Re: [Wien] Potential bug in WIEN2k 21.1 - read_vorb_files

[Peter Blaha]

Dear Joseph Prentice,

Thank you very much for your report and the fix.

Yes, I believe your analysis and the fix is absolutely correct.

Best regards
Peter Blaha

Am 31.03.2022 um 19:29 schrieb Joseph Prentice:

Dear all,

I have been running calculations on iron selenide using WIEN2k 21.1 on 
my local HPC facility, including an external magnetic field. However, 
when I run these calculations using the command:


runsp_lapw -so -orbext -cc 0.1 -ec 0.1

‘runsp_lapw’ crashes when it tries to execute ‘read_vorb_files’. The 
error message is that ‘Variable name must contain alphanumeric characters’.


After some digging, I found where I believe the error was originating. 
In ‘x_lapw’, when the variable ‘exe’ is being set for the 
‘read_vorb_files’ command (around l. 1055), the variable ‘def’ is reset 
incorrectly, using the line:


set $def

This has the effect of trying to set a variable whose name is the 
current value of ‘def’, which is presumably not the intended action, 
particularly as the current value of ‘def’ contains the character ‘.’, 
which is not allowed in variable names.


By changing the above line to

set def

which is in-line with the rest of the script, I have found that the 
calculation now proceeds without crashing.


I hope that this is helpful – please let me know if I have something 
incorrect, or if the above code actually works as intended. I am using 
tcsh v6.20, if that affects how this piece of code runs.


Best wishes,

Joseph Prentice

Cooksey Early Career Teaching and Research Fellow

St Edmund Hall and Department of Materials

University of Oxford


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[Wien] Potential bug in WIEN2k 21.1 - read_vorb_files

[Joseph Prentice]

Dear all,

I have been running calculations on iron selenide using WIEN2k 21.1 on my local 
HPC facility, including an external magnetic field. However, when I run these 
calculations using the command:

runsp_lapw -so -orbext -cc 0.1 -ec 0.1

‘runsp_lapw’ crashes when it tries to execute ‘read_vorb_files’. The error 
message is that ‘Variable name must contain alphanumeric characters’.

After some digging, I found where I believe the error was originating. In 
‘x_lapw’, when the variable ‘exe’ is being set for the ‘read_vorb_files’ 
command (around l. 1055), the variable ‘def’ is reset incorrectly, using the 
line:

set $def

This has the effect of trying to set a variable whose name is the current value 
of ‘def’, which is presumably not the intended action, particularly as the 
current value of ‘def’ contains the character ‘.’, which is not allowed in 
variable names.

By changing the above line to

set def

which is in-line with the rest of the script, I have found that the calculation 
now proceeds without crashing.

I hope that this is helpful – please let me know if I have something incorrect, 
or if the above code actually works as intended. I am using tcsh v6.20, if that 
affects how this piece of code runs.

Best wishes,
Joseph Prentice

Cooksey Early Career Teaching and Research Fellow
St Edmund Hall and Department of Materials
University of Oxford


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Re: [Wien] Potential bug with initso_lapw in version 18.2

[Peter Blaha]

After some additional info I can verify the problem.

It happens in cases WITH inversion symmetry, when you run init_so 
several times and the number of equivalent atoms has been changed by a 
previous init_so.


The problem is in the init_so script, which does not update the original 
case.in2 file, because there is a previous mv instead of a cp command.


You can find in init_so_lapw (wien2k_19) or in initso_lapw (version 18)

...
 if(! -e $file.in2c_so &&  -e $file.in2_so && ! -z $file.in2c_so 
&& ! -z $file.in2_so ) mv $file.in2_so $file.in2c
 if(! -e $file.in2c_so &&  -e $file.in2_so && ! -z $file.in2c_so 
&& ! -z $file.in2_so ) mv $file.in2_so $file.in2


In the first line above, the "mv" should be a "cp" (copy instead of 
move), otherwise case.in2 cannot be updated anymore in the next line and 
the next init_so produces a wrong in2c file.


Regards and thanks for the report


Am 03.07.2019 um 04:51 schrieb Huseyin Ucar:

Dear Developers,

I was having similar problems to what is described in the mail below:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07758.html

Basically, when I do initso_lapw, and wanted to use the new structure 
for SO calculations, the case.in2c file was causing the lapw2 to crash. 
I did realize that the reason is because the case.in2c file is not 
taking the GMAX value from case.in2 at all. I had to manually enter it 
myself into case.in2c after initso_lapw is done. I want to emphasize it 
again: case.in2c does not have the GMAX at the last row only when you 
accept the new structure for SO calculations.


The question I would have at this point is: Will I need to manually fix 
the case.in2c from this point on, or is there a patch I can use to fix 
this issue once and for all. I also want to add that this particular 
problem does not occur in the older versions.


