Re: [QE-users] Supercell and surface creation

[Zack Gainsforth]

Also atomsk is good for this type of task.  https://atomsk.univ-lille.fr/

Zack

> On Mar 24, 2023, at 4:55 AM, mkondrin  wrote:
> 
> On 03/24/2023 02:51 PM, IBRAHIM SA'ADU wrote:
>> Please how can create a 5x5x1 supercell and (0,0,1) surface.
>> Regard
>> 
>> 
>> 
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> Hi,
> 
> Learn more about cif2cell utility.
> 
> Hope this helps,
> 
> Regards,
> 
> M. V. Kondrin
> 
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[QE-users] Number of cores and number of steps to convergence

[Zack Gainsforth]

Hi Folks,I installed a new i9-13900k and I was just curious to see how the P cores and E cores compared.  I did an SCF of a phyllosilicate using each and I find that it converges nicely in all cases but that the number of iterations to reach convergence is different.  I’m just curious why.Run on the 16 E cores only:mpirun —cpu-set 8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 —bind-to core -n 16 pw.x < Cronstedtite.scf | tee Cronstedtite.scf.16Ecore.outRun on the 8 P cores only:mpirun —cpu-set 0,1,2,3,4,5,6,7 —bind-to core -n 8 pw.x < Cronstedtite.scf | tee Cronstedtite.scf.8Pcore.outRun on all 24 cores:mpirun —bind-to core -n 24 pw.x < Cronstedtite.scf | tee Cronstedtite.scf.8P16Ecore.outI find 1 hour for the E cores, 53 mins for the P cores, and 29 mins for all cores — which is practically linear scaling.However, 22 iterations to converge on E cores, 26 to converge on P cores, and 15 to converge on all cores.  It looks like the more cores the fewer the number of convergence steps?  (Input and output files and a spreadsheet attached if anyone is interested.)Thanks,Zack GainsforthSpace Sciences LaboratoryUniversity of California, Berkeley

Cronstedtite.scf
Description: Binary data


Cronstedtite.scf.8P16Ecore.out
Description: Binary data


Cronstedtite.scf.8Pcore.out
Description: Binary data


Cronstedtite.scf.16Ecore.out
Description: Binary data


CalculationSpeed.ods
Description: application/vnd.oasis.opendocument.spreadsheet
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Re: [QE-users] Installation Help

[Zack Gainsforth]

I run it on Kali under WSL because there is an easy path to having a full linux 
desktop with menus etc.  This is useful for running programs like xcrysden.  
(https://www.kali.org/docs/wsl/win-kex/ 
)  If a linux GUI desktop is not 
important to you and you are only interested in the command line, my guess is 
that Ubuntu will be easier to get a successful compile.

Cheers,

Zack

> On Nov 21, 2022, at 10:15 PM, Md. Jahid Hasan Sagor  
> wrote:
> 
> Hi, 
> 
> Actually, I am not familiar with Linux. Do you recommend to start it with 
> Ubuntu?
> 
> Best
> Jahid
> 
> 
> On Tue, Nov 22, 2022, 1:12 AM mailto:chama...@uom.lk>> 
> wrote:
> Dear Jahid,
> 
> Why don't you try to compile it inside a linux distribusion under the wsl?
> 
> Chamara
> 
> November 22, 2022 9:41 AM, "Md. Jahid Hasan Sagor"  >
>  wrote:
> Hi,
> I am trying to install version 7.1 in pc. I am facing a problem when I type 
> ./configure. It does not work.
> Noted: I am using WIndows 11 and Windows Powershell
> 
> Best
> Md Jahid Hasan
> 
> 
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[QE-users] IR calculation for oriented single crystal

[Zack Gainsforth]

Hi All,

I have set up a calculation using pw.x -> ph.x -> dynmat.x successfully and 
plotted myself an IR spectrum.  The match to the experimental spectrum is good. 
 However, this is an IR spectrum assuming a powder where the photons are 
exciting all the modes.  I’d now like to calculate the spectrum for a single 
crystal and specify the electric vector of the photon relative to the crystal.  
It should preferentially excite certain modes.

Is there a straightforward way to do this using ph.x + dynmat.x?  Or perhaps a 
way to read/print the dipole vectors for each mode so I can dot it with my 
photon’s e-field?  Or another way of thinking about this which is more 
efficient?  (Maybe I missed something in the documentation!)

