1. Introduction

1.1. What is ABCrystal?

ABCrystal is a light-weighted but powerful program for atomic and molecular crystal structure predictions. In one sentence, with a molecular structure and its Z, ABCrystal will give you a set of possible crystal structures (both atomic positions and cell are optimized) under specified pressure and crystal family in several seconds or hours by itself without any third-party software.

1.2. ABCrystal Information

ABCrystal was initialized by Dr. Jun Zhang since 2015 and is still actively developed. If you have any bug reports, comments, suggestions or the possibility of cooperation on ABCrystal, please feel free to contact to Dr. Jun Zhang via E-mail:

mailto:zhangjun@szbl.ac.cn

The latest version of ABCrystal can be obtained from:

http://www.zhjun-sci.com/abcrystal

1.3. ABCrystal Citation

Attention

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

1.4. Installation of ABCrystal

ABCrystal is an out-of-box program. When you download ABCrystal, it is a .zip or .tar.gz file. Once you decompress it, ABCrystal is ready to work so actually no installation is needed. Please note that the current version of ABCrystal does not have a graphic user interface (GUI). One must use it in the command line of Windows or Linux.

Below are some tips about running ABCrystal.

1.4.1. For Windows Users

You can call ABCrystal with its absolute path every time, or set path variable to the directory where ABCrystal resides.

Assume you put ABCrystal in the directory D:\ABCrystal, then right-click This PC and click Properties, Advanced System Settings, and Environment Variables. In System variables, select PATH and click Edit. In the editbox, add ;D:\ABCrystal at the end of the texts in it, and click OK to confirm it.

Tip

Now, you can press Shift and right-click in any explorer window and click Open cmd window here to call the command line. Type abcrystal to confirm that you can already call ABCrystal commands.

1.4.2. For Linux Users

You can call ABCrystal with its absolute path every time, or set path variable to the directory where ABCrystal resides.

Assume you put ABCrystal in the directory /home/you/bin/ABCrystal, then open your .bashrc and at the end of the file, add the following statement:

.bashrc
1export PATH=$PATH:/home/you/bin/ABCrystal
2export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/you/bin/ABCrystal

then run source ~/.bashrc. Type abcrystal to confirm that you can already call ABCrystal commands.

Sometimes you may encounter some errors during running ABCrystal on Linux. Here are some useful tips.

Tip

/usr/lib64/libstdc++.so.6: version `GLIBCXX 3.4.21’ not found

Please install or activate a GCC of higher version, like GCC 8.1.0. Sometimes you can try commands like module load gcc/8.1.0 to solve this problem.

Tip

Incorrect format near …

If you prepare an input file on Windows and copy it to Linux, ABCrystal may not recognize its format and report such an error. In this case, please transform the Windows file format into Linux one by dos2unix or using :set fileformat=unix in VIM.

1.4.3. For OpenMP

ABCrystal is parallelized by OpenMP. By default, it will use up all the CPU cores by default. If you want to change this behavior, please set OMP_NUM_THREADS variable to the number of CPU cores you want to use.

1.5. ABCrystal Files

When you decompress ABCrystal, you will find several files, including executables and some plain text files:

  • abcrystal The ABCrystal essential file.

  • topgen It generates topology information for a molecule to be calculated.

  • testfiles Files for testing ABCrystal functions.

  • misc/charmm36 Some collected CHARMM force field parameter files for rigidmol.

  • misc/crystal-cp2k-dft.inp An input template file for CP2K to perform DFT calculations for crystals.