[Pw_forum] Total energy vs PP and some beginner questions

Konrad Gruszka kgruszka at wip.pcz.pl
Fri Apr 10 17:00:27 CEST 2015

Dear Giovanni and Giuseppe,

Thank you very much for taking the discussion. I think it will benefit 
many beginners. I try to read as much as possible but some important 
things escape me at the accumulation of a lot of information, not yet 
know how to siftit.

The answers given by you are very kind, and after reading them I raise 
further questions:

1.If different potentials have different cutoff energies, is it "safe" 
tooverestimate them (ecutwfc), losing only the time of calculationbut 
maintaining good quality?

2. "I guess (but maybe I’m wrong!) that you are wondering whether it is 
possible to mix spin polarised and non spin polarised pseudo potentials 
because you are mislead by the “sp “ and “nsp” found in the pseudo file 
name." - yes. Of course it was clearly my mistake. Question was about 
spin polarization and I've also mistaken name conventions... sorry for 

3. I understand that the various "pp" for the same elements have a 
different number of electrons. How do I know wchichPP I "want" to use? 
<- Perhaps this question is more in physics than QE

4. This will be a very basic question: If I want to do to optimize the 
positions of the atoms in the unit cell should I calculate the 'relax' 
or 'vc-relax'? If I want to optimize for example'a' and 'c' cell width 
parameters I have to use the 'vc-relax' and if I do not want to optimize 
the size of the unit cell but only atomic positions I do the 'relax' 
calculation? What when I need to do both atomic positions and cell 

5. "But, introducing an even small perturbation to the linear geometry 
[...]"- In optimizing the geometry should I always slightly "move" atoms 
from theoretical (Wyckoff) positions?

6. And finally, the last (sorry for the number of questions!) question: 
I know what is google, butI would like to take advantage of Your 
experience:  Is there somewhere a "guide by the hand" which would allow 
me to feel more confident, and more specifically have less doubt which 
solutions are good and which are not? For now I'm trying to read and 
understand "Electronic Structure" by Richard M. Martin and I feel that 
it is a very good quality book.

The questions that I asked clearly show how much novice I am. I hope 
that my lack of knowledge is not very blatant, because my curiosity in 
this topic sometimes keeps me awake :)

"so it is hard to give the correct answer without your input file(s) [...]
Below I attach the input file with the 'relax' calculation I was asking 
before in the "same Z cooridinate" question.

With your permission, I would like to ask for assistance how to take 
into account that the below system is magnetic (ferromagnetic)

     outdir = '/home/darnok/qe/espresso-5.1.2/tempdir/'
     tstress = .true.
     tprnfor = .true.
     nstep = 55
     etot_conv_thr = 1.0E-5
     forc_conv_thr = 1.0D-4
     verbosity = 'high'
     ibrav=  4, celldm(1) =9.505, nat=  6, ntyp= 2, celldm(3)= 0.77,
     ecutwfc = 80.0, ecutrho = 900, smearing = 'gaussian', occupations = 
"smearing", degauss=0.02,
  mixing_mode = 'plain'
  mixing_beta = 0.7

  Fe  55.845  Fe.pbe-sp-van.UPF
  Y  88.906  Y.pbe-nsp-van.UPF
  Y 0.00 0.00 0.00
  Fe 0.3333 0.6666 0.00
  Fe 0.6666 0.3333 0.00
  Fe 0.50 0.00 0.50
  Fe 0.00 0.50 0.50
  Fe 0.50 0.50 0.50
K_POINTS {automatic}
    1 1 1 0 0 0

Again, thank you in advance for your kindly answer,
  Konrad Gruszka, PhD.

