g. to calculate a temperature needed for a thermostat fix or to generate thermodynamic or dump file output. See the Howto output doc page for a summary of various LAMMPS output options, many of which involve computes.

The ID of a compute can only contain alphanumeric characters and underscores.

Computes calculate one of three styles of quantities: global, per-atom, or local. A global quantity is one or more system-wide values, e.g. the temperature of the system. A per-atom quantity is one or more values per atom, e.g. the kinetic energy of each atom. Per-atom values are set to 0.0 for atoms not in the specified compute group. Local quantities are calculated by each processor based on the atoms it owns, but there may be zero or more per atom, e.g. a list of bond distances. Computes that produce per-atom quantities have the word “atom” in their style, e.g. ke/atom. Computes that produce local quantities have the word “local” in their style, e.g. bond/local. Styles with neither “atom” or “local” in their style produce global quantities.

Note that a single compute can produce either global or per-atom or local quantities, but not both global and per-atom. It can produce local quantities in tandem with global or per-atom quantities. The compute doc page will explain.

Global, per-atom, and local quantities each come in three kinds: a single scalar value, a vector of values, or a 2d array of values. The doc page for each compute describes the style and kind of values it produces, e.g. a per-atom vector. Some computes produce more than one kind of a single style, e.g. a global scalar and a global vector.

When a compute quantity is accessed, as in many of the output commands discussed below, it can be referenced via the following bracket notation, where ID is the ID of the compute:

c_ID

entire scalar, vector, or array

c_ID[I]

one element of vector, one column of array

c_ID[I][J]

one element of array

In other words, using one bracket reduces the dimension of the quantity once (vector -> scalar, array -> vector). Using two brackets reduces the dimension twice (array -> scalar). Thus a command that uses scalar compute values as input can also process elements of a vector or array.

Note that commands and variables which use compute quantities typically do not allow for all kinds, e.g. a command may require a vector of values, not a scalar. This means there is no ambiguity about referring to a compute quantity as c_ID even if it produces, for example, both a scalar and vector. The doc pages for various commands explain the details.

In LAMMPS, the values generated by a compute can be used in several ways:

The results of computes that calculate global quantities can be either “intensive” or “extensive” values. Intensive means the value is independent of the number of atoms in the simulation, e.g. temperature. Extensive means the value scales with the number of atoms in the simulation, e.g. total rotational kinetic energy. Thermodynamic output will normalize extensive values by the number of atoms in the system, depending on the “thermo_modify norm” setting. It will not normalize intensive values. If a compute value is accessed in another way, e.g. by a variable, you may want to know whether it is an intensive or extensive value. See the doc page for individual computes for further info.

LAMMPS creates its own computes internally for thermodynamic output. Three computes are always created, named “thermo_temp”, “thermo_press”, and “thermo_pe”, as if these commands had been invoked in the input script:

compute thermo_temp all temp
compute thermo_press all pressure thermo_temp
compute thermo_pe all pe

Additional computes for other quantities are created if the thermo style requires it. See the documentation for the thermo_style command.

Fixes that calculate temperature or pressure, i.e. for thermostatting or barostatting, may also create computes. These are discussed in the documentation for specific fix commands.

In all these cases, the default computes LAMMPS creates can be replaced by computes defined by the user in the input script, as described by the thermo_modify and fix modify commands.

Properties of either a default or user-defined compute can be modified via the compute_modify command.

Computes can be deleted with the uncompute command.

Code for new computes can be added to LAMMPS; see the Modify doc page for details. The results of their calculations accessed in the various ways described above.

Each compute style has its own doc page which describes its arguments and what it does. Here is an alphabetic list of compute styles available in LAMMPS. They are also listed in more compact form on the Commands compute doc page.

There are also additional accelerated compute styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. The individual style names on the Commands compute doc page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist.

Restrictions

none