| 1. |
- Smith, Daniel G. A., et al.
(författare)
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Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine) : Automation and interoperability among computational chemistry programs
- 2021
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 155:20
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Tidskriftsartikel (refereegranskat)abstract
- Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.
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| 2. |
- Galván, Ignacio Fdez., et al.
(författare)
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OpenMolcas : From Source Code to Insight
- 2019
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:11, s. 5925-5964
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Tidskriftsartikel (refereegranskat)abstract
- In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.
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| 3. |
- Rehn, D. R., et al.
(författare)
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Gator : A Python-driven program for spectroscopy simulations using correlated wave functions
- 2021
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : John Wiley and Sons Inc. - 1759-0876 .- 1759-0884. ; 11:6
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Tidskriftsartikel (refereegranskat)abstract
- The Gator program has been developed for computational spectroscopy and calculations of molecular properties using real and complex propagators at the correlated level of wave function theory. Currently, the focus lies on methods based on the algebraic diagrammatic construction (ADC) scheme up to the third order of perturbation theory. An auxiliary Fock matrix-driven implementation of the second-order ADC method for excitation energies has been realized with an underlying hybrid MPI/OpenMP parallelization scheme suitable for execution in high-performance computing cluster environments. With a modular and object-oriented program structure written in a Python/C++ layered fashion, Gator additionally enables time-efficient prototyping of novel scientific approaches, as well as interactive notebook-driven training of students in quantum chemistry. This article is categorized under: Computer and Information Science > Computer Algorithms and Programming Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry.
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| 4. |
- Dreuw, A., et al.
(författare)
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Using core-hole reference states for calculating X-ray photoelectron and emission spectra
- 2022
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084.
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Tidskriftsartikel (refereegranskat)abstract
- For the calculation of core-ionization energies (IEs), X-ray photoelectron spectra (XPS), and X-ray emission spectra (XES), a commonly applied approach is to use non-Aufbau reference states with a core-hole as either final (IE and XPS) or initial (XES) state. However, such reference states can introduce numerical instabilities in post-HF methods, relating to the denominator of the energy corrections involved. This may become arbitrarily close to zero if a negative virtual orbital is present, e.g. a core-hole, leading to near-singularities. The resulting instabilities lead to severe convergence issues of the calculation schemes and, in addition, can strongly affect both energies and intensities, with oscillator strengths seen to reach values up to 4 × 107. For the K-edge we propose freezing the highest-energy virtual orbitals which contribute to any denominator below a threshold of 0.1 Hartree. Stable and reliable spectra are then produced, with minimal influence due to freezing energetically high-lying virtual orbitals (typically removing <5% of the total number of MOs). The developed protocol is here tested for Møller-Plesset perturbation theory and for the algebraic diagrammatic construction scheme for the polarization propagator, and it is also relevant for coupled cluster theory and other related methods.
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| 5. |
- Hodecker, M., et al.
(författare)
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Algebraic-diagrammatic construction scheme for the polarization propagator including ground-state coupled-cluster amplitudes. II. Static polarizabilities
- 2019
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics Inc.. - 0021-9606 .- 1089-7690. ; 150:17
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Tidskriftsartikel (refereegranskat)abstract
- The modification of the algebraic-diagrammatic construction (ADC) scheme for the polarization propagator using ground-state coupled-cluster (CC) instead of Møller-Plesset (MP) amplitudes, referred to as CC-ADC, is extended to the calculation of molecular properties, in particular, dipole polarizabilities. Furthermore, in addition to CC with double excitations (CCD), CC with single and double excitations (CCSD) amplitudes can be used, also in the second-order transition moments of the ADC(3/2) method. In the second-order CC-ADC(2) variants, the MP correlation coefficients occurring in ADC are replaced by either CCD or CCSD amplitudes, while in the F/CC-ADC(2) and F/CC-ADC(3/2) variants, they are replaced only in the second-order modified transition moments. These newly implemented variants are used to calculate the static dipole polarizability of several small- to medium-sized molecules, and the results are compared to the ones obtained by full configuration interaction or experiment. It is shown that the results are consistently improved by the use of CC amplitudes, in particular, for aromatic systems such as benzene or pyridine, which have proven to be difficult cases for standard ADC approaches. In this case, the second-order CC-ADC(2) and F/CC-ADC(2) variants yield significantly better results than the standard third-order ADC(3/2) method, at a computational cost amounting to only about 1% of the latter.
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| 6. |
- Knippenberg, Stefan, et al.
(författare)
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Strong Electronic Coupling Dominates the Absorption and Fluorescence Spectra of Covalently Bound BisBODIPYs
- 2015
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 119:8, s. 1323-1331
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Tidskriftsartikel (refereegranskat)abstract
- The absorption spectrum of a representative BisBODIPY molecule is investigated using high-level quantum chemical methodology; the results are compared with experimental data. The S1 and S2 excited states are examined in detail to illuminate and to understand the electronic coupling between them. With the help of model systems in which the distance between the BODIPY monomers is increased or in which the dihedral angle between the subunits is changed, the electronic coupling is quantified, and its influence on energetics and oscillator strengths is highlighted. For the explanation of the experimental spectrum, orbital interaction effects are found to be important. Because of the large experimental Stokes shift of BisBODIPY, the nature of the emissive state is investigated and found to remain C2 symmetric as the ground state, and no localization of the excitation on one BODIPY subunit occurs. The excitonic coupling is in BisBODIPY still larger than the geometry relaxation energy, which explains the absence of a pseudo-Jahn-Teller effect.
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| 7. |
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| 8. |
- Rinkevicius, Zilvinas, et al.
(författare)
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VeloxChem : A Python-driven density-functional theory program for spectroscopy simulations in high-performance computing environments
- 2019
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : Blackwell Publishing Inc.. - 1759-0876 .- 1759-0884.
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Tidskriftsartikel (refereegranskat)abstract
- An open-source program named VeloxChem has been developed for the calculation of electronic real and complex linear response functions at the levels of Hartree–Fock and Kohn–Sham density functional theories. With an object-oriented program structure written in a Python/C++ layered fashion, VeloxChem enables time-efficient prototyping of novel scientific approaches without sacrificing computational efficiency, so that molecular systems involving up to and beyond 500 second-row atoms (or some 10,000 contracted and in part diffuse Gaussian basis functions) can be routinely addressed. In addition, VeloxChem is equipped with a polarizable embedding scheme for the treatment of the classical electrostatic interactions with an environment that in turn is modeled by atomic site charges and polarizabilities. The underlying hybrid message passing interface (MPI)/open multiprocessing (OpenMP) parallelization scheme makes VeloxChem suitable for execution in high-performance computing cluster environments, showing even slightly beyond linear scaling for the Fock matrix construction with use of up to 16,384 central processing unit (CPU) cores. An efficient—with respect to convergence rate and overall computational cost—multifrequency/gradient complex linear response equation solver enables calculations not only of conventional spectra, such as visible/ultraviolet/X-ray electronic absorption and circular dichroism spectra, but also time-resolved linear response signals as due to ultra-short weak laser pulses. VeloxChem distributed under the GNU Lesser General Public License version 2.1 (LGPLv2.1) license and made available for download from the homepage https://veloxchem.org. This article is categorized under: Software > Quantum Chemistry Electronic Structure Theory > Density Functional Theory Theoretical and Physical Chemistry > Spectroscopy.
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