PyADF — A scripting framework for multiscale quantum chemistry

Jacob, Christoph R.; Beyhan, Selami; Bulo, Rosa E.; Gomes, André Severo Pereira; Götz, Andreas W.; Kiewisch, Karin; Sikkema, Jetze; Visscher, Lucas

doi:10.1002/jcc.21810

Cited by 100 publications

(115 citation statements)

References 56 publications

(74 reference statements)

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“…MolcAs [59] has been used for all wavefunction calculations. WF/DFT calculations are carried out through an interface [60] integrated into the PyAdf scripting framework [61]. The strategy used within that interface corresponds to the splitSCF scheme presented in Ref.…”

Section: Computational Detailsmentioning

confidence: 99%

Part and whole in wavefunction/DFT embedding

Dresselhaus

Neugebauer

2015

Theor Chem Acc

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Section: Computational Detailsmentioning

confidence: 99%

Part and whole in wavefunction/DFT embedding

Dresselhaus

Neugebauer

2015

Theor Chem Acc

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“…72 To allow for the treatment of spin-unrestricted target densities, we extended our recent implementation 31 of the WY direct optimization algorithm and of the subsequent step for singling out an unambiguous optimized potential. 48 The TZ2P and QZ4P Slater-type orbital (STO) basis sets of ADF were used as orbital basis.…”

Section: Computational Methodologymentioning

confidence: 99%

Optimized unrestricted Kohn–Sham potentials from ab initio spin densities

Boguslawski

Jacob

Reiher

2013

The Journal of Chemical Physics

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The reconstruction of the exchange-correlation potential from accurate ab initio electron densities can provide insights into the limitations of the currently available approximate functionals and provide guidance for devising improved approximations for density-functional theory (DFT). For openshell systems, the spin density is introduced as an additional fundamental variable in spin-DFT. Here, we consider the reconstruction of the corresponding unrestricted Kohn-Sham (KS) potentials from accurate ab initio spin densities. In particular, we investigate whether it is possible to reconstruct the spin exchange-correlation potential, which determines the spin density in unrestricted KS-DFT, despite the numerical difficulties inherent to the optimization of potentials with finite orbital basis sets. We find that the recently developed scheme for unambiguously singling out an optimal optimized potential [Ch. R. Jacob, J. Chem. Phys. 135, 244102 (2011)] can provide such spin potentials accurately. This is demonstrated for two test cases, the lithium atom and the dioxygen molecule, and target (spin) densities from full configuration interaction and complete active space self-consistent field calculations, respectively.

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“…An initial surface charge distribution was always determined from the MFCC density. Most of the calculations were set up with the PyAdf framework [58], which uses OpenBabel routines [59,60].…”

Section: Quantum-chemical Calculationsmentioning

confidence: 99%

Including protein density relaxation effects in first-principles embedding calculations of cofactor excitation energies

Goez

Neugebauer

2016

Molecular Physics

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The Three-Partition Frozen Density Embedding (3-FDE) method is applied to the photosynthetic Fenna-Matthews-Olson (FMO) complex of green sulphur bacteria in order to determine cofactor excitation energies. We present a sophisticated multi-layer embedding protocol, which allows to choose fragments of arbitrary size. This is useful in order to limit the total number of calculations, which can create a significant overhead. The approach allows to determine fully polarised densities for realistic proteins in this framework for the first time. A solvent shell around the total system is described in terms of the LoCOSMO algorithm, which tremendously simplifies the computational effort of a continuum description around a system of this size. The solvent response to the excitation is incorporated by a new extension of the LoCOSMO scheme to time-dependent density functional theory. Excitation energies for the chromophores are calculated under the influence of density-based embedding potentials obtained with different technical settings. It is found that protein density relaxation in this particular example hardly influences the transitions, indicating that embedding of the pigments in the initial protein density is sufficient to determine site energy modulations with our approach.

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PyADF — A scripting framework for multiscale quantum chemistry

Cited by 100 publications

References 56 publications

Part and whole in wavefunction/DFT embedding

Part and whole in wavefunction/DFT embedding

Optimized unrestricted Kohn–Sham potentials from ab initio spin densities

Including protein density relaxation effects in first-principles embedding calculations of cofactor excitation energies

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