[QE-users] Guidance Required for modelling CaCO3

[Saiyed Tasnim Md Fahim]

Dear QE users,
I am trying to model the Calcite structure for adsorption study in quantum
espresso. I am getting the following error:

At line 813 of file xmltools.f90

Fortran runtime error: End of file


I have used the following input file:



calculation = 'scf'

etot_conv_thr = 3.00d-04

forc_conv_thr = 1.00d-04

outdir = './.'

prefix = 'calcite2'

pseudo_dir = './.'

tprnfor = .true.

tstress = .true.

verbosity = 'high'

/





degauss = 1.4699723600d-02

ecutrho = 4.00d+02

ecutwfc = 5.00d+01

ibrav = 0

nat = 30

nosym = .false.

ntyp = 3

occupations = 'smearing'

smearing = 'cold'

/





conv_thr = 6.00d-09

electron_maxstep = 80

mixing_beta = 4.00d-01

/



ATOMIC_SPECIES

C 12.0107 C.pbesol-n-kjpaw_psl.1.0.0.UPF

Ca 40.078 Ca.rel-pbesol-spn-kjpaw_psl.1.0.0.UPF

O 15.9994 O.pbesol-n-kjpaw_psl.1.0.0.UPF



ATOMIC_POSITIONS crystal

Ca 0.00 0.666700 0.166700
Ca 0.00 0.00 0.00

Ca 0.00 0.00 0.50

Ca 0.666700 0.00 0.00

Ca 0.666700 0.00 0.833300

Ca 0.00 0.666700 0.666700

C 0.666700 0.00 0.083300

C 0.00 0.00 0.25

C 0.00 0.666700 0.416700

C 0.666700 0.00 0.583300

C 0.00 0.00 0.75

C 0.00 0.666700 0.916700

O 0.666700 0.0755010400 0.083300

O 0.9244989600 0.5911656200 0.083300

O 0.2578322900 0.00 0.25

O -0.00 0.2578322900 0.25

O 0.7421677100 0.7421677100 0.25

O 0.4088343800 0.00 0.083300

O 0.00 0.4088343800 0.416700

O 0.5911656200 0.9244989600 0.416700

O 0.9244989600 0.00 0.583300

O 0.666700 0.5911656200 0.583300

O 0.4088343800 0.0755010400 0.583300

O 0.0755010400 0.666700 0.416700

O 0.00 0.7421677100 0.75

O 0.2578322900 0.2578322900 0.75

O 0.5911656200 0.666700 0.916700

O 0.00 0.9244989600 0.916700

O 0.0755010400 0.4088343800 0.916700

O 0.7421677100 0.00 0.75



K_POINTS automatic

8 8 2 0 0 0



CELL_PARAMETERS angstrom

5.0068012800   0.00   0.00

-2.5034006400  4.3360171002   0.00

0.00   0.00  16.9901279000


I generated the input file from the pwscf input generator as a starting
point. Does anyone know how to solve the problem?


Sincerely,
Saiyed Tasnim Md Fahim,
Ph.D. Student,
Environmental Engineering,
University of Southern California.
___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
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Re: [QE-users] Spatial dependency of the wave functions for the spin-orbit coupling calculation

[Alireza Shabani via users]

Thank you, Paolo, for clarifying it.
So, is it right to say that the wave functions are not scalar anymore when we 
use non-collinear calculations, as they have two components for up and down 
spin?

Best wishes,
Alireza Shabani

Postdoc researcher,
Denmark Technical University
Copenhagen, Denmark
 

-Original Message-
From: Paolo Giannozzi  
Sent: Tuesday, December 12, 2023 11:38 AM
To: Alireza Shabani ; Quantum ESPRESSO users Forum 

Subject: Re: [QE-users] Spatial dependency of the wave functions for the 
spin-orbit coupling calculation

Plane-wave coefficients are complex: the real part is followed by imaginary 
part. The first 2*npw coefficients are for the "up" components of the spinor; 
the following 2*npw are for the "down" component

Paolo
--
Paolo Giannozzi, DMIF, Univ. Udine, Italy
*** AVAILABLE POST-DOC POSITION:
*** https://physicslab.uniud.it/persone/paolo-giannozzi/advert