Best,

Ucar


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Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
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Re: [Wien] Potential bug with initso_lapw in version 18.2

[Peter Blaha]

Hi,

I cannot verify this problem. In my tests I always get a proper and 
complete in2c file.


Can you send me privately your struct file and describe your 
magnetization direction, where the problem occurs.


Am 03.07.2019 um 04:51 schrieb Huseyin Ucar:

Dear Developers,

I was having similar problems to what is described in the mail below:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07758.html

Basically, when I do initso_lapw, and wanted to use the new structure 
for SO calculations, the case.in2c file was causing the lapw2 to crash. 
I did realize that the reason is because the case.in2c file is not 
taking the GMAX value from case.in2 at all. I had to manually enter it 
myself into case.in2c after initso_lapw is done. I want to emphasize it 
again: case.in2c does not have the GMAX at the last row only when you 
accept the new structure for SO calculations.


The question I would have at this point is: Will I need to manually fix 
the case.in2c from this point on, or is there a patch I can use to fix 
this issue once and for all. I also want to add that this particular 
problem does not occur in the older versions.


Best,

Ucar


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Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
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[Wien] Potential bug with initso_lapw in version 18.2

[Huseyin Ucar]

Dear Developers,

I was having similar problems to what is described in the mail below:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07758.html

Basically, when I do initso_lapw, and wanted to use the new structure for SO 
calculations, the case.in2c file was causing the lapw2 to crash. I did realize 
that the reason is because the case.in2c file is not taking the GMAX value from 
case.in2 at all. I had to manually enter it myself into case.in2c after 
initso_lapw is done. I want to emphasize it again: case.in2c does not have the 
GMAX at the last row only when you accept the new structure for SO calculations.

The question I would have at this point is: Will I need to manually fix the 
case.in2c from this point on, or is there a patch I can use to fix this issue 
once and for all. I also want to add that this particular problem does not 
occur in the older versions.

Best,
Ucar
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Re: [Wien] potential

[Yundi Quan]

I'm doing spin polarized calculation. So  I should delete case.clmcorup and
and case.clmcordn and case.clmsum_old. Does it seem right?

On Fri, Sep 2, 2016 at 6:02 AM, Peter Blaha 
wrote:

> Yes. You can "miss use" mixer for that.
>
> Make sure there is no case.clmcore nor an clmsum_old file, just a
> case.clmval.   x mixer will just convert the clmval file into clmsum.
>
> On 09/02/2016 02:58 PM, Yundi Quan wrote:
>
>> Is there a way to automatically convert case.clmval into case.clmsum
>> format? case.clmsum has slightly different Y00 term from case.clmval.
>>
>>
>>
>>
>> On Fri, Sep 2, 2016 at 1:26 AM, Víctor Luaña Cabal
>> >
>> wrote:
>>
>> On Fri, Sep 02, 2016 at 12:21:24AM -0700, Yundi Quan wrote:
>> > The lowest value is -0.35234088194673E-02. I'm using modified
>> Beck-John.
>>
>> I should not consider that numerical inaccuracy. Something else is at
>> work. As Peter Blaha, says converging RMT's and kpoints can be quite
>> important. If you can't solve the problem you may plot the density on
>> an important plane to guess where the problem appears.
>>
>> Best,
>>  Víctor Luaña
>> ___
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> --
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> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
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Re: [Wien] potential

[Peter Blaha]

Yes. You can "miss use" mixer for that.

Make sure there is no case.clmcore nor an clmsum_old file, just a 
case.clmval.   x mixer will just convert the clmval file into clmsum.


On 09/02/2016 02:58 PM, Yundi Quan wrote:

Is there a way to automatically convert case.clmval into case.clmsum
format? case.clmsum has slightly different Y00 term from case.clmval.




On Fri, Sep 2, 2016 at 1:26 AM, Víctor Luaña Cabal
>
wrote:

On Fri, Sep 02, 2016 at 12:21:24AM -0700, Yundi Quan wrote:
> The lowest value is -0.35234088194673E-02. I'm using modified Beck-John.

I should not consider that numerical inaccuracy. Something else is at
work. As Peter Blaha, says converging RMT's and kpoints can be quite
important. If you can't solve the problem you may plot the density on
an important plane to guess where the problem appears.

Best,
 Víctor Luaña
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Re: [Wien] potential

[Yundi Quan]

Is there a way to automatically convert case.clmval into case.clmsum
format? case.clmsum has slightly different Y00 term from case.clmval.




