This paper mainly discusses the multiscale computation from a chemical engineering perspective.From the application designer's perspective,we propose a new approach to investigate and develop both flexible and eff...This paper mainly discusses the multiscale computation from a chemical engineering perspective.From the application designer's perspective,we propose a new approach to investigate and develop both flexible and efficient computer architectures. Based on the requirements of applications within one category,we first induce and extract some inherent computing patterns or core computing kernels from the applications.Some computing models and innovative computing architectures will then be developed for these patterns or kernels,as well as the software mapping techniques. Finally those applications which can share and utilize those computing patterns or kernels can be executed very efficiently on those novel computing architectures. We think that the proposed approach may not be achievable within the existing technology. However,we believe that it will be available in the near future. Hence,we will describe this approach from the following four aspects:multiscale environment in the world,mesoscale as a key scale,energy minimization multiscale(EMMS)paradigm and our perspective.展开更多
Discrete computer simulations are quite helpful in understanding dynamic structures in complex systems.Recently,using the Mole-8.5 supercomputer and molecular dynamics simulations as a"computational microscope&qu...Discrete computer simulations are quite helpful in understanding dynamic structures in complex systems.Recently,using the Mole-8.5 supercomputer and molecular dynamics simulations as a"computational microscope",we simulated the dynamic structure of a whole H1N1 influenza virion in solution for the first time at the atomic level.In total,300 million atoms in a periodic cube with an edge length of 148.5 nm were simulated.Using 288 low level hybrids with 1728 C2050 GPUs and a software package developed specifically for the hardware,the simulation executed 770 ps/d with an integration time step of 1 fs,and analyzed the dynamic structure.With the tremendous computational power of GPUs,efficient software packages for various hardware designs,and consistent physical models,more challenging applications will be carried out in the near future.展开更多
As a fully Lagrangian, particle-based numerical method, the traditional smoothed particle hydrodynamics (SPH) generally suffers from the accuracy problem. To investigate the physical origins of this numerical error, t...As a fully Lagrangian, particle-based numerical method, the traditional smoothed particle hydrodynamics (SPH) generally suffers from the accuracy problem. To investigate the physical origins of this numerical error, the elastic effect between SPH particles is specifically identified by analogy with physical entities, and a unique non-dimensional number is proposed to evaluate the relative dominance of viscous to elastic effect. Through the simulation of two-dimensional Couette flow, the velocity profile and arrangement of particles are examined for various ratios of viscous to elastic effect. The effective viscosity of SPH particles decreases as this non-dimensional number increases, while the increase of particle number significantly reduces the effective viscosity only at lower ratio of viscous to elastic effect. The disparity among nominal viscous dissipation, total dissipation, and theoretical dissipation further confirms the presence of unphysical dissipation resulting from the elastic effect. In summary, due to the constraints from the Mach number and the ratio of viscous to elastic effect, there exists a critical Reynolds number below which the Newtonian behavior could be approximately obtained through suitable choice of model parameters.展开更多
