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晶体结构预测-example 解读:变胞预测

已有 4952 次阅读 2015-2-22 14:43 |个人分类:物质结构及其预测|系统分类:科研笔记

关注:

1) 变胞预测理念及算例分析 如CALYPSO、USPEX等

2) 变组成结构预测-T7_varcomp_GULP算例分析 ......calculationType- 301

3) 变胞预测:1倍分子式,2倍分子式,3倍分子式等等.....calculationType300? 仍用301



You can also do fixed-composition calculations with a variable number of formula units【最常用的,但多少倍分子式上限如何确定?】;

in this
case set just one line (and calculationType=301), for example for compound A2BC4:
% numSpecies
2 1 4
% EndNumSpecies




手册摘录解读:Specify the following varcomp-only options:

$.triangleright $variable  firstGeneMax 【变量  第一代产生的different compositions数量】

Meaning: How many different compositions 【怎样确保产生自己想要的组成?!】are sampled in the first generation. If 0, then the number is equal to initialPopSize/4. For binaries, we recommend firstGeneMax=11, for ternaries a higher value is needed, e.g. 30.

Default: 11

Format:

10 : firstGeneMax


$.triangleright $variable  minAt

Meaning: Minimum number of atoms (for calculationType=301/201/300) or molecules (for calculationType=311) in the unit cell for the first generation.

Default: No default

Format:

10 : minAt

$.triangleright $variable  maxAt

Meaning: Maximum number of atoms (for calculationType=301/201/300 or in META calculations) or molecules (for calculationType=311) in the unit cell for the first generation.

Default: No default   【没有默认值,需自己指定】

Format:

20 : maxAt




算例分析:(**)T7_varcomp_GULP

Lennard-Jones binary system, GULP, and variable-composition method of Wang, Lyakhov and Oganov (2008, 2010, 2012). Test created by ARO, updated by AOL.


1. README 文件解读


Since 9.3.8, we slightly change the definition of Lattice values
in the INPUT.txt for variable composition
.


Instead of the atomic
volume, the estimated volume for each block is now required.

For instance, suppose the two blocks are Ar and Kr.


One should put the volumes for single Ar and Kr atom.
% atomType
Ar Kr
% EndAtomType


% numSpecices
1 0
0 1
% EndNumSpecices

% Latticevalues (this word MUST stay here, type values below)
2.2 17.5
% Endvalues (this word MUST stay here)


If the blocks are ArKr and Kr.
One should put the volumes for ArKr and Kr.

% numSpecices
1 1
0 1
% EndNumSpecices

% Latticevalues (this word MUST stay here, type values below)
20 17
% Endvalues (this word MUST stay here)

The set up is very trivial. One can take an known structure as the reference.
Meanwhile, results1/approximate_volumes give the reference values as well.

approximate volume for each specie:
19.8415 17.9282



2.  INPUT文件解读

PARAMETERS EVOLUTIONARY ALGORITHM

******************************************
******************************************
*      TYPE OF RUN AND SYSTEM            *
******************************************
******************************************
USPEX : calculationMethod (USPEX, VCNEB, META)
301   : calculationType (dimension: 0-3; molecule: 0/1; varcomp: 0/1)
1     : optType (1=enthalpy, 2=volume, 3=hardness, 4=struc_order, 5=aver_dist)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% What symmetry(s) have to be satisfied by the randomly created structures
% symmetries
2-230
% endSymmetries

% numbers of specices (ions/molecules/blocks) of each type
% numSpecices
1 0
0 1

% EndNumSpecices
%%%%%%%%%%%%%%%%%%%%
% Here come the atomic numbers of the atoms involved
% atomType
Ar Kr
% EndAtomType
%%%%%%%%%%%%%%%%%%%%
% valences
1 1
% endValences

******************************************
*               POPULATION               *
******************************************
40    : populationSize (how many individuals per generation)
120   : initialPopSize
40    : numGenerations (how many generations shall be calculated)
30    : stopCrit 【什么意思, 不解】

******************************************
%       FIRST VAR. COMP. GENERATION      *
******************************************
20    : firstGeneMax (how many different compositions for first generation)
8     : minAt (minimum amount of atoms/cell for first generation)     【最少几个原子】
16    : maxAt (maximum amount of atoms/cell for first generation)【最多几个原子】

******************************************
*  SURVIVAL OF THE FITTEST AND SELECTION *
******************************************
0     : reoptOld
0.6   : bestFrac

******************************************
******************************************
*          VARIATION OPERATORS           *
******************************************
******************************************
0.60  : fracGene (fraction of generation produced by heredity)
0.10  : fracRand (fraction of generation produced randomly from space groups)
0.20  : fracAtomsMut (fraction of the generation produced by softmutation)
0.10  : fracTrans (fraction of the generation produced by transmutations)

****************************************
*             CONSTRAINTS              *
****************************************
1.3   : minVectorLength ( minimal length of any lattice vector)
%%%%%%%%%%%%%%%%
% IonDistances
0.4 0.4
0.0 0.4
% EndDistances
%%%%%%%%%%%%%%%%

*****************************************
*                 CELL                  *
*****************************************
% The following is what you know about the lattice. If you know the lattice
% vectors, type them in as 3x3 matrix. If not, type the estimated volume.
% For variable composition - type the estimated atomic volume for each element.
% Latticevalues (this word MUST stay here, type values below)
2.2 17.5
% Endvalues (this word MUST stay here)

*****************************************
*   DETAILS OF AB INITIO CALCULATIONS   *
*****************************************
% supported:  1-vasp, 2-siesta, 3-gulp, 4-LAMMPS, 5-NeuralNetworks
% 6-dmacrys, 7-cp2k, 8-QuantumEspresso, 9-ASE, 10-ATK, 11-CASTEP
abinitioCode (which code from CommandExecutable shall be used for calculation? )
3 3 3 3 3
ENDabinit

%Resolution for KPOINTS - one number per step or just one number in total)
% KresolStart
0.16 0.12 0.09 0.07
%  Kresolend

% commandExecutable
gulp <input >output
% EndExecutable
%%%%%%%%%%%%%%%%%%

1     : numParallelCalcs (how many parallel calculations shall be performed)
0     : whichCluster (0: no-job-script, 1: local submission, 2: remote submission)
0.010 : toleranceFing (tolerance for identical structures)

*****************************************
*               RESTART                 *
*****************************************
0    : pickUpYN (if pickUpYN~=0 , then a previous calculation will be continued )
0    : pickUpGen (at which generation shall the previous calculation be picked up? If = 0 , then a new calculation is started)
0    : pickUpFolder (number of the results folder to be used. If = 0 , then the highest existing number is taken)



CALYPSO:

#### The parameters for structure prediction with variational stoichiometry #####
################# Examples are given in section 3.5 #################
VSC=logical: If this tag is set as “True”, structure prediction of automatic variation of
chemical compositions will be performed
.

This technique is designed to explore all possible
stoichiometries for given binary systems (e.g., AxBy system) at once. However, one has to
take his/her own risk for the use of this technique. The search space has been significantly
enlarged due to the existence of large number of possible stoichiometries. We highly recommend separate simulations with fixed stoichiometries for confirmation of their results.
Default value: False


2.6.3.3
The Output Files

(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.










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