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@zerothi
zerothi committed Apr 29, 2021
2 parents 4b93d53 + 936751a commit ad0047e
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271 changes: 91 additions & 180 deletions install_tutorial.sh
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@@ -1,31 +1,32 @@
#!/bin/bash

url=www.student.dtu.dk/~nicpa/sisl/workshop/20
url=www.student.dtu.dk/~nicpa/sisl/workshop/21
indir=$HOME/TBT-TS-sisl-workshop

function _help {
echo "This script may be used to install the dependencies for the"
echo "tutorial such as Python, numpy, scipy matplotlib, jupyter and sisl."
echo "tutorial such as Python, numpy, scipy matplotlib, jupyter, sisl and z2pack."
echo ""
echo "This script is a two-step script. Please read below."
echo ""
echo "If you do not have Python, numpy, scipy, jupyter, matplotlib or sisl installed"
echo "you should probably run this script in installation mode:"
echo "Running this script in installation mode will download and install conda"
echo "conda provides both Siesta executables as well as the sisl and dependency packages"
echo "so once installed all required infrastructure is available."
echo "It does, however, require a disk space of approximately >4GB"
echo ""
echo " $0 install"
echo "To use the conda framework, run this script in installation mode:"
echo ""
echo "If you have a working Python installation with pip3 you may only need"
echo "to run"
echo " $0 install"
echo ""
echo " pip3 install --upgrade numpy scipy matplotlib netCDF4 jupyter pyamg sisl z2pack"
echo "If you can install Siesta 4.1.5 and sisl 0.11.0 and the rest of the dependencies"
echo "manually then you won't be needing the above installation procedure."
echo "However, we cannot assist installing the packages manually."
echo ""
echo "Once the above steps are fulfilled you should run the download part"
echo "Once the above step is fulfilled you should run the download part"
echo "of the script. It will download the required files for the tutorial:"
echo ""
echo " $0 download"
echo ""
echo "During the download part a new directory will be created:"
echo " $HOME/TBT-TS-sisl-workshop"
echo ""
}

if [ $# -eq 0 ]; then
Expand Down Expand Up @@ -55,7 +56,7 @@ case "x$OSTYPE" in
os=macos
;;
*)
echo "Are you using MingGW or FreeBSD? Or a third?"
echo "Are you using MingGW or FreeBSD? Or a ($(uname -s))?"
echo "Either way this installation script does not work for your distribution..."
exit 1
;;
Expand Down Expand Up @@ -101,110 +102,66 @@ case $1 in
esac


# Function for installation on Linux
function linux_install {
function dwn_file {
local rname=$1
local outname=$1
if [ $# -eq 2 ]; then
outname=$2
fi
if [ ! -e $outname ]; then
wget -O $outname $url/$(basename $rname)
if [ $? -eq 0 ]; then
chmod u+x $outname
else
rm -f $outname
fi
fi
}

# Update lists
sudo apt-get update

# First ensure that the correct packages are installed
for p in gcc gfortran libhdf5-dev libnetcdf-dev libnetcdff-dev python3-dev python3-tk python3-pip libatlas3-base liblapack3 libfreetype6-dev libpng-dev
do
sudo apt-get install $p
done

# Perform the Python installation
pip3 install --upgrade six numpy scipy matplotlib netCDF4 jupyter pyamg sisl z2pack
if [ $? -ne 0 ]; then
echo "pip3 failed to install the packages, will try to install"
echo "in your user directory, if this fails you will have to fix it"
pip3 install --user --upgrade six numpy scipy matplotlib netCDF4 jupyter pyamg sisl z2pack
if [ $? -ne 0 ]; then
echo ""
echo "pip3 failed to install the packages, in either the global or user domain."
echo "Please try and get pip3 to work and re-run the installation proceduce."
fi
function conda_install {
local exe=$1 ; shift

[ ! -e $exe ] && wget -O $exe https://repo.anaconda.com/miniconda/$exe

if [ -e $indir/miniconda3/etc/profile.d/conda.sh ]; then
# it should already be installed
source $indir/miniconda3/etc/profile.d/conda.sh
else
sh ./$exe -b -s -f -p $indir/miniconda3
source $indir/miniconda3/etc/profile.d/conda.sh
fi

# Figure out the local pip3 version
# Note that sometimes this may be wrong since Python should be `python3`.
local py_v=$(pip3 -V | awk '{print $NF}' | tr -d ')')
conda install -c conda-forge -y siesta=4.1.5 sisl=0.11.0 matplotlib jupyter pyamg

