| 1. |
- Brand, Manuel, et al.
(författare)
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Efficient and Parallel Implementation of Real and Complex Response Functions Employing the Second-Order Algebraic-Diagrammatic Construction Scheme for the Polarization Propagator
- 2023
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 20:1, s. 103-113
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Tidskriftsartikel (refereegranskat)abstract
- We present the implementation of an efficient matrix-folded formalism for the evaluation of complex response functions and the calculation of transition properties at the level of the second-order algebraic-diagrammatic construction (ADC(2)) scheme. The underlying algorithms, in combination with the adopted hybrid MPI/OpenMP parallelization strategy, enabled calculations of the UV/vis spectra of a guanine oligomer series ranging up to 1032 contracted basis functions, thereby utilizing vast computational resources from up to 32,768 CPU cores. Further analysis of the convergence behavior of the involved iterative subspace algorithms revealed the superiority of a frequency-separated treatment of response equations even for a large spectral window, including 101 frequencies. We demonstrate the applicability to general quantum mechanical operators by the first reported electronic circular dichroism spectrum calculated with a complex polarization propagator approach at the ADC(2) level of theory.
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| 2. |
- Brand, Manuel, et al.
(författare)
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Efficient parallel implementation of complex response functions employing the algebraic-diagrammatic construction scheme
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We present the derivation and implementation of an efficient matrix-folded formalism for the evaluation of complex response functions at the level of the second-order algebraic-diagrammatic construction ADC(2) scheme. The adopted hybrid MPI/OpenMP parallelization strategy enables the utilization of vast computational resources without significant performance losses as demonstrated by consistent size-scalings for the computationally most demanding steps obtained from calculations of the UV/vis spectra of a guanine oligomer series ranging up to 1,032 contracted basis functions. Further analysis of the convergence behavior of the involved iterative subspace algorithm revealed the superiority of a frequency-separated treatment of response equations even for a large spectral window including 101 frequencies. We demonstrate the applicability to general quantum mechanical operators by the first reported electric circular dichroism spectrum calculated with the complex polarization propagator approach at the ADC(2) level of theory.
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| 3. |
- Brumboiu, Iulia E., 1987-, et al.
(författare)
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Analytical gradients for core-excited states in the algebraic diagrammatic construction (ADC) framework
- 2021
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 155:4
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Tidskriftsartikel (refereegranskat)abstract
- Expressions for analytical molecular gradients of core-excited states have been derived and implemented for the hierarchy of algebraic diagrammatic construction (ADC) methods up to extended second-order within the core-valence separation (CVS) approximation. We illustrate the use of CVS-ADC gradients by determining relaxed core-excited state potential energy surfaces and optimized geometries for water, formic acid, and benzene. For water, our results show that in the dissociative lowest core-excited state, a linear configuration is preferred. For formic acid, we find that the O K-edge lowest core-excited state is non-planar, a fact that is not captured by the equivalent core approximation where the core-excited atom with its hole is replaced by the "Z + 1" neighboring atom in the periodic table. For benzene, the core-excited state gradients are presented along the Jahn-Teller distorted geometry of the 1s -> pi* excited state. Our development may pave a new path to studying the dynamics of molecules in their core-excited states.
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| 4. |
- Dempwolff, Adrian L., et al.
(författare)
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Vertical ionization potential benchmark for unitary coupled-cluster and algebraic-diagrammatic construction methods
- 2022
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 156:5, s. 054114-
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Tidskriftsartikel (refereegranskat)abstract
- The performance of several methods for the calculation of vertical ionization potentials (IPs) or, more generally, electron-detachment energies based on unitary coupled-cluster (UCC) theory and the algebraic-diagrammatic construction (ADC) scheme is evaluated with respect to benchmark data computed at the level of equation-of-motion coupled-cluster theory, including single, double, and triple excitations (IP-EOM-CCSDT). Based on a statistical evaluation of about 200 electron-detached states of 41 molecules, the second-order methods IP-ADC(2) and IP-UCC2 show modest accuracies with IP-EOM-CCSDT as reference, exposing a mean signed error and a standard deviation of the error of -0.54 & PLUSMN; 0.50 and -0.49 & PLUSMN; 0.54 eV, respectively, accompanied by a mean absolute error (MAE) of 0.61 and 0.58 eV, respectively. The strict third-order IP-ADC method demonstrates an accuracy of 0.26 & PLUSMN; 0.35 eV (MAE = 0.35 eV), while the IP-UCC3 method is slightly more accurate with 0.24 & PLUSMN; 0.26 eV (MAE = 0.29 eV). Employing the static self-energy computed using the Dyson expansion method (DEM) improves the IP-ADC(3) performance to 0.27 & PLUSMN; 0.28 eV, with the mean absolute error of this method being 0.32 eV. However, employing the simpler improved fourth-order scheme sigma(4+) for the static self-energy provides almost identical results as the DEM. Based on the quality of the present benchmark results, it therefore appears not necessary to use the computationally more demanding DEM.
