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小木虫论坛-学术科研互动平台 » 计算模拟区 » 第一性原理 » 其他 » ATAT中gensqs工具如何改变取代浓度
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llh2010

至尊木虫 (著名写手)

[求助] ATAT中gensqs工具如何改变取代浓度

请问各位高手们，使用ATAT软件包的gensqs工具产生sqs结构时，如何改变取代的浓度？例如对于一个bcc结构，体心上的一种原子不变，而想让立方体八个顶点上的另一种原子有一个或几个被其它原子取代，请问应该如何写lat.in和conc.in文件。
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1楼2012-03-06 19:27:46
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llh2010

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引用回帖:
7楼: Originally posted by linggang87 at 2012-06-22 19:58:45
看来楼主可能不是用超晶胞方法材料计算方向的。SQS是基于超晶胞方法，用相对较小的晶胞去模拟无序情况，这要求SQS超胞内各个原子的周围环境‘尽可能’和无序时相近，而且误差可以衡量。

超晶胞方法进行晶体学计 ...

谢谢！
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8楼2012-06-23 14:26:45
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linggang87

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【答案】应助回帖

★ ★ ★ ★ ★ ★
fzx2008: 金币+1, 谢谢回帖！ 2012-06-22 08:58:50
llh2010: 金币+5, ★★★很有帮助 2012-06-22 10:01:17
楼主表述中貌似有个错误。周期性结构中立方体八个顶点是等价的，相等于一个原子，不存在取代其中几个的问题。

改变浓度我想方法可以是改变超胞的大小。比如2*2*2的体心立方，含16个原子，取代1个原子浓度为 1/16,取代两个原子，浓度为2/16......

至于具体怎么写你说的文件，不了解，抱歉。。。
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3楼2012-06-21 23:55:49
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linggang87

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【答案】应助回帖

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fzx2008: 金币+3, 谢谢分享 2012-06-22 08:59:52
llh2010: 金币+5, ★★★很有帮助 2012-06-22 09:41:26
我看到过一个人写的ATAT产生SQS的笔记，贴在这里，你可以看看：

SQS “Tutorial”
Amy Bengtson
1 June 2007

Here are my notes on setting up SQS (with many thanks from Yueh-Lin for teaching me).  Setting up the most random SQS cells can be subtle, and my notes aren’t perfect, so please make sure you double check everything here. I make special note of the files you may want to double check with Dane.

For more explanations, please see the atat manual (section 6.1.8):
http://www.its.caltech.edu/~avdw/atat/
http://www.its.caltech.edu/~avdw/atat/manual.pdf

I am using CoFe as an example since it is an SQS structure I have set up in the past.

In order to get sqs structure for 50% Fe in BCC CoFe:

1. Create a lat.in file. This is the structure from which you want to get the disorded structure.  lat.in is of this format:

2.810643  0.000000 0.000000
0.000000 2.810643 0.000000
0.000000 0.000000 2.810643
0.500000 0.500000 0.500000
0.500000 -0.500000 0.500000
0.500000 0.500000 -0.500000
0.000000 0.000000 0.000000 Co,Fe










This lat.in is for primitive BCC with one atom. If your primitive cell has more than 1 atom, then continue to list all atomic positions after 0.000000 0.000000 0.000000 Co,Fe.

2. Make conc.in. This tells ATAT what concentration you want to create.  conc.in is of the same format as lat.in, only with all atomic positions listed.
2.810643 0.000000 0.000000
0.000000 2.810643 0.000000
0.000000 0.000000 2.810643
-1.000000 0.000000 0.000000
0.000000 0.000000 1.000000
0.000000 1.000000 0.000000
-1.000000 1.000000 1.000000 Fe
-0.500000 0.500000 0.500000 Co



3. Now create the clusters by using this command:
corrdump -l lat.in -2=maxradius -clus

The maxradius is the length of the longest pair desired.  A reasonable starting guess is:
-2=3


4. Find the correlation of the clusters you created in step 3.  Here, maxradius should be the same number as in 3.  
corrdump -noe -2=maxradius -rnd -s=conc.in > tcorr.out


5. Generate the sqs structure (disorded structures) using this command:
gensqs -n=Natoms > sqs.out

Where Natoms = the size of the cell you want to create. sqs.out will contain all of the sqs structures, there may be more than 1! The structures will be in the formation of str.out (like conc.in – some conversions will be needed to make them into POSCARs – see step *).


