Re: [QE-users] pw.x malloc failed

[Aziz Ogutlu]

Hi Paolo,

Thank you for your response. If you say where is bad syntax, I can 
correct it and try to run.


Best regards,

On 7/24/23 18:23, Paolo Giannozzi wrote:
The input data you report contain several cases of bad syntax. Please 
provide an input file with correct syntax, the output file and a 
pointer to the pseudopotential files


Paolo

On 7/24/23 13:49, Aziz Ogutlu wrote:


You don't often get email from aziz.ogu...@eduline.com.tr. Learn why 
this is important 



Hi there all,

We're using Quantum Espresso 7.1 with Intel compiler 2022.3 on HPC 
system.


When we call pw.x like below, we're getting an error:

/mpirun pw.x -i < scf_step1.in/

...

/Atomic wfc used for Hubbard projectors are NOT orthogonalized//
//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) 
>= (unsigned long) (nb)' failed.//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) 
>= (unsigned long) (nb)' failed.//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) 
>= (unsigned long) (nb)' failed.//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) 
>= (unsigned long) (nb)' failed.//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) 
>= (unsigned long) (nb)' failed.//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) 
>= (unsigned long) (nb)' failed.//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) 
>= (unsigned long) (nb)' failed.//

//munmap_chunk(): invalid pointer//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) 
>= (unsigned long) (nb)' failed.//

//free(): invalid pointer//
//free(): invalid size//
//munmap_chunk(): invalid pointer//
//forrtl: severe (174): SIGSEGV, segmentation fault occurred/

...

scf_step1.in file is below:

...

/&CONTROL//
//    calculation = 'scf'//
//    title = cri3//
//    prefix = cri3//
//    verbosity = high//
//    tprnfor = false//
//    tstress = false//
//    !wf_collect=.true.,//
//    nstep = 100//
//    outdir = '.'//
//    pseudo_dir = '.'//
/
//&SYSTEM//
//    ibrav = 0//
//    celldm(1) = 13.2422737624//
//    nat = 8//
//    ntyp = 2//
//    ecutwfc = 40//
//    ecutrho = 480//
//    occupations = smearing//
//    smearing = cold//
//    degauss = 1.0D-1//
//    starting_magnetization(1) = 3.0//
//    starting_magnetization(2) = 3.0//
//    noncolin = true//
//    !lspinorb = true//
//    !force_symmorphic=.true.//
/
//&ELECTRONS//
//    conv_thr = 1.0D-10//
//    mixing_beta = 1.0D-1//
//    diagonalization = david//
//    electron_maxstep = 100//
/
//CELL_PARAMETERS (alat= 13.24227376)//
//   1.009850542  -0.00028   0.0//
//  -0.504925295   0.874557247   0.0//
//   0.0   0.0   3.053010270//
//
//ATOMIC_SPECIES//
//    Cr   51.9961   Cr.upf//
//    I   126.90447  I.upf//
//
//ATOMIC_POSITIONS (crystal)//
//Cr    0.373212    0.740955 0.537747//
//Cr    0.736698    0.478677 0.537830//
//I 0.6394274459    0.6394360520 0.4263871618//
//I 0.074173    0.3605885769 0.4263860947//
//I 0.3605789168    0.160499 0.4263887410//
//I 0.3605798499    0.3605872226 0.5736275567//
//I 0.6394379899    1.158469 0.5736249512//
//I 1.085003    0.6394365107 0.5736265856//
//
//K_POINTS AUTOMATIC//
//  12 12 1 0 0 0//
//
//HUBBARD atomic//
//U Cr-3d 1.5/

...

--
İyi çalışmalar,
Aziz Öğütlü

Eduline Bilişim Sanayi ve Ticaret Ltd. Şti.www.eduline.com.tr
Merkez Mah. Ayazma Cad. No:37 Papirus Plaza
Kat:6 Ofis No:118 Kağıthane -  İstanbul - Türkiye 34406
Tel : +90 212 324 60 61 Cep: +90 541 350 40 72


___
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--
İyi çalışmalar,
Aziz Öğütlü

Eduline Bilişim Sanayi ve Ticaret Ltd. Şti.  www.eduline.com.tr
Merkez Mah. Ayazma Cad. No:37 Papirus Plaza
Kat:6 Ofis No:118 Kağıthane -  İstanbul - Türkiye 34406
Tel : +90 212 324 60 61 Cep: +90 541 350 40 72

___
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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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users maili

Re: [QE-users] pw.x malloc failed

[Stefano Baroni]

With all due respect, it seems to me that trying to identify the mistakes, once 
you know that there are some/several, would be a sign of respect to those who 
spend lots of time helping others and to keep the project running. For free. 
Every minute spent addressing questions that could have not been asked, is a 
minute less devoted to the improvement of the code and to correct bugs. I am 
sure you will understand. SB

