disable default TranslationGenerator

[Robert Koch]

Hi everyone,

If I wanted to just run fullrmc (at least at some point in the process) with only swapping of certain species, no translations, is there a way to disable the default TranslationGenerator assigned to each atom? using "set_refine(False) doesn't seem to work. I guess if I set the amplitude to close to zero, this could have the desired effect, but would create a lot of unnecessary small moves?

cheers,

Rob

[Bachir Aoun]

Robert,

you must set SwapPositionsGenerator for the groups that you want to swap. you need to check fullrmc provided examples and in particular atomicNiTi.

This is an exact copy from the example

def run_swap(nsteps, saveFrequency, engineFilePath):

    # activate coordination number. Play with definition and set_used to True

    ACN_CONSTRAINT.set_coordination_number_definition( [ ('ti','ti',2.5, 3.5, 4, 8),

                                                         ('ti','ni',2.2, 3.1, 6, 10),

                                                         ('ni','ni',2.5, 3.5, 4, 8),

                                                         ('ni','ti',2.2, 3.1, 6, 10) ] )

    ACN_CONSTRAINT.set_used(False)

    # reset groups

    ENGINE.set_groups_as_atoms()

    #### set swap generators Ni-->Ti and Ti-->Ni ###

    allElements = ENGINE.allElements

    niSwapList = [[idx] for idx in range(len(allElements)) if allElements[idx]=='ni']

    tiSwapList = [[idx] for idx in range(len(allElements)) if allElements[idx]=='ti']

    # create swap generator

    toNiSG = SwapPositionsGenerator(swapList=niSwapList)

    toTiSG = SwapPositionsGenerator(swapList=tiSwapList)

    # set swap generator to groups

    for g in ENGINE.groups:

        if allElements[g.indexes[0]]=='ni':

            g.set_move_generator(toTiSG)

        elif allElements[g.indexes[0]]=='ti':

            g.set_move_generator(toNiSG)

    # run

    ENGINE.run(numberOfSteps=nsteps, saveFrequency=saveFrequency)

[Robert Koch]

Hi Bachir,

Thanks! This mirrors what I've implemented, but consider the case where we only want to swap a subet of the elements, like this case:

https://bachiraoun.github.io/fullrmc/fullrmc.Generators.html#fullrmc.Generators.Swaps.SwapPositionsGenerator

The last line in that example states "# the rest are oxygen atoms. Default RandomTranslation generator are kept."

Is there any way to turn off these "Default RandomTranslations" for, say oxygen or any other elements not involved in swapping?

thanks!

Rob

[Bachir Aoun]

Robert,

Moves are performed upon groups. You must define the groups you need and set the move generator upon those. By default, when you set your engine pdb file, fullrmc automatically creates atomic groups for you using all atoms. All what you need todo now is to reset the groups to the atoms you need and set the moves generators accordingly

[Robert Koch]

Hi Bachir,

Thanks, this was helpful! 

The issue is that "ENGINE.set_groups_as_atoms()" adds all the atoms as groups, and gives them a translation generator. If we omit this line, then add atoms as groups manually, specifically based on chemical symbol matching, everything runs fine, no atoms translate and we only swap the atoms we intended to.

Thanks!

Rob