Category Archives: Methodology

A multi-GPU implementation of real-time time-dependent auxiliary density functional theory for the investigation of nanosystems irradiations

Electron dynamics simulations, Methodology

Pablo Antonio Martínez, Theresa Vock, Liliane Racha Kharchi, Jesus Nain Pedroza-Montero, Xiaojing Wu, Karim Hasnaoui, Aurélien de la Lande. Comput. Phys. Comm. 2023, 108946, in press.https://doi.org/10.1016/j.cpc.2023.108946

This article belongs to Special Issue on Attosecond Chemistry software in Computer Physics Communications

We report a new Multi-GPU (Graphical Processor Unit) implementation of real-time time-dependent Auxiliary Density Functional Theory (DFT) for simulations of attosecond electronic dynamics in molecular systems subjected to strong perturbations. Our code relies on the Kohn-Sham formalism of DFT and has been implemented in the deMon2k Fortran code. We expand single-particle wave functions (i.e molecular orbitals) as linear combinations of Gaussian-type-orbitals centered on atoms. The density matrix propagation is carried out on GPU while the Kohn-Sham potential is operated on CPUs (Central Processor Unit) with the help of variationally fitted densities. We propose a parallelization strategy using the MAGMA/CUDA libraries to calculate the exponential of dense Hermitian matrices entering the mathematical definition of the propagator, here using Taylor expansions. We report performance benchmarks on water droplets and on fullerenes (C50 to C540). They show a clear advantage of GPU over CPU (using the Scalapack library). The benchmarks also show the benefit of using more than one GPU for systems comprised of up to more than 10,000 basis functions. There, a speed-up of almost 40 between pure 40 CPU and four 4 GPU is obtained. Attosecond electron dynamics simulation in molecular systems comprised of several thousands of electrons becomes amenable to routine simulations in our code. We assess the accuracy of the GPU implementation considering various applications, namely, the calculation of extreme UV absorption spectra with non-Hermitian dynamics, the response of C180 to an electric perturbation, and finally the irradiation of a DNA/protein complex by a 0.4 MeV proton. The results demonstrate the robustness of the implementation. This work also paves the way for future even more efficient implementations.

Irradiation of Plutonium Tributyl Phosphate Complexes by Ionizing Alpha Particles: A Computational Study

Density Functional Theory, Electron dynamics simulations, Methodology, Radiation chemistry

Damien Tolu, Dominique Guillaumont, Aurélien de la Lande. J. Phys. Chem. A. 2023, 127, 34, 7045–7057. doi.org/10.1021/acs.jpca.3c02117. Link to full text in HAL.

The PUREX solvent extraction process, widely used for recovering uranium and plutonium from spent nuclear fuel, utilizes an organic solvent composed of tributyl phosphate (TBP). The emission of ionizing particles such as alpha particles, resulting from the decay of plutonium, makes the organic solvent vulnerable to degradation. Here, we study the ultrashort time alpha irradiation of tributylphosphate (TBP) and Pu(NO3)4(TBP)2 complex formed in the PUREX process. Electron dynamics is propagated by Real-Time-Dependent Auxiliary Density Functional Theory (RT-TD-ADFT). We investigate the use of previously proposed absorption boundary conditions (ABC) in the molecular orbital space to treat secondary electron emission. Basis set and exchange correlation functional effects with ABC are reported as well as a detailed analysis of the ABC parametrization. Preliminary results on the water molecule and then on TBP show that the phenomenological nature of the ABC parameters necessitates selecting appropriate values for each system under study. Irradiation of free and complexed TBP shows an influence of the ligands on the variation of atomic charges on the femtosecond time scale. An accumulation of atomic charges in the alkyl chains of TBP is observed in the case where the nitrate groups are predominantly irradiated. In addition, we find that the Pu atom regains its electric charge very rapidly after being hit by the projectile, with the coordination sphere serving as an electron reservoir to preserve its formal redox state. This study paves the road toward a full understanding of the degradation of organic extracants employed in the nuclear industry.