--
Stefano Baroni, Trieste -- swift message written and sent on the go

> Il giorno 25 lug 2023, alle ore 09:17, Aziz Ogutlu 
>  ha scritto:
> 
> Hi Paolo,
> 
> Thank you for your response. If you say where is bad syntax, I can correct it 
> and try to run.
> 
> Best regards,
> 
>> On 7/24/23 18:23, Paolo Giannozzi wrote:
>> The input data you report contain several cases of bad syntax. Please 
>> provide an input file with correct syntax, the output file and a pointer to 
>> the pseudopotential files
>> 
>> Paolo
>> 
>>> On 7/24/23 13:49, Aziz Ogutlu wrote:
>>> 
>>> You don't often get email from aziz.ogu...@eduline.com.tr. Learn why this 
>>> is important 
>>> 
>>> 
>>> Hi there all,
>>> 
>>> We're using Quantum Espresso 7.1 with Intel compiler 2022.3 on HPC system.
>>> 
>>> When we call pw.x like below, we're getting an error:
>>> 
>>> /mpirun pw.x -i < scf_step1.in/
>>> 
>>> ...
>>> 
>>> /Atomic wfc used for Hubbard projectors are NOT orthogonalized//
>>> //
>>> //pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
>>> (unsigned long) (nb)' failed.//
>>> //pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
>>> (unsigned long) (nb)' failed.//
>>> //pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
>>> (unsigned long) (nb)' failed.//
>>> //pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
>>> (unsigned long) (nb)' failed.//
>>> //pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
>>> (unsigned long) (nb)' failed.//
>>> //pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
>>> (unsigned long) (nb)' failed.//
>>> //pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
>>> (unsigned long) (nb)' failed.//
>>> //munmap_chunk(): invalid pointer//
>>> //pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
>>> (unsigned long) (nb)' failed.//
>>> //free(): invalid pointer//
>>> //free(): invalid size//
>>> //munmap_chunk(): invalid pointer//
>>> //forrtl: severe (174): SIGSEGV, segmentation fault occurred/
>>> 
>>> ...
>>> 
>>> scf_step1.in file is below:
>>> 
>>> ...
>>> 
>>> /&CONTROL//
>>> //calculation = 'scf'//
>>> //title = cri3//
>>> //prefix = cri3//
>>> //verbosity = high//
>>> //tprnfor = false//
>>> //tstress = false//
>>> //!wf_collect=.true.,//
>>> //nstep = 100//
>>> //outdir = '.'//
>>> //pseudo_dir = '.'//
>>> /
>>> //&SYSTEM//
>>> //ibrav = 0//
>>> //celldm(1) = 13.2422737624//
>>> //nat = 8//
>>> //ntyp = 2//
>>> //ecutwfc = 40//
>>> //ecutrho = 480//
>>> //occupations = smearing//
>>> //smearing = cold//
>>> //degauss = 1.0D-1//
>>> //starting_magnetization(1) = 3.0//
>>> //starting_magnetization(2) = 3.0//
>>> //noncolin = true//
>>> //!lspinorb = true//
>>> //!force_symmorphic=.true.//
>>> /
>>> //&ELECTRONS//
>>> //conv_thr = 1.0D-10//
>>> //mixing_beta = 1.0D-1//
>>> //diagonalization = david//
>>> //electron_maxstep = 100//
>>> /
>>> //CELL_PARAMETERS (alat= 13.24227376)//
>>> //   1.009850542  -0.00028   0.0//
>>> //  -0.504925295   0.874557247   0.0//
>>> //   0.0   0.0   3.053010270//
>>> //
>>> //ATOMIC_SPECIES//
>>> //Cr   51.9961   Cr.upf//
>>> //I   126.90447  I.upf//
>>> //
>>> //ATOMIC_POSITIONS (crystal)//
>>> //Cr0.3732120.740955 0.537747//
>>> //Cr0.7366980.478677 0.537830//
>>> //I 0.63942744590.6394360520 0.4263871618//
>>> //I 0.0741730.3605885769 0.4263860947//
>>> //I 0.36057891680.160499 0.4263887410//
>>> //I 0.36057984990.3605872226 0.5736275567//
>>> //I 0.63943798991.158469 0.5736249512//
>>> //I 1.0850030.6394365107 0.5736265856//
>>> //
>>> //K_POINTS AUTOMATIC//
>>> //  12 12 1 0 0 0//
>>> //
>>> //HUBBARD atomic//
>>> //U Cr-3d 1.5/
>>> 
>>> ...
>>> 
>>> -- 
>>> İyi çalışmalar,
>>> Aziz Öğütlü
>>> 
>>> Eduline Bilişim Sanayi ve Ticaret Ltd. Şti.www.eduline.com.tr
>>> Merkez Mah. Ayazma Cad. No:37 Papirus Plaza
>>> Kat:6 Ofis No:118 Kağıthane -  İstanbul - Türkiye 34406
>>> Tel : +90 212 324 60 61 Cep: +90 541 350 40 72
>>> 
>>> 
>>> ___
>>> The Quantum ESPRESSO community stands by the Ukrainian
>>> people and expresses its concerns a

[QE-users] Missing d orbital in projected band structure of CaC6

[Bruce Wang]

Dear QE users and developers,

I am currently working on calculating the projected band structure of CaC6 
using quantum espresso with GGA+UItrasoft pseudopotential 
(Ca.pbe-spn-rrkjus_psl.1.0.0.UPF). However, I have encountered an issue with 
obtaining the 3d orbital wavefunctions for Calcium.