The behavior of a single polyethylene polymer in aqueous solution confined between two hydrophilic walls is studied with molecular dynamics (MD) simulations. The thickness of the nano-slit ranges from 1.26 to 3.15 nm,...The behavior of a single polyethylene polymer in aqueous solution confined between two hydrophilic walls is studied with molecular dynamics (MD) simulations. The thickness of the nano-slit ranges from 1.26 to 3.15 nm, which is comparative to the polymer dimension. A monotonic transition from 3D- to 2D-like configurations is observed as the distance between the two walls narrows. Monomers are compressed into several layers and the preferred bond orientations alternate between parallel and normal to the walls accordingly. The diffusivity in the direction parallel to the wall is always larger than the one perpendicular to it. Calculation of the entropy and enthalpy changes during the folding of the polymer chain alone cannot explain the spontaneous process. The corresponding increase in water entropy due to volume expansion may be large enough to result in the overall free energy decrease.展开更多
Compute Unified Device Architecture (CUDA) was used to design and implement molecular dynamics (MD) simulations on graphics processing units (GPU). With an NVIDIA Tesla C870, a 20-60 fold speedup over that of one core...Compute Unified Device Architecture (CUDA) was used to design and implement molecular dynamics (MD) simulations on graphics processing units (GPU). With an NVIDIA Tesla C870, a 20-60 fold speedup over that of one core of the Intel Xeon 5430 CPU was achieved, reaching up to 150 Gflops. MD simulation of cavity flow and particle-bubble interaction in liquid was implemented on multiple GPUs using a message passing interface (MPI). Up to 200 GPUs were tested on a special network topology, which achieves good scalability. The capability of GPU clusters for large-scale molecular dynamics simulation of meso-scale flow behavior was, therefore, uncovered.展开更多
This paper is devoted to exploring approaches to understanding the stochastic characteristics of particle-fluid two-phase flow. By quantifying the forces dominating the particle motion and modelling the less important...This paper is devoted to exploring approaches to understanding the stochastic characteristics of particle-fluid two-phase flow. By quantifying the forces dominating the particle motion and modelling the less important and/or unclear forces as random forces, a stochastic differential equation is proposed to describe the complex behavior of a particle motion. An exploratory simulation has shown satisfactory agreement with phase doppler particle analyzer (PDPA) measurements, which indicates that stochastic analysis is a potential approach for revealing the details of particle-fluid flow phenomena.展开更多
文摘砂颗粒流在石英砂滤层反冲洗流场中的速度分布,对滤层流化状态的稳定性和反冲洗效果起决定性作用。为了对滤层反冲洗过程砂颗粒的速度场进行分析,并确定最佳反冲洗速度,该文以厚度为400 mm,粒径范围为1.0～1.18 mm的石英砂滤层为研究对象,基于颗粒流运动理论,采用Eulerian-Eulerian模型对滤层反冲洗过程砂粒的速度场进行3维动态模拟。为了验证模拟结果的准确性,作者开展了室内模型试验,并将模拟结果与试验结果进行对比,结果显示,滤层膨胀高度的最大模拟误差为9.8%,能够控制在10%以内,说明数值模拟结果是可信的。在此基础上,分析了反冲洗流化倍数为1.3、1.5、1.7和1.9时,滤层高度分别为15、25和35 cm 3个横截面上,在不同的反冲洗时间,砂粒的轴向速度沿横坐标的分布规律。根据砂粒在3个横截面上运动速度的大小和方向,判断砂滤层是否达到完全流化;根据砂粒在3个横截面上运动趋势是否一致,砂粒的上升区是否保持稳定,判断滤层流化状态是否稳定。结果显示,当反冲洗流化倍数不小于1.7时,滤层才能达到稳定的流化状态,从而达到比较理想的反冲洗效果,并得出滤层最佳反冲洗流化倍数为1.7。研究结论为砂过滤器的反冲洗研究提供了理论基础和技术支撑,为反冲洗性能参数的确定提供了参考。
文摘This paper mainly discusses the multiscale computation from a chemical engineering perspective.From the application designer's perspective,we propose a new approach to investigate and develop both flexible and efficient computer architectures. Based on the requirements of applications within one category,we first induce and extract some inherent computing patterns or core computing kernels from the applications.Some computing models and innovative computing architectures will then be developed for these patterns or kernels,as well as the software mapping techniques. Finally those applications which can share and utilize those computing patterns or kernels can be executed very efficiently on those novel computing architectures. We think that the proposed approach may not be achievable within the existing technology. However,we believe that it will be available in the near future. Hence,we will describe this approach from the following four aspects:multiscale environment in the world,mesoscale as a key scale,energy minimization multiscale(EMMS)paradigm and our perspective.
