[QE-users] cDFT with PAW
Małgorzata Wawrzyniak-Adamczewska
mwaw at amu.edu.pl
Wed Feb 27 13:16:13 CET 2019
Dear Quantum Espresso Users and Developers,
I have a question regarding a constrained DFT with the PAW/US-PAW. Is it
possible to perform calculations in the constrained scheme with QE
package. I would like to calculate possible charge transfer in a
system.
Regards,
Malgorzata Wawrzyniak
W dniu 2019-02-26 12:00, users-request at lists.quantum-espresso.org
napisał(a):
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> Today's Topics:
>
> 1. Phonons with images (Malte Sachs)
> 2. Re: The virtual.x problems (Pietro Delugas)
> 3. Re: Phonons with images (Paolo Giannozzi)
> 4. Re: The virtual.x problems (Fabio Costa)
> 5. Re: The virtual.x problems (Pietro Delugas)
> 6. Phonon Calculation erroneous (Offermans Willem)
> 7. Re: Phonon Calculation erroneous (Lorenzo Paulatto)
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 25 Feb 2019 13:53:06 +0100
> From: Malte Sachs <malte.sachs at chemie.uni-marburg.de>
> To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
> Subject: [QE-users] Phonons with images
> Message-ID:
> <4383cd38-085c-8751-b0af-3df917f6ae96 at chemie.uni-marburg.de>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Dear all,
>
> I have tested the image-example for phonon calculations using
> QuantumEspresso 6.3. In the case I am using these commands:
>
> mpirun -np 4 pw.x < ...
>
> mpirun -np 4 ph.x -ni 2 < ...
>
> mpirun -np 4 ph.x < ....
>
> everything works fine. However, using this:
>
> mpirun -np 2 pw.x < ...
>
> mpirun -np 4 ph.x -ni 2 < ...
>
> mpirun -np 2 ph.x < ....
>
> yields an error in the last step: "pw.x run with a different number of
> processors. Use wf_collect=.true."? However, I have the same number of
> processors in pw.x and ph.x and the wf_collect option is activated by
> default. So I don't know what is going on.
>
> Best regards,
> Malte Sachs
>
> --
> Malte Sachs
> Anorganische Chemie, Fluorchemie
> Philipps-Universit?t Marburg
> Hans-Meerwein-Stra?e 4
> 35032 Marburg (Paketpost: 35043 Marburg)
> Tel.: +49 (0)6421 28 - 25 68 0
> http://www.uni-marburg.de/fb15/ag-kraus/
>
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> ------------------------------
>
> Message: 2
> Date: Mon, 25 Feb 2019 15:46:17 +0100
> From: Pietro Delugas <pdelugas at sissa.it>
> To: users at lists.quantum-espresso.org
> Subject: Re: [QE-users] The virtual.x problems
> Message-ID: <16cd1aa5-a416-4e6f-c85c-a2936505bce1 at sissa.it>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> Hi Fabio
>
> Pseudos from pseudo-dojo are perfect, they are norm-conserving and they
> are in upf format.
>
> ?You have to keep in mind that VCA has sense? for isovalent atoms e. g
> C? with Si. Ga.? and In.
>
> Also pseudos would better? be built with the same number of projectors.
>
> Mixing pseudos with a different number of valence electrons like B and
> Si is most likely not going to work.
>
> I checked B with Si though,? and disappointingly the program produces an
> upf file.? I think that it would be useful at least to print out a very
> evident? warning about the usability of such? file.
>
> Pietro
>
> The problem is the
>
> On 25/02/19 11:58, Fabio Costa wrote: Thanks for the quick reply
>
> To perform this task, I downloaded the full table of PP?from pseudo
> dojo, with the following settings:
>
> Type:NC SR (ONCVPSP v0.4)
> XC: PBE
> Accuracy: standard
> Format: upf
>
> My attempts so far were to mix B-C and Si-Al, both unsuccessful. Maybe
> my mistake is in the choice of these PP files, and if so, where can I
> get the adequate ones to work with the virtual.x?