I followed the QE PP examples, and I have managed to obtain the 4s and 3p 
orbitals. The 3d orbital was missing while it should existed.

I would greatly appreciate any guidance on how to retrieve the 3d orbital 
character of Calcium for my projected band structure calculations.

Thank you for your time and assistance.


Regards,
Bruce
___
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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users mailing list users@lists.quantum-espresso.org
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Re: [QE-users] Missing d orbital in projected band structure of CaC6

[Giuseppe Mattioli]

Dear Bruce (please sign always your posts to this forum with full name  
and affiliation, we appreciate it)
You should add many more details (code version, list of simulations,  
input and relevant parts of output, ...). From your post it is  
impossible to understand what you have exactly done and whether there  
is any error or not.

HTH
Giuseppe

Quoting Bruce Wang :


Dear QE users and developers,

I am currently working on calculating the projected band structure  
of CaC6 using quantum espresso with GGA+UItrasoft pseudopotential  
(Ca.pbe-spn-rrkjus_psl.1.0.0.UPF). However, I have encountered an  
issue with obtaining the 3d orbital wavefunctions for Calcium.


I followed the QE PP examples, and I have managed to obtain the 4s  
and 3p orbitals. The 3d orbital was missing while it should existed.


I would greatly appreciate any guidance on how to retrieve the 3d  
orbital character of Calcium for my projected band structure  
calculations.


Thank you for your time and assistance.


Regards,
Bruce




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: 

___
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@lists.quantum-espresso.org
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[QE-users] How does one calculate dipole moments or access (readable) wave functions from e.g. PW?

[Brian de Keijzer]

Hi all, 


New QE users here. I’ve used QE so far to compute band structures for crystals. 
I am however very much interested in calculating the dipole matrix elements for 
said crystals. Does QE have a module that allows one to do this? If so, how 
would that work?

Moreover, I have read that it is possible to use the wave functions directly. 
That would allow me to compute the dipole elements. Unfortunately most posts 
that I come across appear to be a bit dated tho. What would be the best way to 
access the wave functions using more recent versions of e.g. Python? I’ve come 
across postqe but that appears to no longer be in development nor does the 
installation work on my Python 3.9 distribution. 

Anyhow; I’m looking to learn how to compute k-dependent transition dipole 
moments in QE. It would be awesome if anyone would want to provide an outline 
of how such a thing is to be done using the latest version of QE. 


Bests, 

Brian de Keijzer
___
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and economic cooperation amongst peoples
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Re: [QE-users] Missing d orbital in projected band structure of CaC6

[Giovanni Cantele]

Dear Bruce,

if I'm not wrong you're using this pseudopotential:
http://pseudopotentials.quantum-espresso.org/upf_files/Ca.pbe-spn-rrkjus_psl.1.0.0.UPF

If you look inside you see that it has been generate with this valence
configuration:
nl pn  l   occ   RcutRcut US   E pseu
3S  1  0  2.00  1.200  1.300-3.461142
4S  2  0  2.00  1.200  1.300-0.276804
3P  2  1  6.00  1.400  1.600-2.058527
4P  3  1  0.00  1.400  1.600-0.103085

As such, when you try to project a band structure of a system containing
this atom, it will only be able to project on 3S, 4S, 3P and 4P states.
You may also check this by looking, inside the UPF file, for the string
PP_GIPAW_ORBITAL
After lines such that

you find the radial part of the corresponding atomic wfc to be used for the
projection. Therefore, if an orbital is not included, the code does not
have access to the radial part of the wfc and will not be able to make any
projection.

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 mar 25 lug 2023 alle ore 09:40 Bruce Wang 
ha scritto:

> Dear QE users and developers,
>
> I am currently working on calculating the projected band structure of CaC6
> using quantum espresso with GGA+UItrasoft pseudopotential (
> Ca.pbe-spn-rrkjus_psl.1.0.0.UPF). However, I have encountered an issue
> with obtaining the 3d orbital wavefunctions for Calcium.
>
> I followed the QE PP examples, and I have managed to obtain the 4s and 3p
> orbitals. The 3d orbital was missing while it should existed.
>
> I would greatly appreciate any guidance on how to retrieve the 3d orbital
> character of Calcium for my projected band structure calculations.
>
> Thank you for your time and assistance.
>
>
> Regards,
> Bruce
> ___
> 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
>
___
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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
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Re: [QE-users] Missing d orbital in projected band structure of CaC6

[Giuseppe Mattioli]

Dear Giovanni
I've found this one into the psl-1.0.0 library.

