\(\renewcommand{\AA}{\text{Å}}\)
fix command
Syntax
fix ID group-ID style args
ID = user-assigned name for the fix
group-ID = ID of the group of atoms to apply the fix to
style = one of a long list of possible style names (see below)
args = arguments used by a particular style
Examples
fix 1 all nve
fix 3 all nvt temp 300.0 300.0 0.01
fix mine top setforce 0.0 NULL 0.0
Description
Set a fix that will be applied to a group of atoms. In LAMMPS, a “fix” is any operation that is applied to the system during timestepping or minimization. Examples include updating of atom positions and velocities due to time integration, controlling temperature, applying constraint forces to atoms, enforcing boundary conditions, computing diagnostics, etc. There are hundreds of fixes defined in LAMMPS and new ones can be added; see the Modify page for details.
Fixes perform their operations at different stages of the timestep. If two or more fixes operate at the same stage of the timestep, they are invoked in the order they were specified in the input script.
The ID of a fix can only contain alphanumeric characters and underscores.
Fixes can be deleted with the unfix command.
Note
The unfix command is the only way to turn off a fix; simply specifying a new fix with a similar style will not turn off the first one. This is especially important to realize for integration fixes. For example, using a fix nve command for a second run after using a fix nvt command for the first run will not cancel out the NVT time integration invoked by the “fix nvt” command. Thus, two time integrators would be in place!
If you specify a new fix with the same ID and style as an existing fix, the old fix is deleted and the new one is created (presumably with new settings). This is the same as if an “unfix” command were first performed on the old fix, except that the new fix is kept in the same order relative to the existing fixes as the old one originally was. Note that this operation also wipes out any additional changes made to the old fix via the fix_modify command.
The fix modify command allows settings for some fixes to be reset. See the page for individual fixes for details.
Some fixes store an internal “state” which is written to binary restart files via the restart or write_restart commands. This allows the fix to continue on with its calculations in a restarted simulation. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file. See the doc pages for individual fixes for info on which ones can be restarted.
Some fixes calculate and store any of four styles of quantities: global, per-atom, local, or per-grid.
A global quantity is one or more system-wide values, e.g. the energy of a wall interacting with particles. A per-atom quantity is one or more values per atom, e.g. the original coordinates of each atom at time 0. Per-atom values are set to 0.0 for atoms not in the specified fix 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. values for each bond. 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.
As a general rule of thumb, fixes that produce per-atom quantities have the word “atom” at the end of their style, e.g. ave/atom. Fixes that produce local quantities have the word “local” at the end of their style, e.g. store/local. Fixes that produce per-grid quantities have the word “grid” at the end of their style, e.g. ave/grid.
Global, per-atom, local, and per-grid quantities can also be of three kinds: a single scalar value (global only), a vector of values, or a 2d array of values. For per-atom, local, and per-grid quantities, a “vector” means a single value for each atom, each local entity (e.g. bond), or grid cell. Likewise an “array”, means multiple values for each atom, each local entity, or each grid cell.
Note that a single fix can produce any combination of global, per-atom, local, or per-grid values. Likewise it can produce any combination of scalar, vector, or array output for each style. The exception is that for per-atom, local, and per-grid output, either a vector or array can be produced, but not both. The doc page for each fix explains the values it produces, if any.
When a fix output is accessed by another input script command it is referenced via the following bracket notation, where ID is the ID of the fix:
f_ID |
entire scalar, vector, or array |
f_ID[I] |
one element of vector, one column of array |
f_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, for example, a command that uses global scalar fix values as input can also process elements of a vector or array. Depending on the command, this can either be done directly using the syntax in the table, or by first defining a variable of the appropriate style to store the quantity, then using the variable as an input to the command.
Note that commands and variables which take fix outputs as input typically do not allow for all styles and kinds of data (e.g., a command may require global but not per-atom values, or it may require a vector of values, not a scalar). This means there is typically no ambiguity about referring to a fix output as c_ID even if it produces, for example, both a scalar and vector. The doc pages for various commands explain the details, including how any ambiguities are resolved.