>
> Thank you all for the assistance
> F?bio Costa
> ------------------------------------------------------------------------
> *De:* users <users-bounces at lists.quantum-espresso.org> em nome de
> Pietro Delugas <pdelugas at sissa.it>
> *Enviado:* segunda-feira, 25 de fevereiro de 2019 09:05
> *Para:* users at lists.quantum-espresso.org
> *Assunto:* Re: [QE-users] The virtual.x problems
>
> Hi Fabio
>
> I just tried current version with Al-Ga Ga-In Al-In C-Si Si-Ge P-As,
> which are more or less all of pairs which come to my mind where
> virtual can be used, and apart from Al-Ga where it doesn't work
> because Ga pseudo has usually d semicores every seems to work fine.
>
> Please le me have the 2 pseudos you are trying to mix.
>
> Pietro
>
> On 24/02/19 23:41, Fabio Costa wrote:
> Hello everybody
>
> Sorry for reopening this post, but Im currently struggling to work
> with this virtual.x tool.
>
> I?m working with QE v.6.3, and tried to do the task with both the
> updated and original version of virtual.x. After inputting the PP to
> mix together, the program generates the output file, but ends with
> the message:
>
> At line 215 of file write_upf_v2.f90
>
> Fortran runtime error: End of file
>
> Also, when I open the output PP, NewPseudo.UPF, it contains the
> following text:
>
> <?xml version ?1.0? encoding=?UTF-8??>
>
> <UPF version=?2.0.1?>
>
> Thank you all for any assistance
>
> Cheers
>
> F?bio Costa
>
> _______________________________________________
> users mailing list
> users at lists.quantum-espresso.org <mailto:users at lists.quantum-espresso.org>
> https://lists.quantum-espresso.org/mailman/listinfo/users
> _______________________________________________
> users mailing list
> users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
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Message: 3
Date: Mon, 25 Feb 2019 15:59:50 +0100
From: Paolo Giannozzi <p.giannozzi at gmail.com>
To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] Phonons with images
Message-ID:
<CAPMgbCvp3+-7J6HAeD9HxQ83otkHzOLJ8Gs+-17+8wo5TWUMXw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
I recently removed many such checks that had become obsolete. Try
commenting out the check.
Paolo
On Mon, Feb 25, 2019 at 1:53 PM Malte Sachs <
malte.sachs at chemie.uni-marburg.de> wrote:
> Dear all,
>
> I have tested the image-example for phonon calculations using
> QuantumEspresso 6.3. In the case I am using these commands:
>
> mpirun -np 4 pw.x < ...
>
> mpirun -np 4 ph.x -ni 2 < ...
>
> mpirun -np 4 ph.x < ....
>
> everything works fine. However, using this:
>
> mpirun -np 2 pw.x < ...
>
> mpirun -np 4 ph.x -ni 2 < ...
>
> mpirun -np 2 ph.x < ....
>
> yields an error in the last step: "pw.x run with a different number of
> processors. Use wf_collect=.true." However, I have the same number of
> processors in pw.x and ph.x and the wf_collect option is activated by
> default. So I don't know what is going on.
>
> Best regards,
> Malte Sachs
>
> --
> Malte Sachs
> Anorganische Chemie, Fluorchemie
> Philipps-Universit?t Marburg
> Hans-Meerwein-Stra?e 4
> 35032 Marburg (Paketpost: 35043 Marburg)
> Tel.: +49 (0)6421 28 - 25 68 0
> http://www.uni-marburg.de/fb15/ag-kraus/
>
> _______________________________________________
> users mailing list
> users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
--
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: 4
Date: Mon, 25 Feb 2019 19:14:42 +0000
From: Fabio Costa <fabiocosta4 at hotmail.com>
To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] The virtual.x problems
Message-ID:
<RO1PR80MB3660456258DA73D35F7A73BFF27A0 at RO1PR80MB3660.lamprd80.prod.outlook.com>
Content-Type: text/plain; charset="windows-1252"
Thanks for the assistance Pietro
I understood the point of mixing elements with different valence
electrons. But even when I try to mix together isoelectronic species
(such as Si and C), the generated output file NewPseudo.UPF has no
information.
At first I tried to use the virtual.x that comes within QE 6.3, and also
tried with this updated version , after making a new virtual.x, based on
these instructions:
https://www.mail-archive.com/users@lists.quantum-espresso.org/msg33969.html
The outcome is always the same: the program ends with this fortran
runtime error, and the output file comes with two lines of text:
<?xml version="1.0" encoding="UTF-8"?>
<UPF version="2.0.1">
I already tried to reinstall the whole QE, but nothing has changed.
