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Daniel Sanchezportal - One of the best experts on this subject based on the ideXlab platform.
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toward efficient gw calculationsusing numerical Atomic Orbitals benchmarking and application to moleculardynamics simulations
Journal of Chemical Theory and Computation, 2019Co-Authors: Peter Koval, Daniel Sanchezportal, Mathias P Ljungberg, Moritz MullerAbstract:The use of Atomic Orbitals in Hedin’s GW approximation provides, in principle, an inexpensive alternative to plane-wave basis sets, especially when modeling large molecules. However, benchmarking of the algorithms and basis sets is essential for a careful balance between cost and accuracy. In this paper, we present an implementation of the GW approximation using numerical Atomic Orbitals and a pseudopotential treatment of core electrons. The combination of a contour deformation technique with a one-shot extraction of quasiparticle energies provides an efficient scheme for many applications. The performance of the implementation with respect to the basis set convergence and the effect of the use of pseudopotentials has been tested for the 117 closed-shell molecules from the G2/97 test set and 24 larger acceptor molecules from another recently proposed test set. Moreover, to demonstrate the potential of our method, we compute the thermally averaged GW density of states of a large photochromic compound by sa...
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toward efficient gw calculations using numerical Atomic Orbitals benchmarking and application to molecular dynamics simulations
Journal of Chemical Theory and Computation, 2019Co-Authors: Peter Koval, Daniel Sanchezportal, Mathias P Ljungberg, Moritz MullerAbstract:The use of Atomic Orbitals in Hedin’s GW approximation provides, in principle, an inexpensive alternative to plane-wave basis sets, especially when modeling large molecules. However, benchmarking o...
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pyscf nao an efficient and flexible implementation of linear response time dependent density functional theory with numerical Atomic Orbitals
Computer Physics Communications, 2019Co-Authors: Marc Barbry, Daniel Sanchezportal, Peter KovalAbstract:Abstract We present an algorithm and its implementation to calculate the propertiesof electronic excitations in molecules and clusters from first principles, using time-dependent density functional theory (TDDFT). The algorithm assumes the use of some localized functions as a basis set to represent the spatial degrees of freedom. It relies on an iterative computation of the induced density according to the Dyson-like equation for the linear response function. The current implementation is built upon so-called numerical Atomic Orbitals. It is suitable for a wide variety of density functional theory (DFT) software. In this work, we demonstrate TDDFT calculations starting from preceding DFT runs with SIESTA , GPAW and PySCF packages, while a coupling with the other DFT packages such as Fireball and OpenMX is planned. The mentioned packages are capable of performing ab initio molecular dynamics simulations, and the speed of our TDDFT implementation makes feasible to perform a configuration average of the optical absorption spectra. Our code is written mostly in Python language allowing for a quick and compact implementation of most numerical methods and data-managing tasks with the help of NumPy/SciPy libraries and Python intrinsic constructs. Part of the code is written in C and Fortran to achieve a competitive speed in particular sections of the algorithm. Many parts of the current algorithm and implementation are useful in other ab initio methods for electronic excited states, such as Hedin’s G W , Bethe–Salpeter equation and DFT with hybrid functionals. Corresponding proof-of-principles implementations are already part of the code. Program summary Program Title: PySCF-NAO Program Files doi: http://dx.doi.org/10.17632/9wgp6255hn.1 Licensing provisions: Apache License, Version 2.0 Programming language: Python (2 or 3), Fortran90 and C Supplementary material: We provide the source code and input files to organize example and benchmark calculations discussed in the paper. Nature of the problem: The study of the interaction of photons and charged particles with matter depends upon understanding of electronic excitations in matter. A description of the electronic excitations within time-dependent density functional theory (TDDFT) is popular due to the combination of its reasonable accuracy and its relatively low computational cost. Despite the relative simplicity of TDDFT, its application becomes difficult for quantum systems containing several hundreds of atoms. Such microscopically small systems are relevant in organic electronics, plasmonics