Anik Sen, Pavlin D. Mitev, Anders Eriksson, and Kersti Hermansson,
International Journal of Quantum Chemistry, 116, ( 2016), 67-80
DOI: 10.1002/qua.25022
ASE format database with all structures, Bader and Wannier analysis, and OH stretching frequency published in the article.
$> 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)
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]