关注：

1)  版本更新过程体现的新技术、新方法

2)  版本更新过程中参数设置的变更

CALYPSO4.0 的几个关键命令摘录：

1) calypso.x  不需要 可直接使用

2) 常压不能设成完全等于0

3) 采用 CALYPSO_ANALYSIS_KIT中编译好的cak.py直接使用可对结果进行分析

./cak.py --cif -m 0.01

./cak.py --cif

CALYPSO.log文件中Step与input文件中的代对应，如每一代30个结构，则每一个Step下出现30个结构

连续提交calypso.pbs任务，提上去后又掉下来，产生多个result文件夹的 的处理方法，保留合理的results文件夹如results 1、results2，删掉其他的，将results2 mv成results 后，从新续算提交。

YY-中物院(12248580) 4:32:16 PM
    CALYPSO4.0，设置PickUp= T续算时，没有出现result1文件夹，请问是怎么回事？
LLL_吉大(100334400) 4:38:00 PM
pickup 续算，会在原来的results文件下面进行

LLL_吉大(100334400) 4:39:27 PM
最好把之前没算完的那代对应的文件删除掉
YYY-中物院(12248580) 4:41:36 PM
即，对应的PSO_ini_X等文件删掉？
还有PSO_opt_X

CALYPSO4.0 -input 参数摘录

如果你保留了 outcar 和 的话，比较容易判断。 (最新版可以在 input.dat 里面用 RecordOUTCAR = T 来保留优化过程)。  或者你再把 结构重新优化一下，看一下能量，就知道了，这样更保险一些。

Ialgo =integer: It defines which PSO algorithm should be adopted in the simulation.

1: global PSO algorithm
2: local PSO algorithm
3: ABC algorithm with symmetry
Default value: 2

ICode =integer: It defines which code should be used for local structure optimization during
the structure prediction.

1: VASP
2: SIESTA
3: GULP
4: PWSCF
5: CASTEP
6: CP2K
7: Gaussian
8: DFTB+
9: LAMMPS
Default value: 1

CALYPSO3.0 -input 参数摘录

# It determines which algorithm should be adopted in the simulation.
Ialgo = 2
# Ialgo = 1 for Global PSO
# Ialgo = 2 for Local PSO (default value)

# The number of lbest for local PSO
NumberOfLbest=4
# The Number of local optimization for each structure.
NumberOfLocalOptim= 3

CALYPSO1.2-input 参数摘录

Ialgo (integer): It determines which algorithm should be adopted in the simulation.

1: local PSO algorithm
2: Hybrid PSO (implemented, testing now)
3: global PSO algorithm.
Default value: 3

CALYPSO1.0-input 参数摘录

1: local PSO algorithm (implemented, testing now)

2: PSO algorithm for molecules (implemented, testing now)
3: global PSO algorithm.
Default value: 3

CALYPSO4.0 的几个关键命令：

1) calypso.x  不需要 可直接使用

2) 常压不能设成完全等于0

3) 采用 CALYPSO_ANALYSIS_KIT中编译好的cak.py直接使用可对结果进行分析

./cak.py --cif -m 0.01

./cak.py --cif

Analysis of Results： CALYPSO calculations typically generate a large number of structures. It is necessary to
devise a versatile tool for data analyses. We here develop a CALYPSO_ANALYSIS
KIT(CAK),allowing automatic structure analysis.

  cak.py 现在功能很强大，具体参考Mannual

$cak.py
An output file named as ‘Analysis_Output.dat’ will be generated. By default,
Analysis_Output.dat contains space-group and enthalpy information of 50 energetically best
structures. Note that space groups of structures are determined with a tolerance of 0.1 Å by
default. Below we show several more advanced analyzing options.

$cak.py -n integer
The specified number of best structures will be analyzed and output.

$cak.py -t real
One of the specified values ranging from 0.01 to 1.0 Å will be used as the tolerance for
symmetry analyses of given structures. The default value is 0.1.

$cak.py -m ‘real1 real2 … realn’
Allowing multi-tolerance values (separated by space) for symmetry analyses of given
structures.

$cak.py --cif -m ‘real1 real2 … realn’

  The structure files with .cif format will be generated in directories of ‘dir_n’ (n indicates the
tolerance value for symmetry analysis).

$cak.py --vasp -m ‘real1 real2 … realn’
  The VASP POSCAR files containing structure information will be generated in directories
‘dir_n’ (n indicates the tolerance value for symmetry analysis).