On 12/12/23 11:25, Alireza Shabani via users wrote:
> Dear Giovanni,
> 
> Thank you for your explanation. Yes, I think for the number of KS 
> states, you are right, as the spin-orbit coupled states are twice the 
> non-spin-orbit coupled states. But I am going to focus on just one of 
> these states and calculate the wave function using the information in 
> the .hdf5 file and equation psi = sigma (C_real + i C_imag) * 
> exp(iG.r), which I know I must change a little bit because of the 
> two-component spinor.
> 
> My question is, is it right to say for every single 'Miller Indices' 
> in the .hdf5,we have four complex 'evc'? If so, how should we write 
> the vector to form the desired wave function? Is it a vector with two 
> complex components like this: (c_1 + j c_2   c_3 +j c_4) *
> exp(iG.r)   ,here c_i are the 'evc'.
> 
> Unfortunately, I didn’t find the mathematical description for 
> constructing the spinor plane wave in QE, so I would appreciate it if 
> anybody could introduce a reference for it.
> 
> Thank you for your suggestions.
> 
> Alireza Shabani
> 
> Postdoc researcher,
> Denmark Technical University
> Copenhagen, Denmark
> 
> *From:*Giovanni Cantele 
> *Sent:* Monday, December 11, 2023 2:14 PM
> *To:* Alireza Shabani ; Quantum ESPRESSO users Forum 
> 
> *Subject:* Re: [QE-users] Spatial dependency of the wave functions for 
> the spin-orbit coupling calculation
> 
> I'm not expert about HDF5 files, however because you are seeking for 
> wave function coefficients, the answer might be that, as explained for 
> example here
> 
> https://www.quantum-espresso.org/Doc/pw_user_guide/node10.html#SECTION
> 00043030 
>  N00043030>
> 
> when spin-orbit is turned on the wave functions are two-component spinors.
> This also reflect the fact that, with nelec electrons, the 
> ground-state density suffices nelec/2 Kohn-Sham states (using spin 
> degeneracy) in the absence of spin-orbit
> 
> coupling, whereas including the latter you need to compute (for
> semiconductors) at least nelec states.
> 
> Giovanni
> 
> 
> --
> 
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6 Via Cintia, I-80126, 
> Napoli, Italy
> e-mail: giovanni.cant...@spin.cnr.it 
> 
> Phone: +39 081 676910
> Skype contact: giocan74
> 
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> 
> Web page: https://sites.google.com/view/giovanni-cantele/home
> 
> 
> Il giorno lun 11 dic 2023 alle ore 13:49 Alireza Shabani via users 
>  > ha scritto:
> 
> Dear QE users,
> 
> I am going to calculate the spatial dependency of the wave function
> from the output HDF5 files from QE (for one specific k-point, such
> as Gamma). I know that the number 'evc' should be twice the 'Miller
> Indices' because it includes real and imaginary coefficients in the
> wave function: psi = sigma (C_real + i C_imag) * exp(iG.r).
> 
> Everything looks fine, and I can calculate the wave function in a
> normal DFT calculation (I mean without spin-orbit coupling!!). But,
> when I use spin-orbit coupling, the number of 'evc' in the final
> .hdf5 file becomes four times the 'Miller Indices.' For instance, if
> I have 100 'Miller Indices, ' I will have 400 'evc' which is a bit
> confusing. Does anybody know how we can interpret it?
> 
> Thank you for your suggestions.
> 
> Kind regards,
> 
> Alireza Shabani
> 
> Postdoc researcher,
> Denmark Technical University
> Copenhagen, Denmark
> 
> ___
> The Quantum ESPRESSO community stands by the Ukrainian
> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> 

Re: [QE-users] Thermodynamics with DFT+U

[BARRETEAU Cyrille]

Hi


In fact I faced the same type of problem when modelling spin-crossover 
molecules.

In such molecular systems the standard DFT fails to describe the energy balance 
between Low Spin (LS) and High Spin (HS) state.

The LS being strongly favoured.  Adding U is a way to circumvent this issue.


But trying to determine U self-consistently does not work (at least for our 
system).

Indeed we face the same nasty question that you raised: we have a drastically 
different U for LS and HS and the energy balance obtained is clearly incorrect. 
In addition in such system the atomic relaxation is very crucial, hence one 
also has to take into account a combined scf+relax determination of U that 
rapidly drives you crazy:-)

We have finally abandoned this procedure to keep a constant a U, that we 
determine from experimental estimation of E_LS-E_HS.


Another approach consists in using hybrid functional. But we also have a 
similar problem due to the ratio of exact exchange..

Indeed the "traditional" 1/4 ratio is too large to describe the energy balance, 
strongly favouring HS this time!

Hence one has to decrease the ratio down to something like 0.15...


Cyrille




Cyrille Barreteau
CEA Saclay, IRAMIS, SPEC Bat. 771
91191 Gif sur Yvette Cedex, FRANCE

+33 1 69 08 38 56 /+33  6 47 53 66 52  (mobile)
email: cyrille.barret...@cea.fr
Website: http://iramis.cea.fr/Pisp/cyrille.barreteau/
COSMICS: http://cosmics-h2020.eu/



De : users  de la part de Timrov 
Iurii 
Envoyé : lundi 11 décembre 2023 12:03:32
À : users@lists.quantum-espresso.org
Objet : Re: [QE-users] Thermodynamics with DFT+U

Dear Eduardo,

Your questions are tricky. There is a lot one can say. Please see my comments 
below. Maybe someone else can have a different viewpoint and comment as well.