cat > Ca.$fct-spn-rrkjus_psl.1.0.0.in << EOF
 &input
   title='Ca',
   zed=20.,
   rel=$nrel,
   config='[Ar] 4s2 4p0 3d-1',
   iswitch=3,
   dft='$gfun'
 /
 &inputp
   lpaw=.false.,
   pseudotype=3,
   file_pseudopw='Ca.$fct-spn-rrkjus_psl.1.0.0.UPF',
   author='ADC',
   lloc=-1,
   rcloc=1.5,
   which_augfun='PSQ',
   rmatch_augfun_nc=.true.,
   nlcc=.true.,
   new_core_ps=.true.,
   rcore=1.0,
   tm=.true.
 /
6
3S  1  0  2.00  0.00  1.20  1.30  0.0
4S  2  0  2.00  0.00  1.20  1.30  0.0
3P  2  1  6.00  0.00  1.40  1.60  0.0
4P  3  1  0.00  0.00  1.40  1.60  0.0
3D  3  2  0.00  0.05  1.20  1.70  0.0
3D  3  2  0.00  1.00  1.20  1.70  0.0
EOF

Are there two different PPs with the same name out there?
Best
Giuseppe


Quoting Giovanni Cantele :


Dear Bruce,

if I'm not wrong you're using this pseudopotential:
http://pseudopotentials.quantum-espresso.org/upf_files/Ca.pbe-spn-rrkjus_psl.1.0.0.UPF

If you look inside you see that it has been generate with this valence
configuration:
nl pn  l   occ   RcutRcut US   E pseu
3S  1  0  2.00  1.200  1.300-3.461142
4S  2  0  2.00  1.200  1.300-0.276804
3P  2  1  6.00  1.400  1.600-2.058527
4P  3  1  0.00  1.400  1.600-0.103085

As such, when you try to project a band structure of a system containing
this atom, it will only be able to project on 3S, 4S, 3P and 4P states.
You may also check this by looking, inside the UPF file, for the string
PP_GIPAW_ORBITAL
After lines such that

you find the radial part of the corresponding atomic wfc to be used for the
projection. Therefore, if an orbital is not included, the code does not
have access to the radial part of the wfc and will not be able to make any
projection.

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 mar 25 lug 2023 alle ore 09:40 Bruce Wang 
ha scritto:


Dear QE users and developers,

I am currently working on calculating the projected band structure of CaC6
using quantum espresso with GGA+UItrasoft pseudopotential (
Ca.pbe-spn-rrkjus_psl.1.0.0.UPF). However, I have encountered an issue
with obtaining the 3d orbital wavefunctions for Calcium.

I followed the QE PP examples, and I have managed to obtain the 4s and 3p
orbitals. The 3d orbital was missing while it should existed.

I would greatly appreciate any guidance on how to retrieve the 3d orbital
character of Calcium for my projected band structure calculations.

Thank you for your time and assistance.


Regards,
Bruce
___
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





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: 

___
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
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Re: [QE-users] Missing d orbital in projected band structure of CaC6

[Paolo Giannozzi]

The "3d-1" field in 'config' means - in the rather questionable logic of 
the atomic code - that the 3d orbitals are not bound. In fact the 
pseudization energies for 3d have non-zero values (fourth column below):

3D  3  2  0.00  0.05  1.20  1.70  0.0
3D  3  2  0.00  1.00  1.20  1.70  0.0
The 3d states are thus not saved as atomic states and not usable for 
projection.


Paolo

On 7/25/23 11:12, Giuseppe Mattioli wrote:


Dear Giovanni
I've found this one into the psl-1.0.0 library.

cat > Ca.$fct-spn-rrkjus_psl.1.0.0.in << EOF
  &input
    title='Ca',
    zed=20.,
    rel=$nrel,
    config='[Ar] 4s2 4p0 3d-1',
    iswitch=3,
    dft='$gfun'
  /
  &inputp
    lpaw=.false.,
    pseudotype=3,
    file_pseudopw='Ca.$fct-spn-rrkjus_psl.1.0.0.UPF',
    author='ADC',
    lloc=-1,
    rcloc=1.5,
    which_augfun='PSQ',
    rmatch_augfun_nc=.true.,
    nlcc=.true.,
    new_core_ps=.true.,
    rcore=1.0,
    tm=.true.
  /
6
3S  1  0  2.00  0.00  1.20  1.30  0.0
4S  2  0  2.00  0.00  1.20  1.30  0.0
3P  2  1  6.00  0.00  1.40  1.60  0.0
4P  3  1  0.00  0.00  1.40  1.60  0.0
3D  3  2  0.00  0.05  1.20  1.70  0.0
3D  3  2  0.00  1.00  1.20  1.70  0.0
EOF

Are there two different PPs with the same name out there?
Best
Giuseppe


Quoting Giovanni Cantele :


Dear Bruce,

if I'm not wrong you're using this pseudopotential:
http://pseudopotentials.quantum-espresso.org/upf_files/Ca.pbe-spn-rrkjus_psl.1.0.0.UPF

If you look inside you see that it has been generate with this valence
configuration:
    nl pn  l   occ   Rcut    Rcut US   E pseu
    3S  1  0  2.00  1.200  1.300    -3.461142
    4S  2  0  2.00  1.200  1.300    -0.276804
    3P  2  1  6.00  1.400  1.600    -2.058527
    4P  3  1  0.00  1.400  1.600    -0.103085

As such, when you try to project a band structure of a system containing
this atom, it will only be able to project on 3S, 4S, 3P and 4P states.
You may also check this by looking, inside the UPF file, for the string
PP_GIPAW_ORBITAL
After lines such that
cutoff_radius="0.e0" 
ultrasoft_cutoff_radius="0.e0">
you find the radial part of the corresponding atomic wfc to be used 
for the

projection. Therefore, if an orbital is not included, the code does not
have access to the radial part of the wfc and will not be able to make 
any

projection.

