Merge pull request #45 from mathiasbockwoldt/master

Updated application documentation
uit-no · Jun 4, 2018 · 0c73cd4 · 0c73cd4
2 parents 1df534a + 8a511dd
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diff --git a/applications/chemistry/ADF/firsttime_adf.rst b/applications/chemistry/ADF/firsttime_adf.rst
@@ -46,7 +46,7 @@ These files are also available on Stallo
 
    module load ADF/adf2017.108
    cd <to whatever you call your test folder> # for instance ADFFIRSTJOB
-   cp -R $RUNEX/* .
+   cp -R /global/hds/software/notur/apprunex/ADF/* .
 
 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.
 

diff --git a/applications/chemistry/ADF/firsttime_band.rst b/applications/chemistry/ADF/firsttime_band.rst
@@ -46,7 +46,7 @@ These files are also available on Stallo
 
    module load ADF/adf2017.108
    cd <to whatever you call your test folder> # for instance BANDFIRSTJOB
-   cp -R $RUNEX/* .
+   cp -R /global/hds/software/notur/apprunex/ADF/* .
 
 To verify that the jobs has worked fine, check the outputfile. If it says EXIT and print Energy of Formation at the end of the file, you are likely on the safe side.
 

diff --git a/applications/chemistry/Dalton/Dalton.rst b/applications/chemistry/Dalton/Dalton.rst
@@ -0,0 +1,57 @@
+.. _Dalton:
+
+======
+Dalton
+======
+
+Related information
+===================
+
+.. toctree::
+ :maxdepth: 1
+
+ firsttime_dalton.rst
+
+
+General information
+===================
+
+Description
+-----------
+
+Dalton is an ab initio quantum chemistry computer program. It is capable of calculating various molecular properties using the Hartree-Fock, MP2, MCSCF and coupled cluster theories. Dalton also supports density functional theory calculations.
+
+
+Online information from vendor
+------------------------------
+
+* Homepage: http://daltonprogram.org/
+* Documentation: http://daltonprogram.org/documentation/
+* For download: http://daltonprogram.org/download/
+
+
+License and access policy
+-------------------------
+
+Dalton is licensed under the GPL 2. That basically means that everyone may freely use the program.
+
+Citation
+--------
+
+When publishing results obtained with the referred software referred, check the following page to find the correct citation(s): http://daltonprogram.org/citation/
+
+
+Usage
+=====
+
+You load the application by typing:
+
+.. code-block:: bash
+
+	module load Dalton/2016-130ffaa0-intel-2017a
+
+For more information on available versions of Dalton, type:
+
+.. code-block:: bash
+
+	module avail Dalton
diff --git a/applications/chemistry/Dalton/firsttime_dalton.rst b/applications/chemistry/Dalton/firsttime_dalton.rst
@@ -0,0 +1,44 @@
+.. _first_time_dalton:
+
+================================
+First time you run a Dalton job?
+================================
+
+This page contains info aimed at first time
+users of Dalton on Stallo. 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, copy the input example and the job script example shown below
+into your test job folder (which I assume you have created in advance).
+
+Dalton needs one molecule file and one input file. For simplicity, we have tarred them together and you
+may download them here: :download:`Dalton files<../files/dalton_example_files.tar.gz>`
+
+Molcas runscrip example
+-----------------------
+
+.. include:: ../files/job_dalton.sh
+   :literal:
+
+
+You can also download the runscript file here: :download:`Dalton run script<../files/job_dalton.sh>`
+
+
+The runscript example and the input are also on Stallo
+------------------------------------------------------
+
+Type:
+
+.. code-block:: bash
+
+	cd <whatever_test_folder_you_have> # For instance testdalton
+	cp -R /global/hds/software/notur/apprunex/dalton/* .
+
+When you have all the necessary files in the correct folders, submit the job by typing:
+
+.. code-block:: bash
+
+	sbatch job_dalton.sh
+
+Good luck.
diff --git a/applications/chemistry/Gaussian/firsttime_gaussian.rst b/applications/chemistry/Gaussian/firsttime_gaussian.rst
@@ -47,7 +47,7 @@ Type:
 
 	module load Gaussian/9.d01
 	cd <whereevertestfolderyouhave> # For instance testgau
-	cp -R $RUNEX/* .
+	cp -R /global/hds/software/notur/apprunex/Gaussian/* .
 
 
 When you have all the necessary files in the correct folders, submit the job by typing:

diff --git a/applications/chemistry/Molcas/firsttime_molcas.rst b/applications/chemistry/Molcas/firsttime_molcas.rst
@@ -38,7 +38,7 @@ Type:
 
 	module load Molcas/molcas82-intel-2015a
 	cd <whereevertestfolderyouhave> # For instance testmolcas
-	cp -R $RUNEX/* .
+	cp -R /global/hds/software/notur/apprunex/Molcas/* .
 
 
 When you have all the necessary files in the correct folders, submit the job by typing:

diff --git a/applications/chemistry/Schrodinger/install_schrod.rst b/applications/chemistry/Schrodinger/install_schrod.rst
@@ -1,13 +1,13 @@
 .. _install_schrodinger:
 
 Installing Schrodinger on your local client machine
-====================================================
+===================================================
 
 This page contains info about how to download and install the Schrodinger suite on your local client machine.
 
