ABCluster

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Release Note

Last update: Dec. 4, 2024

🔥 ABCluster 3.3 available! This is a bug-fixed version. To download it, click Download Current Release.

  • Add xTB-GFN0 and GFN-FF support in geom. See Input File for geom and geom with xTB.

  • A bug in rigidmol has been fixed. Many thanks to Dr. Jakub Kubecka for reporting this bug.

Introduction

Briefly, ABCluster searches the global as well as the local minima of flexible molecules and clusters.

ABCluster searches the global minimum of a cluster by mimicing the foraging behavior of honey bee colonies. Don’t worry if you are not familiar with it. Since ABCluster is a black-box program, you can perform a global optimization readily without any knowledge about heuristic algorithms. Therefore you can completely focus on your chemical problem!

Would like to download ABClsuter? Click Download Current Release!

Would like to use ABClsuter? Click ABCluster Manual!

Would like to see successful stories of ABCluster? Click ABCluster Applications!

Download Current Source Code

Released on: Dec. 4, 2024

Below is the source code of ABCluster. For compilation guidance, see ABCluster Manual.

  • 📦 ABCluster Source Code (~ 2 MB) This is the lean source code of ABCluster. To compile it, you may have to compile some libraries and set optimization, link options by yourself. The bonus is that you can optimize ABCluster at a better level on your machine.

  • 📦 ABCluster Source Code with Environment (~ 180 MB) This is the ABCluster source code with compilation environment. In principle, on most Linux and macOS systems, you can compile it with just one command ./build.sh. This is recommended if you want to compile ABCluster rapidly.

Download Current Release

Released on: Dec. 4, 2024

Cite ABCluster

Note

The best way to support the development of ABCluster is that in any published works using ABCluster, please include the following references:

Below is a review of recent development of global optimization algorithms for chemical clusters, including many applications of ABCluster:

Below is the graph representation learning-enabled automatic atom typing algorithm used in ABCluster:

Download Old Releases

About NWPEsSe

NWPEsSe is a flexible and efficient software to search global minimum of potential energy surface in computational chemistry problems. Please refer to Github for details.

Reference:

Release History

  • Version 3.3 (Released on: Dec. 4, 2024): 1) Add xTB-GFN0 and GFN-FF support in geom. See Input File for geom and geom with xTB. 2) A bug in rigidmol has been fixed. Many thanks to Dr. Jakub Kubecka for reporting this bug.

  • Version 3.2 (Released on: Dec. 4, 2023): 1) The stability and computational efficiency of rigidmol is improved significantly. 2) rigidmol can now be accelerated by single or multiple GPU cards! 3) For geom xTB engine, implicit solvation model can be used.

  • Version 3.1 (Released on: May 25, 2022): 1) bee can be used to check if an update is available for ABCluster. 2) Calculations with geom can be restarted or continued. 3) New interfaces to third-party programs: VASP. 4) topgen can automatically type atoms without manual typing. 5) Some typos are fixed.

  • Version 3.0 (Released on: Oct. 29, 2021): 1) ABCluster can perform conformation search for flexible molecules now! This is as easy as the global optimization of clusters! 2) ABCluster can manipulate clusters of both rigid and flexible molecules, i.e., doing global optimization and conformation search simultaneously. 3) ABCluster can generate atomic clusters with assigned point group symmetry! 4) ABCluster can treat complicated clusters more flexible and easily at the nanometer scale: gas phase, ligated, surface-supported, and assemble of clusters. 5) ABCluster has integrated xTB and CHARMM calculation engine internally. 5) Interfaces to third-party programs are provided officially: Gaussian, CP2K. 6) The manual is completely rewritten and is available both online and in a PDF version.

  • Version 2.0 (Released on: Aug. 1, 2018): 1) For rigidmol-optimizer, ABCluster can study the molecular clusters in an external electric field. 2) For isomer and lego, the algorithm to generate initial guesses (thus the search efficiency) have been improved significantly (For example, clashes removing, coarse optimization)! 3) isomer and lego has been parallelized for both single and multi-nodes. 4) Official support for isomer and lego with DMol3 is provided (Courtesy of Prof. Dr. Lei Ma and Mr. Kai Wang, Tianjin International Center for Nanoparticles and Nanosystems (TICNN)).

  • Version 1.5.1 (Released on: Dec. 18, 2017): 1) Official support for isomer and lego with ORCA, NWChem, and xTB-GFN are provided. 2) The evaluation codes have been optimized.

  • Version 1.5 (Released on: Dec. 18, 2016): 1) A component cg-optimizer is added to support the anistropic, coarse-grained particles, including electric multipole interaction and Paramonov-Yaliraki potential. 2) The component rigidmol-optimizer supports 1D, 2D and 3D periodic boundary conditions. 3) New modified Sutton-Chen and extended Lennard-Jones potential are supported. 3) A new keyword surface is added to lego for better supporting surface absorption. 4) The output of isomer and lego are optimized.

  • Version 1.4 (Released on: Apr. 5, 2016): 1) The new component lego has been added to support to search by third-party programs for both molecular and atomic clusters. 2) New Tersoff potential is supported.

  • Version 1.3 (Released on: Jan. 22, 2016): New algorithm has been introduced. Now the efficiency of multi-component atomic clusters (e.g. Ag14Cu24) has been improved by 100 times!

  • Version 1.2 (Released on: Nov. 6, 2015): The interfaces for third-party programs are available! Now ABCluster can do the global optimization with any quantum chemistry programs!

  • Version 1.1 (Released on: Oct. 19, 2015): The optimization of Gupta and Sutton-Chen potential is siginificantly improved.

  • Version 1.0 (Released on: Oct. 1, 2015): The first released version.