A Parallel Implementation of Tight-Binding Molecular Dynamics Based on Reordering of Atoms and the Lanczos Eigen-Solver

1995 ◽  
Vol 408 ◽  
Author(s):  
Luciano Colombot ◽  
William Sawyer ◽  
Djordje Marict
Keyword(s):  
Molecular Dynamics ◽  
Parallel Machines ◽  
Materials Science ◽  
Parallel Implementation ◽  
Tight Binding ◽  
Hamiltonian Matrix ◽  
Time Step ◽  
Full Spectrum ◽  
Eigen Values ◽  
Storage Format

AbstractWe introduce an efficient and scalable parallel implementation of tight-binding molecular dynamics (TBMD) which employs reordering of the atoms in order to maximize datalocality of the distributed tight-binding (TB) Hamiltonian matrix. Reordering of the atom labels allows our new algorithm to scale well on parallel machines since most of the TB hopping integrals for a given atom are local to the processing element (PE) therefore minimizing communication. The sparse storage format and the distribution of the required eigenvectors reduces memory requirements per PE. The sparse storage format and a stabilized parallel Lanczos eigen-solver allow consideration of large problem sizes relevant to materials science. In addition, the implementation allows the calculation of the full spectrum of individual eigen-values/-vectors of the TB matrix at each time-step. This feature is a key issue when the dielectric and optical response must be computed during a TBMD simulation. We present a benchmark of our code and an analysis of the overall efficiency.

An Ab-Initio Multicenter Tight-Binding Model for Molecular Dynamics Simulations

1988 ◽  
Vol 141 ◽  
Author(s):  
Otto F. Sankey ◽  
David J. Niklewski
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Local Density ◽  
Tight Binding ◽  
Real Space ◽  
Hamiltonian Matrix ◽  
Binding Model ◽  
Annealing Study ◽  
Total Energies ◽  
Dynamics Simulations

AbstractA new, approximate method has been developed for computing total energies and forces for a variety of applications including molecular dynamics simulations of covalent materials. The method is tight-binding-like and is based on the local density approximation within the pseudopotential scheme. Slightly excited pseudo-atomic-orbitals are used, and the tight-binding Hamiltonian matrix is obtained in real space. The method is used to find the total energies for five crystalline phases of Si and the Si 2 molecule. Excellent agreement is found with experiment. A molecular dynamics simulated annealing study has been performed on the Si 3 molecule to determine the ground state configuration.

Tight-Binding Molecular Dynamics of Ceramic Nanocrystals Using Pc-Based Parallel Machines

1999 ◽  
Vol 581 ◽  
Author(s):  
Kenji Tsuruta ◽  
Hiroo Totsuji ◽  
Chieko Totsuji
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structures ◽  
Parallel Machines ◽  
Tight Binding ◽  
Expansion Method ◽  
Surface Structures ◽  
Electronic Density ◽  
Pc Cluster ◽  
Fermi Operator ◽  
Gap States

ABSTRACTEvolution of atomic and electronic structures of silicon-carbide (SiC) nanocrystals during sintering is investigated by a tight-binding molecular dynamics (TBMD) method. An O(N) algorithm (the Fermi-operator expansion method) is employed for calculating electronic contributions in the energy and forces. Simulations are performed on our eight-node parallel PC cluster. In a sintering simulation of aligned (no tilt or twist) SiC nanocrystals at T = 1000K, we find that a neck is formed promptly without formation of defects. Analyses of local electronic density-of-states (DOS) and effective charges reveal that unsaturated bonds exist only in grain surfaces accompanying the gap states. In the case of tilted (<122>) nanocrystals, surface structures formed before sintering affect significantly the grainboundary formation.

Large-Scale Molecular Dynamics Simulations of Interstitial Defect Diffusion in Silicon

2002 ◽  
Vol 731 ◽  
Author(s):  
David A. Richie ◽  
Jeongnim Kim ◽  
Richard Hennig ◽  
Kaden Hazzard ◽  
Steve Barr ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Tight Binding ◽  
Md Simulations ◽  
Binding Potential ◽  
Interstitial Defect ◽  
Long Time ◽  
Computational Materials ◽  
Dynamics Simulations

AbstractThe simulation of defect dynamics and evolution is a technologicaly relevant challenge for computational materials science. The diffusion of small defects in silicon unfolds as a sequence of structural transitions. The relative infrequency of transition events requires simulation over extremely long time scales. We simulate the diffusion of small interstitial clusters (I1, I2, I3) for a range of temperatures using large-scale molecular dynamics (MD) simulations with a realistic tight-binding potential. A total of 0.25 μ sec of simulation time is accumulated for the study. A novel real-time multiresolution analysis (RTMRA) technique extracts stable structures directly from the dynamics without structural relaxation. The discovered structures are relaxed to confirm their stability.

