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

[Manocha, Pratyush]

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 "" 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 "spin_component" keyword in the bands.x
> input file to extract the spin separated bands. So my question is: if I
> am using "lspinorb=.true." and "noncolin=.true.", is there a way to
> extract the spin-up and spin-down conduction and valence bands
> separately?
>
> Any help would be appreciated.
>
>
> Regards,
> Pratyush Manocha
> Graduate Student | M.S. Electrical & Computer Engineering
> School of Electrical and Computer Engineering
> Georgia Institute of Technology
> [cid:f2b1f8a4-9ef8-4579-9715-844bf6b1658b]
>
>


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[QE-users] Error: problems computing cholesky

[Chandrima Chakravarty via users]

Hi everyone,
I am very new as a QE user. I am wondering if anyone
can suggest me a direction to get rid of this error. I am running a scf
calculation with blyp and LSDA flag on. After few iteration steps the job
is stopping with this error.

Please show me some direction. I can send the input/output if needed.

%%
 Error in routine  cdiaghg (856):
  problems computing cholesky
 %%

 stopping ...

 %%
 Error in routine  cdiaghg (856):
  problems computing cholesky
 %%

 stopping ...

Best regards
Chandrima
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Re: [QE-users] Orthorhombic unit cell

[Paolo Giannozzi]

If you know the space group number N, set variable "space_group=N", then 
set "nat" to the number of wyckoff positions (not of atoms), then 
provide atomic positions as follows


ATOMIC_POSITIONS crystal_sg
X 4c y

where X=your atomic symbol, y=the value of parameter "y".

Paolo

On 09/03/2023 18:03, sally issa wrote:


You don't often get email from sally.is...@outlook.com. Learn why this 
is important 



Good morning all,

Is there anyone have worked with orthorhombic cell?
I want to define the unit cell for orthorhombic with 4 
atoms:(0,y,1/4),(0,-y, 3/4), (1/2, y+1/2, 1/4) and (-1/2, -y+1/2, 3/4).

With wyckoff position (4c).
I don’t have idea how define y.
Do you have suggestions ?

Thank you

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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] Orthorhombic unit cell

[Vahid Askarpour]

Usually, if there is x-ray data on single crystals, the wyckoff positions are 
given there. Alternatively, one can use evolutionary algorithms such as USPEX 
to generate stable structures but this could be time consuming.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, Canada

On Mar 9, 2023, at 1:03 PM, sally issa  wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Good morning all,

Is there anyone have worked with orthorhombic cell?
I want to define the unit cell for orthorhombic with 4 atoms:(0,y,1/4),(0,-y, 
3/4), (1/2, y+1/2, 1/4) and (-1/2, -y+1/2, 3/4).
With wyckoff position (4c).
I don’t have idea how define y.
Do you have suggestions ?

Thank you
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Re: [QE-users] How to Obtain External Parameters calculated through Self-Consistency calculations

[Fabrizio Ferrari Ruffino]

Hello,
I am not sure what you mean with self-consistent calculated parameters.
The ones you see in xc-infos.x are the default values of the libxc-functional 
external parameters, as you said. Maybe you mean that some of these parameters 
can be 'iteration dependent'? Can you point the equations in the paper you 
refer to?
However, in general, QE always assumes the default values for the Libxc 
external parameters (with a few exceptions for hybrid parameters starting from 
the next release). If you want to change these values, you need to work a bit 
on the code and enforce them by using the subroutine 'set_libxc_ext_param' in 
XClib.

Cheers,
Fabrizio

CNR-IOM

From: users  on behalf of Peter Lai 
via users 
Sent: Thursday, March 9, 2023 5:27 PM
To: users@lists.quantum-espresso.org 
Subject: [QE-users] How to Obtain External Parameters calculated through 
Self-Consistency calculations

Hello whomever this may concern,

I am currently using the TB09 and TPSS exchange-correlation for a 
self-consistency calculation for Strontium Hexaboride (SrB6). We use Libxc for 
these calculatiosn as well. An important value I would like to find is the 
self-consistent calculated parameters used for TB09 and TPSS. While there are 
default values given by xc_infos.x (as stated in the User Guide), they are not 
the external values calculated by the self-consistency calculations (scf). I 
would like to know if there is a way to find these external parameters given a 
self-consistency calculation. Thank you!