$cak.py --pri –vasp/cif
The primitive cells of structures will output.

$cak.py -p

Plotting the figure of lowest enthalpy as a function of generations.

$cak.py --hard
The structures will output in the descending order of hardness.

The Output Files
(1) Analysis_Output.dat
At least three columns are present in this file by default. The first column is the index of
the structures sorted by enthalpies in the ascending order (the numbers in bracket indicate the
structure number out of all structures generated in the CALYPSO calculation). The second
column shows the enthalpy data. The corresponding space-group numbers as obtained by the
desirable tolerance value for the structures are listed in the third column.

(2) Convexhull.dat
This file contains two columns. The first column shows various stoichiometries for a given
binary system. The second column presents the lowest enthalpy for each stoichiometry.

(3) plot.dat
This file contains two columns. The first column shows the generation number, while the
second gives the lowest enthalpy for each generation.

(4)UCell_m_n.vasp
This file contains the structure data in conventional cell in the POSCAR format of VASP. m
and n indicate the enthalpy ranking number and the space group number of the structure,
respectively.

(5) PCell_m_n.vasp
This file contains the structure data in primitive cell in the POSCAR format of VASP. m and
n indicate the enthalpy ranking number and the space group number of the structure,
respectively.

(7) m_n.cif
This file contains the structure data in conventional cell in the .cif format. m and n indicate the
enthalpy ranking number and the space group number of the structure, respectively.

(8) m_n_p.cif

This file contains the structure data in primitive cell in the .cif format. m and n indicate the
enthalpy ranking number and the space group number of the structure, respectively.

参考网址：

http://www.calypso.cn/releasenotes/

Release Notes for CALYPSO 4.0-September,2014

Binary packages of CALYPSO_4.0 are available in the Mac and Linux.

• Interfaced CALYPSO with LAMMPS code.

• Implemented the structure prediction of 2D material with adsorption.

• Implemented the design of optical materials with desirable electronic band gap.

• Implemented new algorithm of Artificial Bee Colony for large system.

Release Notes for CALYPSO 3.7 - May, 2014

• Fixed an issue with generating structures in 2D layer structure prediction.

Release Notes for CALYPSO 3.6 - April, 2014

• Fixed an issue of the interface with CP2K code.

• Redesigned and reimplemented the interface with CASTEP code.

• Upgrade the spglib to version 1.6.

Release Notes for CALYPSO 3.5 - January, 2014

• Fixed an issue with handling the crystal symmetries.

Release Notes for CALYPSO 3.4 - November, 2013

• Fixed an issue of the interface with Gaussian code.

• Fixed an issue of the lattice-pso operator.

Release Notes for CALYPSO 3.3 - October, 2013

• Interfaced CALYPSO with DFTB+ code.

• Fixed an issue of the similar function.

Release Notes for CALYPSO 3.2 - September, 2013

• Fixed an issue with generating new structrues using GPSO in cluster prediction.

Release Notes for CALYPSO 3.1 - July, 2013

• Upgraded the spglib to the version 1.5.

• Fixed an issue with parsing the CONTCAR.

Release Notes for CALYPSO 3.0 - June, 2013

• Refactor most source files and eliminate redundant code.

• Implemented the variational stochemistry structure prediction.

• Implemented the hardness structure design.

• Implemented the surface structure prediction.

• Implemented the Split mode for submit the job.

• Implemented the structural generation based on nucleation growth technique.

• Implemented the prediction of 2D layer (single/multi and buckle layers) structures.

• Interface with VASP, Quantum Espresso, GULP, SIESTA, CP2K and Gaussian codes.

• Refactor the analysis script based on spglib.

Release Notes for CALYPSO 1.3 - October 28, 2011

• Implemented the prediction of Cluster structures.

• Implemented the prediction of 2D structures.

• The parallel local optimization.

• The generation of structures based on the grid and supercell method.

Release Notes for CALYPSO 1.2 - January 12, 2011

• A new Local PSO was implemented now.

• Interface with VASP, SIESTA and GULP.

• Implemented prediction of cluster(testing).

• Usage of the new similar function (bond characterization matrix).

• MaxTime used to control the local optimization.

Release Notes for CALYPSO beta version - Auguest, 2009

• Symmetry constraints on structural generation.

• Generation of new structures by PSO.

• Interface with VASP.