Parallel Simulation Research Articles

Nano-friction behavior and deformation study of hydroxyapatite in ultra-precision polishing process.

In order to study the effect of ultra-precision machining on the surface quality of hydroxyapatite semiconductor materials as well as the material removal mechanism of hydroxyapatite, the mechanical polishing behaviors of hydroxyapatite at different polishing depths were studied by molecular dynamics method. The results show that the subsurface damage of hydroxyapatite increases with increasing polishing depth. The polishing temperature and the polishing force showed a positive correlation with the polishing depth, and the variation of the polishing force was related to the accumulation-release effect of the potential energy of hydroxyapatite material. In addition, the variation of stresses in hydroxyapatite during polishing is mainly influenced by the thermal softening effect. With a smaller polishing depth, the hydroxyapatite semiconductor material has fewer structural defects, fewer atoms undergoing phase transitions, lower surface roughness, and better surface quality. Therefore, to ensure the long-lasting service life of hydroxyapatite semiconductor materials, a small polishing depth should be used in ultra-precision machining. Additionally, this study also provides a theoretical reference for future research on the mechanical properties of hydroxyapatite-based composites. A Large-Scale Atomic/Molecular Parallel Simulator (LAMMPS) was utilized to perform molecular dynamics simulations. The output was visualized and analyzed by the Open Visualization Tools (OVITO) software. The intermolecular interactions were described by the polymer consistent force-field and the 12/6 Lennard-Jones potential functions. The workpiece was polished under a micro-canonical ensemble with the temperature settled at 300 K. Periodic boundary conditions were adopted and the velocity-Verlet algorithm was used to integrate the atomic motion with a timestep of 0.1 femtoseconds (fs).

Genetic algorithm for multilayer shield optimization with a custom parallel computing architecture

This paper introduces a novel architecture for optimizing radiation shielding using a genetic algorithm with dynamic penalties and a custom parallel computing architecture. A practical example focuses on minimizing the Total Ionizing Dose for a silicon slab, considering only the layer number and the total thickness (additional constraints, e.g., cost and density, can be easily added). Genetic algorithm coupled with Geant4 simulations in a custom parallel computing architecture demonstrates convergence for the Total Ionizing Dose values. To address genetic algorithm issues (premature convergence, not perfectly fitted search parameters), a Total Ionizing Dose Database Vault object was introduced to enhance search speed (data persistence) and to preserve all solutions’ details independently. The Total Ionizing Dose Database Vault analysis highlights boron carbide as the best material for the first layer for neutron shielding and high-Z material (e.g., Tungsten) for the last layers to stop secondary gammas. A validation point between Geant4 and MCNP was conducted for specific simulation conditions. The advantages of the custom parallel computing architecture introduced here, are discussed in terms of resilience, scalability, autonomy, flexibility, and efficiency, with the benefit of saving computational time. The proposed genetic algorithm-based approach optimizes radiation shielding materials and configurations efficiently benefiting space exploration, medical devices, nuclear facilities, radioactive sources, and radiogenic devices.

2D parallel simulation of seismic wave propagation in poroelastic media to monitor a CO2 geological sequestration process

Geological sequestration of carbon dioxide CO2 involves storing CO2 beneath geological formations to reduce atmospheric emissions. Typically, CO2 is pressurized into a liquid state and injected into porous rock formations. Monitoring this process relies on seismic data. For the effective monitoring of seismic wave propagation in extensive formations, a highly efficient and robust algorithm is essential. We developed an efficient approach to alleviate the computational workload associated with simulating CO2 sequestration using the staggered grid finite difference method. The method developed was applied to a moderately complex medium which represents pre- and post-CO2 injection of Utsira Formation, North Sea. The model was developed for two scenarios, representing the stages before and after the injection of CO2 into the Formation. The effect of CO2 was observed and picked efficiently in the reservoir by the algorithm developed for the scenarios before and after the injection of CO2. We could see the brightening of reflections with an increased CO2 saturation in the post-CO2 injection cases. The method developed greatly reduces the computational requirement of the simulation which makes it more efficient for large scale applications.

