JUSTUS2/Software/Dalton: Difference between revisions
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After loading the Dalton module ('module load chem/dalton/version') it's path is |
After loading the Dalton module ('module load chem/dalton/version') it's path is |
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also set to the local $PATH- and [[#Dalton-Specific Environments|$DALTON_BIN_DIR environments]]. |
also set to the local $PATH- and [[#Dalton-Specific Environments|$DALTON_BIN_DIR environments]]. |
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<br> |
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$DALTON_BIN_DIR=/opt/bwhpc/common/chem/ |
$DALTON_BIN_DIR=/opt/bwhpc/common/chem/ |
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<pre> |
<pre> |
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Revision as of 10:36, 16 December 2015
| Description | Content |
|---|---|
| module load | chem/dalton |
| Availability | bwUniCluster |
| License | License/Distribution policy | ...more infos here... |
| Citing | Citation Includes | Dalton references |
| Links | Dalton Homepage | Dalton 2013 Manual |
| Graphical Interface | No |
Description
The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilites.
General Features
- First- and second-order methods for geometry optimizations
- Robust second-order methods for locating transition states
- Constrained geometry optimizations; bonds, angles and dihedral angles can be fixed during optimizations
- General numerical derivatives that automatically makes use of the highest order analytical derivative available
- Vibrational analysis and vibrational averaging, including anharmonic effects
- HF and DFT code MPI parallel for direct Fock matrix constructions and for DFT integrations over grid points
- Effective core-potentials (ECPs)
- Multiscale models (continuum and QM/MM using PE)
- Most sections can exploit point-group symmetry D2h and subgroups
For more information on features please visit Description of the Dalton program features web page.
Versions and Availability
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the
Cluster Information System CIS
{{#widget:Iframe |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/dalton |width=99% |height=150 |border=0 }} On the command line interface of any bwHPC cluster you'll get a list of available versions by using the command 'module avail chem/dalton'.
$ module avail chem/dalton ------------------------ /opt/bwhpc/common/modulefiles ------------------------- chem/dalton/2013
License
Code is distributed freely to individuals, but require the users to agree to a personal licence agreement. Site licenses are available, on the condition that the site keeps the source code confidential. Additionally, benchmark licences, valid for a restricted period of time, are available.
Obtaining a licence
A licence to use the Dalton programs can be obtained after filling in the
Dalton2015 Dalton Licence Application Form.
Usage
Loading the module
You can load the default version of Dalton with the command:
$ module load chem/dalton
The module will try to load modules it needs to function (e.g. compiler, mpi, numlibs). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Dalton. If you wish to load a specific (older) version (if available), you can do so using e.g. 'module load chem/dalton/version' to load the version you desires.
$ module avail chem/dalton ------------------------ /opt/bwhpc/common/modulefiles ------------------------- chem/dalton/2013 $ module load chem/dalton/2013
Program Binaries
You can find the Dalton binaries in the main folder of the Dalton system.
After loading the Dalton module ('module load chem/dalton/version') it's path is
also set to the local $PATH- and $DALTON_BIN_DIR environments.
$DALTON_BIN_DIR=/opt/bwhpc/common/chem/
$ : Example with Dalton 2013 $ echo $DALTON_BIN_DIR /opt/bwhpc/common/chem/dalton/2013/bin $ ls -F $DALTON_BIN_DIR basis/ DALTON.STAT GIT_HASH lsdalton.x* tools/ dalton* dalton.x* lsdalton* lslib_tester.x* VERSION
- A '/' at the end of a file name indicates a directory/folder.
- '*' is an executable file.
Disk Usage
Scratch files are written to the current directory by default. Please change to a local directory or to your local workspace (preferred) before starting your calculations.
'dalton_repo' is an example name of a repository you created by using the command 'ws_allocate'.
