| 1. |
- Aguilar, Xavier, et al.
(författare)
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Scalability analysis of Dalton, a molecular structure program
- 2013
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Ingår i: Future generations computer systems. - : Elsevier BV. - 0167-739X .- 1872-7115. ; 29:8, s. 2197-2204
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Tidskriftsartikel (refereegranskat)abstract
- Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a performance characterization and optimization of Dalton. We also propose a solution to avoid the master/worker design of Dalton to become a performance bottleneck for larger process numbers. With these improvements we obtain speedups of 4x, increasing the parallel efficiency of the code and being able to run in it in a much bigger number of cores.
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| 2. |
- Aguilar, Xavier, et al.
(författare)
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Scaling Dalton, a molecular electronic structure program
- 2011
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Ingår i: Seventh International Conference on e-Science, e-Science 2011, 5-8 December 2011, Stockholm, Sweden. - : IEEE conference proceedings. - 9781457721632 ; , s. 256-262
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Konferensbidrag (refereegranskat)abstract
- Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a characterization and performance optimization of Dalton that increases the scalability and parallel efficiency of the application. We also propose asolution that helps to avoid the master/worker design of Daltonto become a performance bottleneck for larger process numbers and increase the parallel efficiency.
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| 3. |
- Ahmadzadeh, Karan, et al.
(författare)
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Efficient implementation of isotropic cubic response functions for two-photon absorption cross sections within the self-consistent field approximation
- 2021
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 154:2
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Tidskriftsartikel (refereegranskat)abstract
- Within the self-consistent field approximation, computationally tractable expressions for the isotropic second-order hyperpolarizability have been derived and implemented for the calculation of two-photon absorption cross sections. The novel tensor average formulation presented in this work allows for the evaluation of isotropic damped cubic response functions using only similar to 3.3% (one-photon off-resonance regions) and similar to 10% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of the two-photon absorption cross section in the one-photon off-resonance and resonance regions are provided for alanine-tryptophan and 2,5-dibromo-1,4-bis(2-(4-diphenylaminophenyl)vinyl)-benzene. Furthermore, a benchmark set of 22 additional small- and medium-sized organic molecules is considered. In all these calculations, a quantitative assessment is made of the reduced and approximate forms of the cubic response function in the one-photon off-resonance regions and results demonstrate a relative error of less than similar to 5% when using the reduced expression as compared to the full form of the isotropic cubic response function.
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| 4. |
- Aidas, Kestutis, et al.
(författare)
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The Dalton quantum chemistry program system
- 2014
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Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 4:3, s. 269-284
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Tidskriftsartikel (refereegranskat)abstract
- Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.
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| 5. |
- Carravetta, V., et al.
(författare)
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Ab initio calculations of molecular resonant photoemission spectra
- 2000
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 113:18, s. 7790-7798
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Tidskriftsartikel (refereegranskat)abstract
- An ab initio method for calculations of molecular resonant photoemission (RPE) spectra is described. The method includes a multicenter expansion of both the dipole matrix element-direct emission-and the Hamiltonian matrix element between the resonant state and the autoionizing states-resonant emission. These quantities are relevant for the description of the process both in the two-step model, where the spectrum is computed at the resonance energy only, and in the one-step model where, by a K-matrix approach, the direct-to-resonant interference is taken into account and the electronic line profile is fully described. The resonant two-electron matrix elements are evaluated over the core-excited relaxed orbitals with the outgoing Auger electron orbital expanded on an augmented multicentered Gaussian basis set. Stieltjes imaging is shown to work excellently for such Gaussian basis sets giving correct continuum normalization matrix elements even for RPE electron energies as high as 100-1000 eV. A numerical investigation is carried out for the participator decay of the C 1s --> pi* and O 1s --> pi* states of CO.
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| 6. |
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| 7. |
- Chen, Xing, et al.