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 mar 25 lug 2023 alle ore 09:40 Bruce Wang 


ha scritto:


Dear QE users and developers,

I am currently working on calculating the projected band structure of 
CaC6

using quantum espresso with GGA+UItrasoft pseudopotential (
Ca.pbe-spn-rrkjus_psl.1.0.0.UPF). However, I have encountered an issue
with obtaining the 3d orbital wavefunctions for Calcium.

I followed the QE PP examples, and I have managed to obtain the 4s 
and 3p

orbitals. The 3d orbital was missing while it should existed.

I would greatly appreciate any guidance on how to retrieve the 3d 
orbital

character of Calcium for my projected band structure calculations.

Thank you for your time and assistance.


Regards,
Bruce
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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: 

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--
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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[QE-users] Fwd: Missing d orbital in projected band structure of CaC6

[Lorenzo Paulatto]

 Forwarded Message 
Subject: 	Re: [QE-users] Missing d orbital in projected band structure 
of CaC6

Date:   Tue, 25 Jul 2023 10:15:26 +0200
From:   Lorenzo Paulatto 
Organization:   CNRS
To: Bruce Wang 



Hello Bruce.


You can see in hte input file (which is at the beginning of the UPF 
file) that the 3d orbital occupancy has been set to "-1". This mean that 
the name is reserved for later use, but the orbital has not actually 
been computed. Later on, two arbitrary energies (0.05Ry and 1Ry) have 
been defined to construct two reference scattering states for the "d" 
orbitals. These states cannot be used for projecting because they are 
not normalizable.



You can try to set 3d0 and pass the input to ld1:

  ld1.x < input

But if the 3d state is unbound, this will not converge. In that case the 
only solution, is to use a slightly excited configuration, i.e.e take 
away some charge from 4s2 and put it in 3d, but I cannot guarantee that 
the resulting pseudopotential will be accurate.



hth

 &input
   title='Ca',
   zed=20.,
   rel=1,
config='[Ar] 4s2 4p0 3d-1', iswitch=3,
   dft='PBE'
 /
 &inputp
   lpaw=.false.,
   use_xsd=.FALSE.,
   pseudotype=3,
   file_pseudopw='Ca.pbe-spn-rrkjus_psl.1.0.0.UPF',
   author='ADC',
   lloc=-1,
   rcloc=1.5,
   which_augfun='PSQ',
   rmatch_augfun_nc=.true.,
   nlcc=.true.,
   new_core_ps=.true.,
   rcore=1.0,
   tm=.true.
 /
6
3S  1  0  2.00  0.00  1.20  1.30  0.0
4S  2  0  2.00  0.00  1.20  1.30  0.0
3P  2  1  6.00  0.00  1.40  1.60  0.0
4P  3  1  0.00  0.00  1.40  1.60  0.0
3D  3  2  0.000.05   1.20  1.70  0.0
3D  3  2  0.001.00   1.20  1.70  0.0



On 7/25/23 09:40, Bruce Wang wrote:

Dear QE users and developers,

I am currently working on calculating the projected band structure of 
CaC6 using quantum espresso with GGA+UItrasoft pseudopotential 
(Ca.pbe-spn-rrkjus_psl.1.0.0.UPF). However, I have encountered an 
issue with obtaining the 3d orbital wavefunctions for Calcium.


I followed the QE PP examples, and I have managed to obtain the 4s and 
3p orbitals. The 3d orbital was missing while it should existed.


I would greatly appreciate any guidance on how to retrieve the 3d 
orbital character of Calcium for my projected band structure 
calculations.


Thank you for your time and assistance.


Regards,
Bruce

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--
Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05___
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Re: [QE-users] How does one calculate dipole moments or access (readable) wave functions from e.g. PW?

[Paolo Giannozzi]

I think code "bands.x" can compute dipole matrix elements.

About direct access to wavefunctions: the default fortran binary format 
is basically unreadable except via the routines of QE. One may 
optionally write hdf5 files that are much easier to read with external 
utilities, though.


Paolo

On 7/25/23 10:40, Brian de Keijzer wrote:

[You don't often get email from briandekey...@hotmail.com. Learn why this is 
important at https://aka.ms/LearnAboutSenderIdentification ]

Hi all,


New QE users here. I’ve used QE so far to compute band structures for crystals. 
I am however very much interested in calculating the dipole matrix elements for 
said crystals. Does QE have a module that allows one to do this? If so, how 
would that work?

