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Nonequilibrium Free-Energy Calculations of Fluids using LAMMPS

What is this?

This repository contains a set of source codes and input scripts that allows to perform nonequilibrium free-energy calculations of fluid-phase systems using LAMMPS code. Details about the code implementation, capabilities and obtained results with these methods will be found in:

"Nonequilibrium Free-Energy Calculations of Fluids using LAMMPS"
Rodolfo Paula Leite, Maurice de Koning
Computational Material Science 159, 316-326 (2019)
DOI: 10.1016/j.commatsci.2018.12.029

What are the repository contents?

doc: This directory contains an updated user manual.

examples: This directory contains input scripts to run MD simulations.

source codes: The main directory contains our LAMMPS source codes.

README: A brief overview of the distribution.

What is new in these source codes?

Code Name Already exists? Modification
angle.cpp / .h yes Added extract method and reinit function.
angle_harmonic.cpp / .h yes Added a fscale variable (which multiplies only the forces) and the extract() method to adapt parameter over the time.
bond_harmonic.cpp / .h yes Added a fscale variable (which multiplies only the forces) and the extract() method to adapt parameter over the time.
fix_adapt.cpp / .h yes Added a fscale keyword for kspace pppm and pppm/tip4p styles to adapt only the forces during MD simulations. Also added the possibility to adapt angle potential (such as angle_harmonic that is used in the examples).
kspace.cpp / .h yes Added a fscale variable in extract() method.
meam_force.cpp yes Added a fscale variable into meam_force function.
meam.h yes Added a fscale variable into meam_force function.
pair_lj_cut_coul_long.cpp / .h yes Added a fscale variable (which multiplies only the forces) in the extract() method.
pair_lj_cut_tip4p_long.cpp / .h yes Added a fscale variable (which multiplies only the forces) in the extract() method.
pair_meam.cpp / .h yes Added a fscale variable (which multiplies only the forces) and the extract() method to adapt parameter over the time.
pair_sw.cpp / .h yes Added a fscale variable (which multiplies only the forces) and the extract() method to adapt parameter over the time.
pair_ufm.cpp / .h yes Added citation information inside the code.
pair_ufm_rw.cpp / .h no A new pair style which is based on LAMMPS implementation of TIP4P water model.
pppm_tip4p.cpp / .h yes Added an option to set fscale variable (which multiplies only the forces) when pppm_tip4p styles is invoked.
pppm.cpp / .h yes Added an option to set fscale variable (which multiplies only the forces) when pppm styles is invoked.

How to install?

To install these source codes, please follow the steps below:

  1. Go to LAMMPS webpage (https://lammps.sandia.gov/download.html) and download the source code at your local machine.

  2. Clone this repository to a subdirectory named USER-FFE inside the src/ directory of your LAMMPS installation:

cd <your-local-lammps>/src/
git clone https://github.com/plrodolfo/FluidFreeEnergyforLAMMPS.git USER-FFE

WARNING: The next step will overwrite some native source codes in your src folder. However, our source codes have compatibility with old versions. Make a backup of your src folder if you want.

  1. Choose some machine file (e.g. Makefile.mpi) and build LAMMPS using the following commands:

i) make yes-manybody

ii) make yes-kspace

iii) make yes-molecule

iv) make yes-rigid

v) make yes-user-meamc

vi) make yes-user-ffe

vii) make mpi

NOTE: Steps (i-vi) are necessary to install the required packages to reproduce the results presented in our paper.

  1. If LAMMPS was successully built, an executable called "lmp_mpi" will be created in the src directory. Otherwise, an error message is reported. For futher details, please visit the "Build LAMMPS" section on user documentation.

How to use these codes?

Instructions of how to use these codes can be found inside each LAMMPS input script in the examples directory and in our paper.

Current compatibility:

lammps-22Aug18

Contact:

Rodolfo Paula Leite - [email protected]

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Fluid-phase Free-energy Calculation package for LAMMPS

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