and surface science. Therefore, much work has been devoted to the development of adequate electronic structure methods. Moreover, thermal motion of atoms and the presence of solvents affects the properties of electronic excited states in a decisive manner. Modeling of the electronic excited states including the system’s dynamics within the Born–Oppenheimer approximation leads to even stronger efficiency requirements from the corresponding electronic structure methods. Solution method: We discretize the Kohn–Sham Hamiltonian using a basis of numerical Atomic Orbitals. The induced electronic density is determined in response to a dipolar external perturbation, according to linear response TDDFT, using an iterative algorithm. The method takes advantage of the sparsity generated by the finite support of the numerical Atomic Orbitals. This allows computing the dynamical polarizability of molecules and clusters containing up to several thousands of atoms. Additional comments including Restrictions and Unusual features: The current algorithm is formulated within the formalism of density response functions. Therefore, one needs to know explicitly an exchange–correlation kernel (second-derivative of energy with respect to variation of the density). The exchange–correlation kernel is analytically known for (semi-)local density functionals, but not for the hybrid density functionals. To date, we implemented only the local density approximation (LDA) for the exchange–correlation kernel to be used with the iterative TDDFT in PySCF-NAO . Spin-restricted formalism for finite systems is covered in the current implementation. Moreover, although our code is prepared to compute the electronic response of all-electron systems, our current implementation of an auxiliary product basis (density-fitting basis) is working best in combination with the use of pseudopotentials.
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projection of plane wave calculations into Atomic Orbitals
arXiv: Condensed Matter, 1995Co-Authors: Daniel Sanchezportal, Emilio Artacho, Jose M SolerAbstract:The projection of the eigenfunctions obtained in standard plane-wave first-principle electronic-structure calculations into Atomic-orbital basis sets is proposed as a formal and practical link between the methods based on plane waves and the ones based on Atomic Orbitals. Given a candidate Atomic basis, ({\it i}) its quality is evaluated by its projection into the plane-wave eigenfunctions, ({\it ii}) it is optimized by maximizing that projection, ({\it iii}) the associated tight-binding Hamiltonian and energy bands are obtained, and ({\it iv}) population analysis is performed in a natural way. The proposed method replaces the traditional trial-and-error procedures of finding appropriate Atomic bases and the fitting of bands to obtain tight-binding Hamiltonians. Test calculations of some zincblende semiconductors are presented.
Peter Koval - One of the best experts on this subject based on the ideXlab platform.
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toward efficient gw calculations using numerical Atomic Orbitals benchmarking and application to molecular dynamics simulations
Journal of Chemical Theory and Computation, 2019Co-Authors: Peter Koval, Daniel Sanchezportal, Mathias P Ljungberg, Moritz MullerAbstract:The use of Atomic Orbitals in Hedin’s GW approximation provides, in principle, an inexpensive alternative to plane-wave basis sets, especially when modeling large molecules. However, benchmarking o...
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toward efficient gw calculationsusing numerical Atomic Orbitals benchmarking and application to moleculardynamics simulations
Journal of Chemical Theory and Computation, 2019Co-Authors: Peter Koval, Daniel Sanchezportal, Mathias P Ljungberg, Moritz MullerAbstract:The use of Atomic Orbitals in Hedin’s GW approximation provides, in principle, an inexpensive alternative to plane-wave basis sets, especially when modeling large molecules. However, benchmarking of the algorithms and basis sets is essential for a careful balance between cost and accuracy. In this paper, we present an implementation of the GW approximation using numerical Atomic Orbitals and a pseudopotential treatment of core electrons. The combination of a contour deformation technique with a one-shot extraction of quasiparticle energies provides an efficient scheme for many applications. The performance of the implementation with respect to the basis set convergence and the effect of the use of pseudopotentials has been tested for the 117 closed-shell molecules from the G2/97 test set and 24 larger acceptor molecules from another recently proposed test set. Moreover, to demonstrate the potential of our method, we compute the thermally averaged GW density of states of a large photochromic compound by sa...
