GTOBAS is a program for fitting Gaussian-type orbitals (GTOs) to Bessel and Coulomb functions over a finite range. The exponents of the GTOs are optimized using the method of Nestmann and Peyerimhoff [J. Phys. B 23 (1990) L773]. The appended module NUMCBAS provides the numerical Bessel and Coulomb functions required as input for the program. The use of GTO continuum basis sets is particularly important in electron–molecule scattering calculations when polyatomic targets are involved. Sample results for such calculations are also discussed.
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UKRmol-scripts is a set of Perl scripts to automatically run the UKRmol+ codes, a complex software suite based on the R-matrix method to model fixed-nuclei photoionization and electron- and positron-scattering for polyatomic molecules. Starting with several basic parameters, the scripts operatively produce all necessary input files and run all codes for electronic structure and scattering calculations as well as gather the more frequently required outputs. The scripts provide a simple way to run such calculations for many molecular geometries concurrently and collect the resulting data for easier post-processing and visualization. We describe the structure of the scripts and the input parameters as well as provide examples for photoionization and electron and positron collisions with molecules. The codes are freely available from Zenodo.
Nature of problem: Performing ab initio photoionization and low energy electron- and positron-scattering on polyatomic molecules requires selecting and setting a significant number of input parameters in order to model the physics in a numerically accurate way. These scripts streamline setting up and analyzing calculations based on the R-matrix method [1] using the UKRmol+ suite [2].
Solution method: The scripts provide automatic generation of input files and execution of programs from the UKRmol+ suite [2] using a number of parameters that describe both physical models and machine-dependent settings, and also outputs of the previous programs in the suite which are automatically read and analyzed. The resulting output files are then post-processed to collect target and scattering data for further analysis and simple plotting.
Additional comments including restrictions and unusual features: The scripts should be used with releases 3.2 of UKRmol-in and UKRmol-out [3] although they are compatible with earlier versions.
[1]
P.G. Burke, R-Matrix Theory of Atomic Collisions: Application to Atomic, Molecular and Optical Processes, Springer, Berlin, 2011.
[2]
Z. Mašín et al., UKRmol+: a suite for modelling electronic processes in molecules interacting with electrons, positrons and photons using the R-matrix method, Comput. Phys. Commum. 249 (2020) 107092.
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.
External routines/libraries: MPI, BLAS/LAPACK, CUDA, MAGMA
Supplementary material: User manual, installation instructions, test cases.
Nature of problem: Electron dynamics within molecular systems is amenable to simulation with Real-Time Time-Dependent Density Functional Theory (RT-TD-DFT). The methodology consists in propagating on the attosecond time scale the single particle electronic wave functions on the underlying Kohn-Sham potential [1,2]. In deMon2k-RT-TDDFT, the propagation is coupled to the Auxiliary DFT framework for fast evaluation of the potential [3]. A remaining computational bottleneck is the matrix exponential calculation of the Hermitian Hamiltonian matrix. This task is achieved in deMon2k via diagolanization or expansions formulas (Taylor, Chebychev or Baker-Campbell-Hausdorff). The operation is cumbersome on central-processor-unit machines for large matrices (e.g. > 5000 × 5000), which corresponds to molecular systems comprising around 2,000 electrons. Alternatives are needed to overcome this bottleneck.
Solution method: We propose to carry out the matrix exponentiation on graphical-processor-units thanks to the MAGMA[4]/CUDA libraries. The code permits a drastic reduction of the computational cost, opening the attosecond dynamic simulations of large molecular systems comprised thousands of electrons with controlled accuracy. The method is tested here for Taylor expansions.
Additional comments including restrictions and unusual features: The code described in this article opens the realization of RT-TD-ADFT simulations. The code is linked to the Master version 6.1.6 of deMon2k (http://www.demon-software.com), which must be pre-installed by the user.
References:
[1] E. Runge, E.K.U. Gross, Phys. Rev. Lett. 52 (1984) 997–1000.
[2] K. Yabana, G.F. Bertsch, Phys. Rev. B 54 (1996) 4484–4487.
[3] A. Alvarez-Ibarra, K.A. Omar, K. Hasnaoui, A. de la Lande, in: Multiscale Dynamics Simulations: Nano and Nano-Bio Systems in Complex Environments, The Royal Society of Chemistry, 2022, pp. 117–143.
The HF– SCF (self-consistent-field) accompanied by the Gaussian-type orbitals are utilized to build the occupied and virtual molecular orbitals (MO). The continuum orbitals are described by orbitals specified by Faure et al. (Alexandre et al., 2002). Now, n-butanol being polar in nature due to permanent dipole moment of 1.66 debye, leads to accounts for more partial waves for convergence i.e. l > 4.
A detailed theoretical investigation of electron impact collision on n-butanol, a potential biofuel, is carried out over a wide energy impact range from 0.1 to 5000 eV. The low energy scattering calculations from 0.1 to 20 eV are performed using UK molecular R-matrix method via Quantemol-N software. This scattering investigation aims to predict various resonances by providing dissociative electron attachment via C–O bond cleavage. Furthermore, the study focuses on estimating several cross-sections namely elastic, differential, momentum transfer, excitation, ionization and total cross-section. In addition, we also computed higher energy cross-section from the ionization threshold to 5000 eV using the spherical complex optical potential (SCOP) method. A good agreement is observed between the computed cross-section at the overlapping energies of employing (SCOP and R-matrix) formalisms. Apart from the scattering study, we also obtained various resonances having significance at low energy. Theoretically predicted resonance peaks agree well with previously reported data and a few new resonance states are also identified. The cross-sectional data presented here will be beneficial as an input parameter modelling electron transport processes during the spark ignition.