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

Density Functional Theory, Electron dynamics simulations, Methodology, QM/MM, Radiation chemistry, Review

Karwan A Omar, Feven A Korsaye, Rika Tandiana, Damien Tolu, Jean Deviers, Xiaojing Wu, Angela Parise, Aurelio Alvarez-Ibarra, Felix Moncada, Jesus Nain Pedroza-Montero, Daniel Mejía-Rodriguez, Nguyen-Thi Van-Oanh, Fabien Cailliez, Carine Clavaguéra, Karim Hasnaoui, Aurélien de la Lande. Eur. J. Special Topics, 2023. doi.org/10.1140/epjs/s11734-023-00905-6. Full text in HAL.

Special collection: Ultrafast Phenomena from attosecond to picosecond timescales: theory and experiments

We summarize in this article the recent progress made in our laboratories in the development of numerical approaches dedicated to investigating ultrafast physicochemical responses of biological matter subjected to ionizing radiations. Our modules are integrated into the deMon2k software which is a readily available program with highly optimized algorithms for conducting Auxiliary Density Functional Theory (ADFT) calculations. We have developed a computational framework based on Real-Time Time-dependent ADFT to simulate the electronic responses of molecular systems to strong perturbations, while molecular dynamics simulations in the ground and excited states (Ehrenfest dynamics) are available to simulate irradiation-induced ultrafast bond breaking/formation. Constrained ADFT and Multi-component ADFT have also been incorporated to simulate charge transfer processes and nuclear quantum effects, respectively. Finally, a coupling to polarizable force fields further permits to realistically account for the electrostatic effects that the systems’ environment has on the perturbed electron density. The code runs on CPU or hybrid CPU/GPU architectures affording simulations of systems comprised up to 1000 atoms at the DFT level with controlled numerical accuracy. We illustrate the applications of these methodologies by taking results from our recent articles that aimed principally at understanding experimental data from pulse radiolysis experiments.

Following the density evolution using real time density functional theory and density based indexes: Application to model push–pull molecules

Density Functional Theory, Electron dynamics simulations, Methodology

Feven Alemu Korsaye, Aurélien de la Lande, Ilaria Ciofini. J. Comput. Chem. 2023, 43, 1464. doi.org/10.1002/jcc.26932. Full text in HAL

Considering as test case a family of organic rod like push–pull molecules, we derived and applied density based index enabling the description and diagnostic of the electronic density evolution in real time-time dependent density functional theory (RT-TDDFT) simulations. In particular, both the charge transfer (CT) distance and a diagnostic index, the DCT and MACRT respectively, were computed on the fly from the density distribution obtained at a given time and the reference ground state density and their mean values were compared with what obtained at Linear Response-TDDFT level. Besides giving a way of analyzing the density redistribution occurring in time, these tools allowed to show how RT-TDDFT, which is definitely a powerful method to model the evolution of the density in CT or charge separation processes, can be affected by the same artifacts known for LR-TDDFT approaches and, particularly, to those related to the use of approximate exchange correlation functionals. The analysis here performed allowed to identify and discard on fly the electronic configurations corresponding to spurious situations.

QM/MM with Auxiliary DFT in deMon2k

Density Functional Theory, Methodology, QM/MM

J. D Samaniego-Rojas, L. I. Hernández-Segura, L. López-Sosa, R. I Delgado-Venegas, B. Gomez, J.-C. Lambry, A. de la Lande, T. Mineva, J. Alejandre, B. A Zúñiga-Gutiérrez, R. Flores-Moreno, P. Calaminici, G. Geudtner, A. M Köster.Andreas in Multiscale Dynamics Simulations: Nano and Nano-bio Systems in Complex Environments.Edited by D. Wei and D. R. Salahub. 2021. Royal Chemical Society. doi.org/10.1039/9781839164668-00001

This chapter describes the theoretical background of the quantum mechanical/molecular mechanical (QM/MM) implementation in deMon2k within the framework of auxiliary density functional theory (ADFT). It aims to give the reader an overview of the current state of the art of this QM/MM implementation and perspectives for its future development. To this end, we first derive the ADFT working equations for the QM and QM/MM energy and gradient expressions. Based on the joint QM/MM gradient expression, we present algorithms for QM/MM structure optimizations, transition-state searches and molecular dynamics simulations. The use of auxiliary density perturbation theory (ADPT) in the framework of QM/MM is discussed using illustrative implementations including analytic second-order ADFT energy derivatives, nuclear magnetic resonance chemical shift calculations and excited state calculations using time-dependent ADFT. The chapter closes with the description of a transformation program used to generate deMon2k QM/MM inputs.