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pyscf nao an efficient and flexible implementation of linear response time dependent density functional theory with numerical Atomic Orbitals
Computer Physics Communications, 2019Co-Authors: Marc Barbry, Daniel Sanchezportal, Peter KovalAbstract:Abstract We present an algorithm and its implementation to calculate the propertiesof electronic excitations in molecules and clusters from first principles, using time-dependent density functional theory (TDDFT). The algorithm assumes the use of some localized functions as a basis set to represent the spatial degrees of freedom. It relies on an iterative computation of the induced density according to the Dyson-like equation for the linear response function. The current implementation is built upon so-called numerical Atomic Orbitals. It is suitable for a wide variety of density functional theory (DFT) software. In this work, we demonstrate TDDFT calculations starting from preceding DFT runs with SIESTA , GPAW and PySCF packages, while a coupling with the other DFT packages such as Fireball and OpenMX is planned. The mentioned packages are capable of performing ab initio molecular dynamics simulations, and the speed of our TDDFT implementation makes feasible to perform a configuration average of the optical absorption spectra. Our code is written mostly in Python language allowing for a quick and compact implementation of most numerical methods and data-managing tasks with the help of NumPy/SciPy libraries and Python intrinsic constructs. Part of the code is written in C and Fortran to achieve a competitive speed in particular sections of the algorithm. Many parts of the current algorithm and implementation are useful in other ab initio methods for electronic excited states, such as Hedin’s G W , Bethe–Salpeter equation and DFT with hybrid functionals. Corresponding proof-of-principles implementations are already part of the code. Program summary Program Title: PySCF-NAO Program Files doi: http://dx.doi.org/10.17632/9wgp6255hn.1 Licensing provisions: Apache License, Version 2.0 Programming language: Python (2 or 3), Fortran90 and C Supplementary material: We provide the source code and input files to organize example and benchmark calculations discussed in the paper. Nature of the problem: The study of the interaction of photons and charged particles with matter depends upon understanding of electronic excitations in matter. A description of the electronic excitations within time-dependent density functional theory (TDDFT) is popular due to the combination of its reasonable accuracy and its relatively low computational cost. Despite the relative simplicity of TDDFT, its application becomes difficult for quantum systems containing several hundreds of atoms. Such microscopically small systems are relevant in organic electronics, plasmonics and surface science. Therefore, much work has been devoted to the development of adequate electronic structure methods. Moreover, thermal motion of atoms and the presence of solvents affects the properties of electronic excited states in a decisive manner. Modeling of the electronic excited states including the system’s dynamics within the Born–Oppenheimer approximation leads to even stronger efficiency requirements from the corresponding electronic structure methods. Solution method: We discretize the Kohn–Sham Hamiltonian using a basis of numerical Atomic Orbitals. The induced electronic density is determined in response to a dipolar external perturbation, according to linear response TDDFT, using an iterative algorithm. The method takes advantage of the sparsity generated by the finite support of the numerical Atomic Orbitals. This allows computing the dynamical polarizability of molecules and clusters containing up to several thousands of atoms. Additional comments including Restrictions and Unusual features: The current algorithm is formulated within the formalism of density response functions. Therefore, one needs to know explicitly an exchange–correlation kernel (second-derivative of energy with respect to variation of the density). The exchange–correlation kernel is analytically known for (semi-)local density functionals, but not for the hybrid density functionals. To date, we implemented only the local density approximation (LDA) for the exchange–correlation kernel to be used with the iterative TDDFT in PySCF-NAO . Spin-restricted formalism for finite systems is covered in the current implementation. Moreover, although our code is prepared to compute the electronic response of all-electron systems, our current implementation of an auxiliary product basis (density-fitting basis) is working best in combination with the use of pseudopotentials.
Klaus Ruedenberg - One of the best experts on this subject based on the ideXlab platform.