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Re: [QE-users] error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory

[Paolo Giannozzi]

1. It's not  a problem of QE but of your machine
2. If you have MKL you should use the DFTI FFT libraries

Paolo

On 3/8/23 23:56, Abdul Muhaymin via users wrote:

Dear users,

I am trying to run pw.x in a cluster (centos) that requires loading 
three modules: intel, impi, and quantum-espresso. Now, I am getting an 
error saying: `pw.x: error while loading shared libraries: 
libfftw3.so.3: cannot open shared object file: No such file or 
directory`. According to the instruction I find in QE troubleshooting 
guide, I added the `export LD_LIBRARY_PATH=/lib64:"$LD_LIBRARY_PATH"` 
line in my script because libfftw3.so.3 exists in `/lib64/`. However, it 
still gives the same error.


So, I ran a `ldd pw.x` command to check what happened, and I saw that:

... (truncated )

libmkl_scalapack_ilp64.so => 
/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64_lin/libmkl_scalapack_ilp64.so (0x7fe15c6ea000)


libfftw3.so.3 => Not found

... (truncated)

That means only libfftw3.so.3 is not linked. When I checked the value of 
$LD_LIBRARY_PATH, it successfully added the `/lib64` part but still I 
get the same error. What could be the reason for this error? Do I need 
to recompile QE? The version of QE running is 6.4.1. Thanks.


Sincerely,

Abdul Muhaymin

Undergraduate – Bilkent University


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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] Fwd: Hydrogen atom pseudopotential files with q=1.5e and q=0.75e (PBE, USPP)

[Lorenzo Paulatto]

Again, to be checked, but I believe that just chaning Zval you can also use it 
as a Cooulomb pseudo for heavier atoms, e.g. the second row from Li onwards, 
that can be useful to do all-electron tests with QE (mind you, for second row 
you easily need 1000 Ry of ecutrho).

Any comments on this actually much appreciated,


Already for H you need several hundred Ry for a converged calculation 
(around 400-600 if I remember correctly), the reason is the divergence 
of 1/r which is an absolute pain to reproduce in plane waves.






nicola


On 08/03/2023 09:13, Paolo Giannozzi wrote:

 Forwarded Message 
Subject: Hydrogen atom pseudopotential files with q=1.5e and q=0.75e (PBE, 
USPP)
Date: Tue, 7 Mar 2023 19:58:51 +0300
From: gökhan haseki 
To: users-ow...@lists.quantum-espresso.org


Dear Quantum Espresso users, I would like to passivate the surface of a III-V 
nanowire with pseudo-Hydrogen atoms. So I need Hydrogen atom pseudopotential 
files with q=1.5e and q=0.75e (PBE, USPP). I've searched many pessupotential 
libraries but haven't been able to find it. your help and suggestions will 
guide me in this regard. Kind regards..
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[QE-users] [SPAM] Re: Pw2wan unexpectedly exceeding memory limit

[Stefan Velja]

Dear QE and W90 users,


As I am new to this mailing list, I want to make sure my previous e-mail didn't 
get lost somewhere and reached you successfully. In either case, you can find 
it below.


Kind regards,

Stefan Velja
PhD Student,
Electronic Structure Theory group (Prof. Dr. Caterina Cocchi)
Carl von Ossietzky University of Oldenburg




From: Stefan Velja
Sent: Saturday, March 4, 2023 8:33 PM
To: users@lists.quantum-espresso.org
Subject: Pw2wan unexpectedly exceeding memory limit


Dear QE and W90 users,


I've used QE for several months running multiple calculations on very large 
MoSe2 supercells (including 200+ atoms) without trouble. Recently, I have been 
trying to run Wannier90 on such a configuration with 96 atoms. I ran the NSCF 
calculation easily on a "standard96" HLRN Göttingen mode (362 GB of usable 
memory) and tried to run a corresponding pw2wan calculation, resulting in the 
following error:


