| 查看: 361 | 回复: 0 | |||
| 当前主题已经存档。 | |||
HiPC至尊木虫 (初入文坛)
thinker
|
[交流]
推荐一篇优秀论文【已搜无重复】
|
||
|
论文题目:Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters 对该篇论文的评价(http://ergodicity.iamganesh.com/ ... lecular-dynamics/): One of the papers nominated for the best paper award at Supercomputing 06 is titled “Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters” from the DE Shaw Research group. If your standard of a modern molecular dynamics code is Computer Simulations of Liquids, then this paper is definitely worth a look. I’ve summarized the innovations below: Midpoint method Published earlier this year in the Journal of Chemical Physics, this is a parallelizing algorithm which is a hybrid between spatial decompositions and force decompositions. The major innovation of this method is the reduced communication bandwidth, which can be a problem when you scale simulations to hundreds of computers. Bitwise Time Reversibility One of the most important requirements for an integrator solving Newton’s equations of motion is symplecticity. One way to check to check for this is by running your integrator in negative time. Doing so should return the system to the initial state. Though not an absolute requirement, this is a nice thing to have for minimizing the energy drift, which ultimately leads to a more realistic simulation. These guys have an integrator that does this. Constraints in single precision To reduce high frequency motions (like vibrations of Carbon-Hydrogen bonds for example), simulations typically make use of constraints to hold bond lengths or atom velocities fixed. Typical codes RATTLE and SHAKE need to be done in double precision for accuracy and to maintain energy conservation. This paper talks about the use of an (unpublished) algorithm that is stable in single precision. Normalized local coordinates Instead of representing coordinates in an absolute global frame, these guys normalize coordinates. This gives them more precision (due to operations done on floating points of the same magnitudes.) It also makes handling periodic boundary conditions simple. Another advantage they mention is that doing pressure control is time reversible. Interpolation schemes Personally, I think this is the cornerstone of the paper. The paper mentions that instead of interactions being a function of distance between the particles, they compute it as a function of . The advantage is that the same set of polynomial coefficients can be used for computing both forces and energies. SIMD instructions I’m just mentioning this for completeness. As far as I know, every high performance engine makes use of these instructions. In fact, GROMACS has hand tuned kernels written using these instructions. In theory, this makes your code four times faster. In conclusion, I was pretty impressed with the quality of work and the innovations these guys have brought to the community. |
回复此楼» 猜你喜欢
调剂招生
已经有0人回复
-
调剂招生
已经有1人回复
-
物理化学论文润色/翻译怎么收费?
已经有144人回复
-
实际气体内压强的微观机制或将改写--------从一个基本的力学佯谬说起
已经有2人回复
-
调剂招生
已经有0人回复
-
调剂招生
已经有0人回复
-
调剂招生
已经有5人回复
-
招收0703开头的学硕调剂生 线上复试
已经有5人回复
-
求助：三乙酰丙酮铁（Fe(acac)₃）标准红外(IR)与XRD谱图/数据
已经有1人回复
-
微纳hub，微纳加工的宝库
已经有0人回复
-
微纳加工里的 lift-off 工艺
已经有0人回复
10