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identification and characterization of molecular bonding structures by ab initio quasi Atomic orbital analyses
Journal of Physical Chemistry A, 2017Co-Authors: Aaron C West, Mark S. Gordon, Juan J Duchimazaheredia, Klaus RuedenbergAbstract:The quasi-Atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-Atomic Orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-Atomic Orbitals are the rigorous ab initio counterparts to the conceptual bond forming Atomic hybrid Orbitals of qualitative chemical reasoning. In the present work, the quasi-Atomic Orbitals are identified as bonding Orbitals, lone pair Orbitals, radical Orbitals, vacant Orbitals and Orbitals with intermediate character. A program determines the bonding characteristics of all quasi-Atomic Orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules...
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relativistic ab initio accurate Atomic minimal basis sets quantitative lumos and oriented quasi Atomic Orbitals for the elements li xe
Journal of Physical Chemistry A, 2017Co-Authors: George Schoendorff, Aaron C West, Michael W Schmidt, Klaus Ruedenberg, Angela K Wilson, Mark S. GordonAbstract:Valence virtual Orbitals (VVOs) are a quantitative and basis set independent method for extracting chemically meaningful lowest unoccupied molecular Orbitals (LUMOs). The VVOs are formed based on a singular value decomposition (SVD) with respect to precomputed and internally stored ab initio accurate Atomic minimal basis sets (AAMBS) for the atoms. The occupied molecular Orbitals and VVOs together form a minimal basis set that can be transformed into orthogonal oriented quasi-Atomic Orbitals (OQUAOs) that provide a quantitative description of the bonding in a molecular environment. In the present work, relativistic AAMBS are developed that span the full valence orbital space. The impact of using full valence AAMBS for the formation of the VVOs and OQUAOs and the resulting bonding analysis is demonstrated with applications to the cuprous chloride, scandium monofluoride, and nickel silicide diAtomic molecules.
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a comprehensive analysis in terms of molecule intrinsic quasi Atomic Orbitals iv bond breaking and bond forming along the dissociative reaction path of dioxetane
Journal of Physical Chemistry A, 2015Co-Authors: Aaron C West, Mark S. Gordon, Michael W Schmidt, Klaus RuedenbergAbstract:The quantitative analysis of molecular density matrices in terms of oriented quasi-Atomic Orbitals (QUAOs) is shown to yield detailed conceptual insight into the dissociation of dioxetane on the basis of ab initio wave functions. The QUAOs persist and can be followed throughout the reaction path. The kinetic bond orders and the orbital populations of the QUAOs quantitatively reveal the changes of the bonding interactions along the reaction path. At the transition state the OO bond is broken, and the molecule becomes a biradical. After the transition state the reaction path bifurcates. The minimum energy path gently descends from the transition state via a valley-ridge inflection point to a second saddle point, from which two new minimum energy paths lead to two equivalent formaldehyde dimers. The CC bond breaks, and the π-bonds of the formaldehyde fragments form in close vicinity of the second saddle point. The changes of the interactions in this region are elucidated by the analysis of the rearrangements of the QUAOs.
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a comprehensive analysis in terms of molecule intrinsic quasi Atomic Orbitals iii the covalent bonding structure of urea
Journal of Physical Chemistry A, 2015Co-Authors: Aaron C West, Mark S. Gordon, Michael W Schmidt, Klaus RuedenbergAbstract:The analysis of molecular electron density matrices in terms of quasi-Atomic Orbitals, which was developed in previous investigations, is quantitatively exemplified by a detailed application to the urea molecule. The analysis is found to identify strong and weak covalent bonding interactions as well as intramolecular charge transfers. It yields a qualitative as well as quantitative ab initio description of the bonding structure of this molecule, which raises questions regarding some traditional rationalizations.
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a comprehensive analysis in terms of molecule intrinsic quasi Atomic Orbitals ii strongly correlated mcscf wave functions
Journal of Physical Chemistry A, 2015Co-Authors: Aaron C West, Mark S. Gordon, Michael W Schmidt, Klaus RuedenbergAbstract:A methodology is developed for the quantitative identification of the quasi-Atomic Orbitals that are embedded in a strongly correlated molecular wave function. The wave function is presumed to be generated from configurations in an internal orbital space whose dimension is equal to (or slightly larger) than that of the molecular minimal basis set. The quasi-Atomic Orbitals are found to have large overlaps with corresponding Orbitals on the free atoms. They separate into bonding and nonbonding Orbitals. From the bonding quasi-Atomic Orbitals, localized bonding and antibonding molecular Orbitals are formed. The resolution of molecular density matrices in terms of these Orbitals furnishes a basis for analyzing the interAtomic bonding patterns in molecules and the changes in these bonding patterns along reaction paths. A new bond strength measure, the kinetic bond order, is introduced.
