Departament de Física Aplicada, EUETII, Universitat Politècnica de Catalunya, Pça del Rei 15, Igualada 08700, Spain.
J Comput Chem. 2010 Nov 15;31(14):2669-76. doi: 10.1002/jcc.21553.
The PUPIL system is a combination of software and protocols for the systematic linkage and interoperation of molecular dynamics and quantum mechanics codes to perform QM/MD (sometimes called QM/MM) calculations. The Gaussian03 and Amber packages were added to the PUPIL suite recently. However, efficient parallel QM codes are critical because calculation of the QM forces is the overwhelming majority of the computational load. Here we report details of incorporation of the deMon2k density functional suite as a new parallel QM code. An additional motivation is to add a highly optimized, purely DFT code. We illustrate with a demonstration study of the influence of perchlorate as a dopant ion of the poly(3,4-ethylenedioxythiophene) conducting polymer in explicit acetonitrile solvent using Amber and deMon2k. We discuss unanticipated requirements for use of a scheme for semi-empirical correction of Kohn-Sham eigenvalues to give physically meaningful one-electron gap energies. We provide comparison of both geometric parameters and electronic properties for nondoped and doped systems. We also present results comparing deMon2k and Gaussian03 calculation of forces for a short sequence of steps. We discuss briefly some difficult problems of quantum zone SCF convergence for the anionically doped system. The difficulties seem to be caused by well-know deficiencies in simple approximate exchange-correlation functionals.
PUPIL 系统是一个软件和协议的组合，用于对分子动力学和量子力学代码进行系统的链接和互操作，以执行 QM/MD（有时称为 QM/MM）计算。最近，Gaussian03 和 Amber 软件包已被添加到 PUPIL 套件中。然而，高效的并行量子力学代码是至关重要的，因为计算量子力学力占据了绝大部分的计算负载。在这里，我们报告了将 deMon2k 密度泛函套件作为一个新的并行量子力学代码进行整合的详细信息。另一个动机是添加一个高度优化的、纯粹的 DFT 代码。我们通过使用 Amber 和 deMon2k 对聚（3,4-亚乙二氧基噻吩）导电聚合物在明确的乙腈溶剂中作为掺杂离子的高氯酸根的影响进行演示研究来说明这一点。我们讨论了使用半经验校正 Kohn-Sham 本征值以给出物理意义上的单电子能隙能量的方案的意外要求。我们提供了未掺杂和掺杂体系的几何参数和电子性质的比较。我们还展示了 deMon2k 和 Gaussian03 对短序列步骤的力计算的结果比较。我们简要讨论了阴离子掺杂体系中量子区 SCF 收敛的一些困难问题。这些困难似乎是由简单近似交换相关泛函的已知缺陷引起的。
