[QE-users] It is neccesary to make a vc-relax in each DFT U+V calculation?
ROBERT MIKHAIL GUZMAN ARELLANO
rguzmana at unmsm.edu.pe
Tue Oct 1 19:33:50 CEST 2024
Dear Iurii and Lorenzo.
I am very grateful for your responses. I have just finished a calculation
with hp.x, using the parallelization characterized by the
"perturb_only_atom" command. I ran an SCF calculation to generate the
density, with the output folder named "tmp." After that, I copied the "tmp"
folder four times, naming them "tmp1," "tmp2," "tmp3," and "tmp4," because
I chose four atoms to define the U and V values. Part of the SCF input is
as follows:
&control
calculation='scf',
restart_mode='from_scratch',
prefix='graphane',
pseudo_dir = './PP',
outdir='./tmp',
.
.
.
ATOMIC_SPECIES
C 12.0107 C.pbe-n-kjpaw_psl.1.0.0.UPF
H 1.008 H.pbe-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
C 0.0000000000 0.0489411798 4.0736189551
C 0.0000000000 1.5156118708 3.6147177498
H 0.0000000000 0.0493473355 5.1835009290
H 0.0000000000 1.5152618823 2.5048489230
K_POINTS {automatic}
12 12 1 0 0 0
HUBBARD ortho-atomic
V C-2P C-2P 1 1 1.d-5
V C-2P C-2P 2 2 1.d-5
V C-2P C-2P 1 2 1.d-5
V C-2P H-1S 1 3 1.d-5
V C-2P H-1S 2 4 1.d-5
V H-1S H-1S 3 3 1.d-5
V H-1S H-1S 4 4 1.d-5
I then ran four hp.x calculations simultaneously, where one of the inputs
is:
&INPUTHP
prefix='graphane',
outdir='./tmp1',
nq1=6, nq2=6, nq3=1,
conv_thr_chi = 1.d-8,
dist_thr = 1.d-4
alpha_mix(1) = 0.05,
docc_thr = 1.d-4
iverbosity = 2
determine_num_pert_only = .false.
perturb_only_atom(1) = .true.
niter_max = 200
/
The inputs for the others are similar, with the difference that:
outdir='./tmpJ', perturb_only_atom(J) = .true.
where J=2,3,4.
Inside the tmpJ folder, there is an HP folder (J = 1, 2, 3, 4). I renamed
the tmp1 folder to tmp and copied all the files from "tmpJ/HP" to "tmp/HP."
Finally, I ran hp.x with the following input:
&INPUTHP
prefix='graphane',
outdir='./tmp',
nq1=6, nq2=6, nq3=1,
iverbosity = 2
compute_hp=.true.
/
which produced the .dat file with the Hubbard parameters.
Could you say me if it is ok? I would like to do the same with the q-points
parallelization method. However, I am wondering if copying the tmp folder
is necessary for this last method.
On the other hand, is it possible to run pw.x and hp.x to calculate V
values between different orbitals of the same atom? where part of the
hubbard card would be:
HUBBARD ortho-atomic
V C-2P C-2S 1 1 1.d-3
V C-2P C-2S 2 2 1.d-3
Best regards.
El mar, 1 oct 2024 a las 3:17, Lorenzo Bastonero (<lbastone at uni-bremen.de>)
escribió:
> Dear Robert and everyone,
>
> Indeed, as Iurii wrote, for each individual Hubbard atoms being perturbed
> you can use the `start_q` and `last_q`, along with the
> `determine_q_mesh_only` to just “initialise” the calculation and find the
> number of q-points needed for each Hubbard atom. After that, you should
> collect the perturbation matrices and use `sum_pertq`.
>
> You can think of automating this by scripting, but allow me to make a
> small advertisement. Recently, we developed some nice code written in AiiDA
> that automates all of this (parallelisation over atoms and q-points, plus
> some great additional features to find nearest neighbours). The code is
> under beta version here:
> https://github.com/aiidateam/aiida-quantumespresso-hp.
> We are about to publish a preprint about it explaining all the details. If
> you are interested, I am happy to help you out if you needed any assistance.
>
> An interesting plus is that you can then use the `aiida-vibroscopy` plugin
> (also developed by myself) to perform phonon, IR and Raman calculations
> using finite-displacements and finite-fields with very little knowledge
> (where DFT+U+V and any other functional are supported). See for instance
> these tutorials (and e.g. the related paper) to have an idea:
> https://aiida-vibroscopy.readthedocs.io/en/latest/tutorials/index.html
>
> Cheers,
> Lorenzo
>
> ********************************
> Lorenzo Bastonero
>
> PhD Student
> U Bremen Excellence Chair,
> Bremen Center for Computational Materials Science,
> and MAPEX Center for Materials and Processes
>
> University of Bremen
> Faculty of Production Engineering
> TAB-Building, Room 3.32
> Am Fallturm 1
> 28359 Bremen, DE
>
> http://www.hmi.uni-bremen.de/
>
> Il giorno 1 ott 2024, alle ore 08:30, ROBERT MIKHAIL GUZMAN ARELLANO via
> users <users at lists.quantum-espresso.org> ha scritto:
>
> Thanks a lot for your response Iurii.
