[QE-users] General questions on pw.x's SCF output using pw2casino flag
Wai-Ga Ho
wdh17 at my.fsu.edu
Tue Mar 12 16:22:51 CET 2019
Dear Paolo and Katharina,
Thank you for the equations/insight! All my questions are answered now haha. It's just one thing teaching understanding the theory and problem-solving approach, and another thing to make this connection to the program outputs so that you can use your results meaningfully and confidently.
Anyways, this helped shed a lot of light on what the physical meaning behind each energy contribution is, and helped me understand some other things as well.
I thank you all for your time ❤ (:
David, FSU Physics Dept and NHMFL
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Today's Topics:
1. Re: users Digest, Vol 140, Issue 8
(Mw. Dr. K. Doblhoff-Dier (k.doblhoff-dier))
2. Re: General questions on pw.x's SCF output using pw2casino
flag (Paolo Giannozzi)
3. Re: turbo_lanczos error (Michal Krompiec)
4. Re: turbo_lanczos error (Paolo Giannozzi)
5. extracting wavefunctions (Wenfei Li)
6. Re: extracting wavefunctions (dv009200 at fh-muenster.de)
----------------------------------------------------------------------
Message: 1
Date: Fri, 8 Mar 2019 12:53:47 +0100 (CET)
From: "Mw. Dr. K. Doblhoff-Dier (k.doblhoff-dier)"
<k.doblhoff-dier at umail.leidenuniv.nl>
To: users at lists.quantum-espresso.org
Subject: Re: [QE-users] users Digest, Vol 140, Issue 8
Message-ID:
<876992562.3222.1552046027671.JavaMail.open-xchange at webmail.leidenuniv.nl>
Content-Type: text/plain; charset="utf-8"
Dear Wai-Ga David Ho,
Without having looked into the code, from what I recall:
ad 1 and 2: I would be careful in calling the explicitly treated electrons
"valence states", but yes, the energies should refer to the energies resulting
from the explicitly treated electrons and the pseudo-cores in your system.
ad 3.: Modern pseudo-potentials are non-local in nature. In a single determinant
picture, this means that a different potentials applies for electrons having
different l,m-quantum numbers (semi-local form) or different n-l-m orbitals
(separable or fully non-local form). Usually, part of the potential, containing
the long range part, (or the total potential of one of the channels) is defined
as "local" and applies to all l,m-quantum numbers/orbitals. A "correction" is
then still needed for the other channels, this is the "non-local" part of the
interaction energy. There are lots of good introductions around, but for a quick
view of the equations, you could, for example, have a look at the PhD thesis of
Peter David Haynes: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.tcm.phy.cam.ac.uk_-7Epdh1001_thesis_node19.html&d=DwICAg&c=MNHwOqQ8N1u91SoMLfIblwuGXKgp50OPUXjl8uRAbak&r=B7toNJkJN9wC1at1deS0cQ&m=9LMiMknXz94xEFb5pHEGi2iJ61xoiCrrYme9su-wI8g&s=HNV3k-I6Pa5ny4w_20X3QCyQdrGetmFi2YuQbFC2_uk&e=
<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.tcm.phy.cam.ac.uk_-7Epdh1001_thesis_node19.html&d=DwICAg&c=MNHwOqQ8N1u91SoMLfIblwuGXKgp50OPUXjl8uRAbak&r=B7toNJkJN9wC1at1deS0cQ&m=9LMiMknXz94xEFb5pHEGi2iJ61xoiCrrYme9su-wI8g&s=HNV3k-I6Pa5ny4w_20X3QCyQdrGetmFi2YuQbFC2_uk&e=> (see eqns. 3.75 an
3.76).
Hope that helps,
Best regards,
Katharina Doblhoff-Dier, Leiden University
> Hello QE community,
>
>
> Some time ago, I was attempting to use the -pw2casino flag to deconstruct the
> total energy in terms of its physical contributions, such as its kinetic
> energy term, etc (see
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_users-40lists.quantum-2Despresso.org_msg35391.html&d=DwICAg&c=MNHwOqQ8N1u91SoMLfIblwuGXKgp50OPUXjl8uRAbak&r=B7toNJkJN9wC1at1deS0cQ&m=9LMiMknXz94xEFb5pHEGi2iJ61xoiCrrYme9su-wI8g&s=QV3AZdZBhvYaUF3GuNPUTFtwRq_Xx6XOn5YiF5YRysA&e=
> for my previous post).