F?bio Costa
________________________________
De: users <users-bounces at lists.quantum-espresso.org> em nome de Pietro
Delugas <pdelugas at sissa.it>
Enviado: segunda-feira, 25 de fevereiro de 2019 14:46
Para: users at lists.quantum-espresso.org
Assunto: Re: [QE-users] The virtual.x problems
Hi Fabio
Pseudos from pseudo-dojo are perfect, they are norm-conserving and they
are in upf format.
You have to keep in mind that VCA has sense for isovalent atoms e. g C
with Si. Ga. and In.
Also pseudos would better be built with the same number of projectors.
Mixing pseudos with a different number of valence electrons like B and
Si is most likely not going to work.
I checked B with Si though, and disappointingly the program produces an
upf file. I think that it would be useful at least to print out a very
evident warning about the usability of such file.
Pietro
The problem is the
On 25/02/19 11:58, Fabio Costa wrote:
Thanks for the quick reply
To perform this task, I downloaded the full table of PP from pseudo
dojo, with the following settings:
Type:NC SR (ONCVPSP v0.4)
XC: PBE
Accuracy: standard
Format: upf
My attempts so far were to mix B-C and Si-Al, both unsuccessful. Maybe
my mistake is in the choice of these PP files, and if so, where can I
get the adequate ones to work with the virtual.x?
Thank you all for the assistance
F?bio Costa
________________________________
De: users
<users-bounces at lists.quantum-espresso.org><mailto:users-bounces at lists.quantum-espresso.org>
em nome de Pietro Delugas <pdelugas at sissa.it><mailto:pdelugas at sissa.it>
Enviado: segunda-feira, 25 de fevereiro de 2019 09:05
Para:
users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
Assunto: Re: [QE-users] The virtual.x problems
Hi Fabio
I just tried current version with Al-Ga Ga-In Al-In C-Si Si-Ge P-As,
which are more or less all of pairs which come to my mind where virtual
can be used, and apart from Al-Ga where it doesn't work because Ga
pseudo has usually d semicores every seems to work fine.
Please le me have the 2 pseudos you are trying to mix.
Pietro
On 24/02/19 23:41, Fabio Costa wrote:
Hello everybody
Sorry for reopening this post, but Im currently struggling to work with
this virtual.x tool.
I?m working with QE v.6.3, and tried to do the task with both the
updated and original version of virtual.x. After inputting the PP to mix
together, the program generates the output file, but ends with the
message:
At line 215 of file write_upf_v2.f90
Fortran runtime error: End of file
Also, when I open the output PP, NewPseudo.UPF, it contains the
following text:
<?xml version ?1.0? encoding=?UTF-8??>
<UPF version=?2.0.1?>
Thank you all for any assistance
Cheers
F?bio Costa
_______________________________________________
users mailing list
users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
https://lists.quantum-espresso.org/mailman/listinfo/users
_______________________________________________
users mailing list
users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
https://lists.quantum-espresso.org/mailman/listinfo/users
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Message: 5
Date: Tue, 26 Feb 2019 08:43:14 +0100
From: Pietro Delugas <pdelugas at sissa.it>
To: users at lists.quantum-espresso.org
Subject: Re: [QE-users] The virtual.x problems
Message-ID: <271ec9f3-93b3-3cc4-83b2-bf4e6d0f3686 at sissa.it>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"
Hi Fabio
can you try to download the 6.3-backports version from here
https://gitlab.com/QEF/q-e/tree/qe-6.3-backports ?
or better? you can download directly the? development version from
gitlab or github.
Pietro
On 25/02/19 20:14, Fabio Costa wrote:
> Thanks for the assistance Pietro
>
> I understood the point of mixing elements with different valence
> electrons. But even when I try to mix together isoelectronic species
> (such as Si and C), the generated output file NewPseudo.UPF has no
> information.
>
> At first I tried to use the virtual.x that comes within QE 6.3, and
> also tried with this updated version , after making a new virtual.x,
> based on these instructions:
> https://www.mail-archive.com/users@lists.quantum-espresso.org/msg33969.html
>
> The outcome is always the same: the program ends with this fortran
> runtime error, and the output file comes with two lines of text:
> <?xml version="1.0" encoding="UTF-8"?>
> <UPF version="2.0.1">
>
> I already tried to reinstall the whole QE, but nothing has changed.
