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Abcluster User Manual Version 2.1

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Abcluster User Manual Version 2.1 ABCluster User Manual Version 2.1 for the global optimization of chemical clusters by Jun Zhang more information: http://www.zhjun-sci.com/software-abcluster-download.php Contents Contents i 1 Introduction1 1.1 What is ABCluster?.............................1 1.2 Program Citation...............................1 1.3 Contacting the Author............................2 1.4 Copyright and Disclaimer..........................2 1.5 Files of ABCluster..............................2 1.6 Installation of ABCluster..........................3 1.6.1 For Windows Users..........................3 1.6.2 For Linux and Mac OS X Users...................3 1.6.3 For Linux and Mac OS X Users: Possible Issues.........4 1.6.4 For OpenMP.............................4 1.6.5 If you see Incorrect format near ... ..............4 1.7 Support ABCluster..............................4 2 Theoretical Background5 2.1 Rule of Thumb................................5 2.2 Choose Your Cluster and Potential Energy Function...........5 2.2.1 When does Force Field Perform Well?...............5 2.2.2 When Must Quantum Chemistry be Used?............6 2.2.3 Some Force Fields Preferred by Physicists.............6 2.3 The Artificial Bee Colony Algorithm....................6 2.4 Interfaces to Third-party Programs.....................7 3 Rigid Molecular Clusters with Force Fields9 3.1 Introduction..................................9 3.2 Example 1: (H2O)6 .............................. 10 + + + 3.3 Example 2: Li , Na and Cs in (C6H6)6 ................. 12 3.4 Example 3: (CH2 {CH2)13 and Build New Force Fields.......... 14 3.5 Example 4: HNO3(H2O)10 in an Electric Field.............. 16 4 Optimization with Third-party Programs: isomer 19 4.1 Introduction.................................. 19 4.2 isomer with Gaussian............................ 19 4.2.1 Configuration of Gaussian...................... 19 + 4.2.2 Example 1: Al3O4 ......................... 20 4.2.3 More About optfile ........................ 22 4.2.4 Example 2: Au6 ........................... 23 4.3 ABCluster Interfaces with Third-Party Programs............. 26 4.4 Clusters with Specific Point Group Symmetry............... 27 i ii CONTENTS 4.4.1 Point Group Grammar........................ 28 4.4.2 Example 3: Au20 under Point Group Symmetries......... 28 5 Optimization with Third-party Programs: lego 31 5.1 Introduction.................................. 31 5.2 lego by Itself: Generate Complex Clusters................ 31 5.2.1 Preparation.............................. 31 5.2.2 Example 1: Na4(SO4)2(H2O)300 ................... 34 5.2.3 Example 2: (H2O)1000(C6H5CCH)150 ................ 35 5.2.4 Example 3-9: All Structural Features................ 36 5.3 lego with Gaussian............................. 44 { 5.3.1 Example 10: (IO3 )(H2O)4 ..................... 44 { 5.3.2 Example 11: ((NH3)4 )....................... 46 5.3.3 Theoretical Background....................... 47 5.4 lego with xTB................................ 48 2+ 5.4.1 Example 12: Au8(PPh3)7 ..................... 48 5.4.2 Example 13: Co6Te8(PEt3)6 ..................... 50 5.4.3 Theoretical Background....................... 52 5.5 lego with CP2K............................... 53 5.5.1 Example 14: Au8 on O-Defected Rutile (110) Surface...... 53 5.5.2 Theoretical Background....................... 55 5.6 lego with Gromacs.............................. 55 5.6.1 An Additional Input Option in inp File.............. 56 5.6.2 Example 15: A Reversed Micelle of POPC............. 56 5.6.3 Example 16: Two Layers of POPC................. 58 5.6.4 Theoretical Background....................... 59 5.7 lego with Lammps.............................. 60 5.7.1 Example 17: Ni38(CO)36 ....................... 60 5.7.2 Theoretical Background....................... 62 5.8 lego with NWChem, ORCA, MOPAC................... 62 5.9 lego with DMol3............................... 63 5.10 Energy Boundary Setting.......................... 63 2− 5.10.1 Example 18: EMIM3Cl5 ...................... 63 5.11 lego with More Programs.......................... 66 6 Atomic Clusters with Force Fields 69 6.1 Introduction.................................. 69 6.2 Example 1: 38 Lennard-Jones Particles................... 72 6.3 About abcinp ................................. 72 Q+ Q− 6.4 Example 2: (Mg O )20 .......................... 75 6.5 Example 3: Silve and Copper Clusters................... 76 6.5.1 Ag38 and Cu38 ............................ 76 6.5.2 Ag32Cu6 ................................ 77 6.6 Example 4: Perovskite Clusters (CaTiO3)5 ................ 77 6.7 Example 5: C16 and Ge16 Clusters..................... 