initial commit after rudimentary conversion from gitit

applications/applications.rst

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+---
+toc: no
+title: Applications
+...
+
+Overview over SW installed on Stallo
+--------------------------------------
+
+For a complete list of applications see the :doc:`software page <software>`.
+
+Missing / new SW?
+...................
+
+If there is any SW missing on this list that you would like to have
+installed on Stallo, or you need help to install your own SW, please
+feel free to contact the support personal about this:
+:doc:`support-uit@notur.no <support-uit@notur.no>`
+
+Changes in application software
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+New and updated software will be announced on `UiT
+News <http://docs.notur.no/uit/uit-news>`_.
+Headlines from the above news page will also be displayed on the login
+screen.
+The easiest way to check which software and versions available is to use
+the  ``module`` command.
+List all software available::
+
+    module avail
+List all version of a specific software::
+
+    module avail software-name
+
+Modules
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Software installations on the clusters span many applications, and many
+different version numbers of the same application. It is not possible
+(nor desirable) to use them all at the same time, since different
+versions of the same application may conflict with each other. In order
+to simplify the control of which application versions are available in a
+specific session, there is a system for loading and unloading 'modules'
+which activate and deactivate the relevant parts of your user session.
+
+The modules command
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+An introduction to the Modules Command; a way to navigate between
+various settings, libraries and SW versions
+
+Software installations on the clusters span many applications, and many
+different version numbers of the same application. It is not possible
+(nor desirable) to use them all at the same time, since different
+versions of the same application may conflict with each other. In order
+to simplify the control of which application versions are available in a
+specific session, there is a system for loading and unloading 'modules'
+which activate and deactivate the relevant parts of your user session.
+
+To learn about Modules, please follow this link to the `Metasenter
+page about link about Modules 
+<../../../metacenter/metacenter-documentation/metacenter_user_guide/the-modules-command>`_.
+
+
+Which modules are loaded?
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+To see the modules currently active in your session, use the
+command  
+
+::
+
+    module list
+
+
+
+Which modules are available?
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In order to see a complete list of available modules, issue the
+command 
+
+::
+
+    module avail
+
+The resulting list will contain module names conforming to the following
+pattern:
+
+*  name of the module
+*  /
+*  version
+*  (default) if default version
+
+How are modules loaded?
+~~~~~~~~~~~~~~~~~~~~~~~
+
+In order to enable to make available, for instance, the netcdf library,
+issue the command  
+
+::
+
+    module load netcdf
+
+
+
+This will load the default netcdf version. To load a specific version,
+just include the version:
+
+::
+
+    module load netcdf/3.6.2
+
+
+
+How are modules unloaded?
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Keeping with the above example, use the following command to unload the
+GLView module again:  
+
+::
+
+    module unload netcdf
+
+Which version of a module is the default?
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In order to see, for instance, which version of netcdf is loaded by the
+module, use:
+
+::
+
+    module show netcdf
+
+This will show the version and path of the module.
+
+
+
+How do I switch to a different version of a module?
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Switching to another version is similar to loading a specific version.
+As an example, if you want to switch from the default (current) Intel
+compilers version to version 8.0, type
+
+::
+
+    module switch intelcomp intelcomp/8.0
+
+How do I switch to a different version of a module?
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Say you want to switch from the intel compilers  version 11.1 to, e.g.
+version 11.0, use  
+
+::
+
+    module switch intel-compiler/11.1 intel-compiler/11.0
+
+.. :vim:ft=rst

applications/biology.rst

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+
+Biology
+~~~~~~~~~~~~~~~~~
+
+*  :doc:`Amber <application-support/chemistry-applications/amber>`
+*  `Genomics
+   applications <application-support/genomics-applications/genomics-applications>`_
+*  :doc:`Gromacs <application-support/chemistry-applications/gromacs>`
+*  :doc:`NAMD <application-support/chemistry-applications/namd>`
+*  :doc:`OpenBabel <application-support/chemistry-applications/openbabel>`
+*  :doc:`Schroedinger <application-support/chemistry-applications/schroedinger>`

