Re: [QE-users] Requesting Help With Spin Orbit Coupling Spin-Separated Bands Extraction

[Luiz Gustavo Davanse da Silveira via users]

Dear Pratyush Manocha,

Now I'm the one who has to apologize about a delayed response.

> Thank you for informing me about the "lsigma" keyword. While it doesn't
> solve my problem of segregating spin-up bands from spin-down ones, it
> gives me the expectation values of the total angular momentum along the
> x, y, and z axes, right?

It gives you the expectation values of the spin operator.

> I tried extracting the data for GaAs, and I noticed from the results that
> often, the expectation values are values other than 0.5, 0, and -0.5;
> does this mean that, at these points, the band has a mix of both spin-up
> and spin-down electrons?

Well, you might find sources that describe it like that, but, as I see it,
in noncollinear calculations each electronic state can have its own spin
quantization axis. Therefore, global spin-up and spin-down states may not
be a good description. Rather, depending on the complexity of your system,
at each k-point of a given band spins may be align in a particular
direction. You could, in principle, determine which direction this is and
define locally what is spin up and spin down, I don't know if it's worth
it, though. Simply put, "lsigma = 1,2,3" gives you the three orthogonal
components of the spin vector. If you take the modulus, the result should
be 0.5 (or close to it).

> Another question I had is: when you say that I can color the bands
> according to the spin values like a fatband plot, do you mean that each
> band would individually be coloured from "colour a" to "colour b" based
> on the spin values at the different k points along the chosen "k-path?"

Exactly. This form of showing the data might not be useful if bands are
degenerate. But if the bands are splitted and spin-polarized you will end
up with a graph showing something similar to spin-up and spin-down bands.

Best regards,

Luiz Gustavo Silveira
Assistant professor, Department of Physics - Federal University of Paraná
Curitiba - Brazil


Em Qui, Março 9, 2023 11:47 pm, Manocha, Pratyush escreveu:
> Dear Professor Luiz,
>
>
> I apologize for my delayed response; I had exams to appear for.
>
>
> Thank you for informing me about the "lsigma" keyword. While it doesn't
> solve my problem of segregating spin-up bands from spin-down ones, it
> gives me the expectation values of the total angular momentum along the
> x, y, and z axes, right?
>
> I tried extracting the data for GaAs, and I noticed from the results that
> often, the expectation values are values other than 0.5, 0, and -0.5;
> does this mean that, at these points, the band has a mix of both spin-up
> and spin-down electrons?
>
> Another question I had is: when you say that I can color the bands
> according to the spin values like a fatband plot, do you mean that each
> band would individually be coloured from "colour a" to "colour b" based
> on the spin values at the different k points along the chosen "k-path?"
>
> Thank you very much for helping me with this!
>
>
> Regards,
> Pratyush Manocha
> Graduate Student | M.S. Electrical & Computer Engineering
> School of Electrical and Computer Engineering
> Georgia Institute of Technology
> 
> From: Luiz Gustavo Davanse da Silveira 
> Sent: Thursday, February 16, 2023 14:03
> To: Manocha, Pratyush 
> Cc: users@lists.quantum-espresso.org 
> Subject: Re: [QE-users] Requesting Help With Spin Orbit Coupling
> Spin-Separated Bands Extraction
>
>
> Dear Pratyush Manocha,
>
>
> I believe the spin_component variable doesn't work with noncollinear
> calculations. You can however use the lsigma variable in bands.x input to
> get the spin components at each k-point for every band. Then, for
> instance, you can use this information to color the band plot according
> to spin values (like a fatbands plot).
>
> Best Regards,
>
>
> Luiz Gustavo Silveira
> Assistant professor, Department of Physics - Federal University of Paraná
> Curitiba - Brazil
>
>
> Em Seg, Dezembro 19, 2022 7:22 pm, Manocha, Pratyush escreveu:
>
>> Dear All,
>>
>>
>>
>> I am using QE-7.1 and want to plot the spin-orbit coupled bands for
>> Silicon and later on, GaN. I ran a few simulations for Silicon (with a
>> fully relativistic pseudopotential obtained from PSLibrary 1.0.0) by
>> turning on the "lspinorb" and "noncolin" keywords and specifying a
>> non-zero "starting_magnetization" in the "&system" namecard.  The
>> simulation runs smoothly, however, when I try to extract the bands for
>> just spin-down electrons using "spin_component=2" in the input file
>> given to the bands.x code, it returns the following error: Error in
>> routine punch_bands (1):  incorrect spin_component???.
>>
>> I went through the archive and also tried simulating with various
>> different keyword combinations using "nspin" and "lspinorb", and I found
>>  that "lspinorb" requires non-colinear spin vectors whereas "nspin=2"
>> requires colinear spins, therefore, they would not work simultaneously.
>>  As a result, I can not use the "sp

Re: [QE-users] Best way to extract eigenvectors from pwscf output?