On Fri, Sep 2, 2016 at 1:26 AM, Víctor Luaña Cabal <
vic...@fluor.quimica.uniovi.es> wrote:

> On Fri, Sep 02, 2016 at 12:21:24AM -0700, Yundi Quan wrote:
> > The lowest value is -0.35234088194673E-02. I'm using modified Beck-John.
>
> I should not consider that numerical inaccuracy. Something else is at
> work. As Peter Blaha, says converging RMT's and kpoints can be quite
> important. If you can't solve the problem you may plot the density on
> an important plane to guess where the problem appears.
>
> Best,
>  Víctor Luaña
> ___
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> SEARCH the MAILING-LIST at:  http://www.mail-archive.com/
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Re: [Wien] potential

[Peter Blaha]

Vcxoul can have pos and neg. values.

Rho should be positive everywhere. However, when you plot the density of 
only one state, rho can get zero easily in large parts of the unit cell 
and thus by numerical inaccuracies even small !!! negative densities may 
pop up, in particular if you are not well converged (RKMAX) or have a 
density with sharp nodes, ...


On 09/02/2016 09:26 AM, Yundi Quan wrote:

I wanted to plot only the charge density of a particular state. So I
changed the k-mesh to only one point and then used
x lapw1 -up -c
x lapw1 -dn -c
x lapw2 -vresp -c -all emin emax
The resulting case.clmval is used as the input charge density. I know
that the Y00 term in case.clmval is different from Y00 term in
case.clmsum. Could this be the problem?






On Fri, Sep 2, 2016 at 12:21 AM, Yundi Quan > wrote:

The lowest value is -0.35234088194673E-02. I'm using modified Beck-John.


Yundi

On Thu, Sep 1, 2016 at 11:30 PM, Víctor Luaña Cabal
> wrote:

On Thu, Sep 01, 2016 at 11:15:32PM -0700, Yundi Quan wrote:
> What's the sign convention used in the output files of critic2? I 
notice
> that there are positive and negative values in both vcoul.cube and
> rho.cube. Maybe it is OK to have both positive and negative 
vcoul.cube. But
> what does it mean to have both positive and negative date in 
rho.cube? Or
> is it just numerical inaccuracy?

It should be, as rho >= 0. I should not worry if it is *quite*
close to xero.
Otherwise, please, tell me the lowest value you find.

Best,
 Víctor Luaña
--
 .  ."Las mujeres suelen ser menos fanáticas que los
hombres,
/ `' \más prácticas y más responsables."
   /(o)(o)\   --John Carlin (ElPaís, 2016-07-03)
  /`. \/ .'\  Women USE to be less fanatical than men, more
practical
 /   '`'`   \ and more responsible."
 |  \'`'`/  |
 |  |'`'`|  | "let's hope our world learns from UK what
political lies
  \/`'`'`'\/   and false patrioterism can comdemn a generation
to suffer"
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:  >  !
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Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
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Re: [Wien] potential

[Yundi Quan]

I wanted to plot only the charge density of a particular state. So I
changed the k-mesh to only one point and then used
x lapw1 -up -c
x lapw1 -dn -c
x lapw2 -vresp -c -all emin emax
The resulting case.clmval is used as the input charge density. I know that
the Y00 term in case.clmval is different from Y00 term in case.clmsum.
Could this be the problem?






On Fri, Sep 2, 2016 at 12:21 AM, Yundi Quan  wrote:

> The lowest value is -0.35234088194673E-02. I'm using modified Beck-John.
>
>
> Yundi
>
> On Thu, Sep 1, 2016 at 11:30 PM, Víctor Luaña Cabal <
> vic...@fluor.quimica.uniovi.es> wrote:
>
>> On Thu, Sep 01, 2016 at 11:15:32PM -0700, Yundi Quan wrote:
>> > What's the sign convention used in the output files of critic2? I notice
>> > that there are positive and negative values in both vcoul.cube and
>> > rho.cube. Maybe it is OK to have both positive and negative vcoul.cube.
>> But
>> > what does it mean to have both positive and negative date in rho.cube?
>> Or
>> > is it just numerical inaccuracy?
>>
>> It should be, as rho >= 0. I should not worry if it is *quite* close to
>> xero.
>> Otherwise, please, tell me the lowest value you find.
>>
>> Best,
>>  Víctor Luaña
>> --
>>  .  ."Las mujeres suelen ser menos fanáticas que los hombres,
>> / `' \más prácticas y más responsables."
>>/(o)(o)\   --John Carlin (ElPaís, 2016-07-03)
>>   /`. \/ .'\  Women USE to be less fanatical than men, more practical
>>  /   '`'`   \ and more responsible."
>>  |  \'`'`/  |
>>  |  |'`'`|  | "let's hope our world learns from UK what political lies
>>   \/`'`'`'\/   and false patrioterism can comdemn a generation to suffer"
>> ===(((==)))==+=
>> ! Dr.Víctor Luaña, in silico chemist & prof. !
>> ! Departamento de Química Física y Analítica !
>> ! Universidad de Oviedo, 33006-Oviedo, Spain !
>> ! e-mail:    !
>> ! phone: +34-985-103491  fax: +34-985-103125 !
>> ++
>>  GroupPage: 
>>  Articles:  
>>  git-hub:   
>>
>> ___
>> Wien mailing list
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>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>> SEARCH the MAILING-LIST at:  http://www.mail-archive.com/wi
>> e...@zeus.theochem.tuwien.ac.at/index.html
>>
>
>
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Re: [Wien] potential