Moreover, I have read that it is possible to use the wave functions directly. 
That would allow me to compute the dipole elements. Unfortunately most posts 
that I come across appear to be a bit dated tho. What would be the best way to 
access the wave functions using more recent versions of e.g. Python? I’ve come 
across postqe but that appears to no longer be in development nor does the 
installation work on my Python 3.9 distribution.

Anyhow; I’m looking to learn how to compute k-dependent transition dipole 
moments in QE. It would be awesome if anyone would want to provide an outline 
of how such a thing is to be done using the latest version of QE.


Bests,

Brian de Keijzer
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--
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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Re: [QE-users] How does one calculate dipole moments or access (readable) wave functions from e.g. PW?

[Brian de Keijzer]

Hi Paolo,

Thank you for your answer’

Bands.x had caught my eye before but I did not notice how to make it output 
transition dipole moments. How would one compute those?

Meanwhile I managed to indeed get hdf5 output. That’s great! If there is a 
native way to obtain the values I want it’s preferable tho.

Best regards,

Brian de Keijzer

> On 25 Jul 2023, at 13:37, Paolo Giannozzi  wrote:
> 
> I think code "bands.x" can compute dipole matrix elements.
> 
> About direct access to wavefunctions: the default fortran binary format is 
> basically unreadable except via the routines of QE. One may optionally write 
> hdf5 files that are much easier to read with external utilities, though.
> 
> Paolo
> 
>> On 7/25/23 10:40, Brian de Keijzer wrote:
>> [You don't often get email from briandekey...@hotmail.com. Learn why this is 
>> important at https://aka.ms/LearnAboutSenderIdentification ]
>> Hi all,
>> New QE users here. I’ve used QE so far to compute band structures for 
>> crystals. I am however very much interested in calculating the dipole matrix 
>> elements for said crystals. Does QE have a module that allows one to do 
>> this? If so, how would that work?
>> Moreover, I have read that it is possible to use the wave functions 
>> directly. That would allow me to compute the dipole elements. Unfortunately 
>> most posts that I come across appear to be a bit dated tho. What would be 
>> the best way to access the wave functions using more recent versions of e.g. 
>> Python? I’ve come across postqe but that appears to no longer be in 
>> development nor does the installation work on my Python 3.9 distribution.
>> Anyhow; I’m looking to learn how to compute k-dependent transition dipole 
>> moments in QE. It would be awesome if anyone would want to provide an 
>> outline of how such a thing is to be done using the latest version of QE.
>> Bests,
>> Brian de Keijzer
>> ___
>> 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
> 
> -- 
> 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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[QE-users] DFT + Hubbard error with ccECP pseudopotentials in QE 7.1 and 7.2

[Anirudh Adavi]

Hello,

I am attempting to run some SCF calculations with QE on transition metal oxide 
systems to generate orbitals for subsequent QMC. As such, I have been using the 
ccECP and ccECP-soft pseudopotentials from https://pseudopotentiallibrary.org/. 
However, adding a U correction to either the Mn-3d or O-2p orbitals gives the 
following error.

 from offset_atom_wfc : error # 1
 Mismatch between the requested and available manifolds

My input is as follows.

...
ATOMIC_SPECIES
   Mn 54.938 Mn.ccECP-soft.upf
   Na 22.99 Na.ccECP.upf
   O  15.999 O.ccECP.upf
ATOMIC_POSITIONS bohr
   Na  -1.78117929   5.36667723   6.05419528
   Na   6.41143191   0.16710178   6.13034248
   Mn  -0.16407059  -0.52879762   2.66509362
   ...
K_POINTS automatic
   6 6 5  0 0 0
...
HUBBARD ortho-atomic
U Mn-3d 3.9
U O-2p 6.0

The calculation works well with the ccECP potentials with no Hubbard 
correction. It also runs with Hubbard corrections when using the ONCV-SR 
pseudopotentials from D. R. Hamann, but I would prefer to keep the ccECP 
pseudopotentials for use in QMC. I encountered the same error when using QE 
7.2. Any help in correcting my mistakes is greatly appreciated.

I apologize if this is the wrong channel for this question. Please let me know 
if further information is needed, or if there is a more appropriate place to 
ask.

Thank you,
Anirudh Adavi
MIT DMSE
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Re: [QE-users] SCF Calculation Issue with PBE0 Functional

[Rameswar Bhattacharjee]

Hi Kazume,
thanks for the suggestion. I tried with an older version but gave the
same error. However, I solved it by changing the "exxdiv_treatment" to
'vcut_spherical' and it converged.