>
> F?bio Costa
> ------------------------------------------------------------------------
> *De:* users <users-bounces at lists.quantum-espresso.org> em nome de
> Pietro Delugas <pdelugas at sissa.it>
> *Enviado:* segunda-feira, 25 de fevereiro de 2019 14:46
> *Para:* users at lists.quantum-espresso.org
> *Assunto:* Re: [QE-users] The virtual.x problems
>
> Hi Fabio
>
> Pseudos from pseudo-dojo are perfect, they are norm-conserving and
> they are in upf format.
>
> ?You have to keep in mind that VCA has sense for isovalent atoms e. g
> C? with Si. Ga.? and In.
>
> Also pseudos would better? be built with the same number of projectors.
>
> Mixing pseudos with a different number of valence electrons like B and
> Si is most likely not going to work.
>
> I checked B with Si though,? and disappointingly the program produces
> an upf file.? I think that it would be? useful at least to print out a
> very evident? warning about the usability of such? file.
>
> Pietro
>
> The problem is the
>
> On 25/02/19 11:58, Fabio Costa wrote: Thanks for the quick reply
>
> To perform this task, I downloaded the full table of PP?from pseudo
> dojo, with the following settings:
>
> Type:NC SR (ONCVPSP v0.4)
> XC: PBE
> Accuracy: standard
> Format: upf
>
> My attempts so far were to mix B-C and Si-Al, both unsuccessful.
> Maybe my mistake is in the choice of these PP files, and if so, where
> can I get the adequate ones to work with the virtual.x?
>
> Thank you all for the assistance
> F?bio Costa
> ------------------------------------------------------------------------
> *De:* users <users-bounces at lists.quantum-espresso.org>
> <mailto:users-bounces at lists.quantum-espresso.org> em nome de Pietro
> Delugas <pdelugas at sissa.it> <mailto:pdelugas at sissa.it>
> *Enviado:* segunda-feira, 25 de fevereiro de 2019 09:05
> *Para:* users at lists.quantum-espresso.org
> <mailto:users at lists.quantum-espresso.org>
> *Assunto:* Re: [QE-users] The virtual.x problems
>
> Hi Fabio
>
> I just tried current version with Al-Ga Ga-In Al-In C-Si Si-Ge P-As,
> which are more or less all of pairs which come to my mind where
> virtual can be used, and apart from Al-Ga where it doesn't work
> because Ga pseudo has usually d semicores every seems to work fine.
>
> Please le me have the 2 pseudos you are trying to mix.
>
> Pietro
>
> On 24/02/19 23:41, Fabio Costa wrote:
> Hello everybody
>
> Sorry for reopening this post, but Im currently struggling to work
> with this virtual.x tool.
>
> I?m working with QE v.6.3, and tried to do the task with both the
> updated and original version of virtual.x. After inputting the PP to
> mix together, the program generates the output file, but ends with
> the message:
>
> At line 215 of file write_upf_v2.f90
>
> Fortran runtime error: End of file
>
> Also, when I open the output PP, NewPseudo.UPF, it contains the
> following text:
>
> <?xml version ?1.0? encoding=?UTF-8??>
>
> <UPF version=?2.0.1?>
>
> Thank you all for any assistance
>
> Cheers
>
> F?bio Costa
>
> _______________________________________________
> users mailing list
> users at lists.quantum-espresso.org <mailto:users at lists.quantum-espresso.org>
> https://lists.quantum-espresso.org/mailman/listinfo/users
> _______________________________________________
> users mailing list
> users at lists.quantum-espresso.org <mailto:users at lists.quantum-espresso.org>
> https://lists.quantum-espresso.org/mailman/listinfo/users
_______________________________________________
users mailing list
users at lists.quantum-espresso.org
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Message: 6
Date: Tue, 26 Feb 2019 08:05:32 +0000
From: Offermans Willem <willem.offermans at vito.be>
To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
Subject: [QE-users] Phonon Calculation erroneous
Message-ID: <D0B1C418-BC0D-4D0C-AABB-C8C14F69D686 at Vito.be>
Content-Type: text/plain; charset="utf-8"
Dear Quantum Espresso friends,
I?m running a phonon calculation and all seems to run well.
But mode 5 cannot converge:
<snip>
...
