fix adapt command¶

Syntax¶

fix ID group-ID adapt N attribute args ... keyword value ...

ID, group-ID are documented in fix command
adapt = style name of this fix command
N = adapt simulation settings every this many timesteps
one or more attribute/arg pairs may be appended

attribute = pair or bond or kspace or atom

pair args = pstyle pparam I J v_name
  pstyle = pair style name, e.g. lj/cut
  pparam = parameter to adapt over time
  I,J = type pair(s) to set parameter for
  v_name = variable with name that calculates value of pparam
bond args = bstyle bparam I v_name
  bstyle = bond style name, e.g. harmonic
  bparam = parameter to adapt over time
  I = type bond to set parameter for
  v_name = variable with name that calculates value of bparam
kspace arg = v_name
  v_name = variable with name that calculates scale factor on K-space terms
atom args = aparam v_name
  aparam = parameter to adapt over time
  v_name = variable with name that calculates value of aparam

zero or more keyword/value pairs may be appended

keyword = scale or reset or mass

scale value = no or yes
  no = the variable value is the new setting
  yes = the variable value multiplies the original setting
reset value = no or yes
  no = values will remain altered at the end of a run
  yes = reset altered values to their original values at the end of a run
mass value = no or yes
  no = mass is not altered by changes in diameter
  yes = mass is altered by changes in diameter

Examples¶

fix 1 all adapt 1 pair soft a 1 1 v_prefactor
fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 pair coul/cut scale 3 3 v_scale2 scale yes reset yes
fix 1 all adapt 10 atom diameter v_size

variable ramp_up equal "ramp(0.01,0.5)"
fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up

Description¶

Change or adapt one or more specific simulation attributes or settings over time as a simulation runs. Pair potential and K-space and atom attributes which can be varied by this fix are discussed below. Many other fixes can also be used to time-vary simulation parameters, e.g. the “fix deform” command will change the simulation box size/shape and the “fix move” command will change atom positions and velocities in a prescribed manner. Also note that many commands allow variables as arguments for specific parameters, if described in that manner on their doc pages. An equal-style variable can calculate a time-dependent quantity, so this is another way to vary a simulation parameter over time.

If N is specified as 0, the specified attributes are only changed once, before the simulation begins. This is all that is needed if the associated variables are not time-dependent. If N > 0, then changes are made every N steps during the simulation, presumably with a variable that is time-dependent.

Depending on the value of the reset keyword, attributes changed by this fix will or will not be reset back to their original values at the end of a simulation. Even if reset is specified as yes, a restart file written during a simulation will contain the modified settings.

If the scale keyword is set to no, which is the default, then the value of the altered parameter will be whatever the variable generates. If the scale keyword is set to yes, then the value of the altered parameter will be the initial value of that parameter multiplied by whatever the variable generates. I.e. the variable is now a “scale factor” applied in (presumably) a time-varying fashion to the parameter.

Note that whether scale is no or yes, internally, the parameters themselves are actually altered by this fix. Make sure you use the reset yes option if you want the parameters to be restored to their initial values after the run.

The pair keyword enables various parameters of potentials defined by the pair_style command to be changed, if the pair style supports it. Note that the pair_style and pair_coeff commands must be used in the usual manner to specify these parameters initially; the fix adapt command simply overrides the parameters.

The pstyle argument is the name of the pair style. If pair_style hybrid or hybrid/overlay is used, pstyle should be a sub-style name. If there are multiple sub-styles using the same pair style, then pstyle should be specified as “style:N” where N is which instance of the pair style you wish to adapt, e.g. the first, second, etc. For example, pstyle could be specified as “soft” or “lubricate” or “lj/cut:1” or “lj/cut:2”. The pparam argument is the name of the parameter to change. This is the current list of pair styles and parameters that can be varied by this fix. See the doc pages for individual pair styles and their energy formulas for the meaning of these parameters:

