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Multi-level grid algorithms for faster molecular energetics 更快分子能量学的多级网格算法
Pub Date : 2010-09-01 DOI: 10.1145/1839778.1839799
R. Chowdhury, C. Bajaj
Bio-molecules reach their stable configuration in solvent which is primarily water with a small concentration of salt ions. One approximation of the total free energy of a bio-molecule includes the classical molecular mechanical energy EMM (which is understood as the self intra-molecular energy in vacuum) and the solvation energy Gsol which is caused by the change of the environment of the molecule from vacuum to solvent (and hence also known as the molecule-solvent interaction energy). This total free energy is used to model and study the stability of bio-molecules in isolation or in their interactions with drugs. In this paper we present fast O (N log N) multi-level grid based approximation algorithms (where N is the number of atoms) for efficiently estimating the compute-intensive terms of EMM and Gsol. The fast octree-based algorithm for Gsol is additionally dependent on an O (N) size computation of the biomolecular surface and its spatial derivatives (normals). We also provide several examples with timing results, and speed/accuracy tradeoffs, demonstrating the efficiency and scalability of our fast free energy estimation of bio-molecules, potentially with millions of atoms.
生物分子在溶剂中达到稳定构型,溶剂主要是水和少量盐离子。生物分子总自由能的一种近似包括经典的分子机械能EMM(被理解为真空中的自身分子内能量)和溶剂化能Gsol,这是由分子从真空到溶剂的环境变化引起的(因此也称为分子-溶剂相互作用能)。该总自由能用于模拟和研究生物分子在分离或与药物相互作用中的稳定性。在本文中,我们提出了快速的O (N log N)基于多级网格的近似算法(其中N是原子数),用于有效地估计EMM和Gsol的计算密集型项。基于八叉树的快速Gsol算法还依赖于生物分子表面及其空间衍生物(法线)的O (N)大小的计算。我们还提供了几个计时结果和速度/精度权衡的例子,展示了我们对生物分子的快速自由能估计的效率和可扩展性,可能有数百万个原子。
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引用次数: 4
Merging and smoothing machining boundaries on cutter location surfaces 合并和平滑刀具定位表面的加工边界
Pub Date : 2010-09-01 DOI: 10.1145/1839778.1839803
W. Li, Ralph Robert Martin, F. Langbein
In region machining, neighbouring regions may be close together, but disconnected. Boundary curves may also have unwanted geometric artifacts caused by approximation and discretisation. We present a strategy to improve the topology and geometry of such boundary curves, allowing the generation of better tool paths, and in turn, improved tool wear and surface quality of the machined part. We make such improvements in three steps: firstly, disconnected regions are merged where appropriate, using a method based on morphological operations from image processing. Secondly, boundary segments with undesirable geometric properties are identified and replaced by simpler segments, using a vertex deletion operation. Finally, flaws at a smaller geometric scale are removed, using a curve shortening algorithm. Experimental results are given to illustrate our algorithm.
在区域加工中,相邻的区域可能很近,但不相连。边界曲线也可能由于近似和离散化而产生不需要的几何伪影。我们提出了一种策略来改进这种边界曲线的拓扑和几何形状,从而产生更好的刀具路径,从而改善刀具磨损和加工零件的表面质量。我们分三步进行改进:首先,使用基于图像处理形态学操作的方法,在适当的地方合并断开的区域。其次,使用顶点删除操作,识别具有不良几何属性的边界段并将其替换为更简单的边界段。最后,使用曲线缩短算法去除较小几何尺度上的缺陷。实验结果验证了算法的有效性。
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引用次数: 1
Accurate moment computation using the GPU 使用GPU进行精确的力矩计算
Pub Date : 2010-09-01 DOI: 10.1145/1839778.1839790
A. Krishnamurthy, Sara McMains
We present algorithms for computing accurate moments of solid models that are represented using multiple trimmed NURBS surfaces. Our algorithms make use of programmable Graphics Processing Units (GPUs) to accelerate the computations. We evaluate the surface coordinates and normals accurately, with theoretical bounds, using our GPU NURBS evaluator. We have developed a framework that makes use of this data to evaluate surface integrals of trimmed NURBS surfaces in real time. With our framework, we can compute volume and moments of solid models with theoretical guarantees. The framework also supports local geometry changes, which is useful for providing interactive feedback to the designer while the solid model is being designed. We can compute the center of mass and check for stability of the solid model interactively. Applications of such real-time moment computation include deformation modeling, animation, and physically based simulations.
