\(\renewcommand{\AA}{\text{Å}}\)
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 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 or more of four styles of quantities: global, per-atom, local, or per-atom. 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. Per-grid quantities are calculated on a regular 2d or 3d grid which overlays a 2d or 3d simulation domain. The grid points and the data they store are distributed across processors; each processor owns the grid points which fall within its subdomain.
Computes that produce per-atom quantities have the word “atom” at the end of their style, e.g. ke/atom. Computes that produce local quantities have the word “local” at the end of their style, e.g. bond/local. Computes that produce per-grid quantities have the word “grid” at the end of their style, e.g. property/grid. Styles with neither “atom” or “local” or “grid” at the end of their style name produce global quantities.
Note that a single compute typically produces either global or per-atom or local or per-grid values. It does not compute both global and per-atom values. It can produce local values or per-grid values in tandem with global or per-atom quantities. The compute doc page will explain the details.
Global, per-atom, local, and per-grid quantities 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 \(\to\) scalar, array \(\to\) vector). Using two brackets reduces the dimension twice (array \(\to\) 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 a global temperature or pressure can be used by fixes that do thermostatting or barostatting or when atom velocities are created.
Global values can be output via the thermo_style custom or fix ave/time command. Or the values can be referenced in a variable equal or variable atom command.
Per-atom values can be output via the dump custom command. Or they can be time-averaged via the fix ave/atom command or reduced by the compute reduce command. Or the per-atom values can be referenced in an atom-style variable.
Local values can be reduced by the compute reduce command, or histogrammed by the fix ave/histo command, or output by the dump local command.
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 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 page for details. The results of their calculations accessed in the various ways described above.
Each compute style has its own 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 page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist.
ackland/atom - determines the local lattice structure based on the Ackland formulation
adf - angular distribution function of triples of atoms
aggregate/atom - aggregate ID for each atom
angle - energy of each angle sub-style
angle/local - theta and energy of each angle
angmom/chunk - angular momentum for each chunk
ave/sphere/atom - compute local density and temperature around each atom
basal/atom - calculates the hexagonal close-packed “c” lattice vector of each atom
body/local - attributes of body sub-particles
bond - energy of each bond sub-style
bond/local - distance and energy of each bond
born/matrix - second derivative or potential with respect to strain
centro/atom - centro-symmetry parameter for each atom
centroid/stress/atom - centroid based stress tensor for each atom
chunk/atom - assign chunk IDs to each atom
chunk/spread/atom - spreads chunk values to each atom in chunk
cluster/atom - cluster ID for each atom
cna/atom - common neighbor analysis (CNA) for each atom
cnp/atom - common neighborhood parameter (CNP) for each atom
com - center of mass of group of atoms
com/chunk - center of mass for each chunk
contact/atom - contact count for each spherical particle
coord/atom - coordination number for each atom
count/type - count of atoms or bonds by type
damage/atom - Peridynamic damage for each atom
dihedral - energy of each dihedral sub-style
dihedral/local - angle of each dihedral
dilatation/atom - Peridynamic dilatation for each atom
dipole - dipole vector and total dipole
dipole/chunk - dipole vector and total dipole for each chunk
dipole/tip4p - dipole vector and total dipole with TIP4P pair style
dipole/tip4p/chunk - dipole vector and total dipole for each chunk with TIP4P pair style
displace/atom - displacement of each atom
dpd - total values of internal conductive energy, internal mechanical energy, chemical energy, and harmonic average of internal temperature
dpd/atom - per-particle values of internal conductive energy, internal mechanical energy, chemical energy, and internal temperature
edpd/temp/atom - per-atom temperature for each eDPD particle in a group
efield/atom - electric field at each atom
efield/wolf/atom - electric field at each atom
entropy/atom - pair entropy fingerprint of each atom
erotate/asphere - rotational energy of aspherical particles
erotate/rigid - rotational energy of rigid bodies
erotate/sphere - rotational energy of spherical particles
erotate/sphere/atom - rotational energy for each spherical particle
event/displace - detect event on atom displacement
fabric - calculates fabric tensors from pair interactions
fep - compute free energies for alchemical transformation from perturbation theory
fep/ta - compute free energies for a test area perturbation
force/tally - force between two groups of atoms via the tally callback mechanism
fragment/atom - fragment ID for each atom
global/atom - assign global values to each atom from arrays of global values
group/group - energy/force between two groups of atoms
gyration - radius of gyration of group of atoms
gyration/chunk - radius of gyration for each chunk
gyration/shape - shape parameters from gyration tensor
gyration/shape/chunk - shape parameters from gyration tensor for each chunk
heat/flux - heat flux through a group of atoms
heat/flux/tally - heat flux through a group of atoms via the tally callback mechanism
heat/flux/virial/tally - virial heat flux between two groups via the tally callback mechanism
hexorder/atom - bond orientational order parameter q6
hma - harmonically mapped averaging for atomic crystals
improper - energy of each improper sub-style
improper/local - angle of each improper
inertia/chunk - inertia tensor for each chunk
ke - translational kinetic energy
ke/atom - kinetic energy for each atom
ke/atom/eff - per-atom translational and radial kinetic energy in the electron force field model
ke/eff - kinetic energy of a group of nuclei and electrons in the electron force field model
ke/rigid - translational kinetic energy of rigid bodies
composition/atom - local composition for each atom
