scholarly journals High performance wave packet molecular dynamics with density functional exchange-correlation term for non-ideal plasma simulations

2021 ◽  
Vol 1787 (1) ◽  
pp. 012043
Author(s):  
Ya S Lavrinenko ◽  
I V Morozov ◽  
I A Valuev
Keyword(s):  
Molecular Dynamics ◽  
Wave Packet ◽  
High Performance ◽  
Density Functional ◽  
Exchange Correlation ◽  
Plasma Simulations ◽  
Correlation Term ◽  
Ideal Plasma

scholarly journals Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory

2018 ◽  
Vol 19 (8) ◽  
pp. 2346 ◽  
Author(s):  
Esko Makkonen ◽  
Patrick Rinke ◽  
Olga Lopez-Acevedo ◽  
Xi Chen
Keyword(s):  
Molecular Dynamics ◽  
Density Functional ◽  
Time Dependent ◽  
Basis Set ◽  
Dna Nanostructures ◽  
Exchange Correlation ◽  
Hartree Fock ◽  
Spurious Peak ◽  
20 Nm ◽  
Dependent Density

We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag + -mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range. However, a spurious positive peak is present in the CAM-B3LYP ECD spectra. We trace the origins of this spurious peak and find that is likely due to the sensitivity of silver atoms to the amount of Hartree–Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag + -mediated DNA species.

scholarly journals On the Efficient Evaluation of the Exchange Correlation Potential on Graphics Processing Unit Clusters

2020 ◽  
Vol 8 ◽  
Author(s):  
David B. Williams-Young ◽  
Wibe A. de Jong ◽  
Hubertus J. J. van Dam ◽  
Chao Yang
Keyword(s):  
Graphics Processing Units ◽  
High Performance ◽  
Density Functional ◽  
Materials Science ◽  
Basis Set ◽  
Theoretical Treatment ◽  
Processing Unit ◽  
Multiple Gpus ◽  
Exchange Correlation ◽  
Graphics Processing

The predominance of Kohn–Sham density functional theory (KS-DFT) for the theoretical treatment of large experimentally relevant systems in molecular chemistry and materials science relies primarily on the existence of efficient software implementations which are capable of leveraging the latest advances in modern high-performance computing (HPC). With recent trends in HPC leading toward increasing reliance on heterogeneous accelerator-based architectures such as graphics processing units (GPU), existing code bases must embrace these architectural advances to maintain the high levels of performance that have come to be expected for these methods. In this work, we purpose a three-level parallelism scheme for the distributed numerical integration of the exchange-correlation (XC) potential in the Gaussian basis set discretization of the Kohn–Sham equations on large computing clusters consisting of multiple GPUs per compute node. In addition, we purpose and demonstrate the efficacy of the use of batched kernels, including batched level-3 BLAS operations, in achieving high levels of performance on the GPU. We demonstrate the performance and scalability of the implementation of the purposed method in the NWChemEx software package by comparing to the existing scalable CPU XC integration in NWChem.

The effect of impurities in ultra-thin hydrogenated silicene and germanene: a first principles study

2015 ◽  
Vol 17 (34) ◽  
pp. 22210-22216 ◽  
Author(s):  
Caroline J. Rupp ◽  
Sudip Chakraborty ◽  
Rajeev Ahuja ◽  
Rogério J. Baierle
Keyword(s):  
Density Functional Theory ◽  
Electronic Properties ◽  
First Principles ◽  
Density Functional ◽  
Functional Theory ◽  
Exchange Correlation ◽  
Spin Polarized ◽  
Effect Of Impurities ◽  
The Stability ◽  
Correlation Term

Spin polarized density functional theory within the GGA–PBE and HSE06 approach for the exchange correlation term has been used to investigate the stability and electronic properties of nitrogen and boron impurities in single layers of silicane and germanane.

Exchange-Correlation Energy Densities and Response Potentials: Connection Between Two Definitions and Analytical Model for the Strong-Coupling Limit of a Stretched Bond

2019 ◽  
Author(s):  
S. Giarrusso ◽  
Paola Gori-Giorgi
Keyword(s):  
Density Functional Theory ◽  
Strong Coupling ◽  
Density Functional ◽  
Correlation Energy ◽  
Order Term ◽  
Strong Coupling Limit ◽  
Local Form ◽  
Coupling Constant ◽  
Functional Theory ◽  
Exchange Correlation

We analyze in depth two widely used definitions (from the theory of conditional probablity amplitudes and from the adiabatic connection formalism) of the exchange-correlation energy density and of the response potential of Kohn-Sham density functional theory. We introduce a local form of the coupling-constant-dependent Hohenberg-Kohn functional, showing that the difference between the two definitions is due to a corresponding local first-order term in the coupling constant, which disappears globally (when integrated over all space), but not locally. We also design an analytic representation for the response potential in the strong-coupling limit of density functional theory for a model single stretched bond.<br>

Evaluating Transition Metal Barrier Heights with the Latest DFT Exchange–Correlation Functionals – the MOBH35 Benchmark Dataset