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| 5. |
- Fransson, Thomas, et al.
(författare)
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Computational Chemistry from Laptop to HPC : A notebook exploration of quantum chemistry
- 2022. - 1
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- Quantum chemistry is a powerful tool. It is now possible to model complex chemical processes even on a laptop getting insights into matter at its fundamental scale.But quantum chemistry is also very complex. Answering a chemical question requires selecting parameters among a wide variety of choices. Choosing a model system, an electronic structure method, a basis set, a set of properties, and a wide array of parameters which can affect the results in small but sometimes meaningful way… It can be a very daunting task, even for veterans of the field.Similarly, for those who wish to get a deeper understanding of a method, going through the pages of equation often riddled with inconsistent notations and formulations is very challenging. And at the end, the link between the equation and the computer implementation found in existing softwares can be vague at best.We believe that a core issue is that humans are not good at learning in abstract terms. We can get very far with a lecture or a textbook, but we will never build as much intuition about how a clock work as by simply breaking one apart and rebuilding it from scratch.This is exactly the aim of this page, allowing a hands-on approach to computational chemistry. Together we will dismantle the black box that a computational chemistry code often seems to be, go through all the cogs and gears, and build back together some of the main computational methods of modern computational chemistry. We will do this by presenting the underlying equations, all expressed with consistent notations, as well as by suggesting a simple python implementation, to really display in action how the theory is implemented into a practical tool. Additionally, we will put these methods in context by showing how they can be used to address concrete chemical questions, discussing the strengths and weaknesses of each method and how to best use them to solve practical problems.
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| 6. |
- Fransson, Thomas, et al.
(författare)
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eChem : A Notebook Exploration of Quantum Chemistry
- 2023
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Ingår i: Journal of Chemical Education. - : American Chemical Society (ACS). - 0021-9584 .- 1938-1328. ; 100:4, s. 1664-1671
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Tidskriftsartikel (refereegranskat)abstract
- The eChem project features an e-book published as a web page (10.30746/978-91-988114-0-7), collecting a repository of Jupyter notebooks developed for the dual purpose of explaining and exploring the theory underlying computational chemistry in a highly interactive manner as well as providing a tutorial-based presentation of the complex workflows needed to simulate embedded molecular systems of real biochemical and/or technical interest. For students ranging from beginners to advanced users, the eChem book is well suited for self-directed learning, but workshops led by experienced instructors and targeting student bodies with specific needs and interests can readily be formed from its components. This has been done by using eChem as the base for a workshop directed toward graduate students learning the theory and practices of quantum chemistry, resulting in very positive assessment of the interactive nature of this framework. The members of the eChem team are engaged in both education and research, and as a mirroring activity, we develop the open-source software upon which this e-book is predominantly based. The overarching vision and goal of our work is to provide a science- and education-enabling software platform for quantum molecular modeling on contemporary and future high-performance computing systems, and to document the resulting development and workflows in the eChem book.
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| 7. |
- Fransson, Thomas, et al.
