Dalton

Please note that this application page is referring to the old CentOS software stack which is obsolete and does not work any more with the new Ubuntu setup. You can find an overview on the Ubuntu software stack on this wiki page.

Category

Chemistry, Quantum chemistry, DFT

Description

The Dalton2016 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, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilites.

Available versions (Euler, old software stack)

Legacy versions	Supported versions	New versions
		2016.1, 2016.1_64

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Environment modules (Euler, old software stack)

Version	Module load command	Additional modules loaded automatically
2016.1	module load new gcc/4.8.2 openblas/0.2.13_seq open_mpi/1.6.5 dalton/2016.1
2016.1_64	module load new gcc/4.8.2 mkl/14.0.1 dalton/2016.1_64

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

How to submit a job

You can submit a Dalton job (test.dal, test.mol) with the following command

sbatch [Slurm options] --wrap="dalton [Dalton options] test"

Here you need to replace [Dalton options] with Dalton command line options and [Slurm options] with Slurm parameters for the resource requirements of the job. Please find a documentation about the parameters of sbatch on the wiki page about the batch system.

Example

As an example for running a Dalton job, we are running a DFT (B3LYP) calculation for a water molecule.

[leonhard@euler07 ~]$ ls
water.dal  water.mol
[leonhard@euler07 ~]$ cat water.dal
**DALTON INPUT
.RUN PROPERTIES
.PARALLEL
**WAVE FUNCTIONS
.DFT
 B3LYP
**END OF DALTON INPUT

[leonhard@euler07 ~]$ cat water.mol
INTGRL
H20
Test including f-functions
C   2    
        8.    1    4    1    1    1    1
O     0.0  0.0000000000          0.0
    4    0    
87.0
18.34
3.23
1.0
    2    0    
3.67
1.0
    1    0    
1.0
    1    0    
1.0
        1.    2    2    1    1
H1    1.430    0.0  1.1
H2   -1.430    0.0  1.1
    2    0 
4.2321
1.22
    1    0   
1.0 

[leonhard@euler07 ~]$ module load new gcc/4.8.2 openblas/0.2.13_seq open_mpi/1.6.5 dalton/2016.1
[leonhard@euler07 ~]$ bsub -n 4 -W 1:00 -R "rusage[mem=2048]" "dalton -N 4 water"
Generic job.
Job <33781881> is submitted to queue <normal.4h>.
[leonhard@euler07 ~]$ bjobs
JOBID      USER       STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
33781881   leonhard   PEND  normal.4h  euler07                 *N 4 water Dec  9 16:30
[leonhard@euler07 ~]$ bjobs
JOBID      USER       STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
33781881   leonhard   RUN   normal.4h  euler07     4*e1090     *N 4 water Dec  9 16:30
[leonhard@euler07 ~]$ bjobs
No unfinished job found
[leonhard@euler07 ~]$ grep -A3 LUMO water.out
    E(LUMO) :     0.90088950 au (symmetry 3)
  - E(HOMO) :     0.14886297 au (symmetry 2)
  ------------------------------------------
    gap     :     0.75202654 au

The resource usage summary of the job is written to the corresponding LSF log file.

License information

Dalton license

Links

http://daltonprogram.org