[Yundi Quan]

The lowest value is -0.35234088194673E-02. I'm using modified Beck-John.


Yundi

On Thu, Sep 1, 2016 at 11:30 PM, Víctor Luaña Cabal <
vic...@fluor.quimica.uniovi.es> wrote:

> On Thu, Sep 01, 2016 at 11:15:32PM -0700, Yundi Quan wrote:
> > What's the sign convention used in the output files of critic2? I notice
> > that there are positive and negative values in both vcoul.cube and
> > rho.cube. Maybe it is OK to have both positive and negative vcoul.cube.
> But
> > what does it mean to have both positive and negative date in rho.cube? Or
> > is it just numerical inaccuracy?
>
> It should be, as rho >= 0. I should not worry if it is *quite* close to
> xero.
> Otherwise, please, tell me the lowest value you find.
>
> Best,
>  Víctor Luaña
> --
>  .  ."Las mujeres suelen ser menos fanáticas que los hombres,
> / `' \más prácticas y más responsables."
>/(o)(o)\   --John Carlin (ElPaís, 2016-07-03)
>   /`. \/ .'\  Women USE to be less fanatical than men, more practical
>  /   '`'`   \ and more responsible."
>  |  \'`'`/  |
>  |  |'`'`|  | "let's hope our world learns from UK what political lies
>   \/`'`'`'\/   and false patrioterism can comdemn a generation to suffer"
> ===(((==)))==+=
> ! Dr.Víctor Luaña, in silico chemist & prof. !
> ! Departamento de Química Física y Analítica !
> ! Universidad de Oviedo, 33006-Oviedo, Spain !
> ! e-mail:    !
> ! phone: +34-985-103491  fax: +34-985-103125 !
> ++
>  GroupPage: 
>  Articles:  
>  git-hub:   
>
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Re: [Wien] potential

[Víctor Luaña Cabal]

On Thu, Sep 01, 2016 at 11:15:32PM -0700, Yundi Quan wrote:
> What's the sign convention used in the output files of critic2? I notice
> that there are positive and negative values in both vcoul.cube and
> rho.cube. Maybe it is OK to have both positive and negative vcoul.cube. But
> what does it mean to have both positive and negative date in rho.cube? Or
> is it just numerical inaccuracy?

It should be, as rho >= 0. I should not worry if it is *quite* close to xero.
Otherwise, please, tell me the lowest value you find.

Best,
 Víctor Luaña
--
 .  ."Las mujeres suelen ser menos fanáticas que los hombres,
/ `' \más prácticas y más responsables." 
   /(o)(o)\   --John Carlin (ElPaís, 2016-07-03)
  /`. \/ .'\  Women USE to be less fanatical than men, more practical
 /   '`'`   \ and more responsible."
 |  \'`'`/  |
 |  |'`'`|  | "let's hope our world learns from UK what political lies
  \/`'`'`'\/   and false patrioterism can comdemn a generation to suffer"
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:    !
! phone: +34-985-103491  fax: +34-985-103125 !
++
 GroupPage: 
 Articles:  
 git-hub:   

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Re: [Wien] potential

[Yundi Quan]

What's the sign convention used in the output files of critic2? I notice
that there are positive and negative values in both vcoul.cube and
rho.cube. Maybe it is OK to have both positive and negative vcoul.cube. But
what does it mean to have both positive and negative date in rho.cube? Or
is it just numerical inaccuracy?

In WIEN2k the energy zero point is the average of the potential in the
interstitial region. Is it already shifted in case.vcoul?