born	a,b,c	type pairs
born/coul/long, born/coul/msm	coulombic_cutoff	type global
buck, buck/coul/cut	a,c	type pairs
buck/coul/long, buck/coul/msm	a,c,coulombic_cutoff	type pairs
buck/mdf	a,c	type pairs
coul/cut	scale	type pairs
coul/cut/soft	lambda	type pairs
coul/debye	scale	type pairs
coul/dsf	coulombic_cutoff	type global
coul/long, coul/msm	coulombic_cutoff, scale	type pairs
coul/long/soft	scale, lambda, coulombic_cutoff	type pairs
eam, eam/alloy, eam/fs	scale	type pairs
gauss	a	type pairs
lennard/mdf	A,B	type pairs
lj/class2	epsilon,sigma	type pairs
lj/class2/coul/cut, lj/class2/coul/long	epsilon,sigma,coulombic_cutoff	type pairs
lj/cut	epsilon,sigma	type pairs
lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm	epsilon,sigma,coulombic_cutoff	type pairs
lj/cut/coul/cut/soft, lj/cut/coul/long/soft	epsilon,sigma,lambda,coulombic_cutoff	type pairs
lj/cut/coul/dsf	cutoff	type global
lj/cut/tip4p/cut	epsilon,sigma,coulombic_cutoff	type pairs
lj/cut/soft	epsilon,sigma,lambda	type pairs
lj/expand	epsilon,sigma,delta	type pairs
lj/mdf	epsilon,sigma	type pairs
lj/sf/dipole/sf	epsilon,sigma,scale	type pairs
lubricate	mu	global
mie/cut	epsilon,sigma,gamma_repulsive,gamma_attractive	type pairs
morse, morse/smooth/linear	D0,R0,alpha	type pairs
morse/soft	D0,R0,alpha,lambda	type pairs
nm/cut	E0,R0,m,n	type pairs
nm/cut/coul/cut, nm/cut/coul/long	E0,R0,m,n,coulombic_cutoff	type pairs
reaxff	chi, eta, gamma	type global
snap	scale	type pairs
spin/dmi	coulombic_cutoff	type global
spin/exchange	coulombic_cutoff	type global
spin/magelec	coulombic_cutoff	type global
spin/neel	coulombic_cutoff	type global
table	table_cutoff	type pairs
ufm	epsilon,sigma	type pairs
soft	a	type pairs

Note

It is easy to add new pairwise potentials and their parameters to this list. All it typically takes is adding an extract() method to the pair_*.cpp file associated with the potential.

Some parameters are global settings for the pair style, e.g. the viscosity setting “mu” for pair_style lubricate. Other parameters apply to atom type pairs within the pair style, e.g. the prefactor “a” for pair_style soft.

Note that for many of the potentials, the parameter that can be varied is effectively a prefactor on the entire energy expression for the potential, e.g. the lj/cut epsilon. The parameters listed as “scale” are exactly that, since the energy expression for the coul/cut potential (for example) has no labeled prefactor in its formula. To apply an effective prefactor to some potentials, multiple parameters need to be altered. For example, the Buckingham potential needs both the A and C terms altered together. To scale the Buckingham potential, you should thus list the pair style twice, once for A and once for C.

If a type pair parameter is specified, the I and J settings should be specified to indicate which type pairs to apply it to. If a global parameter is specified, the I and J settings still need to be specified, but are ignored.

Similar to the pair_coeff command, I and J can be specified in one of two ways. Explicit numeric values can be used for each, as in the first example above. I <= J is required. LAMMPS sets the coefficients for the symmetric J,I interaction to the same values.

A wild-card asterisk can be used in place of or in conjunction with the I,J arguments to set the coefficients for multiple pairs of atom types. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). Note that only type pairs with I <= J are considered; if asterisks imply type pairs where J < I, they are ignored.

IMPROTANT NOTE: If pair_style hybrid or hybrid/overlay is being used, then the pstyle will be a sub-style name. You must specify I,J arguments that correspond to type pair values defined (via the pair_coeff command) for that sub-style.

The v_name argument for keyword pair is the name of an equal-style variable which will be evaluated each time this fix is invoked to set the parameter to a new value. It should be specified as v_name, where name is the variable name. Equal-style variables can specify formulas with various mathematical functions, and include thermo_style command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify parameters that change as a function of time or span consecutive runs in a continuous fashion. For the latter, see the start and stop keywords of the run command and the elaplong keyword of thermo_style custom for details.

