Merge branch 'master' of github.com:uit-no/hpc-doc

applications/chemistry/ADF/ADF.rst

@@ -7,11 +7,12 @@ The Amsterdam Density Functional modeling suite
 This page contains general information about the ADF modeling suite installed on Stallo:
 
 Related information:
-====================
-
-* `Info about the ADF program on Stallo <ADFprog.rst>`_
-* `Info abut the Band program on Stallo <Band.rst>`_
+---------------------
+.. toctree:: :maxdepth: 1
+ :titlesonly:
 
+ ADFprog
+ Band
 
 General Information:
 ====================
@@ -71,10 +72,16 @@ ion(s).
 Here are links to more information about ADF and Band on Stallo:
 -----------------------------------------------------------------
 
-* `Info about the ADF program on Stallo <ADFprog.rst>`_
-* `First time run of ADF <firstime_adf.rst>`_
-* `Info abut the Band program on Stallo <Band.rst>`_
-* `First time run of Band <firsttime_band.rst>`_
+.. toctree:: :maxdepth: 1
+   :titlesonly:
+
+   ADFprog
+   firsttime_adf
+   Band
+   firsttime_band
+
+
+
 
 
 

applications/chemistry/ADF/ADFprog.rst

@@ -1,14 +1,13 @@
 .. _ADFprog:
 
-===============================================================
+=================================================
 Amsterdam Density Functional program
-=====================================
+=================================================
 
 Information regarding the quantum chemistry code ADF on Stallo
 
 Related information:
-====================
-
+---------------------
 .. toctree::
  :maxdepth: 1
 
@@ -26,13 +25,10 @@ The underlying theory is the Kohn-Sham approach to Density-Functional Theory (DF
 
 
 Online documentation from vendor:
-----------------------------------
+------------------------------------
 
 * 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).
 
 Usage
 ======
@@ -50,11 +46,10 @@ to see which versions of ADF which are available. Use
 
 .. code-block:: bash
 
- $ module load ADF/<version> # i.e 2016.106
+ $ module load ADF/<version> # i.e adf2017.108
 
 to get access to any given version of ADF.  
 
-
 The first time you run an ADF job?
 ----------------------------------
 
@@ -70,7 +65,3 @@ Get the information you need here:
 Here we hold information for how to run on Stallo for the first time, and for using SLURM for the first time. 
 
 
-
-
-
-

applications/chemistry/ADF/Band.rst

@@ -1,14 +1,13 @@
 .. _Band:
 
-===============================================================
-Amsterdam Density Functional program
-=====================================
+============================
+The periodic DFT code Band
+============================
 
-Information regarding the periodic DFT code Band on Stallo
+Information regarding the periodic DFT code Band on Stallo:
 
 Related information:
-====================
-
+---------------------
 .. toctree::
  :maxdepth: 1
 
@@ -27,15 +26,11 @@ The Amsterdam Density Functional Band-structure program - BAND - can be used for
 BAND makes use of atomic orbitals, it can handle elements throughout the periodic table, and has several analysis options available. BAND can use numerical atomic orbitals, so that the core is described very accurately. Because of the numerical orbitals BAND can calculate accurate total energies. Furthermore it can handle basis functions for arbitrary l-values.
 
 
-Online documentation from vendor:
-----------------------------------
+Online info from vendor:
+------------------------
 
 * Documentation: https://www.scm.com/doc/BAND
 
-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).
-
 Usage
 ======
 
@@ -52,7 +47,7 @@ to see which versions of Band which are available. Use
 
 .. code-block:: bash
 
- $ module load ADF/<version> # i.e 2016.106
+ $ module load ADF/<version> # i.e adf2017.108
 
 to get access to any given version of Band.  
 
@@ -74,5 +69,3 @@ Here we hold information for how to run on Stallo for the first time, and for us
 
 
 
-
-

applications/chemistry/Schrodinger/Schrodinger.rst

@@ -9,7 +9,7 @@ A description of the Schrödinger product suites that are available for norwegia
 General Information:
 ====================
 
-NOTUR is, together with the user community, funding a national license of Schrödinger´s Small Molecule Drug Discovery Suite and PyMol.
+NOTUR is, together with the user community, funding a national license of Schrödinger´s Small Molecule Drug Discovery Suite and PyMol. This implies that users are allowed to download and install their own copies of the software, and using the license server for providing license tokens. More about that in another document: :ref:`install_schrodinger`. 
 
 Online info from vendor:
 ------------------------
@@ -60,8 +60,6 @@ Usage
 The most commot usage of schrodinger on Stallo is through the Maestro gui. Log in with x11-tunneling enabled, or through the web-interface http://stallo-gui.uit.no/.
 Load the module of choice: 
 
-One important note: All new installs will be made through the new software scheme on Stallo. Please confer the documentation for :ref:`new_scheme`.
-
 Use
 
 .. code-block:: bash
@@ -87,7 +85,7 @@ For examples on how to submit Schrodinger jobs on Stallo, look here :ref:`run_sc
 Finding available licenses
 ===========================
 
-This should in principle be obsolete for users, since we are promised unlimited licenses in the national system. But still, for the curious soles:
+This should in principle be obsolete for users, since we are promised unlimited licenses in the national system. But still, for the curious souls:
 
 If you want to know about avaible licenses; do the following