Introduction

Le noyau de la suite logicielle Dalton2016 est constitué de deux puissantes applications pour l'étude des structures électroniques de molécules : Dalton et LSDalton. Ensemble, ces applications offrent des fonctionnalités étendues pour le calcul des propriétés moléculaires aux niveaux théoriques HF, DFT, MCSCF et CC. Plusieurs de ses propriétés sont uniques à la suite Dalton2016.

site web du projet : http://daltonprogram.org/
documentation : http://daltonprogram.org/documentation/
forum : http://forum.daltonprogram.org/

Modules

$ module load nixpkgs/16.09 intel/2016.4 openmpi/2.0.2 dalton/2017-alpha

Remarquez que dalton/2017-alpha dépend d’une version OpenMPI autre que la version par défaut. Pour de l’information sur la commande module voyez Utiliser des modules.

Utilisation

Voici un exemple ː

fichier d'entrée : dft_rspexci_nosym.dal (voir les exemples ci-dessous)
spécification de la molécule : H2O_cc-pVDZ_nosym.mol (voir les exemples ci-dessous)
To use the atomic basis set installed with the program, supply the option -b ${BASLIB}.
pour définir le nombre de processus avec une option en ligne de commande ou une variable d’environnement :
- ajoutez l’option -N ${SLURM_NTASKS} en ligne de commande pour le lanceur (voir Script 1 dans les exemples ci-dessous)
- ou export DALTON_NUM_MPI_PROCS=${SLURM_NTASKS} (voir Script 2 dans les exemples ci-dessous).

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

Example 1: dft_rspexci_nosym

INPUTMOLECULEScript 1Script 2

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

INPUTMOLECULEScript 1Script 2

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`"