In LAMMPS, the values generated by a fix can be used in several ways:
Global values can be output via the thermo_style custom or fix ave/time command. Alternatively, the values can be referenced in an equal-style variable 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. Alternatively, 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. They can also be output by the dump local command.
See the Howto output page for a summary of various LAMMPS output options, many of which involve fixes.
The results of fixes 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 fix 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 fix styles for further info.
Each fix style has its own page that describes its arguments and what it does, as listed below. Here is an alphabetical list of fix styles available in LAMMPS. They are also listed in more compact form on the Commands fix doc page.
There are also additional accelerated fix styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. The individual style names on the Commands fix doc page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist.
accelerate/cos - apply cosine-shaped acceleration to atoms
acks2/reaxff - apply ACKS2 charge equilibration
adapt - change a simulation parameter over time
adapt/fep - enhanced version of fix adapt
addforce - add a force to each atom
add/heat - add a heat flux to each atom
addtorque - add a torque to a group of atoms
alchemy - perform an “alchemical transformation” between two partitions
amoeba/bitorsion - torsion/torsion terms in AMOEBA force field
amoeba/pitorsion - 6-body terms in AMOEBA force field
append/atoms - append atoms to a running simulation
atc - initiates a coupled MD/FE simulation
atom/swap - Monte Carlo atom type swapping
ave/atom - compute per-atom time-averaged quantities
ave/chunk - compute per-chunk time-averaged quantities
ave/correlate - compute/output time correlations
ave/correlate/long - alternative to ave/correlate that allows efficient calculation over long time windows
ave/grid - compute per-grid time-averaged quantities
ave/histo - compute/output time-averaged histograms
ave/histo/weight - weighted version of fix ave/histo
ave/time - compute/output global time-averaged quantities
aveforce - add an averaged force to each atom
balance - perform dynamic load-balancing
brownian - overdamped translational brownian motion
brownian/asphere - overdamped translational and rotational brownian motion for ellipsoids
brownian/sphere - overdamped translational and rotational brownian motion for spheres
bocs - NPT style time integration with pressure correction
bond/break - break bonds on the fly
bond/create - create bonds on the fly
bond/create/angle - create bonds on the fly with angle constraints
bond/react - apply topology changes to model reactions
bond/swap - Monte Carlo bond swapping
box/relax - relax box size during energy minimization
charge/regulation - Monte Carlo sampling of charge regulation
cmap - CMAP torsion/torsion terms in CHARMM force field
colvars - interface to the collective variables “Colvars” library
controller - apply control loop feedback mechanism
damping/cundall - Cundall non-viscous damping for granular simulations
deform - change the simulation box size/shape
deform/pressure - change the simulation box size/shape with additional loading conditions
deposit - add new atoms above a surface
dpd/energy - constant energy dissipative particle dynamics
drag - drag atoms towards a defined coordinate
drude - part of Drude oscillator polarization model
drude/transform/direct - part of Drude oscillator polarization model
drude/transform/inverse - part of Drude oscillator polarization model
dt/reset - reset the timestep based on velocity, forces
edpd/source - add heat source to eDPD simulations
efield - impose electric field on system
efield/tip4p - impose electric field on system with TIP4P molecules
ehex - enhanced heat exchange algorithm
electrode/conp - impose electric potential
electrode/conq - impose total electric charge
electrode/thermo - apply thermo-potentiostat
electron/stopping - electronic stopping power as a friction force
electron/stopping/fit - electronic stopping power as a friction force
enforce2d - zero out z-dimension velocity and force
eos/cv - applies a mesoparticle equation of state to relate the particle internal energy to the particle internal temperature
