scholarly journals KIMERA: A Kinetic Montecarlo Code for Mineral Dissolution

Minerals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 825
Author(s):  
Pablo Martin ◽  
Juan J. Gaitero ◽  
Jorge S. Dolado ◽  
Hegoi Manzano
Keyword(s):  
Monte Carlo ◽  
Dissolution Rate ◽  
Point Defects ◽  
Open Source Software ◽  
Kinetic Monte Carlo ◽  
Object Oriented ◽  
Mineral Dissolution ◽  
Atomic Scale ◽  
Mineral Structure ◽  
Scientific Tool

KIMERA is a scientific tool for the study of mineral dissolution. It implements a reversible Kinetic Monte Carlo (KMC) method to study the time evolution of a dissolving system, obtaining the dissolution rate and information about the atomic scale dissolution mechanisms. KIMERA allows to define the dissolution process in multiple ways, using a wide diversity of event types to mimic the dissolution reactions, and define the mineral structure in great detail, including topographic defects, dislocations, and point defects. Therefore, KIMERA ensures to perform numerous studies with great versatility. In addition, it offers a good performance thanks to its parallelization and efficient algorithms within the KMC method. In this manuscript, we present the code features and show some examples of its capabilities. KIMERA is controllable via user commands, it is written in object-oriented C++, and it is distributed as open-source software.

Formation of embedded Co nanostructures in Cu(001) surface under electromigration

2020 ◽  
pp. 2150090
Author(s):  
S. V. Kolesnikov ◽  
A. L. Klavsyuk ◽  
A. M. Saletsky
Keyword(s):  
Monte Carlo ◽  
Current Density ◽  
Kinetic Monte Carlo ◽  
The Self ◽  
Atomic Scale ◽  
Self Organization ◽  
Simulation Results ◽  
Self Learning

Formation of embedded Co nanostructures in Cu(001) surface under electromigration is investigated on the atomic scale by performing self-learning kinetic Monte Carlo (kMC) simulations. The analysis of simulation results reveals the following important result. The electromigration of vacancies does not influence on the self-organization of Co nanostructures in the first layer of Cu(001) surface at all values of current density, which can be achieved in experiments.

Kinetics of Precipitation: Comparison between Monte Carlo Simulations, Cluster Dynamics and the Classical Laws

2005 ◽  
Vol 237-240 ◽  
pp. 671-676 ◽  
Author(s):  
Philippe Maugis ◽  
Frédéric Soisson ◽  
Ludovic Lae
Keyword(s):  
Monte Carlo ◽  
Kinetic Monte Carlo ◽  
Diffusion Mechanism ◽  
Interface Energy ◽  
Atomic Scale ◽  
Atomistic Simulations ◽  
Model Based ◽  
Kinetics Of Precipitation ◽  
Kinetics Of ◽  
Nucleation Growth

We test the main approximations of the classical laws for nucleation, growth and coarsening by comparison with atomistic simulations of the kinetics of precipitation. We investigate the kinetics of phase separation in dilute A-B solid solutions by precipitation of B atoms in the Arich matrix. Classically, the kinetics is represented by the time evolution of the total number of particles and their mean radius. In this work, the kinetics is predicted by three types of models: (a) an Atomic-scale Kinetic Monte Carlo (AKMC) model based on a vacancy diffusion mechanism, (b) a Cluster Dynamics model, and (c) the MultiPreci model, based on the coupling of the classical laws of nucleation, growth and coarsening. Cluster Dynamics and the Multipreci model have been parameterized such that the thermodynamic and kinetic parameters (solubility, diffusion coefficient, interface energy) be identical to that of the AKMC. Under these conditions we find that the classical laws are in good agreement with the atomistic simulations as long as the thermodynamics of the solid solution remains strictly regular. As expected, Cluster Dynamics compares better with the atomistic simulations, especially if a precise description of the energetics of the smallest clusters is applied.

