fix mol/swap command — LAMMPS documentation

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# fix mol/swap command

## Syntax

    fix ID group-ID mol/swap N X itype jtype seed T keyword value ...

- ID, group-ID are documented in fix command

- atom/swap = style name of this fix command

- N = invoke this fix every N steps

- X = number of swaps to attempt every N steps

- itype,jtype = two atom types (1-Ntypes or type label) to swap with each other

- seed = random # seed (positive integer)

- T = scaling temperature of the MC swaps (temperature units)

- zero or more keyword/value pairs may be appended to args

- keyword = ke

      ke value = no or yes
        no = no conservation of kinetic energy after atom swaps
        yes = kinetic energy is conserved after atom swaps

## Examples

    fix 2 all mol/swap 100 1 2 3 29494 300.0 ke no
    fix mySwap fluid mol/swap 500 10 1 2 482798 1.0

    labelmap atom 1 A 2 B
    fix mySwap fluid mol/swap 500 10 A B 482798 1.0

## Description

This fix performs Monte Carlo swaps of two specified atom types within a randomly selected molecule. Two possible use cases are as follows.

First, consider a mixture of some molecules with atoms of itype and other molecules with atoms of jtype. The fix will select a random molecule and attempt to swap all the itype atoms to jtype for the first kind of molecule, or all the jtype atoms to itype for the second kind. Because the swap will only take place if it is energetically favorable, the fix can be used to determine the miscibility of 2 different kinds of molecules much more quickly than just dynamics would do it.

Second, consider diblock co-polymers with two types of monomers itype and jtype. The fix will select a random molecule and attempt to do a itype <–> jtype swap of all those monomers within the molecule. Thus the fix can be used to find the energetically favorable fractions of two flavors of diblock co-polymers.

Intra-molecular swaps of atom types are attempted every N timesteps. On that timestep, X swaps are attempted. For each attempt a single molecule ID is randomly selected. The range of possible molecule IDs from loID to hiID is pre-computed before each run begins. The loID/hiID is set for the molecule with the smallest/largest ID which has any itype or jtype atoms in it. Note that if you define a system with many molecule IDs between loID and hiID which have no itype or jtype atoms, then the fix will be inefficient at performing swaps. Also note that if atoms with molecule ID = 0 exist, they are not considered molecules by this fix; they are assumed to be solvent atoms or molecules.

Candidate atoms for swapping must also be in the fix group. Atoms within the selected molecule which are not itype or jtype are ignored.

When an atom is swapped from itype to jtype (or vice versa), if charges are defined, the charge values for itype versus jtype atoms are also swapped. This requires that all itype atoms in the system have the same charge value. Likewise all jtype atoms in the system must have the same charge value. If this is not the case, LAMMPS issues a warning that it cannot swap charge values.

If the ke keyword is set to yes, which is the default, and the masses of itype and jtype atoms are different, then when a swap occurs, the velocity of the swapped atom is rescaled by the sqrt of the mass ratio, so as to conserve the kinetic energy of the atom.

The potential energy of the entire system is computed before and after each swap is performed within a single molecule. The specified temperature T is used in the Metropolis criterion to accept or reject the attempted swap. If the swap is rejected all swapped values are reversed.

The potential energy calculations can include systems and models with the following features:

- manybody pair styles, including EAM

- hybrid pair styles

- long-range electrostatics (kspace)

- triclinic systems

- potential energy contributions from other fixes

For the last bullet point, fixes can have an associated potential energy. Examples of such fixes include: efield, gravity, addforce, langevin, restrain, temp/berendsen, temp/rescale, and wall fixes. For that energy to be included in the total potential energy of the system (the quantity used for the swap accept/reject decision), you MUST enable the fix_modify energy option for that fix. The doc pages for individual fix commands specify if this should be done.

Note

One comment on computational efficiency. If the cutoff lengths defined for the pair style are different for itype versus jtype atoms (for any of their interactions with any other atom type), then a new neighbor list needs to be generated for every attempted swap. This is potentially expensive if N is small or X is large.

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

This fix writes the state of the fix to binary restart files. This includes information about the random number generator seed, the next timestep for MC exchanges, the number of exchange attempts and successes etc. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion.

Note

For this to work correctly, the timestep must not be changed after reading the restart with reset_timestep. The fix will try to detect it and stop with an error.

None of the fix_modify options are relevant to this fix.

This fix computes a global vector of length 2, which can be accessed by various output commands. The vector values are the following global cumulative quantities:

> 1. swap attempts

> 2. swap accepts

The vector values calculated by this fix are “intensive”.

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

This fix is part of the MC package. It is only enabled if LAMMPS was built with that package. See the Build package doc page for more info.

## Related commands

fix atom/swap, fix gcmc

## Default

The option default is ke = yes.