Development of a measure for assessing malingered incompetency in criminal proceedings: Denney competency related test (D-CRT)

ABSTRACT Introduction Experts frequently assess competency in criminal settings where the rate of feigning cognitive deficit is demonstrably elevated. We describe the construction and validation of the Denney Competency Related Test (D-CRT) to assess feigned incompetency of defendants in the criminal adjudicative setting. It was expected the D-CRT would prove effective at identifying feigned incompetence based on its two alternative, forced-choice and performance curve characteristics. Method Development and validation of the D-CRT occurred in described phases. Items were developed to measure competency based upon expert review. Item analysis and adjustments were completed with 304 young teenage volunteers to obtain a proper spread of item difficulty in preparation for eventual performance curve analysis (PCA). Test-retest reliability was assessed with 44 adult community volunteers. Validation included an analog simulation design with 101 jail detainees using MacArthur Competency Assessment Test-Criminal Adjudication and Word Memory Test as criterion measures. Effects of racial/ethnic demographic differences were examined in a separate study of 208 undergraduate volunteers. D-CRT specificity was identified with 46 elderly clinic referrals diagnosed with mild cognitive impairment and dementia. Results Item development, adjustment, and repeat analysis resulted in item probabilities evenly spread from .28 to 1.0. Test-retest correlation was good (.83). Internal consistency of items was excellent (KR-20 > .91). D-CRT demonstrated convergent validity in regard to measuring competency related information and as well as malingering. The test successfully differentiated between jail inmates asked to perforfm their best and inmates asked to simulate incompetency (AUC = .945). There were no statistically significant differences found in performance across racial/ethnic backgrounds. D-CRT specificity remained excellent among elderly clinic referrals with significant cognitive compromise at the recommended total score cutoff. Conclusions D-CRT is an effective measure of feigned criminal incompetency in the context of potential cognitive deficiency, and PCA is assistive in the determination. Additional validation using knowns groups designs with various mental health-related conditions are needed.

One-step formation of three-dimensional interconnected T-shaped microstructures inside composites by orthogonal bidirectional self-assembly method

ABSTRACT The fillers inside a polymer matrix should typically be self-assembled in both the horizontal and vertical directions to obtain 3-dimentional (3D) percolation pathways, whereby the fields of application can be expanded and the properties of organic-inorganic composite films improved. Conventional dielectrophoresis techniques can typically only drive fillers to self-assemble in only one direction. We have devised a one-step dielectrophoresis-driven approach that effectively induces fillers self-assembly along two orthogonal axes, which results in the formation of 3D interconnected T-shaped iron microstructures (3D-T CIP) inside a polymer matrix. This approach to carbonyl iron powder (CIP) embedded in a polymer matrix results in a linear structure along the thickness direction and a network structure on the top surface of the film. The fillers in the polymer were controlled to achieve orthogonal bidirectional self-assembly using an external alternating current (AC) electric field and a non-contact technique that did not lead to electrical breakdown. The process of 3D-T CIP formation was observed in real time using in situ observation methods with optical microscopy, and the quantity and quality of self-assembly were characterized using statistical and fractal analysis. The process of fillers self-assembly along the direction perpendicular to the electric field was explained by finite element analogue simulations, and the results indicated that the insulating polyethylene terephthalate (PET) film between the electrode and the CIP/prepolymer suspension was the key to the formation of the 3D-T CIP. In contrast to the traditional two-step method of fabricating sandwich-structured film, the fabricated 3D-T CIP film with 3D electrically conductive pathways can be applied as magnetic field sensor.

More with less: Harvesting transition mechanism, free energy, and rates from short parallel molecular dynamics simulations

More with less: Harvesting transition mechanism, free energy, and rates from short parallel molecular dynamics simulations

Investigation of some thermal properties of iron and chromium-based core-shell nanowires

Fe and Cr based core–shell nanowires (CSNWs) are modeled as cylindrical structures in which the atoms are arranged in a bcc crystal structure. Two different sizes with diameters of 2.5 nm and 4.5 nm for nanowires (NWs) are created and their lengths are set as four times their diameters. Their structural and thermodynamic properties are investigated through the molecular dynamics (MD) simulation technique in the canonical (NVT) statistical ensemble implemented in the open-source Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) software package. Atomic interactions between the atoms are described by using the many-body potentials based on the Embedded Atom Model (EAM). The melting temperatures of the NWs have been determined by investigating the behavior of the potential energy, specific heat capacity, radial distribution function, Lindemann melting criterion, the mean square displacement, and diffusion coefficients as a variation of temperature. The same melting temperatures are acquired from all these temperature-dependent physical properties for all NWs considered in this study. To the best of our knowledge, our simulation results are presented for the first time in this work and have the potential to guide experimental studies.

