基于高通量计算平台的过渡态搜索算法及自动流程实现
|
摘要
本文针对寻找反应过程中过渡态结构的问题,基于高通量计算平台设计并实现了一种过渡态搜索算法及其自动计算流程。实现了包括中间结构自动产生功能在内的过渡态搜索的自动流程计算,具体包括计算的准备文件产生、结构筛选、结果后处理等各个流程。同时,在整个自动计算过程中还引入自动纠错机制,可以实现自动根据错误类型实现对错误的恢复与处理功能,以提高过渡态搜索计算的可靠性。最后,本文进行了H原子在Mg晶体表面扩散的研究,将计算结果与文献数据进行了对照,以验证计算结果的合理性。
In this paper, we design and implement a transition state search algorithm and its automatic calculation process based on the high-throughput computational platform to find the transition state structure in the reaction process. The automatic flow calculation of transition state search including the automatic generation of intermediate structure is implemented, which includes the processes of generation of preparation files, structure filtering and post-processing of results. At the same time, to improve the reliability of the transition state search calculation, automatic error correction mechanism is introduced in the whole automatic calculation process, which can automatically recover and process the error according to the error type. At last, to verify the rationality of the calculated results, the diffusion of H atoms on the surface of Mg crystal is studied in this paper, and the results are compared with the literature data.
In this paper, we design and implement a transition state search algorithm and its automatic calculation process based on the high-throughput computational platform to find the transition state structure in the reaction process. The automatic flow calculation of transition state search including the automatic generation of intermediate structure is implemented, which includes the processes of generation of preparation files, structure filtering and post-processing of results. At the same time, to improve the reliability of the transition state search calculation, automatic error correction mechanism is introduced in the whole automatic calculation process, which can automatically recover and process the error according to the error type. At last, to verify the rationality of the calculated results, the diffusion of H atoms on the surface of Mg crystal is studied in this paper, and the results are compared with the literature data.
引文
[1]傅献彩,沈文霞,姚天扬.物理化学[M].北京:高等教育出版社,2006.235-245.
[2]罗渝然.过渡态理论的进展[J].化学通报,1983,1(10):8-14.
[3]Laidler K,King C.A lifetime of transition-state theory[J].The chemical intelligencer,1998,4(3):39-39.
[4]王沁泌,蒋华良,陈凯先,陈建忠,嵇汝运.化学反应过渡态的计算方法[J].化学进展,1997,9(3):253-263.
[5]戴东旭,杨学明.化学反应过渡态的结构和动力学[J].中国科学辑:化学,2009,39(10):1089-1101.
[6]Hrant P Hratchian,H Bernhard Schlegel.Finding minima,transition states,and following reaction pathways on ab initio potential energy surfaces in Theory and Applications of Computational Chemistry:The First Forty Years[M].Elsevier B V,2005.195-243.
[7]Maeda S,K Ohno,et al.Automated Global Mapping of Minimal Energy Points on Seams of Crossing by the Anharmonic Downward Distortion Following Method:A Case Study of H2CO[J].Physical Chemistry A,2009,113(9):1704-1710.
[8]刘跃,王骐,刘颖.几种过渡态结构的有效优化方法[J].分子科学学报,2003,19(3):181-185.
[9]刘一骏,杨小渝,任杰,王宗国.高可用面向材料基因工程的高通量材料计算任务管理系统[J].科研信息化技术与应用,2015,6(6):74-82.
[10]D Gunter,S Cholia,A Jain,M Kocher,K Persson,et al.Community accessible datastore of high-throughput calculations:experiences from the Materials Project[C].//High Performance Computing,Networking,Storage and Analysis.USA,IEEE,2012:1244-1251.
[11]KF Aguey-Zinsou,JR Ares-Fernández.Hydrogen in magnesium:new perspectives toward functional stores[J].Energy&Environmental Science,2010,3(5):526-543.
[12]吴广新.镁基储氢合金吸放氢热力学和动力学研究[D].上海:上海大学材料科学与工程学院,2009.
[13]吴广新,张捷宇,吴永全,李谦,周国治,包新华.H在Mg(0001)表面吸附、解离和扩散的第一性原理研究[J].物理化学学报,2008,24(1):55-60.
[14]N Jacobson,B Tegner,E Schroder,P Hyldgaard,BI Lundqvist.Hydrogen dynamics in magnesium and graphite[J].Computational Materials Science,2002,24(1):273-277.
[15]T Vegge.Locating the rate-limiting step for the interaction of hydrogen with Mg(0001)using density-functional theory calculations and rate theory[J].Physical Review B,2004,70(3):2199-2208.
[2]罗渝然.过渡态理论的进展[J].化学通报,1983,1(10):8-14.
[3]Laidler K,King C.A lifetime of transition-state theory[J].The chemical intelligencer,1998,4(3):39-39.
[4]王沁泌,蒋华良,陈凯先,陈建忠,嵇汝运.化学反应过渡态的计算方法[J].化学进展,1997,9(3):253-263.
[5]戴东旭,杨学明.化学反应过渡态的结构和动力学[J].中国科学辑:化学,2009,39(10):1089-1101.
[6]Hrant P Hratchian,H Bernhard Schlegel.Finding minima,transition states,and following reaction pathways on ab initio potential energy surfaces in Theory and Applications of Computational Chemistry:The First Forty Years[M].Elsevier B V,2005.195-243.
[7]Maeda S,K Ohno,et al.Automated Global Mapping of Minimal Energy Points on Seams of Crossing by the Anharmonic Downward Distortion Following Method:A Case Study of H2CO[J].Physical Chemistry A,2009,113(9):1704-1710.
[8]刘跃,王骐,刘颖.几种过渡态结构的有效优化方法[J].分子科学学报,2003,19(3):181-185.
[9]刘一骏,杨小渝,任杰,王宗国.高可用面向材料基因工程的高通量材料计算任务管理系统[J].科研信息化技术与应用,2015,6(6):74-82.
[10]D Gunter,S Cholia,A Jain,M Kocher,K Persson,et al.Community accessible datastore of high-throughput calculations:experiences from the Materials Project[C].//High Performance Computing,Networking,Storage and Analysis.USA,IEEE,2012:1244-1251.
[11]KF Aguey-Zinsou,JR Ares-Fernández.Hydrogen in magnesium:new perspectives toward functional stores[J].Energy&Environmental Science,2010,3(5):526-543.
[12]吴广新.镁基储氢合金吸放氢热力学和动力学研究[D].上海:上海大学材料科学与工程学院,2009.
[13]吴广新,张捷宇,吴永全,李谦,周国治,包新华.H在Mg(0001)表面吸附、解离和扩散的第一性原理研究[J].物理化学学报,2008,24(1):55-60.
[14]N Jacobson,B Tegner,E Schroder,P Hyldgaard,BI Lundqvist.Hydrogen dynamics in magnesium and graphite[J].Computational Materials Science,2002,24(1):273-277.
[15]T Vegge.Locating the rate-limiting step for the interaction of hydrogen with Mg(0001)using density-functional theory calculations and rate theory[J].Physical Review B,2004,70(3):2199-2208.