SIESTA-SIPs: Massively parallel spectrum-slicing eigensolver for an ab initio molecular dynamics package

2018 ◽  
Vol 39 (22) ◽  
pp. 1806-1814 ◽  
Author(s):  
Murat Keçeli ◽  
Fabiano Corsetti ◽  
Carmen Campos ◽  
Jose E. Roman ◽  
Hong Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Massively Parallel ◽  
Ab Initio Molecular Dynamics ◽  
Spectrum Slicing

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

2019 ◽  
Author(s):  
Liqun Cao ◽  
Jinzhe Zeng ◽  
Mingyuan Xu ◽  
Chih-Hao Chin ◽  
Tong Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Large Scale ◽  
Methane Combustion ◽  
Combustion Method ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Computational Time ◽  
Combustion Mechanism ◽  
Daily Lives

Combustion is a kind of important reaction that affects people's daily lives and the development of aerospace. Exploring the reaction mechanism contributes to the understanding of combustion and the more efficient use of fuels. Ab initio quantum mechanical (QM) calculation is precise but limited by its computational time for large-scale systems. In order to carry out reactive molecular dynamics (MD) simulation for combustion accurately and quickly, we develop the MFCC-combustion method in this study, which calculates the interaction between atoms using QM method at the level of MN15/6-31G(d). Each molecule in systems is treated as a fragment, and when the distance between any two atoms in different molecules is greater than 3.5 Å, a new fragment involved two molecules is produced in order to consider the two-body interaction. The deviations of MFCC-combustion from full system calculations are within a few kcal/mol, and the result clearly shows that the calculated energies of the different systems using MFCC-combustion are close to converging after the distance thresholds are larger than 3.5 Å for the two-body QM interactions. The methane combustion was studied with the MFCC-combustion method to explore the combustion mechanism of the methane-oxygen system.

scholarly journals A Review on Combination of Ab Initio Molecular Dynamics and NMR Parameters Calculations

2021 ◽  
Vol 22 (9) ◽  
pp. 4378
Author(s):  
Anna Helena Mazurek ◽  
Łukasz Szeleszczuk ◽  
Dariusz Maciej Pisklak
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Small Amplitude ◽  
Ab Initio Molecular Dynamics ◽  
Quantum Mechanical ◽  
Time Step ◽  
Noticeable Effect ◽  
Nmr Parameters ◽  
Mechanical Methods ◽  
Simulation Time

This review focuses on a combination of ab initio molecular dynamics (aiMD) and NMR parameters calculations using quantum mechanical methods. The advantages of such an approach in comparison to the commonly applied computations for the structures optimized at 0 K are presented. This article was designed as a convenient overview of the applied parameters such as the aiMD type, DFT functional, time step, or total simulation time, as well as examples of previously studied systems. From the analysis of the published works describing the applications of such combinations, it was concluded that including fast, small-amplitude motions through aiMD has a noticeable effect on the accuracy of NMR parameters calculations.

scholarly journals Temperature-Dependent Properties of Molten Li2BeF4 Salt Using Ab Initio Molecular Dynamics

ACS Omega ◽  
2021 ◽  
Author(s):  
Khagendra Baral ◽  
Saro San ◽  
Ridwan Sakidja ◽  
Adrien Couet ◽  
Kumar Sridharan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Ab Initio Molecular Dynamics ◽  
Temperature Dependent ◽  
Temperature Dependent Properties

scholarly journals Ab initio molecular dynamics study of AlCl4− adsorption on PEDOT conducting polymer chains

2021 ◽  
Vol 7 ◽  
pp. 111-119
Author(s):  
Ben Craig ◽  
Chris-Kriton Skylaris ◽  
Carlos Ponce de Leon ◽  
Denis Kramer
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Conducting Polymer ◽  
Polymer Chains ◽  
Ab Initio Molecular Dynamics

scholarly journals Effects of applied voltage on water at a gold electrode interface from ab initio molecular dynamics

2021 ◽  
Vol 12 (16) ◽  
pp. 5865-5873
Author(s):  
Zachary K. Goldsmith ◽  
Marcos F. Calegari Andrade ◽  
Annabella Selloni
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Applied Voltage ◽  
Gold Electrode ◽  
Ab Initio Molecular Dynamics ◽  
Dynamic Effects ◽  
Electrode Interface

Ab initio molecular dynamics of an aqueous electrode interface reveal the electrostatic, structural, and dynamic effects of quantifiable voltage biases on water.

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