For example, these commands would change the prefactor coefficient of the pair_style soft potential from 10.0 to 30.0 in a linear fashion over the course of a simulation:

variable prefactor equal ramp(10,30)
fix 1 all adapt 1 pair soft a * * v_prefactor

The bond keyword uses the specified variable to change the value of a bond coefficient over time, very similar to how the pair keyword operates. The only difference is that now a bond coefficient for a given bond type is adapted.

A wild-card asterisk can be used in place of or in conjunction with the bond type argument to set the coefficients for multiple bond types. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive).

Currently bond does not support bond_style hybrid nor bond_style hybrid/overlay as bond styles. The only bonds that currently are working with fix_adapt are

class2	r0	type bonds
fene	k, r0	type bonds
gromos	k, r0	type bonds
harmonic	k,r0	type bonds
morse	r0	type bonds
nonlinear	r0	type bonds

The kspace keyword used the specified variable as a scale factor on the energy, forces, virial calculated by whatever K-Space solver is defined by the kspace_style command. If the variable has a value of 1.0, then the solver is unaltered.

The kspace keyword works this way whether the scale keyword is set to no or yes.

The atom keyword enables various atom properties to be changed. The aparam argument is the name of the parameter to change. This is the current list of atom parameters that can be varied by this fix:

charge = charge on particle
diameter or diameter/disc = diameter of particle

The v_name argument of the atom keyword is the name of an equal-style variable which will be evaluated each time this fix is invoked to set, or scale the parameter to a new value. It should be specified as v_name, where name is the variable name. See the discussion above describing the formulas associated with equal-style variables. The new value is assigned to the corresponding attribute for all atoms in the fix group.

If the atom parameter is diameter and per-atom density and per-atom mass are defined for particles (e.g. atom_style granular), then the mass of each particle is, by default, also changed when the diameter changes. The mass is set from the particle volume for 3d systems (density is assumed to stay constant). For 2d, the default is for LAMMPS to model particles with a radius attribute as spheres. However, if the atom parameter is diameter/disc, then the mass is set from the particle area (the density is assumed to be in mass/distance^2 units). The mass of the particle may also be kept constant if the mass keyword is set to no. This can be useful to account for diameter changes that do not involve mass changes, e.g., thermal expansion.

For example, these commands would shrink the diameter of all granular particles in the “center” group from 1.0 to 0.1 in a linear fashion over the course of a 1000-step simulation:

variable size equal ramp(1.0,0.1)
fix 1 center adapt 10 atom diameter v_size

This fix can be used in long simulations which are restarted one or more times to continuously adapt simulation parameters, but it must be done carefully. There are two issues to consider. The first is how to adapt the parameters in a continuous manner from one simulation to the next. The second is how, if desired, to reset the parameters to their original values at the end of the last restarted run.

Note that all the parameters changed by this fix are written into a restart file in their current changed state. A new restarted simulation does not know their original time=0 values, unless the input script explicitly resets the parameters (after the restart file is read), to their original values.

Also note, that the time-dependent variable(s) used in the restart script should typically be written as a function of time elapsed since the original simulation began.

With this in mind, if the scale keyword is set to no (the default) in a restarted simulation, original parameters are not needed. The adapted parameters should seamlessly continue their variation relative to the preceding simulation.

If the scale keyword is set to yes, then the input script should typically reset the parameters being adapted to their original values, so that the scaling formula specified by the variable will operate correctly. An exception is if the atom keyword is being used with scale yes. In this case, information is added to the restart file so that per-atom properties in the new run will automatically be scaled relative to their original values. This will only work if the fix adapt command specified in the restart script has the same ID as the one used in the original script.

In a restarted run, if the reset keyword is set to yes, and the run ends in this script (as opposed to just writing more restart files, parameters will be restored to the values they were at the beginning of the run command in the restart script. Which as explained above, may or may not be the original values of the parameters. Again, an exception is if the atom keyword is being used with reset yes (in all the runs). In that case, the original per-atom parameters are stored in the restart file, and will be restored when the restarted run finally completes.

Restart, fix_modify, output, run start/stop, minimize info¶

If the atom keyword is used and the scale or reset keyword is set to yes, then this fix writes information to a restart file so that in a restarted run scaling can continue in a seamless manner and/or the per-atom values can be restored, as explained above.

None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

For rRESPA time integration, this fix changes parameters on the outermost rRESPA level.

Restrictions¶

none

Default¶

The option defaults are scale = no, reset = no, mass = yes.