JUSTUS2/Software/Dalton: Difference between revisions

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{{Softwarepage}}
{{Softwarepage|chem/dalton}}


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'''Dalton''' (named after [https://en.wikipedia.org/wiki/John_Dalton John Dalton]) is an ab initio quantum chemistry computer program designed to to allow convenient, automated determination of a large number of molecular properties based on an HF, HF-srDFT, DFT, MP2, CC, CI, MCSCF, or MC-srDFT reference wave function. For additional information on features please visit the [https://daltonprogram.org/features/ Description of the Dalton suite features] web page.
'''Dalton''' (named after [https://en.wikipedia.org/wiki/John_Dalton John Dalton]) is an ab initio quantum chemistry computer program designed to to allow convenient, automated determination of a large number of molecular properties based on an HF, HF-srDFT, DFT, MP2, CC, CI, MCSCF, or MC-srDFT reference wave function. For additional information on features please visit the [https://daltonprogram.org/features/ Description of the Dalton suite features] web page.


= License =

Dalton is free, open-source software released under the GNU Lesser General Public License (LGPL). Anyone interested in using the Dalton program suite must read the conditions described in its [https://gitlab.com/dalton/dalton/-/blob/master/LICENSE license agreement].


= Usage =
= Usage =
== Hints for using Dalton ==
== Loading the module ==
See [[Software Modules]] documentation

== Input Files ==

For information about how to construct input files (dalinp{.dal} [molinp{.mol} [potinp{.pot}]]) for Dalton, please consult the [https://daltonprogram.org/manuals/dalton2020manual.pdf vendor documentation].

== Environment Variables ==

Environment variables understood by Dalton:
<pre>
DALTON_TMPDIR : scratch directory
DALTON_USE_GLOBAL_SCRATCH : use global scratch directory, do not copy any files to worker nodes
DALTON_NODELIST : list of nodes, dalton.x will be copied to DALTON_TMPDIR on each node unless
DALTON_USE_GLOBAL_SCRATCH is defined
DALTON_LAUNCHER : launcher for the dalton.x binary (if defined, -N flag not allowed)
</pre>

== Disk Usage ==


Scratch files are written to <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$SCRATCH</span> by default. This configuration option can be changed by setting the environment variable <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$DALTON_TMPDIR</span> (e.g., to a dedicated [[workspace]]) before starting your calculations with Dalton.
Scratch files are written to <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$SCRATCH</span> by default. This configuration option can be changed by setting the environment variable <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$DALTON_TMPDIR</span> (e.g., to a dedicated [[workspace]]) before starting your calculations with Dalton.

= Examples =

As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system.

Example scripts are available in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$DALTON_EXA_DIR</span>:
<pre>
$ module load chem/dalton # load module
$ ls $DALTON_EXA_DIR # show content of directory $DALTON_EXA_DIR
$ cat $DALTON_EXA_DIR/README # show examples README
</pre>

Run a first simple example job on JUSTUS2:
<pre>
$ module load chem/dalton # load module
$ WORKSPACE=`ws_allocate dalton 3` # allocate workspace
$ cd $WORKSPACE # change to workspace
$ cp -a $DALTON_HOME/bwhpc-examples . # copy example files to workspace
$ cd bwhpc-examples # change to test directory
$ sbatch dalton-2020.0.slurm # submit job
$ squeue # obtain JOBID
$ scontrol show job <JOBID> # check state of job
$ ls # when job finishes the results will be visible in this directory
</pre>


= FAQ =
= FAQ =
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* [https://en.wikipedia.org/wiki/Dalton_(program) Wikipedia article (english)]
* [https://en.wikipedia.org/wiki/Dalton_(program) Wikipedia article (english)]
* [https://daltonprogram.org/tools/ Plugins for Dalton (english)]
* [https://daltonprogram.org/tools/ Plugins for Dalton (english)]
----
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]

Latest revision as of 11:30, 23 April 2024

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


Description Content
module load chem/dalton
License GNU Lesser General Public License (LGPL).
Citing Publications
Links Homepage | Documentation
Graphical Interface No

Description

Dalton (named after John Dalton) is an ab initio quantum chemistry computer program designed to to allow convenient, automated determination of a large number of molecular properties based on an HF, HF-srDFT, DFT, MP2, CC, CI, MCSCF, or MC-srDFT reference wave function. For additional information on features please visit the Description of the Dalton suite features web page.


Usage

Loading the module

See Software Modules documentation

Input Files

For information about how to construct input files (dalinp{.dal} [molinp{.mol} [potinp{.pot}]]) for Dalton, please consult the vendor documentation.

Environment Variables

Environment variables understood by Dalton: 

DALTON_TMPDIR             : scratch directory
DALTON_USE_GLOBAL_SCRATCH : use global scratch directory, do not copy any files to worker nodes
DALTON_NODELIST           : list of nodes, dalton.x will be copied to DALTON_TMPDIR on each node unless
                            DALTON_USE_GLOBAL_SCRATCH is defined
DALTON_LAUNCHER           : launcher for the dalton.x binary (if defined, -N flag not allowed)

Disk Usage

Scratch files are written to $SCRATCH by default. This configuration option can be changed by setting the environment variable $DALTON_TMPDIR (e.g., to a dedicated workspace) before starting your calculations with Dalton.

Examples

As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system.

Example scripts are available in the directory $DALTON_EXA_DIR: 

$ module load chem/dalton                # load module
$ ls $DALTON_EXA_DIR                     # show content of directory $DALTON_EXA_DIR
$ cat $DALTON_EXA_DIR/README             # show examples README

Run a first simple example job on JUSTUS2: 

$ module load chem/dalton                           # load module
$ WORKSPACE=`ws_allocate dalton 3`                  # allocate workspace
$ cd $WORKSPACE                                     # change to workspace
$ cp -a $DALTON_HOME/bwhpc-examples .               # copy example files to workspace
$ cd bwhpc-examples                                 # change to test directory
$ sbatch dalton-2020.0.slurm                        # submit job
$ squeue                                            # obtain JOBID
$ scontrol show job <JOBID>                         # check state of job
$ ls                                                # when job finishes the results will be visible in this directory

FAQ

Q: What to do if my simulations abort with MEMGET ERROR, insufficient work space in memory ?

A: Increase Dalton's usable work memory with either -mb or -gb on the command line.

Useful links

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