On Thu, Sep 1, 2016 at 4:39 AM, <t...@theochem.tuwien.ac.at> wrote:

> yes
>
> On Thursday 2016-09-01 12:56, Yundi Quan wrote:
>
> Date: Thu, 1 Sep 2016 12:56:49
>> From: Yundi Quan <quanyu...@gmail.com>
>> Reply-To: A Mailing list for WIEN2k users <w...@zeus.theochem.tuwien.ac.
>> at>
>> To: A Mailing list for WIEN2k users <wien@zeus.theochem.tuwien.ac.at>
>> Subject: Re: [Wien] potential
>>
>>
>> Does the procedure stay the same if I use modified Becke-John potential?
>>
>> Yundi
>>
>> On Wed, Aug 31, 2016 at 5:12 PM, Yundi Quan <quanyu...@gmail.com> wrote:
>>  Thanks.
>> Yundi
>>
>> On Wed, Aug 31, 2016 at 11:27 AM, Peter Blaha
>> <pbl...@theochem.tuwien.ac.at> wrote:
>>  As mentioned before, you should not use case.vsp/vns.
>>
>>  But there is a more or less "standard" method:
>>
>>  Instead use the R2V option in lapw0 and create
>>  case.vtotal.
>>
>>  The potential in this format can be used in lapw5 (see UG)
>>  to create V on a grid in a single plane.
>>
>>  You can also use   prepare_xsf_lapw   (see UG) to create a
>>  3D grid of the potential (in a format suitable for viewing
>>  in xcrysden, but I'm sure it can be converted easily to
>>  other formats).
>>
>>
>>  Am 31.08.2016 um 16:25 schrieb Yundi Quan:
>>  Is there a way to convert the potential in case.vns
>>  and case.vsp into a
>>  real space grid with Nx, Ny, Nz number of points
>>  along \vec{a}, \vec{b}
>>  and \vec{c} respectively? Thanks.
>>
>>
>>  Yundi
>>
>>
>> ___
>> Wien mailing list
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>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
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>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>
>>
>> --
>> 
>> --
>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060
>> Vienna
>> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
>> Email: bl...@theochem.tuwien.ac.atWIEN2k:
>> http://www.wien2k.at
>> WWW:   http://www.imc.tuwien.ac.at/staff/tc_group_e.php
>> 
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>>
>>
>>
>>
>>
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Re: [Wien] potential

[tran]

yes

On Thursday 2016-09-01 12:56, Yundi Quan wrote:


Date: Thu, 1 Sep 2016 12:56:49
From: Yundi Quan <quanyu...@gmail.com>
Reply-To: A Mailing list for WIEN2k users <wien@zeus.theochem.tuwien.ac.at>
To: A Mailing list for WIEN2k users <wien@zeus.theochem.tuwien.ac.at>
Subject: Re: [Wien] potential

Does the procedure stay the same if I use modified Becke-John potential?

Yundi

On Wed, Aug 31, 2016 at 5:12 PM, Yundi Quan <quanyu...@gmail.com> wrote:
 Thanks.
Yundi

On Wed, Aug 31, 2016 at 11:27 AM, Peter Blaha
<pbl...@theochem.tuwien.ac.at> wrote:
 As mentioned before, you should not use case.vsp/vns.

 But there is a more or less "standard" method:

 Instead use the R2V option in lapw0 and create
 case.vtotal.

 The potential in this format can be used in lapw5 (see UG)
 to create V on a grid in a single plane.

 You can also use   prepare_xsf_lapw   (see UG) to create a
 3D grid of the potential (in a format suitable for viewing
 in xcrysden, but I'm sure it can be converted easily to
 other formats).


 Am 31.08.2016 um 16:25 schrieb Yundi Quan:
 Is there a way to convert the potential in case.vns
 and case.vsp into a
 real space grid with Nx, Ny, Nz number of points
 along \vec{a}, \vec{b}
 and \vec{c} respectively? Thanks.


 Yundi


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--
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Vienna
Phone: +43-1-58801-165300             FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.at    WIEN2k:
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Re: [Wien] potential

[Yundi Quan]

Does the procedure stay the same if I use modified Becke-John potential?


Yundi

On Wed, Aug 31, 2016 at 5:12 PM, Yundi Quan  wrote:

> Thanks.
>
> Yundi
>
> On Wed, Aug 31, 2016 at 11:27 AM, Peter Blaha <
> pbl...@theochem.tuwien.ac.at> wrote:
>
>> As mentioned before, you should not use case.vsp/vns.
>>
>> But there is a more or less "standard" method:
>>
>> Instead use the R2V option in lapw0 and create case.vtotal.
>>
>> The potential in this format can be used in lapw5 (see UG) to create V on
>> a grid in a single plane.
>>
>> You can also use   prepare_xsf_lapw   (see UG) to create a 3D grid of the
>> potential (in a format suitable for viewing in xcrysden, but I'm sure it
>> can be converted easily to other formats).
>>
>>
>>
>> Am 31.08.2016 um 16:25 schrieb Yundi Quan:
>>
>>> Is there a way to convert the potential in case.vns and case.vsp into a
>>> real space grid with Nx, Ny, Nz number of points along \vec{a}, \vec{b}
>>> and \vec{c} respectively? Thanks.
>>>
>>>
>>> Yundi
>>>
>>>
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>>> Wien mailing list
>>> Wien@zeus.theochem.tuwien.ac.at
>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>> SEARCH the MAILING-LIST at:  http://www.mail-archive.com/wi
>>> e...@zeus.theochem.tuwien.ac.at/index.html
>>>
>>>
>> --
>> 
>> --
>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
>> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
>> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
>> WWW:   http://www.imc.tuwien.ac.at/staff/tc_group_e.php
>> 
>> --
>>
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>> e...@zeus.theochem.tuwien.ac.at/index.html
>>
>
>
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Re: [Wien] potential

[Yundi Quan]

Thanks.