我们提出了计算使用多个修剪NURBS表面表示的实体模型的精确力矩的算法。我们的算法利用可编程图形处理单元(gpu)来加速计算。我们使用我们的GPU NURBS评估器精确地评估表面坐标和法线,具有理论界限。我们开发了一个框架,利用这些数据来评估实时修剪的NURBS表面的表面积分。利用我们的框架,我们可以计算出具有理论保证的实体模型的体积和矩。该框架还支持局部几何变化,这对于在设计实体模型时向设计人员提供交互式反馈非常有用。我们可以交互式地计算实体模型的质心和稳定性校核。这种实时力矩计算的应用包括变形建模、动画和基于物理的仿真。
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引用次数: 6
Geometric reasoning via internet CrowdSourcing 通过互联网众包进行几何推理
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629296
A. Jagadeesan, A. Lynn, J. Corney, Xiu-Tian Yan, J. Wenzel, A. Sherlock, W. Regli
The ability to interpret and reason about shapes is a peculiarly human capability that has proven difficult to reproduce algorithmically. So despite the fact that geometric modeling technology has made significant advances in the representation, display and modification of shapes, there have only been incremental advances in geometric reasoning. For example, although today's CAD systems can confidently identify isolated cylindrical holes, they struggle with more ambiguous tasks such as the identification of partial symmetries or similarities in arbitrary geometries. Even well defined problems such as 2D shape nesting or 3D packing generally resist elegant solution and rely instead on brute force explorations of a subset of the many possible solutions. Identifying economic ways to solving such problems would result in significant productivity gains across a wide range of industrial applications. The authors hypothesize that Internet Crowdsourcing might provide a pragmatic way of removing many geometric reasoning bottlenecks. This paper reports the results of experiments conducted with Amazon's mTurk site and designed to determine the feasibility of using Internet Crowdsourcing to carry out geometric reasoning tasks as well as establish some benchmark data for the quality, speed and costs of using this approach. After describing the general architecture and terminology of the mTurk Crowdsourcing system, the paper details the implementation and results of the following three investigations; 1) the identification of "Canonical" viewpoints for individual shapes, 2) the quantification of "similarity" relationships with-in collections of 3D models and 3) the efficient packing of 2D Strips into rectangular areas. The paper concludes with a discussion of the possibilities and limitations of the approach.
对形状进行解释和推理的能力是人类特有的能力,事实证明这种能力很难通过算法重现。因此,尽管几何建模技术在形状的表示、显示和修改方面取得了重大进展,但在几何推理方面却只有渐进式的进展。例如,虽然今天的CAD系统可以自信地识别孤立的圆柱形孔,但它们在更模糊的任务中挣扎,例如识别任意几何形状的部分对称性或相似性。即使是定义明确的问题,如2D形状嵌套或3D包装,通常也会抵制优雅的解决方案,而是依赖于对许多可能解决方案子集的蛮力探索。确定解决这些问题的经济方法将导致在广泛的工业应用中显著提高生产率。作者假设,互联网众包可能提供一种实用的方式来消除许多几何推理瓶颈。本文报告了在亚马逊的mTurk网站上进行的实验结果,旨在确定使用互联网众包来执行几何推理任务的可行性,并为使用这种方法的质量、速度和成本建立一些基准数据。在描述了mTurk众包系统的总体架构和术语之后,论文详细介绍了以下三项调查的实施和结果;1)单个形状的“规范”视点识别,2)三维模型集合内“相似”关系的量化,3)二维条形条在矩形区域内的有效填充。文章最后讨论了这种方法的可能性和局限性。
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引用次数: 19
Mesh clustering by approximating centroidal Voronoi tessellation 通过逼近质心Voronoi镶嵌的网格聚类
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629294
Fengtao Fan, F. Cheng, Conglin Huang, Yong Li, Jianzhong Wang, S. Lai
An elegant and efficient mesh clustering algorithm is presented. The faces of a polygonal mesh are divided into different clusters for mesh coarsening purpose by approximating the Centroidal Voronoi Tessellation of the mesh. The mesh coarsening process after clustering can be done in an isotropic or anisotropic fashion. The presented algorithm improves previous techniques in local geometric operations and parallel updates. The new algorithm is very simple but is guaranteed to converge, and generates better approximating meshes with the same computation cost. Moreover, the new algorithm is suitable for the variational shape approximation problem with L2, 1 distortion error metric and the convergence is guaranteed. Examples demonstrating efficiency of the new algorithm are also included in the paper.