Thanks,

Zack

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Re: [QE-users] local magnetic moment zero.

[Zack Gainsforth]

Hi,

I notice from the ld1.x input help file under config:

"Negative occupancies are used to flag unbound states;
they are not actually used.”

Though it is worth noting that PAW UFP files generated by such a configuration 
do have channels corresponding to those level/momenta.

Cheers,

Zack

> On Sep 5, 2020, at 12:30 AM, Poonam Kaushik  wrote:
> 
> Dear Stephen Zhang,
> >I don't think sulfur should have any d electrons
> yes, you are right. I also don't know the meaning of 3d-2 in S.
> I took these pseudopotentials from the QE website.
> Here is the occupations of both as mention in pseudopotentials 
> S: Valence configuration:
> nl pn  l   occ   
> 3S  1  0  2.00   
> 3P  2  1  4.00 
> Fe:
> nl pn  l   occ  
> 4S  1  0  1.00  
> 4S  1  0  0.00  
> 4P  2  1  0.00  
> 4P  2  1  0.00  
> 3D  3  2  7.00  
> 3D  3  2  0.00 
> 
> Thanks and regards,
> Poonam Sharma.
> 
> 
> 
> 
> -
> Poonam Sharma
> Research Scholar 
> Department of Physics
> Indian Institute of Technology Bombay
> Mumbai - 400076
> India.
> 
> 
> 
> On Sat, Sep 5, 2020 at 12:27 PM Poonam Kaushik  > wrote:
> Dear Stephen Zhang,
> Thank you so much for your response.
> If this is the case, then will it create a problem in the rest part of the 
> calculations?
> Should I need to change my pseudopotentials?
> Here is the configuration of pseudopotentials
>  Fe: LDA 3d7 4s1
> S:   [Ne] 3s2 3p4 3d-2
> 
> Thanks and regards,
> Poonam Sharma
> 
> 
> 
> 
> -
> Poonam Sharma
> Research Scholar 
> Department of Physics
> Indian Institute of Technology Bombay
> Mumbai - 400076
> India.
> 
> 
> 
> On Sat, Sep 5, 2020 at 10:56 AM Poonam Kaushik  > wrote:
> Dear Experts,
> I have one general question. During spin polarised calculations I am getting 
> zero local magnetic moments for all the atoms in LDA approximations, this is 
> something that I am not expecting. I am defining some initial magnetizations 
> also in the input file.
> Is this depends on the choice of pseudopotentials or something else.
> 
> Thanks and regards,
> Poonam Sharma
> 
> 
> 
> -
> Poonam Sharma
> Research Scholar 
> Department of Physics
> Indian Institute of Technology Bombay
> Mumbai - 400076
> India.
> 
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Re: [QE-users] Testing Al PBE pseudo

[Zack Gainsforth]

Hi all,

I figured this out and since the question seems to have popped up at least
twice before in the QE forum without a clear answer I thought it may be
worth mentioning the solution.

The answer seems to be that the configts card needs to use the valence
states only.  Namely, in my case:

configts(1)='1s2 2s2 2p6 3s2 3p1'

fails, while

configts(1)='3s2 3p1'

is fine.  Looking at
http://www.democritos.it/pipermail/pw_forum/2012-April/023896.html and
https://lists.quantum-espresso.org/pipermail/users/2012-October/025269.html,
one can see that the same error is occurring and in those cases the
configts card either misses some states, or includes too many.

Hopefully this saves someone a little time down the road.

Cheers,

Zack


On Fri, Aug 21, 2020 at 11:56 AM Zack Gainsforth  wrote:

