Link'O'Rama




Gnuplot extrapolations with errorbars


Adding errorbars on your extrapolations using Gnuplot requires a bit of tinkering. To create a plot with errorbars like the one on the right a temporary file tmp is used to store the extrapolated value and its error estimate. In order to access the error estimates from the fit one needs to invoke set fit errorvariables before fitting. The fitted function is then plotted together with a single point with errorbars at x = 0.

Here is an example, where I extrapolate the data points with errors stored in data to
x → 0 using the fit function f(x) = a + b x + c x2. The mean value and its errorbars for the extrapolation at x = 0 are the simply given by the values of a and a_err, respectively.


                  data = "/tmp/gnuplot.data"
                  set print data
                  print "1 0.549846 0.450154\n2 4.9544 0.954397\n3 9.49577 0.49577\n4 15.3761 0.623939\n"

                  tmp = "/tmp/gnuplot.xtrapolated"
                  set print tmp

                  set fit errorvariables
                  f(x) = a + b*x + c*x**2
                  fit f(x) data u 1:2:3 yerr via a,b,c
                  set print tmp
                  print "\n\n0.0 ",a,a_err

                  p data u 1:2:3 w yerr lt 3 pt 1, f(x) lt 1 t '', tmp u 1:2:3 w yerr lt 1 pt 0 t ''
               

arXiv Logo

Ever needed a vector graphics version of the awesome arXiv logo? No? Anyways, here is a the EPS and the PDF version of what I've cooked up. Feel free to use and modify it!   Creative Commons License

Linux → MacOSX

Linux rocks! Nevertheless I spent too much time tinkering with the operating system, which made me rethink my priorities: configurability vs. operability. As a numerical physicist I spent most of my time in the shell, coding, writing TeX and preparing figures for papers, lectures or notes. Mac provides me the perfect blend of software and OS. I have compiled a list of steps for the initial setup of on this page

RSS-feed
PRL's newly accepted

With the help from Howto Create an RSS 2.0 Feed I've created a feed which post-processes the "Condensed Matter: Electronic Properties" section of PRL's newly accepted (not yet published) papers list. You can checkout and subscribe to the feed here.

Job sites

The are several job-sites our there. Maybe the most popular are by the APS and Physics today. For faculty job postings, shortlist rumors and faculty shuffle check out the CM & AMO Physics Rumor Mill, @cmamorumor (unfortunatley, this seems to be dead). If you know more, please leave a comment!

RSS-feed
cond-mat with authors

Although the arXiv provides a multitude of RSS-feeds, I don't like their format. In particular I'm missing the list of authors. So I've tinkered another RSS-feed using the arXiv API export function to fetch the latest publications and post-processes them into a valid RSS-feed which also includes the authors, here.

MathJax

Check out MathJax to use TeX formulas on your webpages, e.g., $$ \int d\varepsilon \frac{1}{{\rm e}^{(\varepsilon-\mu) / {\rm k} T}\,+ 1} $$ is JavaScript interpreted, easily editable TeX code without the need to use images.


TeX word count for Physical Review Letters


This little script uses the CTAN Perl-script texcount to count the number of word in a TeX file (omitting TeX-statements) and computes the number of words equivalent used by figures according to the standards of the Physical Review Letters. For simplicity the script does not extract the used figures from the manuscript, but assumes all eps-figures in the current directory are to be used.

                  #!/bin/bash

                  texcount=$(which texcount)

                  sum=0
                  for file in $@; do
                     if [[ $file == *.eps ]]; then
                        words=$(grep '%%BoundingBox' $file | awk '{print int(150/(($4-$1)/($5-$2))+21)}')
                     elif [[ $file == *.tex ]]; then
                        words=$($texcount -1 -sum $file)
                     fi
                     sum=$((sum+words))
                     echo $words $file| awk '{ printf "%6d  %s\n",$1,$2 }'
                  done
                  echo $sum | awk '{ printf "%6d  total\n",$1 }'
               

Following the guidelines for calculating length the word equivalent for figures can be simplified estimated from the figures's aspect ratio (width / height) using the formula [(150 / aspect ratio) + 20 words] for single-column figures, and {[300 / (0.5 * aspect ratio)] + 40 words} for double column figures. In the script above I have considered single-column figures only.