eos/table - applies a tabulated mesoparticle equation of state to relate the particle internal energy to the particle internal temperature
eos/table/rx - applies a tabulated mesoparticle equation of state to relate the concentration-dependent particle internal energy to the particle internal temperature
evaporate - remove atoms from simulation periodically
external - callback to an external driver program
ffl - apply a Fast-Forward Langevin equation thermostat
filter/corotate - implement corotation filter to allow larger timesteps with r-RESPA
flow/gauss - Gaussian dynamics for constant mass flux
freeze - freeze atoms in a granular simulation
gcmc - grand canonical insertions/deletions
gld - generalized Langevin dynamics integrator
gle - generalized Langevin equation thermostat
gravity - add gravity to atoms in a granular simulation
grem - implements the generalized replica exchange method
halt - terminate a dynamics run or minimization
heat - add/subtract momentum-conserving heat
heat/flow - plain time integration of heat flow with per-atom temperature updates
hyper/global - global hyperdynamics
hyper/local - local hyperdynamics
imd - implements the “Interactive MD” (IMD) protocol
indent - impose force due to an indenter
ipi - enable LAMMPS to run as a client for i-PI path-integral simulations
langevin - Langevin temperature control
langevin/drude - Langevin temperature control of Drude oscillators
langevin/eff - Langevin temperature control for the electron force field model
langevin/spin - Langevin temperature control for a spin or spin-lattice system
lb/fluid - lattice-Boltzmann fluid on a uniform mesh
lb/momentum - fix momentum replacement for use with a lattice-Boltzmann fluid
lb/viscous - fix viscous replacement for use with a lattice-Boltzmann fluid
lineforce - constrain atoms to move in a line
manifoldforce - restrain atoms to a manifold during minimization
mdi/qm - LAMMPS operates as a client for a quantum code via the MolSSI Driver Interface (MDI)
mdi/qmmm - LAMMPS operates as client for QM/MM simulation with a quantum code via the MolSSI Driver Interface (MDI)
meso/move - move mesoscopic SPH/SDPD particles in a prescribed fashion
mol/swap - Monte Carlo atom type swapping with a molecule
momentum - zero the linear and/or angular momentum of a group of atoms
momentum/chunk - zero the linear and/or angular momentum of a chunk of atoms
move - move atoms in a prescribed fashion
msst - multi-scale shock technique (MSST) integration
mvv/dpd - DPD using the modified velocity-Verlet integration algorithm
mvv/edpd - constant energy DPD using the modified velocity-Verlet algorithm
mvv/tdpd - constant temperature DPD using the modified velocity-Verlet algorithm
neb - nudged elastic band (NEB) spring forces
neb/spin - nudged elastic band (NEB) spring forces for spins
nonaffine/displacement - calculate nonaffine displacement of atoms
nph - constant NPH time integration via Nose/Hoover
nph/asphere - NPH for aspherical particles
nph/body - NPH for body particles
nph/eff - NPH for nuclei and electrons in the electron force field model
nph/sphere - NPH for spherical particles
nphug - constant-stress Hugoniostat integration
npt - constant NPT time integration via Nose/Hoover
npt/asphere - NPT for aspherical particles
npt/body - NPT for body particles
npt/cauchy - NPT with Cauchy stress
npt/eff - NPT for nuclei and electrons in the electron force field model
npt/sphere - NPT for spherical particles
npt/uef - NPT style time integration with diagonal flow
numdiff - numerically approximate atomic forces using finite energy differences
numdiff/virial - numerically approximate virial stress tensor using finite energy differences
nve - constant NVE time integration
nve/asphere - NVE for aspherical particles
nve/asphere/noforce - NVE for aspherical particles without forces
nve/awpmd - NVE for the Antisymmetrized Wave Packet Molecular Dynamics model
nve/body - NVE for body particles
nve/dot - rigid body constant energy time integrator for coarse grain models
nve/dotc/langevin - Langevin style rigid body time integrator for coarse grain models
nve/eff - NVE for nuclei and electrons in the electron force field model
nve/limit - NVE with limited step length
nve/line - NVE for line segments
nve/manifold/rattle - NVE time integration for atoms constrained to a curved surface (manifold)
nve/noforce - NVE without forces (update positions only)
nve/sphere - NVE for spherical particles
nve/bpm/sphere - NVE for spherical particles used in the BPM package