>
> I have a question about how to use hp.x in parallel. In the article "HP –
> A Code for the Calculation of Hubbard Parameters Using Density-Functional
> Perturbation Theory," four levels of parallelization are mentioned.
>
> The first can be done using the command "perturb_only_atom(i)." The second
> is parallelization over "q" points, the third is parallelization over "k"
> points, and the last is plane wave parallelization, which I assume is
> automatically enabled, as in pw.x. However, how can I set the "q" and "k"
> parallelization for hp.x?
>
> I run hp.x with the assumption that the -nq label is necessary if it
> exists. So I use the command:
>
> *mpirun -np 4 hp.x -nq 2 -nk 2 -in name.in <http://name.in/> > name.out*
> Is it ok?
>
> Please let me know. I was searching on the internet but I did not find an
> example of how to run hp.x in parallel using "q" and "k" levels.
>
> Best regards.
>
> El lun, 30 sept 2024 a las 9:38, Timrov Iurii (<iurii.timrov at psi.ch>)
> escribió:
>
>> Dear Giuseppe,
>>
>> The developers of ACBN0 are interested to make it public, but it is not
>> clear yet if and when this will happen.
>>
>> Greetings,
>> Iurii
>>
>> ----------------------------------------------------------
>> Dr. Iurii TIMROV
>> Tenure-track scientist
>> Laboratory for Materials Simulations (LMS)
>> Paul Scherrer Institut (PSI)
>> CH-5232 Villigen, Switzerland
>> +41 56 310 62 14
>> https://www.psi.ch/en/lms/people/iurii-timrov
>> ------------------------------
>> *From:* users <users-bounces at lists.quantum-espresso.org> on behalf of
>> Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
>> *Sent:* Monday, September 30, 2024 16:18
>> *To:* users at lists.quantum-espresso.org <users at lists.quantum-espresso.org>
>> *Subject:* Re: [QE-users] It is neccesary to make a vc-relax in each DFT
>> U+V calculation?
>>
>>
>> Dear Iurii
>> Is there any hope to have the ACBN0 pseudo-hybrid functional or its
>> adapted implementation by Lee and Son you mentioned soon available in
>> a regular QE version?
>> Thanks in advance
>> Giuseppe
>>
>> Quoting Timrov Iurii <iurii.timrov at psi.ch>:
>>
>> > Dear Robert,
>> >
>> > Originally, DFT+U and DFT+U+V were introduced to study
>> > transition-metal and rare-earth compounds. So usually, U has been
>> > applied to d and f electrons, and V for d-p and similar couples.
>> >
>> > In your system, you have only s and p electrons. Now there are more
>> > and more studies where U and V are applied to these electronic
>> > states (see e.g.
>> >
>> https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.2.043410).
>> I do not have much experience in using DFT+U and DFT+U+V with U and V from
>> linear response for these systems. But I know that ACBN0 is used quite
>> extensively for these systems and U and V are
>> > positive.
>> >
>> > HTH
>> >
>> > Greetings,
>> > Iurii
>> >
>> >
>> > ----------------------------------------------------------
>> > Dr. Iurii TIMROV
>> > Tenure-track scientist
>> > Laboratory for Materials Simulations (LMS)
>> > Paul Scherrer Institut (PSI)
>> > CH-5232 Villigen, Switzerland
>> > +41 56 310 62 14
>> > https://www.psi.ch/en/lms/people/iurii-timrov
>> > ________________________________
>> > From: ROBERT MIKHAIL GUZMAN ARELLANO <rguzmana at unmsm.edu.pe>
>> > Sent: Saturday, September 28, 2024 02:03
>> > To: Timrov Iurii <iurii.timrov at psi.ch>
>> > Cc: users at lists.quantum-espresso.org <users at lists.quantum-espresso.org>
>> > Subject: Re: [QE-users] It is neccesary to make a vc-relax in each
>> > DFT U+V calculation?
>> >
>> > Thanks a lot for your response.
>> >
>> > I was reading the paper that you recommended to me and I notice that
>> > your U and V values are positive.
>> >
>> > I am practicing the DFT U + V in graphane (graphene -C- completely
>> > hydrogenated - 4 atoms in the unit cell) with the objective to
>> > calculate U and V values of carbon and hydrogen orbitals or between
>> > them. I used the protocol of your paper and I am considering the HSE
>> > band structure calculation as a target, where the last gives a
>> > greater gap energy than the GGA DFT calculations.
>> >
>> > I obtained positive U values but the V values are negatives.