applications/chemistry/ADF/ADF.rst

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+---
+title: Amsterdam Density Functional program system
+...
+
+A description of the quantum chemistry and material science package ADF/BAND
+
+General Information:
+--------------------
+The Amsterdam Density Functional (ADF) software is used for electronic structure calculations. As the name implies, only DFT calculations can be run. In ADF, basis sets are of Slater-type (instead of Gaussian-type), giving improved performance and good convergence results for especially metal compounds. Note that also naming of basis sets is somewhat different from standard gaussian type basis sets, which makes basis set comparison less trivial. All-electron basis sets are available for the entire periodic table. See: http://www.scm.com/Products/Overview/ADFinfo.html.
+
+*Functionality:*
+
+* Single Point calculation, Geometry Optimization and Transition States
+* Frequencies and thermodynamic properties
+* Tracing a Reaction Path
+* Computation of any electronic configuration
+* Excitation energies, oscillator strengths, transition dipole moments, (hyper)polarizabilities, Van der Waals dispersion coefficients, CD spectra, ORD, using Time-Dependent Density Functional Theory (TDDFT)
+* ESR (EPR) g-tensors, A-tensors, NQCCs
+* NMR chemical shifts and spin-spin coupling constants and Various other molecular properties
+* Treatment of large systems and environment by the QM/MM (Quantum Mechanics / Molecular Mechanics) hybrid approach.
+* Implementation of the Noodleman spin-flip method. See the online manual for more information: `http://www.scm.com/Doc/Doc2009.01/ADF/ADFUsersGuide/page85.html#keyscheme%20SPINFLIP <http://www.scm.com/Doc/Doc2009.01/ADF/ADFUsersGuide/page85.html#keyscheme%20SPINFLIP>`_
+
+ADF on Stallo:
+--------------
+
+*The current default version* on Stallo is ADF 2012.01c
+
+ 2009.01, 2010.02b, 2012.01 and 2013 - the latter included the latest bug fix release. We also do install the development version every now and then.
+
+You load the application by typing:
+
+.. code-block:: bash
+
+    $ module load adf
+
+This command will give you the default version, which is currently 2012.01c.
+
+For more information on available versions, type:
+
+.. code-block:: bash
+
+    $ module avail adf
+
+If you want to run other versions of ADF, change the <module load> parameter in the script file to the version you want to run, for instance:
+
+.. code-block:: bash
+
+ $ module load adf/2013.01
+
+will load the version adf2013.01. For more information on ADF/BAND, see: http://www.scm.com/
+
+JOB SUBMISSION GUIDELINES
+::::::::::::::::::::::::::
+
+* Download the run script adf2012.run and move the file to your $HOME/bin directory (if necessary create directory first).
+* Submit job (s) from any directory:
+
+.. code-block::
+
+ $ adf2012.run input 2 8 20:30 
+
+Job-name is here input.inp, number of nodes is 2 with 8 processors per node and 20 hrs 30 minutes run time (walltime). If you want to look at a typical input file for geometry optimizations with ADF, look at inputfile for ADF geometry optimization.
+
+**Note:** 
+
+* Generated output and TAPE21 files are named based on input file. Example: input.inp gives input-a12.out and input-a12.t21 outputs if using the adf2012.run script. 
+* ADF jobs are run in /global/work/$LOGNAME/$PBS_JOBID (one 'kid' directory per requested node). This is a measure to ease support efforts from our side. Temporary directories are removed upon job completion. If job aborted prematurely, temporary directories need to be removed manually. Remember to move the TAPE21 file before deleting the temporary kid0 folder.
+* The output file is continuously updated to the $HOME directory (from where the job was submitted).
+* Since ADF is a very complex code, able to solve a vast range of chemistry problems - giving a unified advice regarding scaling is difficult. For a standard geometry optimization, it seems to scale well in the region of 4-6 full nodes (64-96 cores) at least. For linear transit we would currently stay at no more than 4 full nodes or less currently.Unless having tests indicating otherwise, users who want to run large jobs should allocate no more than the prescribed numbers of processors. More information will come. 
+
+Further information:
+---------------------
+
+* `How to restart a job<adf_restart>`_. 
+* `How to run using *fragments*<adf_fragments>`_.
+* `Troubleshooting ADF-jobs<adf_troubleshoot>`_.
+* `Information about inputfiles<adf_input>`_.
+* `Runscript examples<adf_runscripts>`_.
+
+
+ADF 2009.01 run script: adf2009.run
+
+ADF 2010.01 run script: adf2010.run
+
+LINKS
+------
+General: http://www.scm.com/
+
+Online Manual: http://www.scm.com/Doc/Doc2008.01/ADF/ADFUsersGuide/page1.html
+
+Utilities: http://www.scm.com/Doc/Doc2009.01/ADF/Utilities/page1.html
+
+Email Technical Support: support@scm.com (only for ADF specific questions)

applications/chemistry/ADF/adf_fragments.rst

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+---
+title: How to run ADF using fragments
+...
+
+This is a brief introduction to how to create fragments necessary for among other things, BSSE calculations and proper broken symmetry calculations.
+
+**Running with fragments:**
+
+* Download and modify script for fragment create run, e.g. this template: Create.TZP.sh  (modify ACCOUNT, add desired atoms and change to desired basis and desired functional)
+* Run the create job in the same folder as the one where you want to run your main job(s) (qsub Create.TZP.sh).
+* Put the line cp $init/t21.* .  in your ADF run script (in your $HOME/bin directory)
+* In job.inp, specify correct file name in FRAGMENT section, e.g. “H   t21.H_tzp”. * Submit job.inp as usual. 
+
+
+Running with fragments is only necessary when you want to run a BSSE calculations or manipulate charge and/or atomic mass for a given atom (for instance modeling heavy isotope labelled samples for frequency calculations).  

