\(\renewcommand{\AA}{\text{Å}}\)
fix adapt/fep command
Syntax
fix ID group-ID adapt/fep N attribute args ... keyword value ...
ID, group-ID are documented in fix command
adapt/fep = 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 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 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 I = type(s) to set parameter for v_name = variable with name that calculates value of aparam
zero or more keyword/value pairs may be appended
keyword = scale or reset or after
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 after value = no or yes no = parameters are adapted at timestep N yes = parameters are adapted one timestep after N
Examples
fix 1 all adapt/fep 1 pair soft a 1 1 v_prefactor
fix 1 all adapt/fep 1 pair soft a 2* 3 v_prefactor
fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
fix 1 all adapt/fep 10 atom diameter 1 v_size
Example input scripts available: examples/PACKAGES/fep
Description
Change or adapt one or more specific simulation attributes or settings over time as a simulation runs.
This is an enhanced version of the fix adapt command with two differences:
It is possible to modify the charges of chosen atom types only, instead of scaling all the charges in the system.
There is a new option after for better compatibility with fix ave/time.
This version is suited for free energy calculations using compute ti or compute fep.
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, then the value the parameter is set to 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). Internally, the parameters themselves are actually altered; make sure you use the reset yes option if you want the parameters to be restored to their initial values after the run.
If the after keyword is set to yes, then the parameters are changed one timestep after the multiple of N. In this manner, if a fix such as “fix ave/time” is used to calculate averages at every N timesteps, all the contributions to the average will be obtained with the same values of the parameters.
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. For example, pstyle could be specified as “soft” or “lubricate”. 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:
a,b,c |
type pairs |
|
a,c |
type pairs |
|
a,c |
type pairs |
|
scale |
type pairs |
|
lambda |
type pairs |
|
scale |
type pairs |
|
scale, lambda |
type pairs |
|
scale |
type pairs |
|
a |
type pairs |
|
a,b |
type pairs |
|
epsilon,sigma |
type pairs |
|
epsilon,sigma |
type pairs |
|
epsilon,sigma |
type pairs |
|
epsilon,sigma,lambda |
type pairs |
|
epsilon,sigma |
type pairs |
|
epsilon,sigma,lambda |
type pairs |
|
epsilon,sigma |
type pairs |
|
epsilon,sigma,lambda |
type pairs |
|
epsilon,sigma,delta |
type pairs |
|
epsilon,sigma |
type pairs |
|
epsilon,sigma,scale |
type pairs |
|
epsilon,sigma,gamR,gamA |
type pairs |
|
d0,r0,alpha |
type pairs |
|
d0,r0,alpha,lambda |
type pairs |
|
e0,r0,nn,mm |
type pairs |
|
e0,r0,nn,mm |
type pairs |
|
scale |
type pairs |
|
a |
type pairs |
|
epsilon,sigma,scale |
type pairs |
Note
It is easy to add new 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.
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. \(I \le J\) 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 “m*” or “m*n”. If \(N\) is 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 m to \(N\) (inclusive). A middle asterisk means all types from m to n (inclusive). Note that only type pairs with \(I \le J\) 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 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 = diameter of particle
The \(I\) argument indicates which atom types are affected. A wild-card asterisk can be used in place of or in conjunction with the \(I\) argument to set the coefficients for multiple atom types.
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 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 also changed when the diameter changes (density is assumed to stay constant).
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
For rRESPA time integration, this fix changes parameters on the outermost rRESPA level.
Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to binary restart files. 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.
Restrictions
none
Default
The option defaults are scale = no, reset = no, after = no.