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Brand, M., Dreuw, A., Norman, P. & Li, X. (2023). Efficient and Parallel Implementation of Real and Complex Response Functions Employing the Second-Order Algebraic-Diagrammatic Construction Scheme for the Polarization Propagator. Journal of Chemical Theory and Computation, 20(1), 103-113
Open this publication in new window or tab >>Efficient and Parallel Implementation of Real and Complex Response Functions Employing the Second-Order Algebraic-Diagrammatic Construction Scheme for the Polarization Propagator
2023 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 20, no 1, p. 103-113Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2023
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-342465 (URN)10.1021/acs.jctc.3c01065 (DOI)001139474200001 ()38117937 (PubMedID)2-s2.0-85181012222 (Scopus ID)
Note

QC 20240122

Available from: 2024-01-22 Created: 2024-01-22 Last updated: 2024-01-22Bibliographically approved
Brand, M. (2022). Implementation of complex polarization propagator theory for linear response properties of large molecular systems. (Doctoral dissertation). Stockholm: KTH Royal Institute of Technology
Open this publication in new window or tab >>Implementation of complex polarization propagator theory for linear response properties of large molecular systems
2022 (English)Doctoral 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.

Abstract [sv]

Den anmärkningsvärda utvecklingen som inom enbart loppet av en livstid gått från de första kommersiellt tillgängliga datorerna mot exascale superdatorer har varit nära sammanflätad med en strävan att kunna utnyttja den uppgraderade beräkningskraften för att kunna lösa mer komplexa problem inom den teoretisk kemin. I syfte att ytterligare tänja på gränserna för beräkningsmässigt tillgängliga molekylära systemstorlekar, inkluderar denna avhandling en presentation av programmeringsinsatser som ledde till utvecklingen av två kvantkemiska mjukvarukoder, såväl som en rad ab initio studier på kolbaserade system, där de två mjukvarukoderna applicerades.

VeloxChem- och Gator-programmen som är utvecklade för spektroskopi-simuleringar på nivån för density-functional theory (DFT) respektive korrelerade vågfunktionsmetoder, använder ett hybrid-message passing interface (MPI)/open multiprocessing (OpenMP) parallelliseringsschema som är inbäddat i en modulär programstruktur skriven i lager av  Python/C++ för exekvering i nutida hög-prestandaberäkningsmiljöer (HPC). De inkluderade numeriska lösningsalgoritmerna för utvärdering av reella och komplexa linjära responsfunktioner i kombination med den parallella konstruktionen av extra Fock-matriser möjliggör effektiv beräkning av både en-fotonabsorption eller elektronisk cirkulär dikroism (CD)-spektra i ultravioletta/synliga (UV/vis) eller röntgen områden, samt beräkningar av van der Waals C6 dispersionskoefficienter.

Genom att använda VeloxChem-programmet i två omfattande undersökningar har dispersionskoefficienterna C6 för kolfullerener upp till en systemstorlek på C540 och CD-spektra av kolhelicener från CH[5] till CH[30] varit beräknade på DFT-nivå. Den första undersökningen avslöjade en icke-additiv skalning med avseende på antalet kolatomer av N2,2. Den andra identifierade icke-triviala CD-bandprogressioner, som förmodligen är kopplat till antalet överlappande lager i de spiralformade konjugerade systemen. Resultaten från dessa studier utmanar den nuvarande uppfattningen inom undersökningarnas respektive områden.

I en jämförelse på en serie guanin-oligomerer utförda med Gator-programmet, beräknades hela UV/vis-spektrumet för en tetrad på nivån av ett andra-ordningens algebraic-diagrammatic construction (ADC(2)) scheme på mindre än 15 timmar genom effektivt nyttjande av 32 768 kärnor för centralprocessorer (CPU).

Genom att överskrida gränsen på 10 000 och 1 000 kontrakterade basfunktioner för en behandling med DFT- respektive ADC(2)-metoderna, visar dessa applicerade exempel på VeloxChems och Gators förmåga att utnyttja enorma beräkningsresurser som görs tillgängliga av både nutida och framtida HPC-system och därmed tillåter rutinmässiga beräkningar av systemstorlekar som tidigare var utom räckhåll.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2022. p. 87
Series
TRITA-CBH-FOU ; 2022:54
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
Identifiers
urn:nbn:se:kth:diva-320270 (URN)978-91-8040-394-8 (ISBN)
Public defence
2022-11-18, D37, Lindstedtsvägen 5, Zoom: https://kth-se.zoom.us/j/67595336394, Stockholm, 09:00 (English)
Opponent
Supervisors
Note

QC 2022-10-18

Available from: 2022-10-18 Created: 2022-10-17 Last updated: 2022-11-16Bibliographically approved
Brand, M. & Norman, P. (2022). Nontrivial spectral band progressions in electronic circular dichroism spectra of carbohelicenes revealed by linear response calculations. Physical Chemistry, Chemical Physics - PCCP, 24(32), 19321-19332
Open this publication in new window or tab >>Nontrivial spectral band progressions in electronic circular dichroism spectra of carbohelicenes revealed by linear response calculations
2022 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 32, p. 19321-19332Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Royal Society of Chemistry (RSC), 2022
National Category
Chemical Process Engineering Energy Engineering Medical Biotechnology
Identifiers
urn:nbn:se:kth:diva-316719 (URN)10.1039/d2cp02371g (DOI)000837448700001 ()35929836 (PubMedID)2-s2.0-85135689319 (Scopus ID)
Note