Pert. # 1: Fermi energy shift (Ry) = -2.5081E-03 1.6156E-27
iter # 63 total cpu time : 26867.7 secs av.it.: 23.9
thresh= 1.297E-06 alpha_mix = 0.100 |ddv_scf|^2 = 6.099E-11
End of self-consistent calculation
Convergence has been achieved
Representation # 5 mode # 5
Self-consistent Calculation
Pert. # 1: Fermi energy shift (Ry) = -1.7279E-02 0.0000E+00
iter # 1 total cpu time : 26946.8 secs av.it.: 15.7
thresh= 1.000E-02 alpha_mix = 0.100 |ddv_scf|^2 = 3.581E-06
kpoint 1 ibnd 99 solve_linter: root not converged 1.031E-03
Pert. # 1: Fermi energy shift (Ry) = -7.0043E-02 0.0000E+00
iter # 2 total cpu time : 27058.6 secs av.it.: 33.4
thresh= 1.892E-04 alpha_mix = 0.100 |ddv_scf|^2 = 2.379E-04
Pert. # 1: Fermi energy shift (Ry) = -5.5995E-02 0.0000E+00
iter # 3 total cpu time : 27143.0 secs av.it.: 20.6
thresh= 1.542E-03 alpha_mix = 0.100 |ddv_scf|^2 = 3.080E-05
Pert. # 1: Fermi energy shift (Ry) = -1.9838E-03 0.0000E+00
iter # 4 total cpu time : 27233.3 secs av.it.: 23.0
thresh= 5.550E-04 alpha_mix = 0.100 |ddv_scf|^2 = 3.693E-06
kpoint 1 ibnd 99 solve_linter: root not converged 4.283E-04
Pert. # 1: Fermi energy shift (Ry) = 3.4490E-03 0.0000E+00
iter # 5 total cpu time : 27335.3 secs av.it.: 28.2
thresh= 1.922E-04 alpha_mix = 0.100 |ddv_scf|^2 = 2.869E-05
Pert. # 1: Fermi energy shift (Ry) = -1.0061E-02 0.0000E+00
iter # 6 total cpu time : 27426.0 secs av.it.: 23.5
?
Pert. # 1: Fermi energy shift (Ry) = -2.7921E-02 0.0000E+00
iter # 98 total cpu time : 36344.4 secs av.it.: 29.4
thresh= 1.701E-04 alpha_mix = 0.100 |ddv_scf|^2 = 6.016E-06
kpoint 1 ibnd 99 solve_linter: root not converged 9.021E-04
Pert. # 1: Fermi energy shift (Ry) = 2.8328E-03 0.0000E+00
iter # 99 total cpu time : 36444.3 secs av.it.: 27.6
thresh= 2.453E-04 alpha_mix = 0.100 |ddv_scf|^2 = 1.921E-05
Pert. # 1: Fermi energy shift (Ry) = 2.4610E-02 0.0000E+00
iter # 100 total cpu time : 36536.3 secs av.it.: 23.9
thresh= 4.382E-04 alpha_mix = 0.100 |ddv_scf|^2 = 1.317E-05
End of self-consistent calculation
No convergence has been achieved
</snip>
As you might notice, the second value of Fermi energy shift remains
0.0000E+00.
What does it mean?
On request, I can send you the input files.
Met vriendelijke groeten,
Mit freundlichen Gr??en,
With kind regards,
Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073
Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>
[cid:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local]
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If you plan to visit VITO at Mol, then please note that the main
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VITO Disclaimer: http://www.vito.be/e-maildisclaimer
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Message: 7
Date: Tue, 26 Feb 2019 09:11:18 +0100
From: Lorenzo Paulatto <paulatz at gmail.com>
To: users at lists.quantum-espresso.org
Subject: Re: [QE-users] Phonon Calculation erroneous
Message-ID: <16b94d99-987b-5112-c243-4385f962b424 at gmail.com>
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> As you might notice, the second value of Fermi energy shift remains
> ?0.0000E+00.
This is normal: if the positions of the atoms are all fixed by symmetry
the Fermi shift is zero.
Regarding the convergence, it is not converging but it is not exploding
either, which may indicate that it is just a question of reducing the
alpha_mix of phonon to have it converge, by default it is
alpha_mix(1) = 0.7
You can try
alpha_mix(1) = 0.3
alpha_mix(2) = 0.1
hth
--
Lorenzo Paulatto - Paris
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