You can download the script here: PRLtexcount (make sure to put it in a directory in your $PATH and make it executable).


Histograms in the shell & gnuplot


This is a nice shell script which uses awk to produce a histogram from a data set. This can be especially useful in combination with gnuplot, e.g., for the original data set data.dat use the line

gnuplot> p "< histogram data.dat 100" u 1:2 w boxes

in gnuplot to plot the histogram of data.dat with 100 subdivisions (bins) of the whole data range. Unfortunately, the script's origin is lost - I apologize for not being able to crediting the original author. You can download the script here: histogram (make sure to put it in a directory in your $PATH and make it executable).

                  #!/bin/bash
                  # This is script which uses awk to produce a histogram of 

                  FILE=$1 # input file
                  BINS=$2 # number of bins

                  if [ "$#" != "2" ] || [ ! -f $FILE ]; then
                     echo 'usage: histogram <file> <#bins>'
                     exit 1
                  fi

                  # determine border values
                  MIN=$(awk 'NR == 1 || $1 < min {line = $0; min = $1} END {print line}' $FILE)
                  MAX=$(awk 'NR == 1 || $1 > max {line = $0; max = $1} END {print line}' $FILE)

                  # use awk to bin data
                  awk -v m=$MIN -v M=$MAX -v b=$BINS 'BEGIN { 

                    w = (M-m)/b      # width of each bin

                    # set up arrays
                    for (i = 1 ; i <= b; ++i) {
                      n[i] = m+(i*w)        # upper bound of bin
                      c[i] = n[i] - (w/2)   # centre of bin
                      f[i] = 0              # frequency count
                    }
                  }

                  { 
                    # bin the data
                    for (i = 1; i <= b; ++i)
                      if ($1 <= n[i]) {
                           ++f[i]
                           break       
                      } 
                  }

                  END {
                    # print results to a file for plotting

                    for (i = 1; i <= b; ++i) {
                      if (f[i] > 0) {
                        print c[i],"\t", f[i]
                      }
                      else {
                        print c[i], 0
                      }
                    }
                  }' $FILE
               

Note, that gnuplot of course can create histograms intrinsically using the commands

gnuplot> binwidth=5
gnuplot> bin(x,width)=width*floor(x/width)
gnuplot> p 'data.dat' u (bin($1,binwidth)):(1.0) smooth freq with boxes


SSH keys


SSH keys serve as a means of identifying yourself to an SSH server using public-key cryptography without the need of passwords. SSH key authentication offers additional security and convenience, but is not without drawbacks and may not be appropriate for all environments. One of the many introductions onto the SSH keys framework can be found in this article.

Below is a shell script which essentially voids the need to remember the last two lines. Its purpose is to distribute your public SSH key to a remote host, such that future use of your password becomes obsolete. You can download the script here: ssh-keyput (make sure to put it in a directory in your $PATH and make it executable).

                  #!/bin/bash

                  RHOST=$1
                  if [ "$RHOST" = "" ]; then
                     echo -e "usage: ssh-keyput <host>\n"
                     exit 1
                  fi

                  if [ ! -e "${HOME}/.ssh/id_dsa.pub" ]; then
                     echo "No public key has been found in ${HOME}/.ssh/"
                     ssh-keygen -t dsa
                  fi

                  cat ${HOME}/.ssh/id_dsa.pub | ssh $RHOST 'sh -c "cat - >>~/.ssh/authorized_keys"'
                  ssh-agent sh -c 'ssh-add < /dev/null && bash'
               

The script tests if you have an existing dsa-key (stored by default in $HOME/.ssh/id_dsa.pub) and transfers the public part to the new host, in order to avoid the the password query. Invoke

$ ssh-keyput user@remotehost

and you'll be asked for the last time to enter your password on the remote host. Then make sure you enter a new shell and test your password-free connection using ssh keyes.