Investigation of dislocation and twinning behavior in HMX under high-velocity impact employing molecular dynamics simulations.

Under the ReaxFF/lg force field, the multiscale shock technique (MSST) was employed to investigate the decomposition behavior of perfect, dislocated, and twinned octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) at a velocity of 11 km/s. This study aimed to analyze the changes in system temperature, bond formation and breaking, variations in the number of small molecules, and the number of clusters. The results indicated that the sensitivity of dislocated HMX was the lowest, while the sensitivity of twinned and perfect HMX was comparable. Comparing the formation and breaking of bonds in HMX during the shock process, it was found that the change in the number of bonds in dislocated HMX was similar to that in perfect HMX, whereas twinning accelerated the breaking of bonds. By analyzing the changes in small molecular fragments (CO, CO2, H, H2, H2O, N2, N2H, NH2, NO, NO2, and O) during the shock process of HMX, it was found that dislocation had a relatively minor effect on the small molecular fragments, while twinning promoted the generation of CO, H, NO, and O and accelerated the decomposition of NO. A comparison of the number, weight, and atomic ratio of clusters under perfect, dislocated, and twinned conditions revealed that under the influence of shock, the number of clusters initially increased sharply and then decreased slowly. Meanwhile, compared to the perfect and dislocated explosives, the number of clusters under the twinned structure was significantly fewer, indicating that the twinned structure could reduce cluster formation. The proportion of oxygen to carbon in the twinned HMX was lower than that in the perfect and dislocated explosives, possibly due to the higher content of small molecular fragment O in twinned HMX. Different structures of HMX crystals were constructed, including twinned defect structure (with a supercell containing 6458 atoms), dislocation defect structure (with a supercell containing 2352 atoms), and perfect structure (also with a supercell containing 2352 atoms). The modeling of defect crystal structures was carried out using the Atomsk software. For the twinned defect structure, we first constructed a mirror symmetric structure of the original configuration and then merged these two structures together. For the dislocation defect structure, we shifted a segment of the originally ordered perfect crystal structure by a certain distance using Atomsk. Before conducting the simulations, we performed geometric optimization of the models using the conjugate gradient (CG) algorithm and carried out 10 ps of NVT and NPT simulations to equilibrate the energy, temperature, and other parameters within the system. Finally, a 50-ps MSST impact simulation was performed using Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS).

Acoustic emission characteristic of sandstone and sandstone like material under multi-path loading.

Using spline interpolation to select proportions of similar materials, a comparative analysis of the fracturing behavior of sandstone specimens and similar material specimens was conducted through Brazilian splitting tests under multi-path loading. The study revealed that during stepwise loading, both sandstone and similar materials exhibited memory effects and plastic deformation. However, under constant velocity loading, the relationship between force and displacement in sandstone showed linearity after compaction. Employing MATLAB optimization algorithms for the inversion of acoustic emission event information, the distribution of fracture points, and the evolution of cracks were analyzed. The findings indicated that under stepwise loading, both sandstone and similar materials exhibited banded distribution of peak frequencies, with sandstone concentrated in the mid-low-frequency range and similar materials leaning towards the low-frequency range. The amplitude-frequency characteristics of acoustic emission signals suggested that initially, sandstone produced low-frequency, low-amplitude signals. As cracks developed, these signals gradually transformed into high-frequency, high-amplitude signals, ultimately leading to macroscopic failure. The ringing counts and b-values of sandstone displayed an approximate "W" shape distribution, with a subsequent decrease in b-values during final failure. In contrast, the acoustic emission counts were inversely related to b-values. Similar materials exhibited slightly more acoustic emission counts than sandstone, with relatively lower b-values. The crack development process of both sandstone and similar materials was confirmed through these observations. From the perspective of section initiation and local damage, sandstone and similar materials exhibited similar failure characteristics. The proportions of quartz sand: cement: water = 9:1:0.9 in similar materials demonstrated the most similar characteristics to sandstone in terms of mechanical loading, acoustic emission features, and failure morphology. This suggests that these similar materials can be used as substitutes for sandstone in analogous simulation experiments. The study provides theoretical support for understanding rock fracture mechanisms, offers guidance for the selection and proportioning of similar materials, and holds significance for predicting and controlling rock fracture behavior in engineering applications.