[Manocha, Pratyush]

Dear Prof. Paolo,

Thank you for your prompt response.

I want to extract the Hamiltonian and eigenvectors (not necessarily Kohn-Sham, 
whatever eigenvectors QE solves for; I am aware that QE solves the Kohn-Sham 
equation, so I think it outputs the Kohn-Sham eigenvectors, please correct me 
if I am wrong).

The reasons for extracting the eigenvectors and the Hamiltonian are multiple. 
Primarily to calculate a couple of matrix elements for my research project. But 
I want to extract this data in a human-readable format so that I can get a 
better understanding of the QE DFT package as a whole.

Would the simple_output code provided by you in the post I linked earlier be 
the best way to go about doing this?

Regards,
Pratyush Manocha
Graduate Student | M.S. Electrical & Computer Engineering
School of Electrical and Computer Engineering
Georgia Institute of Technology
[cid:25bb8cf8-c47e-4cd7-b1d6-4838034fb6c7]

From: Paolo Giannozzi 
Sent: Monday, March 20, 2023 11:52
To: Quantum ESPRESSO users Forum 
Cc: Manocha, Pratyush 
Subject: Re: [QE-users] Best way to extract eigenvectors from pwscf output?

On 3/20/23 16:32, Manocha, Pratyush wrote:

>  I also saw a code posted by Prof. Paolo Giannozzi, which is not
> supposed to be used for anything greater than simple crystals

the first code (simple_output) can be used for large systems as well. It
will produce large files, though. The second code (simple_test) is
provided just as a test: it fills and diagonalizes a matrix containing
the hamiltonian in plane waves. This is possible only for small systems.
QE never fills the hamiltonian matrix.

> What would be the most robust way of extracting the
> Hamiltonian and eigenvectors of the Kohn-Sham equation in a
> human-readable format for such a large input cell size?

Once you have Kohn-Sham human-readable eigenvectors, what do you plan to
do: (human-)read all of them?

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
___
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

Re: [QE-users] Best way to extract eigenvectors from pwscf output?

[Paolo Giannozzi]

On 3/20/23 16:32, Manocha, Pratyush wrote:

 I also saw a code posted by Prof. Paolo Giannozzi, which is not 
supposed to be used for anything greater than simple crystals 


the first code (simple_output) can be used for large systems as well. It 
will produce large files, though. The second code (simple_test) is 
provided just as a test: it fills and diagonalizes a matrix containing 
the hamiltonian in plane waves. This is possible only for small systems. 
QE never fills the hamiltonian matrix.


What would be the most robust way of extracting the 
Hamiltonian and eigenvectors of the Kohn-Sham equation in a 
human-readable format for such a large input cell size?


Once you have Kohn-Sham human-readable eigenvectors, what do you plan to 
do: (human-)read all of them?


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
___
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

[QE-users] Best way to extract eigenvectors from pwscf output?

[Manocha, Pratyush]

Dear all,

What is the best way to extract the eigenvectors from the output of pw.x?

I searched the forum for a solution, but most of them rely on the qexml.f90, 
which is nowhere to be found on my QE installation (I'm using qe-7.1). I also 
saw a code posted by Prof. Paolo Giannozzi, which is not supposed to be used 
for anything greater than simple crystals (linked 
here).

I am simulating 10x10x10 (or larger) supercells of GaN to investigate doping in 
them. What would be the most robust way of extracting the Hamiltonian and 
eigenvectors of the Kohn-Sham equation in a human-readable format for such a 
large input cell size?

I apologize if the question is too basic, I am not familiar with Fortran yet, 
so understanding the codes has become a challenge in itself. Any help would be 
greatly appreciated.

Regards,
Pratyush Manocha
Graduate Student | M.S. Electrical & Computer Engineering
School of Electrical and Computer Engineering
Georgia Institute of Technology
[cid:e17f39ac-3312-4490-8f52-60f3597fa010]
___
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

Re: [QE-users] Compilation Issue

[Paolo Giannozzi]

It looks like you do not have the mpi libraries installed (or they are 
not compatible with your linker or compiler)


Paolo

On 3/20/23 10:06, Vinky Chow via users wrote:

Hi Dr Lorenzo,

I was following the instructions here 
.

