SQS “Tutorial”.doc

SQS “Tutorial” Amy Bengtson1 June 2007Here 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 arent 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): /avdw/atat//avdw/atat/manual.pdfI 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: Lengths of each side of the cellLattice vectors (that form BCC)Atomic position(s). Tell which species can substitute (here Co and Fe can both be at this position)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 0.0000000.000000 2.810643 0.0000000.000000 0.000000 2.8106430.500000 0.500000 0.5000000.500000 -0.500000 0.5000000.500000 0.500000 -0.5000000.000000 0.000000 0.000000 Co,FeThis 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 0.0000000.000000 2.810643 0.0000000.000000 0.000000 2.810643-1.000000 0.000000 0.0000000.000000 0.000000 1.0000000.000000 1.000000 0.000000-1.000000 1.000000 1.000000 Fe-0.500000 0.500000 0.500000 Co3. Now create the clusters by using this command: corrdump -l lat.in -2=maxradius -clusThe maxradius is the length of the longest pair desired. A reasonable starting guess is:-2=34. 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.out5. Generate the sqs structure (disorded structures) using this command: gensqs -n=Natoms sqs.outWhere 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 cluscorrdump -noe -2=maxradius -3=another_radius -rnd -s=conc.in tcorr.outThe “-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.outYou 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 dont 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.outii. Find the target correlation out to the LargerRadiuscorrdump -noe -2= LargerRadius -rnd -s=sqs.out tcorr_finalRND.outiii. 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: INCARSYSTEM = CoFeENCUT=455ISPIND = 2 #makes spin-polarized calc. possibleISPIN = 2 #does spin-polarized calc.MAGMOM= 5 5 5 5 5 5 5 5ISTART = 0 INIWAV = 1 NSW = 191 IBRION = 2ISIF = 3 ISMEAR = 1 SIGMA = 0.2PREC = AccurateLWAVE = .FALSE.KPPRA = 17576 KSCHEME=Monkorst-PackDOGGASUBATOM = 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.ino conc,ino tcorr.outo rms ranking (show the Excel sheet where you rank tcorr_final.out)o And confirm that maxradius is a reasonable value. Appendix: Example of ranking tcorr_final.out in Excel. NOTE: This tcorr_final.out is NOT from the above lat.in and conc.in, it is just an example: These are the target correlations from step 6ii. (tcorr_finalRND.out)RandomPoint1st Pair2nd Pair3rd PairCorr0-0.750.56250.5625SQS #Point1st Pair2nd Pair3rd Pairrms|1st Pair|2nd Pair|3rd Pair|10-0.750.56250.50.062500-0.062520-0.750.50.583330.0658797310-0.06250.0208330-0.7883883480-0.0625-0.062540-0.7883883480-0.0625-0.062550-0.750.50.583330.0658797310-0.06250.02083These are from tcorr_final.outSQS# = the structure associated with