  *   Should we choose one average value, or use the computed value for each 
system?

Both options are used in the literature. From my experience, it is better to 
use the second one.

  *   In DFT+U with empirical U people often use one value and compare the 
total energies. Why? One reason is because how would you choose different U 
values for different systems (e.g. FM vs AFM)? Maybe this can be done, but it 
is easier to use one empirical value. And it is claimed that the total energies 
must be compared with the same U value. But why? Is there a theorem or a proof? 
See below for the discussion why I would not use the same U value.
  *   In the second case, one uses different U values for different structures, 
provided that these U value are computed ab initio. Does this make sense? At 
least to me, yes. Why? Because different structures require different 
corrections. And, indeed, if one computes U e.g. for the Co-3d states in LiCoO2 
and CoO2, the U values appear to be different. Why? Because the electronic 
screening is different, and the magnitude of self-interaction errors is 
different in LiCoO2 and CoO2. One can make an approximation and use an average 
U value for these two systems, but why doing so? From our experience using 
different ab initio U values and comparing total energies gives results in good 
agreement with experiments (e.g. voltages for batteries). But we do not have a 
(mathematical) justification for doing so, as well as we do not have a proof 
why one should not do it. Hence, at present there is no consensus in the 
literature on this topic. More investigations for various systems is needed to 
see trends. But for me, comparing total energies with different U values 
obtained from linear-response theory makes sense and it provides reasonable 
results.


  *   Concerning the advantage of self consistency, let me rise the example 
LiCoO2 that comes with the HP code. The example produces U for Co and also for 
O, as well as V(Co-O). U(O-2p)=8.0439 eV. Is this parameter useful? As the 
example is not converged w.r.t. to k-points and cutoffs the number may change, 
but U(O-2p) is still there. I read PRB101, 064305 (2020) by Floris et al, and 
it seems that U(O-2p) is discarded. I am curious why, but I couldn't find a 
discussion. Maybe there is another article. My point here is that using self 
consistent parameters for some elements and shells, and discarding others is 
just a partial self-consistency.

We did not apply the U correction to O-2p states. The question of whether to 
apply or not the U correction to O-2p is another big question. Many things can 
be said here, and you will possibly receive different answers from different 
people. A few comments from my side:

  *   We generally do not apply U to O-2p, when U is computed from 
linear-response theory, because it is large (8-9 eV) and from our experience 
the accuracy of some properties (e.g. voltages) are worsened.
  *   If you use ACBN0 to compute U, you might get 2-3 eV, and applying this 
correction to O-2p might improve the results. 

Re: [QE-users] Spatial dependency of the wave functions for the spin-orbit coupling calculation

[Paolo Giannozzi]

Plane-wave coefficients are complex: the real part is followed by 
imaginary part. The first 2*npw coefficients are for the "up" components 
of the spinor; the following 2*npw are for the "down" component


Paolo
--
Paolo Giannozzi, DMIF, Univ. Udine, Italy
*** AVAILABLE POST-DOC POSITION:
*** https://physicslab.uniud.it/persone/paolo-giannozzi/advert

On 12/12/23 11:25, Alireza Shabani via users wrote:

Dear Giovanni,

Thank you for your explanation. Yes, I think for the number of KS 
states, you are right, as the spin-orbit coupled states are twice the 
non-spin-orbit coupled states. But I am going to focus on just one of 
these states and calculate the wave function using the information in 
the .hdf5 file and equation psi = sigma (C_real + i C_imag) * exp(iG.r), 
which I know I must change a little bit because of the two-component 
spinor.


My question is, is it right to say for every single 'Miller Indices' in 
the .hdf5,we have four complex 'evc'? If so, how should we write the 
vector to form the desired wave function? Is it a vector with two 
complex components like this: (c_1 + j c_2   c_3 +j c_4) * 
exp(iG.r)   ,here c_i are the 'evc'.


Unfortunately, I didn’t find the mathematical description for 
constructing the spinor plane wave in QE, so I would appreciate it if 
anybody could introduce a reference for it.


Thank you for your suggestions.

Alireza Shabani

Postdoc researcher,
Denmark Technical University
Copenhagen, Denmark

*From:*Giovanni Cantele 
*Sent:* Monday, December 11, 2023 2:14 PM
*To:* Alireza Shabani ; Quantum ESPRESSO users Forum 

*Subject:* Re: [QE-users] Spatial dependency of the wave functions for 
the spin-orbit coupling calculation


I'm not expert about HDF5 files, however because you are seeking for 
wave function coefficients, the answer might be that, as explained for 
example here


https://www.quantum-espresso.org/Doc/pw_user_guide/node10.html#SECTION00043030
 


when spin-orbit is turned on the wave functions are two-component spinors.
This also reflect the fact that, with nelec electrons, the ground-state 
density suffices nelec/2 Kohn-Sham states (using spin degeneracy) in the 
absence of spin-orbit


coupling, whereas including the latter you need to compute (for 
semiconductors) at least nelec states.