$ cd $(ws_find dalton_repo) ['your-id'-dalton_repo-0]$ pwd /work/workspace/scratch/'your-id'-dalton_repo-0 ['your-id'-dalton_repo-0]$
Examples
bwHPC examples
You can copy a simple interactive example to your workspace and run it, using 'msub'
$ cd $(ws_find dalton_repo) $ cp $DALTON_EXA_DIR/bwunicluster-dalton-example.moab . $ cp bwunicluster-dalton-example.moab mydaltonjob.moab § vi mydaltonjob.moab # do your own modifications $ msub mydaltonjob.moab # start job submission
It is strongly recommended to use $DALTON_EXA_DIR to find the bwHPC examples.
bwHPC Moab submit script
Here is an excerpt from the supplied bwunicluster-dalton-example.moab script as found in $DALTON_EXA_DIR.
[...]
echo " "
echo "### Copying input test files for job (if required):"
echo " "
cp -vr ${DALTON_EXA_DIR}/ethane-blyp-benchmark.{dal,mol} .
echo " "
echo "### Redefine TMPDIR for storing temporary Dalton files ..."
echo " "
export TMPDIR="${TMP_WORK_DIR}/dalton_tmp"
export DALTON_TMPDIR="${TMP_WORK_DIR}/dalton_tmp"
echo "TMPDIR = ${TMPDIR}"
echo "DALTON_TMPDIR = ${TMPDIR}"
echo " "
echo "### Calling dalton command ..."
echo " "
# Here is the main Dalton command showing how to run a regular
# Dalton job (mpirun is invoked within the 'dalton' script automatically).
# For details on the Dalton job see 'ethane-blyp-benchmark.info'.
# Example job input: ethane-blyp-benchmark.{dal,mol}
# Example job output: bwhpc-example.out ethane-blyp-benchmark.tar.gz.
export workdir=${TMP_WORK_DIR}
cd ${TMP_WORK_DIR}
time $DALTON_BIN_DIR/dalton -N ${MOAB_PROCCOUNT} -o bwhpc-example.out ethane-blyp-benchmark.dal ethane-blyp-benchmark.mol
[...]
|
Dalton-Specific Environments
To see a list of all Dalton environments set by the 'module load'-command use 'env | grep DALTON'. Or use the command 'module display chem/dalton'.
$ : Example with Dalton 2013 $ env | grep DALTON DALTON_VERSION=2013 DALTON_EXA_DIR=/opt/bwhpc/common/chem/dalton/2013/bwhpc-examples DALTON_BIN_DIR=/opt/bwhpc/common/chem/dalton/2013/bin DALTON_HOME=/opt/bwhpc/common/chem/dalton/2013
Version-Specific Information
For a more detailed information specific to a specific Dalton version, see the information available via the module system with the command 'module help chem/dalton/version'.
For a small abstract what Dalton is about use the command 'module whatis chem/dalton/version'.
$ : Dalton 2013 examples $ module whatis chem/dalton chem/dalton : Moleculare electronic structure package DALTON 2013 (command 'dalton' and 'lsdalton') $ : $ module help chem/dalton ----------- Module Specific Help for 'chem/dalton/2013' ----------- This module provides the quantum chemistry program Dalton version 2013 (see also http://dirac.chem.sdu.dk/daltonprogram.org/). The Dalton2013 suite consists of two separate executables, 'dalton' and 'lsdalton'. The DALTON code is a powerful tool for a wide range of molecular properties at different levels of theory (e.g. MCSCF or CC), whereas LSDALTON is a linear-scaling HF and DFT code suitable for large molecular systems. [...] Documentation: * For 'dalton' command line options see output of 'dalton -h'. This includes the specification of the memory, the number of workers and how the tmp work dir is used. * An Moab example script for dalton including a short example calculation can be found here: /opt/bwhpc/common/chem/dalton/2013/bwhpc-examples/bwunicluster-dalton-example.moab You can copy the example and submit it to the queueing system. [...]