Yundi

On Wed, Aug 31, 2016 at 11:27 AM, Peter Blaha 
wrote:

> As mentioned before, you should not use case.vsp/vns.
>
> But there is a more or less "standard" method:
>
> Instead use the R2V option in lapw0 and create case.vtotal.
>
> The potential in this format can be used in lapw5 (see UG) to create V on
> a grid in a single plane.
>
> You can also use   prepare_xsf_lapw   (see UG) to create a 3D grid of the
> potential (in a format suitable for viewing in xcrysden, but I'm sure it
> can be converted easily to other formats).
>
>
>
> Am 31.08.2016 um 16:25 schrieb Yundi Quan:
>
>> Is there a way to convert the potential in case.vns and case.vsp into a
>> real space grid with Nx, Ny, Nz number of points along \vec{a}, \vec{b}
>> and \vec{c} respectively? Thanks.
>>
>>
>> Yundi
>>
>>
>> ___
>> Wien mailing list
>> Wien@zeus.theochem.tuwien.ac.at
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>> SEARCH the MAILING-LIST at:  http://www.mail-archive.com/wi
>> e...@zeus.theochem.tuwien.ac.at/index.html
>>
>>
> --
> --
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
> WWW:   http://www.imc.tuwien.ac.at/staff/tc_group_e.php
> --
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Re: [Wien] potential

[Peter Blaha]

As mentioned before, you should not use case.vsp/vns.

But there is a more or less "standard" method:

Instead use the R2V option in lapw0 and create case.vtotal.

The potential in this format can be used in lapw5 (see UG) to create V 
on a grid in a single plane.


You can also use   prepare_xsf_lapw   (see UG) to create a 3D grid of 
the potential (in a format suitable for viewing in xcrysden, but I'm 
sure it can be converted easily to other formats).



Am 31.08.2016 um 16:25 schrieb Yundi Quan:

Is there a way to convert the potential in case.vns and case.vsp into a
real space grid with Nx, Ny, Nz number of points along \vec{a}, \vec{b}
and \vec{c} respectively? Thanks.


Yundi


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--
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Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
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Re: [Wien] potential

[Alberto Otero de la Roza]

Hi Yundi,

You can write real-space grids of WIEN2k potentials, densities, or
combinations of them using critic2
(https://github.com/aoterodelaroza/critic2). Use this input:

crystal case.struct
load wien case.vcoul case.struct vnorm id vcoul
load wien case.clmsum case.struct id rho

cube cell 50 50 50 field vcoul file vcoul.cube
cube cell 50 50 50 field rho file rho.cube
cube cell 50 50 50 field "$vcoul*$rho" file vrho.cube

You load the crystal structure with "crystal", then the electrostatic
potential (case.vcoul) and the total density (clmsum). Note the
"vnorm" keyword selects the correct normalization for the
potential. The following cube entries write 3d grids in Gaussian cube
format with 50 points along each axis for the potential (first line),
the density (second), and the product of the two.

Best,

Alberto

* Yundi Quan  [2016-08-31 07:58:49 -0700]:
> Thanks Professor Marks. What I'm trying to do is to visualize \psi(r)^*
> V(r) \psi (r) in real space for a layered material so as to show how the
> potential changes from layer to layer.
> 
> 
> 
> On Wed, Aug 31, 2016 at 7:50 AM, Laurence Marks 
> wrote:
> 
> > I am 99% certain that there is nothing which will do this
> > automatically for you, some work will be required.
> >
> > I am pretty certain that you can use the R2V option in case.in0 to
> > output vtotal. You would then need to do something like use lapw5 to
> > generate a number of different slices, or use lapw3 (modified input)
> > to generate the Fourier coefficients than do your own Fourier
> > transform of them.
> >
> > N.B., you will have to pay attention to norms and be careful otherwise
> > it will be GIGO.
> >
> > On Wed, Aug 31, 2016 at 9:25 AM, Yundi Quan  wrote:
> > > Is there a way to convert the potential in case.vns and case.vsp into a
> > real
> > > space grid with Nx, Ny, Nz number of points along \vec{a}, \vec{b} and
> > > \vec{c} respectively? Thanks.
> > >
> > >
> > > Yundi
> >
> >
> >
> > --
> > Professor Laurence Marks
> > "Research is to see what everybody else has seen, and to think what
> > nobody else has thought", Albert Szent-Gyorgi
> > www.numis.northwestern.edu ; Corrosion in 4D:
> > MURI4D.numis.northwestern.edu
> > Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
> > Co-Editor, Acta Cryst A
> > ___
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> > SEARCH the MAILING-LIST at:  http://www.mail-archive.com/
> > wien@zeus.theochem.tuwien.ac.at/index.html
> >