2019 ◽  
Author(s):  
Mark Iron ◽  
Trevor Janes
Keyword(s):  
Transition Metal ◽  
Density Functional ◽  
Computational Cost ◽  
Basis Set ◽  
Functional Theory ◽  
Exchange Correlation ◽  
Barrier Heights ◽  
Complete Basis Set ◽  
Complete Basis Set Limit ◽  
Hybrid Functionals

A new database of transition metal reaction barrier heights – MOBH35 – is presented. Benchmark energies (forward and reverse barriers and reaction energy) are calculated using DLPNO-CCSD(T) extrapolated to the complete basis set limit using a Weizmann1-like scheme. Using these benchmark energies, the performance of a wide selection of density functional theory (DFT) exchange–correlation functionals, including the latest from the Truhlar and Head-Gordon groups, is evaluated. It was found, using the def2-TZVPP basis set, that the ωB97M-V (MAD 1.8 kcal/mol), ωB97X-V (MAD 2.1 kcal/mol) and SCAN0 (MAD 2.1 kcal/mol) hybrid functionals are recommended. The double-hybrid functionals PWPB95 (MAD 1.6 kcal/mol) and B2K-PLYP (MAD 1.8 kcal/mol) did perform slightly better but this has to be balanced by their increased computational cost.

scholarly journals Sensitivity of Intra- and Intermolecular Interactions of Benzo[h]quinoline from Car–Parrinello Molecular Dynamics and Electronic Structure Inspection

2021 ◽  
Vol 22 (10) ◽  
pp. 5220
Author(s):  
Jarosław J. Panek ◽  
Joanna Zasada ◽  
Bartłomiej M. Szyja ◽  
Beata Kizior ◽  
Aneta Jezierska
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Quantum Effects ◽  
Potential Of Mean Force ◽  
Probability Density Distribution ◽  
Donor And Acceptor ◽  
Nuclear Quantum Effects ◽  
Vibrational Features

The O-H...N and O-H...O hydrogen bonds were investigated in 10-hydroxybenzo[h]quinoline (HBQ) and benzo[h]quinoline-2-methylresorcinol complex in vacuo, solvent and crystalline phases. The chosen systems contain analogous donor and acceptor moieties but differently coupled (intra- versus intermolecularly). Car–Parrinello molecular dynamics (CPMD) was employed to shed light onto principle components of interactions responsible for the self-assembly. It was applied to study the dynamics of the hydrogen bonds and vibrational features as well as to provide initial geometries for incorporation of quantum effects and electronic structure studies. The vibrational features were revealed using Fourier transformation of the autocorrelation function of atomic velocity and by inclusion of nuclear quantum effects on the O-H stretching solving vibrational Schrödinger equation a posteriori. The potential of mean force (Pmf) was computed for the whole trajectory to derive the probability density distribution and for the O-H stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The electronic structure changes of the benzo[h]quinoline-2-methylresorcinol dimer and trimers were studied based on Constrained Density Functional Theory (CDFT) whereas the Electron Localization Function (ELF) method was applied for all systems. It was found that the bridged proton is localized on the donor side in both investigated systems in vacuo. The crystalline phase simulations indicated bridged proton-sharing and transfer events in HBQ. These effects are even more pronounced when nuclear quantization is taken into account, and the quantized Pmf allows the proton to sample the acceptor area more efficiently. The CDFT indicated the charge depletion at the bridged proton for the analyzed dimer and trimers in solvent. The ELF analysis showed the presence of the isolated proton (a signature of the strongest hydrogen bonds) only in some parts of the HBQ crystal simulation. The collected data underline the importance of the intramolecular coupling between the donor and acceptor moieties.

scholarly journals Strain Investigation on Spin-Dependent Transport Properties of γ-Graphyne Nanoribbon Between Gold Electrodes

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Yun Li ◽  
Xiaobo Li ◽  
Shidong Zhang ◽  
Liemao Cao ◽  
Fangping Ouyang ◽  
...  
Keyword(s):  
Transport Properties ◽  
High Performance ◽  
Density Functional ◽  
Strain Engineering ◽  
Molecular Junctions ◽  
Spin Splitting ◽  
Functional Theory ◽  
Spin Dependent Transport ◽  
The Density Functional Theory ◽  
Dependent Transport

AbstractStrain engineering has become one of the effective methods to tune the electronic structures of materials, which can be introduced into the molecular junction to induce some unique physical effects. The various γ-graphyne nanoribbons (γ-GYNRs) embedded between gold (Au) electrodes with strain controlling have been designed, involving the calculation of the spin-dependent transport properties by employing the density functional theory. Our calculated results exhibit that the presence of strain has a great effect on transport properties of molecular junctions, which can obviously enhance the coupling between the γ-GYNR and Au electrodes. We find that the current flowing through the strained nanojunction is larger than that of the unstrained one. What is more, the length and strained shape of the γ-GYNR serves as the important factors which affect the transport properties of molecular junctions. Simultaneously, the phenomenon of spin-splitting occurs after introducing strain into nanojunction, implying that strain engineering may be a new means to regulate the electron spin. Our work can provide theoretical basis for designing of high performance graphyne-based devices in the future.

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