Tom Ziegler - One of the best experts on this subject based on the ideXlab platform.
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a theoretical study of 31p and 95mo nmr chemical shifts in m co 5pr3 m cr mo r h ch3 c6h5 f and cl based on density functional theory and gauge including Atomic Orbitals
Journal of Physical Chemistry A, 1998Co-Authors: Yosadara Ruizmorales, Tom ZieglerAbstract:A theoretical study has been carried out on 31P NMR chemical shifts in the phosphine-substituted metal carbonyls of the type M(CO)5PR3 (M = Cr and Mo; R = H, CH3, C6H5, F, and Cl) as well as the 95Mo NMR chemical shift of Mo(CO)5P(C6H5)3 and Mo(CO)5PX3 (X = F and Cl). The study was based on density functional theory (DFT) and gauge-including Atomic Orbitals (GIAO). The calculated chemical shifts and the components of the chemical shift tensor are in good agreement with the available experimental data. The coordination chemical shift expressed as the difference in the isotropic shifts Δδ = δΜ(CO)5PR3 − δPR3 between PR3 as a ligand, δM(CO)5PR3, and free PR3, was analyzed in detail. It was shown that the paramagnetic coupling between the π Orbitals of the complexed PR3 ligand πPR3 and the dσ metal-based LUMO of the M(CO)5PR3 complex has a positive contribution to the coordination chemical shift, Δδ, whereas the paramagnetic couplings between σPR3 and π*PR3 as well as πPR3 and π*PR3 of the complexed ligand ha...
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calculation of the g tensor of electron paramagnetic resonance spectroscopy using gauge including Atomic Orbitals and density functional theory
Journal of Physical Chemistry A, 1997Co-Authors: Tom ZieglerAbstract:An implementation of the g-tensor of electron paramagnetic resonance (EPR) spectroscopy is presented. This implementation is based on density functional theory (DFT) and the use of gauge-including Atomic Orbitals (GIAO). Contributions from the spin−other-orbit operators are neglected, while all the other relevant perturbation operators are included. The new method is an extension of an existing DFT−GIAO program package for the calculation of the chemical shift of nuclear magnetic resonance spectroscopy; full use is made of the conceptual analogy between the g-tensor and the chemical shift. The new program is applied to various small radicals. The agreement of calculated and experimental g-tensors is good for radicals of first-row elements; experimental trends are generally well reproduced. The quality of calculated results is worse if the scheme is applied to compounds of heavier elements. Possible reasons for these apparent shortcomings of the method are discussed.
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calculation of the g tensor of electron paramagnetic resonance spectroscopy using gauge including Atomic Orbitals and density functional theory
Journal of Physical Chemistry A, 1997Co-Authors: Georg Schreckenbach, Tom ZieglerAbstract:An implementation of the g-tensor of electron paramagnetic resonance (EPR) spectroscopy is presented. This implementation is based on density functional theory (DFT) and the use of gauge-including Atomic Orbitals (GIAO). Contributions from the spin−other-orbit operators are neglected, while all the other relevant perturbation operators are included. The new method is an extension of an existing DFT−GIAO program package for the calculation of the chemical shift of nuclear magnetic resonance spectroscopy; full use is made of the conceptual analogy between the g-tensor and the chemical shift. The new program is applied to various small radicals. The agreement of calculated and experimental g-tensors is good for radicals of first-row elements; experimental trends are generally well reproduced. The quality of calculated results is worse if the scheme is applied to compounds of heavier elements. Possible reasons for these apparent shortcomings of the method are discussed.
Trygve Helgaker - One of the best experts on this subject based on the ideXlab platform.
