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  • 1.
    Ahmadzadeh, Karan
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Scott, Mikael
    Ruprecht Karls Univ Heidelberg, Interdisciplinary Ctr Sci Comp, Neuenheimer Feld 205, D-69120 Heidelberg, Germany..
    Brand, Manuel
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Kaunas Univ Technol, Fac Math & Nat Sci, Dept Phys, LT-51368 Kaunas, Lithuania..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Efficient implementation of isotropic cubic response functions for two-photon absorption cross sections within the self-consistent field approximation2021In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, no 2, article id 024111Article in journal (Refereed)
    Abstract [en]

    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.

  • 2.
    Brand, Manuel
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Implementation of complex polarization propagator theory for linear response properties of large molecular systems2022Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Since its beginning, the remarkable development from the first commercially available computers toward exascale supercomputers just within the span of a lifetime has been closely intertwined with the perpetual quest for the utilization of the arising computing power for the avail of theoretical chemistry. With the aim of further pushing the limits of computationally accessible molecular system sizes, this thesis includes the presentation of programming efforts, which brought forth two quantum chemical software codes, as well as a range of ab initio studies on carbon-based systems, enabled by the former.

    The VeloxChem and Gator programs, developed for spectroscopy simulations at the level of density-functional theory (DFT) and correlated wave function methods, respectively, employ a hybrid message passing interface (MPI)/open multiprocessing (OpenMP) parallelization scheme embedded in a modular program structure written in a Python/C++ layered fashion for the execution in contemporary high-performance computing (HPC) environments. Included numerical solvers for the evaluation of real and complex linear response functions in combination with the parallel construction of auxiliary Fock matrices enable the efficient calculation of one-photon absorption or electronic circular dichroism (CD) spectra in the ultraviolet/visible (UV/vis) or X-ray spectral region, as well as van der Waals C6 dispersion coefficients.

    Employing the VeloxChem program in two comprehensive investigations, the C6 dispersion coefficients of carbon fullerenes up to a system size of C540 and the CD spectra of carbohelicenes ranging from CH[5] to CH[30] have been calculated at the DFT level of theory. The revealed non-additive scaling with respect to the number of carbon atoms of N2.2 in the former and nontrivial CD band progressions, arguably linked to the number of overlapping layers in the helical conjugated systems, in the latter rectify the current conception in their respective fields.

    In a benchmark for the Gator program on a series of guanine oligomers, the full UV/vis spectrum for a tetrad was calculated at the level of a second-order algebraic-diagrammatic construction (ADC(2)) scheme in just under 15 hours by efficient employment of 32,768 central processing unit (CPU) cores.

    Exceeding the limit of 10,000 and 1,000 contracted basis functions for a treatment with the DFT and ADC(2) methods, respectively, these practical examples demonstrate the capability of VeloxChem and Gator to harness vast computational resources made available by contemporary and future HPC systems and thereby routinely address scopes of system sizes that were previously out of reach.

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  • 3.
    Brand, Manuel
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH Royal Inst Technol, Dept Theoret Chem & Biol, Sch Engn Sci Chem Biotechnol & Hlth, SE-10691 Stockholm, Sweden..
    Ahmadzadeh, Karan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH Royal Inst Technol, Dept Theoret Chem & Biol, Sch Engn Sci Chem Biotechnol & Hlth, SE-10691 Stockholm, Sweden..
    Li, Xin
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH Royal Inst Technol, Dept Theoret Chem & Biol, Sch Engn Sci Chem Biotechnol & Hlth, SE-10691 Stockholm, Sweden..
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Department of Physics, Faculty of Mathematics and Natural Sciences, Kaunas University of Technology, LT-51368 Kaunas, Lithuania.
    Saidi, Wissam A.
    Univ Pittsburgh, Dept Mech Engn & Mat Sci, Pittsburgh, PA 15261 USA..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH Royal Inst Technol, Dept Theoret Chem & Biol, Sch Engn Sci Chem Biotechnol & Hlth, SE-10691 Stockholm, Sweden..
    Size-dependent polarizabilities and van der Waals dispersion coefficients of fullerenes from large-scale complex polarization propagator calculations2021In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, no 7, article id 074304Article in journal (Refereed)
    Abstract [en]

