Added documentation for Band

applications/chemistry/ADF/ADF.rst

@@ -1,18 +1,17 @@
 .. _ADF:
 
-===========================================
-Amsterdam Density Functional program system
-===========================================
+===============================================================
+Amsterdam Density Functional program
+=====================================
 
-Information regarding the quantum chemistry and material science package ADF/BAND on Stallo
+Information regarding the quantum chemistry code ADF on Stallo
 
 Related information:
 ====================
 
 .. toctree::
  :maxdepth: 1
 
- Band.rst
  firstime_adf.rst
 
 General Information:
@@ -21,51 +20,20 @@ General Information:
 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.
+According to the vendor, ADF (Amsterdam Density Functional) is a DFT program particularly strong in understanding and predicting structure, reactivity, and spectra of molecules. It 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. 
 
 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:
-------------------------
+Online documentation from vendor:
+----------------------------------
 
-* Homepage: http://www.scm.com
 * 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).
 
-
-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\
-ists 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 type license; meaning that research institutes not being part of Norwegian Universities must provide their own l\
-icense to be able to use and publish results obtained with this code on NOTUR installlations.`
-
-
-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
 ======
 
@@ -78,7 +46,7 @@ Use
 
     $ module avail ADF
 
-to see which versions of Gaussian are available. Use
+to see which versions of ADF which are available. Use
 
 .. code-block:: bash
 

applications/chemistry/ADF/ADF_modeling_suite.rst

@@ -0,0 +1,88 @@
+.. _ADFsuite:
+
+====================================================================================
+The Amsterdam Density Functional modeling suite
+=================================================
+
+This page contains general information about the ADF modeling suite installed on Stallo:
+
+Related information:
+====================
+
+.. toctree::
+ :maxdepth: 1
+
+ ADF.rst
+ firstime_adf.rst
+ Band.rst
+ firstime_band.rst
+
+General Information:
+====================
+
+Description:
+-------------
+
+The DFT code ADF is used in many areas of chemistry and materials science, and consists of the following parts:
+
+* The pure DFT code based on Slater type orbitals; ADF.
+* The periodic DFT code BAND shares a lot of functionality with ADF.d for treating large periodic molecular systems.
+* DFTB and MOPAC are fast approximate methods to study large molecules and big periodic systems, employing DFT-based and semi-empirical data, respectively.
+* Reaction dynamics in large complex systems can be studied with bond order based ReaxFF.
+* COSMO-RS uses quantum mechanical data from ADF to predict thermodynamic properties of solutions and mixtures (LogP, VLE, pKa, …)
+
+
+Online info from vendor:
+------------------------
+
+* Homepage: http://www.scm.com
+* Documentation: https://www.scm.com/doc/
+
+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).
+
+
+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\
+ists 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 type license; meaning that research institutes not being part of Norwegian Universities must provide their own l\
+icense to be able to use and publish results obtained with this code on NOTUR installlations.`
+
+
+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).
+
+More info on ADF and Band:
+---------------------------
+
+Here are links to more information about ADF and Band on Stallo:
+
+
+.. toctree::
+ :maxdepth: 1
+
+ ADF.rst
+ Band.rst
+
+
+
+

applications/chemistry/ADF/Band.rst

@@ -1,12 +1,76 @@
-.. _Band.rst
+.. _ADF:
+
+===============================================================
+Amsterdam Density Functional program
+=====================================
+
+Information regarding the quantum chemistry code ADF on Stallo
+
+Related information:
+====================
+
+.. toctree::
+ :maxdepth: 1
+
+ firstime_adf.rst
+
+General Information:
+====================
+
+Description:
+-------------
+
+According to the vendor, ADF (Amsterdam Density Functional) is a DFT program particularly strong in understanding and predicting structure, reactivity, and spectra of molecules. It 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. 
+
+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 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
+======
+
+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 which are available. Use
+
+.. code-block:: bash
+
+ $ module load ADF/<version> # i.e 2016.106
+
+to get access to any given version of ADF.  
+
+
+The first time you run an ADF job?
+----------------------------------
+
+Get the information you need here:
+
+
+.. toctree::
+ :maxdepth: 1
+
+ firstime_adf.rst
+
+
+Here we hold information for how to run on Stallo for the first time, and for using SLURM for the first time. 
+
 
-===========================================
-Amsterdam Density Functional program system
-===========================================
 
-This is a description of the BAND part of the ADF/Band program system.
 
