[QE-users] Problem using SCAN calculating energy of atomic oxygen
Filippo Savazzi
filo.savazzi at gmail.com
Thu Nov 22 09:52:24 CET 2018
Thank you very much Natalie, Paolo and Giuseppe
You’ve been very helpful, cause I had the suspect SCAN wasn’t applicable to this subject but I was stuck trying to find tricks to make it work.
I’d have just a last question on the topic. I was able to calculate the single point energy of molecular oxygen (O2) using SCAN, hence calculate the absorption energy for a bridged oxygen on coronene at least with respect to O2. Shall I consider this result satisfactory, having used the same grid that I used for other functionals (PBE, PBE0, …)? The absorption energy is consistent with the others.
Thank you again for your help, have a great day!
Filippo
Filippo Savazzi, PhD Student
Politecnico di Torino, Torino, Italy
> On 21 Nov 2018, at 21:26, Paolo Giannozzi <p.giannozzi at gmail.com> wrote:
>
> I tend to agree with Natalie's conclusions. Unfortunately I am not aware of any simple solution. All meta-GGA functionals do strange things in systems with regions of vanishing charge, and SCAN is the one that gives less problems (!). SCF divergence is maybe extreme, but there are also problems like this one: https://gitlab.com/QEF/q-e/issues/32 <https://gitlab.com/QEF/q-e/issues/32>, indicating that one may need a surprisingly dense FFT grid to get reliable results
>
> Paolo
>
> On Wed, Nov 21, 2018 at 8:22 PM Holzwarth, Natalie <natalie at wfu.edu <mailto:natalie at wfu.edu>> wrote:
> I have looked into the SCAN functional for an isolated atom, also finding that Vxc increases to unphysically large values as the density decreases exponentially. We were able to demonstrate for ourselves that the SCAN functional itself is responsible for this behavior due to the appearance of the density in denominators of various terms. It is my understanding that the SCAN developers are aware of this issue and are working on a remedy. In the meantime, perhaps it would be good to use the SCAN functional only for systems that do not have exponentially decreasing densities. At least that was my conclusion. Sincerely, Natalie Holzwarth
>
> N. A. W. Holzwarth email: natalie at wfu.edu <mailto:natalie at wfu.edu>
> Department of Physics web: http://www.wfu.edu/~natalie <http://www.wfu.edu/~natalie>
> Wake Forest University phone: 1-336-758-5510
> Winston-Salem, NC 27109 USA office: Rm. 300 Olin Physical Lab
>
>
> On Wed, Nov 21, 2018 at 1:26 PM Filippo Savazzi <filo.savazzi at gmail.com <mailto:filo.savazzi at gmail.com>> wrote:
> Thanks Giuseppe,
> I’ll give it a try, I didn’t think about setting the occupation from input.
> Thank you for your help.
>
> Best,
>
> Filippo
>
>
>
> Filippo Savazzi, PhD Student
> Politecnico di Torino, Torino, Italy
>
> > On 21 Nov 2018, at 19:00, Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it <mailto:giuseppe.mattioli at ism.cnr.it>> wrote:
> >
> >
> > Dear Filippo
> > Isolated open-shell atoms are tricky. Please look here for hints
> >
> > yourpathtoQE6.3/PW/examples/example05
> >
> > HTH
> > Giuseppe
> >
> > Quoting Filippo Savazzi <filo.savazzi at gmail.com <mailto:filo.savazzi at gmail.com>>:
> >
> >> Dear QE users,
> >>
> >> I’m Filippo Savazzi, a PhD student from Politecnico di Torino, Italy.
> >> I’m using QE since a couple of years, and just browsing the archives of this mailing list or enquiring the mighty google I’ve been lucky enough that this is actually the first time I have to post a question.
> >> Thanks everybody for the indirect support you gave me in these years.
> >>
> >> I’m calculating absorption energies of oxygen on a coronene molecule, as part of a little evaluation of different available XC functionals that I’m doing. I’m calculating the absorption energy both with respect to the molecular oxygen and with atomic oxygen.
> >> My problems arise when I try to calculate the energy of a single atom of oxygen using SCAN. In this case the energy diverges until the SCF fails. I have no troubles running the calculation on the actual system (coronene + bridged O), neither on a molecular oxygen (triplet O2); the issue is just localised on the single oxygen atom. My first guess was that the implementation of SCAN has either troubles in dealing with isolated systems or with spin polarization, but I ruled out these issues when I was able to calculate the single point energy of an oxygen molecule. Are you aware of any other problems using SCAN in these conditions?