6. In many cases you will find you have many structures in sqs.out.  The problem is how to choose which structures to run.  You can do two things:
a. Redo everything above with a larger maxradius – this will give more correlations to match.  Or you can add another radius to match:
corrdump -l lat.in -2=maxradius -3=another_radius –clus
corrdump -noe -2=maxradius -3=another_radius  -rnd -s=conc.in > tcorr.out
The “-2” matches pairs, the “-3” matches triplets.

b. Rank the sqs structures that you have in sqs.out to find the “most random” structures.  To do this:
        i. Find the correlation on the sqs structures in sqs.out:
        corrdump -noe -2=LargerRadius -s=sqs.out > tcorr_final.out
You want LargerRadius to be larger than maxradius because you are trying find the correlations beyond the original correlation given in tcorr.out.  Usually you want to rank based on the first 3 pairs.  The columns in tcorr_final.out are:
[point correlation] [1st pair] [2nd pair] [3rd pair] [4th pair] …  
If you don’t have at least 4 columns in your tcorr_final.out, then you need to increase LargerRadius until you have at least 4 columns.
Each row corresponds to an sqs structure in sqs.out

ii. Find the target correlation out to the LargerRadius
corrdump -noe -2= LargerRadius -rnd -s=sqs.out > tcorr_finalRND.out
               
iii. Open tcorr_final.out in excel and rank the structures based on most random.  
       
7. Once you have found which structures from sqs.out you are going to use, split them up and make each structure into its own str.out file.

8. Create a vasp.wrap file that gives the VASP input information. Here is an example:
[INCAR]
SYSTEM = CoFe
ENCUT=455
ISPIND = 2 #makes spin-polarized calc. possible
ISPIN = 2 #does spin-polarized calc.
MAGMOM=  5 5 5 5 5 5 5 5
ISTART = 0     
INIWAV = 1   
NSW = 191  
IBRION = 2
ISIF = 3   
ISMEAR = 1
SIGMA = 0.2
PREC = Accurate
LWAVE = .FALSE.
KPPRA = 17576
KSCHEME=Monkorst-Pack
DOGGA
SUBATOM = s/Co/Co/g
SUBATOM = s/Fe/Fe_pv/g


9. In the directory with sqs.out, create the VASP input files using this command:
runstruct_vasp -nr

10. Run as you normally do.

If you make a mistake and need to start over, remove all of these files:
rm clusters.out corrdump.log gensqs_0_1.stat sqscell.out sqs* sym.out tcorr.out


Important!!! These are the files you should double check with Dane to make sure they were set up correctly.
o        lat.in
o        conc,in
o        tcorr.out
o        rms ranking (show the Excel sheet where you rank tcorr_final.out)
o        And confirm that maxradius is a reasonable value.
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4楼2012-06-22 00:17:13
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llh2010

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引用回帖:
4楼: Originally posted by linggang87 at 2012-06-22 00:17:13
我看到过一个人写的ATAT产生SQS的笔记，贴在这里，你可以看看：

SQS “Tutorial”
Amy Bengtson
1 June 2007

Here are my notes on setting up SQS (with many thanks from Yueh-Lin for teaching me).  S ...

恩，非常感谢！这个笔记我也看过了。虽然说的比较清楚，但是他只给出了Fe和Co是1:1的情况，就是各占50%。想产生其它比例需要修改conc.in这个文件，笔记中conc.in文件没有说清楚基矢和原子坐标是怎么来的，不知道如何修改。
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5楼2012-06-22 09:40:27
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