nve/spin - NVE for a spin or spin-lattice system
nve/tri - NVE for triangles
nvk - constant kinetic energy time integration
nvt - NVT time integration via Nose/Hoover
nvt/asphere - NVT for aspherical particles
nvt/body - NVT for body particles
nvt/eff - NVE for nuclei and electrons in the electron force field model
nvt/manifold/rattle - NVT time integration for atoms constrained to a curved surface (manifold)
nvt/sllod - NVT for NEMD with SLLOD equations
nvt/sllod/eff - NVT for NEMD with SLLOD equations for the electron force field model
nvt/sphere - NVT for spherical particles
nvt/uef - NVT style time integration with diagonal flow
oneway - constrain particles on move in one direction
orient/bcc - add grain boundary migration force for BCC
orient/fcc - add grain boundary migration force for FCC
orient/eco - add generalized grain boundary migration force
pafi - constrained force averages on hyper-planes to compute free energies (PAFI)
pair - access per-atom info from pair styles
phonon - calculate dynamical matrix from MD simulations
pimd/langevin - Feynman path-integral molecular dynamics with stochastic thermostat
pimd/nvt - Feynman path-integral molecular dynamics with Nose-Hoover thermostat
planeforce - constrain atoms to move in a plane
plumed - wrapper on PLUMED free energy library
poems - constrain clusters of atoms to move as coupled rigid bodies
polarize/bem/gmres - compute induced charges at the interface between impermeable media with different dielectric constants with generalized minimum residual (GMRES)
polarize/bem/icc - compute induced charges at the interface between impermeable media with different dielectric constants with the successive over-relaxation algorithm
polarize/functional - compute induced charges at the interface between impermeable media with different dielectric constants with the energy variational approach
pour - pour new atoms/molecules into a granular simulation domain
precession/spin - apply a precession torque to each magnetic spin
press/berendsen - pressure control by Berendsen barostat
press/langevin - pressure control by Langevin barostat
print - print text and variables during a simulation
propel/self - model self-propelled particles
property/atom - add customized per-atom values
python/invoke - call a Python function during a simulation
python/move - move particles using a Python function during a simulation run
qbmsst - quantum bath multi-scale shock technique time integrator
qeq/comb - charge equilibration for COMB potential
qeq/ctip - charge equilibration for CTIP potential
qeq/dynamic - charge equilibration via dynamic method
qeq/fire - charge equilibration via FIRE minimizer
qeq/point - charge equilibration via point method
qeq/reaxff - charge equilibration for ReaxFF potential
qeq/shielded - charge equilibration via shielded method
qeq/slater - charge equilibration via Slater method
qmmm - functionality to enable a quantum mechanics/molecular mechanics coupling
qtb - implement quantum thermal bath scheme
qtpie/reaxff - apply QTPIE charge equilibration
rattle - RATTLE constraints on bonds and/or angles
reaxff/bonds - write out ReaxFF bond information
reaxff/species - write out ReaxFF molecule information
recenter - constrain the center-of-mass position of a group of atoms
restrain - constrain a bond, angle, dihedral
rheo - integrator for the RHEO package
rheo/thermal - thermal integrator for the RHEO package
rheo/oxidation - create oxidation bonds for the RHEO package
rheo/pressure - pressure calculation for the RHEO package
rheo/viscosity - viscosity calculation for the RHEO package
rhok - add bias potential for long-range ordered systems
rigid - constrain one or more clusters of atoms to move as a rigid body with NVE integration
rigid/meso - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
rigid/nph - constrain one or more clusters of atoms to move as a rigid body with NPH integration
rigid/nph/small - constrain many small clusters of atoms to move as a rigid body with NPH integration
rigid/npt - constrain one or more clusters of atoms to move as a rigid body with NPT integration
rigid/npt/small - constrain many small clusters of atoms to move as a rigid body with NPT integration
rigid/nve - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
rigid/nve/small - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
rigid/nvt - constrain one or more clusters of atoms to move as a rigid body with NVT integration