applications/chemistry/ADF/adf_restart.rst

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+---
+title: How to restart an ADF job
+...
+
+**Restarting a job:**
+
+#. In the directory where you started your job, rename or copy the job-output t21 file into $SCM_TMPDIR/TAPE21.
+
+#. In job.inp file, put RESTART TAPE21 just under the comment line.
+
+#. Submit job.inp file as usual. 
+
+This might also be automized, we are working on a solution for restart after unexpected downtime. 

applications/chemistry/ADF/adf_troubleshoot.rst

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+Troubleshooting ADF calculations
+by Kathrin Helen Hopmann — last modified Jun 30, 2010 03:09 PM
+Collection of some error messages and possible solutions
+
+
+
+Errors in .out file: 
+Attempt to open nonexistent file TAPE__0
+or
+
+master does not have RSFILE. iexist=0
+Solution: RESTART was specified in the .inp file, but name of TAPE21 file was not correct, or run script was unable to transport TAPE21 to the running directory. See here for details how to restart ADF calculations.
+
+
+
+ EOF INPUT WHILE READING A BLOCK KEY
+or
+
+Error: Could not parse line in ATOMS key:
+Solution: Check that all sections in the .inp file are terminated correctly with end.
+
+
+
+Error: Could not find matching basis file for X
+Solution: Basis set for atom X was not found. Check that atom labels are chemically correct.
+
+
+
+If  you are running ADF 2008.01 and get an empty output-file, apart from the fragment calculations, you might have forgotten to specify the infiniband interconnects for the job.

applications/chemistry/CFOUR/CFOUR.rst

@@ -0,0 +1,6 @@
+---
+toc: no
+title: Index
+...
+
+To be written...

applications/chemistry/Dalton/Dalton.rst

@@ -0,0 +1,6 @@
+---
+toc: no
+title: Index
+...
+
+To be written...

applications/chemistry/Gaussian/Gaussian.rst

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+---
+title: The GAUSSIAN program system
+...
+
+`Back to Applications top page<../index>`_
+
+Gaussian is a computational chemistry software program system initially released in 1970. The name comes from, then groundbreaking, the use of gaussian type basis functions – which later more or less has become the “trade standard”. Gaussian has a rather low user threshold and a tidy user setup, which, together with a broad range of possibilities and a graphical user interface (gaussview), might explain its popularity in academic institutions. 
+
+- For information about the latest Gaussian release, see http://www.gaussian.com/g_prod/g09b.htm.
+- For a list of 
functionality: see http://www.gaussian.com/g_prod/g09_glance.htm
+- For information about Gaussian 09 job types, see http://www.gaussian.com/g_tech/g_ur/m_jobtypes.htm
+
+GAUSSIAN on NOTUR installations
+================================
+
+Currently there are two available main release versions in the NOTUR system; Gaussian 03 and Gaussian 09. Gaussian 09 is the latest in the Gaussian series of programs and Gaussian 03 is its predecessor. For differences between the two, please check the gaussian web page http://www.gaussian.com/g_tech/g_ur/a_gdiffs09.htm.
+
+Headings in inputfiles for parallel runs.
+Content in the .tsnet.config file.
+Content in the g09parallel.job script.
+Advised number of nodes and cpus in parallel runs.
+Please do read these sections carefully. 
+
+For distribution in the NOTUR system, see `the NOTUR software pages<http://www.notur.no/software/chemistry/>`_.
+
+For more information on:
+
+- Gaussian 03 - go to `Gaussian 03<g03>`_
+- Gaussian 09 - go to `Gaussian 09<g09>`_
+
+Generally, we advice users to run the latest version of the software. This rule has some important exceptions: 
+
+#. As a rule of thumb you should always complete a project using the same software as you started with. 
+#. If you by experience know that your kind of problem behaves better (runs faster, uses less memory or scales better) on older versions of the program we of course encourage you to run your jobs the more efficient way.
+
+
+
+LINKS
+======
+Software home-page: http://www.gaussian.com/
+
+Technical support from software vendor: http://www.gaussian.com/g_email/em_help.htm 
+
+Technical support for Stallo: support-uit@notur.no