QC 20220830

Available from: 2022-08-30 Created: 2022-08-30 Last updated: 2022-10-17Bibliographically approved
Ahmadzadeh, K., Scott, M., Brand, M., Vahtras, O., Li, X., Rinkevicius, Z. & Norman, P. (2021). Efficient implementation of isotropic cubic response functions for two-photon absorption cross sections within the self-consistent field approximation. Journal of Chemical Physics, 154(2), Article ID 024111.
Open this publication in new window or tab >>Efficient implementation of isotropic cubic response functions for two-photon absorption cross sections within the self-consistent field approximation
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2021 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, no 2, article id 024111Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
AIP Publishing, 2021
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-289893 (URN)10.1063/5.0031851 (DOI)000609824200001 ()33445884 (PubMedID)2-s2.0-85099407136 (Scopus ID)
Note

QC 20210215

Available from: 2021-02-15 Created: 2021-02-15 Last updated: 2023-10-03Bibliographically approved
Rehn, D. R., Rinkevicius, Z., Herbst, M. F., Li, X., Scheurer, M., Brand, M., . . . Norman, P. (2021). Gator: A Python-driven program for spectroscopy simulations using correlated wave functions. Wiley Interdisciplinary Reviews. Computational Molecular Science, 11(6), Article ID e1528.
Open this publication in new window or tab >>Gator: A Python-driven program for spectroscopy simulations using correlated wave functions
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2021 (English)In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, E-ISSN 1759-0884, Vol. 11, no 6, article id e1528Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
John Wiley and Sons Inc, 2021
Keywords
computational spectroscopy, electronic structure theory, propagator theory, response theory, Algebra, Calculations, Cluster computing, Computation theory, Computer software, Electronic structure, High level languages, Perturbation techniques, Quantum chemistry, Wave functions, Ab initio electronic structure methods, Algebraic diagrammatic constructions, Correlated wave functions, High-performance computing clusters, Molecular properties, Object-oriented program, Object oriented programming
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-307209 (URN)10.1002/wcms.1528 (DOI)000629781400001 ()2-s2.0-85102706759 (Scopus ID)
Note

QC 20220118

Available from: 2022-01-18 Created: 2022-01-18 Last updated: 2022-10-17Bibliographically approved
Brand, M., Ahmadzadeh, K., Li, X., Rinkevicius, Z., Saidi, W. A. & Norman, P. (2021). Size-dependent polarizabilities and van der Waals dispersion coefficients of fullerenes from large-scale complex polarization propagator calculations. Journal of Chemical Physics, 154(7), Article ID 074304.
Open this publication in new window or tab >>Size-dependent polarizabilities and van der Waals dispersion coefficients of fullerenes from large-scale complex polarization propagator calculations
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2021 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, no 7, article id 074304Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
AMER INST PHYSICS, 2021
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-292491 (URN)10.1063/5.0040009 (DOI)000630521400004 ()33607910 (PubMedID)2-s2.0-85100915441 (Scopus ID)
Note

QC 20210412

Available from: 2021-04-12 Created: 2021-04-12 Last updated: 2022-10-17Bibliographically approved
Rinkevicius, Z., Xin, L., Vahtras, O., Brand, M., Ahmadzadeh, K., Ringholm, M., . . . Norman, P. (2019). New and efficient Python/C plus plus modular library for real and complex response functions at the level of Kohn-Sham density functional theory. Paper presented at 257th National Meeting of the American-Chemical-Society (ACS), MAR 31-APR 04, 2019, Orlando, FL. Abstracts of Papers of the American Chemical Society, 257
Open this publication in new window or tab >>New and efficient Python/C plus plus modular library for real and complex response functions at the level of Kohn-Sham density functional theory
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2019 (English)In: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 257Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
American Chemical Society (ACS), 2019
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-257663 (URN)000478861204497 ()
Conference
257th National Meeting of the American-Chemical-Society (ACS), MAR 31-APR 04, 2019, Orlando, FL
Note

QC 20190904

Available from: 2019-09-04 Created: 2019-09-04 Last updated: 2024-03-15Bibliographically approved
Rinkevicius, Z., Li, X., Vahtras, O., Ahmadzadeh, K., Brand, M., Ringholm, M., . . . Norman, P. (2019). VeloxChem: A Python-driven density-functional theory program for spectroscopy simulations in high-performance computing environments. Wiley Interdisciplinary Reviews. Computational Molecular Science, Article ID e1457.
Open this publication in new window or tab >>VeloxChem: A Python-driven density-functional theory program for spectroscopy simulations in high-performance computing environments
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2019 (English)In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, E-ISSN 1759-0884, article id e1457Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Blackwell Publishing Inc., 2019
Keywords
circular dichroism, density functional theory (DFT), ECD, high-performance computing (HPC), MPI, OpenMP, response theory, UV/vis, Application programming interfaces (API), Cluster computing, Computation theory, Computational efficiency, Dichroism, Electronic structure, High level languages, Message passing, Object oriented programming, Open source software, Physical chemistry, Program processors, Quantum chemistry, Circular dichroism spectra, Electronic structure theory, High performance computing, High performance computing (HPC), High-performance computing clusters, Density functional theory
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-268434 (URN)10.1002/wcms.1457 (DOI)000502095100001 ()2-s2.0-85076863228 (Scopus ID)
Note

QC 20200429

Available from: 2020-04-29 Created: 2020-04-29 Last updated: 2024-03-18Bibliographically approved
Brand, M., Dreuw, A., Norman, P. & Li, X.Efficient parallel implementation of complex response functions employing the algebraic-diagrammatic construction scheme.
Open this publication in new window or tab >>Efficient parallel implementation of complex response functions employing the algebraic-diagrammatic construction scheme
(English)Manuscript (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.

National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
Identifiers
urn:nbn:se:kth:diva-320268 (URN)
Note

QC 20221018

Available from: 2022-10-17 Created: 2022-10-17 Last updated: 2023-05-03Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-3992-043x

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