>
>
> I've succeeded when using ultrasoft pseudopotentials, but I now have some
> further questions related to the output from the -pw2casino SCF option. I
> attempted to find some answers online, but was unable to find documentation or
> forum discussions, and I was also unable to figure out what was being
> implemented in the pw2casino.f90 and pw2casino_write.f90 codes I found on
> github...
>
>
> Anyways, my questions mainly have to deal with the physical interpretations of
> the deconstructed energy values.
>
>
> When using the pw2casino flag, the contributions given to us are:
>
> - Kinetic energy
> - Local energy
> - Non-Local energy
> - Ewald energy
> - xc contribution
> - hartree energy
>
>
> Now from my understanding of KS density functional theory, the total energy is
> comprised of the following:
>
> -Kinetic energy (itinerancy of electrons in their KS orbitals)
>
> -Hartree energy (the classical Coulomb interaction between electrons)
>
> -Ewald energy (the classical Coulomb interaction between nuclei)
>
> -External energy (the classical Coulomb interaction between the electron
> density and the nuclei)
>
> -XC energy (everything else i.e. exchange, correlation, and a bit of kinetic
> energy error from taking the KS ansatz)
>
>
> Furthermore, from a DFT approach that uses PAW pseudopotentials, I know that
> we have to map between all-electron and pseudo expectation values, so that we
> make a distinction between pseudoenergies and the more physical all-electron
> energies (see here for more information
> https://urldefense.proofpoint.com/v2/url?u=https-3A__journals.aps.org_prb_abstract_10.1103_PhysRevB.50.17953&d=DwICAg&c=MNHwOqQ8N1u91SoMLfIblwuGXKgp50OPUXjl8uRAbak&r=B7toNJkJN9wC1at1deS0cQ&m=9LMiMknXz94xEFb5pHEGi2iJ61xoiCrrYme9su-wI8g&s=3rU3gEl3kkbph3H2fWafxdAkpYqMuD4l2SNGQ4ilG78&e=). Now the PAW
> formalisms and approach are generalizable to other pseudopotential methods, so
> I assume that we deal with the same kind of all-electron vs pseudo distinction
> when using ultrasoft pseudopotentials.
>
>
>
> Now that I've laid out the basic prerequisite knowledge I currently have, my
> questions about the pw2casino energy deconstruction are as follows:
>
> 1) The output of the total energy is understood to be the pseudoenergy (i.e.
> the energy of the system in the pseudospace of ultrasoft potentials where the
> hard nuclear potentials are being weakened by the core electrons). Am I
> correct in assuming the deconstructed contributions are pseudoenergies well?
> Because they sum up to the total pseudoenergy that is output.
> 2) As a continuation off of 1), does this mean that the Kinetic Energy
> produced using the pw2casino flag only sums over the valence states (since our
> core electrons are approximately frozen out in this pseudopotential approach)?
> 3) What are the physical meanings behind the "Local energy" and "Non-local
> energy" values that are being output by pw2casino? If we compare my list of
> contributions to the list produced by pw2casino, it seems as if these two
> energy contributions are connected to the External energy i.e. the energy
> between electron and nuclei. If this is correct, and in light of our
> pseudopotential approach, does this mean that the "Local energy" corresponds
> to that of the core electrons while the "Non-local" energy are for the valence
> electrons?
> 4) Question 3) was asked assuming that the output from pw2casino for the
> kinetic, ewald, XC, and hartree contributions are in line with my
> understanding of the energy contributions. Am I missing anything in this
> respect, or do they all match up?
>
> If anyone can answer any of my questions or offer any further insight into the
> physical meaning behind these energy values or how they are calculated, it
> would be very much appreciated.