Honeycomb lattice graphics


Since I have been repeatedly asked for graphics I used in talks and papers I here provide high resolution versions of a few popular images for use under Creative Commons License . Click on the preview images to obtain the high-res version.


YouTube Science


There is a huge number of small and large experiments, educational channels and the fair amount of woo on YouTube. Here are a few of my favorite physics related posts/channels:

An intruiging phenomenon from the Earth Unplugged YouTube channel, that should remind you that classical mechanics can still be fascinating. Can you spot the mistake in one of the explanations? UPDATE

This is an example by Tim Hutton of Stephan Rafler's SmoothLife - a generalization of Conway's "Game of Life" to the continuous domain. Details are presented in this paper. Here are more examples.

The The Royal Institution YouTube channel is a source of high quality science clips as well as longer presentations including the famous RI Christmas Lectures.

The YouTube channel MinutePhysics tackles questions, such as Why is it Dark at Night? in 60 seconds bites (sometimes in only 9.9999s) - and that well researched and presented.

Veritasium is a YouTube on popular scientific topics and everyday questions. Their explainations are fairly well researched, but more on the entertainment side.

Vsauce is collaborating infrequently with Veritasium and MinutePhysics is actually a collection of channels, which covers a broad selection of topics from to science and technology to fictional worlds.


Shellscript grepskip


Ever so often I need to grep a certain line from a file. The problem is, I do not need the line of the regular expression I can provide, but the n-th line after. For this purpose I wrote the little script grepskip.

#!/usr/bin/perl

if (@ARGV < 3)
{  die "usage: grepskip <expr> [expr] ... <nskip> <file>\n\n";
} 

@expressions = ();
for ($i=0;$i<@ARGV-2;$i++)
{  push(@expressions,@ARGV[$i]);
}

$file = $ARGV[@ARGV-1];
$nskip = $ARGV[@ARGV-2];

open(FID,"<$file") || die "unable to open $file";
@line = <FID>;
close(FID);

for ($i=0;$i<@line;$i++)
{  foreach $exp (@expressions)
   {  if ($line[$i] =~ m/.*$exp.*/) 
      {  print $line[$i+$nskip];
      }
   }
}
               

Here is an example, how it works. Let the file data.dat contain the lines:

                  0.0   0.0
                     0.283084   0.040688
                     0.364561   0.155806
                  1.0   0.0
                     0.998068   0.215512
                     0.812932   0.552596
                  0.0   1.0
                     0.884292   0.177753
                     0.764657   0.142434
               

To extract the second line after the pattern '   0.0$', without knowing which lines match the pattern we can use

$ grepskip '   0.0$' 2 data.dat
   0.364561   0.155806
   0.812932   0.552596


Keynote 6 sucks


iWork 2013 has been getting flag a lot, already. Here I add my bit trashing Keynote 6 in particular. While Apple has been trying to make their iWork suite iCloud-compatible, it has thrown out functionality. In the case of Keynote, Apple apparently dropped the use of vector graphics: Once you have imported/copied/dropped your Illustrator, EPS, or PDF file into Keynote it no longer is in vector format, but rather a bitmap (albeit high-res). That not only implies you've lost all decent scalability, but it also renders the editing of formulas created with LaTeXit obsolete.

In case you were not aware of this feature using LaTeXit and Keynote - here is how it works with Keynote versions < 6: Compile your LaTeX expression in LaTeXit, copy it as 'PDF w.o.f.' and paste it into Keynote (or drag). If you then want to replace the expression, but do not want to retype everything, copy the formula and paste it into LaTeXit - voila, you have your LaTeX code back.

In short: Stay away from the Keynote 2013, the new shadow-styles are not worth the loss of functionality. Let's hope Apple will reconsider (I know, I know, ...).


