EmDee: A Molecular Dynamics Laboratory

EmDee is a minimalist library that can perform, in a very efficient way, the most computationally demanding tasks of classical molecular dynamics simulations:

1. Calculation of pairwise interaction forces, energies, and virials.
2. Building and manipulation of neighbor lists.
3. Scaling and/or translation of atom coordinates and conjugate momenta.

The purpose of EmDee is to serve as a platform to test simulation methods that involve the mechanics of many atoms, such as different thermostats and barostats, hybrid Monte Carlo algorithms, etc.

Contents

This repository contains:

• Source code (fortran) and build instructions (Makefile) for the EmDee library
• A test program in 3 versions:
  • A fortran source code + build instructions (Makefile)
  • A C source code + build instructions (Makefile)
  • A julia script
• An example input data file for the test program

Standard compilation and testing

Dependencies (considering a Ubuntu 16.04.1 LTS fresh install):

Basic for compiling the library

• gfortran

Tested with:

• GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 20160609

Can usually be installed via apt:

 sudo apt-get install gfortran

Further dependencies for running the test

To run the julia script test:

• julia

Tested with:

• julia version 0.4.5

Can usually be installed via apt:

 sudo apt install julia

Compiling the library:

• Clone the repository

    git clone https://github.com/craabreu/EmDee
  

  This will create a local copy of the repository on your device.

• Execute the Makefile in the root directory of the repository tree

    make
  

  This will build the shared library (lib/libemdee.so).

Running the tests:

• Use building option test

    make test
  

  This will compile the c and fortran test programs and create a copy of the default julia testscript inside the test directory.

• Run each test using the input file provided in the example directory.

    test/testfortran <N_threads> examples/data.inp
    test/testc <N_threads> examples/data.inp
    test/testjulia <N_threads> examples/data.inp
  

  In the commands above, N_threads (optional) is the number of parallel threads to be used for the calculations.

Installing the library in the system path:

• Use building option install

    make install
  

  This will copy the static library (lib/libemdee.so) to /usr/local/lib and the C header file (include/emdee.h) and fortran module (include/emdee.f03) to /usr/local/include.