Relative path

../fullrmc/Examples/SiOxNanosphere/

Description

Isolated Silicon oxide spherical nano-particle is create using 2315 silicon atom and 1094 oxygen atom dispersed in the outer layers at different concentration ratios that decreases with the depth of the nano-particle.

Files

1. SiOx.pdb: The initial configuration input file.
2. SiOx.gr: 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 constraint data.
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.

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. Starting from fullrmc version 1.0.0, fitting non-periodic boundary conditions is possible. This is done by computing a shape function that corrects for density fluctuation and void at large distances. Here, set_shape_function_parameters method is used to fit a shape function ShapeFunction upon computing the experimental constraint PairDistributionConstraint.

DIFFERENT RUNS:

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

1. run_normal_rmc: Runs a normal traditional RMC fit.
2. run_explore: Sets RecursiveGroupSelector group selector and runs explore mode.
3. expand_nanoparticule: Sets DirectionalOrderSelector group selector and wraps it with RecursiveGroupSelector to allow different fitting modes. DirectionalOrderSelector is initialized with both expand and adjustMoveGenerators set to True. This means that it will automatically select groups starting from outer layers to the deapest ones and will automatically set and adjust groups move generators to a collection of randomRotation and TranslationTowardsCenterGenerator using MoveGeneratorCollector.

RUN SIMULATION:

run the different functions to fit the system.

PLOT PDF CONSTRAINT:

Plotting PairDistributionConstraint data after fitting.