ABCluster: Download Manual Gallery Stories
ABCluster 3.1 available! Several useful functions are added!
- bee can be used to check if an update is available for ABCluster.
- Calculations with geom can be restarted or continued.
- New interfaces to third-party programs: VASP.
- topgen can automatically type atoms without manual typing.
- Some typos are fixed.
Download it immediately!
Get latest binaries and manual (Released on: Dec. 20, 2022)
Citation
When you use ABCluster in your work, I will appreciate you if you can cite the following publications:
Zhang, J.; Dolg, M. ABCluster: The Artificial Bee Colony Algorithm for Cluster Global Optimization. Phys. Chem. Chem. Phys. 2015, 17, 24173-24181.
Zhang, J.; Dolg, M. Global Optimization of Rigid Molecular Clusters by the Artificial Bee Colony Algorithm. Phys. Chem. Chem. Phys. 2016, 18, 3003-3010.
If you use the automatic atom typing algorithm with graph representation learning in topgen, please cite:
Zhang, J. Atom Typing Using Graph Representation Learning: How Do Models Learn Chemistry? J. Chem. Phys. 2022, 156, 204108.
A review of state-of-the-art global optimization theory and applications is highly recommended:
Zhang, J.; Glezakou, V.-A. Global Optimization of Chemical Cluster Structures: Methods, Applications, and Challenges. Int. J. Quantum Chem. 2021, 121, e26553.
What can ABCluster do?
Briefly, ABCluster searches the global as well as the local minima of flexible molecules and clusters.
ABCluster is a software developed by Jun Zhang to perform the global optimization and conformation search of molecules and clusters with the so-called "atificial bee colony" (ABC) algorithm. ABC is an unbiased, population-based, swarm-intelligence global optimization algorithm. The software 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 software, you can perform a global optimization readily without any knowledge about heuristic algorithms. Therefore you can completely focus on the chemical problem!
Would like to download ABClsuter? Click to Download!
Would like to see what kinds of molecules and clusters can ABCluster treat? Click Gallery for many beautiful graphs!
Would like to see successful stories of ABCluster? Click Stories for many exciting stories!
Copyright and disclaimer
ABCluster is Copyright © 2015-2023 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.
Get previous binaries and manual
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.
Download: Github
Reference:
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.
History
- 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), http://ticnn.tju.edu.cn).
- 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.
