Description:
pyvdw 0.1.0
vdw (my naïve wrapper of existing vDW packages for PySCF)
This package is my naïve wrapper of various existing vDW libraries for PySCF. Should be able to evaluate energy or force
(gradient) of van der Waals correction to density functional methods.
This package is not aimed to be a pyscf extension module. It's just a wrapper.
Install
To install this package, you may download from pypi:
pip install pyvdw
To use DFTD3, DFTD4, or TS-vDW (from libmbd) or MBD methods, you may also manually install those libraries.
This package is only an interface to those existing libraries.
conda install simple-dftd3 dftd3-python dftd4 dftd4-python libmbd
pip install pyscf, pymbd
I know that leaving the task of dependency packages installation to user is really inconvenient, but currently
I don't know how to handle conda, pip and advanced packaging elegently. So if any pratical ideas on this, raise
your issue >w<
Included vDW models
DFTD3
Package: simple-dftd3, https://github.com/awvwgk/simple-dftd3
Usage:
from pyscf import gto, dft
from vdw import to_dftd3
mol = gto.Mole(atom="O; H 1 0.94; H 1 0.94 2 104.5", basis="cc-pVDZ").build()
# Modified/Revisited BJ/Rational damping
mf = to_dftd3(dft.RKS(mol, xc="PBE"), version="bjm").run()
print(mf.e_vdw) # -0.000347885
Versions and Citations:
For any version of DFTD3, please first cite 10.1063/1.3382344. This is not formal citation recommendation,
thus refer to original site DFTD3
and package simple-dftd3 for formal citation guide.
Original DFTD3 (version = "zero"):
Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. J. Chem. Phys. 2010, 132 (15), 154104.
https://doi.org/10.1063/1.3382344.
Goerigk, L.; Hansen, A.; Bauer, C.; Ehrlich, S.; Najibi, A.; Grimme, S.
Phys. Chem. Chem. Phys. 2017, 19 (48), 32184–32215. https://doi.org/10.1039/C7CP04913G.
BJ/Rational damping (version = "bj", which is default):
Grimme, S.; Ehrlich, S.; Goerigk, L. J. Comput. Chem. 2011, 32 (7), 1456–1465.
https://doi.org/10.1002/jcc.21759.
Modified zero damping and BJ damping (version = "zerom" or "bjm"):
Smith, D. G. A.; Burns, L. A.; Patkowski, K.; Sherrill, C. D.
J. Phys. Chem. Lett. 2016, 7 (12), 2197–2203. https://doi.org/10.1021/acs.jpclett.6b00780.
Optimized Power (version = "op"):
Witte, J.; Mardirossian, N.; Neaton, J. B.; Head-Gordon, M.
J. Chem. Theory Comput. 2017, 13 (5), 2043–2052. https://doi.org/10.1021/acs.jctc.7b00176.
DFTD4
Package: dftd4, https://github.com/dftd4/dftd4
Usage:
from pyscf import gto, dft
from vdw import to_dftd4
mol = gto.Mole(atom="O; H 1 0.94; H 1 0.94 2 104.5", basis="cc-pVDZ").build()
# DFTD4 default bj-eeq-atm version
mf = to_dftd4(dft.RKS(mol, xc="PBE")).run()
print(mf.e_vdw) # -0.000192782
Citations:
For any version of DFTD4, please first cite 10.1063/1.5090222. This is not formal citation recommendation,
thus refer to package dftd4 for formal citation guide.
Original DFTD4:
Caldeweyher, E.; Ehlert, S.; Hansen, A.; Neugebauer, H.; Spicher, S.; Bannwarth, C.; Grimme, S.
J. Chem. Phys. 2019, 150 (15), 154122. https://doi.org/10.1063/1.5090222.
Newly SCAN related functionals:
Ehlert, S.; Huniar, U.; Ning, J.; Furness, J. W.; Sun, J.; Kaplan, A. D.; Perdew, J. P.; Brandenburg, J. G.
J. Chem. Phys. 2021, 154 (6), 061101. https://doi.org/10.1063/5.0041008.
Bursch, M.; Neugebauer, H.; Ehlert, S.; Grimme, S.
J. Chem. Phys. 2022, 156 (13), 134105. https://doi.org/10.1063/5.0086040.
Doubly hybrid functionals:
Santra, G.; Sylvetsky, N.; Martin, J. M. L.
J. Phys. Chem. A 2019, 123 (24), 5129–5143. https://doi.org/10.1021/acs.jpca.9b03157.
TS and MBD
Package: libmbd, https://github.com/libmbd/libmbd
Usage:
from pyscf import gto, dft
from vdw import to_mbd
mol = gto.Mole(atom="""
O 0. 0. 0.
H 0. 0. 1.
H 0. 1. 0.
O 0. 0. 2.
H 0. 0. 3.
H 0. 1. 2.""", basis="cc-pVDZ").build()
# Tkatchenko-Scheffler
mf = to_mbd(dft.RKS(mol, xc="PBE"), variant="ts").run()
print(mf.e_vdw) # -0.000212847
# MBD@rsSCS
mf = to_mbd(dft.RKS(mol, xc="PBE"), variant="rsscs").run()
print(mf.e_vdw) # -0.001245831
Notice
To calculate MBD or TS-vDW, free atomic volume is required. This is calculated, instead of preloaded,
using basis set aug-cc-pVQZ. Value of this volume may be close to FHI-aims and Quantum Espresso. However,
this calculation is relatively costly if your molecule and basis set is not large. Basis set error also
occurs (where FHI-aims give free folume by highly efficient numerical radial Schrödinger equation).
Citations:
This is not formal citation recommendation
TS (Tkatchenko-Scheffler)
Tkatchenko, A.; Scheffler, M.
Phys. Rev. Lett. 2009, 102 (7), 073005. https://doi.org/10.1103/PhysRevLett.102.073005.
MBD (Many-Body Dispersion)
Tkatchenko, A.; DiStasio, R. A.; Car, R.; Scheffler, M.
Phys. Rev. Lett. 2012, 108 (23), 236402. https://doi.org/10.1103/PhysRevLett.108.236402.
Ambrosetti, A.; Reilly, A. M.; DiStasio, R. A.; Tkatchenko, A.
J. Chem. Phys. 2014, 140 (18), 18A508. https://doi.org/10.1063/1.4865104.
More Examples
Refer to example folder for more examples.
Code Sources
This package uses or modifies existing codes.
Hirshfeld analysis utilizes atomic spherically averaged DFT pyscf/pyscf #1143.
Wrapper code utilizes pyscf/dftd3.
Functional default parameters of TS-vDW and MBD are from libmbd/libmbd.
The author is aware of previous efforts to implement vDW for PySCF, such as pyscf/dftd3
and pyscf/mbd. However, due to my own requirement for usage and API convenience, as well
as my need to use TS-vDW, this simple hundreds-lines-of-code tiny package is built from existing various libraries.
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
Files:
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