Dalton: Difference between revisions
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= Introduction = | = Introduction = <!--T:1--> | ||
<!--T:2--> | |||
The kernel of the Dalton2016 suite is the two powerful molecular electronic structure programs, Dalton and LSDalton. Together, the two programs provide extensive functionality for the calculations of molecular properties at the HF, DFT, MCSCF, and CC levels of theory. Many of these properties are only available in the Dalton2016 suite. | The kernel of the Dalton2016 suite is the two powerful molecular electronic structure programs, Dalton and LSDalton. Together, the two programs provide extensive functionality for the calculations of molecular properties at the HF, DFT, MCSCF, and CC levels of theory. Many of these properties are only available in the Dalton2016 suite. | ||
<!--T:3--> | |||
* Project web site: http://daltonprogram.org/ | * Project web site: http://daltonprogram.org/ | ||
* Documentation: http://daltonprogram.org/documentation/ | * Documentation: http://daltonprogram.org/documentation/ | ||
* Forum: http://forum.daltonprogram.org/ | * Forum: http://forum.daltonprogram.org/ | ||
= Modules = | = Modules = <!--T:4--> | ||
<!--T:5--> | |||
<source lang="bash"> | <source lang="bash"> | ||
$ module load nixpkgs/16.09 intel/2016.4 openmpi/2.0.2 dalton/2017-alpha | $ module load nixpkgs/16.09 intel/2016.4 openmpi/2.0.2 dalton/2017-alpha | ||
</source> | </source> | ||
<!--T:6--> | |||
Notice that <code>dalton/2017-alpha</code> depends on a non-default version of Open MPI. | Notice that <code>dalton/2017-alpha</code> depends on a non-default version of Open MPI. | ||
For more on the <code>module</code> command see [[Utiliser des modules/fr|Using modules]]. | For more on the <code>module</code> command see [[Utiliser des modules/fr|Using modules]]. | ||
= Usage = | = Usage = <!--T:7--> | ||
<!--T:8--> | |||
Here is an example: | Here is an example: | ||
<!--T:9--> | |||
* Dalton input file: <code>dft_rspexci_nosym.dal</code> (see Examples below) | * Dalton input file: <code>dft_rspexci_nosym.dal</code> (see Examples below) | ||
* Molecule specification: <code>H2O_cc-pVDZ_nosym.mol</code> (see Examples below) | * Molecule specification: <code>H2O_cc-pVDZ_nosym.mol</code> (see Examples below) | ||
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** Or, <code>export DALTON_NUM_MPI_PROCS=${SLURM_NTASKS}</code> (refer to '''Script 2''' in the examples below). | ** Or, <code>export DALTON_NUM_MPI_PROCS=${SLURM_NTASKS}</code> (refer to '''Script 2''' in the examples below). | ||
<!--T:10--> | |||
To run Dalton, load the module and use the launcher <code>dalton</code>: | To run Dalton, load the module and use the launcher <code>dalton</code>: | ||
<!--T:11--> | |||
<source lang="bash"> | <source lang="bash"> | ||
dalton -b ${BASLIB} -N ${SLURM_NTASKS} -dal dft_rspexci_nosym.dal -mol H2O_cc-pVDZ_nosym.mol | dalton -b ${BASLIB} -N ${SLURM_NTASKS} -dal dft_rspexci_nosym.dal -mol H2O_cc-pVDZ_nosym.mol | ||
</source> | </source> | ||
<!--T:12--> | |||
or | or | ||
<!--T:13--> | |||
<source lang="bash"> | <source lang="bash"> | ||
export DALTON_NUM_MPI_PROCS=${SLURM_NTASKS} | export DALTON_NUM_MPI_PROCS=${SLURM_NTASKS} | ||
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</source> | </source> | ||
= Examples: scripts and input files = | = Examples: scripts and input files = <!--T:14--> | ||
== Example 1: dft_rspexci_nosym == | == Example 1: dft_rspexci_nosym == <!--T:15--> | ||
</translate> | </translate> | ||
<tabs> | <tabs> | ||
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</tabs> | </tabs> | ||
<translate> | <translate> | ||
== Example 2: dft_rspexci_sym.dal == | == Example 2: dft_rspexci_sym.dal == <!--T:16--> | ||
</translate> | </translate> | ||
<tabs> | <tabs> | ||
Revision as of 15:41, 7 September 2018
Introduction[edit]
The kernel of the Dalton2016 suite is the two powerful molecular electronic structure programs, Dalton and LSDalton. Together, the two programs provide extensive functionality for the calculations of molecular properties at the HF, DFT, MCSCF, and CC levels of theory. Many of these properties are only available in the Dalton2016 suite.
- Project web site: http://daltonprogram.org/
- Documentation: http://daltonprogram.org/documentation/
- Forum: http://forum.daltonprogram.org/
Modules[edit]
$ module load nixpkgs/16.09 intel/2016.4 openmpi/2.0.2 dalton/2017-alpha
Notice that dalton/2017-alpha depends on a non-default version of Open MPI.
For more on the module command see Using modules.
