ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

7.8.2 Molecules
Example:
$ ase abinit H2 -p ecut=200,xc=LDA -F 5,1 --atomize
ASE Manual, Release 3.6.1.2828
This will calculate the energy of a H2 molecule using Abinit with a planewave cutoff of 200 eV and the LDA
XC-functional. A fit using 5 points and a variation of the bond length from -1 % to +1 % is made and in addition
the energy of a single hydrogen atom is also calculated.
Results are written to json files and can be analysed with:
$ ase abinit H H2 -s
name E E-E0 d0 hnu Ea Ea0
eV eV Ang meV eV eV
H2 -29.703 0.022 0.770 556.096 4.852 4.873
H -12.426
Note: The json files are simple text files that can be more or less’ed or pretty printed with python -m
json.tool H2-molecule-abinit.jon.
7.8.3 Bulk systems
Example:
$ ase bulk Ni Cu Pd Ag Pt Au -F 5,1
Here we used the default EMT potential and the result is:
$ ase bulk Ni Cu Pd Ag Pt Au -s
name E E-E0 V0 B
eV eV Ang^3 GPa
Ni -0.009 0.005 10.600 175.978
Ag 0.002 0.002 16.775 100.151
Pt -0.000 0.000 15.080 278.087
Au 0.003 0.003 16.684 173.868
Pd 0.000 0.001 14.588 179.105
Cu -0.006 0.001 11.565 134.439
More examples
Anti-ferromagnetic bcc iron:
$ ase vasp bulk -x bcc Fe -C -M 2.3,-2.3 -p xc=PBE -k 8,8,8
Bulk silicon (128 atoms, Gamma point only):
$ ase abinit bulk Si -r 4,4,4 -k 1,1,1 -a 5.46
Bulk aluminum in orthorhombic cell with LDA and fixed rmt:
$ ase elk bulk --orthorhombic Al -k 4,4,4 -a 4.05 -p "swidth=0.1,rmt={’Al’: 1.9}"
7.8.4 Batch jobs
Suppose you want to run a large number of similar calculations like relaxing the structure of all the molecules in
the G2-1 database. You could do that by submitting this job to your compute cluster:
7.8. Command line tools 81