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 LIGGGHTS(R)-PUBLIC, 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 dozens of fixes defined in LIGGGHTS(R)-PUBLIC and new ones can be added; see this section for a discussion.

The full list of fixes defined in LIGGGHTS(R)-PUBLIC is on this page.

Fixes perform their operations at different stages of the timestep. If 2 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.

Warning

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 doc 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 one of three styles of quantities: global, per-atom, or local, which can be used by other commands or output as described below. 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 displacement vector for each atom since 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 atoms.

Note that a single fix may produces either global or per-atom or local quantities (or none at all), but never more than one of these.

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 fix describes the style and kind of values it produces, e.g. a per-atom vector. Some fixes produce more than one kind of a single style, e.g. a global scalar and a global vector.

When a fix 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 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 -> scalar, array -> vector). Using two brackets reduces the dimension twice (array -> scalar). Thus a command that uses scalar fix values as input can also process elements of a vector or array.

Note that commands and variables which use fix 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 fix quantity as f_ID even if it produces, for example, both a scalar and vector. The doc pages for various commands explain the details.

In LIGGGHTS(R)-PUBLIC, the values generated by a fix can be used in several ways:

See this howto section for a summary of various LIGGGHTS(R)-PUBLIC 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 doc page for individual fixes for further info.

Each fix style has its own documentation page which describes its arguments and what it does, as listed below.

The full list of fixes defined in LIGGGHTS(R)-PUBLIC is on this page.

Restrictions

Some fix styles are part of specific packages. They are only enabled if LIGGGHTS(R)-PUBLIC was built with that package. See the Making LIGGGHTS(R)-PUBLIC section for more info on packages. The doc pages for individual fixes tell if it is part of a package.