Computational Magnetism York

cropping pdfs from terminal

2009-10-15T12:43:00.001+01:00

From terminal you can use pdfcrop, which should be installed on most linux systems. As its terminal based it is easier to script.

example

pdfcrop --margins '5 0 5 10' --clip input.pdf output.pdf

Make tar.gz

2009-09-04T11:25:00.000+01:00

tar czvf myarchive.tar.gz myfile

Multiple files in gnuplot

2009-06-15T12:47:00.000+01:00

Seems obvious now but you can use paste

e.g.

plot "< paste file1.dat file2.dat" using 1:($2/$4) w points

Searching for tabs with grep

2009-06-15T11:43:00.004+01:00

I was trying to search for an integer number, which had tabs after is
i.e grep 300 and it would come up with something like
300 -0.0137598 -0.00228325 0.930859 0.932037 -1.04561e+27 -1.73505e+26 7.07363e+28 7.08259e+28 -0.0129162 -0.00224769 0.874459 0.875568 0.00575037 0.00194563 -0.395375 0.396846 1.46282e+24
450 -0.00449249 -0.00663059 0.858427 0.869783 -3.41386e+26 -5.03861e+26 6.52322e+28 6.60951e+28 -0.00415084 -0.00613002 0.795084 0.805603 0.00124869 0.00187794 -0.257016 0.262097 1.46282e+24
etc....

i.e. where there is 300 within any number. To search for 300 i used
grep 300[[:space:]]

Wireless with Linux

2009-05-22T09:19:00.001+01:00

This link shows how it is set up using the gnome GUI network manager

http://www.york.ac.uk/services/cserv/net/wireless/help/naslinuxnew.html

Getting xorg to recognise two GPU's

2009-04-02T09:08:00.003+01:00

In Ubuntu 8.10, after installation of the nvidia driver, xorg is unable to decide which card to use. To fix this, login in to a terminal, and then type

sudo lspci grep VGA

On my machine this gave the following output:
02:00.0 VGA compatible controller: nVidia Corporation Device 05e2 (rev a1)
04:00.0 VGA compatible controller: nVidia Corporation Device 05e2 (rev a1)

So to get the xserver working, you need to add the following line oin the device section of /etc/X11/xorg.conf:

Section "Device"
Identifier "Configured Video Device"
Busid "PCI:2:0:0"
Driver "nvidia"
EndSection

Then run:

sudo service gdm restart

to get the xserver working as normal.

Bash extract function

2009-03-31T14:11:00.001+01:00

Extract function for bash. Put in .bashrc

function extract() # Handy Extract Program.
{
if [ -f $1 ] ; then
case $1 in
*.tar.bz2) tar xvjf $1 ;;
*.tar.gz) tar xvzf $1 ;;
*.bz2) bunzip2 $1 ;;
*.rar) unrar x $1 ;;
*.gz) gunzip $1 ;;
*.tar) tar xvf $1 ;;
*.tbz2) tar xvjf $1 ;;
*.tgz) tar xvzf $1 ;;
*.zip) unzip $1 ;;
*.Z) uncompress $1 ;;
*.7z) 7z x $1 ;;
*) echo "'$1' cannot be extracted via >extract<" ;;
esac
else
echo "'$1' is not a valid file"
fi
}

epstopdf

2009-03-27T14:32:00.000Z

It's epstopdf joe not eps2pdf

Fixing backspace on edred vim

2009-03-27T10:40:00.001Z

To fix the backspace key on the vim on edred add this to .vimrc

set backspace=indent,eol,start

latex figures

2009-03-26T16:15:00.001Z

To get rid of strange behaviour in latex where it does weird things with figure numbers its has to be done in a strict order.

\begin{figure}
\begin{center}
\includegraphics{...}
\end{center}
\caption{...}
\label{...}
\end{figure}

I think caption can go above \begin{center} but it must be outside of the centre section

Gnuplot PDF+Latex files

2009-03-26T13:38:00.002Z

To create a pdf file from gnuplot with latex text do the following:

In the plot use the terminal:

set terminal epslatex

Then convert the eps to a pdf file.

Include the figure using

\input{figure.tex}

Printing variables from gnuplot to a file

2009-03-25T14:38:00.004Z

To output variables such as fitting parameters from gnuplot use.

set fit errorvariables # creates a_err type variables for fitting errors
set print "tmp.dat"
print a,a_err,b,b_err

Cross Product

2009-03-25T11:49:00.006Z

I got sick of working out cross products by hand. So i wrote a C program to calculate it. Bit over the top but oh well. I won't save the source code just when i need it I will get it from here. If anyone can be arsed to change/edit it or make an applet then go ahead.

