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EmDee: A Molecular Dynamics Laboratory

Build Status

codecov.io

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.