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--- exercises:common:reading_list [2022/11/14 14:13] – created jglan
+++ exercises:common:reading_list [2023/12/05 13:43] (current) – [Papers] fnunes
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-Understanding Molecular Simulation From Algorithms to Applications, 作者： Daan Frenkel and Berend Smit
+==== Books ====
-Statistical Mechanics: Theory and Molecular Simulation, 作者： Mark E. Tuckerman
+  * Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory, Attila Szabo
+  * Molecular Electronic-Structure Theory, Trygve Helgaker, Poul Jørgensen, and Jeppe Olsen
+  * Electronic Structure: Basic Theory and Practical Methods, Richard M. Martin
+  * Understanding Molecular Simulation From Algorithms to Applications, Daan Frenkel and Berend Smit
+  * Computer Simulation of Liquids: Second Edition, Michael P. Allen and Dominic J. Tildesley
+  * Statistical Mechanics: Theory and Molecular Simulation, Mark E. Tuckerman
+  * Ab Initio Molecular Dynamics Basic Theory and Advanced Methods, Dominik Marx and Jürg Hutter
+  * Time-Dependent Density-Functional Theory: Concepts and Applications, Carsten A. Ullrich
-Computer Simulation of Liquids: Second Edition， 作者：Michael P. Allen and Dominic J. Tildesley
-从头计算法分子动力学：
-Ab Initio Molecular Dynamics Basic Theory and Advanced Methods, 作者：Dominik Marx, Ruhr-Universität, Jürg Hutter
+==== Papers ====
-电子结构：
+  * CPMD: Unified Approach for Molecular Dynamics and Density-Functional Theory, Roberto Car and Michele Parrinello (DOI: https://doi.org/10.1103/PhysRevLett.55.2471)
-Molecular Electronic-Structure Theory，作者：Trygve Helgaker, Poul Jørgensen, Jeppe Olsen
+  * Metadynamics: Escaping free-energy minima, Alessandro Laio and Michele Parrinello (DOI: https://doi.org/10.1073/pnas.202427399)
-Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory,作者：Attila Szabo
+  * Real-time methods: Real-Time Time-Dependent Electronic Structure Theory, Xiaosong Li, Niranjan Govind, Christine Isborn, A. Eugene DePrince III, and Kenneth Lopata (DOI: https://doi.org/10.1021/acs.chemrev.0c00223); Real-time time-dependent electronic structure theory, Joshua J. Goings, Patrick J. Lestrange, and Xiaosong Li (DOI: https://doi.org/10.1002/wcms.1341)
-分子动力学相关论文：
-CPMD论文：Unified Approach for Molecular Dynamics and Density-Functional Theory， R. Car and M. Parrinello
+Electronic Structure：
+  * GPW: A hybrid Gaussian and plane wave density functional scheme, Gerald Lippert, Jürg Hutter, and Michele Parrinello (DOI: https://doi.org/10.1080/002689797170220)
-Meta-dynamics论文：Escaping free-energy minima, Alessandro Laio and Michele Parrinello
+  * GAPW: The Gaussian and augmented-plane-wave density functional method for ab initio molecular dynamics simulations, Gerald Lippert, Jürg Hutter, and Michele Parrinello (DOI: https://doi.org/10.1007/s002140050523); All-electron ab-initio molecular dynamics, Matthias Krack and Michele Parrinello (DOI: https://doi.org/10.1039/B001167N); Inner-shell spectroscopy by the Gaussian and augmented plane wave method, Marcella Iannuzzi and Jürg Hutter (DOI: https://doi.org/10.1039/B615522G)
-CSVR控温器论文：Canonical sampling through velocity rescaling， Giovanni Bussi, Davide Donadio, and Michele Parrinello
+  * PBE：Generalized Gradient Approximation Made Simple, John P. Perdew, Kieron Burke, and Matthias Ernzerhof (DOI: https://doi.org/10.1103/PhysRevLett.77.3865)
+  * SCAN： Strongly Constrained and Appropriately Normed Semilocal Density Functional, Jianwei Sun, Adrienn Ruzsinszky, and John P. Perdew (DOI: https://doi.org/10.1103/PhysRevLett.115.036402)
+  * HSE： Hybrid functionals based on a screened Coulomb potential, Jochen Heyd, Gustavo E. Scuseria, and Matthias Ernzerhof (DOI: https://doi.org/10.1063/1.1564060)
+  * DFT-D-Grimme: A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu, Stefan Grimme, Jens Antony, Stephan Ehrlich, and Helge Krieg (DOI: https://doi.org/10.1063/1.3382344)
-TRPMD控温论文：How to remove the spurious resonances from ring polymer molecular dynamicsHow to remove the spurious resonances from ring polymer molecular dynamicsTRPMD控温论文：How to remove the spurious resonances from ring polymer molecular dynamics
-电子结构类论文：
+Machine learning：
-PBE论文：Generalized Gradient Approximation Made Simple John P. Perdew, Kieron Burke, and Matthias Ernzerhof
+  * BPNN： Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces, Jörg Behler and Michele Parrinello (DOI: https://doi.org/10.1103/PhysRevLett.98.146401)
-SCAN论文：Strongly Constrained and Appropriately Normed Semilocal Density Functional Jianwei Sun, Adrienn Ruzsinszky, and John P. Perdew
+  * DeepMD： Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics, Linfeng Zhang, Jiequn Han, Han Wang, Roberto Car, and Weinan E (DOI: https://doi.org/10.1103/PhysRevLett.120.143001)
-HSE论文：Hybrid functionals based on a screened Coulomb potential， Jochen Heyd and Gustavo E. Scuseria
-DFT-D-Grimme: A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
-机器学习类论文：
-BPNN神经网络论文：Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces Jörg Behler and Michele Parrinello
-DeepMD论文：Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics, Linfeng Zhang, Jiequn Han, Han Wang, Roberto Car, and Weinan E