Tagged: ASE

MacOS Sierra for Computational Materials Science in 2017

An update of previous entries for setting up an Apple computer for scientific computing. It is not an absolute guide, but simply one way to get going.  I started with a clean install of Mac OS 10.12 (Sierra).

  • Awaken UNIX

The first step is to install the command line tools. Open a Terminal and type make which triggers the system to install Xcode (if missing) and the command line tools module (basic UNIX commands including a gcc compiler). Be sure to set up your bash_profile, ssh config, and vimrc files to make working faster and more comfortable.

  • Basics

My base applications include: (standard office) Dropbox, Slack, MS Office (Imperial link), Mactex, Texmaker, Mendeley; (scientific computing) latest gcc/gfortraniTerm, Textmate, XQuartz, Atom, Cyberduck, GitHub client(materials modelling) VESTA, Avogadro. For video and image editing ffmpeg and imagemagick are essential.

  • Python

Python package and environment maintenance can cause headaches, so this time I went with Conda for Mac. I am happy with the results so far, and the standard install gives a good base set of packages.

  • Fortran and C

It is possible to survive using gnu compilers and freely available maths libraries, but Intel Fortran and MKL tend to be faster and better tested (easier to compile). For non-commericial purposes Intel Composer is now free for OS X. The package installs in a few clicks, but be sure source the variables in your .bash_profile:
source /opt/intel/mkl/bin/mklvars.sh intel64
source /opt/intel/bin/compilervars.sh intel64


The outcome:
% which ifort
/usr/local/bin/ifort
% ifort --version
ifort (IFORT) 17.0.4 20170411

  • Openmpi

To enable parallelism, I downloaded the latest source code of openmpi (2.1.1).
./configure -prefix=/usr/local/openmpi-2.1.1 CC=icc FC=ifort F77=ifort
make
sudo make install

be patient… it can easily take 20 minutes. Finally add to your .bash_profile:
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/usr/local/openmpi-2.1.1/lib/
export PATH=./:/usr/local/openmpi-2.1.1/bin:$PATH
export OMP_NUM_THREADS=1

The outcome:
% which mpif90
/usr/local/openmpi-2.1.1/bin/mpif90
% mpif90 --version
ifort (IFORT) 17.0.4 20170411

  • Phonopy

I use this open-source lattice-dynamics package a lot. The installation used to be multi-step, but Conda makes life easier (adapted from Togo’s official guide):
% conda install numpy scipy h5py pyyaml matplotlib openblas
% git clone https://github.com/atztogo/phonopy.git
% export CC=gcc
% cd phonopy
% python setup.py install --user

To run: phonopy

If harmonic phonons are not enough for you, then Phono3py lets you calculate phonon-phonon interactions, but it gets very expensive to compute.
% git clone https://github.com/atztogo/phono3py.git
% cd phono3py
% python setup.py install --user

To run: phono3py

  • VASP

I use a range of electronic structure packages, but VASP is the old reliable. I downloaded the latest version (5.4.4), which has streamlined the install process. Enter the main folder and
cp ./arch/makefile.include.linux_intel ./makefile.include

The file needs to be modified to point to the correct compilers (I used icc, icpc, and mpifort). We will also remove DscaLAPACK from the pre-compiler options and set SCALAPACK =  . There is one bug to fix before you type make: in ./src/lib/getshmem.c add #define SHM_NORESERVE 010000 to the end of the include statements.

The outcome:
% mpirun -np 4 ../vasp_std
running on 4 total cores
distrk: each k-point on 4 cores, 1 groups
distr: one band on 1 cores, 4 groups
using from now: INCAR
vasp.5.4.4

  • ASE

The atomistic simulation environment is a useful set of Python tools and modules. It now installs, including the gui, in one command:
pip install --user ase gpaw

The outcome:
ase-gui

ASE

I will update with more codes and tools as I find time, and always happy to receive suggestions.

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Installing ASE on Mac OSX

“ASE is an Atomistic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations.” It links to a wide variety of electronic structure packages and automates many tedious processes. Best of all it’s free and open source.

There is a Homebrew installation option, but sometimes it is nice to know what you are installing. The basic starting point is a system with XCode and SciPy (following the Phonopy installation guide).

1. Feed your Python with GTK
– An “object-oriented widget toolkit” in a simple self-installing package.

2. Water your Python with Libpng
– A png reference library in a simple self-installing package.

3. Download & Link ASE
tar -zxf python-ase-3.8.0.3420.tar.gz
ln -s python-ase-3.8.1.3440 ase
cd ase
python setup.py install --user

4. Nearly there…
– Add to your .bash_profile (with the right pathway):
export PYTHONPATH=$HOME/progs/ase:$PYTHONPATH
export PATH=$HOME/progs/ase/tools:$PATH

5. Test (and have fun)!
mkdir tmp; cd tmp
python -c "from ase.test import test; test(verbosity=2, display=False)" 2>&1 | tee testase.log

OUTPUT:
Ag-Cu100.py (ScriptTestCase) ... ok
CO2_Au111.py (ScriptTestCase) ... ok
COCu111_2.py (ScriptTestCase) ... ok
...