DL-FIND: An Open-Source Geometry Optimizer for Atomistic Simulations
DL-FIND: An Open-Source Geometry Optimizer for Atomistic Simulations
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DOI：
10.1021/jp9028968
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发表时间：
2009-10-29
影响因子：
2.9
通讯作者：
Sherwood, Paul
中科院分区：
文献类型：
--
作者：
Kaestner, Johannes;Carr, Joanne M.;Sherwood, Paul
几何优化，包括寻找过渡态，占了量子化学，计算表面科学和固态物理中花费的大部分CPU时间，并且在使用经典力场的模拟中也起着重要作用。我们已经实现了一个几何优化器，称为DL-FIND，包括在原子模拟代码。它可以在笛卡尔坐标系、冗余内坐标系、混合离域内坐标系以及与原子结构无关的多变量函数中优化结构。优化算法的实现与所使用的坐标变换无关。最速下降、共轭梯度、拟牛顿和L-BFGS算法以及阻尼分子动力学可用作最小化方法。分区有理函数优化算法，二聚体方法和轻推弹性带方法的修改版本提供过渡状态搜索的能力。罚函数，梯度投影，拉格朗日-牛顿法实现圆锥相交优化。各种随机搜索方法，包括遗传算法，可用于全局或局部最小化，并可作为并行算法运行。该代码在开源GNU LGPL许可证下发布。文中介绍了DL-FIND的一些应用。
Geometry optimization, including searching for transition states, accounts for most of the CPU time spent in quantum chemistry, computational surface science, and solid-state physics, and also plays an important role in simulations employing classical force fields. We have implemented a geometry optimizer, called DL-FIND, to be included in atomistic simulation codes. It can optimize structures in Cartesian coordinates, redundant internal coordinates, hybrid-delocalized internal coordinates, and also functions of more variables independent of atomic structures. The implementation of the optimization algorithms is independent of the coordinate transformation used. Steepest descent, conjugate gradient, quasi-Newton, and L-BFGS algorithms as well as damped molecular dynamics are available as minimization methods. The partitioned rational function optimization algorithm, a modified version of the dimer method and the nudged elastic band approach provide capabilities for transition-state search. Penalty function, gradient projection, and Lagrange-Newton methods are implemented for conical intersection optimizations. Various stochastic search methods, including a genetic algorithm, are available for global or local minimization and can be run as parallel algorithms. The code is released under the open-source GNU LGPL license. Some selected applications of DL-FIND are surveyed.