W dniu 10.04.2015 o 12:50, Giovanni Cantele pisze:
>> On 10 Apr 2015, at 11:33, Konrad Gruszka <kgruszka at wip.pcz.pl> wrote:
>> Dear Users,
>> Recently while making some tests on simple systems I've found very
>> strange behaviour of pw.x. It is obvious that choosing different pseudo
>> potentials should give to some extent different total energies. Since
>> I'm a beginner,  I would therefore ask a few questions:
>> 1. To what extent has the pseudopotentials of two different elements
>> must be the same? Can I use spin polarized together with none spin
>> polarized PP? Or can I for example use Fe.pbe-sp-van.upf with
>> Y.pbe-nsp-van.UPF? Or even combine for example Fe.pbe-sp-van.upf with
>> Y.pbe-mt_fhi.UPF ?
>> 2. I have noticed that combining some PP together gives very different
>> total energies: for example for the same system first run with Fe and Y
>> with ",pbe-mt_fhi.UPF" gives total = -200 Ry and when using
>> Fe.pbe-sp-van.upf with Y.pbe-nsp-van.upf gives total energy = -1333 Ry.
>> Why those two PP give so big difference?
>> 3. The last one noob-like question:  While doing a 'relax' calc. only
>> the X and Y coordinates change during calculation, the Z always is such
>> as set on the begining. Is that normal? (or maybe it is only fortuity
>> for my atomic system?)
>> The lecture of pwscf manual did not answer my questions. I regret to
>> note that the beginnings with QE are wery hard for novice...
>> Thank you in advice for your kindly answer
>> Konrad Gruszka, PhD.
>> Czestochowa University of Technology, Poland
>> -- dr inż. Konrad Gruszka Politechnika Częstochowska Instytut Fizyki
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
> actually, the lecture of the pwscf documentation does answer your questions:
> 1. I guess (but maybe I’m wrong!) that you are wondering whether it is possible to mix spin polarised and non spin polarised pseudo potentials because
> you are mislead by the “sp “ and “nsp” found in the pseudo file name. As you can read here:
> http://www.quantum-espresso.org/pseudopotentials/naming-convention/
> the “s”, “p” and “n” stand for
> 	• s: semicore state s in valence
> 	• p: semicore state p in valence
> 	• n: nonlinear core-correction
> So you can mix the mentioned pseudos, provided you know the features of the pseudo you are using (norm conserving versus ultrasoft,
> with versus without non linear core correction, ect.)
> 2. see here: http://www.quantum-espresso.org/faq/pseudopotentials/#2.4
> as explained in the above link, mostly when two different pseudos of the same elements are built with a different number of electrons, the two total energies differ a lot. If you look carefully inside the pseudo files, you (not that hardly) discover that Y.pbe-mt_fhi.UPF has 3 valence electrons, with only 5s and 4d orbitals occupied,
>      5s  5  0  2.00      0.000      0.000     0.000000
>      5p  5  1  0.00      0.000      0.000     0.000000
>      4d  4  2  1.00      0.000      0.000     0.000000
>      4f  4  3  0.00      0.000      0.000     0.000000
> whereas Y.pbe-nsp-van.UPF has 11 valence electrons with 4s and 4p orbitals occupied as well
> Wavefunctions         nl  l   occ
>                         4S  0  2.00
>                         4P  1  6.00
>                         4D  2  1.00
>                         5S  0  2.00
> 3. see here: http://www.quantum-espresso.org/faq/self-consistency/#6.14
> so it is hard to give the correct answer without your input file(s), but what is likely going on is that you system has a symmetry that forces the z component of the forces to zero.
> Beware: when finding a symmetry, pw.x always keeps that symmetry during the run. How? For example, all the forces that, consistently with the found symmetry, should be zero, are NOT calculated but set to zero. A typical example is try to run a relax run for an H2O molecule. If you start with the following positions:
> H    0.0    0.0   -1.0
> O    0.0    0.0    0.0
> H    0.0    0.0    1.0
> then pw.x relaxes to
> H        0.000000000   0.000000000  -0.945242812
> O        0.000000000   0.000000000   0.000000000
> H        0.000000000   0.000000000   0.945242812
> because the molecule initially starts with a linear geometry (in this case along the z axis). The found symmetry is such that any force between atoms cannot have either an x or an y component, so pw.x is able (unless otherwise instructed) to output a relaxed structure constrained to lie along the z axis (which in this case is not the lowest energy one!).
> But, introducing an even small perturbation to the linear geometry, such as
> H    0.0    0.1   -1.0
> O    0.0    0.0    0.0
> H    0.0    0.1    1.0
> the right experimental geometry is found:
> H        0.000000000   0.264981368  -0.771676756
> O        0.000000000  -0.329962735   0.000000000
> H        0.000000000   0.264981368   0.771676756
> (OH bond: 0.97 A, H-O-H angle: 104.7)
> In the first case 16 symmetry operations are found, whereas in the second only 4!
> Giovanni

dr inż. Konrad Gruszka
Politechnika Częstochowska
Instytut Fizyki

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