From tone.kokalj at ijs.si  Fri Jun 11 13:14:49 2021
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 11 Jun 2021 13:14:49 +0200
Subject: [xcrysden] Saving the grid for an expanded system
In-Reply-To: <1506966585.67296069.1619190127584.JavaMail.zimbra@unex.es>
References: <1506966585.67296069.1619190127584.JavaMail.zimbra@unex.es>
Message-ID: <0546b2eb79c4837f78b7a07e8dbfd3286fa0abe3.camel@ijs.si>

On Fri, 2021-04-23 at 17:02 +0200, Juan Jose Melendez Martinez wrote:
> Dear all
> 
> I have generated a supercell by expanding a single unit cell along
> each crystal axis; xcrysden behaves very nicely for this. I can also
> expand a 3D grid defined for the unit cell to the whole supercell,
> and then I can see the charge distribution within the latter, for
> instance. Once I got the grid (say the charge density) in the whole
> supercell, I saved it via the "Save Grid" command. And then I found a
> couple of issues:
> 
> 1) The xsf file saved from the previous procedure contains the atoms
> in the supercell. However, when I load the file, I get the unit cell,
> not the supercell that I expected. 

This is the programmed behavior. If you want to load the structure with
the same setting, use File-->Current State and Structure instead. But
beware that in case of datagrids, this will make very large file.

> 
> 2) I realized that the grid was saved for the unit cell only, not for
> the whole supercell. I can expand the grid again, but I cannot use it
> to compute charge differences, for instance. 

This is also the programmed behavior. Why would you save more than is
needed, especially with datagrids which results in large files? I do
not understand the problem you are describing about the charge
differences.

> Did any of you experience something like this before? Any help,
> please?

Of course: this is how it is meant to be.

Best regards, Tone
-- 
Jo?ef Stefan Institute, Ljubljana, Slovenia



From melendez at unex.es  Fri Jun 11 22:41:44 2021
From: melendez at unex.es (Juan Jose Melendez Martinez)
Date: Fri, 11 Jun 2021 22:41:44 +0200 (CEST)
Subject: [xcrysden] Saving the grid for an expanded system
In-Reply-To: <0546b2eb79c4837f78b7a07e8dbfd3286fa0abe3.camel@ijs.si>
References: <1506966585.67296069.1619190127584.JavaMail.zimbra@unex.es>
	<0546b2eb79c4837f78b7a07e8dbfd3286fa0abe3.camel@ijs.si>
Message-ID: <134637557.23088912.1623444104048.JavaMail.zimbra@unex.es>

Dear Tone

Thanks for your answer. I understand the issue now.

Best regards

Juanjo

----- Mensaje original -----
De: Tone Kokalj <tone.kokalj at ijs.si>
Para: XCrySDen mailing list <xcrysden at democritos.it>
Enviado: Fri, 11 Jun 2021 13:14:49 +0200 (CEST)
Asunto: Re: [xcrysden] Saving the grid for an expanded system

On Fri, 2021-04-23 at 17:02 +0200, Juan Jose Melendez Martinez wrote:
> Dear all
> 
> I have generated a supercell by expanding a single unit cell along
> each crystal axis; xcrysden behaves very nicely for this. I can also
> expand a 3D grid defined for the unit cell to the whole supercell,
> and then I can see the charge distribution within the latter, for
> instance. Once I got the grid (say the charge density) in the whole
> supercell, I saved it via the "Save Grid" command. And then I found a
> couple of issues:
> 
> 1) The xsf file saved from the previous procedure contains the atoms
> in the supercell. However, when I load the file, I get the unit cell,
> not the supercell that I expected. 

This is the programmed behavior. If you want to load the structure with
the same setting, use File-->Current State and Structure instead. But
beware that in case of datagrids, this will make very large file.

> 
> 2) I realized that the grid was saved for the unit cell only, not for
> the whole supercell. I can expand the grid again, but I cannot use it
> to compute charge differences, for instance. 

This is also the programmed behavior. Why would you save more than is
needed, especially with datagrids which results in large files? I do
not understand the problem you are describing about the charge
differences.

> Did any of you experience something like this before? Any help,
> please?

Of course: this is how it is meant to be.

Best regards, Tone
-- 
Jo?ef Stefan Institute, Ljubljana, Slovenia


_______________________________________________
XCrySDen mailing list
XCrySDen at democritos.it
http://www.democritos.it/mailman/listinfo/xcrysden


From deb.jyotirmoy11 at gmail.com  Mon Jun 14 03:58:56 2021
From: deb.jyotirmoy11 at gmail.com (Jyotirmoy Deb)
Date: Mon, 14 Jun 2021 07:28:56 +0530
Subject: [xcrysden] How to get the numerical value of electron density?
Message-ID: <CAH7ahTMYjHxtwQXbpXUew8TncDZZHNS=s4Di+pNsbkLYv-nBGA@mail.gmail.com>

I want to get the numerical value of electron density rho (x,y,z) along X,
Y, Z grid points in a human-readable file format. i.e in a text or dat file
I want to save X, Y, Z vs rho (x,y,z). How to do it?

