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llh2010

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[求助] ATAT中g(shù)ensqs工具如何改變?nèi)〈鷿舛?

請(qǐng)問(wèn)各位高手們，使用ATAT軟件包的gensqs工具產(chǎn)生sqs結(jié)構(gòu)時(shí)，如何改變?nèi)〈臐舛龋坷鐚?duì)于一個(gè)bcc結(jié)構(gòu)，體心上的一種原子不變，而想讓立方體八個(gè)頂點(diǎn)上的另一種原子有一個(gè)或幾個(gè)被其它原子取代，請(qǐng)問(wèn)應(yīng)該如何寫(xiě)lat.in和conc.in文件。

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1樓 2012-03-06 19:27:46

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linggang87

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franch: 金幣+2, 謝謝回帖交流。 2012-06-25 17:29:51

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6樓: Originally posted by llh2010 at 2012-06-22 10:01:05
周期性結(jié)構(gòu)中八個(gè)頂角是等價(jià)的，在隨機(jī)排布中一個(gè)單胞中的八個(gè)頂角可能排不同的原子。隨機(jī)排布的晶體很多情況下只具有短程有序。
你說(shuō)的方法我也看到其他人做過(guò)，這種方法計(jì)算出來(lái)的結(jié)果不是很準(zhǔn)，原因是這種方法 ...

看來(lái)樓主可能不是用超晶胞方法材料計(jì)算方向的。SQS是基于超晶胞方法，用相對(duì)較小的晶胞去模擬無(wú)序情況，這要求SQS超胞內(nèi)各個(gè)原子的周?chē)h(huán)境‘盡可能’和無(wú)序時(shí)相近，而且誤差可以衡量。

超晶胞方法進(jìn)行晶體學(xué)計(jì)算中，周期性是必須的，而且如果你用的超胞能夠模擬無(wú)序情況了，這個(gè)超胞之外的和它等價(jià)的那些自然也可以模擬無(wú)序。

超晶胞方法模擬不同濃度時(shí)是有限制的，比如2%濃度，你只能建一個(gè)50個(gè)原子的胞，取代其中一個(gè)原子，進(jìn)行模擬，你不能取代半個(gè)原子。對(duì)于這個(gè)限制VCA 和CPA模擬無(wú)序就有優(yōu)勢(shì)了，濃度可以隨意，不過(guò)VCA和CPA都不能進(jìn)行原子位置的弛豫，有時(shí)候這是很大的劣勢(shì)。

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llh2010

7樓2012-06-22 19:58:45

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linggang87

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fzx2008: 金幣+1, 謝謝回帖！ 2012-06-22 08:58:50
llh2010: 金幣+5, ★★★很有幫助 2012-06-22 10:01:17

樓主表述中貌似有個(gè)錯(cuò)誤。周期性結(jié)構(gòu)中立方體八個(gè)頂點(diǎn)是等價(jià)的，相等于一個(gè)原子，不存在取代其中幾個(gè)的問(wèn)題。

改變濃度我想方法可以是改變超胞的大小。比如2*2*2的體心立方，含16個(gè)原子，取代1個(gè)原子濃度為 1/16,取代兩個(gè)原子，濃度為2/16......

至于具體怎么寫(xiě)你說(shuō)的文件，不了解，抱歉。。。

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3樓2012-06-21 23:55:49

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fzx2008: 金幣+3, 謝謝分享 2012-06-22 08:59:52
llh2010: 金幣+5, ★★★很有幫助 2012-06-22 09:41:26

我看到過(guò)一個(gè)人寫(xiě)的ATAT產(chǎn)生SQS的筆記，貼在這里，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樓2012-06-22 00:17:13

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llh2010

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引用回帖:

4樓: Originally posted by linggang87 at 2012-06-22 00:17:13
我看到過(guò)一個(gè)人寫(xiě)的ATAT產(chǎn)生SQS的筆記，貼在這里，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，非常感謝！這個(gè)筆記我也看過(guò)了。雖然說(shuō)的比較清楚，但是他只給出了Fe和Co是1:1的情況，就是各占50%。想產(chǎn)生其它比例需要修改conc.in這個(gè)文件，筆記中conc.in文件沒(méi)有說(shuō)清楚基矢和原子坐標(biāo)是怎么來(lái)的，不知道如何修改。

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5樓2012-06-22 09:40:27

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