The error appears during the make all command.
Thank you.

Regards,
Vinky


On Mon, 20 Mar 2023 at 16:41, Lorenzo Paulatto > wrote:





/usr/bin/ld: cannot find -lmpi_usempif08


Hello Vinky,

normally you do not link fortran code with ld, but with the fortran
compiler itself, which should be the default unless you tamper with
the ./configure parameters. If you want more help, please provide
more detail about what you are doing (i.e.e every command you type
to arrive at the error and teh entire configure output)



make[2]: Leaving directory
'/home/student/qe-7.1-ReleasePack/qe-7.1/PW/src'


At your institute, students do not have the right to a name?

cheers




make[1]: *** [Makefile:9: pw] Error 1
make[1]: Leaving directory
'/home/student/qe-7.1-ReleasePack/qe-7.1/PW'
make: *** [Makefile:71: pw] Error 1

Could anyone help solving this?
Thank you!

Regards,
Vinky

___
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 listus...@lists.quantum-espresso.org  

https://lists.quantum-espresso.org/mailman/listinfo/users  

-- 
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
 ___
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

Re: [QE-users] Compilation Issue

[Vinky Chow via users]

Hi Dr Lorenzo,

I was following the instructions here
.
The error appears during the make all command.
Thank you.

Regards,
Vinky


On Mon, 20 Mar 2023 at 16:41, Lorenzo Paulatto 
wrote:

>
>
> /usr/bin/ld: cannot find -lmpi_usempif08
>
> Hello Vinky,
>
> normally you do not link fortran code with ld, but with the fortran
> compiler itself, which should be the default unless you tamper with the
> ./configure parameters. If you want more help, please provide more detail
> about what you are doing (i.e.e every command you type to arrive at the
> error and teh entire configure output)
>
> make[2]: Leaving directory '/home/student/qe-7.1-ReleasePack/qe-7.1/PW/src'
>
> At your institute, students do not have the right to a name?
>
> cheers
>
>
>
> make[1]: *** [Makefile:9: pw] Error 1
> make[1]: Leaving directory '/home/student/qe-7.1-ReleasePack/qe-7.1/PW'
> make: *** [Makefile:71: pw] Error 1
>
> Could anyone help solving this?
> Thank you!
>
> Regards,
> Vinky
>
> ___
> 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.orghttps://lists.quantum-espresso.org/mailman/listinfo/users
>
> --
> 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
> ___
> 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
___
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

Re: [QE-users] Compilation Issue

[Lorenzo Paulatto]

/usr/bin/ld: cannot find -lmpi_usempif08


Hello Vinky,

normally you do not link fortran code with ld, but with the fortran 
compiler itself, which should be the default unless you tamper with the 
./configure parameters. If you want more help, please provide more 
detail about what you are doing (i.e.e every command you type to arrive 
at the error and teh entire configure output)



make[2]: Leaving directory 
'/home/student/qe-7.1-ReleasePack/qe-7.1/PW/src'


At your institute, students do not have the right to a name?

cheers




make[1]: *** [Makefile:9: pw] Error 1
make[1]: Leaving directory '/home/student/qe-7.1-ReleasePack/qe-7.1/PW'
make: *** [Makefile:71: pw] Error 1

Could anyone help solving this?
Thank you!

Regards,
Vinky

___
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 listus...@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

--
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___
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

[QE-users] Compilation Issue

[Vinky Chow via users]

Hello,

I am facing some errors during compilation (QE version: 7.1 O.S.: Ubuntu
Linux 20.04).

/usr/bin/ld: cannot find -lmpi_usempif08
/usr/bin/ld: cannot find -lmpi_usempi_ignore_tkr
/usr/bin/ld: cannot find -lmpi_mpifh
/usr/bin/ld: cannot find -lmpi
/usr/bin/ld: cannot find -lopen-rte
/usr/bin/ld: cannot find -lopen-pal
/usr/bin/ld: cannot find -lhwloc
/usr/bin/ld: cannot find -levent
/usr/bin/ld: cannot find -levent_pthreads
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:314: pw.x] Error 1
make[2]: Leaving directory '/home/student/qe-7.1-ReleasePack/qe-7.1/PW/src'
make[1]: *** [Makefile:9: pw] Error 1
make[1]: Leaving directory '/home/student/qe-7.1-ReleasePack/qe-7.1/PW'
make: *** [Makefile:71: pw] Error 1

Could anyone help solving this?
Thank you!

Regards,
Vinky
___
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