Giovanni


--

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cant...@spin.cnr.it 
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009 

Web page: https://sites.google.com/view/giovanni-cantele/home 



Il giorno lun 11 dic 2023 alle ore 13:49 Alireza Shabani via users 
> ha scritto:


Dear QE users,

I am going to calculate the spatial dependency of the wave function
from the output HDF5 files from QE (for one specific k-point, such
as Gamma). I know that the number 'evc' should be twice the 'Miller
Indices' because it includes real and imaginary coefficients in the
wave function: psi = sigma (C_real + i C_imag) * exp(iG.r).

Everything looks fine, and I can calculate the wave function in a
normal DFT calculation (I mean without spin-orbit coupling!!). But,
when I use spin-orbit coupling, the number of 'evc' in the final
.hdf5 file becomes four times the 'Miller Indices.' For instance, if
I have 100 'Miller Indices, ' I will have 400 'evc' which is a bit
confusing. Does anybody know how we can interpret it?

Thank you for your suggestions.

Kind regards,

Alireza Shabani

Postdoc researcher,
Denmark Technical University
Copenhagen, Denmark

___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu
)
users mailing list users@lists.quantum-espresso.org

https://lists.quantum-espresso.org/mailman/listinfo/users



___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and 

Re: [QE-users] Spatial dependency of the wave functions for the spin-orbit coupling calculation

[Alireza Shabani via users]

Dear Giovanni,

Thank you for your explanation. Yes, I think for the number of KS states, you 
are right, as the spin-orbit coupled states are twice the non-spin-orbit 
coupled states. But I am going to focus on just one of these states and 
calculate the wave function using the information in the .hdf5 file and 
equation psi = sigma (C_real + i C_imag) * exp(iG.r), which I know I must 
change a little bit because of the two-component spinor.

My question is, is it right to say for every single 'Miller Indices' in the 
.hdf5, we have four complex 'evc'? If so, how should we write the vector to 
form the desired wave function? Is it a vector with two complex components like 
this: (c_1 + j c_2   c_3 +j c_4) * exp(iG.r)   ,here c_i are the 'evc'.

Unfortunately, I didn’t find the mathematical description for constructing the 
spinor plane wave in QE, so I would appreciate it if anybody could introduce a 
reference for it.

Thank you for your suggestions.
Alireza Shabani
Postdoc researcher,
Denmark Technical University
Copenhagen, Denmark


From: Giovanni Cantele 
Sent: Monday, December 11, 2023 2:14 PM
To: Alireza Shabani ; Quantum ESPRESSO users Forum 

Subject: Re: [QE-users] Spatial dependency of the wave functions for the 
spin-orbit coupling calculation

I'm not expert about HDF5 files, however because you are seeking for wave 
function coefficients, the answer might be that, as explained for example here
https://www.quantum-espresso.org/Doc/pw_user_guide/node10.html#SECTION00043030
when spin-orbit is turned on the wave functions are two-component spinors.
This also reflect the fact that, with nelec electrons, the ground-state density 
suffices nelec/2 Kohn-Sham states (using spin degeneracy) in the absence of 
spin-orbit
coupling, whereas including the latter you need to compute (for semiconductors) 
at least nelec states.

Giovanni

--

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cant...@spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: https://sites.google.com/view/giovanni-cantele/home


Il giorno lun 11 dic 2023 alle ore 13:49 Alireza Shabani via users 
mailto:users@lists.quantum-espresso.org>> ha 
scritto:
Dear QE users,
I am going to calculate the spatial dependency of the wave function from the 
output HDF5 files from QE (for one specific k-point, such as Gamma). I know 
that the number 'evc' should be twice the 'Miller Indices' because it includes 
real and imaginary coefficients in the wave function: psi = sigma (C_real + i 
C_imag) * exp(iG.r).
Everything looks fine, and I can calculate the wave function in a normal DFT 
calculation (I mean without spin-orbit coupling!!). But, when I use spin-orbit 
coupling, the number of 'evc' in the final .hdf5 file becomes four times the 
'Miller Indices.' For instance, if I have 100 'Miller Indices, ' I will have 
400 'evc' which is a bit confusing. Does anybody know how we can interpret it?
Thank you for your suggestions.

Kind regards,
Alireza Shabani
Postdoc researcher,
Denmark Technical University
Copenhagen, Denmark

___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX 
(www.max-centre.eu)
users mailing list 
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users
___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users