Major update of chemistry software documentation.

applications/chemistry/ADF/ADF.rst

@@ -1,31 +1,46 @@
+.. _ADF:
+
 ===========================================
 Amsterdam Density Functional program system
 ===========================================
 
-A description of the quantum chemistry and material science package ADF/BAND
+Information regarding the quantum chemistry and material science package ADF/BAND on Stallo
+
+Related information:
+====================
+
+.. toctree::
+ :maxdepth: 1
+
+ Band.rst
+ firsttime_adf.rst
+
 
 General Information:
 ====================
 
-The ADF software is a DFT-only first-principles electronic structure calculations program system, and consists of a rich variety of packages.
+Description:
+-------------
+
+ADF (Amsterdam Density Functional) is a Fortran program for calculations on atoms and molecules (in gas phase or solution). It can be used for the study of such diverse fields as molecular spectroscopy, organic and inorganic chemistry, crystallography and pharmacochemistry. A separate program BAND is available for the study of periodic systems: crystals, surfaces, and polymers. The COSMO-RS program is used for calculating thermodynamic properties of (mixed) fluids.
+
+The underlying theory is the Kohn-Sham approach to Density-Functional Theory (DFT).  The software is a DFT-only first-principles electronic structure calculations program system, and consists of a rich variety of packages.
+
 
 Online info from vendor:
 ------------------------
 
 Homepage: http://www.scm.com
-Documentation: http://www.scm.com/Doc
+Documentation: https://www.scm.com/doc/ADF/
 
 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. For ADF/BAND we advise to search in general documentation, se\
 nding emails to support(either notur or scm) or trying the ADF mailing list (see http://www.scm.com/Support for more info).
 
-Citation
---------
-When publishing results obtained with the referred software referred, please do check the developers web page in order to find the correct citat\
-ion(s).
 
-License information:
---------------------
+License and access policy:
+---------------------------
+
 The license of ADF/Band is commercial.
 
 NOTUR holds a national license of the ADF program system, making usage of ADF/BAND available for all academic scient\
@@ -46,72 +61,39 @@ We have a national license for the following packages:
 icense to be able to use and publish results obtained with this code on NOTUR installlations.`
 
 
-
-is software for first-principles electronic structure calculations. The program suite shows good scaling behaviour, and we have tested in the 80-160 core region but not beyond. For statements from vendor related to scaling, please visit their home page as shown on top of this page. 
-
-(link to general info about license policy notur when available; currently contact: www.sigma2.no)
+Citation
+--------
+When publishing results obtained with the referred software referred, please do check the developers web page in order to find the correct citat\
+ion(s).
 
 
 Usage
 ======
 
-We generally advise to run ADF on more than one node, unless you do know that your particular problem does not make the code scale well. 
+The ADF/BAND suite of software is currently installed as precompiled binaries on Stallo. We install the intel-mpi version, since it has proven to collaborate the better with our mpi setup. We generally advise to run ADF on more than one node, unless you do know that your particular problem does not make the code scale well.
 
-Use
-
-.. code-block:: bash
 
-    $ module avail adf 
-
-to see which versions of ADF are available. Use
+Use
 
 .. code-block:: bash
 
-    $ module load ADF
+    $ module avail ADF
 
-or 
+to see which versions of Gaussian are available. Use
 
 .. code-block:: bash
 
- $ module load ADF/<version> # i.e 2014.10 (default)
-
-to get access to ADF.  
-
-
-First run of ADF/BAND:
---------------------------------
-
-To get download the jobscript example(s), type the following:
-
-.. code-block::bash
+ $ module load ADF/<version> # i.e 2016.106
 
-    module load notur
-    cd $APPEX/adf 
+to get access to any given version of ADF.  
 
-Copy the contents of this folder to your home directory.
 
-Then, submit the job by typing:
+The first time you run an ADF job?
+--------------------------------------
 
-.. code-block::bash
-
-    sbatch job_adf.sh
-
-Compare the energy of adf_caffeine.out with the Bond Energy =  -156.75317227 eV in adf_example_correct_stallo.output. The energy should ideally be identical or close to identical. When this is the case, you may alter variables in the shell script as much as you like to adapt to your own jobs. Good luck.
-
-- NB: ADF is installed as precompiled binaries, they come with their own mpi (intel MPI). So if you are not using the provided runscript example, please make sure that the default openmpi is swapped with the default intel-MPI module.
-
-
-- On Stallo, we holds the nbo6 plug in license that allows users of adf to produce files that can be read with the nb06 software.
-
-ADF input example:
---------------------
-
-.. include:: adf.inputex
-   :literal:
-
-ADF runscrip example:
-------------------------
+Get the information you need here:
 
-.. include:: adf.jobscriptex
-   :literal:
+.. toctree::
+   :maxdepth: 1
 
+   firsttime_adf.rst

applications/chemistry/ADF/Band.rst

@@ -1,73 +1,12 @@
+.. _Band.rst
+
 ===========================================
 Amsterdam Density Functional program system
 ===========================================
 