(författare)
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Spectral character of intermediate state in solid-state photoarrangement of alpha-santonin
- 2012
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Ingår i: Chemical Physics. - : Elsevier BV. - 0301-0104 .- 1873-4421. ; 405, s. 40-45
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Tidskriftsartikel (refereegranskat)abstract
- The vibronically resolved spectra of an intermediate and a product involved in the photoreaction of alpha-santonin have been explored by the density functional theory and the post-SCF methodologies, and a detailed comparison of theory with experiment was conducted to obtain reliable assignments to the observed spectra. The predicted emission energies of photosantonic acid and a topochemical product are found to match with the experimental values reasonably. The further calculations manifest that the absorption spectrum of photosantonic acid exhibits vibrationally resolved features, while the absorption band of topochemical product without vibrational resolution is opposite to the experimental observation. These new computational findings lead to a revised assignment to the observed bands and provide a basis for experimentalists to draw a convinced reaction mechanism for the alpha-santonin photorearrangement.
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| 8. |
- Chen, Xing
(författare)
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Theoretical Studies on Magnetic and Photochemical Properties of Organic Molecules
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The present thesis is concerned with the theoretical studies on magnetic and photochemical properties of organic molecules. The ab initio and first principles theories were employed to investigate the vibrational effects on the isotropic hyperfine coupling constant (HFCC) known as the critical parameter in electron paramagnetic resonance spectrum, the theoretical simulations of the vibronically resolved molecular spectra, the photo-induced reaction mechanism of α-santonin and the spin-forbidden reaction of triplet-state dioxygen with cofactor-free enzyme. The theoretical predictions shed light on the interpretation of experimental observations, the understanding of reaction mechanism, and importantly the guideline and perspective in respect of the popularized applications. We focused on the vibrational corrections to the isotropic HFCCs of hydrogen and carbon atoms in organic radicals. The calculations indicate that the vibrational contributions induce or enhance the effect of spin polarization. A set of rules were stated to guide experimentalist and theoretician in identification of the contributions from the molecular vibrations to HFCCs. And the coupling of spin density with vibrational modes in the backbone is significant and provides the insight into the spin density transfer mechanism in organic π radicals. The spectral characters of the intermediates in solid-state photoarrangement of α-santonin were investigated in order to well understand the underlying experimental spectra. The molecular spectra simulated with Franck-Condon principle show that the positions of the absorption and emission bands of photosantonic acid well match with the experimental observations and the absorption spectrum has a vibrationally resolved character. α-Santonin is the first found organic molecule that has the photoreaction activities. The photorearrangement mechanism is theoretically predicted that the low-lying excited state 1(nπ*) undergoing an intersystem crossing process decays to 3(ππ*) state in the Franck-Condon region. A pathway which is favored in the solid-state reaction requires less space and dynamic advantage on the excited-state potential energy surface (PES). And the other pathway is predominant in the weak polar solvent due to the thermodynamical and dynamical preferences. Lumisantonin is a critical intermediate derived from α-santonin photoreaction. The 3(ππ*) state plays a key role in lumisantonin photolysis. The photolytic pathway is in advantage of dynamics and thermodynamics on the triplet-state PES. In contrast, the other reaction pathway is facile for pyrolysis ascribed to a stable intermediate formed on the ground-state PES. The mechanism of the oxidation reaction involving cofactor-free enzyme and triplet-state dioxygen were studied. The theoretical calculations show that the charge-transfer mechanism is not a sole way to make a spin-forbidden oxidation allowed. It is more likely to take place in the reactant consisting of a non-conjugated substrate. The other mechanism involving the surface hopping between the triplet- and singlet-state PESs via a minimum energy crossing point (MECP) without a significant charge migration. The electronic state of MECP exhibits a mixed characteristic of the singlet and triplet states. The enhanced conjugation of the substrate slows down the spin-flip rate, and this step can in fact control the rate of the reaction that a dioxygen attaches to a substrate.
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