Diffusion in the AlMo3 Ordered Intermetallic

2008 ◽  
Vol 272 ◽  
pp. 51-60
Author(s):  
M.I. Pascuet ◽  
Julián R. Fernández ◽  
A.M. Monti
Keyword(s):  
Monte Carlo ◽  
Point Defects ◽  
Interatomic Potential ◽  
Kinetic Monte Carlo ◽  
Statistical Thermodynamics ◽  
Monte Carlo Technique ◽  
Vacancy Mechanism ◽  
Ordered Intermetallic ◽  
Equilibrium Concentrations

An EAM interatomic potential for the ordered AlMo3 intermetallic is developed and applied to the study of point defects in the AlMo3. The equilibrium concentrations of vacancies and antisites are calculated using statistical thermodynamics. Results show that antisites are the most abundant type of defect in a range of temperatures and compositions close to stoichiometry. Finally, the diffusion by vacancy mechanism in the same structure is studied through the kinetic Monte Carlo technique. Possible atomic mechanisms of diffusion are suggested and analyzed in some detail.

scholarly journals Effect of atomic scale plasticity on hydrogen diffusion in iron: Quantum mechanically informed and on-the-fly kinetic Monte Carlo simulations

2008 ◽  
Vol 23 (10) ◽  
pp. 2757-2773 ◽  
Author(s):  
A. Ramasubramaniam ◽  
M. Itakura ◽  
M. Ortiz ◽  
E.A. Carter
Keyword(s):  
Monte Carlo ◽  
Density Functional ◽  
Hydrogen Diffusion ◽  
Kinetic Monte Carlo ◽  
Computational Cost ◽  
Bulk Diffusion ◽  
Density Functional Theory Calculations ◽  
Atomic Scale ◽  
Energy Barriers ◽  
Eam Potential

We present an off-lattice, on-the-fly kinetic Monte Carlo (KMC) model for simulating stress-assisted diffusion and trapping of hydrogen by crystalline defects in iron. Given an embedded atom (EAM) potential as input, energy barriers for diffusion are ascertained on the fly from the local environments of H atoms. To reduce computational cost, on-the-fly calculations are supplemented with precomputed strain-dependent energy barriers in defect-free parts of the crystal. These precomputed barriers, obtained with high-accuracy density functional theory calculations, are used to ascertain the veracity of the EAM barriers and correct them when necessary. Examples of bulk diffusion in crystals containing a screw dipole and vacancies are presented. Effective diffusivities obtained from KMC simulations are found to be in good agreement with theory. Our model provides an avenue for simulating the interaction of hydrogen with cracks, dislocations, grain boundaries, and other lattice defects, over extended time scales, albeit at atomistic length scales.

scholarly journals Cluster Dynamics Modeling of Materials: Advantages and Limitations

2007 ◽  
Vol 129 ◽  
pp. 51-58 ◽  
Author(s):  
Alain Barbu ◽  
Emmanuel Clouet
Keyword(s):  
Monte Carlo ◽  
Point Defects ◽  
Source Term ◽  
Kinetic Monte Carlo ◽  
Short Review ◽  
Metallic Materials ◽  
Dynamics Modeling ◽  
Term Evolution ◽  
Primary Damage

The aim of this paper is to give a short review on cluster dynamics modeling in the field of atoms and point defects clustering in materials. It is shown that this method, due to its low computer cost, can handle long term evolution that cannot, in many cases, be obtained by Lattice Kinetic Monte Carlo methods. Indeed, such a possibility is achieved thanks to an important drawback that is the loss of space correlations of the elements of the microstructures. Some examples, in the field of precipitation and irradiation of metallic materials are given. The limitations and difficulties of this method are also discussed. Unsurprisingly, it is shown that it goes in a very satisfactory way when the objects are distributed homogeneously. Conversely, the source term describing the primary damage under irradiation, by nature heterogeneous in space and time, is tricky to introduce especially when displacement cascades are produced.