mliap - gradients of energy and forces with respect to model parameters and related quantities for training machine learning interatomic potentials
momentum - translational momentum
msd - mean-squared displacement of group of atoms
msd/chunk - mean-squared displacement for each chunk
msd/nongauss - MSD and non-Gaussian parameter of group of atoms
nbond/atom - calculates number of bonds per atom
omega/chunk - angular velocity for each chunk
orientorder/atom - Steinhardt bond orientational order parameters Ql
pair - values computed by a pair style
pair/local - distance/energy/force of each pairwise interaction
pe - potential energy
pe/atom - potential energy for each atom
pe/mol/tally - potential energy between two groups of atoms separated into intermolecular and intramolecular components via the tally callback mechanism
pe/tally - potential energy between two groups of atoms via the tally callback mechanism
plasticity/atom - Peridynamic plasticity for each atom
pressure - total pressure and pressure tensor
pressure/alchemy - mixed system total pressure and pressure tensor for fix alchemy runs
pressure/uef - pressure tensor in the reference frame of an applied flow field
property/atom - convert atom attributes to per-atom vectors/arrays
property/chunk - extract various per-chunk attributes
property/grid - convert per-grid attributes to per-grid vectors/arrays
property/local - convert local attributes to local vectors/arrays
ptm/atom - determines the local lattice structure based on the Polyhedral Template Matching method
rdf - radial distribution function \(g(r)\) histogram of group of atoms
reduce - combine per-atom quantities into a single global value
reduce/chunk - reduce per-atom quantities within each chunk
reduce/region - same as compute reduce, within a region
rigid/local - extract rigid body attributes
saed - electron diffraction intensity on a mesh of reciprocal lattice nodes
slice - extract values from global vector or array
smd/contact/radius - contact radius for Smooth Mach Dynamics
smd/damage - damage status of SPH particles in Smooth Mach Dynamics
smd/hourglass/error - error associated with approximated relative separation in Smooth Mach Dynamics
smd/internal/energy - per-particle enthalpy in Smooth Mach Dynamics
smd/plastic/strain - equivalent plastic strain per particle in Smooth Mach Dynamics
smd/plastic/strain/rate - time rate of the equivalent plastic strain in Smooth Mach Dynamics
smd/rho - per-particle mass density in Smooth Mach Dynamics
smd/tlsph/defgrad - deformation gradient in Smooth Mach Dynamics
smd/tlsph/dt - CFL-stable time increment per particle in Smooth Mach Dynamics
smd/tlsph/num/neighs - number of particles inside the smoothing kernel radius for Smooth Mach Dynamics
smd/tlsph/shape - current shape of the volume of a particle for Smooth Mach Dynamics
smd/tlsph/strain - Green–Lagrange strain tensor for Smooth Mach Dynamics
smd/tlsph/strain/rate - rate of strain for Smooth Mach Dynamics
smd/tlsph/stress - per-particle Cauchy stress tensor for SPH particles
smd/triangle/vertices - coordinates of vertices corresponding to the triangle elements of a mesh for Smooth Mach Dynamics
smd/ulsph/effm - per-particle effective shear modulus
smd/ulsph/num/neighs - number of neighbor particles inside the smoothing kernel radius for Smooth Mach Dynamics
smd/ulsph/strain - logarithmic strain tensor for Smooth Mach Dynamics
smd/ulsph/strain/rate - logarithmic strain rate for Smooth Mach Dynamics
smd/ulsph/stress - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
smd/vol - per-particle volumes and their sum in Smooth Mach Dynamics
snap - gradients of SNAP energy and forces with respect to linear coefficients and related quantities for fitting SNAP potentials
sna/atom - bispectrum components for each atom
sna/grid - global array of bispectrum components on a regular grid
sna/grid/local - local array of bispectrum components on a regular grid
snad/atom - derivative of bispectrum components for each atom
snav/atom - virial contribution from bispectrum components for each atom
sph/e/atom - per-atom internal energy of Smooth-Particle Hydrodynamics atoms
sph/rho/atom - per-atom density of Smooth-Particle Hydrodynamics atoms
sph/t/atom - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
spin - magnetic quantities for a system of atoms having spins
stress/atom - stress tensor for each atom
stress/cartesian - stress tensor in cartesian coordinates
stress/cylinder - stress tensor in cylindrical coordinates
stress/mop - normal components of the local stress tensor using the method of planes
stress/mop/profile - profile of the normal components of the local stress tensor using the method of planes
stress/spherical - stress tensor in spherical coordinates
stress/tally - stress between two groups of atoms via the tally callback mechanism
tdpd/cc/atom - per-atom chemical concentration of a specified species for each tDPD particle
temp - temperature of group of atoms
temp/asphere - temperature of aspherical particles
temp/body - temperature of body particles
temp/chunk - temperature of each chunk
temp/com - temperature after subtracting center-of-mass velocity
temp/cs - temperature based on the center-of-mass velocity of atom pairs that are bonded to each other
temp/deform - temperature excluding box deformation velocity
temp/deform/eff - temperature excluding box deformation velocity in the electron force field model
temp/drude - temperature of Core–Drude pairs
temp/eff - temperature of a group of nuclei and electrons in the electron force field model
temp/partial - temperature excluding one or more dimensions of velocity
temp/profile - temperature excluding a binned velocity profile
temp/ramp - temperature excluding ramped velocity component
temp/region - temperature of a region of atoms
temp/region/eff - temperature of a region of nuclei and electrons in the electron force field model
temp/rotate - temperature of a group of atoms after subtracting out their center-of-mass and angular velocities
temp/sphere - temperature of spherical particles
temp/uef - kinetic energy tensor in the reference frame of an applied flow field
ti - thermodynamic integration free energy values
torque/chunk - torque applied on each chunk
vacf - velocity auto-correlation function of group of atoms
vcm/chunk - velocity of center-of-mass for each chunk
viscosity/cos - velocity profile under cosine-shaped acceleration
voronoi/atom - Voronoi volume and neighbors for each atom
xrd - X-ray diffraction intensity on a mesh of reciprocal lattice nodes
Restrictions
none
Default
none