Effects of Topological Parameters on Thermal Properties of Carbon Nanotubes via Molecular Dynamics Simulation

Due to their unique properties, carbon nanotubes (CNTs) are finding a growing number of applications across multiple industrial sectors. These properties of CNTs are subject to influence by numerous factors, including the specific chiral structure, length, type of CNTs used, diameter, and temperature. In this topic, the effects of chirality, diameter, and length of single-walled carbon nanotubes (SWNTs) on the thermal properties were studied using the reverse non-equilibrium molecular dynamics (RNEMD) method and the Tersoff interatomic potential of carbon–carbon based on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). For the shorter SWNTs, the effect of chirality on the thermal conductivity is more obvious than for longer SWNTs. Thermal conductivity increases with increasing chiral angle, and armchair SWNTs have higher thermal conductivity than that of zigzag SWNTs. As the tube length becomes longer, the thermal conductivity increases while the effect of chirality on the thermal conductivity decreases. Furthermore, for SWNTs with longer lengths, the thermal conductivity of zigzag SWNTs is higher than that of the armchair SWNTs. Thermal resistance at the nanotube–nanotube interfaces, particularly the effect of CNT overlap length on thermal resistance, was studied. The simulation results were compared with and in agreement with the experimental and simulation results from the literature. The presented approach could be applied to investigate the properties of other advanced materials.

Massively parallel simulations of multi-stage compressors on Sunway TaihuLight

Massively parallel simulations of multi-stage compressors on Sunway TaihuLight

A simple efficient algorithm for molecular simulations of constant potential electrodes.

Increasingly, society requires high power, high energy storage devices for applications ranging from electric vehicles to buffers on the electric grid. Supercapacitors are a promising contribution to meeting these demands, though there still remain unsolved practical problems. Molecular dynamics simulations can shed light on the relevant molecular level processes in electric double layer capacitors, but these simulations are computationally very demanding. Our focus here is on the algorithmic complexity of the constant potential method (CPM), which uses dedicated electrostatics solvers to maintain a fixed potential difference between two conducting electrodes. We show how any standard electrostatics solver-capable of calculating the energies and forces on all atoms-can be used to implement CPM with a minimum of coding. As an example, we compare our generalized implementation of CPM, based on invocations of the particle-particle-particle-mesh routine of the Large-scale Atomic/Molecular Massively Parallel Simulator, with a traditional implementation based on a dedicated re-implementation of Ewald summation. Both methods yield comparable results on four test systems, with the former achieving a substantial gain in speed and improved scalability. The step from dedicated electrostatic solvers to generic routines is made possible by noting that CPM's traditional narrow Gaussian point-spread of atomic charges on the electrodes effectively endows point-like atoms with chemical hardness, i.e., an intra-atomic energy quadratic in the charge.