>
> And if this is helpful for anyone, I am using PWSCF v.5.0.2 and the following
> pseudopotentials for MgO:
> - Mg.pbe-spnl-rrkjus_psl.1.0.0.UPF
> - O.pbe-nl-rrkjus_psl.1.0.0.UPF
>
> Thank you,
> Wai-Ga David Ho, Dept of Physics at Florida State University and NHMFL
>
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Message: 2
Date: Fri, 8 Mar 2019 13:13:46 +0100
From: Paolo Giannozzi <p.giannozzi at gmail.com>
To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] General questions on pw.x's SCF output using
pw2casino flag
Message-ID:
<CAPMgbCuMDJ7haXG=7t6X6c0fbTXjch7=zARyiqKeORXYBBVj7g at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
On Thu, Mar 7, 2019 at 5:18 PM Wai-Ga Ho <wdh17 at my.fsu.edu> wrote:
- Kinetic energy
>
\sum_k \sum_v <\psi_{k,v}|\hbar^2\nabla^2/2m|\psi_{k,v}>
(v runs over valence bands only)
- Local energy
>
>
\int V_{loc}(r)\rho(r) dr
(V_loc(r)=local pseudopotential, \rho = valence charge)
- Non-Local energy
>
>
\sum_k \sum_v <\psi_{k,v}|V_{NL}|\psi_{k,v}>
(V_{NL} = nonlocal pseudopotential)
The sum of these three terms should correspond to the "one-electron
contribution" reprinted on output by PWscf
- Ewald energy
> - xc contribution
> - hartree energy
>
>
These three should be the same as in PWscf
Paolo
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Message: 3
Date: Fri, 8 Mar 2019 14:48:59 +0000
From: Michal Krompiec <michal.krompiec at gmail.com>
To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] turbo_lanczos error
Message-ID:
<CAOWoSSOUh2BaAOX7fgW0fZbbBKSoPAEYznXLFBFkVALjrM4kWA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Thanks Pietro,
Indeed adding -i8 to FF_FLAGS and FOX_FLAGS in make.inc helped, but I had
to comment line 352 in qmmm.f90 which was causing ifort to complain (I
don't plan to use qmmm anyway):
qmmm.f90(352): warning #6075: The data type of the actual argument does not
match the definition. [NAT_MM]
CALL ec_fill_radii( aradii, nat_mm, mass, types, ntypes, 1 )
------------------------------------^
qmmm.f90(352): error #6633: The type of the actual argument differs from
the type of the dummy argument. [TYPES]
CALL ec_fill_radii( aradii, nat_mm, mass, types, ntypes, 1 )
--------------------------------------------------^
qmmm.f90(352): warning #6075: The data type of the actual argument does not
match the definition. [NTYPES]
CALL ec_fill_radii( aradii, nat_mm, mass, types, ntypes, 1 )
---------------------------------------------------------^
compilation aborted for qmmm.f90 (code 1)
However, subsequent run of the test suite failed, I get the following error
for each test run:
Attempting to use an MPI routine before initializing MPI
*** error in Message Passing (mp) module ***
*** error code: 8000
What could be the cause? Just to double-check, I re-built from the same
source (QE 6.4) without -i8 and the tests went OK.
Thanks,
Michal
On Fri, 8 Mar 2019 at 10:14, Pietro Davide Delugas <pdelugas at sissa.it>
wrote:
> hello Michal
>
> in the make.inc you should add the -i8 flag also to FOX_FLAGS in order
> that routines in FoX library are also compiled using long integers
>
> after editing the make.inc file do a make clean before compiling.