#include < iostream>
#include < cstdlib>
#include < cmath>

void cross_product(double*&,double*&,double*&);

int main()
{

double *vec1=NULL,*vec2=NULL,*vec3=NULL;

try
{
vec1 = new double[3];
}
catch(...)
{
std::cerr << "Error Allocating vec1" << std::endl;
exit(0);
}
try
{
vec2 = new double[3];
}
catch(...)
{
std::cerr << "Error Allocating vec2" << std::endl;
exit(0);
}
try
{
vec3 = new double[3];
}
catch(...)
{
std::cerr << "Error Allocating vec3" << std::endl;
exit(0);
}

//Initialise Arrays
for(unsigned int i = 0 ; i < 3 ; i++)
{
vec1[i] = 0.0;
vec2[i] = 0.0;
vec3[i] = 0.0;
}

for(unsigned int i = 0 ; i < 3 ; i++)
{
std::cout << "Enter element " << i+1 << " of the first array and press enter" << std::endl;
std::cin >> vec1[i];
}

for(unsigned int i = 0 ; i < 3 ; i++)
{
std::cout << "Enter element " << i+1 << " of the second array and press enter" << std::endl;
std::cin >> vec2[i];
}

std::cout << "The vectors you entered were \nvec1 = " << vec1[0] << "\t" << vec1[1] << "\t" << vec1[2] <<
"\nvec2 = " << vec2[0] << "\t" << vec2[1] << "\t" << vec2[2] << std::endl;

cross_product(vec1,vec2,vec3);

std::cout << "The results of the cross product of the vector you entered is \n" << vec3[0] << "\t" << vec3[1] << "\t" << vec3[2] << std::endl;

return(0);
}

void cross_product(double*& vec1,double*& vec2,double*& vec3)
{
vec3[0] = vec1[1]*vec2[2] - vec1[2]*vec2[1];
vec3[1] = vec1[2]*vec2[0] - vec1[0]*vec2[2];
vec3[2] = vec1[0]*vec2[1] - vec1[1]*vec2[0];
}

Labeling figures in Latex

2009-03-24T13:06:00.000Z

If labeling of figures has gone wrong in latex it's probably because the \label{} must be at the end of the figure block after the includegraphics and caption.

Compiling OpenMPI with Intel Compilers on Ubuntu

2009-03-24T11:57:00.001Z

Compiling OpenMPI with Intel compilers can be a bit of a nuisance, and so the following seems to work with version 11.074 Intel Compilers, OpenMPI v 2.8.1 and Ubuntu 8.10:

1) Install The Intel Compilers with defaults
2) Put iccvars.sh and ifortvars.sh into /etc/profile.d, and comment out the lines referring to non 64 bit binaries
3) source /etc/profile
4) Unpack the OpenMPI
5) Run ./configure --with-fortran CXX=icc FC=ifort LIBS=-lstdc++
6) type LANG=C
7) make all
8) sudo make all install
9) sudo ldconfig
10) type mpiCC --showme to verify the compiler wrappers are working correctly

Awk Scripting, combining columns

2009-03-24T11:16:00.001Z

If you have multiple files named filename.< a number > e.g. filename.0, filename.1, filename.2,filename.3 etc then you can take an average of multiple columns using awk as below:

you need to know how many files you have, in this num_files=16, and you need to know the total number of columns per file in this tot_num_cols=13. Here I wanted to average colums 1 and 4. Using the paste command which pastes a number of files to the screen side by side and piping to awk the script will output the average of columns 1 and 4 to a file called anewfile.txt

paste filename.* | awk 'BEGIN{num_col=4;num_files=16;timecol=1;tot_num_cols} {c=0; for (j=0;j < num_files;j++){c+=$(timecol+tot_num_cols*j)}}; s="0;" i="0;i < ="num_files;i++){s+="$(num_col+tot_num_cols*i)};" > | anewfile.txt

Bash number formatting

2009-03-24T11:04:00.000Z

Use printf as in c. For zero padding add a 0 infront of the field length, eg: %06i

So to delete more files than rm can handle

for i in `seq 0 100`; do file=`printf "%06i" "$i"`; echo $file; done