[QE-users] Problem using SCAN calculating energy of atomic oxygen

[Filippo Savazzi]

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> 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>:
> 
>> 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>
> 
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