SimTK Core Toolset (obsolete project)

Prior to June, 2011 this project was used to distribute the Simbios-developed Simbody and Molmodel packages in the SimTK biosimulation toolkit. These are now distributed separately from the Simbody and Molmodel projects (https://simtk.org/home/simbody, https://simtk.org/home/molmodel). Please use those projects instead of this one.The other major component of SimTK is the GPU-accelerated molecular dynamics package OpenMM, see https://simtk.org/home/openmm if you are interested.<b>The text below refers to the pre-June, 2011 packaging and has been superseded as described above.</b><b><i>SimTK Core subprojects</i></b> This SimTK Core project collects together all the binaries needed for the various SimTK Core subprojects. These include Simbody, Molmodel, Simmath (including Ipopt), Simmatrix, CPodes, SimTKcommon, and Lapack. See the individual projects for descriptions.<b><i>SimTK overview</i></b>SimTK brings together in a robust, convenient, open source form the collection of highly-specialized technologies necessary to building successful physics-based simulations of biological structures. These include: strict adherence to an important set of abstractions and guiding principles, robust, high-performance numerical methods, support for developing and sharing physics-based models, and careful software engineering.<b><i>Accessible High Performance Computing</i></b><br/>We believe that a primary concern of simulation scientists is performance, that is, speed of computation. We seek to build valid, approximate models using classical physics in order to achieve reasonable run times for our computational studies, so that we can hope to learn something interesting before retirement. In the choice of SimTK technologies, we are focused on achieving the best possible performance on hardware that most researchers actually have. In today's practice, that means commodity multiprocessors and small clusters.The difference in performance between the best methods and the do-it-yourself techniques most people use can be astounding—easily an order of magnitude or more. The growing set of SimTK Core libraries seeks to provide the best implementation of the best-known methods for widely used computations such as:Linear algebra, numerical integration and Monte Carlo sampling, multibody (internal coordinate) dynamics, molecular force field evaluation, nonlinear root finding and optimization. All SimTK Core software is in the form of C++ APIs, is thread-safe, and quietly exploits multiple CPUs when they are present.The resulting pre-built binaries are available for download and immediate use.<b><i>Citation:</i></b> Any work that uses SimTK Core (including Simbody) should cite the following paper: Jeanette P. Schmidt, Scott L. Delp, Michael A. Sherman, Charles A. Taylor,Vijay S. Pande, Russ B. Altman, "The Simbios National Center: SystemsBiology in Motion", Proceedings of the IEEE, special issue on Computational System Biology. Volume 96, Issue 8:1266 - 1280. (2008) <br/><br/>This project includes the following software/data packages: <br/> <ul> <li> <a href="https://simtk.org/frs?group_id=97#pack_399">Example programs using SimTK </a> : Source code examples for release 2.0 of SimTKCore. </li> <li> <a href="https://simtk.org/frs?group_id=97#pack_108">Linux </a> : SimTK core software for Linux </li> <li> <a href="https://simtk.org/frs?group_id=97#pack_259">Mac OS X (intel) </a> : SimTK core software for intel based Max OS X. As of SimTK 2.0 we no longer provide binaries for other Mac OS platforms. </li> <li> <a href="https://simtk.org/frs?group_id=97#pack_234">Windows </a> : SimTK core software for Windows </li> </ul>

在2011年6月之前，本项目曾用于在SimTK生物模拟工具包中分发Simbios开发的Simbody和Molmodel软件包。如今，Simbody和Molmodel项目已独立分发，详情请参阅https://simtk.org/home/simbody和https://simtk.org/home/molmodel。请使用这些项目替代本项目的相关内容。SimTK的另一个主要组件是GPU加速的分子动力学软件包OpenMM，如需了解更多信息，请访问https://simtk.org/home/openmm。以下文本涉及2011年6月之前的软件包，已被上述描述所取代。<b>SimTK核心子项目</b>本SimTK核心项目汇集了所有必需的二进制文件，以支持各种SimTK核心子项目。这些子项目包括Simbody、Molmodel、Simmath（包括Ipopt）、Simmatrix、CPodes、SimTKcommon和Lapack。具体项目的描述请参阅各自的项目页面。<b>SimTK概述</b>SimTK以稳健、便捷、开源的形式汇集了构建成功的基于物理的生物学结构模拟所需的高度专业化的技术集合。这包括：严格遵循一系列重要的抽象和指导原则、稳健、高性能的数值方法、支持开发与共享基于物理的模型，以及细致的软件工程。<b>可访问的高性能计算</b><br/>我们坚信，模拟科学家的主要关注点是性能，即计算的速率。我们致力于使用经典物理学构建有效、近似的模型，以实现计算研究的合理运行时间，以便我们能够在退休之前有所收获。在选择SimTK技术时，我们专注于在大多数研究人员实际拥有的硬件上实现最佳性能。在当今的实践中，这意味着通用多处理器和小型集群。最佳方法与大多数人所采用的自行开发技术之间的性能差异可能令人震惊——甚至可能达到一个数量级或更多。SimTK核心库的日益增长旨在提供已知方法的最佳实现，这些方法广泛应用于线性代数、数值积分和蒙特卡洛采样、多体（内部坐标）动力学、分子力场评估、非线性根查找和优化等计算。所有SimTK核心软件均以C++ API的形式提供，线程安全，并在存在多个CPU时自动利用。<b>引用：</b>任何使用SimTK核心（包括Simbody）的研究工作均应引用以下论文：Jeanette P. Schmidt, Scott L. Delp, Michael A. Sherman, Charles A. Taylor, Vijay S. Pande, Russ B. Altman, “The Simbios National Center: SystemsBiology in Motion”，IEEE汇刊，关于计算系统生物学的特刊。第96卷，第8期：1266 - 1280.（2008）<br/><br/>本项目包含以下软件/数据包：<br/> <ul> <li><a href="https://simtk.org/frs?group_id=97#pack_399">使用SimTK的示例程序</a>：SimTKCore 2.0版本的源代码示例。</li> <li><a href="https://simtk.org/frs?group_id=97#pack_108">Linux</a>：适用于Linux的SimTK核心软件。</li> <li><a href="https://simtk.org/frs?group_id=97#pack_259">Mac OS X (intel)</a>：适用于基于Intel的Mac OS X的SimTK核心软件。自SimTK 2.0版本起，我们不再提供其他Mac OS平台的可执行文件。</li> <li><a href="https://simtk.org/frs?group_id=97#pack_234">Windows</a>：适用于Windows的SimTK核心软件。</li> </ul>