3.7. Fix styles

In LAMMPS, a “fix” is any operation that is computed during timestepping that alters some property of the system. Essentially everything that happens during a simulation besides force computation, neighbor list construction, and output, is a “fix”. This includes time integration (update of coordinates and velocities), force constraints or boundary conditions (SHAKE or walls), and diagnostics (compute a diffusion coefficient). New styles can be created to add new options to LAMMPS.

Fix_setforce.cpp is a simple example of setting forces on atoms to prescribed values. There are dozens of fix options already in LAMMPS; choose one as a template that is similar to what you want to implement.

Here is a brief description of methods you can define in your new derived class. See fix.h for details.

setmask	determines when the fix is called during the timestep (required)
init	initialization before a run (optional)
setup_pre_exchange	called before atom exchange in setup (optional)
setup_pre_force	called before force computation in setup (optional)
setup	called immediately before the first timestep and after forces are computed (optional)
min_setup_pre_force	like setup_pre_force, but for minimizations instead of MD runs (optional)
min_setup	like setup, but for minimizations instead of MD runs (optional)
initial_integrate	called at very beginning of each timestep (optional)
pre_exchange	called before atom exchange on re-neighboring steps (optional)
pre_neighbor	called before neighbor list build (optional)
pre_force	called before pair & molecular forces are computed (optional)
post_force	called after pair & molecular forces are computed and communicated (optional)
final_integrate	called at end of each timestep (optional)
end_of_step	called at very end of timestep (optional)
write_restart	dumps fix info to restart file (optional)
restart	uses info from restart file to re-initialize the fix (optional)
grow_arrays	allocate memory for atom-based arrays used by fix (optional)
copy_arrays	copy atom info when an atom migrates to a new processor (optional)
pack_exchange	store atom’s data in a buffer (optional)
unpack_exchange	retrieve atom’s data from a buffer (optional)
pack_restart	store atom’s data for writing to restart file (optional)
unpack_restart	retrieve atom’s data from a restart file buffer (optional)
size_restart	size of atom’s data (optional)
maxsize_restart	max size of atom’s data (optional)
setup_pre_force_respa	same as setup_pre_force, but for rRESPA (optional)
initial_integrate_respa	same as initial_integrate, but for rRESPA (optional)
post_integrate_respa	called after the first half integration step is done in rRESPA (optional)
pre_force_respa	same as pre_force, but for rRESPA (optional)
post_force_respa	same as post_force, but for rRESPA (optional)
final_integrate_respa	same as final_integrate, but for rRESPA (optional)
min_pre_force	called after pair & molecular forces are computed in minimizer (optional)
min_post_force	called after pair & molecular forces are computed and communicated in minimizer (optional)
min_store	store extra data for linesearch based minimization on a LIFO stack (optional)
min_pushstore	push the minimization LIFO stack one element down (optional)
min_popstore	pop the minimization LIFO stack one element up (optional)
min_clearstore	clear minimization LIFO stack (optional)
min_step	reset or move forward on line search minimization (optional)
min_dof	report number of degrees of freedom added by this fix in minimization (optional)
max_alpha	report maximum allowed step size during linesearch minimization (optional)
pack_comm	pack a buffer to communicate a per-atom quantity (optional)
unpack_comm	unpack a buffer to communicate a per-atom quantity (optional)
pack_reverse_comm	pack a buffer to reverse communicate a per-atom quantity (optional)
unpack_reverse_comm	unpack a buffer to reverse communicate a per-atom quantity (optional)
dof	report number of degrees of freedom removed by this fix during MD (optional)
compute_scalar	return a global scalar property that the fix computes (optional)
compute_vector	return a component of a vector property that the fix computes (optional)
compute_array	return a component of an array property that the fix computes (optional)
deform	called when the box size is changed (optional)
reset_target	called when a change of the target temperature is requested during a run (optional)
reset_dt	is called when a change of the time step is requested during a run (optional)
modify_param	called when a fix_modify request is executed (optional)
memory_usage	report memory used by fix (optional)
thermo	compute quantities for thermodynamic output (optional)

Typically, only a small fraction of these methods are defined for a particular fix. Setmask is mandatory, as it determines when the fix will be invoked during the timestep. Fixes that perform time integration (nve, nvt, npt) implement initial_integrate() and final_integrate() to perform velocity Verlet updates. Fixes that constrain forces implement post_force().

Fixes that perform diagnostics typically implement end_of_step(). For an end_of_step fix, one of your fix arguments must be the variable “nevery” which is used to determine when to call the fix and you must set this variable in the constructor of your fix. By convention, this is the first argument the fix defines (after the ID, group-ID, style).

If the fix needs to store information for each atom that persists from timestep to timestep, it can manage that memory and migrate the info with the atoms as they move from processors to processor by implementing the grow_arrays, copy_arrays, pack_exchange, and unpack_exchange methods. Similarly, the pack_restart and unpack_restart methods can be implemented to store information about the fix in restart files. If you wish an integrator or force constraint fix to work with rRESPA (see the run_style command), the initial_integrate, post_force_integrate, and final_integrate_respa methods can be implemented. The thermo method enables a fix to contribute values to thermodynamic output, as printed quantities and/or to be summed to the potential energy of the system.