Merge pull request #60 from uit-no/radovan/gaussian

Trivial changes in Gaussian docs

applications/chemistry/Gaussian/GaussView.rst

@@ -1,16 +1,19 @@
-.. _gaussview:
 
 ======================
 GaussView for Gaussian
 ======================
 
-Gaussview is a visualization program that can be used to open Gaussian output files and checkpoint files (.chk) to display structures, molecular orbitals, normal modes, etc. You can also set up jobs and submit them directly.
+Gaussview is a visualization program that can be used to open Gaussian output
+files and checkpoint files (.chk) to display structures, molecular orbitals,
+normal modes, etc. You can also set up jobs and submit them directly.
 
 
 GaussView on Stallo
 --------------------
 
-The GaussView version for Gaussian 09 is release 5.0.8 To load and run GaussView on Stallo, you first have to load the relevant gaussian module, and then call gaussview::
+The GaussView version for Gaussian 09 is release 5.0.8 To load and run
+GaussView on Stallo, you first have to load the relevant gaussian module, and
+then call gaussview::
 
    $ module load Gaussian/09.d01
    $ gview
@@ -20,4 +23,3 @@ More information about GaussView
 
 * General info about the program: http://www.gaussian.com/g_prod/gv5.htm
 * Online reference: http://www.gaussian.com/g_tech/gv5ref/gv5ref_toc.htm
-

applications/chemistry/Gaussian/Gaussian.rst

@@ -1,4 +1,3 @@
-.. _Gaussian:
 
 ===========================
 The GAUSSIAN program system
@@ -23,7 +22,10 @@ General Information
 Description
 -----------
 
-Gaussian is a computational chemistry software program system initially released in 1970. 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.
+Gaussian is a computational chemistry software program system initially
+released in 1970. 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.
 
 Online info from vendor
 -----------------------
@@ -37,7 +39,12 @@ License information
 
 The license of GAUSSIAN is commercial/proprietary.
 
-The license of Gaussian constitutes of 4 site licenses for the 4 current host institutions of NOTUR installations; NTNU, UiB, UiO, UiT. In principle, only person from one of these institutions have access to the Gaussian Software system installed on Stallo. Note that users that do not come from one of the abovementioned institutions still may be granted access, but they need to document access to a valid license for the verion in question first.
+The license of Gaussian constitutes of 4 site licenses for the 4 current host
+institutions of NOTUR installations; NTNU, UiB, UiO, UiT. In principle, only
+person from one of these institutions have access to the Gaussian Software
+system installed on Stallo. Note that users that do not come from one of the
+above mentioned institutions still may be granted access, but they need to
+document access to a valid license for the version in question first.
 
 * To get access to the code, you need to be in the gaussian group of users.
 * To be in the gaussian group of users, you need be qualified for it - see above.
@@ -46,8 +53,8 @@ The license of Gaussian constitutes of 4 site licenses for the 4 current host in
 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).
+When publishing results obtained with the referred software referred, please do
+check the developers web page in order to find the correct citation(s).
 
 
 Additional online info about Gaussian on Stallo
@@ -56,7 +63,16 @@ Additional online info about Gaussian on Stallo
 Usage
 -----
 
-Since Gaussian is a rather large and versatile program system with a range of different binaries, we would in general advice users to check whether their jobs are parallelized or not before submitting jobs. It would in general, unless every step is entirely well parallelized, always be more efficient to split a complex many-step job into smaller parallel and serial parts/jobs so that also the overall utilization of hardware is improved. I you are in doubt whether or not your job will scale outside one node (=shared memory), go to the Gaussian application home folder and check if there is an \*.exel version of the executable(s) you will be using. If yes, your job will generally work ok in parallel up to approx 300 cores (this is for the more advanced users).
+Since Gaussian is a rather large and versatile program system with a range of
+different binaries, we would in general advice users to check whether their
+jobs are parallelized or not before submitting jobs. It would in general,
+unless every step is entirely well parallelized, always be more efficient to
+split a complex many-step job into smaller parallel and serial parts/jobs so
+that also the overall utilization of hardware is improved. I you are in doubt
+whether or not your job will scale outside one node (=shared memory), go to the
+Gaussian application home folder and check if there is an \*.exel version of
+the executable(s) you will be using. If yes, your job will generally work ok in
+parallel up to approx 300 cores (this is for the more advanced users).
 
 We generally wants users to run as many nodes as possible to limit the walltime length of running jobs.
 
@@ -84,4 +100,3 @@ this here :doc:`gaussian_on_stallo`.
 
 Here we also address issues related to running Gaussian in parallel, number of cores to use,
 memory allocation and special issues taken care of at install.
-

applications/chemistry/Gaussian/firsttime_gaussian.rst

@@ -5,7 +5,7 @@ First time you run a Gaussian job?
 ==================================
 
 This page contains info aimed at first time
-users of Gaussian on Stallo, but may also be usefull to
+users of Gaussian on Stallo, but may also be useful 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.
@@ -20,13 +20,15 @@ Gaussian input example
    :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`
+**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<../files/caffeine.com>`
 
 
-Gaussian runscrip example
--------------------------
+Gaussian runscript example
+--------------------------
 
 .. include:: ../files/job_gaussian.sh
    :literal:
@@ -55,5 +57,5 @@ When you have all the necessary files in the correct folders, submit the job by
 
 	sbatch job_gaussian.sh
 
-To verify that nothing has gone wrong, check the output of the calculations. In Gaussian output, you allways get an entertaining quote at the end. Good luck. 
-
+To verify that nothing has gone wrong, check the output of the calculations. In
+Gaussian output, you always get an entertaining quote at the end. Good luck.