> Pietro
>
> On 03/08/2019 10:55 AM, Michal Krompiec wrote:
>
> Hello,
> I'm trying to run a TDDpFT calculation on a large system, using HSE06
> functional. Turbo_lanczos crashes with the following message:
> Error in routine diropn (3):
> wrong record length
>
> I found a similar (?) problem discussed previously (
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pw-2Dforum.pwscf.narkive.com_6QjNE4Dw_wrong-2Drecord-2Dlength&d=DwICAg&c=MNHwOqQ8N1u91SoMLfIblwuGXKgp50OPUXjl8uRAbak&r=B7toNJkJN9wC1at1deS0cQ&m=9LMiMknXz94xEFb5pHEGi2iJ61xoiCrrYme9su-wI8g&s=q_zBn0BVaKgSSblAm-SUje8kTIlEBTlh2hztzEkGX6o&e= ) but the
> solution posted there (compilation with the -i8 flag to prevent integer
> overflow) doesn't work for me - build fails with the following error:
> fox_init_module.f90(22): error #6285: There is no matching specific
> subroutine for this generic subroutine call. [SETUP_IO]
> CALL setup_io(ERR_CODE = errcodes(1), EOR_CODE = errcodes(2),
> EOF_CODE = errcodes(3))
> -----------^
> compilation aborted for fox_init_module.f90 (code 1)
>
> I would be very grateful for any advice.
> Thanks,
> Michal Krompiec
>
>
> Adjunct Professor
>
> School of Chemistry, University of Southampton
>
> Highfield, Southampton SO17 1BJ, UK
>
> and
>
> Head of Computational Modelling | Performance Materials | Early Research
> and Business Development
>
> Merck
>
>
>
> _______________________________________________
> users mailing listusers at lists.quantum-espresso.orghttps://lists.quantum-espresso.org/mailman/listinfo/users
>
>
> _______________________________________________
> users mailing list
> users at lists.quantum-espresso.org
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.quantum-2Despresso.org_mailman_listinfo_users&d=DwICAg&c=MNHwOqQ8N1u91SoMLfIblwuGXKgp50OPUXjl8uRAbak&r=B7toNJkJN9wC1at1deS0cQ&m=9LMiMknXz94xEFb5pHEGi2iJ61xoiCrrYme9su-wI8g&s=2t2_6sryg7DJpR5der4G5R29jQd4YSUr1jd5MgNZ3u4&e=
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------------------------------
Message: 4
Date: Fri, 8 Mar 2019 17:46:49 +0100
From: Paolo Giannozzi <p.giannozzi at gmail.com>
To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] turbo_lanczos error
Message-ID:
<CAPMgbCtoJ-pJpPruTY+7QWuQF1bZTHzXugs2zBar7Y8CaQksYQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
On Fri, Mar 8, 2019 at 3:49 PM Michal Krompiec <michal.krompiec at gmail.com>
wrote:
Attempting to use an MPI routine before initializing MPI
> *** error in Message Passing (mp) module ***
> *** error code: 8000
>
> What could be the cause?
>
hard to say. May I suggest that you promote to double precision only a few
relevant variables instead of all integer variables? these are: unf_recl,
recl in Modules/io_files,f90, subroutine diropn; and the various "nword*"
variables. First of all, print unf_recl and recl in diropn just before the
error message, in order to locate exactly where the problem arises
Paolo
> Thanks,
> Michal
>
> On Fri, 8 Mar 2019 at 10:14, Pietro Davide Delugas <pdelugas at sissa.it>
> wrote:
>
>> hello Michal
>>
>> in the make.inc you should add the -i8 flag also to FOX_FLAGS in order
>> that routines in FoX library are also compiled using long integers
>>
>> after editing the make.inc file do a make clean before compiling.
>> Pietro
>>
>> On 03/08/2019 10:55 AM, Michal Krompiec wrote:
>>
>> Hello,
>> I'm trying to run a TDDpFT calculation on a large system, using HSE06
>> functional. Turbo_lanczos crashes with the following message:
>> Error in routine diropn (3):
>> wrong record length
>>
>> I found a similar (?) problem discussed previously (
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__pw-2Dforum.pwscf.narkive.com_6QjNE4Dw_wrong-2Drecord-2Dlength&d=DwICAg&c=MNHwOqQ8N1u91SoMLfIblwuGXKgp50OPUXjl8uRAbak&r=B7toNJkJN9wC1at1deS0cQ&m=9LMiMknXz94xEFb5pHEGi2iJ61xoiCrrYme9su-wI8g&s=q_zBn0BVaKgSSblAm-SUje8kTIlEBTlh2hztzEkGX6o&e= ) but
>> the solution posted there (compilation with the -i8 flag to prevent integer
>> overflow) doesn't work for me - build fails with the following error:
>> fox_init_module.f90(22): error #6285: There is no matching specific
>> subroutine for this generic subroutine call. [SETUP_IO]
>> CALL setup_io(ERR_CODE = errcodes(1), EOR_CODE = errcodes(2),
>> EOF_CODE = errcodes(3))
>> -----------^
>> compilation aborted for fox_init_module.f90 (code 1)
>>
>> I would be very grateful for any advice.
