JUSTUS2/Software/ADF: Difference between revisions

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{{Softwarepage|chem/adf}}

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The ADF program suite is available for all users of the cluster. When you publish any results obtained with the ADF program suite you must cite ADF and the used components properly. Therefore please see the [https://www.scm.com/doc/ADF/Required_citations.html required citations]. Furthermore there might be additional [https://www.scm.com/adf-modeling-suite component specific citations] that can be found in documentation of the individual components.
The ADF program suite is available for all users of the cluster. When you publish any results obtained with the ADF program suite you must cite ADF and the used components properly. Therefore please see the [https://www.scm.com/doc/ADF/Required_citations.html required citations]. Furthermore there might be additional [https://www.scm.com/adf-modeling-suite component specific citations] that can be found in documentation of the individual components.

= Versions and Availability =

A list of versions currently available on the bwForCluster Chemistry can be obtained from the [https://cis-hpc.uni-konstanz.de/prod.cis/Justus/chem/adf Cluster Information System (CIS)]:
{{#widget:Iframe
|url=https://cis-hpc.uni-konstanz.de/prod.cis/Justus/chem/adf
|width=99%
|height=120
|border=0
}}
On the command line of a particular bwHPC cluster a list of all available versions is displayed by command
<pre>
$ module avail chem/adf
</pre>



= Usage =
= Usage =


== Loading the module and module help ==
== Creating input files with adfinput ==


Probably the easiest method to create input files is using the graphical user interface '''adfinput''': First start and connect to a [[Start_VNC_Server_-_bwForCluster_Chemistry_-_3D_Acceleration|3D-accelerated VNC session]] via [[TigerVNC]] running on one of our visualization nodes. Then - within the VNC window - load the adf module and run adfinput with 3D acceleration:
You can load the default version of ''ADF'' with the command
<pre>
<pre>
$ module load chem/adf
module load chem/adf
vglrun adfinput
</pre>
</pre>


⚫
With help of ADFinput molecules and periodic systems can be constructed (depending on the selected target program, i.e. '''adf''' or '''band'''). Furthermore one can control most calculational parameters like DFT methods, basis sets, convergence criteria, etc. After saving the calculation via '''File -> Save as''' with name '''MY_JOB''', a '''run'''-shell script with name '''MY_JOB.run''' can be found on disk.
There are no dependencies to other modules. All required components,
e.g. Intel MPI, are included in the ADF module.
<br>


⚫
This '''run'''-shell script contains the job input and executes the appropriate ADF commands like '''adf''', '''band''', etc (the input is piped via STDIN into those commands). The '''run'''-script can be called from within your ADF queueing system shell script, thus the queueing system shell script still defines the queueing system parameters, manages the temporary directories, loads the module, cleans up after the end of the job, etc).
Additional help is available via command
<pre>
$ module help chem/adf
</pre>
<br>

== Creating input files with '''adfinput''' ==

⚫
Probably the easiest method to create input files is using the graphical user interface '''adfinput''' (best called within a [[TigerVNC]] session). With help of ADFinput molecules and periodic systems can be constructed (depending on the selected target program, i.e. '''adf''' or '''band'''). Furthermore one can control most calculational parameters like DFT methods, basis sets, convergence criteria, etc. After saving the calculation via ''File -> Save as'' with name ''MY_JOB'', a ''run''-shell script with name ''MY_JOB.run'' can be found on disk.

⚫
This ''run''-shell script contains the job input and executes the appropriate ADF commands like '''adf''', '''band''', etc (the input is piped via STDIN to those commands). The ''run''-script should be called from within your ADF queueing system shell script, thus the queueing system shell script still defines the queueing system parameters, manages the temporary directories, loads the module, cleans up after job end, etc).


For an introduction how to use the ADF GUI please follow some of the [https://www.scm.com/doc/Tutorials/Introduction/Introduction.html ADF Tutorials]. If you want to change the job input without GUI, you can edit the ''run''-shell scripts manually. All possible keywords and options are documented in the ''manuals'' sections of the [https://www.scm.com/doc/Documentation/index.html documentation of the individual programs].
For an introduction how to use the ADF GUI please follow some of the [https://www.scm.com/doc/Tutorials/Introduction/Introduction.html ADF tutorials]. If you want to change the job input without GUI, you can edit the '''run'''-shell scripts manually. All possible keywords and options are documented in the '''manuals''' sections of the [https://www.scm.com/doc/Documentation/index.html documentation of the individual programs].


== Parallel computing ==
== Parallel computing ==


In queueing system scripts the commands '''adf''', '''band''', ... automatically run on the cores as specified when submitting the script. Neither ''mpirun'' nor any further command line options are required.
In queueing system scripts the commands '''adf''', '''band''', ... automatically use the cores as specified when submitting the job script. Neither '''mpirun''' nor any further command line options are required.


In case of interactive single-node test jobs one can limit the number of cores via command line option ''-n NB_OF_CORES'', i.e. ''-n 8''.
In case of interactive single-node test jobs one can limit the number of cores via command line option '''-n NB_OF_CORES''', for example '''adf -n 8'''.


