Python package (noblegasmd)

A pip install-able, numba-accelerated Python port of the same NVE Lennard-Jones engine, runnable with zero build step (e.g. in Google Colab). MD.cpp below remains the authoritative physics reference; the port is validated against it (see tests/).

pip install noblegasmd

from noblegasmd import run, sweep

result = run(gas="Ar", T=300.0, rho=40.0)
print(result.Z, result.P_avg, result.T_avg)

df = sweep(gas="Ar", T=[100, 200, 300, 400], rho=[1, 40, 500, 2000], n_replicates=3)

See notebooks/reproduce_figure4.ipynb to regenerate the published quasi-isotherms, and MD_python_port_spec.md for the full port specification. Development install: pip install -e ".[dev]", then pytest.

---

C++ reference implementation (MD.cpp)

• Source code for Molecular Dynamics Program - can compile and run on Linux, Windows, and Mac OSX

• More information about this program, including detailed instructions for its use, can be found here for instructions and here for discussion of its use in an undergraduate laboratory setting

• This folder should containt the source code (MD.cpp) and a makefile which can be used to compile the source to a machine-executable file.

• A copy of the gnu public license (LICENSE.md) should be included.

• To compile this code using a gnu C/C++ compiler and create an executable called 'MD.exe' in a Linux/Unix environment, type

  make

• To run the program in a Linux/Unix environment, type

  ./MD.exe

• The program will run interactively. Follow the prompts to customize your simulation

Note for Windows users on Cygwin installation: Our J. Chem. Ed. article suggests installing all Cygwin packages, which is quite large and time consuming. Success with a much lighter installation has been reported by selecting the default package installation plus 3 additional packages under the "devel" sub-heading. As accessed on 01/08/2020, these packages and version numbers are as follows:

• gcc-g++ (7.4.0-1)
• git (2.21.0-1)
• make (4.2.1-2)