MDEval.jl

Package to evaluate molecular dynamics (MD) simulations.

1. Installation

To register the module locally, type

Pkg> add https://github.com/se-schmitt/MDEval.jl

in package mode (type ] in REPL to enter Pkg mode).

Then, the module can be loaded by

using MDEval

2. Manual

2.1 Function mdeval

mdeval(mode::Symbol, folder::String, keywords::NamedTuple)

Input arguments:

• mode: defines the mode of the simulations/evaluation. Possible values: :single_run, :tdm, :vle, :nemd_shear, or :nemd_heat (see Section 2.1)
• folder: path to main folder containing all simulation data (see Section 2.3)
• keywords: options to define the evaluation parameters (see Section 2.2)

Examples are provided in the examples folder.

2.1 Evaluation Modes

Different simulation types can be evaluated:

• Evaluation of single run simulations for thermodynamic properties (including transport properties) (:single_run)
• Time decomposition method (TDM) for transport properties (:tdm)
• Evaluation of vapou-liquid equilibrium (VLE) simulations (direct two phase simualtions) (:vle)
• Evaluation of non-equilibrium molecular dynamics (NEMD) shear simulations to determine viscosity (:nemd_shear)
• Evaluation of NEMD heat transfer simulation to determine thermal conductivity (:nemd_heat)

2.2 Keywords

Name	Possible values [default value]	Modes	Description
ensemble	NVT, NVE, NpT	:single_run, :tdm, :nemd_shear	ensemble to evaluate
timesteps_equ	interger ≥ 0 [0]	:single_run, :tdm, :vle	number of timesteps to ignore at the start of each simulation
do_single	true, false [true]	:tdm, :nemd_shear	evaluate single folders
do_state	true, false [true]	:tdm, :nemd_shear	evaluate complete thermodynamic state (main folder)
n_boot	integer ≥ 0 [0]	:tdm	number of bootstrapping repetitions
cutcrit	float ≥ 0 [0.4]	:tdm	cut criteria for :tdm method
do_transport	true, false	:single_run	evaluation of transport properties
corr_length	integer ≥ 0	:single_run	length (timesteps) of correlation function
span_corr_fun	integer ≥ 0	:single_run	timesteps between single correlation functions
n_blocks	integer ≥ 0	:single_run	number of blocks for static properties
n_every	integer ≥ 1	:single_run	skip n_every timesteps when calculating acf (useful for slowly converging states, e.g. ideal gas)
debug_mode	true, false	:single_run	if debug mode is enables, errors are thrown directly
acf_calc_mode	autocov, fft [autocov/fft]	:single_run, :tdm	mode for acf calculation (autocov: full acf by Julia autocov command (can be slowly for long signals), fft: acf calculation by FFT (fast, but inaccurate for long times))
do_structure	true, false [false]	all	structure evaluation
n_bin	integer ≥ 0 [100]	all	number of bins for radial pair distribution (RDF) calculation
r_cut	float [10.0]	all	cut-off radius for RDF (unit: Å) calculation
units	metal, reduced [real]	all	units of simulation (real: LAMMPS SI units, reduced: reduced by LJ parameters)
k_L_thermo	float [0.1]	:nemd_heat	reduced length of thermostats (as fraction of total box length)

2.3 Folder structure

• Single run/ NEMD shear/ NEMD heat simulations

├── SIM_1* [contains all output files of a EMD simulation of one state point]
:

• TDM

├── STATE_1 [contains all replica simulations of one state point]
│   ├── Sim_001
│   ├── Sim_002
:   :

• VLE simulations

├── FOLDER_1 [contains all simulations for one substance]
│   ├── Sim_T1 [VLE simulation at temperature T1]
│   ├── Sim_T2 [VLE simulation at temperature T2]
:   :

• NEMD shear simulations

├── STATE_1 [contains all simulations of one state point]
│   ├── Sim_S1 [VLE simulation with shear rate S1]
│   ├── Sim_S2 [VLE simulation with shear rate S2]
:   : 

2.4 Units

Either reduced or real units can be used. The given unit defines the input as well as the output units. reduced units refer to the Lennard-Jones units system. The input units for real units are the LAMMPS metal units. The units of the output are defined in the following table.

Property	Symbol	Unit
mass	m	g/mol
time	t	ps
temperature	T	K
pressure	p	MPa
energy	E	eV
viscosity	η	Pa*s
self-diffusion coefficient	D	m²/s
thermal conductivity	λ	W/(m*K)