Large Scale Atomistic Simulations using the Tight Binding Approach

1997 ◽  
Vol 491 ◽  
Author(s):  
M. Celino ◽  
F. Cleri ◽  
L. Colombo ◽  
M. Rosati ◽  
V. Rosato ◽  
...  
Keyword(s):  
Computer Architecture ◽  
Amorphous Materials ◽  
Large Scale ◽  
Materials Science ◽  
Tight Binding ◽  
Hamiltonian Matrix ◽  
Extended Defects ◽  
Atomistic Modelling ◽  
New Perspective ◽  
Scaling Algorithms

ABSTRACTAtomistic modelling of Materials Science problems often requires the simulation of systems with an irreducibly-large unit cell, such as amorphous materials, fullerites, or systems containing extended defects, such as dislocations, cracks or grain boundaries. Large-scale simulations with the Tight-Binding approach must face the computational obstacle represented by the O(N3)-scaling of the diagonalization of the Hamiltonian matrix. This bottleneck can be overcome by parallel computing techniques and/or the introduction of faster, O(N)-scaling algorithms. We report the activities performed in the frame of a collaboration among several research groups on the porting of TBMD codes on parallel computers. In particular, we describe the porting of a O(N3) TBMD code on different MIMD computers, with either distributed or shared memory, by using appropriate software tools. Furthermore, preliminary results obtained in the porting of an O(N) TBMD code on an experimental, hybrid MIMD-SIMD computer architecture are reported. The new perspective of using specialized platforms to deal with large-scale TBMD simulation is discussed.

MOLECULAR DYNAMICS AND QUANTUM MOLECULAR DYNAMICS SIMULATIONS ON PARALLEL ARCHITECTURES

1994 ◽  
Vol 05 (02) ◽  
pp. 281-283
Author(s):  
PRIYA VASHISHTA ◽  
RAJIV K. KALIA ◽  
AIICHIRO NAKANO ◽  
JIN YU
Keyword(s):  
Molecular Dynamics ◽  
Tight Binding ◽  
Porous Silica ◽  
Interaction Model ◽  
Multiple Time ◽  
Quantum Molecular Dynamics ◽  
Time Step ◽  
Multiple Time Step ◽  
Parallel Molecular Dynamics ◽  
Dynamics Simulations

Efficient parallel molecular dynamics (MD) algorithm based on the multiple-time-step (MTS) approach is developed. The MTS-MD algorithm is used to study structural correlations in porous silica at densities 2.2 g/cm3 to 1.6 g/cm3. Nature of phonons and effects of hydrostatic pressure in solid C60 is studied using the tight-binding MD method within a unified interaction model which includes intermolecular and intra-molecular interactions.

Efficient Treatment of Fixed and Induced Dipolar Interactions

2000 ◽  
Vol 653 ◽  
Author(s):  
Celeste Sagui ◽  
Thoma Darden
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Lagrangian Formalism ◽  
Dipolar Interactions ◽  
Time Step ◽  
Efficient Treatment ◽  
Particle Mesh Ewald ◽  
Fixed Charges ◽  
Self Consistency ◽  
Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

Evolution of Metastable Structures in Bimetallic Catalysts from Microscopy and Machine-Learning Molecular Dynamics

2020 ◽  
Author(s):  
Jin Soo Lim ◽  
Jonathan Vandermause ◽  
Matthijs A. van Spronsen ◽  
Albert Musaelian ◽  
Christopher R. O’Connor ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Complete Characterization ◽  
Layer By Layer ◽  
Surface Restructuring ◽  
Metastable Structures ◽  
Mechanistic Investigation ◽  
Underlying Mechanisms

Restructuring of interface plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different composition and morphology at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of the long-timescale restructuring of Pd deposited on Ag, using microscopy, spectroscopy, and novel simulation methods. Encapsulation of Pd by Ag always precedes layer-by-layer dissolution of Pd, resulting in significant Ag migration out of the surface and extensive vacancy pits. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. The underlying mechanisms are uncovered by performing fast and large-scale machine-learning molecular dynamics, followed by our newly developed method for complete characterization of atomic surface restructuring events. Our approach is broadly applicable to other multimetallic systems of interest and enables the previously impractical mechanistic investigation of restructuring dynamics.

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

2019 ◽  
Author(s):  
Frédéric Célerse ◽  
Louis Lagardere ◽  
Étienne Derat ◽  
Jean-Philip Piquemal
Keyword(s):  
Molecular Dynamics ◽  
Parallel Implementation ◽  
Steered Molecular Dynamics ◽  
Massively Parallel

This paper is dedicated to the massively parallel implementation of Steered Molecular Dynamics in the Tinker-HP softwtare. It allows for direct comparisons of polarizable and non-polarizable simulations of realistic systems.

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