I am eagerly waiting for your response.

Thanking you

with regards

Jyotirmoy






Jyotirmoy Deb

DST-INSPIRE Senior Research Fellow

Department of Physics

Assam University, Silchar

Assam, India-788011

Ph. No: +919435589869

Email: deb.jyotirmoy11 at gmail.com

           jyotirmoy.deb at aus.ac.in
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.democritos.it/pipermail/xcrysden/attachments/20210614/70f4d7dc/attachment.htm 

From tone.kokalj at ijs.si  Mon Jun 14 12:00:39 2021
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 14 Jun 2021 12:00:39 +0200
Subject: [xcrysden] How to get the numerical value of electron density?
In-Reply-To: <CAH7ahTMYjHxtwQXbpXUew8TncDZZHNS=s4Di+pNsbkLYv-nBGA@mail.gmail.com>
References: <CAH7ahTMYjHxtwQXbpXUew8TncDZZHNS=s4Di+pNsbkLYv-nBGA@mail.gmail.com>
Message-ID: <73eaef5f2a88ce18a7b8b3deb426b4c68a2eed77.camel@ijs.si>

On Mon, 2021-06-14 at 07:28 +0530, Jyotirmoy Deb wrote:
> I want to get the numerical value of electron density rho (x,y,z)
> along X, Y, Z grid points in a human-readable file format. i.e in a
> text or dat file I want to save X, Y, Z vs rho (x,y,z). How to do it?
> I am eagerly waiting for your response.

You can write a small program that reads the XSF formatted datagrid 
and prints it in the format of your choosing.

The XSF-datagrid specs are here: 
http://www.xcrysden.org/doc/XSF.html#__toc__11


Best regards, 
Tone
-- 
Jo?ef Stefan Institute, Ljubljana, Slovenia



From carlofedep at gmail.com  Fri Jun 18 10:34:58 2021
From: carlofedep at gmail.com (Carlo Federico Pauletti)
Date: Fri, 18 Jun 2021 10:34:58 +0200
Subject: [xcrysden] XCrysDen issue on Fedora 34
Message-ID: <07662bae-4b07-55e7-d1fe-0495006fd455@gmail.com>

Good morning,

I would like to run XCrysDen on Fedora34. I downloaded and extracted the 
compiled package in my home directory but as soon as I execute:

./xcrysden

I get this error:

/home/carlofedep/xcrysden-1.6.2-bin-shared/bin/xcrys: error while 
loading shared libraries: libTogl.so.2: cannot open shared object file: 
No such file or directory.

I tried to look for it via:

sudo dnf install libTogl.so.2

but it does not work. May I receive some help in solving this issue?

Thanks a lot,

Federico



From matic.poberznik at gmail.com  Fri Jun 18 11:06:14 2021
From: matic.poberznik at gmail.com (Matic)
Date: Fri, 18 Jun 2021 11:06:14 +0200
Subject: [xcrysden] XCrysDen issue on Fedora 34
In-Reply-To: <07662bae-4b07-55e7-d1fe-0495006fd455@gmail.com>
References: <07662bae-4b07-55e7-d1fe-0495006fd455@gmail.com>
Message-ID: <28159aff-debd-7bdf-2a81-66318cfcbf1c@gmail.com>

Dear Federico,

please check the following thread:

http://www.democritos.it/pipermail/xcrysden/2020-February/001980.html

I would suggest you download the package from:

https://sourceforge.net/projects/togl/files/

compile it and add the path to the LD_LIBRARY_PATH (Fedora comes with 
version 2.1 which afaik doesn't work with xcrysden)

I hope this helps,

Best Regards,

Matic Poberznik

> Good morning,
>
> I would like to run XCrysDen on Fedora34. I downloaded and extracted the
> compiled package in my home directory but as soon as I execute:
>
> ./xcrysden
>
> I get this error:
>
> /home/carlofedep/xcrysden-1.6.2-bin-shared/bin/xcrys: error while
> loading shared libraries: libTogl.so.2: cannot open shared object file:
> No such file or directory.
>
> I tried to look for it via:
>
> sudo dnf install libTogl.so.2
>
> but it does not work. May I receive some help in solving this issue?
>
> Thanks a lot,
>
> Federico
>
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden

-- 
Matic Poberznik
CNR-IOM Democritos c/o SISSA, via Bonomea 265, Trieste, Italy