Reliability and performances of real-time time-dependent auxiliary density functional theory

Density Functional Theory, Electron dynamics simulations, Methodology

Rika Tandiana, Carine Clavaguera, Karim Hasnaoui, Jesús Naín Pedroza-Montero, Aurélien de La Lande. Theor. Chem. Acc. 2021, 140, 126. doi.org/10.1007/s00214-021-02819-9. Full text in HAL.

Part of a collection: 20th deMon Developers Workshop

We recently adapted the Auxiliary DFT framework as implemented in deMon2k to the simulation of time-dependent problems via the Runge and Gross equations. Our implementation of the so-called Real-Time-Time-Dependent ADFT (RT-TD-ADFT) fully benefits from the algorithms available in deMon2k to carry out variational density fitting, notably the MINRES algorithm recently proposed for self-consistent-field calculations. We test here MINRES for the first time in the context of RT-TD-ADFT. We report extensive benchmarks calculations to assess the reliability of the ADFT framework. These encompass the construction of absorption spectra in the gas phase and in solvent, the calculation of electronic stopping power curves, the irradiation of zeolites by swift ions and the investigation of charge migrations with attosecond time resolution. All our results are very encouraging. We show that even small auxiliary basis sets are sufficient to obtain results almost undisguisable from those obtained with large and flexible auxiliary bases. Overall, we establish the reliability of RT-TD-ADFT to simulate electronics dynamics in large or very large molecular systems.

Multicomponent density functional theory with density fitting

Density Functional Theory, Methodology, Multicomponent DFT

Daniel Mejía-Rodríguez, Aurélien de La Lande, J. Chem. Phys. 2019, 150, 174115, doi.org/10.1063/1.5078596. Full text in HAL

Multicomponent Density Functional Theory (MDFT) is a promising methodology to incorporate nuclear quantum effects, such as zero-point energy or tunneling, or to simulate other types of particles such as muons or positrons using particle densities as basic quantities. As for standard electronic DFT, a still ongoing challenge is to achieve the most efficient implementations. We introduce a multicomponent DFT implementation within the framework of auxiliary DFT, focusing on molecular systems comprising electrons and quantum protons. We introduce a dual variational procedure to determine auxiliary electron and proton densities which leads to a succession of approximate energy expressions. Electronic and protonic fitted densities are employed in (i) electron-electron, proton-proton, and electron-proton classical Coulomb interactions and (ii) electron exchange-correlation, proton-proton exchange, and electron-proton correlation (EPC) potentials. If needed, exact exchange among electrons or among protons is computed by the variational fitting of the corresponding Fock potential. The implementation is carried out in deMon2k. We test various electron proton correlation functionals on proton affinities. We find that auxiliary densities can be safely used in electron-electron, proton-proton, and electron-proton classical Coulomb interactions, as well as in EPC, albeit with some precautions related to the choice of the electronic auxiliary basis set that must be flexible enough. Computational tests reported indicate that introduction of density fitting in MDFT is clearly advantageous in terms of computational effort with good scaling properties with respect to the number of electrons and protons treated at the DFT level.

Molecular simulations with in-deMon2k QM/MM, a tutorial-review

Density Functional Theory, Methodology, QM/MM, Review

Aurélien de La Lande, Aurelio Alvarez-Ibarra, Karim Hasnaoui, Fabien Cailliez, Xiaojing Wu, Tzonka Mineva, Jérôme Cuny, Patrizia Calaminici, Luis López-Sosa, Gerald Geudtner, Isabelle Navizet, Cristina Garcia Iriepa, Dennis R Salahub, Andreas M Köster. Molecules, 2019, 24, 1653.doi.org/10.3390/molecules24091653. Full text from publisher.

Article from the special issue: Multiscale Chemical Modeling and Simulations Using Quantum Mechanics/Molecular Mechanics (QM/MM))

deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born–Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.