UT theoretical chemistry code forum

Dear Graeme,

When one is using the dosanalyze.pl script, what is right way to call it in order to run over multiple atoms?

I noticed that if one uses something like:

dosanalyze.pl e=-10,0 p 3-4

one obtains an output which is completely different then if one runs:

dosanalyze.pl e=-10,0 p 3,4 (i.e. with comma between 3 and 4)

On a specific case: I used the vtstscripts-964 scripts after a VASP DOS calculation (using LORBIT=11). I run split_dos and then dosanalyze.pl. The following are the results I obtained:

(1) If I run the script for atom 3:

dosanalyze.pl e=-10,0 p 3

I obtain:

#################################
Integrate from -10eV to 0eV.

Total States: 319.64803676
Average Energy (band center): -5.56726181833926
Standard Deviation: 3.31226366780355
#################################

It looks good.

(2) If I run the script for atom 4:

dosanalyze.pl e=-10,0 p 4

I obtain:

#################################
Integrate from -10eV to 0eV.

Total States: 319.64814697
Average Energy (band center): -5.56726264401453
Standard Deviation: 3.31226339638815
#################################

It looks also good.

(3) If I run the script over both atoms 3 and 4, using:

dosanalyze.pl e=-10,0 p 3-4

I obtain:

#################################
Integrate from -10eV to 0eV.

Total States: 639.29618373
Average Energy (band center): -5.56726223117697
Standard Deviation: 3.31226353209585
#################################

If we compare this output with that for the cases (1) and (2) - in terms of total states and band center - this output looks good.

(4) If I run now the script also over both atoms 3 and 4, but using:

dosanalyze.pl e=-10,0 p 3,4 (i.e. with comma)

I obtain:

#################################
Integrate from -10eV to 0eV.

Total States: 2231.69516635
Average Energy (band center): -6.94029205505517
Standard Deviation: 3.02607550862248
#################################

This result cannot be correct. The number of states is too large, and there is no reason for the shift of the p-band center to -6.9 eV (comparing with the output from (1) and (2)).

Is it correct to say that if one has more atoms, then the only way to go over them is by using a syntax like "atom_x - atom_y". Using a syntax which includes a comma, i.e. "atom_x, atom_y" seems not to lead to a correct output. While this is ok for many cases, it can be a problem if one wants to look at atoms which are not consecutive, i.e. 1,2,3,5.

Please let me know if I am doing anything wrong, or this is the way the script works for multiple atoms.

Thank you very much for your time!

With best regards,
Eduard

I'm looking at the dosanalyze.pl code and I see that the #-# format is accepted as an input, but there is no support for the #, # format when specifying atoms. So I'm not sure what the script is doing when you specify p 3,4. If you post a .tar.gz file of your calculation, I will be able to reproduce your results and add this functionality, or at least print a graceful exit message or something - we can't have it giving incorrect results without reporting a problem.

Thank you for reporting this - I appreciate all feedback to help improve our scripts.

Dear Graeme,

Fully agree. It would be actually nice to have the #,# option, particularly for the systems for which one needs to look at a set of non-consecutive atoms.

I sent you the VASP relevant files via a wetransfer link (valid for 7 days).