pytint
Python library for free energy calculations using thermodynamic integration
Installing LAMMPS
pytint works with the standard version of LAMMPS. Currently
supported pair styles are pace(works with
lammps-ace)
and eam (with standard LAMMPS). If you want use other pair styles
such as snap or sw, please
contact.
pytint needs LAMMPS compiled as a library with Python support. It
can be done by the following instructions-
cd lammps
mkdir build_lib
cd build_lib
cmake -D BUILD_LIB=ON -D BUILD_SHARED_LIBS=ON -D BUILD_MPI=ON -D PKG_MANYBODY=ON -D PKG_USER-MISC=ON -D PKG_USER-PACE=ON ../cmake
make # -j${NUM_CPUS}
cp liblammps${SHLIB_EXT}* ../src
cd ../src
make install-python
The include files and compiled files should be available in the
paths. A full set of instructions can be found
here.
Installing pytint
Install dependencies
The following packages need to be installed.
numpy (
conda install -c conda-forge numpy)scipy (
conda install -c conda-forge scipy)pyyaml (
conda install -c conda-forge pyyaml)mendeleev (
conda install -c conda-forge mendeleev)pylammpsmpi (
conda install -c conda-forge pylammpsmpi)pyscal (
conda install -c conda-forge pyscal)
Install pytint
After installing the requirements, pytint can be installed by,
git clone https://git.noc.ruhr-uni-bochum.de/atomicclusterexpansion/pytint.git
cd pytint
python setup.py install
cd pytint/docs
pip install -r requirements.txt
make html
The files will be in pytint/docs/build/html.
pytint can be run as both a Python library and as a command line
tool. The recommended way to use pytint is through the command line.
After installation, pytint can be accessed from the terminal using,
tint --help
The main option one needs to specify is the --input or -i. This
keyword species the location of the input file. The format of the
inputfile is discussed in detail here.
tint -i input.yaml
Such a command will read the input file and start NEHI calculations
for each temperature mentioned in the input file. Alternatively, one
can use the --mode option to launch a reversible scaling
calculation.
tint -i input.yaml -m rs
In this case, one NEHI calculation is done for the first temperature mentioned in the input file, and then a reversible scaling calculation is done to extend the free energy up to the last temperature specified in the input file.
Publications
Freitas, Rodrigo, Mark Asta, and Maurice de Koning. “Nonequilibrium Free-Energy Calculation of Solids Using LAMMPS.” Computational Materials Science 112 (February 2016): 333–41. https://doi.org/10.1016/j.commatsci.2015.10.050.
Paula Leite, Rodolfo, and Maurice de Koning. “Nonequilibrium Free-Energy Calculations of Fluids Using LAMMPS.” Computational Materials Science 159 (March 2019): 316–26. https://doi.org/10.1016/j.commatsci.2018.12.029.
Koning, Maurice de, A. Antonelli, and Sidney Yip. “Optimized Free-Energy Evaluation Using a Single Reversible-Scaling Simulation.” Physical Review Letters 83, no. 20 (November 15, 1999): 3973–77. https://doi.org/10.1103/PhysRevLett.83.3973.