rigid/nvt/small - constrain many small clusters of atoms to move as a rigid body with NVT integration
rigid/small - constrain many small clusters of atoms to move as a rigid body with NVE integration
rx - solve reaction kinetic ODEs for a defined reaction set
saed/vtk - time-average the intensities from compute saed
setforce - set the force on each atom
setforce/spin - set magnetic precession vectors on each atom
sgcmc - fix for hybrid semi-grand canonical MD/MC simulations
shake - SHAKE constraints on bonds and/or angles
shardlow - integration of DPD equations of motion using the Shardlow splitting
smd - applied a steered MD force to a group
smd/adjust_dt - calculate a new stable time increment for use with SMD integrators
smd/integrate_tlsph - explicit time integration with total Lagrangian SPH pair style
smd/integrate_ulsph - explicit time integration with updated Lagrangian SPH pair style
smd/move_tri_surf - update position and velocity near rigid surfaces using SPH integrators
smd/setvel - sets each velocity component, ignoring forces, for Smooth Mach Dynamics
smd/wall_surface - create a rigid wall with a triangulated surface for use in Smooth Mach Dynamics
sph - time integration for SPH/DPDE particles
sph/stationary - update energy and density but not position or velocity in Smooth Particle Hydrodynamics
spring - apply harmonic spring force to group of atoms
spring/chunk - apply harmonic spring force to each chunk of atoms
spring/rg - spring on radius of gyration of group of atoms
spring/self - spring from each atom to its origin
srd - stochastic rotation dynamics (SRD)
store/force - store force on each atom
store/state - store attributes for each atom
tdpd/source - add external concentration source
temp/berendsen - temperature control by Berendsen thermostat
temp/csld - canonical sampling thermostat with Langevin dynamics
temp/csvr - canonical sampling thermostat with Hamiltonian dynamics
temp/rescale - temperature control by velocity rescaling
temp/rescale/eff - temperature control by velocity rescaling in the electron force field model
tfmc - perform force-bias Monte Carlo with time-stamped method
tgnvt/drude - NVT time integration for Drude polarizable model via temperature-grouped Nose-Hoover
tgnpt/drude - NPT time integration for Drude polarizable model via temperature-grouped Nose-Hoover
thermal/conductivity - Mueller-Plathe kinetic energy exchange for thermal conductivity calculation
ti/spring - perform thermodynamic integration between a solid and an Einstein crystal
tmd - guide a group of atoms to a new configuration
ttm - two-temperature model for electronic/atomic coupling (replicated grid)
ttm/grid - two-temperature model for electronic/atomic coupling (distributed grid)
ttm/mod - enhanced two-temperature model with additional options
tune/kspace - auto-tune \(k\)-space parameters
vector - accumulate a global vector every N timesteps
viscosity - Mueller-Plathe momentum exchange for viscosity calculation
viscous - viscous damping for granular simulations
viscous/sphere - viscous damping on angular velocity for granular simulations
wall/body/polygon - time integration for body particles of style rounded/polygon
wall/body/polyhedron - time integration for body particles of style rounded/polyhedron
wall/colloid - Lennard-Jones wall interacting with finite-size particles
wall/ees - wall for ellipsoidal particles
wall/flow - flow boundary conditions
wall/gran - frictional wall(s) for granular simulations
wall/gran/region - fix wall/region equivalent for use with granular particles
wall/harmonic - harmonic spring wall
wall/lj1043 - Lennard-Jones 10–4–3 wall
wall/lj126 - Lennard-Jones 12–6 wall
wall/lj93 - Lennard-Jones 9–3 wall
wall/lepton - Custom Lepton expression wall
wall/morse - Morse potential wall
wall/piston - moving reflective piston wall
wall/reflect - reflecting wall(s)
wall/reflect/stochastic - reflecting wall(s) with finite temperature
wall/region - use region surface as wall
wall/region/ees - use region surface as wall for ellipsoidal particles
wall/srd - slip/no-slip wall for SRD particles
wall/table - Tabulated potential wall wall
widom - Widom insertions of atoms or molecules
Restrictions
Some fix styles are part of specific packages. They are only enabled if LAMMPS was built with that package. See the Build package page for more info. The doc pages for individual fixes tell if it is part of a package.
Default
none