Setup your Raspberry Pi as an AirPrint server


Here are the step-by-step instructions on how to setup your Raspberry Pi running Raspbian (or any other debian system) as an AirPrint server. I am essentially reproducing the HOWTOs found here and here. First of all, let's install cups (if not already installed):

$ sudo apt-get install cups

Add your user (default user name is pi) to the group lpadmin to allow it administrate CUPS.

$ sudo usermod -a -G lpadmin pi

We also need to tell CUPS to alias itself to any hostname as AirPrint communicates with CUPS with a different hostname than the machine-defined one. To do this, we edit the CUPS configuration file and add the directive ServerAlias * before the <Location /> block. (You might want to use vi and do it manually, instead).

$ sudo sed -i -e 's/<Location \/>/ServerAlias *\n<Location \/>/' /etc/cups/cupsd.conf

Connect (as user pi, not root!) to the CUPS web-interface using midori (or better iceweasel)

$ midori https://localhost:631

and setup the new printer. You'll need to authenticate with your systems username and password. Make sure you check 'Share This Printer' during the printer setup! Note, there is no need to set 'Share printers' in the Server Settings: section on CUPS's Administration page. With the aid of Timothy J. Fontaine's python script we can now generate avahi announcements that will make iOS think that our printer is AirPrint capable. For that you’ll need the Python CUPS module and the avahi daemon (again we'll do this in a root-shell):

$ sudo apt-get install python-cups avahi-daemon
$ sudo /etc/init.d/avahi-daemon start

Now, we’ll download Tim’s Python script to generate the avahi announcements for all installed CUPS printers and restart the daemon

$ sudo mkdir /opt/airprint
$ sudo cd /opt/airprint
$ sudo wget -O airprint-generate.py --no-check-certificate \
     https://raw.github.com/tjfontaine/airprint-generate/master/airprint-generate.py
$ sudo chmod +x airprint-generate.py
$ sudo ./airprint-generate.py -d /etc/avahi/services
$ sudo /etc/init.d/avahi-daemon restart

And that's all there is to do. As long as your iOS device is in the same subnet you should now find the AirPrint representatives of your installed printers.


Calling C/C++ routines from Fortran


Here are two examples of frequently used system functions implemented in C and called from Fortran. While these might be available as intrinsic functions in you compiler of choice, their implementation would be specific to your compiler and not part of the Fortran standard and hence not portable, unless implemented in C. Note that the functions are listed twice, once with and once without the trailing underscore - this is to stay compatible with different Fortran compilers which implement different naming conventions.

The first example is a function to obtain the process ID (PID) of the program you are running (fgetpid.c).

#include <unistd.h>

void fgetpid_(int *id)
{
   *id = (int)getpid();
}

void fgetpid(int *id)
{
   *id = (int)getpid();
}

You can call the function from Fortran via:

INTEGER :: pid
CALL fgetpid(pid)
WRITE(*,*) pid               

The second example is execution of system commands using C's system command (exec.c).

#include <stdlib.h>
#include <stdio.h>
#include <string.h>

void exec_(char *cmd, int *cmdLen, int *stat)
{
   char *cmdcpy;

   if(!(cmdcpy=(char*)malloc(*cmdLen+1)))
   {  fprintf(stderr,"exec: malloc failed\n");
      exit(1);
   }
   strncpy(cmdcpy,cmd,*cmdLen);
   cmdcpy[*cmdLen]='\0';
   *stat = system(cmdcpy);

   free(cmdcpy);
   return;
}


void exec(char *cmd, int *cmdLen, int *stat)
{
   char *cmdcpy;

   if(!(cmdcpy=(char*)malloc(*cmdLen+1)))
   {  fprintf(stderr,"exec: malloc failed\n");
      exit(1);
   }
   strncpy(cmdcpy,cmd,*cmdLen);
   cmdcpy[*cmdLen]='\0';
   *stat = system(cmdcpy);

   free(cmdcpy);
   return;
}

Execute system commands in Fortran via:

CHARACTER(len=128) :: cmd
INTEGER :: ierr
cmd = 'touch test.dat'
CALL exec(trim(cmd),len_trim(cmd),ierr)

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