Relative path

../fullrmc/Examples/removes/

Description

A box of 8100 atoms oxide composite of Nickel, Manganese, Cobalt and Lithium and Oxygen. In this example, we show how to use a EmptyGroup and AtomsRemoveGenerator in order to reproduce defects in the system.

Files

1. system.pdb: The initial configuration input file.
2. pdf.exp: The x-rays experimental pair distribution function data.
3. run.py: The script file used to run the simulation.
4. plot.py: The script file to plot the last saved engine state of PairDistributionConstraint.
5. visualize.py: The script file to visualize the last save configuration using VMD. if installed.

run.py explained

IMPORTING USEFUL DEFINITIONS:

All useful packages, modules and definitions are imported.

DECLARE USEFUL VARIABLES:

Initialize and declare useful variables in all the script.

CREATE ENGINE:

Check if engine already saved on disk. In the affirmative load it to continue fitting from last saved configuration. Otherwise, build the engine and the needed constraints.

DIFFERENT RUNS:

Define functions to run the fitting engine. All of the following functions finish running the engine using Engine.run method.

1. normal_run: use set_groups_as_atoms to create groups of single atom. Here the engine runs traditional RMC with random selection of groups using RandomSelector and random atomic translations using TranslationGenerator move generator.
2. swaps_run: use set_groups_as_atoms to create groups of single atom. Create two swapping lists. The first one containing only Lithium atoms indexes and the second all of Cobalt, Nickel and Manganese atom indexes. Create two SwapPositionsGenerator for swapping Lithium atoms with Cobalt, Nickel and Manganese and vice-versa.
3. removes_run: Create remove lists that are lists of atom indexes. First list for oxygen atoms, another one for lithium atoms and a third one for all of nickel, manganese and cobalt. AtomsRemoveGenerator is a especial generator that can only be set to an EmptyGroup. Create three EmptyGroup where by default their move generators are AtomsRemoveGenerator instances. use set_maximum_collected for each and every one to limit the maximum number of allowed removed atoms per generator. The use set_atoms_list to set list of atoms to remove from. If set_maximum_collected is not used, then theres is no boundaries to how many atoms are allowed to be removed and AtomsRemoveGenerator can remove atoms without any control. The same way, if set_maximum_collected is not used the AtomsRemoveGenerator will remove any atom from the system. Finally, use set_groups method to set only the three defined EmptyGroup.

RUN SIMULATION:

launch normal_run then allow experimental constraint to fit its scale factor then launch normal_run again. At this point, one can notice that the fit is not perfect yet. Create ‘swap_1’ frame and set it as used. Launch swaps_run to swap between atoms then launch normal_run again. Then, create and use ‘removes_2’ frame. And Finally, loop for many times all of removes_run, normal_run and swaps_run. Notice that the number of steps for removes_run is as little as 100. It’s very important to remove as little atoms as possible and try to fit again. Excessive atoms removal is irreversible, and even though it decreases total error on the short run but it will drive the system to an impossibility to finding a solution. Removing a lot of atoms can create artificial defects and voids in the system that can’t be explained physically. Notice here the usage of frame is very important. At any time if one thinks that for instance a lot of atoms were removed, then one can simply revert to a previous frame prior to starting atoms removal.