Parallel Quantum Algorithm for Hamiltonian Simulation

We study how parallelism can speed up quantum simulation. A parallel quantum algorithm is proposed for simulating the dynamics of a large class of Hamiltonians with good sparse structures, called uniform-structured Hamiltonians, including various Hamiltonians of practical interest like local Hamiltonians and Pauli sums. Given the oracle access to the target sparse Hamiltonian, in both query and gate complexity, the running time of our parallel quantum simulation algorithm measured by the quantum circuit depth has a doubly (poly-)logarithmic dependence polylog⁡log⁡(1/ϵ) on the simulation precision ϵ. This presents an exponential improvement over the dependence polylog⁡(1/ϵ) of previous optimal sparse Hamiltonian simulation algorithm without parallelism. To obtain this result, we introduce a novel notion of parallel quantum walk, based on Childs' quantum walk. The target evolution unitary is approximated by a truncated Taylor series, which is obtained by combining these quantum walks in a parallel way. A lower bound Ω(log⁡log⁡(1/ϵ)) is established, showing that the ϵ-dependence of the gate depth achieved in this work cannot be significantly improved.Our algorithm is applied to simulating three physical models: the Heisenberg model, the Sachdev-Ye-Kitaev model and a quantum chemistry model in second quantization. By explicitly calculating the gate complexity for implementing the oracles, we show that on all these models, the total gate depth of our algorithm has a polylog⁡log⁡(1/ϵ) dependence in the parallel setting.

Effects of sp3 bond ratio and modulation ratios on nanotribology behaviors of diamond-like carbon coatings investigated using atomistic nanoscratching simulations.

Diamond-like carbon (DLC) films are amorphous solids in which carbon atoms are linked by hybridized sp3, sp2, and sp bonds. The mechanical and tribological properties of DLC films can be adjusted by tuning the sp2/sp3 bond ratio. These films are typically used as protective coatings for components such as dies, automotive engines, mechanical seals, hard disk drives, biological engineering devices, and micro/nano-electromechanical systems. Further exploration of the mechanical and tribological behavior of DLC films is important for enhancing functional design for the above applications. The simulation results show that single-layer DLC with a higher sp3 ratio has better resistance to indentation. Single-layer DLC with a lower initial sp3 ratio has lower friction and a shorter repeated cycle in the friction force curve due to an increase in the graphitization of the friction interface. Single-layer DLC with a higher sp3 ratio has a higher coefficient of friction because compared with the normal force, the friction force is much more sensitive to an increase in the sp3 ratio. Molecular dynamics simulations based on the Tersoff potential were performed using the open-source code LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator).

Development of a Scalable Parallel Compositional Simulator for Thermo-Hydromechanical Coupling in Fractured Rocks Using an Embedded Discrete Fracture Model

Summary Numerical simulation of thermo-hydromechanical (THM) coupling in practical complex fractured rocks is an essential but challenging issue for the evaluation and optimization of underground energy production. In this study, we present our work on a scalable parallel compositional simulator for THM coupling, which is suitable for massive 3D polygonal fractures. In addition, we also present the improvements, parallel implementation, and optimization of an embedded discrete fracture model (EDFM). A unified cell-centered grid system based on the finite volume method (FVM) is used for all governing equations, and an extended stencil is adopted for mechanical equations to resolve the low-resolution defect of the traditional FVM. The deformation of both matrix rock and fractures is considered. A sequential fully implicit (SFI) method is adopted to solve THM coupling. This simulator is validated against three analytical solution models. Finally, we apply the simulator to two cases including a multilayered shale gas reservoir with massive natural fractures and a fractured geothermal model using CO2 as a working fluid. We also test the performance and parallel scalability on 1,024 CPU cores with up to 50 million matrix gridblocks and 5.5 million fracture gridblocks. The results show that this simulator can efficiently solve the THM coupling problem in practical massive fractures.

A Fast Dynamic Simulation Method of an Active Distribution Network with Distributed Generations Based on Decomposition and Coordination

With the penetration of distributed resources into power distribution networks, power distribution networks are transforming into active distribution networks with a high proportion of distributed generations and power electronic equipment. Efficient modeling and simulation methods are essential to perform dynamic response analysis. In order to satisfy the fast/steady/slow multiple time-scale simulation requirements of active distribution networks, a fast/medium/slow time partition model and a network decoupling method for short line characteristic lines is proposed in this paper. Through the decomposition coordination simulation method, the network is decomposed into multiple regions that can be simulated in parallel. Based on the interconnection of fiber optic network cards, a multi-rate parallel simulation and synchronization strategy is proposed, which significantly improves the simulation speed of active distribution networks while ensuring simulation accuracy. The numerical experiments have been conducted based on a modified IEEE 33-bus and a PG&E 69-bus, and simulation results show the feasibility of the proposed method. The verification results of the example show that using adaptive variable-step-size multi-rate parallel simulation technology can increase the subnet computation-time balance rate and simulation acceleration ratio to 119.90% and 121.31% in the same rate-parallel mode.