提出了一种简洁高效的网格聚类算法。通过逼近多边形网格的质心Voronoi镶嵌,将多边形网格的面划分为不同的簇,达到网格粗化的目的。聚类后的网格粗化过程可以采用各向同性或各向异性的方式进行。该算法在局部几何运算和并行更新方面改进了原有的算法。该算法在保证收敛性的同时,简化了算法,并在相同的计算代价下生成了更好的逼近网格。该算法适用于具有L2、1畸变误差度量的变分形状逼近问题,并保证了算法的收敛性。文中还给出了一些实例,证明了新算法的有效性。
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引用次数: 4
An isogeometric BEM for exterior potential-flow problems in the plane 平面外位流问题的等几何边界元
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629302
C. Politis, A. Ginnis, P. Kaklis, K. Belibassakis, C. Feurer
In this paper, the isogeometric concept introduced by Hughes, in the context of Finite Element Method, is applied to Boundary Element Method (BEM), for solving an exterior planar Neumann problem. The developed isogeometric-BEM concept is based on NURBS, for representing the exact body geometry and employs the same basis for representing the potential and/or the density of the single layer. In order to examine the accuracy of the scheme, numerical results for the case of a circle and a free-form body are presented and compared against analytical solutions. This enables performing a numerical error analysis, verifying the superior convergence rate of the isogeometric BEM versus low-order BEM. When starting from the initial NURBS representation of the geometry and then using knot insertion for refinement of the NURBS basis, the achieved rate of convergence is O(DoF-4). This rate may be further improved by using a degree-elevated initial NURBS representation of the geometry (kh-refinement).
本文将Hughes在有限单元法背景下引入的等几何概念应用于边界元法(BEM),用于求解外平面诺依曼问题。开发的等几何边界元概念基于NURBS,用于表示精确的车身几何形状,并采用相同的基础来表示单层的势能和/或密度。为了检验该格式的准确性,给出了圆和自由形体的数值结果,并与解析解进行了比较。这样可以进行数值误差分析,验证等几何边界元与低阶边界元的优越收敛速度。当从几何形状的初始NURBS表示开始,然后使用插入结对NURBS基进行细化时,实现的收敛速度为0 (DoF-4)。通过使用几何形状的初始NURBS表示(kh-细化),可以进一步提高该速率。
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引用次数: 87
Generalized Koebe's method for conformal mapping multiply connected domains 保角映射多连通域的广义Koebe方法
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629267
W. Zeng, Xiaotian Yin, Min Zhang, F. Luo, X. Gu
Surface parameterization refers to the process of mapping the surface to canonical planar domains, which plays crucial roles in texture mapping and shape analysis purposes. Most existing techniques focus on simply connected surfaces. It is a challenging problem for multiply connected genus zero surfaces. This work generalizes conventional Koebe's method for multiply connected planar domains. According to Koebe's uniformization theory, all genus zero multiply connected surfaces can be mapped to a planar disk with multiply circular holes. Furthermore, this kind of mappings are angle preserving and differ by Möbius transformations. We introduce a practical algorithm to explicitly construct such a circular conformal mapping. Our algorithm pipeline is as follows: suppose the input surface has n boundaries, first we choose 2 boundaries, and fill the other n -- 2 boundaries to get a topological annulus; then we apply discrete Yamabe flow method to conformally map the topological annulus to a planar annulus; then we remove the filled patches to get a planar multiply connected domain. We repeat this step for the planar domain iteratively. The two chosen boundaries differ from step to step. The iterative construction leads to the desired conformal mapping, such that all the boundaries are mapped to circles. In theory, this method converges quadratically faster than conventional Koebe's method. We give theoretic proof and estimation for the converging rate. In practice, it is much more robust and efficient than conventional non-linear methods based on curvature flow. Experimental results demonstrate the robustness and efficiency of the method.