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Re: [Wien] potential

[Yundi Quan]

Thanks Professor Marks. What I'm trying to do is to visualize \psi(r)^*
V(r) \psi (r) in real space for a layered material so as to show how the
potential changes from layer to layer.



On Wed, Aug 31, 2016 at 7:50 AM, Laurence Marks 
wrote:

> I am 99% certain that there is nothing which will do this
> automatically for you, some work will be required.
>
> I am pretty certain that you can use the R2V option in case.in0 to
> output vtotal. You would then need to do something like use lapw5 to
> generate a number of different slices, or use lapw3 (modified input)
> to generate the Fourier coefficients than do your own Fourier
> transform of them.
>
> N.B., you will have to pay attention to norms and be careful otherwise
> it will be GIGO.
>
> On Wed, Aug 31, 2016 at 9:25 AM, Yundi Quan  wrote:
> > Is there a way to convert the potential in case.vns and case.vsp into a
> real
> > space grid with Nx, Ny, Nz number of points along \vec{a}, \vec{b} and
> > \vec{c} respectively? Thanks.
> >
> >
> > Yundi
>
>
>
> --
> Professor Laurence Marks
> "Research is to see what everybody else has seen, and to think what
> nobody else has thought", Albert Szent-Gyorgi
> www.numis.northwestern.edu ; Corrosion in 4D:
> MURI4D.numis.northwestern.edu
> Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
> Co-Editor, Acta Cryst A
> ___
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> wien@zeus.theochem.tuwien.ac.at/index.html
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Re: [Wien] potential

[Laurence Marks]

I am 99% certain that there is nothing which will do this
automatically for you, some work will be required.

I am pretty certain that you can use the R2V option in case.in0 to
output vtotal. You would then need to do something like use lapw5 to
generate a number of different slices, or use lapw3 (modified input)
to generate the Fourier coefficients than do your own Fourier
transform of them.

N.B., you will have to pay attention to norms and be careful otherwise
it will be GIGO.

On Wed, Aug 31, 2016 at 9:25 AM, Yundi Quan  wrote:
> Is there a way to convert the potential in case.vns and case.vsp into a real
> space grid with Nx, Ny, Nz number of points along \vec{a}, \vec{b} and
> \vec{c} respectively? Thanks.
>
>
> Yundi



-- 
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what
nobody else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu
Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
Co-Editor, Acta Cryst A
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[Wien] potential

[Yundi Quan]

Is there a way to convert the potential in case.vns and case.vsp into a
real space grid with Nx, Ny, Nz number of points along \vec{a}, \vec{b} and
\vec{c} respectively? Thanks.


Yundi
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Re: [Wien] potential well depth

[Peter Blaha]

Now we start to understand what you want.

You have to create manually some distorted structures (corresponding to the
potential well you want to investigate) and calculate E-tot.
Then plot E-tot vs. distortion.

It is your task, to define the distortions (eg. in SrTiO3 it could be a
simple rigid rotation of the octahedra, but that could be done in various ways,
or there could be (additional) tilting, .

Am 26.02.2015 um 13:45 schrieb Mohammed Abujafar:

Dear WINE2k developers and users,
Hi,
I am concerning about reading the  value of the potential depth well from the 
DFT results ,for an example SrTiO3 compound in perovskite structure.How can I 
get it?Your help
is highly appreciated.Thanks a lot in advance.
With best regards
Mohammed


On Wednesday, February 25, 2015 8:09 AM, Mohammed Abujafar 
mabuja...@yahoo.com wrote:


Dear developers and Wien2k users,,
Hi,
Do you have an idea about implementing the potential well depth in eV   and 
width with certain number of unit cells.
Thank you very much in advance
With best regards
Mohammed





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Re: [Wien] potential well depth

[Mohammed Abujafar]

Dear WINE2k developers and users,Hi,I am concerning about reading the  value of 
the potential depth well from the DFT results ,for an example SrTiO3 compound 
in perovskite structure.How can I get it?Your help is highly appreciated.Thanks 
a lot in advance.With best regardsMohammed
 

