| 1. |
- Manni, Giovanni Li, et al.
(författare)
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The OpenMolcas Web : A Community-Driven Approach to Advancing Computational Chemistry
- 2023
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:20, s. 6933-6991
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Tidskriftsartikel (refereegranskat)abstract
- The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.
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| 2. |
- Aquilante, Francesco, et al.
(författare)
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Modern quantum chemistry with [Open]Molcas
- 2020
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21
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Tidskriftsartikel (refereegranskat)abstract
- MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
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| 3. |
- Blachucki, Wojciech, et al.
(författare)
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Approaching the Attosecond Frontier of Dynamics in Matter with the Concept of X-ray Chronoscopy
- 2022
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Ingår i: Applied Sciences. - : MDPI AG. - 2076-3417. ; 12:3
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Tidskriftsartikel (refereegranskat)abstract
- Featured Application Herein, an innovative methodology, called X-ray chronoscopy, is proposed for exploration of ultrafast processes in matter with attosecond precision using current XFEL sources. The method is based on measuring the change in an X-ray pulse temporal profile induced by interaction with a medium. X-ray free electron lasers (XFELs) have provided scientists opportunities to study matter with unprecedented temporal and spatial resolutions. However, access to the attosecond domain (i.e., below 1 femtosecond) remains elusive. Herein, a time-dependent experimental concept is theorized, allowing us to track ultrafast processes in matter with sub-fs resolution. The proposed X-ray chronoscopy approach exploits the state-of-the-art developments in terahertz streaking to measure the time structure of X-ray pulses with ultrahigh temporal resolution. The sub-femtosecond dynamics of the saturable X-ray absorption process is simulated. The employed rate equation model confirms that the X-ray-induced mechanisms leading to X-ray transparency can be probed via measurement of an X-ray pulse time structure.
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| 4. |
- De Gracia Triviño, Juan Angel, et al.
(författare)
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Complete Active Space Methods for NISQ Devices: The Importance of Canonical Orbital Optimization for Accuracy and Noise Resilience
- 2023
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:10, s. 2863-2872
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Tidskriftsartikel (refereegranskat)abstract
- To avoid the scaling of the number of qubits with the size of the basis set, one can divide the molecular space into active and inactive regions, which is also known as complete active space methods. However, selecting the active space alone is not enough to accurately describe quantum mechanical effects such as correlation. This study emphasizes the importance of optimizing the active space orbitals to describe correlation and improve the basis-dependent Hartree-Fock energies. We will explore classical and quantum computation methods for orbital optimization and compare the chemically inspired ansatz, UCCSD, with the classical full CI approach for describing the active space in both weakly and strongly correlated molecules. Finally, we will investigate the practical implementation of a quantum CASSCF, where hardware-efficient circuits must be used and noise can interfere with accuracy and convergence. Additionally, we will examine the impact of using canonical and noncanonical active orbitals on the convergence of the quantum CASSCF routine in the presence of noise.
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| 5. |
- Delcey, Mickael G., et al.
(författare)
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Exact semi-classical light-matter interaction operator applied to two-photon processes with strong relativistic effects
- 2020
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 153:2
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Tidskriftsartikel (refereegranskat)abstract
- X-ray processes involve interactions with high-energy photons. For these short wavelengths, the perturbing field cannot be treated as constant, and there is a need to go beyond the electric-dipole approximation. The exact semi-classical light-matter interaction operator offers several advantages compared to the multipole expansion such as improved stability and ease of implementation. Here, the exact operator is used to model x-ray scattering in metal K pre-edges. This is a relativistic two-photon process where absorption is dominated by electric-dipole forbidden transitions. With the restricted active space state-interaction approach, spectra can be calculated even for the multiconfigurational wavefunctions including second-order perturbation. However, as the operator itself depends on the transition energy, the cost for evaluating integrals for hundreds of thousands unique transitions becomes a bottleneck. Here, this is solved by calculating the integrals in a molecular-orbital basis that only runs over the active space, combined with a grouping scheme where the operator is the same for close-lying transitions. This speeds up the calculations of single-photon processes and is critical for the modeling of two-photon scattering processes. The new scheme is used to model Kα resonant inelastic x-ray scattering of iron-porphyrin complexes with relevance to studies of heme enzymes, for which the total computational time is reduced by several orders of magnitude with an effect on transition intensities of 0.1% or less.
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| 6. |
- Delcey, Mickaël G.
(författare)
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MultiPsi : A python-driven MCSCF program for photochemistry and spectroscopy simulations on modern HPC environments
- 2023
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Ingår i: Wiley Interdisciplinary Reviews: Computational Molecular Science. - 1759-0876. ; 13:6
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Tidskriftsartikel (refereegranskat)abstract
- We present MultiPsi, an open-source MCSCF program for the calculation of ground and excited states properties of strongly correlated systems. The program currently implements a general MCSCF code with excited states available using either state-averaging or linear response. It is written in a highly modular fashion using Python/C++ which makes it well suited as a development platform, enabling easy prototyping of novel methods, and as a teaching tool using interactive notebooks. The code is also very efficient and designed for modern high-performance computing environments using hybrid OpenMP/MPI parallelization. This efficiency is demonstrated with the calculation of the CASSCF energy and linear response of a molecule with more than 700 atoms as well as a fully optimized conventional CI calculation on more than 400 billion determinants. This article is categorized under: Software > Quantum Chemistry Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy.
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| 7. |
- Delcey, Mickael G, 1988-
(författare)
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MultiPsi: A python-driven MCSCF program for photochemistry and spectroscopy simulations on modern HPC environments
- 2023
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Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 13:6
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Tidskriftsartikel (refereegranskat)abstract
- We present MultiPsi, an open-source MCSCF program for the calculation of ground and excited states properties of strongly correlated systems. The program currently implements a general MCSCF code with excited states available using either state-averaging or linear response. It is written in a highly modular fashion using Python/C++ which makes it well suited as a development platform, enabling easy prototyping of novel methods, and as a teaching tool using interactive notebooks. The code is also very efficient and designed for modern high-performance computing environments using hybrid OpenMP/MPI parallelization. This efficiency is demonstrated with the calculation of the CASSCF energy and linear response of a molecule with more than 700 atoms as well as a fully optimized conventional CI calculation on more than 400 billion determinants. This article is categorized under: Software > Quantum Chemistry Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy.
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| 8. |
- Delcey, Mickael G, 1988-, et al.
(författare)
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Soft X-ray signatures of cationic manganese–oxo systems, including a high-spin manganese(v) complex
- 2022
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 24:6, s. 3598-3610
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Tidskriftsartikel (refereegranskat)abstract
- Limitations in synthesis of high-valent metal–oxo complexes are circumvented by trapping a series of ionic Mn–oxo complexes. One of them is a rare high-spin Mn(v)–oxo, which can serve as a template to identify similar intermediates in catalysis.
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| 9. |
- 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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| 10. |
- 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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