Uppsala University, Department of Chemistry – Ångström Laboratory

Anik Sen, Pavlin D. Mitev, Anders Eriksson, and Kersti Hermansson,
International Journal of Quantum Chemistry
116, ( 2016), 67-80
DOI10.1002/qua.25022

ASE format database with all structures, Bader and Wannier analysis, and OH stretching frequency published in the article.

Download

$> ase db IJQC.116.db -c id,name,method,pbc,charge,volume,energy
id|name         |method|pbc|charge|  volume|  energy
 1|Al(NO3)3.9H2O|PBE-D2|TTT| 0.000|1421.939|-882.352
 2|MgSO4.11H2O  |PBE-D2|TTT| 0.000| 680.318|-405.280
 3|MgSO4.7H2O   |PBE-D2|TTT| 0.000| 933.902|-571.405
 4|Na2CO3.10H2O |PBE-D2|TTT| 0.000|1219.089|-752.414

You can use web browser to look on common prperties

$> ase db IJQC.116.db -w
 * Running on http://0.0.0.0:5000/ (Press CTRL+C to quit)

 

Here is a new version of the tools, rewritten in Python3 and Jupyter Notebooks. (Link to the old version)

ASE-db-tools

The package contains:

  • ASE-db-tools.py module.
  • Jupyter Python3 Notebook with an example how to  extract and calculate properties from the database.
  • Jupyter Python3 Notebook with an example how to  build the database.
  • IJQC.116.db – the database itself.
  • Complete outputs for the four systems.

Look on the complete output from the notebook for the case of Al(NO3)3.9H2O.

Dependencies:

  • Python3
  • ase-3.15.0+
  • pymatgen

Command line interface:

./ASE_db_tools.py -h
usage: ASE_db_tools.py [-h] [-id]
                       (--add-VASP-tructure | --add-VASP-bader | --add-VASP-wannier | --add-VASP-DDEC6 | --add-symmetry | --add-OH-PES | --add-DVR-results | --prop-H2O-bader-dipoles | --prop-H2O-wannier-dipoles | --prop-H2O-DDEC6-dipoles | --EF-H2O-bader | --EF-H2O-wannier | --EF-H2O-DDEC6)
                       [-d] [-f] [-l] [-i] [-s] [-chg] [-v]
                       dbname

ASE database tools

positional arguments:
  dbname                database name

optional arguments:
  -h, --help            show this help message and exit
  -id                   number of the row in the database
  --add-VASP-tructure   Add VASP structre to the database
  --add-VASP-bader      Add VASP Bader calculation results to the database
  --add-VASP-wannier    Add VASP Wannier calculation results to the database
  --add-VASP-DDEC6      Add VASP DDEC6 calculation results to the database
  --add-symmetry        Find and add symmetry for the structure in the
                        database
  --add-OH-PES          Add OH stretch PES in the database
  --add-DVR-results     Add DVR results for the sytructure in the database
  --prop-H2O-bader-dipoles
                        Calculate H2O Bader dipoles for the structure in the
                        database
  --prop-H2O-wannier-dipoles
                        Calculate H2O Wannier dipoles for the structure in the
                        database
  --prop-H2O-DDEC6-dipoles
                        Calculate H2O DDEC6 dipoles for the structure in the
                        database
  --EF-H2O-bader        Calculate Bader EF at H positions for H2O molecules
                        for the structure in the database
  --EF-H2O-wannier      Calculate Wannier EF at H positions for H2O molecules
                        for the structure in the database
  --EF-H2O-DDEC6        Calculate DDEC6 EF at H positions for H2O molecules
                        for the structure in the database
  -d , --directory      Specify folder input
  -f , --file           Specify file input
  -l , --label          Specify label input
  -i , --index          Specify index input
  -s , --symprec        Specify symmetry precision input
  -chg , --core_charges 
                        Specify core_charges in json format. '{ "H" : 1.0 ,
                        "O" : 6.0 }'
  -v, --verbose         Verbose output

Example:

$ ./ASE_db_tools.py IJQC.116.db -id 1 --prop-H2O-wannier-dipoles --core_charges '{"H" : 1, "O": 6 , "W": -2 , "Al": 3 , "N": 5}' | head
  Origin at atom idx: 88  core_charge: 6
============================================
idx:  213   Chg:   -2   dist: 0.478127
idx:  286   Chg:   -2   dist: 0.293650
idx:    5   Chg:    1   dist: 1.000710
idx:  302   Chg:   -2   dist: 0.479148
idx:  337   Chg:   -2   dist: 0.359560
idx:    4   Chg:    1   dist: 0.999393
============================================
  Total Dipole= 3.9117 [Debye]