 Case  : isolated

  AMN: iknum =1

===
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 0 PID 3970 RUNNING AT gsn2002
=   KILLED BY SIGNAL: 9 (Killed)
===


This seems to be a "memory limit exceeded" error message. As seen above, I used 
only 1 k-point to simplify the calculation (after attempts with more k-points 
failed) and used the "huge96" partition (1522 GB of usable memory). The same 
calculation with a pristine MoSe2 cell (3 atoms) ran easily, even with SOC. 
What steps could I take to solve this?


Please find the following excerpts from my NSCF, W90 and pw2wan input files and 
let me know if you need any additional data. I excluded some of the flags for 
brevity.


nscf.in:


calculation = 'nscf'
pseudo_dir = '/home/bepsvelj/pseudopotentials'
prefix = 'mose2'
outdir = 'tmp'
disk_io = 'low'
verbosity = 'high'
/


nbnd = 1088
/// Other sistem properties listed here
/


conv_thr = 0.01
/

ATOMIC_SPECIES
Se 79.  Se_ONCV_PBE-1.2.upf
Mo 96.  Mo_ONCV_PBE-1.2.upf

ATOMIC_POSITIONS (angstrom)
/// Atom positions listed here

K_POINTS crystal
1
  0.  0.  0.  5.00e-02


wannier90.in:
num_bands = 1088
num_wann = 1088
num_iter = 100
num_print_cycles = 10

iprint = 3

auto_projections = .true.

bands_plot = true

begin kpoint_path
G 0.0 0.0 0.0 G 0.0 0.0 0.0
end kpoint_path

mp_grid = 1 1 1
begin kpoints
  0.  0.  0.
end kpoints

begin atoms_cart
/// Atom positions listed here
end atoms_cart

begin unit_cell_cart
/// Cell properties listed here
end unit_cell_cart


pw2wan.in:

  outdir = 'tmp'
  prefix = 'mose2'
  seedname = 'w90'
  write_amn = .true.
  write_mmn = .true.
  scdm_proj = .true.
/

Thank you very much in advance!

Kind regards,
Stefan Velja
PhD Student,
Electronic Structure Theory group (Prof. Dr. Caterina Cocchi)
Carl von Ossietzky University of Oldenburg
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Re: [QE-users] Are my supercell 'vc-relax' calculations seem to run correctly?

[Paolo Giannozzi]

It's a rather large calculation:  200k plane waves, 20 k-points, 42 Gb 
total memory. If you have less than 42 Gb physical RAM in your machine, 
the calculation can take forever


Paolo

On 3/8/23 13:01, NAIMI SALMA wrote:
I want to dope my material. So I created a 2*2*2 supercell then I  used 
a vc-relax to optimize the supercell. It`s been more than one day and 
the calculations still didn't complete. Is that normal?
  I attached my input and output file (The calculations are still 
running so I coppied what's in the output file till now)


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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] How to Obtain External Parameters calculated through Self-Consistency calculations

[Peter Lai via users]

Hello whomever this may concern,

I am currently using the TB09 and TPSS exchange-correlation for a
self-consistency calculation for Strontium Hexaboride (SrB6). We use Libxc
for these calculatiosn as well. An important value I would like to find is
the self-consistent calculated parameters used for TB09 and TPSS. While
there are default values given by xc_infos.x (as stated in the User Guide),
they are not the external values calculated by the self-consistency
calculations (scf). I would like to know if there is a way to find these
external parameters given a self-consistency calculation. Thank you!
___
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[QE-users] Orthorhombic unit cell

[sally issa]

Good morning all,

Is there anyone have worked with orthorhombic cell?
I want to define the unit cell for orthorhombic with 4 atoms:(0,y,1/4),(0,-y, 
3/4), (1/2, y+1/2, 1/4) and (-1/2, -y+1/2, 3/4).
With wyckoff position (4c).
I don’t have idea how define y.
Do you have suggestions ?

Thank you
___
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