Rameswar

On Mon, Jul 24, 2023 at 12:50 AM Kazume NISHIDATE
 wrote:
>
> Dear Rameswar Bhattacharjee,
>
> > these systems, the calculation continues to run for an
> > unusually long time, and I notice that the program prints
> > similar lines (provided below) after each iteration
> > convergence.
>
> What compiler did you use to build the QE?
> Intel's newest one?
>
> I encountered a similar problem in the HSE06 hybrid calculation.
>
> Can you try the same calculation using the QE bult in the older
> Intel compiler (or simply using the older version of QE)?
>
>
>
>
> 西館数芽
> Kazume NISHIDATE Ph.D
>
> Department of Systems Innovation Engineering,
> Graduate School of Science and Engineering, Iwate University
> 4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN
> Phone:+81-19-621-6391
> kazume.nishid...@gmail.com, nisid...@iwate-u.ac.jp
> https://sites.google.com/site/nisidatelab/
>
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> effects that the Russian military offensive has on their
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-- 
Rameswar Bhattacharjee
Department of Chemistry
Georgetown University
Washington, DC 20057
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[QE-users] problems optimizing 2d material with option . ¿ possible bug?

[Wilber Muriel]

Dear QE Developers

I am performing a geometric optimization (vc-relax) for a 2D material, using 
the option "assume_isolated = '2D' " and "cell_dofree ="2Dxy" " ,
and I noticed that the forces do not converge, after 19 steps the forces have 
not changed at all, which is unusual:

 Total force = 1.788117 Total SCF correction = 0.35
  Total force = 1.721481 Total SCF correction = 0.14
  Total force = 1.771077 Total SCF correction = 0.35
  Total force = 1.783843 Total SCF correction = 0.38
  Total force = 1.787049 Total SCF correction = 0.45
  Total force = 1.787844 Total SCF correction = 0.99
  Total force = 1.788047 Total SCF correction = 0.000158
  Total force = 1.788094 Total SCF correction = 0.06
  Total force = 1.721474 Total SCF correction = 0.58
  Total force = 1.771077 Total SCF correction = 0.70
  Total force = 1.783843 Total SCF correction = 0.16
  Total force = 1.787049 Total SCF correction = 0.36
  Total force = 1.787844 Total SCF correction = 0.68
  Total force = 1.788047 Total SCF correction = 0.000117
  Total force = 1.788094 Total SCF correction = 0.000286
  Total force = 1.721480 Total SCF correction = 0.99
  Total force = 1.771077 Total SCF correction = 0.50
  Total force = 1.783843 Total SCF correction = 0.58
  Total force = 1.787048 Total SCF correction = 0.58
  Total force = 1.787845 Total SCF correction = 0.000140
  Total force = 1.788046 Total SCF correction = 0.000172
  Total force = 1.788094 Total SCF correction = 0.04
  Total force = 1.721474 Total SCF correction = 0.55
  Total force = 1.771077 Total SCF correction = 0.35
  Total force = 1.783843 Total SCF correction = 0.39
  Total force = 1.787049 Total SCF correction = 0.45
  Total force = 1.787844 Total SCF correction = 0.000103
  Total force = 1.788046 Total SCF correction = 0.000162

without the option "assume_isolated = '2D' " the optimization can be performed 
without problems.
The inputs are here: 
https://drive.google.com/file/d/1UOj-y4a1k9OQT1zHfVlSAR_YMNPJu_j6/view?usp=drive_link

The version of QE used is: develop - commit : 9ff5b55a (The compilation was 
successful)

 Computation node:
 HP ProLiant SL230s Gen8
 CPU: 2 x Intel Xeon E5-2660v2 @ 2,20GHz, 10 cores c/u
 RAM 46 GB

configure lines

./configure 
--prefix=/home/aecheverri/apps/qsoftw/QE/dev-commit-9ff5b55a-impi-elpa-2023.05.001
--enable-parallel --with-scalapack=intel --with-fox
--with-elpa-lib="-L/home/aecheverri/apps/lib/elpa/2023.05.001-avx-impi-intel-2022/lib
 -lelpa"
--with-elpa-include="/home/aecheverri/apps/lib/elpa/2023.05.001-avx-impi-intel-2022/include/elpa-2023.05.001/modules
 -I${MKLROOT}/include/intel64/lp64 "
CFLAGS="-O3 -axAVX,CORE-AVX512 -fp-model=source " FFLAGS="-O2 
-axAVX,CORE-AVX512 -fp-model=source -assume byterecl -g -traceback "

best regards

Wilver
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[QE-users] problems optimizing 2d material with option "assume_isolated = '2D' " . ¿ possible bug?

[Wilber Muriel]

Dear QE Developers

Note: I apologize for repeating the message. In the previous one the subject 
was incomplete.