 
 Getting an account on www.schrodinger.com
-------------------------------------------
+-----------------------------------------
 
 You need to create an account (free) and log in with the password you create. Then you download the relevant software for your machine and follow install procedures that comes with the software.
 

diff --git a/applications/chemistry/Schrodinger/run_schrod.rst b/applications/chemistry/Schrodinger/run_schrod.rst
@@ -21,12 +21,10 @@ To get download the jobscript example(s), type the following:Direct log in via s
 .. code-block:: bash
 
  	$ module load Schrodinger/2017-2-intel-2016a
- 	$ cp -R $runex/Schrodinger/* ~
+ 	$ cp -r /global/hds/software/notur/apprunex/Schrodinger/* ~
 	# Be sure this do not overwrite any folder or info you may want to keep in your home.
 
-Note: This suite is quite extensive in features, and we generally advice you to either join tutorial courses, talk \
-to experts in your proximity or read the vendor-provided documentation if you have absolutely no knowledge about how to \
-use this suite of software. Here we only provide a couple of rough startup examples to get you up running.
+Note: This suite is quite extensive in features, and we generally advice you to either join tutorial courses, talk to experts in your proximity or read the vendor-provided documentation if you have absolutely no knowledge about how to use this suite of software. Here we only provide a couple of rough startup examples to get you up running.
 
 Then;
 

diff --git a/applications/chemistry/TURBOMOLE/run_turbo.rst b/applications/chemistry/TURBOMOLE/run_turbo.rst
@@ -18,7 +18,7 @@ load the ``notur`` module
 .. code-block:: bash
 
     $ module load notur
-    $ cp -r $RUNEX/TURBOMOLE .
+    $ cp -r /global/hds/software/notur/apprunex/TURBOMOLE .
 
 From this directory you can submit the example script (you need to specify a
 valid account in the script first)
@@ -29,7 +29,7 @@ valid account in the script first)
 
 
 The calculation should take less than 2 min, but may spend much more than this
-in the queue. Verify that the output file ``dscf.out`` ends with 
+in the queue. Verify that the output file ``dscf.out`` ends with
 
 .. code-block:: bash
 

diff --git a/applications/chemistry/VASP/firsttime_vasp.rst b/applications/chemistry/VASP/firsttime_vasp.rst
@@ -41,7 +41,7 @@ These files are also available on Stallo
 
    module load VASP/5.4.1.plain-intel-2016a
    cd <to whatever you call your test folder> # for instance testvasp
-   cp -R $RUNEX/* .
+   cp -R /global/hds/software/notur/apprunex/VASP/* .
    sbatch job_vasp.sh
 
 and you are up running. Happy hunting.
diff --git a/applications/chemistry/files/dalton_example_files.tar.gz b/applications/chemistry/files/dalton_example_files.tar.gz
diff --git a/applications/chemistry/files/job_dalton.sh b/applications/chemistry/files/job_dalton.sh
@@ -0,0 +1,57 @@
+#!/bin/bash -l
+
+# Write the account to be charged here
+# (find your account number with `cost`)
+#SBATCH --account=nnXXXXk
+
+#SBATCH --job-name=daltonexample
+
+# we ask for 20 cores
+#SBATCH --ntasks=20
+
+# run for five minutes
+#              d-hh:mm:ss
+#SBATCH --time=0-00:05:00
+
+# 500MB memory per core
+# this is a hard limit
+#SBATCH --mem-per-cpu=500MB
+
+# Remove percentage signs to turn on all mail notification
+#%%%SBATCH --mail-type=ALL
+
+# You may not place bash commands before the last SBATCH directive!
+
+# Load Dalton
+# You can find all installed Dalton installations with:
+#   module avail dalton
+module load Dalton/2013.2
+
+# Define the input files
+molecule_file=caffeine.mol
+input_file=b3lyp_energy.dal
+
+# Define and create a unique scratch directory
+SCRATCH_DIRECTORY=/global/work/${USER}/daltonexample/${SLURM_JOBID}
+mkdir -p ${SCRATCH_DIRECTORY}
+cd ${SCRATCH_DIRECTORY}
+
+# Define and create a temp directory
+TEMP_DIR=${SCRATCH_DIRECTORY}/temp
+mkdir -p ${TEMP_DIR}
+
+# copy input files to scratch directory
+cp ${SLURM_SUBMIT_DIR}/${input_file} ${SLURM_SUBMIT_DIR}/${molecule_file} ${SCRATCH_DIRECTORY}
+
+# run the code
+dalton -N ${SLURM_NTASKS} -t ${TEMP_DIR} ${input_file} ${molecule_file}
+
+# copy output and tar file to submit dir
+cp *.out *.tar.gz ${SLURM_SUBMIT_DIR}
+
+# we step out of the scratch directory and remove it
+cd ${SLURM_SUBMIT_DIR}
+rm -rf ${SCRATCH_DIRECTORY}
+
+# happy end
+exit 0
diff --git a/applications/sw_guides.rst b/applications/sw_guides.rst
@@ -12,13 +12,14 @@ the module system, and information about changes in application software see :re
    :maxdepth: 2
    :titlesonly:
 
-   chemistry/Gaussian/Gaussian
-   chemistry/VASP/VASP
    chemistry/ADF/ADF
-   chemistry/Schrodinger/Schrodinger
-   chemistry/ORCA/ORCA
+   chemistry/Dalton/Dalton
+   chemistry/Gaussian/Gaussian
    chemistry/Molcas/Molcas
+   chemistry/ORCA/ORCA
+   chemistry/Schrodinger/Schrodinger
    chemistry/TURBOMOLE/TURBOMOLE
+   chemistry/VASP/VASP
 
    physics/COMSOL/COMSOL