Understanding the empirical process of animating to open up the field of stop motion analog simulation

As a stop motion specialist I tend to think it less as a relic than as a persisting medium, especially since this kind of production is still vivid in the film industry but also because I think some practices, or ways to use the medium are still not cleared because they are only considered as effects, not as an entire way of making a whole film.On the one hand it’s not only about theorizing but opening up new fields and developments based on what has already been done, sometimes unconsciously by artists. On the other hand we also feel the urge to free ourselves from discourses and practical tips given by the animators themselves. Most of the time stop motion animators are engaged in an empirical process leading them to a no less empirical knowledge. I myself discussed it with Patar and Aubier from the Beast animation fame and they don’t have much clue they are promptly and punctually disguising, transfiguring and thus transmuting matter, they only think in terms of material and technic limitations and how hint (or elaborated tricks) can help them solving it when trying to convey something on screen.That’s why we would like to engage ourselves into a physics-based analysis that would be a real asset to assert, didactically, what cause leads to what effects when animated one way or another, for example, exactly what kind of material can be used and what kind of manipulation or substitution leads to that effect of matter.

AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD.

All-atom molecular dynamics (MD) simulations are an essential structural biology technique with increasing application to multimillion-atom systems, including viruses and cellular machinery. Classical MD simulations rely on parameter sets, such as the AMBER family of force fields (AMBERff), to accurately describe molecular motion. Here, we present an implementation of AMBERff for use in NAMD that overcomes previous limitations to enable high-performance, massively parallel simulations encompassing up to two billion atoms. Single-point potential energy comparisons and case studies on model systems demonstrate that the implementation produces results that are as accurate as running AMBERff in its native engine.

Exploitation and Utilization of Generated Oil and Gas by Pyrolysis Simulation Modeling of Shale Source Rocks under the Condition of In Situ Conversion

Previous studies have mainly focused on the source rocks of the 7th Member of Yanchang Formation (Chang 7 Member) in the Ordos Basin, with very few studies focusing on the extracts from the source rocks. These extracts have important guiding significance for studying the in situ conversion process of shale oil. Taking the shale source rock of the Chang 7 Member as an example, this paper selected the extract of shale source rock (i.e., retained oil), which has been less studied previously, as the sample to carry out the hydrocarbon-generating pyrolysis simulation experiment of a semi-open–semi-closed system. Seven groups of parallel simulation experiments were designed with a pressure of 20 MPa. The generated oil and gas were collected and quantified, and their geochemical characteristics were researched. In addition, the generated oil and gas were investigated from aspects of cumulative yield and net increased yield, and the chromatographic and mass spectral characteristics of the generated oil were also researched. Based on this, an inductive hydrocarbon generation model of retained oil in shale source rocks was established: slow hydrocarbon generation stage (300–320 °C), rapid hydrocarbon generation stage (320–360 °C), and residual oil pyrolysis stage (0.79%Ro–1.47%Ro). This study is of important significance to guide the research on the in situ conversion process of shale source rock.

Sustainable Material Selection in New Constructions: A Brute‐Force Optimization Framework Using Parallel Computing, Cost Benefits, and Thermal Performance Analysis

Sustainable construction practices rely on carefully selecting building materials and balancing environmental and economic considerations. This study examines the complex link between local climate, market dynamics, and building material selection. Market data analysis, parametric modeling, and brute‐force optimization are used to provide insights into construction decision‐making. Across 5540 simulations, a thorough assessment of the financial and energy performance of various materials for walls, roofs, windows, and floors is conducted. Incorporating Pareto ranking, parallel simulation, and sensitivity analysis, the comprehensive evaluation reveals the intricate tradeoffs between cost, thermal properties, and energy savings. The findings highlight the potential for optimal external wall solutions to reduce U‐values by up to 30% and achieve source energy savings of up to 25% source energy savings across diverse climates. By emphasizing the importance of local context in material selection, this study highlights how energy consumption patterns and transmission losses influence financial and energy performance, thus advancing sustainable construction practices.