# remove unused tarballs (no need for them to be around)
conda clean -t -y

echo ""
echo "This script assumes you are using Python $py_v"
echo "Before you can run exercises etc. you should execute the following:"
echo ""

# You probably need to add to the path, this is a simplistic way of
# adding the default ubuntu installation directories
grep "/.local/bin" ~/.bashrc > /dev/null
if [ $? -eq 1 ]; then
echo "" >> ~/.bashrc
echo "export PATH=\$HOME/.local/bin:\$PATH" >> ~/.bashrc
echo ""
echo "PLEASE RESTART YOUR SHELL!"
fi
grep "/.local/lib/python$py_v" ~/.bashrc > /dev/null
if [ $? -eq 1 ]; then
echo "" >> ~/.bashrc
echo "export PYTHONPATH=\$HOME/.local/lib/python$py_v/site-packages:\$PYTHONPATH" >> ~/.bashrc
echo ""
echo "PLEASE RESTART YOUR SHELL!"
fi
}
echo " source $indir/setup.sh"
echo ""
{
echo "#!/bin/bash"
echo "source $indir/miniconda3/etc/profile.d/conda.sh"
echo "conda activate"
} > $indir/setup.sh

source $indir/setup.sh

# Function for installation on Linux
function my_brew {
brew $@
if [ $? -ne 0 ]; then
echo "Running:"
echo " brew $@"
echo "failed."
echo "If this requests you should do a link brew:"
echo " brew link ..."
echo "then most probably your write access to this folder is prohibited:"
echo " /usr/local/include/Frameworks"
echo "If the folder does not exist, create it."
exit 1
fi
# now install packages not part of conda-forge
pip install z2pack
}

function macos_install {

# Check that brew is installed?
which brew 2>/dev/null
if [ $? -ne 0 ]; then
echo "You have not installed brew, this script requires that you have brew installed"
exit 1
fi

# First we need to install xcode-select
xcode-select --install

# Now try and install gcc (it should also include gfortran)
my_brew install gcc
# Ensure wget is installed
my_brew install wget --with-libressl

# Add the science tap (it HAS been deprecated, so probably not needed
#my_brew tap homebrew/science
# Function for installation on Linux
function linux_install {
conda_install Miniconda3-latest-Linux-x86_64.sh
}

my_brew install szip hdf5
my_brew install netcdf --with-fortran
my_brew install python3
sudo easy_install pip3

pip3 install --upgrade six numpy scipy matplotlib netCDF4 jupyter pyamg sisl z2pack
if [ $? -ne 0 ]; then
echo "pip3 failed to install the packages, will try to install"
echo "in your user directory, if this fails you will have to fix it"
pip3 install --user --upgrade six numpy scipy matplotlib netCDF4 jupyter pyamg sisl z2pack
if [ $? -ne 0 ]; then
echo ""
echo "pip3 failed to install the packages, in either the global or user domain."
echo "Please try and get pip3 to work and re-run the installation proceduce."
fi
fi
function macos_install {
conda_install Miniconda3-latest-MacOSX-x86_64.sh
}

function install_warning {
Expand All @@ -215,117 +172,71 @@ function install_warning {
echo ""
echo " CTRL+^C"
echo ""
echo "Please ensure you have more than 5 GB of disk space available!"
echo ""
sleep 3
}

# Now create a common folder in the top-home directory

function download_warning {
echo ""
echo "This script will create a folder in your $HOME directory:"
echo " $HOME/TBT-TS-sisl-workshop"
echo "where all the tutorials and executable files will be downloaded."
echo ""
}

function install_test_sisl {
echo ""
echo " Will try and run sisl"
echo " import sisl ; print(sisl.geom.graphene())"
python3 -c "import sisl ; print(sisl.geom.graphene())"
echo " import sisl ; print(sisl.__version__, sisl.__file__)"
python -c "import sisl ; print(sisl.__version__, sisl.__file__)"
if [ $? -ne 0 ]; then
echo "Failed running sisl, please mail the organizer with the error message (unless some of the installations failed)"
fi
}