曲面参数化是指将曲面映射到标准平面域的过程,在纹理映射和形状分析中起着至关重要的作用。大多数现有技术都集中在单连通表面上。多连通属零曲面是一个具有挑战性的问题。本文对多连通平面域的Koebe方法进行了推广。根据Koebe的均匀化理论,所有的零属多重连通曲面都可以映射到具有多个圆孔的平面圆盘上。此外,这种映射是保角的,并且通过Möbius变换有所不同。我们介绍了一种实用的算法来显式构造这样一个圆共形映射。我们的算法流程如下:假设输入曲面有n个边界,首先选取2个边界,填充其余的n - 2个边界,得到一个拓扑环;然后应用离散Yamabe流方法将拓扑环空保形映射为平面环空;然后去除填充的小块,得到平面多连通域。对平面域迭代重复此步骤。这两个选择的边界每一步都不同。迭代构造导致所需的保角映射,这样所有的边界都映射到圆上。理论上,该方法的二次收敛速度比传统的Koebe方法快。给出了收敛速度的理论证明和估计。在实际应用中,该方法比传统的基于曲率流的非线性方法具有更高的鲁棒性和效率。实验结果证明了该方法的鲁棒性和有效性。
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引用次数: 39
Constraint-based model synthesis 基于约束的模型综合
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629269
Paul C. Merrell, Dinesh Manocha
We present a method for procedurally modeling general complex 3D shapes. Our approach is targeted towards applications in digital entertainment and gaming and can automatically generate complex models of buildings, man-made structures, or urban datasets in a few minutes based on user-defined inputs. The algorithm attempts to generate results that resemble a user-defined input model and that satisfy various dimensional, geometric, and algebraic constraints. These constraints are used to capture the intent of the user and generate shapes that look more natural. We also describe efficient techniques to handle complex shapes and demonstrate their performance on many different types of models.
我们提出了一种对一般复杂三维形状进行程序化建模的方法。我们的方法是针对数字娱乐和游戏的应用,可以根据用户定义的输入在几分钟内自动生成复杂的建筑、人造结构或城市数据集模型。该算法试图生成类似于用户定义输入模型的结果,并满足各种维度、几何和代数约束。这些约束用于捕捉用户的意图并生成看起来更自然的形状。我们还描述了处理复杂形状的有效技术,并演示了它们在许多不同类型模型上的性能。
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引用次数: 20
A geometric criterion for smooth interpolation of curve networks 曲线网络平滑插值的几何准则
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629277
T. Hermann, J. Peters, T. Strotman
A key problem when interpolating a network of curves occurs at vertices: an algebraic condition called the vertex enclosure constraint must hold wherever an even number of curves meet. This paper recasts the constraint in terms of the local geometry of the curve network. This allows formulating a new geometric constraint, related to Euler's Theorem on local curvature, that implies the vertex enclosure constraint and is equivalent to it where four curve segments meet without forming an X.
当插值曲线网络出现在顶点时,一个关键问题是:一个称为顶点包围约束的代数条件必须在偶数曲线相遇的地方成立。本文从曲线网络的局部几何角度对约束进行了重新定义。这允许形成一个新的几何约束,与欧拉局部曲率定理相关,它隐含顶点包围约束,并且等价于四个曲线段相交而不形成X。
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引用次数: 8
Robust principal curvatures using feature adapted integral invariants 利用特征自适应积分不变量的鲁棒主曲率
Pub Date : 2009-10-05 DOI: 10.1145/1629255.1629298
Yu-Kun Lai, Shimin Hu, T. Fang
Principal curvatures and principal directions are fundamental local geometric properties. They are well defined on smooth surfaces. However, due to the nature as higher order differential quantities, they are known to be sensitive to noise. A recent work by Yang et al. combines principal component analysis with integral invariants and computes robust principal curvatures on multiple scales. Although the freedom of choosing the radius r gives results on different scales, in practice it is not an easy task to choose the most appropriate r for an arbitrary given model. Worse still, if the model contains features of different scales, a single r does not work well at all. In this work, we propose a scheme to automatically assign appropriate radii across the surface based on local surface characteristics. The radius r is not constant and adapts to the scale of local features. An efficient, iterative algorithm is used to approach the optimal assignment and the partition of unity is incorporated to smoothly combine the results with different radii. In this way, we can achieve a better balance between the robustness and the accuracy of feature locations. We demonstrate the effectiveness of our approach with robust principal direction field computation and feature extraction.
主曲率和主方向是局部几何的基本性质。它们在光滑的表面上很清晰。然而,由于它们是高阶微分量的性质,它们对噪声很敏感。Yang等人最近的一项工作将主成分分析与积分不变量结合起来,计算了多尺度上的鲁棒主曲率。虽然选择半径r的自由可以在不同的尺度上得到结果,但在实践中,为任意给定的模型选择最合适的r并不是一件容易的事。更糟糕的是,如果模型包含不同尺度的特征,单个r根本不能很好地工作。在这项工作中,我们提出了一种基于局部表面特征自动分配适当半径的方案。半径r不是恒定的,它适应局部特征的尺度。采用一种高效的迭代算法逼近最优分配,并采用单位分割法将不同半径的结果进行平滑组合。这样,我们可以在特征位置的鲁棒性和准确性之间取得更好的平衡。通过鲁棒主方向场计算和特征提取验证了该方法的有效性。
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引用次数: 12
期刊
Symposium on Solid and Physical Modeling
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