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VeloxChem: A Python-driven density-functional theory program for spectroscopy simulations in high-performance computing environments
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.ORCID iD: 0000-0003-2729-0290
KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.ORCID iD: 0000-0001-6508-8355
KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0002-9123-8174
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
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2019 (English)In: WIREs 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. article id e1457
Keywords [en]
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: urn:nbn:se:kth:diva-268434DOI: 10.1002/wcms.1457ISI: 000502095100001Scopus ID: 2-s2.0-85076863228OAI: oai:DiVA.org:kth-268434DiVA, id: diva2:1427527
Note

QC 20200429

Available from: 2020-04-29 Created: 2020-04-29 Last updated: 2024-09-04Bibliographically approved
In thesis
1. Implementation of complex polarization propagator theory for linear response properties of large molecular systems
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
2. Efficient Calculation of Nonlinear Spectroscopic Properties within the Time-Dependent Density Functional Theory Approximation
Open this publication in new window or tab >>Efficient Calculation of Nonlinear Spectroscopic Properties within the Time-Dependent Density Functional Theory Approximation
2023 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis introduces a novel computational scheme tailored for efficient calculations of nonlinear spectroscopic observables. First, a derivation and implementation of an algorithm designed to harness the linearity of the Fock matrix construction in calculating two-photon absorption cross-sections within the self-consistent field approximation is presented. Subsequently, this computational scheme is extended to the density functional theory approximation for functionals belonging to the generalized gradient approximation. Lastly the derivation and implementation of the nonlinear exchange-correlation kernel for functionals belonging to the meta generalized gradient approximation are presented for the first time.

Collectively, the advancements presented in this thesis contribute new methodologies and insights to the computational realm of nonlinear spectroscopic calculations, offering the potential for large-scale theoretical spectroscopy calculations at the level of density functional theory.

Abstract [sv]

Denna avhandling introducerar en ny beräkningsmetod skräddarsydd för effektiva beräkningar av icke-linjära spektroskopiska observabler. Först presenteras en härledning och implementering av en algoritm utformad för att utnyttja lineariteten i Fock-matrixkonstruktionen vid beräkning av två-fotons absorptions tvärsnitt inom ramen för "the self-consistent field approximation". Därefter utvidgas denna beräkningsmethod till nivån av "density functional theory" för funktionaler som tillhör den generaliserade gradientapproximationen. Slutligen presenteras härledningen och implementeringen av den icke-linjära "exchange-correlation kernelen" för funktionaler som tillhör meta-generaliserade gradientapproximationen för första gången.

Sammantaget bidrar de framsteg som presenteras i denna avhandling med nya metoder och insikter för beräkningen av för icke-linjära spektroskopiska beräkningar, vilket erbjuder potentialen för storskaliga teoretiska spektroskopiberäkningar.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2023. p. 67
Series
TRITA-CBH-FOU ; 2023:46
Keywords
Cubic response, DFT, Response theory
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
Identifiers
urn:nbn:se:kth:diva-337435 (URN)978-91-8040-721-2 (ISBN)
Public defence
2023-10-31, Kollegiesalen, Brinellvägen 6, https://kth-se.zoom.us/j/66109968018, Stockholm, 09:00 (English)
Opponent
Supervisors
Note

QC 20231005

Available from: 2023-10-05 Created: 2023-10-03 Last updated: 2025-12-03Bibliographically approved

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Rinkevicius, ZilvinasLi, XinVahtras, OlavAhmadzadeh, KaranBrand, ManuelRingholm, MagnusNorman, Patrick

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