Relative path

../fullrmc/Examples/benchmark/

Description

A box of 719 molecules of tetrahydrofuran of a total of 9347 atoms is used to benchmark several functionalities of fullrmc. This example is very useful to test the performance of fullrmc. Benchmarking might take several hours. At the end of this example benchmark data will be saved and two matplotlib figures will be plotted.

Files

1. experimental.gr: x-rays pair distribution function data of tetrahydrofuran liquid
2. system.pdb: The initial configuration input file
3. run.py: The script file used to run the simulation

run.py explained

IMPORTING USEFUL DEFINITIONS:

All useful packages, modules and definitions are imported.

SHUT DOWN LOGGING:

Set logger minimum level to maximum possible integer value. This will mute all non-error logging.

CREATE ENGINE:

Create the engine and all of PairDistributionConstraint, InterMolecularDistanceConstraint, BondConstraint, BondsAngleConstraint and ImproperAngleConstraint constraints.

DIFFERENT RUNS:

Define functions to run the fitting engine or to visualize saved benchmarks.

1. run: Allows multiple arguments and sets the engine to run a specific benchmark.
2. benchmark_constraints: run and save benchmarks on constraints using different group sizes.
3. benchmark_nsteps: run and save benchmarks on number of steps using a fixed group size and set of constraints.
4. load_and_plot_constraints_benchmark: load and plot saved constraints benchmarks.
5. load_and_plot_steps_benchmark: load and plot saved number of steps benchmarks.

RUN SIMULATION:

benchmark_constraints and benchmark_nsteps functions are called and benchmarks are shown at the end

PLOT BENCHMARKS:

If uncommented, load_and_plot_steps_benchmark and load_and_plot_constraints_benchmark functions will be called.