基金supported by Ministry of Finance(ZDYZ2008-2)the National Key Science and Technology Project(2008ZX05014-003-006HZ)+1 种基金the Knowledge Innovation Project of Chinese Academy of Sciences (KGCX2-YW-124)the National Natural Science Foundation of China (20821092)
文摘Discrete computer simulations are quite helpful in understanding dynamic structures in complex systems.Recently,using the Mole-8.5 supercomputer and molecular dynamics simulations as a"computational microscope",we simulated the dynamic structure of a whole H1N1 influenza virion in solution for the first time at the atomic level.In total,300 million atoms in a periodic cube with an edge length of 148.5 nm were simulated.Using 288 low level hybrids with 1728 C2050 GPUs and a software package developed specifically for the hardware,the simulation executed 770 ps/d with an integration time step of 1 fs,and analyzed the dynamic structure.With the tremendous computational power of GPUs,efficient software packages for various hardware designs,and consistent physical models,more challenging applications will be carried out in the near future.
基金supported by the National Natural Science Foundation of China (21206167)the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA07080203)
文摘As a fully Lagrangian, particle-based numerical method, the traditional smoothed particle hydrodynamics (SPH) generally suffers from the accuracy problem. To investigate the physical origins of this numerical error, the elastic effect between SPH particles is specifically identified by analogy with physical entities, and a unique non-dimensional number is proposed to evaluate the relative dominance of viscous to elastic effect. Through the simulation of two-dimensional Couette flow, the velocity profile and arrangement of particles are examined for various ratios of viscous to elastic effect. The effective viscosity of SPH particles decreases as this non-dimensional number increases, while the increase of particle number significantly reduces the effective viscosity only at lower ratio of viscous to elastic effect. The disparity among nominal viscous dissipation, total dissipation, and theoretical dissipation further confirms the presence of unphysical dissipation resulting from the elastic effect. In summary, due to the constraints from the Mach number and the ratio of viscous to elastic effect, there exists a critical Reynolds number below which the Newtonian behavior could be approximately obtained through suitable choice of model parameters.
基金the National Natural Science Foundation of China (Grant Nos. 20336040, 20490201 and 20221603)Chinese Academy of Sciences (Grant Nos. KJCX-SW-L01 and KJCX3-SYW-S01)Research Fund of Key Lab for Nanomaterials, Ministry of Education of China (Grant No. 2006-1)
文摘The behavior of a single polyethylene polymer in aqueous solution confined between two hydrophilic walls is studied with molecular dynamics (MD) simulations. The thickness of the nano-slit ranges from 1.26 to 3.15 nm, which is comparative to the polymer dimension. A monotonic transition from 3D- to 2D-like configurations is observed as the distance between the two walls narrows. Monomers are compressed into several layers and the preferred bond orientations alternate between parallel and normal to the walls accordingly. The diffusivity in the direction parallel to the wall is always larger than the one perpendicular to it. Calculation of the entropy and enthalpy changes during the folding of the polymer chain alone cannot explain the spontaneous process. The corresponding increase in water entropy due to volume expansion may be large enough to result in the overall free energy decrease.
基金Supported by the National Natural Science Foundation of China (Grant Nos. 20336040, 20221603 and 20490201)the Chinese Academy of Sciences (Grant No. Kgcxz-yw-124)
文摘Compute Unified Device Architecture (CUDA) was used to design and implement molecular dynamics (MD) simulations on graphics processing units (GPU). With an NVIDIA Tesla C870, a 20-60 fold speedup over that of one core of the Intel Xeon 5430 CPU was achieved, reaching up to 150 Gflops. MD simulation of cavity flow and particle-bubble interaction in liquid was implemented on multiple GPUs using a message passing interface (MPI). Up to 200 GPUs were tested on a special network topology, which achieves good scalability. The capability of GPU clusters for large-scale molecular dynamics simulation of meso-scale flow behavior was, therefore, uncovered.
文摘This paper is devoted to exploring approaches to understanding the stochastic characteristics of particle-fluid two-phase flow. By quantifying the forces dominating the particle motion and modelling the less important and/or unclear forces as random forces, a stochastic differential equation is proposed to describe the complex behavior of a particle motion. An exploratory simulation has shown satisfactory agreement with phase doppler particle analyzer (PDPA) measurements, which indicates that stochastic analysis is a potential approach for revealing the details of particle-fluid flow phenomena.