I am performing a geometric optimization (vc-relax) for a 2D material, using 
the option "assume_isolated = '2D' " and "cell_dofree ="2Dxy" " ,
and I noticed that the forces do not converge, after 19 steps the forces have 
not changed at all, which is unusual:

Total force = 1.788117 Total SCF correction = 0.35
  Total force = 1.721481 Total SCF correction = 0.14
  Total force = 1.771077 Total SCF correction = 0.35
  Total force = 1.783843 Total SCF correction = 0.38
  Total force = 1.787049 Total SCF correction = 0.45
  Total force = 1.787844 Total SCF correction = 0.99
  Total force = 1.788047 Total SCF correction = 0.000158
  Total force = 1.788094 Total SCF correction = 0.06
  Total force = 1.721474 Total SCF correction = 0.58
  Total force = 1.771077 Total SCF correction = 0.70
  Total force = 1.783843 Total SCF correction = 0.16
  Total force = 1.787049 Total SCF correction = 0.36
  Total force = 1.787844 Total SCF correction = 0.68
  Total force = 1.788047 Total SCF correction = 0.000117
  Total force = 1.788094 Total SCF correction = 0.000286
  Total force = 1.721480 Total SCF correction = 0.99
  Total force = 1.771077 Total SCF correction = 0.50
  Total force = 1.783843 Total SCF correction = 0.58
  Total force = 1.787048 Total SCF correction = 0.58
  Total force = 1.787845 Total SCF correction = 0.000140
  Total force = 1.788046 Total SCF correction = 0.000172
  Total force = 1.788094 Total SCF correction = 0.04
  Total force = 1.721474 Total SCF correction = 0.55
  Total force = 1.771077 Total SCF correction = 0.35
  Total force = 1.783843 Total SCF correction = 0.39
  Total force = 1.787049 Total SCF correction = 0.45
  Total force = 1.787844 Total SCF correction = 0.000103
  Total force = 1.788046 Total SCF correction = 0.000162

without the option "assume_isolated = '2D' " the optimization can be performed 
without problems.
The inputs are here: 
https://drive.google.com/file/d/1UOj-y4a1k9OQT1zHfVlSAR_YMNPJu_j6/view?usp=drive_link

The version of QE used is: develop - commit : 9ff5b55a (The compilation was 
successful)

 Computation node:
 HP ProLiant SL230s Gen8
 CPU: 2 x Intel Xeon E5-2660v2 @ 2,20GHz, 10 cores c/u
 RAM 46 GB

configure lines

./configure 
--prefix=/home/aecheverri/apps/qsoftw/QE/dev-commit-9ff5b55a-impi-elpa-2023.05.001
--enable-parallel --with-scalapack=intel --with-fox
--with-elpa-lib="-L/home/aecheverri/apps/lib/elpa/2023.05.001-avx-impi-intel-2022/lib
 -lelpa"
--with-elpa-include="/home/aecheverri/apps/lib/elpa/2023.05.001-avx-impi-intel-2022/include/elpa-2023.05.001/modules
 -I${MKLROOT}/include/intel64/lp64 "
CFLAGS="-O3 -axAVX,CORE-AVX512 -fp-model=source " FFLAGS="-O2 
-axAVX,CORE-AVX512 -fp-model=source -assume byterecl -g -traceback "

best regards

Wilver
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Re: [QE-users] DFT + Hubbard error with ccECP pseudopotentials in QE 7.1 and 7.2

[Timrov Iurii via users]

Dear Anirudh Adavi,


See section "Pseudopotentials" in q-e/Doc/Hubbard_input.pdf.


You need to add labels of the wavefunctions in the pseudopotential file (e.g. 
label = "3d"). This is needed for the DFT+U code to work by knowing what is the 
Hubbard manifold. Otherwise, you can try older versions of QE (<7.1) where this 
is not needed, because the logic is different.


HTH


Iurii


--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334

From: users  on behalf of Anirudh 
Adavi 
Sent: Tuesday, July 25, 2023 11:55:43 PM
To: users@lists.quantum-espresso.org
Subject: [QE-users] DFT + Hubbard error with ccECP pseudopotentials in QE 7.1 
and 7.2

Hello,

I am attempting to run some SCF calculations with QE on transition metal oxide 
systems to generate orbitals for subsequent QMC. As such, I have been using the 
ccECP and ccECP-soft pseudopotentials from https://pseudopotentiallibrary.org/. 
However, adding a U correction to either the Mn-3d or O-2p orbitals gives the 
following error.

 from offset_atom_wfc : error # 1
 Mismatch between the requested and available manifolds

My input is as follows.

…
ATOMIC_SPECIES
   Mn 54.938 Mn.ccECP-soft.upf
   Na 22.99 Na.ccECP.upf
   O  15.999 O.ccECP.upf
ATOMIC_POSITIONS bohr
   Na  -1.78117929   5.36667723   6.05419528
   Na   6.41143191   0.16710178   6.13034248
   Mn  -0.16407059  -0.52879762   2.66509362
   …
K_POINTS automatic
   6 6 5  0 0 0
…
HUBBARD ortho-atomic
U Mn-3d 3.9
U O-2p 6.0

The calculation works well with the ccECP potentials with no Hubbard 
correction. It also runs with Hubbard corrections when using the ONCV-SR 
pseudopotentials from D. R. Hamann, but I would prefer to keep the ccECP 
pseudopotentials for use in QMC. I encountered the same error when using QE 
7.2. Any help in correcting my mistakes is greatly appreciated.

I apologize if this is the wrong channel for this question. Please let me know 
if further information is needed, or if there is a more appropriate place to 
ask.

Thank you,
Anirudh Adavi
MIT DMSE
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