-A description of the quantum chemistry and material science package ADF/BAND
-
-General Information:
-====================
-
-The ADF software is a DFT-only program package used for electronic structure calculations, and consists of a rich variety of packages. See http://www.scm.com/ for more information.
-
-Citation
---------
-When publishing results obtained with the software referred to, please do check the developers web page in order to find the correct citation(s).
-
-
-License information:
---------------------
-NOTUR holds a national license of the ADF program system, making usage of ADF/BAND available for all academic scientists in Norway. 
-
-
-We have a national license for the following packages:
-
-ADF, ADFGUI, BAND, BANDGUI, CRS, DFTB, DFTBGUI, GUI, REAXFF, REAXFFGUI, NBO6 (on Stallo only, but machine license available for all users of Stallo).
-
-Please note that this is an academic license; meaning that research institutes not being part of Norwegian Universities must provide their own license to be able to use and publish results obtained with this code on NOTUR installlations.
-
-Information about versions:
----------------------------
-
-You load the application by typing:
-
-.. code-block:: bash
-
-    $ module load ADF
-
-This command will give you the default version.
-
-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/2014.08
-
-First run of ADF/BAND on Stallo:
-================================
-
-To get download the jobscript example(s), type the following:
-
-.. code-block::bash
-
-    module load notur
-    cd $APPEX/adf 
-
-Copy the contents of this folder to your home directory.
-
-Then, submit the job by typing:
-
-`qsub job_adf_stallo.sh`
-
-Compare the energy of adf_example.out with the Bond Energy =  -156.77666698 eV in adf_example_correct_stallo.output. The energy should ideally be identical or close to identical. When this is the case, you may alter variables in the shell script as much as you like to adapt to your own jobs. Good luck.
-
-> NB: ADF is on Stallo set up with intel mpi, if not using this script - remember to do module swap openmpi impi before loading the adf module.
+This is a description of the BAND part of the ADF/Band program system.
 
-> On Stallo, we holds the nbo6 plug in license that allows users of adf to produce files that can be read with the nb06 software.
 
+More info will come when we gain more experience with this particular code.
 
+In principle, quite a lot should be similar to the ADF part.

applications/chemistry/ADF/firstime_adf.rst

@@ -0,0 +1,62 @@
+.. _first_time_adf:
+
+===================================
+First time you run an ADF job?
+===================================
+
+This page contains info aimed at first time 
+users of ADF 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).
+
+ADF input example:
+--------------------
+
+.. include:: ../files/caffeine.adf
+   :literal:
+
+This file can also be downloaded here: :download:`Caffeine input for ADF <../files/caffeine.adf>`.
+
+Place this file in a job folder of choice, say ADFFIRSTJOB in your home directory on Stallo.
+
+then, copy the job-script as seen here:
+
+.. include:: ../files/job_adf.sh
+   :literal:
+
+(Can also be downloaded from here: :download:`job_vasp.sh <../files/job_adf.sh>`.)
+
+Place this script in the same folder and type:
+
+.. code-block::bash
+
+    sbatch job_adf.sh
+
+You may now have submitted your first adf job.
+
+
+These files are also available on Stallo:
+------------------------------------------
+
+.. code-block:: bash
+
+   module load ADF/2016.106
+   cd <to whatever you call your test folder> # for instance ADFFIRSTJOB
+   cp -R $RUNEX/* .
+
+To verify that the jobs has worked fine, check the outputfile. If it says EXIT and print Bond Energies at the end of the file, you are likely on the safe side. 
+
+Compare the energy of adf_caffeine.out with the Bond Energy =  -156.75317227 eV in adf_example_correct_stallo.output. The Bond Energy should ideally be close to -156.75317227 eV. When this is the case, you may alter variables in the shell script as much as you like to adapt to your own jobs. 
+
+**NB: ADF is installed as precompiled binaries, they come with their own mpi (intel MPI). So if you are not using the provided runscript example, please make sure that the default openmpi is swapped with the default intel-MPI module.**
+
+Also note that, on Stallo, we hold the nbo6 plug in license that allows users of adf to produce files that can be read with the nb06 software.
+
+Good luck with your chemistry!
+

applications/chemistry/Gaussian/Gaussian.rst

@@ -64,7 +64,7 @@ Use
 
 .. code-block:: bash
 
-    $ module avail gaussian
+    $ module avail Gaussian
 
 to see which versions of Gaussian are available. Use
 

applications/chemistry/Gaussian/firsttime_gaussian.rst

@@ -16,25 +16,25 @@ into your test job folder (which I assume you have created in advance).
 Gaussian input example:
 ------------------------
 
-.. include:: caffeine.com
+.. include:: ../files/caffeine.com
    :literal:
 
 
 **NB: Pay special attention to the %mem defined in the beginning of the file. Also note that there are no mentioning of Linda and shared memory cores. This is addressed here:** :ref:`gaussian_on_stallo`
 
-You can also download the input file here: :download:`Caffeine-input<caffeine.com>`
+You can also download the input file here: :download:`Caffeine-input<../files/caffeine.com>`
 
 
 Gaussian runscrip example:
 --------------------------
 
-.. include:: job_g09.sh
+.. include:: ../files/job_g09.sh
    :literal:
 
 
 **NB: Note that we for Gaussian advice to specify both nodes and core/node. This is due to the special way Gaussian sets up parallel jobs!**
 
-You can also download the input file here: :download:`Gaussian run script<job_g09.sh>`
+You can also download the runscript here: :download:`Gaussian run script<../files/job_g09.sh>`
 
 
 
@@ -45,9 +45,9 @@ Type:
 
 .. code-block:: bash
 	
-	module load Gaussian/9.c01
-	cd <whereevertestfolderyouhave>
-	cp -R $RUNEX .
+	module load Gaussian/9.d01
+	cd <whereevertestfolderyouhave> # For instance testgau
+	cp -R $RUNEX/* .
 
 
 When you have all the necessary files in the correct folders, submit the job by typing: