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Installation of Descriptor Codes

Here are the installation instructions for the codes implementing the various descriptors.

Gaussian Approximation Potential (GAP)

Clone the QUIP repository:

git clone --recursive https://github.com/libAtoms/QUIP.git

Define the environment variable QUIP_ROOT as the path of QUIP repository.

cd QUIP
export QUIP_ROOT=${PWD}

Decide your architecture by looking in the ${QUIP_ROOT}/arch/ directory and define the environmental variable QUIP_ARCH, e.g,

export QUIP_ARCH=linux_x86_64_gfortran

Make sure QUIP_ROOT and QUIP_ARCH are in environment path for further auto-detection of building LAMMPS.

Define the environment variable QUIP_INSTALLDIR and add it to the environment path. When the compilation and installation finishes, all compiled programs will be copied to QUIP_INSTALLDIR.

export QUIP_INSTALLDIR=<path_for_executables>

Obtain the support for Gaussian Approximation Potential from GAP, extract the codes in ${QUIP_ROOT}\src directory.

Customise QUIP, set the maths libraries and provide linking options. (It will ask some questions, make sure answer yes to compile with GAP prediction and training support).

make config

Compile all programs, modules and libraries.

make

Copies all compiled programs to QUIP_INSTALLDIR.

make install

Compile QUIP as a library and link to it, this will create a library build/${QUIP_ARCH}/libquip.a.

make libquip

Clone the LAMMPS repository from GitHub. (if LAMMPS package has already been installed, skip this step).

git clone [email protected]:lammps/lammps.git

Assume LMP_ROOT is the path of LAMMPS package, enable the interface neccessary to use QUIP potentials in ${LMP_ROOT}/src directory.

make yes-user-quip

The serial version of LAMMPS containing QUIP interface can then be installed. (Please refer to LAMMPS website for the installation of other versions.)

make serial

Moment Tensor Potential (MTP)

Clone the MLIP repository. This repository is under development, please refer to Alex Shapeev for access to the repository.

git clone http://gitlab.skoltech.ru/shapeev/mlip-dev.git

Assume MLIP_ROOT is the path of MLIP package. Configure the MLIP package build in ${MLIP_ROOT} directory.

./configure

Compile and build the MLIP executable and add the ${MLIP_ROOT}/bin to environment path.

make mlp

Clone the LAMMPS repository from GitHub. (if LAMMPS package has already been installed, skip this step).

git clone [email protected]:lammps/lammps.git

Assume LMP_ROOT is the path of LAMMPS package. Configure MLIP to be used within LAMMPS in ${MLIP_ROOT} directory.

./configure --lammps=${LMP_ROOT}

Install LAMMPS with MLIP interface in ${MLIP_ROOT} directory.

make lammps

An example is provided in mlearn/notebooks/MTP_example/example.ipynb.

Neural Network Potential (NNP)

Clone the n2p2 package from GitHub.

git clone https://github.com/CompPhysVienna/n2p2.git

Assume N2P2_ROOT is the path of the n2p2 package. Build the neccessary executables in ${N2P2_ROOT}/src directory. (Make sure Eigen and GSL are installed and visible in the system).

make

Add the path of ${N2P2_ROOT}/bin to the environment path.

Build the shared libraries of neural network potentials in ${N2P2_ROOT}/src directory.

make libnnpif-shared

Add the path of NNP libraries ${N2P2_ROOT}/lib to library path LD_LIBRARY_PATH.

Clone the LAMMPS repository from GitHub. (if LAMMPS package has already been installed, skip this step).

git clone [email protected]:lammps/lammps.git

Assume LMP_ROOT is the path of LAMMPS package. Link to NNP libraries in ${LMP_ROOT} directory.

ln -s ${N2P2_ROOT} lib/nnp

Copy the USER-NNP package to the LAMMPS source directory.

cp -r ${N2P2_ROOT}/src/interface/LAMMPS/src/USER-NNP ${LMP_ROOT}/src

Enable LAMMPS interface with NNP in ${LMP_PATH}/src directory.

make yes-user-nnp

The serial version of LAMMPS containing NNP interface can then be installed. (Please refer to LAMMPS website for the installation of other versions.)

make serial

Spectral Neighbor Analysis Potential (SNAP)

Note: The current SNAP submodule is guaranteed to be compatible with stable version of LAMMPS-12Dec2018. Further efforts will be made to ensure SNAP submodule compatible with newest version of LAMMPS.

The calculations rely on LAMMPS package itself. Assume LMP_ROOT is the path of LAMMPS package. To install SNAP package, enable the SNAP interface in ${LMP_ROOT}/src directory.

make yes-snap

The serial version of LAMMPS containing SNAP interface can then be installed. (Please refer to LAMMPS website for the installation of other versions.)

make serial