[Pw_forum] Total energy vs PP and some beginner questions

Giuseppe Mattioli giuseppe.mattioli at ism.cnr.it
Fri Apr 10 18:03:42 CEST 2015 

Dear Konrad

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

Yes, it is generally safe (apart from very strange effects that can arise in particular and limited cases).

> 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
Yes, it is! :-)

> 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
> parameters?

vc-relax optimizes both cell parameters and atomic positions

> 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?

It might sometimes be wise to check the quality of your setup by displacing a little the atoms out of their symmetry positions, but they usually tend 
to come back.

> 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.

I suppose that the best thing is to flick through the "tutorials" section of the QE site.

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

Look at nspin=2 and all the related variables in the pw.x input guide. The high-spin (or ferromagnetic, as physicists like to call it :-)) 
configuration of your system should not be very hard to obtain.

HTH

Giuseppe

On Friday, April 10, 2015 05:00:27 PM Konrad Gruszka wrote:
> 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
> that.
> 
> 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
> parameters?
> 
> 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)
> 
>   &control
>      prefix='YFe52',
>      restart_mode='from_scratch'
>      calculation='relax'
>      pseudo_dir='/home/darnok/qe/espresso-5.1.1/pseudo/'
>      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'
>   /
>   &system
>      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,
>   /
>   &electrons
>   mixing_mode = 'plain'
>   mixing_beta = 0.7
>   /
> 
>   &ions
>   /
> ATOMIC_SPECIES
>   Fe  55.845  Fe.pbe-sp-van.UPF
>   Y  88.906  Y.pbe-nsp-van.UPF
> ATOMIC_POSITIONS {crystal}
>   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: ATOMIC_POSITIONS (angstrom)
> > 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
> > ATOMIC_POSITIONS (angstrom)
> > 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

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   Giuseppe Mattioli                            
   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
   v. Salaria Km 29,300 - C.P. 10                
   I 00015 - Monterotondo Stazione (RM), Italy    
   Tel + 39 06 90672836 - Fax +39 06 90672316    
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   ResearcherID: F-6308-2012

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