A multi-GPU implementation of Real-Time Time-Dependent Auxiliary Density Functional Theory for the investigation of nanosystems irradiations

Martínez, Pablo Antonio; Vock, Theresa; Kharchi, Liliane Racha; Pedroza-Montero, Jesus Nain; Wu, Xiaojing; Hasnaoui, Karim; de la Lande, Aurélien

doi:10.1016/j.cpc.2023.108946

Cited by 5 publications

(5 citation statements)

References 71 publications

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“…In a last section, we have then described currently ongoing time resolved measurements to study radiation‐induced molecular processes in DNA and future perspectives using FEL facilities. We anticipate that an increased collaboration between theoreticians and experimentalists will allow significant progress in the field, notably regarding charge transfer and energy deposition, for instance thanks to state‐of‐the‐art methods using graphical processor units to run parallelized calculations using time‐dependent density‐functional theory [60] …”

Section: Discussionmentioning

confidence: 99%

“…We anticipate that an increased collaboration between theoreticians and experimentalists will allow significant progress in the field, notably regarding charge transfer and energy deposition, for instance thanks to state-of-the-art methods using graphical processor units to run parallelized calculations using timedependent density-functional theory. [60]…”

Section: Discussionmentioning

confidence: 99%

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Radiation‐Induced Molecular Processes in DNA: A Perspective on Gas‐Phase Interaction Studies

Schlathölter,

Poully

2024

Chemistry A European J

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Studying the direct effects of DNA irradiation is essential for understanding the impact of radiation on biological systems. Gas‐phase interactions are especially well suited to uncover the molecular mechanisms underlying these direct effects. Only relatively recently, isolated DNA oligonucleotides were irradiated by ionizing particles such as VUV or X‐ray photons or ion beams, and ionic products were analyzed by mass spectrometry. This article provides a comprehensive review of primarily experimental investigations in this field over the past decade, emphasizing the description of processes such as ionization, fragmentation, charge and hydrogen transfer triggered by photoabsorption or ion collision, and the recent progress made thanks to specific atomic photoabsorption. Then, we outline ongoing experimental developments notably involving ion‐mobility spectrometry, crossed beams or time‐resolved measurements. The discussion extends to potential research directions for the future.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Radiation‐Induced Molecular Processes in DNA: A Perspective on Gas‐Phase Interaction Studies

Schlathölter,

Poully

2024

Chemistry A European J

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“…In the case depicted in Figure 3, one could use up to 400 CPUs with appreciable gain and to further strongly decrease the cost of the simulation [19]. To go one step beyond in terms of efficiency, we have recently developed a hybrid CPU/GPU code with very encouraging results [86]. In our current implementation, matrix Note the change of scale between the two graphs.…”

Section: High-performance Computingmentioning

confidence: 99%

“…In our current implementation, matrix Note the change of scale between the two graphs. Adapted with permission from [79] and [86].…”

Section: High-performance Computingmentioning

confidence: 99%

Current status of deMon2k for the investigation of the early stages of matter irradiation by time-dependent DFT approaches

Omar

Korsaye

Tandiana

et al. 2023

Eur. Phys. J. Spec. Top.

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HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

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“…All simulations have been carried out with our multi-GPU implementation of RT-TD-DFT in the deMon2k code (version 6.1.6) using 4 GPU and 40 CPU or 8 GPU and 64 CPU . For electronic integral calculations, we used a mixed scheme for electronic repulsion and adaptive grids of high accuracy for the exchange-correlation contributions (10 –7 Ha, following deMon2k nomenclature). , deMon2k relies on the auxiliary DFT formalism (ADFT) whereby variationally fitted electron densities are introduced to avoid cumbersome four-index electronic-repulsion-integral calculations and to simplify the numerical integration of XC contributions.…”

Section: Gaussian-type Orbitals For the Continuummentioning

confidence: 99%

Use of Gaussian-Type Functions for Describing Fast Ion-Matter Irradiation with Time-Dependent Density Functional Theory

Tandiana,

Omar,

Luppi

et al. 2023

J. Chem. Theory Comput.

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The electronic stopping power is an observable property that quantifies the ability of swift ions to penetrate matter to transfer energy to the electron cloud. The recent literature has proven the value of Real-Time Time-Dependent Density Functional Theory to accurately evaluate this property from first-principles, but questions remain regarding the capability of computer codes relying on atom-centered basis functions to capture the physics at play. In this Perspective, we draw attention to the fact that irradiation by swift ions triggers electron emission into the continuum, especially at the Bragg peak. We investigate the ability of Gaussian atomic orbitals (AOC), which were fitted to mimic continuum wave functions, to improve electronic stopping power predictions. AOC are added to standard correlation-consistent basis sets or STO minimal basis sets. Our benchmarks for water irradiation by fast protons clearly advocate for the use of AOC, especially near the Bragg peak. We show that AOC only need to be placed on the molecules struck by the ion. The number of AOC that are added to the usual basis set is relatively small compared to the total number of atomic orbitals, making the use of such a basis set an excellent choice from a computational cost point of view. The optimum basis set combination is applied for the calculation of the stopping power of a proton in water with encouraging agreement with experimental data.

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A multi-GPU implementation of Real-Time Time-Dependent Auxiliary Density Functional Theory for the investigation of nanosystems irradiations

Cited by 5 publications

References 71 publications

Radiation‐Induced Molecular Processes in DNA: A Perspective on Gas‐Phase Interaction Studies

Radiation‐Induced Molecular Processes in DNA: A Perspective on Gas‐Phase Interaction Studies

Current status of deMon2k for the investigation of the early stages of matter irradiation by time-dependent DFT approaches

Use of Gaussian-Type Functions for Describing Fast Ion-Matter Irradiation with Time-Dependent Density Functional Theory

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