    While the anomalous non-additive size-dependencies of static dipole polarizabilities and van der Waals C-6 dispersion coefficients of carbon fullerenes are well established, the widespread reported scalings for the latter (ranging from N-2.2 to N-2.8) call for a comprehensive first-principles investigation. With a highly efficient implementation of the linear complex polarization propagator, we have performed Hartree-Fock and Kohn-Sham density functional theory calculations of the frequency-dependent polarizabilities for fullerenes consisting of up to 540 carbon atoms. Our results for the static polarizabilities and C-6 coefficients show scalings of N-1.2 and N-2.2, respectively, thereby deviating significantly from the previously reported values obtained with the use of semi-classical/empirical methods. Arguably, our reported values are the most accurate to date as they represent the first ab initio or first-principles treatment of fullerenes up to a convincing system size.

  • 4.
    Brand, Manuel
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Dreuw, Andreas
    Ruprecht Karls Univ Heidelberg, Interdisciplinary Ctr Sci Comp, D-69120 Heidelberg, Germany..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Efficient and Parallel Implementation of Real and Complex Response Functions Employing the Second-Order Algebraic-Diagrammatic Construction Scheme for the Polarization Propagator2023In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 20, no 1, p. 103-113Article in journal (Refereed)
    Abstract [en]

    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.

  • 5.
    Brand, Manuel
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Dreuw, Andreas
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Efficient parallel implementation of complex response functions employing the algebraic-diagrammatic construction schemeManuscript (preprint) (Other academic)
    Abstract [en]

    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.

  • 6.
    Brand, Manuel
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Nontrivial spectral band progressions in electronic circular dichroism spectra of carbohelicenes revealed by linear response calculations2022In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 32, p. 19321-19332Article in journal (Refereed)
    Abstract [en]

    We demonstrate that contemporary computational resources allow for accurate theoretical studies of systems matching recent advances in experimental helicene chemistry. Concerned with first-principles calculations of carbohelicenes, our work surpasses CH[12] as the largest system investigated to date and unravels trends in the electronic structure of the low-lying states of the homologous series. Utilizing a highly efficient implementation of linear response algorithms, we present electronic circular dichroism (CD) spectra of carbohelicenes ranging from CH[5] to CH[30] at the level of Kohn-Sham density-functional theory. Our results for a systematic increase in system size show the emergence of new CD bands that subsequently rise to intensities dominating the spectrum. The spectral band progressions exhibit a periodicity directly linked to the number of overlapping layers of conjugation. While our findings rectify the current understanding of the electronic structure of carbohelicenes, they also serve as a general call for caution regarding the extrapolation of trends from small system ranges.

  • 7. Rehn, D. R.
    et al.
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Department of Physics, Faculty of Mathematics and Natural Sciences, Kaunas University of Technology, Kaunas, Lithuania.
    Herbst, M. F.
    Li, X.
    Scheurer, M.
    Brand, Manuel
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Dempwolff, A. L.
    Brumboiu, Iulia E.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Department of Chemistry, Korea Advanced Institute for Science and Technology, Daejeon, South Korea.
    Fransson, T.
    Dreuw, A.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Gator: A Python-driven program for spectroscopy simulations using correlated wave functions2021In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, E-ISSN 1759-0884, Vol. 11, no 6, article id e1528Article in journal (Refereed)
    Abstract [en]

    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.

  • 8.
    Rinkevicius, Zilvinas
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Vahtras, Olav
    KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ahmadzadeh, Karan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Brand, Manuel
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ringholm, Magnus
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    List, N. H.
    Scheurer, M.
    Scott, M.
    Dreuw, A.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    VeloxChem: A Python-driven density-functional theory program for spectroscopy simulations in high-performance computing environments2019In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, E-ISSN 1759-0884, article id e1457Article in journal (Refereed)
    Abstract [en]

    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.

  • 9.
    Rinkevicius, Zilvinas
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Xin, Li
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Brand, Manuel
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ahmadzadeh, Karan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ringholm, Magnus
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. UiT, Dept Chem, Tromso, Norway..
    List, Nanna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    New and efficient Python/C plus plus modular library for real and complex response functions at the level of Kohn-Sham density functional theory2019In: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 257Article in journal (Other academic)
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