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What is ABIN?

ABIN is a program for performing ab initio molecular dynamics. It was designed specifically to deal with quantum nuclear effects. It can do path integral simulations and also utilizes quantum thermostat based on General Langevin equation. It can also simulate non-adiabatic events using Surface-hoping algorithm.

The basic philosophy of this program is simple. While the program itself handles the propagation of the system according to the equations of motion, the forces and energies are taken from the external electronic structure program such as ORCA or TeraChem. The call to the chosen external program is handled via a simple shell script. Therefore, writing a new interface is rather straightforward and can be done without any changes to ABIN or the ab initio code.

The code is provided under the GNU General Public License. A full text of the license can be found in the file LICENCE.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

A full documentation can be found in the folder DOC.

Installation

To compile the code, you'll need a GFortran and g++ compiler version >=7.0. Earlier versions might work, but always run test to verify. Intel compiler might work, but there is a know issue with restarting GLE based simulations, so this functionality is automatically disabled when using ifort.

For some features, you will also need to install the FFTW library. It is usually provided with your Linux distribution. It can also be downloaded here: http://www.fftw.org/

The compilation can be as easy as:

$ ./configure && make

You can test the installation by:

$ make test

If you modify the source code and want to recompile, you should always clean up before the recompilation:

$ make clean && make

Optional dependencies

Some functionality relies on external libraries. These are optional, and the code automatically recognizes which feature is supported for a given build. Run configure -h to see all the options and how to configure them.

To install the libraries, you can use the install scripts in dev_scripts/. We use these in our Continuous Integration testing suite on Github using the Ubuntu 18.04 image so they are guaranteed to work, though you might need to tweak them a bit for your system.

The optional libraries are:

  • MPICH: An MPI implementation used for Replica Exchange MD and MPI interface with TeraChem.
    • If you just need REMD you can also use other MPI libraries such as OpenMPI.
  • FFTW: Fast Fourier Transform library used for normal mode transformation in Path Integral MD.
  • PLUMED: A collection of very useful tools for free energy calculations (MetaDynamics, Umbrella Sampling etc).

Structure of the repository

Path Description
src/ ABIN source code
sample_inputs Sample input files.
interfaces/ BASH interfaces to common ab initio codes.
utils/ Handy scripts that might be useful in conjuction with the MD code.
unit_tests/ Unit tests; run by make unittest
tests/ End-to-End tests; run by make e2etest
dev_scripts/ Setup for ABIN devs and install scripts for optional libraries.