(författare)
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Simulating X-ray Emission Spectroscopy with Algebraic Diagrammatic Construction Schemes for the Polarization Propagator
- 2019
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:1, s. 546-556
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Tidskriftsartikel (refereegranskat)abstract
- The calculation of X-ray emission spectra has been addressed with the algebraic diagrammatic construction (ADC) scheme, using a core-ionized wave function as the reference state. With this, the valence-to-core transitions are found as the first eigenstates with negative eigenvalues. The performance of the ADC hierarchical methods ADC(2), ADC(2)-x, and ADC(3/2) has been investigated on 17 transition of second row elements (C, N, O, F, and Ne), and 5 transitions of third-row elements (S and Cl). We report ADC(2) results within 0.20 +/- 0.36 eV of experimental values with an appropriate choice of basis set and when accounting for relativistic effects, with a slight tendency toward underestimating emission energies. By comparison, ADC(2)-x yields a similar spread in relative energies, but a consistent overestimation of approximately 1.5 eV. Going to ADC(3/2), we now observe an underestimation of emission energies and a larger error spread. By comparison, calculations of X-ray absorption spectra have been reported to favor the ADC(2)-x method, with ADC(2) showing the largest error when comparing to experimental values. The difference in ADC performance trends between these core spectroscopies are attributed to the different electron rearrangement effects in X-ray absorption and emission processes.
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| 8. |
- Fransson, Thomas, et al.
(författare)
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Static polarizabilities and C-6 dispersion coefficients using the algebraic-diagrammatic construction scheme for the complex polarization propagator
- 2017
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 146:9
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Tidskriftsartikel (refereegranskat)abstract
- An implementation of the damped linear response function, or complex polarization propagator, using the algebraic-diagrammatic construction (ADC) scheme has been developed and utilized for the calculation of electric-dipole polarizabilities and C-6 dispersion coefficients. Four noble gases (He, Ne, Ar, and Kr), five n-alkanes (methane, ethane, propane, butane, and pentane), three carbonyls (formaldehyde, acetaldehyde, and acetone), and three unsaturated hydrocarbons (ethene, acetylene, and benzene) have been treated with the hierarchical set of models ADC(2), ADC(2)-x, and ADC(3/2), and comparison has been made to results obtained with damped linear response Hartree-Fock (HF) and coupled cluster singles and doubles (CCSD) theory as well as high-quality experimental estimates via the dipole oscillator strength distribution approach. This study marks the first ADC calculations of C-6 dispersion coefficients and the first ADC(3/2) calculations of static polarizabilities. Results at CCSD and ADC(3/2) levels of theory are shown to be of similar quality, with electron correlation effects increasing the molecular property values for all calculations except CCSD considerations of ethene and acetylene (attributed to an overestimation of bond electron density at HF level of theory). The discrepancies betweenCCSDand ADC(3/2) are partially due toADCoverestimating anisotropies, and discrepancies with respect to experimental values are partially due to the lack of zero-point vibrational effects in the present study.
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| 9. |
- Fransson, Thomas, et al.
(författare)
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XABOOM : An X-ray Absorption Benchmark of Organic Molecules Based on Carbon, Nitrogen, and Oxygen 1s -> π* Transitions
- 2021
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 17:3, s. 1618-1637
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Tidskriftsartikel (refereegranskat)abstract
- The performance of several standard and popular approaches for calculating X-ray absorption spectra at the carbon, nitrogen, and oxygen K-edges of 40 primarily organic molecules up to the size of guanine has been evaluated, focusing on the low-energy and intense 1s -> pi* transitions. Using results obtained with CVS-ADC(2)-x and fc-CVS-EOM-CCSD as benchmark references, we investigate the performance of CC2, ADC(2), ADC(3/2), and commonly adopted density functional theory (DFT)-based approaches. Here, focus is on precision rather than on accuracy of transition energies and intensities-in other words, we target relative energies and intensities and the spread thereof, rather than absolute values. The use of exchange-correlation functionals tailored for time-dependent DFT calculations of core excitations leads to error spreads similar to those seen for more standard functionals, despite yielding superior absolute energies. Long-range corrected functionals are shown to perform particularly well compared to our reference data, showing error spreads in energy and intensity of 0.2-0.3 eV and similar to 10%, respectively, as compared to 0.3-0.6 eV and similar to 20% for a typical pure hybrid. In comparing intensities, state mixing can complicate matters, and techniques to avoid this issue are discussed. Furthermore, the influence of basis sets in high-level ab initio calculations is investigated, showing that reasonably accurate results are obtained with the use of 6-311++G**. We name this benchmark suite as XABOOM (X-ray absorption benchmark of organic molecules) and provide molecular structures and ground-state self-consistent field energies and spectroscopic data. We believe that it provides a good assessment of electronic structure theory methods for calculating X-ray absorption spectra and will become useful for future developments in this field.
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| 10. |
- 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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