>> >
>> > These are:
>> >
>> > ATOMIC_SPECIES
>> > C 12.0107 C.pbe-n-kjpaw_psl.1.0.0.UPF
>> > H 1.008 H.pbe-kjpaw_psl.1.0.0.UPF
>> > ATOMIC_POSITIONS {angstrom}
>> > C 0.0000000000 0.0489411798 4.0736189551
>> > C 0.0000000000 1.5156118708 3.6147177498
>> > H 0.0000000000 0.0493473355 5.1835009290
>> > H 0.0000000000 1.5152618823 2.5048489230
>> > K_POINTS {automatic}
>> > 12 12 1 0 0 0
>> > HUBBARD ortho-atomic
>> > V C-2P C-2P 1 1 2.8212
>> > V C-2P C-2P 2 2 2.8212
>> > V C-2P H-1S 1 3 -0.0283
>> > V C-2P H-1S 2 4 -0.0283
>> > V C-2P C-2P 1 2 -0.1355
>> > V H-1S H-1S 3 3 4.3467
>> > V H-1S H-1S 4 4 4.3467
>> >
>> > So I am wondering what is the criteria to validate or accept a
>> > negative V, and another question is which orbitals need to be
>> > selected for a V and U calculations. For example in the commented
>> > paper, the Mn-3d and O-2p orbitals are considered but avoided the
>> > others valence orbitals. I am thinking that the most energetic
>> > orbitals of each atom must be considered... Could you recommend
>> > another work where discuss it ?
>> >
>> > Thanks for the attention!!
>> >
>> >
>> >
>> > El vie, 27 sept 2024 a las 3:01, Timrov Iurii
>> > (<iurii.timrov at psi.ch<mailto:iurii.timrov at psi.ch>>) escribió:
>> > Dear Robert,
>> >
>> > Please have a look at this paper:
>> > https://journals.aps.org/prb/abstract/10.1103/PhysRevB.103.045141
>> >
>> > Yes, generally, one should also redo the vc-relax calculations using
>> > updated U and V values using DFT+U+V. But if, for example, one wants
>> > to work with the fixed geometry (e.g. the experimental one), then
>> > obviously there is no need to do the vc-relax calculations.
>> >
>> > Greetings,
>> > Iurii
>> >
>> > ----------------------------------------------------------
>> > Dr. Iurii TIMROV
>> > Tenure-track scientist
>> > Laboratory for Materials Simulations (LMS)
>> > Paul Scherrer Institut (PSI)
>> > CH-5232 Villigen, Switzerland
>> > +41 56 310 62 14
>> > https://www.psi.ch/en/lms/people/iurii-timrov
>> > ________________________________
>> > From: users
>> > <users-bounces at lists.quantum-espresso.org<mailto:
>> users-bounces at lists.quantum-espresso.org>> on behalf of ROBERT MIKHAIL
>> GUZMAN ARELLANO via users
>> > <users at lists.quantum-espresso.org<mailto:
>> users at lists.quantum-espresso.org>>
>> > Sent: Thursday, September 26, 2024 17:34
>> > To:
>> > users at lists.quantum-espresso.org<mailto:
>> users at lists.quantum-espresso.org>
>> > <users at lists.quantum-espresso.org<mailto:
>> users at lists.quantum-espresso.org>>
>> > Subject: [QE-users] It is neccesary to make a vc-relax in each DFT
>> > U+V calculation?
>> >
>> > Dear members,
>> >
>> > I am starting to work in DFT U+V making calculations with pw.x and
>> > hp.x of Quantum Espresso package. So my question is:
>> >
>> > In order to calculate the U and V values with hp.x. What is the path
>> > to follow?
>> >
>> > At his time. I am doing these steps.
>> >
>> > 0. Calibrate pseudo potentials, k-points, and frequency of waves and
>> density.
>> >
>> > 1. Calculate the crystalline structure using vc-relax.
>> >
>> > 2. Make a scf calculation using the best atomic positions and unit
>> > cell parameters obtained in vc-relax calculation. In this
>> > calculation, I put a small value of U and V between orbitals. (1.d-3
>> > eV)
>> >
>> > 3 run hp.x in order to calculate better values of U and V.
>> >
>> > 4 extract the U and V values calculated by hp.x, and put these in a
>> > new scf calculation and run the last.
>> >
>> > 5 repeat the 3 step and after the 4 step until the U and V values
>> > between 2 different calculations look equal or with small difference
>> > (0.01eV).
>> >
>> > My Question is: is it necessary to make a vc-relax between the 3 and
>> > 4 steps? I looked at some examples which do that in order to
>> > calculate U value,but do not do the same when calculating V
>> > (interaction between different orbitals).
>> >
>> > During this month I have been working with atoms whose valence
>> > orbitals are S and P, and I understand that for these orbitals, not
>> > being very localized like the D orbitals, it is necessary to work
>> > with U and V, where V responds to the coulomb interaction between
>> > orbitals of neighboring atoms.
>> >
>> > Thank's for your attention.
>> >
>> > Best regards.
>>
>>
>>
>> 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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>> 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
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>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>> users mailing list users at lists.quantum-espresso.org
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>>
> _______________________________________________
> 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 at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
>
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