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relativistic four component calculations of buckingham birefringence using london Atomic Orbitals
Theoretical Chemistry Accounts, 2011Co-Authors: Radovan Bast, Antonio Rizzo, Kenneth Ruud, Trygve HelgakerAbstract:We present the first relativistic study of the electric-field-gradient induced birefringence (Buckingham birefringence), with application to the series of molecules CX2 (X = O, S, Se, Te). A recently developed Atomic-orbital-driven scheme for the calculation of time-dependent molecular properties using one-, two- and four-component relativistic wave functions (Bast et al. in Chem Phys 356:177, 2009) is extended to first-order frequency-dependent magnetic-field perturbations, using London Atomic Orbitals to ensure gauge-origin independent results and to improve basis-set convergence. Calculations are presented at the Hartree–Fock and Kohn–Sham levels of theory and results for CO2 and CS2 are compared with previous high-level coupled-cluster calculations. Except for the heaviest member of the series, relativistic effects are small—in particular for the temperature-independent contribution to the birefringence. By contrast, the effects of electron correlation are significant. However, the reliability of standard exchange-correlation functionals in describing Buckingham birefringence remains unclear based on the comparison with high-level coupled-cluster singles-and-doubles calculations.
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perturbation dependent Atomic Orbitals for the calculation of spin rotation constants and rotational g tensors
Journal of Chemical Physics, 1996Co-Authors: Jurgen Gauss, Kenneth Ruud, Trygve HelgakerAbstract:Spin‐rotation constants and rotational g tensors can be evaluated as second derivatives of the energy with respect to the rotational angular momentum and nuclear spin or angular momentum and external magnetic field, respectively. To overcome problems with the slow basis set convergence and the unphysical (gauge‐)origin dependence in quantum chemical calculations of these two properties, we suggest the use of perturbation dependent Atomic Orbitals (rotational London Orbitals), which depend explicitly on the angular momentum and the external magnetic field and are a generalization of the conventional London Orbitals (also known as gauge‐including Atomic Orbitals). It is shown that calculations of spin‐rotation constants and rotational g tensors based on rotational London Orbitals are closely related to London‐orbital computations of nuclear shieldings and magnetizabilities. Test calculations at the Hartree–Fock self‐consistent‐field level for HF, N2, CO, and CH2O demonstrate the superior convergence to the basis set limit provided by the rotational London Orbitals. They suggest that future calculations employing rotational London Orbitals in conjunction with highly correlated wave functions will be able to provide results of unprecedented accuracy for spin‐rotation constants and rotational g tensors.
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Multiconfigurational self-consistent field calculations of nuclear shieldings using London Atomic Orbitals
The Journal of Chemical Physics, 1994Co-Authors: Kenneth Ruud, Trygve Helgaker, Rgensen, Rika Kobayashi, Keld L. Bak, Rgen Aa. JensenAbstract:Nuclear shielding calculations are presented for multiconfigurational self‐consistent field wave functions using London Atomic Orbitals (gauge invariant Atomic Orbitals). Calculations of nuclear shieldings for eight molecules (H2O, H2S, CH4, N2, CO, HF, F2, and SO2) are presented and compared to corresponding individual gauges for localized Orbitals (IGLO) results. The London results show better basis set convergence than IGLO, especially for heavier atoms. It is shown that the choice of active space is crucial for determination of accurate nuclear shielding constants.
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vibrational raman optical activity calculations using london Atomic Orbitals
Faraday Discussions, 1994Co-Authors: Trygve Helgaker, Kenneth Ruud, Keld L. Bak, Poul Jorgensen, Jeppe OlsenAbstract:Ab initio calculations of Raman differential intensities are presented at the self-consistent field (SCF) level of theory. The electric dipole–electric dipole, electric dipole–magnetic dipole and electric dipole–electric quadrupole polarizability tensors are calculated at the frequency of the incident light, using SCF linear response theory. London Atomic Orbitals are employed, imposing gauge origin invariance on the calculations. Calculations have been carried out in the harmonic approximation for CFHDT and methyloxirane.