QUIP package

Compiling LAMMPS on Hipergator with QUIP package

The QUIP package is a collection of software tools to carry out molecular dynamics simulations. It implements a variety of interatomic potentials and tight binding quantum mechanics, and is also able to call external packages, and serve as plugins to other software such as LAMMPS, CP2K and also the python framework ASE. Various hybrid combinations are also supported in the style of QM/MM, with a particular focus on materials systems such as metals and semiconductors.

For more details, see the online documentation.

Do not compile on login nodes as those nodes are old opteron 4386 machines. The Intel compilers default to -xhost so they will build in a -m=pentium4 code path as the default and only code path if an alternative is not specified e.g. -ax. Please make sure to compile on a dev node. If you compile packages in login node, your account will have the chance to be suspended.

$ module load ufrc

$ srundev --time=01:00:00

$ module load intel/2018.1.163 openmpi/3.0.0 

To compile QUIP the minimum requirements are:

• A working Fortran compiler. (ifort or gfortran)
• Linear algebra libraries BLAS and LAPACK.

1) Clone the QUIP repository from GitHub. The --recursive option brings in submodules automatically (If you don't do this, then you will need to run git submodule update --init from the top-level QUIP directory after cloning) :

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

2) Enter in QUIP folder and specify QUIP folder path

export QUIP_ROOT=${PWD}

3) Decide your architecture by looking in the arch/ directory, and define an environmental variable QUIP_ARCH .Please note: if you are building QUIP to link it to LAMMPS, the serial version of QUIP must be compiled.

export QUIP_ARCH=linux_x86_64_ifort_icc

4） GAP is needed, it can be downloaded from the `Software' section of libatoms.org, after accepting the terms and conditions of the Academic License Agreement. Extract the tarball under the /path/to/QUIP/src/ directory.

5) If you don't use something it is asking for, just leave it blank. NB make sure to answer `y' to `Do you want to compile with GAP prediction support ? [y/n]'. The answers will be stored in Makefile.inc in the build/${QUIP_ARCH} directory, and you can edit them later (e.g. to change optimisation or debug options). Note that the default state is usually with rather heavy debugging on, including bounds checking, which makes the code quite slow. The make command has to be executed from the top-level directory. Making `libquip' ensures all the necessary libraries will be built.

make config

6) Please note, in the questions please add flags -lmkl_intel_lp64 -lmkl_sequential -lmkl_core in the BLAS and LAPACK options or you can directly change Makefile.inc and edit the row shown below:

MATH_LINKOPTS= -lmkl_intel_lp64 -lmkl_sequential -lmkl_core

If you want to use GAP package make sure to answer `y` to `Do you want to compile with GAP prediction support ? [y/n]'

7) Make this package

make libquip

8) Building LAMMPS

Edit Makefile.lammps in the lib/quip folder, if necessary. If you have cloned, configured, and built QUIP inside this folder, QUIP_ROOT and QUIP_ARCH should be autodetected, even without having to set the environment variables. Otherwise export the environment variables as shown above or edit Makefile.lammps LAMMPS ships with a user package containing the interface necessary to use QUIP potentials, but it needs to be added to the compilation first. To do that, enter the LAMMPS source directory and type:

make yes-user-quip

9) Making LAMMPS

make icc_openmpi

Examples:

There are three example sets in examples/USER/quip:

• a set of input files to compute the energy of an 8-atom cubic diamond cell of silicon with the Stillinger-Weber potential. Use this to benchmark that the interface is working correctly.
• a set of input files demonstrating the use of the QUIP pair style for a molecular system with pair style hybrid/overlay and different exclusion settings for different pair styles. This input is for DEMONSTRATION purposes only, and does not simulate a physically meaningful system.
• a set of input files to demonstrate how GAP potentials are specified in a LAMMPS input file to run a short MD. The GAP parameter file gap_example.xml is intended for TESTING purposes only. Potentials can be downloaded from http://www.libatoms.org or obtained from the authors of QUIP.