Atomic Scale Modeling of the Silicon (100) Thermal Oxidation, A Kinetic Monte Carlo Approach

1999 ◽  
Vol 567 ◽  
Author(s):  
A. Esteve ◽  
M. Djafari Rouhani ◽  
Ph. Faurous ◽  
D. Esteve
Keyword(s):  
Monte Carlo ◽  
Thermal Oxidation ◽  
Large Scale ◽  
Kinetic Monte Carlo ◽  
Atomic Scale ◽  
Scale Modeling ◽  
Temporal Aspect ◽  
Oxidation Modeling ◽  
Original Approach ◽  
Oxidation Mechanisms

ABSTRACTIn this paper, we propose an original approach of the silicon (100) dry thermal oxidation modeling that is capable to reproduce the oxidation dynamics at the atomic level and at a large scale comparing with ab initio methods. This approach is based on the use of a Monte Carlo procedure to manage the temporal aspect. In conjunction with experimental literature data, first principle calculations have been carried out with the objective of isolating some elementary oxidation mechanisms, i.e. basic atomic movements and their corresponding energies. This preliminary list of mechanisms is discussed in detail. A growth mechanism allowing the oxide defect generation is proposed. Finally, we present Monte Carlo calculations with the implemented mechanisms where at least three silicon layers are oxidized.

The Role of Surface Annihilation in Annealing Investigated by Atomic Model Simulation

2005 ◽  
Vol 864 ◽  
Author(s):  
Min Yu ◽  
Xiao Zhang ◽  
Ru Huang ◽  
Xing Zhang ◽  
Yangyuan Wang ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Integrated Circuits ◽  
Point Defects ◽  
Model Simulation ◽  
Kinetic Monte Carlo ◽  
Boron Diffusion ◽  
Junction Depth ◽  
Kinetic Monte Carlo Method ◽  
Enhanced Diffusion

AbstractBehavior of point defects in annealing is investigated a lot in order to suppress the Transient Enhanced Diffusion (TED) of boron as is urged by the development of integrated circuits. Surface annihilation possibility for point defects is very important in determining junction depth in the case of ultra-shallow doping. However the understanding on it is still ambiguous considering the inconsistent results on surface annihilation behavior. In this paper the variation of surface annihilation possibility is studied. The simulation on boron diffusion as well as silicon diffusion is performed. The evolution of Si clusters is simulated. By explaining experimental results with Kinetic Monte Carlo method based simulation, we proposed that surface annihilation possibility varies in different cases.

scholarly journals The complementary graphene growth and etching revealed by large-scale kinetic Monte Carlo simulation

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Xiao Kong ◽  
Jianing Zhuang ◽  
Liyan Zhu ◽  
Feng Ding
Keyword(s):  
Monte Carlo ◽  
Large Scale ◽  
2D Materials ◽  
Kinetic Monte Carlo ◽  
Computational Cost ◽  
Atomic Scale ◽  
Graphene Growth ◽  
Graphene Island ◽  
Atomic Simulations ◽  
Hole Growth

AbstractTo fully understand the kinetics of graphene growth, large-scale atomic simulations of graphene islands evolution up to macro sizes (i.e., graphene islands of a few micrometers or with billions of carbon atoms) during growth and etching is essential, but remains a great challenge. In this paper, we developed a low computational cost large-scale kinetic Monte Carlo (KMC) algorithm, which includes all possible events of carbon attachments and detachments on various edge sites of graphene islands. Such a method allows us to simulate the evolution of graphene islands with sizes up to tens of micrometers during either growth or etching with a single CPU core. With this approach and the carefully fitted parameters, we have reproduced the experimentally observed evolution of graphene islands during both growth or etching on Pt(111) surface, and revealed more atomic details of graphene growth and etching. Based on the atomic simulations, we discovered a complementary relationship of graphene growth and etching—the route of graphene island shape evolution during growth is exactly the same as that of the etching of a hole in graphene and that of graphene island etching is exactly same as that of hole growth. The complementary relation brings us a basic principle to understand the growth and etching of graphene, and other 2D materials from atomic scale to macro size and the KMC algorithm is expected to be further developed into a standard simulation package for investigating the growth mechanism of 2D materials on various substrates.

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