# create installation directory
mkdir -p $indir
pushd $indir

if [ $action == install ]; then
# os will be download
download_warning
install_warning
case $os in
linux)
install_warning
linux_install
;;
macos)
install_warning
macos_install
;;
esac
install_test_sisl

exit 0
else
download_warning
fi

# Now create a common folder in the top-home directory

function download_warning {
echo ""
echo "This script will create a folder in your $HOME directory:"
echo " $HOME/TBT-TS-sisl-workshop"
echo "where all the tutorials and executable files will be downloaded."
echo ""
}

function dwn_file {
local rname=$1
local outname=$1
if [ $# -eq 2 ]; then
outname=$2
fi
if [ ! -e $outname ]; then
wget -O $outname $url/$(basename $rname)
if [ $? -eq 0 ]; then
chmod u+x $outname
else
rm -f $outname
fi
fi
}

download_warning

indir=$HOME/TBT-TS-sisl-workshop
mkdir -p $indir
pushd $indir

# Now download the executables
mkdir -p bin

# Download latest tutorial files
if [ -e sisl-TBT-TS.tar.gz ]; then
rm sisl-TBT-TS.tar.gz
fi
dwn_file sisl-TBT-TS.tar.gz

# Determine the optimization level for the current architecture
_suffix=
case $os in
linux)
# Figure out if the user has AVX
if $(grep "avx2" /proc/cpuinfo > /dev/null) ; then
_suffix=_avx2
elif $(grep "avx" /proc/cpuinfo > /dev/null) ; then
_suffix=_avx
elif $(grep "sse2" /proc/cpuinfo > /dev/null) ; then
_suffix=_sse
fi
;;
esac

case $os in
linux)
dwn_file bin/siesta$_suffix bin/siesta
dwn_file bin/tbtrans$_suffix bin/tbtrans
;;
macos)
dwn_file bin/siesta_mac bin/siesta
dwn_file bin/tbtrans_mac bin/tbtrans
;;
esac

# We will simply add it if it does not exist
# We also assume the SHELL is BASH
if ! `grep $indir ~/.bashrc` ; then
echo "" >> ~/.bashrc
echo "# Variable for the TBT-TS-sisl workshop" >> ~/.bashrc
echo "export PATH=$indir/bin:\$PATH" >> ~/.bashrc
echo "" >> ~/.bashrc
fi

echo ""
echo "In folder"
echo " $indir"
echo "you will find everything needed for the tutorial"
echo "If you use BASH (most likely) you should have siesta and tbtrans in your path."
echo "you will find everything needed for the tutorial."
echo "If you are using the conda installation provided by this script"
echo "please always start your sessions by executing:"
echo ""
echo " source $indir/setup.sh"
echo ""
echo "which will correctly setup the environment for you."
echo "Run (after you have restarted your shell):"
echo " which tbtrans"
echo "and check it returns $indir/bin/tbtrans"
echo "and check it returns $indir/miniconda3/bin/tbtrans"
8 changes: 4 additions & 4 deletions presentations/01/electrodes.tex
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Expand Up @@ -413,10 +413,10 @@ \subsection{Electrodes}
}
\uncover<3->{
\fill (.5,0) circle (\mysize) node[above right] {1};
\fill (1.5,0) circle (\mysize) node[above right] {2};
\fill (2.5,0) circle (\mysize) node[above right] {3};
\fill (.5,1) circle (\mysize) node[above right] {4};
\fill (1.5,1) circle (\mysize) node[above right] {5};
\fill (1.5,0) circle (\mysize) node[above right] {3};
\fill (2.5,0) circle (\mysize) node[above right] {5};
\fill (.5,1) circle (\mysize) node[above right] {2};
\fill (1.5,1) circle (\mysize) node[above right] {4};
\fill (2.5,1) circle (\mysize) node[above right] {6};
}
\foreach \x in {-2.5,-1.5,-.5,3.5,4.5,5.5} {
Expand Down
4 changes: 2 additions & 2 deletions presentations/01/negf.tex
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Expand Up @@ -150,8 +150,8 @@ \subsection{Transmission}

The sum of bond-currents crossing \emph{any} device cross-section is equal to the
current between the leads. Without the prefactor $e/h$ this also applies for the
bond-transmissions\footnote{TBtrans calculates bond-\emph{transmissions}, although
they are named \emph{currents}.}.
bond-transmissions\footnote{TBtrans calculates bond-\emph{transmissions} (without the
prefactor $e/h$), although they are named \emph{currents}.}.

The bond-currents obey Kirchoff's laws.

Expand Down
2 changes: 1 addition & 1 deletion presentations/01/se.tex
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ \subsection{Semi-infinity}
Describes interaction of a system to a semi-infinite region

\item%
Self-energy calculations \emph{require} no more than nearest neighbour interactions between unit-cells!
Self-energy calculations \emph{require} no more than nearest neighbour interactions between unit-cells

\begin{align*}
\SE_{\mrc 11}(E) &= \VV^\dagger\big[E+\im\eta-\HH\big]^{-1}\VV
Expand Down
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