8. Appendix

8.1. Update History

  • Version 3.2 (Released on: Dec 4, 2023):

    1. The stability and computational efficiency of rigidmol is improved significantly. See the table below:

      Reference

      System

      rigidmol 3.1

      rigidmol 3.2

      Example: Li+, Na+, and Cs+ in (C6H6)6

      \(\mathrm{Na}^{+}(\mathrm{C}_6\mathrm{H}_6)_6\)

      60 seconds

      30 seconds

      Example: Performance Comparison Using (Camphor)10

      \((\mathrm{Camphor})_{10}\)

      3361 seconds

      573 seconds

      The calculations were performed on a computer with 96 Intel(R) Xeon(R) Gold 6248R CPU @ 3.00GHz cores.

    2. rigidmol can now be accelerated by single or multiple GPU cards! See rigidmol Accelerated by GPU, for a system of \((\mathrm{CH}_3\mathrm{CN})_{1500}\), the speed comparison is:

      A single Intel(R) Xeon(R) Gold 6248R CPU @ 3.00GHz Core

      56 seconds

      A single Quadro RTX 4000 Card

      3 seconds

      This is very useful for large systems.

    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.

    6. Interfaces to third-party programs: Gaussian, CP2K.

    7. 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.

    4. A new keyword surface is added to lego for better supporting surface absorption.

    5. 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 significantly improved.

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

8.2. Acknowledgement

  • Prof. Benchao Zhu helps translate this manual to simplified Chinese.

  • Prof. Benchao Zhu points out several mistakes in this manual.