Usage[edit]
Here is an example:
- Dalton input file:
dft_rspexci_nosym.dal(see Examples below) - Molecule specification:
H2O_cc-pVDZ_nosym.mol(see Examples below) - To use the atomic basis set installed with the program, supply the option
-b ${BASLIB}. - The number of processes can be set using a command line option or an environment variable:
- Add the option
-N ${SLURM_NTASKS}to the launcher command line (refer to Script 1 in the examples below). - Or,
export DALTON_NUM_MPI_PROCS=${SLURM_NTASKS}(refer to Script 2 in the examples below).
- Add the option
To run Dalton, load the module and use the launcher dalton:
dalton -b ${BASLIB} -N ${SLURM_NTASKS} -dal dft_rspexci_nosym.dal -mol H2O_cc-pVDZ_nosym.mol
or
export DALTON_NUM_MPI_PROCS=${SLURM_NTASKS}
dalton -b ${BASLIB} -dal dft_rspexci_nosym.dal -mol H2O_cc-pVDZ_nosym.mol
Examples: scripts and input files[edit]
Example 1: dft_rspexci_nosym[edit]
File : dft_rspexci_nosym.dal
**DALTON INPUT
.RUN RESPONSE
**INTEGRALS
.PROPRINT
**WAVE FUNCTIONS
.DFT
B3LYP
**RESPONSE
*LINEAR
.SINGLE RESIDUE
.ROOTS
3
**END OF DALTON INPUT
File : H2O_cc-pVDZ_nosym.mol
BASIS
cc-pVDZ
H2O
2 0
8. 1
O 0.0 0.0000000000 0.0
1. 2
H1 1.430 0.0 1.1
H2 -1.430 0.0 1.1
File : run_dalton_job.sh
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --mem-per-cpu=3500M
#SBATCH --time=00-30:00
# Load the module:
module load nixpkgs/16.09 intel/2016.4 openmpi/2.0.2 dalton/2017-alpha
# Setting the variables:
dltonlaun=dalton
dltonexec=dalton.x
daltoninput=dft_rspexci_nosym.dal
daltonmol=H2O_cc-pVDZ_nosym.mol
echo "Starting run at: `date`"
echo "Running the example: INPUT=${daltoninput} - Molecule=${daltonmol}"
${dltonlaun} -b ${BASLIB} -N ${SLURM_NTASKS} -dal ${daltoninput} -mol ${daltonmol}
echo "Program finished with exit code $? at: `date`"
File : run_dalton_job.sh
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --mem-per-cpu=3500M
#SBATCH --time=00-30:00
# Load the module:
module load nixpkgs/16.09 intel/2016.4 openmpi/2.0.2 dalton/2017-alpha
# Setting the variables:
dltonlaun=dalton
dltonexec=dalton.x
daltoninput=dft_rspexci_nosym.dal
daltonmol=H2O_cc-pVDZ_nosym.mol
# Set the number of cores DALTON_NUM_MPI_PROCS to ${SLURM_NTASKS}
export DALTON_NUM_MPI_PROCS=${SLURM_NTASKS}
echo "Starting run at: `date`"
echo "Running the example: INPUT=${daltoninput} - Molecule=${daltonmol}"
${dltonlaun} -b ${BASLIB} -dal ${daltoninput} -mol ${daltonmol}
echo "Program finished with exit code $? at: `date`"
Example 2: dft_rspexci_sym.dal[edit]
File : dft_rspexci_sym.dal
**DALTON INPUT
.RUN RESPONSE
**INTEGRALS
.PROPRINT
**WAVE FUNCTIONS
.DFT
B3LYP
**RESPONSE
*LINEAR
.SINGLE RESIDUE
**END OF DALTON INPUT
File : H2O_cc-pVDZ_sym.mol
BASIS
cc-pVDZ
H2O
2
8. 1
O 0.0 0.0000000000 0.0
1. 2
H1 1.430 0.0 1.1
H2 -1.430 0.0 1.1
File : run_dalton_job.sh
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --mem-per-cpu=3500M
#SBATCH --time=00-30:00
# Load the module:
module load nixpkgs/16.09 intel/2016.4 openmpi/2.0.2 dalton/2017-alpha
# Setting the variables:
dltonlaun=dalton
dltonexec=dalton.x
daltoninput=dft_rspexci_sym.dal
daltonmol=H2O_cc-pVDZ_sym.mol
echo "Starting run at: `date`"
echo "Running the example: INPUT=${daltoninput} - Molecule=${daltonmol}"
${dltonlaun} -b ${BASLIB} -N ${SLURM_NTASKS} -dal ${daltoninput} -mol ${daltonmol}
echo "Program finished with exit code $? at: `date`"
File : run_dalton_job.sh
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --mem-per-cpu=3500M
#SBATCH --time=00-30:00
# Load the module:
module load nixpkgs/16.09 intel/2016.4 openmpi/2.0.2 dalton/2017-alpha
# Setting the variables:
dltonlaun=dalton
dltonexec=dalton.x
daltoninput=dft_rspexci_sym.dal
daltonmol=H2O_cc-pVDZ_sym.mol
# Set the number of cores DALTON_NUM_MPI_PROCS to ${SLURM_NTASKS}
export DALTON_NUM_MPI_PROCS=${SLURM_NTASKS}
echo "Starting run at: `date`"
echo "Running the example: INPUT=${daltoninput} - Molecule=${daltonmol}"
${dltonlaun} -b ${BASLIB} -dal ${daltoninput} -mol ${daltonmol}
echo "Program finished with exit code $? at: `date`"