 On Wednesday, February 25, 2015 8:09 AM, Mohammed Abujafar 
mabuja...@yahoo.com wrote:
   

 Dear developers and Wien2k users,,Hi,Do you have an idea about implementing 
the potential well depth in eV   and width with certain number of unit 
cells.Thank you very much in advanceWith best regardsMohammed


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[Wien] potential well depth

[Mohammed Abujafar]

Dear developers and Wien2k users,,Hi,Do you have an idea about implementing the 
potential well depth in eV   and width with certain number of unit cells.Thank 
you very much in advanceWith best regardsMohammed
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[Wien] Potential Delta-sol

[Peter Blaha]

In principle, yes. But you have to apply your own correction for charged cells.

And in additon: I'd use the mBJ-potential. This is much less effort, more 
general
and accurate.

Am 19.11.2010 15:48, schrieb Amilcar Meneses Viveros:

 Hi there.

 For the potential (Delta-sol) in the reference

 Phys. Rev. Lett. 105, 196403
 (http://prl.aps.org/abstract/PRL/v105/i19/e196403)

 Is possible use this potential in Wien2k?

 Regards
 Amilcar


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Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/
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[Wien] Potential Delta-sol

[Amilcar Meneses Viveros]

Hi there.

For the potential (Delta-sol) in the reference

Phys. Rev. Lett. 105, 196403
(http://prl.aps.org/abstract/PRL/v105/i19/e196403)

Is possible use this potential in  Wien2k?

Regards
Amilcar

[Wien] Potential in the k-point

[Artamonov Oleg]

Dear Wien2k Users,

I produced successfully the band structure calculation by spaghetti for my 
structure. I need now to extract from Wien2k the potential and the field ( 
namely  the gradient of the potential in the real space) for any k-point 
specified by the energy and k-vector.
How is it possible to do that?

Thanks in advance, Oleg Artamonov.

[Wien] Potential in a interstitial

[Oleg Rubel]

Hi Oleg,

are you talking about Coulomb potential? If yes, then it is 0. (Strictly 
speaking 0 is its Fourier coefficient at k = 0.)

I hope this will help.

Oleg

--
Oleg Rubel, PhD
Scientist, Thunder Bay Regional Research Institute
Adjunct Professor, Dept Physics, Lakehead University
290 Munro St, Thunder Bay, P7A 7T1, Ontario, Canada
Phone: +1-807-7663350
Fax: +1-807-3441948
E-mail: rubelo at tbh.net
Homepage: http://www.tbrri.com/~orubel/
 Artamonov Oleg artaoleg at yandex.ru 08/02/10 8:24 AM 
Dear Wien2k users,

Can anybody prompt me what subroutine in the lapw0 produces an average 
potential in the interstitial region.
Thanks in advance,
Oleg Artamonov.
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[Wien] Potential in a interstitial

[Oleg Rubel]

Hi Oleg,

this issue has been addressed several times in the mail-list. Please, search 
for reference energy.

Oleg

 On 8/6/2010 at 6:02 AM, in message 446971281088956 at web122.yandex.ru,
Artamonov Oleg artaoleg at yandex.ru wrote:
 Hi Oleg,
 
 thanks for reply. I am interested in a Coulomb potential in the energy units 
 in the interstitial region, strictly speaking.in the region between atomic 
 potentials. It is easy to see (using lapw5) that the potential is not zero 
 and its average  value should depend on the structure (solid, surface). It 
 seems to me I need to calculate it by hand. Oleg.
 
 
 
 06.08.10, 08:23, Oleg Rubel rubelo at tbh.net:
 
 Hi Oleg,
  
  are you talking about ? If yes, then it is 0. (Strictly speaking 0 is its 
 Fourier coefficient at k = 0.)
  
  I hope this will help.
  
  Oleg
  
  --
  Oleg Rubel, PhD
  Scientist, Thunder Bay Regional Research Institute
  Adjunct Professor, Dept Physics, Lakehead University
  290 Munro St, Thunder Bay, P7A 7T1, Ontario, Canada
  Phone: +1-807-7663350
  Fax: +1-807-3441948
  E-mail: rubelo at tbh.net 
  Homepage: http://www.tbrri.com/~orubel/ 
   Artamonov Oleg  08/02/10 8:24 AM 
  Dear Wien2k users,
  
  Can anybody prompt me what subroutine in the lapw0 produces an average 
 potential in the interstitial region.
  Thanks in advance,
  Oleg Artamonov.
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[Wien] Potential in a interstitial

[Artamonov Oleg]

Dear Wien2k users,

Can anybody prompt me what subroutine in the lapw0 produces an average 
potential in the interstitial region.
Thanks in advance,
Oleg Artamonov.