scholarly journals TeraChem : A graphical processing unit ‐accelerated electronic structure package for large‐scale ab initio molecular dynamics

2020 ◽  
Author(s):  
Stefan Seritan ◽  
Christoph Bannwarth ◽  
Bryan S. Fales ◽  
Edward G. Hohenstein ◽  
Christine M. Isborn ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Ab Initio ◽  
Large Scale ◽  
Graphical Processing Unit ◽  
Ab Initio Molecular Dynamics ◽  
Processing Unit ◽  
Graphical Processing

scholarly journals TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units

2020 ◽  
Vol 152 (22) ◽  
pp. 224110 ◽  
Author(s):  
Stefan Seritan ◽  
Christoph Bannwarth ◽  
B. Scott Fales ◽  
Edward G. Hohenstein ◽  
Sara I. L. Kokkila-Schumacher ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Ab Initio ◽  
Ab Initio Molecular Dynamics ◽  
Graphical Processing Units ◽  
Graphical Processing

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 Long Timestep Molecular Dynamics on the Graphical Processing Unit

2013 ◽  
Vol 9 (8) ◽  
pp. 3267-3281 ◽  
Author(s):  
James C. Sweet ◽  
Ronald J. Nowling ◽  
Trevor Cickovski ◽  
Christopher R. Sweet ◽  
Vijay S. Pande ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Graphical Processing Unit ◽  
Processing Unit ◽  
Graphical Processing

A web-deployed interface for performing ab initio molecular dynamics, optimization, and electronic structure in Fireball

2009 ◽  
Vol 180 (3) ◽  
pp. 418-426 ◽  
Author(s):  
J. Brandon Keith ◽  
Jacob R. Fennick ◽  
Chad E. Junkermeier ◽  
Daniel R. Nelson ◽  
James P. Lewis
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Ab Initio ◽  
Ab Initio Molecular Dynamics

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.

An adaptive finite-element method for large-scale ab initio molecular dynamics simulations

2015 ◽  
Vol 17 (47) ◽  
pp. 31444-31452 ◽  
Author(s):  
Eiji Tsuchida ◽  
Yoong-Kee Choe ◽  
Takahiro Ohkubo
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Polymer Electrolyte Membrane ◽  
Ab Initio Molecular Dynamics ◽  
Adaptive Finite Element Method ◽  
Adaptive Finite Element ◽  
Electrolyte Membrane ◽  
Dynamics Simulations

A snapshot of ab initio molecular dynamics simulations for a polymer electrolyte membrane at low hydration.

Ab-Initio Molecular Dynamics Approach to the Study of Grain Boundaries in Semiconductors

1988 ◽  
Vol 141 ◽  
Author(s):  
E. Tarnow ◽  
P. D. Bristowe ◽  
J. D. Joannopoulos ◽  
M. C. Payne
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Ab Initio ◽  
Local Density ◽  
Ab Initio Molecular Dynamics ◽  
Local Density Of States ◽  
High Angle ◽  
Surface Information ◽  
Atomic And Electronic Structure ◽  
Translation State

AbstractUsing an ab-initio molecular dynamics approach based on the Car-Parrinello method, the detailed atomic and electronic structure of a high-angle grain boundary in germanium is determined by investigating its energy-translation surface. Information concerning the coordination of the lowest energy configuration, its translation state, volume change, structure factor and local density of states is obtained.

Electronic Structure and Dynamics of Defect in a-Si:H by Ab-Initio Molecular Dynamics

1993 ◽  
Vol 297 ◽  
Author(s):  
N. Orita ◽  
T. Sasaki ◽  
H. Katayama–Yoshida
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Ab Initio ◽  
Hydrogenated Amorphous Silicon ◽  
Ab Initio Molecular Dynamics ◽  
Dangling Bond ◽  
Structure And Dynamics ◽  
Dynamics Simulations ◽  
Hydrogenated Amorphous

Electronic structure and dynamics of defects in hydrogenated amorphous silicon (a-Si:H) are investigated based upon ab–initio molecular–dynamics simulations. It is shown that (i) the hydrogen–passivated dangling bond (Si-H), (ii) the positively-ionized three–centered bond (Si– H+–Si), (iii) the negatively–ionized three–coordinated dangling bond (D−) and (iv) the five- coordinated floating bond (F5) are the intrinsic defects in a–Si:H. Based upon the calculated result, we discuss the role of hydrogen and the origin of the photo–induced defect in a-Si:H.

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