Miscellaneous

MKL install
Register to get the MKL (register at https://registrationcenter.intel.com/en/forms/?productid=2558&licensetype=2); untar the tar-ball and use the installation provided (usually called something like install_GUI.sh).

To use the library, use

source /opt/intel/mkl/bin/mklvars.sh intel64

Upgrade gcc/g++ for CentOS
Use the devtoolset:

wget http://people.centos.org/tru/devtools-2/devtools-2.repo -O /etc/yum.repos.d/devtools-2.repo

yum install devtoolset-2-gcc devtoolset-2-binutils

yum install devtoolset-2-gcc-c++ devtoolset-2-gcc-gfortran

To enable:

scl enable devtoolset-2 bash

source /opt/rh/devtoolset-2/enable

Look for standard installations
Sometimes it has handy to look for installed packages. This can be done with (here hdf5 is used as an example)

rpm -ql hdf5

will look for hdf5 files

Operations on files
Copy full name (path/name) of the target files into a gile e.g. called "list.txt" - if you want to delete the files, use

for i in `cat list`; do rm "$i" ; done

-can also be used to make a backups...

for i in `cat list`; do cp "$i" "$i".bak ; done

and of course much more...

Copy and paste problems (indentation problems)
open vi and type :set paste

Starting the program
java -jar /path/jmol/Jmol.jar

java -jar /home/erik/programs/jmol/Jmol.jar

Known problems
DALTON: The molden file from dalton cannot be opened by jmol. Open the molden.inp file with molden and write out a new file (select "write" in the moden menu). The new file can be opened by jmol

Orbital plots script
background white for (i=1; i<10; i++) { isosurface color yellow blue mo @{i} opaque fname = "orb" + @{i} + ".jpg" write jpg @{fname} }