> Hello all,
>
> I’m having difficulty with testing a pseudo.
>
> I started with the Al.pbe-n-kjpaw_psl.1.0.0.in file from the PS Library.
> I’m using QE installed through synaptic, which is ld1.x version 6.4.1.  I
> also tried this with 6.6 that I downloaded from the website and compiled.
>
> In both cases, I can run the .in file to generate the pseudo without
> complaint, and I see no obvious issues in the output.  When I plot the log
> derivatives they seem to match up very nicely.  When I try to run a test
> configuration though, it fails.
>
> It looked like it was complaining about the wavefunctions having nodes, so
> I tried adding rho0=0.01 and out of desperation 0.1!  To no avail.
>
> My question is whether I am doing something else incorrect in how I’m
> setting up the test?
>
> Thanks,
>
> Zack
>
> Here is the .in file I’m using to run the test (the original file from PS
> Library is exactly the same except I’ve added a &test section and changed
> iswitch=2 instead of 3):
>
>  &input
>title='Al',
>zed=13.,
>rel=1,
>config='[Ne] 3s2 3p1 3d-1',
>iswitch=2,
>dft='PBE'
>  /
>  &inputp
>lpaw=.true.,
>pseudotype=3,
>file_pseudopw='Al.pbe-n-kjpaw_psl.1.0.0.UPF',
>author='ADC',
>lloc=-1,
>rcloc=1.9,
>which_augfun='PSQ',
>rmatch_augfun_nc=.true.,
>nlcc=.true.,
>new_core_ps=.true.,
>rcore=1.8,
>tm=.true.
>  /
> 6
> 3S  1  0  2.00  0.00  1.70  1.90  0.0
> 3S  1  0  0.00  6.00  1.70  1.90  0.0
> 3P  2  1  1.00  0.00  1.70  2.00  0.0
> 3P  2  1  0.00  3.50  1.70  2.00  0.0
> 3D  3  2  0.00  0.10  1.70  1.90  0.0
> 3D  3  2  0.00  0.30  1.70  1.90  0.0
> &test
> file_pseudo='Al.pbe-n-kjpaw_psl.1.0.0.UPF'
> nconf=1
> configts(1)='1s2 2s2 2p6 3s2 3p1'
> /
>
> With both versions, the test runs the AE calculation OK, and then when it
> starts to run the pseudo:
>
> With 6.6 I see:
>
>Warning: n=1, l=0 expected 0 nodes, found *
>Setting wfc to zero for this iteration
>(This warning will only be printed once per wavefunction)
>
>Zero norm: self consistency problem; state:  1 (l=  0, j=0.0)
>
>Warning: n=2, l=0 expected 1 nodes, found *
>Setting wfc to zero for this iteration
>(This warning will only be printed once per wavefunction)
>
>Zero norm: self consistency problem; state:  2 (l=  0, j=0.0)
>
>Warning: n=2, l=1 expected 0 nodes, found *
>Setting wfc to zero for this iteration
>(This warning will only be printed once per wavefunction)
>
>Zero norm: self consistency problem; state:  3 (l=  1, j=0.0)
>
>Warning: n=3, l=0 expected 2 nodes, found *
>Setting wfc to zero for this iteration
>(This warning will only be printed once per wavefunction)
>
>Zero norm: self consistency problem; state:  4 (l=  0, j=0.0)
>
>Warning: n=3, l=1 expected 1 nodes, found *
>Setting wfc to zero for this iteration
>(This warning will only be printed once per wavefunction)
>
>Zero norm: self consistency problem; state:  5 (l=  1, j=0.0)
>Zero norm: self consistency problem; state:  1 (l=  0, j=0.0)
>Zero norm: self consistency problem; state:  2 (l=  0, j=0.0)
>Zero norm: self consistency problem; state:  3 (l=  1, j=0.0)
>Zero norm: self consistency problem; state:  4 (l=  0, j=0.0)
>Zero norm: self consistency problem; state:  5 (l=  1, j=0.0)
> [many lines removed]
>  Message from routine run_pseudo:
>  Warning: convergence not achieved
>Zero norm: self consistency problem; state:  1 (l=  0, j=0.0)
>Zero norm: self consistency problem; state:  2 (l=  0, j=0.0)
>Zero norm: self consiste

[QE-users] Testing Al PBE pseudo

[Zack Gainsforth]

Hello all,

I’m having difficulty with testing a pseudo.

I started with the Al.pbe-n-kjpaw_psl.1.0.0.in file from the PS Library.  I’m 
using QE installed through synaptic, which is ld1.x version 6.4.1.  I also 
tried this with 6.6 that I downloaded from the website and compiled.

In both cases, I can run the .in file to generate the pseudo without complaint, 
and I see no obvious issues in the output.  When I plot the log derivatives 
they seem to match up very nicely.  When I try to run a test configuration 
though, it fails.

It looked like it was complaining about the wavefunctions having nodes, so I 
tried adding rho0=0.01 and out of desperation 0.1!  To no avail.

My question is whether I am doing something else incorrect in how I’m setting 
up the test?  