== Disk usage ==
== Disk usage ==


Temporary files are stored below directory ''SCM_TMPDIR''. Typically this variable is defined within the queing system script and points to some local directory below ''TMPDIR''. In case of multi-node jobs, ''SCM_TMPDIR'' must point to the same directory and must exist on every node.
Temporary files are stored below directory '''SCM_TMPDIR'''. Typically this environment variable is defined within the queueing system script and points to some node-local directory below '''TMPDIR'''. In case of multi-node jobs, '''SCM_TMPDIR''' must point to the same directory on every node and must exist on every node.


When loading the adf module, '''SCM_TMPDIR''' is defined automatically and usually points to '''TMPDIR'''. When running under control of the queueing system, '''TMPDIR''' is the node-local scratch directory of the job.
⚫
Please never put temporary files on any central file system like ''HOME'' or ''SCRATCH''.


⚫
Please never put temporary files of ADF on central file systems like '''HOME''' or '''SCRATCH''' or workspaces.
= Input and queueing system examples =

Links to input and queuing system example files can be found via
<pre>
$ module help chem/vasp
</pre>
<br>

== Interactive parallel example ==
The example shows, how to load the vasp module,
extract some example input files and run vasp on an
interactive node using 4 cores:

<pre>
$ module load chem/adf
$ mkdir ~/ADF-example-job/
$ cd ~/ADF-example-job/
$ adf -n 4 < $ADF_EXA_DIR/adf-Energy_H2O-all_electron-example.inp
</pre>
<br>

= Version-specific information =

For specific information about version X, see the output of command
<pre>
$ module help chem/adf/X
</pre>

To load and use a specific ADF version X, use the command
<pre>
$ module load chem/adf/X
</pre>
<br>


----
----
[[Category:Chemistry software]]

Latest revision as of 11:30, 23 April 2024

The main documentation is available via module help chem/adf on the cluster. Most software modules for applications provide working example batch scripts.


Description Content
module load chem/adf
License Commercial - see SCM License Terms
Citing Required citations as well as module specific citations
Links ADF Homepage and product specific documentation pages
Graphical Interface ADF GUI
User forum ADF Discussion List

Description

The ADF Modeling Suite by SCM (Software for Chemistry & Materials) is a collection of programs for modeling chemical and physical properties of molecules and solids. The suite consists of the following components:

  • With help of the graphical user interface adfinput one can construct molecules, solids and slabs. All kinds of calculational parameters like functionals, basis sets, convergence parameters can be defined as well. The calculation and its parameters can be saved as a run-file which is suitable for inclusion in our queueing system scripts. For details see the Tutorials of SCM.
  • adfjobs can used for interactive job control. This is intended only for short test jobs running in background for some minutes. For longer jobs one should save the job as run-file which can be called from within a queueing system script. For details see the Tutorials of SCM.
  • adf is a powerful molecular DFT (density functional theory) code applicable in many areas of chemistry and materials science. One strength of ADF is in the field of inorganic chemistry.
  • band is a DFT code for periodic systems using local slater type orbital basis sets.
  • dftb provides fast approximate methods for studying large molecules and large periodic systems.
  • reaxff is a bond order based force field program for studying reaction dynamics in large complex systems.
  • The COSMO-RS method allows to predict thermodynamic properties of solutions and mixtures (LogP, VLE, pKa, ...) based on quantum mechanical data from ADF.

License and citing

The ADF program suite is available for all users of the cluster. When you publish any results obtained with the ADF program suite you must cite ADF and the used components properly. Therefore please see the required citations. Furthermore there might be additional component specific citations that can be found in documentation of the individual components.

Usage

Creating input files with adfinput

Probably the easiest method to create input files is using the graphical user interface adfinput: First start and connect to a 3D-accelerated VNC session via TigerVNC running on one of our visualization nodes. Then - within the VNC window - load the adf module and run adfinput with 3D acceleration: 

module load chem/adf
vglrun adfinput

With help of ADFinput molecules and periodic systems can be constructed (depending on the selected target program, i.e. adf or band). Furthermore one can control most calculational parameters like DFT methods, basis sets, convergence criteria, etc. After saving the calculation via File -> Save as with name MY_JOB, a run-shell script with name MY_JOB.run can be found on disk.

This run-shell script contains the job input and executes the appropriate ADF commands like adf, band, etc (the input is piped via STDIN into those commands). The run-script can be called from within your ADF queueing system shell script, thus the queueing system shell script still defines the queueing system parameters, manages the temporary directories, loads the module, cleans up after the end of the job, etc).

For an introduction how to use the ADF GUI please follow some of the ADF tutorials. If you want to change the job input without GUI, you can edit the run-shell scripts manually. All possible keywords and options are documented in the manuals sections of the documentation of the individual programs.

Parallel computing

In queueing system scripts the commands adf, band, ... automatically use the cores as specified when submitting the job script. Neither mpirun nor any further command line options are required.

In case of interactive single-node test jobs one can limit the number of cores via command line option -n NB_OF_CORES, for example adf -n 8.

Disk usage

Temporary files are stored below directory SCM_TMPDIR. Typically this environment variable is defined within the queueing system script and points to some node-local directory below TMPDIR. In case of multi-node jobs, SCM_TMPDIR must point to the same directory on every node and must exist on every node.

When loading the adf module, SCM_TMPDIR is defined automatically and usually points to TMPDIR. When running under control of the queueing system, TMPDIR is the node-local scratch directory of the job.

Please never put temporary files of ADF on central file systems like HOME or SCRATCH or workspaces.

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