CALYPSO教程

U s e r' s G u i d e

CALYPSO version 1.3.0

October 28, 2011

Written by Yanming Ma, Yanchao Wang, Jian Lv and Li zhu

State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, China Please contact with Yanchao Wang (wyc09@), Jian Lv (jianlv10@), Li Zhu (zhuli10@) and Yanming Ma (mym@) for any technical questions or any bugs.

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Copyright © 2011 Jilin University. All Rights Reserved.

CONTENTS

1. INTRODUCTION (3)

2. COMPILATION (4)

3. EXECUTION OF THE PROGRAM (4)

4. INPUT FILE (5)

5. OUTPUT FILES (11)

6. THE RESULTS ANALYSIS (12)

7. SOME PUBLICATIONS FROM USE OF CALYPSO (13)

8. FUTURE DEVELOPMENT (13)

9. ACKNOWLEDGMENTS (13)

1.INTRODUCTION

CALYPSO (Crystal structure AnaLYsis by Particle Swarm Optimization) is a package for crystal structure prediction through particle swarm optimization algorithm. The approach requires only chemical compositions for a given compound to predict stable or metastable structures at given external conditions (e.g., pressure and temperature), thus the CALYPSO package can be used to identify/determine the crystal structure and design the multi-functional materials. Its main characteristics are:

z The Crystal Structure Prediction uses no experimental information, with just the chemical compositions and external conditions.

z The symmetry constraint is imposed in the structure generation.

z A particularly devised geometrical structure parameter is implemented to enhance the structure search efficiency.

z Incorporation of partial structural information is possible, e.g., fixed experimental cell parameters, fixed space group or fixed partial atomic positions.

z It is written in Fortran 95 and memory is allocated dynamically.

It routinely provides:

z crystal structure prediction

z molecular crystal structure prediction

z cluster structure prediction

z2-dimensional structure prediction

For more details on the formalism, see the reference cited below.

Reference:

“Crystal structure prediction via particle-swarm optimization” Yanchao Wang, Jian Lv, Li Zhu and Yanming Ma*, Phys. Rev. B 82, 094116 (2010).

PILATION

For CALYPSO installation, basic UNIX knowledge is required. The user should be acquainted with the tar, gzip, awk, sed and make commands of the UNIX environment. To install CALYPSO, you need:

z A minimal UNIX/LINUX environment.

z Fortran-95(Intel Fortran Compiler) compilers.

z VASP should be installed on your computer. There are development interfaces with other codes (SIESTA and GULP ).

If you want to compile the program, please simply use the following commands.

$ tar zvxf Calypso_*.tar.gz

$ cd CALYPSO_*

$ sh install.sh

A new folder "Workspace" will be built for CALYPSO run.

3.EXECUTION OF THE PROGRAM

A fast way to check your installation of CALYPSO code can be found in the directory of “Tests”. Please simply run the commands.

$ cd CALYPSO_*/Tests

$ ./calypso.x > log &

Other examples are provided in the “path-to-package/Examples” directory. This directory contains basic input.dat and shell scripts for running CALYPSO.

We describe here in details how to run crystal structure prediction on Silicon. It is advisable to create independent directories for each job, so that everything is clean and neat. Please go to your working directory and:

$ mkdir Si

$ cd Si

$ cp path-to-package/Examples/Si/* ./ .

The working directory should contain the following necessary files:

(1)The CALYPSO input file: input.dat