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:
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.
| 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. |
To install these source codes, please follow the steps below:
-
Go to LAMMPS webpage (https://lammps.sandia.gov/download.html) and download the source code at your local machine.
-
Clone this repository to a subdirectory named
USER-FFEinside thesrc/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.
- 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.
- 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.
Instructions of how to use these codes can be found inside each LAMMPS input script in the examples directory and in our paper.
lammps-22Aug18
Rodolfo Paula Leite - [email protected]