78 A Version History 81 Bibliography 83 Chapter 1 Introduction I know that many people (including me) are very reluctant to read lengthy and tedious manuals, thus the manual is kept as short as possible. If you want to start as soon as possible, please go over Contents and just read Chapter2 and the sections starting with \Examples". 1.1 What is ABCluster? Briefly, ABCluster searches the global as well as the local minima of atomic and molec- ular clusters. ABCluster is a program developed by Dr. Jun Zhang to perform the global opti- mization of atomic and molecular clusters. It is an efficient and user-friendly program. It is designed in a way that non-experts, as well as experts, can perform a global op- timization readily without knowing too much about the internal algorithms, being a black-box. The latest version of ABCluster and related resources can be obtained online: http://www.zhjun-sci.com/software-abcluster-download.php ABCluster has been applied to a lot of realistic chemical problems by many authors, please refer to: http://www.zhjun-sci.com/software-abcluster-stories.php ABCluster uses very efficient global optimization algorithm, i.e. \the artificial bee colony algorithm", which was developed in 2005, to perform the search. The algorithm has been modified and improved specifically for chemical problems. ABCluster supports a large number of force fields by itself, and also provide interfaces for any other third- party computational chemistry programs, meaning that ABCluster is able to generate reasonable initial structures of complex topology quickly by itself and also can generate optimized cluster structures using highly accurate ab initio quantum chemistry methods! 1.2 Program Citation For any published works using ABCluster please include the following references: Zhang, J.; Dolg, M. ABCluster: The Artificial Bee Colony Algorithm for Cluster Global Optimization. Phys. Chem. Chem. Phys. 2015, 17, 24173{24181. 1 2 CHAPTER 1. INTRODUCTION Zhang, J.; Dolg, M. Global Optimization of Clusters of Rigid Molecules Using the Artificial Bee Colony Algorithm. Phys. Chem. Chem. Phys. 2016, 18, 3003{3010. Zhang, J.; Glezakou, V.-A.; Rousseau, R.; Nguyen, M.-T. NWPEsSe: An Adaptive-Learning Global Optimization Algorithm for Nanosized Cluster Systems. J. Chem. Theory Comput. 2020, 16, 3947{3958. 1.3 Contacting the Author If you have any bug reports, comments, suggestions or the possibility of cooperation on ABCluster, please feel free to contact to Dr. Jun Zhang via E-mail: [email protected] 1.4 Copyright and Disclaimer ABCluster is Copyright c 2015-2019 Jun Zhang. ABCluster is free of charge to non- profit academic use. The use of ABCluster in commercial packages is not allowed without a prior written commercial license agreement. The following codes used by ABCluster have special restrictions: • libLBFGS (see http://www.chokkan.org/software/liblbfgs) libLBFGS is the C realization of the limited-memory Broyden{Fletcher{Goldfarb{ Shanno (L-BFGS) method[1]. It is Copyright c 2002-2014 Naoaki Okazaki. libLBFGS is distributed under the term of the MIT license. • Boost (see http://www.boost.org) Boost is a set of C++ libraries. It is Copyright c 2004-2006 Joe Coder. Boost is distributed under the Boost Software License, Version 1.0. 1.5 Files of ABCluster When you download ABCluster and unzip it, you can get several files: • rigidmol-optimizer For the global optimization of rigid molecular clusters with CHARMM-like force fields. • isomer For the global optimization of atomic clusters with third-party programs. • lego For the global optimization or fast initial structure guess of any clusters with third-party programs. • atom-optimizer For the global optimization of atomic clusters using empirical force fields. • abcinp For Generating input files for atom-optimizer. • xyz2gaussian A small program for ABCluster using Gaussian. • gaussian2xyz A small program for ABCluster using Gaussian. • manual.pdf The user manual of ABCluster. • misc/atomic-force-field.txt Some collected parameters for atom-optimizer. 1.6. INSTALLATION OF ABCLUSTER 3 • misc/dmol34abcluster.sh A script for ABCluster using DMol3 (Courtesy of Prof. Dr. Lei Ma and Mr. Kai Wang, Tianjin International Center for Nanopar- ticles and Nanosystems (TICNN), http://ticnn.tju.edu.cn). • misc/mopac4abcluster.sh A script for ABCluster using MOPAC. • misc/nwchem4abcluster.sh A script for ABCluster using NWChem. • misc/orca4abcluster.sh A script for ABCluster using ORCA. • misc/cp2k4abcluster/* Scripts for ABCluster using CP2K. • misc/gromacs4abcluster/* Scripts for ABCluster using Gromacs. • misc/lammps4abcluster/* Scripts for ABCluster using Lammps. • testfiles This folder contains all test input files. Attention: From ABCluster 2.1, a part of functionality of lego has been moved to another software called NWPEsSe, which could be obtained free of charge from: https://store.pnnl.gov/content/north-west-potential-energy-surface-search-engine- nwpesse 1.6 Installation
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