> >> In the following I attach the input for pw.x I’m using, as well as a brief example of the SCF part in the output. I already played with cell dimension (thinking too much vacuum could have been the problem), as well as with ecutwfc and ecutrho (so indirectly with the integration grid), and then, just to give it a chance, with the diagonalization method and beta-mixing.
> >>
> >> Thank you in advance for your attention.
> >>
> >> Best,
> >> Filippo
> >>
> >>
> >> Filippo Savazzi, PhD Student
> >> Politecnico di Torino, Torino, Italy
> >>
> >>
> >>
> >>
> >> &CONTROL
> >> calculation = ’scf',
> >> restart_mode='from_scratch',
> >> pseudo_dir = '/home/filippo/pseudo',
> >> outdir='./tmp_o',
> >> prefix='oxy',
> >> /
> >> &SYSTEM
> >> ibrav=6,
> >> celldm(1)=20,
> >> celldm(3)=1,
> >> nat=1,
> >> ntyp=1,
> >> input_dft='scan',
> >> ecutwfc=100,
> >> tot_magnetization=2,
> >> nspin=2,
> >> /
> >> &ELECTRONS
> >> diagonalization = 'cg',
> >> electron_maxstep = 300,
> >> mixing_mode = 'local-TF',
> >> mixing_beta = 0.7,
> >> conv_thr = 1.0d-7,
> >> /
> >> &IONS
> >> ion_dynamics='damp',
> >> upscale=1000,
> >> /
> >> ATOMIC_SPECIES
> >> O 15.99 O_ONCV_PBE-1.0.upf
> >> ATOMIC_POSITIONS {angstrom}
> >> O 0.0000 0.0000 0.0000
> >> K_POINTS{gamma}
> >>
> >>
> >>
> >>
> >> EXTRACT OF OUTPUT:
> >>
> >> Dense grid: 540376 G-vectors FFT dimensions: ( 128, 128, 128)
> >>
> >> Estimated max dynamical RAM per process > 116.06 MB
> >>
> >> Estimated total dynamical RAM > 1.36 GB
> >> Generating pointlists ...
> >> new r_m : 0.4125 (alat units) 8.2500 (a.u.) for type 1
> >>
> >> Initial potential from superposition of free atoms
> >>
> >> starting charge 5.99905, renormalised to 6.00000
> >>
> >> negative rho (up,down): 4.917E-05 4.917E-05
> >> Starting wfcs are random
> >>
> >> total cpu time spent up to now is 3.1 secs
> >>
> >> Self-consistent Calculation
> >>
> >> iteration # 1 ecut= 100.00 Ry beta= 0.70
> >> CG style diagonalization
> >> ethr = 1.00E-02, avg # of iterations = 9.6
> >>
> >> negative rho (up,down): 1.044E-03 1.363E-03
> >>
> >> total cpu time spent up to now is 240.5 secs
> >>
> >> total energy = 2429.63502350 Ry
> >> Harris-Foulkes estimate = -31.41616940 Ry
> >> estimated scf accuracy < 3.28037744 Ry
> >>
> >> total magnetization = 2.00 Bohr mag/cell
> >> absolute magnetization = 2.00 Bohr mag/cell
> >>
> >> iteration # 2 ecut= 100.00 Ry beta= 0.70
> >> CG style diagonalization
> >> c_bands: 4 eigenvalues not converged
> >> ethr = 1.00E-02, avg # of iterations = 13.6
> >>
> >> negative rho (up,down): 2.824E-03 3.815E-03
> >>
> >> total cpu time spent up to now is 331.7 secs
> >>
> >> total energy = 33638.43350785 Ry
> >> Harris-Foulkes estimate = 318.68713998 Ry
> >> estimated scf accuracy < 0.37936007 Ry
> >>
> >> total magnetization = 2.00 Bohr mag/cell
> >> absolute magnetization = 2.00 Bohr mag/cell
> >
> >
> >
> > GIUSEPPE MATTIOLI
> > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> > Via Salaria Km 29,300 - C.P. 10
> > I-00015 - Monterotondo Scalo (RM)
> > Mob (*preferred*) +39 373 7305625
> > Tel + 39 06 90672342 - Fax +39 06 90672316
> > E-mail: <giuseppe.mattioli at ism.cnr.it <mailto:giuseppe.mattioli at ism.cnr.it>>
> >
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> --
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> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
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