Added first_time_adf

applications/firstime_run_template.rst

@@ -0,0 +1,48 @@
+.. _first_time_vasp:
+
+===================================
+First time you run a VASP job?
+===================================
+
+This page contains info aimed at first time 
+users of VASP on Stallo, but may also be usefull to 
+more experienced users. Please look carefully through the 
+provided examples. Also note that the job-script example is rather richly 
+commented to provide additional and relevant info.
+
+
+
+If you want to run this testjob, download the copies of the scripts and put them 
+into your test job folder (which I assume you have created in advance).
+
+VASP input example:
+--------------------
+
+Download the tarred job :download:`CeO2job-files <../files/CeO2.tar.gz>`.
+
+move this file to your test job folder on Stallo and type
+
+.. code-block:: bash
+
+   tar -zxf CeO2.tar.gz
+
+Then; download the job-script as seen here:
+
+.. include:: ../files/job_vasp.sh
+   :literal:
+
+Download it here :download:`job_vasp.sh <../files/job_vasp.sh>`.
+
+
+These files are also available on Stallo:
+------------------------------------------
+
+.. code-block:: bash
+
+   module load VASP/5.4.1.plain-intel-2016a
+   cd <to whatever you call your test folder> # for instance testvasp
+   cp -R $RUNEX/* .
+   sbatch job_vasp.sh
+
+and you are up running. Happy hunting.
+

applications/sw_guides.rst

@@ -16,8 +16,9 @@ the module system, and information about changes in application software see :re
    chemistry/ADF/ADF
    chemistry/Schrodinger/Schrodinger
    chemistry/ORCA/ORCA
+   chemistry/Molcas/Molcas
 
-   math-stat/MATLAB.rst
-   math-stat/Mathematica.rst
-   math-stat/R.rst
-   math-stat/STATA.rst
+   math-stat/MATLAB/MATLAB
+   math-stat/Mathematica/Mathematica
+   math-stat/R/R
+   math-stat/STATA/STATA

applications/template.rst

@@ -0,0 +1,96 @@
+.. _vasp:
+
+==========================================
+VASP (Vienna Ab initio Simulation Package)
+==========================================
+
+Information regarding the Vienna Ab initio Simulation Package (VASP) installed on Stallo.
+
+Related information:
+=====================
+
+.. toctree::
+   :maxdepth: 1
+
+   firsttime_vasp.rst
+   vasp_on_stallo.rst
+
+
+General information:
+=====================
+
+Description 
+------------
+VASP is a complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmented wave method and a plane wave basis set. The approach implemented in VASP is based on the (finite-temperature) local-density approximation with the free energy as variational quantity and an exact evaluation of the instantaneous electronic ground state at each MD time step.
+
+VASP uses efficient matrix diagonalisation schemes and an efficient Pulay/Broyden charge density mixing. These techniques avoid all problems possibly occurring in the original Car-Parrinello method, which is based on the simultaneous integration of electronic and ionic equations of motion.
+
+The interaction between ions and electrons is described by ultra-soft Vanderbilt pseudopotentials (US-PP) or by the projector-augmented wave (PAW) method. US-PP (and the PAW method) allow for a considerable reduction of the number of plane-waves per atom for transition metals and first row elements. Forces and the full stress tensor can be calculated with VASP and used to relax atoms into their instantaneous ground-state.
+
+There are various type plug ins and added functionality to VASP. On Stallo, we have added support for the Texas transition state tools (`vTST <http://theory.cm.utexas.edu/vtsttools/>`_), the `VASPsol <http://vaspsol.mse.ufl.edu>`_ implicit solvation model made by Hennig and Mathew from University of Florida and the `Bayesian Error Estimation Functionals <http://suncat.stanford.edu/about/facilities/software>`_ from the SUNCAT center, Standford. 
+
+Online information from vendor:
+-------------------------------
+* Homepage: http://www.vasp.at
+* Documentation: http://cms.mpi.univie.ac.at/wiki/index.php/The_VASP_Manual
+
+
+License and access policy:
+----------------------------
+
+The VASP license is proprietary and commercial. It is based on group license policy, and for NOTUR systems VASP packages falls in the "bring your own license" category. See :ref:`About_licenses`.
+
+
+The Vasp program is not distributed via site licences. However, HPC-staff in NOTUR have access to the VASP code to be able to support any research groups that have a valid VASP license. 
+
+VASP is a commercial software package that requires a license for all who wants to run on Stallo. To get access you would need to prove that the group you are a m\
+ember of holds a valid licence; a representative for the research group needs to contact VASP and ask for an aknowledgement of you connection to the license. A VASP representative sends this acknowledgement to support@notur.no. Then your name is put into the VASP group, granting you access to the VASP 5 release of VASP on Stallo.
+
+The support people in NOTUR, do not provide trouble shooting guides anymore, due to a national agreement that it is better for the community as a whole to add to the community info/knowledge pool where such is made available. Also, HPC staff from UiT does not provide any support to VASP 4 anymore, basically due to age of the code.  
+
+Citation
+---------
+When publishing results obtained with the referred software referred, please do check the developers web page in order to find the correct citation(s).
+
+Usage
+=====
+
+You load the application by typing:
+
+.. code-block:: bash
+
+    $ module load VASP
+
+This command will give you the default version.
+
+For more information on available versions, type:
+
+.. code-block:: bash
+
+    $ module avail VASP
+
+Experiencewise, VASP is a rather memory intensive code. Users are advised to read up on the general job script example(s) for SLURM and Stallo, and also how to specify memory in `SLURM <https://slurm.schedmd.com>`_.
+
+
+First time you run a VASP job on Stallo?
+----------------------------------------
+
+Get the information you need here:
+
+.. toctree::
+   :maxdepth: 1
+
+   firsttime_vasp.rst
+
+
+About the VASP version(s) installed on Stallo:
+--------------------------------------------------
+
+Since the installation we made on Stallo is rather taylor made, we have gathered information about this here:
+
+.. toctree::
+   :maxdepth: 1
+
+   vasp_on_stallo.rst
+
+Here we also adress compilation relevant information for those who would like to do it themselves.