Abinit/Example

As an example for running an Abinit job, we will perform some calculations on a $H_2$ molecule. This requires two files, an input file and a file, which specifies the name of the files created during the job.

[leonhard@euler04 ~]$ ls
test.files  test.in
[leonhard@euler04 ~]$ cat test.in
# H2 molecule in a big box

acell 10 10 10
ntypat 1      
znucl 1        
natom 2       
typat 1 1     
xcart         
              
  -0.7 0.0 0.0
   0.7 0.0 0.0
ecut 10.0     
kptopt 0      
nkpt 1        
nstep 10      
toldfe 1.0d-6 
diemac 2.0    
optforces 1
[leonhard@euler04 ~]$ cat test.files
test.in
test.out
testi
testo
test
/cluster/apps/abinit/7.10.5/x86_64/share/abinit-test/Psps_for_tests/01h.pspgth

After preparing the input file, we need to load the required module for using Abinit 7.10.5 and then we can submit the job.

[leonhard@euler04 ~]$ module load intel/15.0.0 open_mpi/1.6.5 python/2.7.6 abinit/7.10.5
[leonhard@euler04 ~]$ bsub -n 1 -W 0:30 -R "rusage[mem=512]" "abinit < test.files > log"
Generic job.
Job <33703710> is submitted to queue <normal.4h>.
[leonhard@euler04 ~]$ bjobs
JOBID      USER       STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
33703710   leonhard   PEND  normal.4h  euler04                 *les > log Dec  7 16:06
[leonhard@euler04 ~]$ bjobs
JOBID      USER       STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
33703710   leonhard   PEND  normal.4h  euler04                 *les > log Dec  7 16:06
[leonhard@euler04 ~]$ bjobs
No unfinished job found
[leonhard@euler04 ~]$ grep etotal log 
           etotal     -1.1037224213E+00

You can find the resource usage summary of the job in the corresponding LSF log file.