 
-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/files/job_adf.sh

@@ -33,7 +33,8 @@ cores=40  # Number of cores potentially used by mpi engine in submit procedure
 
 # We load all the default program system settings with module load:
 
-module load ADF/2016.106
+module purge
+module load ADF/adf2017.108
 
 #-------------------------------
 
@@ -49,7 +50,7 @@ submitdir=$SLURM_SUBMIT_DIR
 tempdir=$SCM_TMPDIR
 
 cd $submitdir
-cp ${input}.${ext} $temdir
+cp ${input}.${ext} $tempdir
 cd $tempdir
 
 # In case necessary, set SCM_IOBUFFERSIZE

applications/chemistry/files/job_band.sh

@@ -0,0 +1,92 @@
+#!/bin/bash -l
+################### ADF Job Batch Script Example ###################
+# Section for defining queue-system variables:
+#-------------------------------------
+# This script asks for a given set of cores nodes and cores. Stallo has got 16 or 20 cores/node,
+# asking for something that adds up to both is our general recommodation (80, 160 etc), you would
+# then need to use --ntasks instead of -N and --ntasks-per-node. (replace both).
+# Runtime for this job is 59 minutes; syntax is hh:mm:ss. 
+# Memory is set to the maximum advised for a full node,
+# of 30000MB/node and leaving some for the system to use. Memory  
+# can be specified pr core, virtual or total pr job (be carefull).   
+#-------------------------------------
+# SLURM-section 
+#SBATCH --job-name=band_runex
+#SBATCH -N 2
+#SBATCH --ntasks-per-node=20
+#SBATCH --time=00:59:00
+#SBATCH --mem-per-cpu=1500MB # Be ware of memory needs!
+#SBATCH --output=band_runex.log
+#SBATCH --mail-type=ALL
+#SBATCH --exclusive
+#SBATCH --partition=multinode
+######################################
+# Section for defining job variables and settings:
+#-------------------------------------
+# Area for defining variables:
+
+input=silicone # Name of input without extention 
+ext=adf # We use the same naming scheme as the software default, also for extention
+cores=40  # Number of cores potentially used by mpi engine in submit procedure
+
+#-------------------------------
+
+# We load all the default program system settings with module load:
+
+module purge
+module load ADF/adf2017.108
+
+#-------------------------------
+
+# Now we create working directory and temporary scratch for the job(s):
+# Necessary variables are defined in the notur and the software modules.
+
+export SCM_TMPDIR=/global/work/$USER/$SLURM_JOBID
+mkdir -p $SCM_TMPDIR
+
+# Preparing and moving inputfiles to tmp:
+
+submitdir=$SLURM_SUBMIT_DIR
+tempdir=$SCM_TMPDIR
+
+cd $submitdir
+cp ${input}.${ext} $tempdir
+cd $tempdir
+
+# In case necessary, set SCM_IOBUFFERSIZE
+#export SCM_IOBUFFERSIZE=1024 # Or higher if necessary.
+
+######################################
+# Section for running the program and cleaning up:
+#-------------------------------------
+
+# Running the program:
+
+time band  -n $cores < ${input}.${ext} > band_$input.out
+
+# Cleaning up and moving files back to home/submitdir:
+# Make sure to move all essential files 
+# specific for the given job/software.
+
+cp band_$input.out $submitdir/band_$input.out
+cp TAPE21 $submitdir/$input.t21
+
+# To zip some of the output might be a good idea!
+#gzip $input.t21
+#mv $input.t21.gz $submitdir/
+
+# Investigate potentially other files to keep:
+echo `pwd`
+echo `ls -ltr`
+
+# ALLWAYS clean up after yourself. Please do uncomment the following line
+#cd $submitdir
+#rm  $tempdir/*
+#rmdir $tempdir
+
+
+echo "Job finished at"
+date
+################### Job Ended ###################
+exit 0
+