>> Thanks,
>> Michal Krompiec
>>
>>
>> Adjunct Professor
>>
>> School of Chemistry, University of Southampton
>>
>> Highfield, Southampton SO17 1BJ, UK
>>
>> and
>>
>> Head of Computational Modelling | Performance Materials | Early Research
>> and Business Development
>>
>> Merck
>>
>>
>>
>> _______________________________________________
>> users mailing listusers at lists.quantum-espresso.orghttps://lists.quantum-espresso.org/mailman/listinfo/users
>>
>>
>> _______________________________________________
>> users mailing list
>> users at lists.quantum-espresso.org
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.quantum-2Despresso.org_mailman_listinfo_users&d=DwICAg&c=MNHwOqQ8N1u91SoMLfIblwuGXKgp50OPUXjl8uRAbak&r=B7toNJkJN9wC1at1deS0cQ&m=9LMiMknXz94xEFb5pHEGi2iJ61xoiCrrYme9su-wI8g&s=2t2_6sryg7DJpR5der4G5R29jQd4YSUr1jd5MgNZ3u4&e=
>
> _______________________________________________
> users mailing list
> users at lists.quantum-espresso.org
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.quantum-2Despresso.org_mailman_listinfo_users&d=DwICAg&c=MNHwOqQ8N1u91SoMLfIblwuGXKgp50OPUXjl8uRAbak&r=B7toNJkJN9wC1at1deS0cQ&m=9LMiMknXz94xEFb5pHEGi2iJ61xoiCrrYme9su-wI8g&s=2t2_6sryg7DJpR5der4G5R29jQd4YSUr1jd5MgNZ3u4&e=
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Message: 5
Date: Fri, 8 Mar 2019 16:52:24 -0800
From: Wenfei Li <liwenfei94 at gmail.com>
To: users at lists.quantum-espresso.org
Subject: [QE-users] extracting wavefunctions
Message-ID:
<CA+EXCtv_PGVRZLZLntZyJwCNP_GyZdWpBLr02bbUe9q5JuSF9A at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi,
I'm wondering if there's a way to extract all the orbital wavefunctions at
once? I've been using pp.x to extract them one by one, but it takes a very
long time for large systems.
Is there any other applications that can be used to extract orbitals?
Thanks for your time!
Best,
Wenfei
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Message: 6
Date: Sat, 9 Mar 2019 09:45:46 +0100
From: dv009200 at fh-muenster.de
To: "Quantum Espresso users Forum" <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] extracting wavefunctions
Message-ID:
<d773fb86833534e164a3881bf67f54a9.squirrel at webmail.fh-muenster.de>
Content-Type: text/plain;charset=iso-8859-1
pp.x has the option to plot a range of wavefunctions you just have to
specify kband(1)=min and kband(2)=max.
Have a look at the pp.x input description:
"kband(i), i=1,2
Band(s) to be plotted. To plot a single band ibnd, specify kband=ibnd or
kband(1)=ibnd To plot a range of bands [imin, imax], specify kband(1)=imin
and kband(2)=imax"
Regards
Dominik
M.Sc. Dominik Voigt PhD Student
M?nster University of Applied Sciences
Email: dv009200 at fh-muenster.de
> Hi,
>
> I'm wondering if there's a way to extract all the orbital wavefunctions at
> once? I've been using pp.x to extract them one by one, but it takes a very
> long time for large systems.
> Is there any other applications that can be used to extract orbitals?
> Thanks for your time!
>
> Best,
> Wenfei
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