Thanks,

Zack

Here is the .in file I’m using to run the test (the original file from PS 
Library is exactly the same except I’ve added a &test section and changed 
iswitch=2 instead of 3):

 &input
   title='Al',
   zed=13.,
   rel=1,
   config='[Ne] 3s2 3p1 3d-1',
   iswitch=2,
   dft='PBE'
 /
 &inputp
   lpaw=.true.,
   pseudotype=3,
   file_pseudopw='Al.pbe-n-kjpaw_psl.1.0.0.UPF',
   author='ADC',
   lloc=-1,
   rcloc=1.9,
   which_augfun='PSQ',
   rmatch_augfun_nc=.true.,
   nlcc=.true.,
   new_core_ps=.true.,
   rcore=1.8,
   tm=.true.
 /
6
3S  1  0  2.00  0.00  1.70  1.90  0.0
3S  1  0  0.00  6.00  1.70  1.90  0.0
3P  2  1  1.00  0.00  1.70  2.00  0.0
3P  2  1  0.00  3.50  1.70  2.00  0.0
3D  3  2  0.00  0.10  1.70  1.90  0.0
3D  3  2  0.00  0.30  1.70  1.90  0.0
&test
file_pseudo='Al.pbe-n-kjpaw_psl.1.0.0.UPF'
nconf=1
configts(1)='1s2 2s2 2p6 3s2 3p1'
/

With both versions, the test runs the AE calculation OK, and then when it 
starts to run the pseudo:

With 6.6 I see:

   Warning: n=1, l=0 expected 0 nodes, found *
   Setting wfc to zero for this iteration
   (This warning will only be printed once per wavefunction)

   Zero norm: self consistency problem; state:  1 (l=  0, j=0.0)

   Warning: n=2, l=0 expected 1 nodes, found *
   Setting wfc to zero for this iteration
   (This warning will only be printed once per wavefunction)

   Zero norm: self consistency problem; state:  2 (l=  0, j=0.0)

   Warning: n=2, l=1 expected 0 nodes, found *
   Setting wfc to zero for this iteration
   (This warning will only be printed once per wavefunction)

   Zero norm: self consistency problem; state:  3 (l=  1, j=0.0)

   Warning: n=3, l=0 expected 2 nodes, found *
   Setting wfc to zero for this iteration
   (This warning will only be printed once per wavefunction)

   Zero norm: self consistency problem; state:  4 (l=  0, j=0.0)

   Warning: n=3, l=1 expected 1 nodes, found *
   Setting wfc to zero for this iteration
   (This warning will only be printed once per wavefunction)

   Zero norm: self consistency problem; state:  5 (l=  1, j=0.0)
   Zero norm: self consistency problem; state:  1 (l=  0, j=0.0)
   Zero norm: self consistency problem; state:  2 (l=  0, j=0.0)
   Zero norm: self consistency problem; state:  3 (l=  1, j=0.0)
   Zero norm: self consistency problem; state:  4 (l=  0, j=0.0)
   Zero norm: self consistency problem; state:  5 (l=  1, j=0.0)
[many lines removed]
 Message from routine run_pseudo:
 Warning: convergence not achieved
   Zero norm: self consistency problem; state:  1 (l=  0, j=0.0)
   Zero norm: self consistency problem; state:  2 (l=  0, j=0.0)
   Zero norm: self consistency problem; state:  3 (l=  1, j=0.0)
   Zero norm: self consistency problem; state:  4 (l=  0, j=0.0)
   Zero norm: self consistency problem; state:  5 (l=  1, j=0.0)


With 6.4, 

   Warning: n=2, l=0 expected 1 nodes, found 0
   Setting wfc to zero for this iteration
   (This warning will only be printed once per wavefunction)

   Zero norm: self consistency problem; state:  2 (l=  0, j=0.0)

   Warning: n=3, l=0 expected 2 nodes, found 0
   Setting wfc to zero for this iteration
   (This warning will only be printed once per wavefunction)

   Zero norm: self consistency problem; state:  4 (l=  0, j=0.0)

   Warning: n=3, l=1 expected 1 nodes, found 0
   Setting wfc to zero for this iteration
   (This warning will only be printed once per wavefunction)

   Zero norm: self consistency problem; state:  5 (l=  1, j=0.0)

 %%
 Error in routine new_paw_hamiltonian (1):
 negative rho
 %%

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