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.democritos.it/pipermail/xcrysden/attachments/20210618/5284c2cb/attachment.htm 

From matic.poberznik at gmail.com  Fri Jun 18 12:43:26 2021
From: matic.poberznik at gmail.com (Matic)
Date: Fri, 18 Jun 2021 12:43:26 +0200
Subject: [xcrysden] XCrysDen issue on Fedora 34
In-Reply-To: <b1e06896-6c4c-b22d-fef7-6d4b997d9763@gmail.com>
References: <07662bae-4b07-55e7-d1fe-0495006fd455@gmail.com>
	<28159aff-debd-7bdf-2a81-66318cfcbf1c@gmail.com>
	<b1e06896-6c4c-b22d-fef7-6d4b997d9763@gmail.com>
Message-ID: <aed4fcb5-1a65-d188-d6fd-cc7478acd1b1@gmail.com>

Hi,

I don't think you need to do that (you need it only to use with the 
tclsh); I suggest you unpack it somewhere in your home directory and 
then add the following to your ~/.bashrc:

export LD_LIBRARY_PATH=$HOME/path/to/Togl:$LD_LIBRARY_PATH

(replace /path/to/Togl/ with the correct path that contains libTogl.so.2 
(i suppose "lib/Togl2.0")
the either open a new terminal or type: source ~/.bashrc

you can check if the changes were accepted with: echo $LD_LIBRARY_PATH

finally to see if xcrysden finds the library try:

ldd ~/path/to/xcrysden/bin/xcrys

(this command will list all the libraries connected to xcrysden and 
their locations, check for libTogl2.0 to see if it points to the right 
file, i.e., libTogl.so.2 => /path/to/Togl/libTogl.so.2 ):

Best,

Matic


> Hi Matic, thank you for your answer.
>
> I downloaded the package you linked and followed the README file. It 
> says:
>
> For users:
>
> ??? Only the lib/Togl2.X directory (and its contents) need to be 
> installed
> ??? in your Tcl library.? laaExecute the following Tcl script to find the
> ??? directories Tcl looks for packages in:
>
> ??? puts $tcl_libPath
>
> ??? and then copy the lib/Togl2.X directory into one of those 
> directories.
>
> However I don't know how to execute the "puts $tcl_libPath" to locate 
> the folder where to copy the lib/Togl2.0 folder. Do you have any 
> suggestion?
>
> Thanks, Federico
>
> Il 18/06/21 11:06, Matic ha scritto:
>>
>> Dear Federico,
>>
>> please check the following thread:
>>
>> http://www.democritos.it/pipermail/xcrysden/2020-February/001980.html
>>
>> I would suggest you download the package from:
>>
>> https://sourceforge.net/projects/togl/files/
>>
>> compile it and add the path to the LD_LIBRARY_PATH (Fedora comes with 
>> version 2.1 which afaik doesn't work with xcrysden)
>>
>> I hope this helps,
>>
>> Best Regards,
>>
>> Matic Poberznik
>>
>>> Good morning,
>>>
>>> I would like to run XCrysDen on Fedora34. I downloaded and extracted 
>>> the
>>> compiled package in my home directory but as soon as I execute:
>>>
>>> ./xcrysden
>>>
>>> I get this error:
>>>
>>> /home/carlofedep/xcrysden-1.6.2-bin-shared/bin/xcrys: error while
>>> loading shared libraries: libTogl.so.2: cannot open shared object file:
>>> No such file or directory.
>>>
>>> I tried to look for it via:
>>>
>>> sudo dnf install libTogl.so.2
>>>
>>> but it does not work. May I receive some help in solving this issue?
>>>
>>> Thanks a lot,
>>>
>>> Federico
>>>
>>>
>>> _______________________________________________
>>> XCrySDen mailing list
>>> XCrySDen at democritos.it
>>> http://www.democritos.it/mailman/listinfo/xcrysden
>> -- 
>> Matic Poberznik
>> CNR-IOM Democritos c/o SISSA, via Bonomea 265, Trieste, Italy

-- 
Matic Poberznik
CNR-IOM Democritos c/o SISSA, via Bonomea 265, Trieste, Italy


From gabo13279 at gmail.com  Fri Jun 18 13:54:16 2021
From: gabo13279 at gmail.com (Gavin Abo)
Date: Fri, 18 Jun 2021 04:54:16 -0700
Subject: [xcrysden] XCrysDen issue on Fedora 34
In-Reply-To: <07662bae-4b07-55e7-d1fe-0495006fd455@gmail.com>
References: <07662bae-4b07-55e7-d1fe-0495006fd455@gmail.com>
Message-ID: <CAEOUph0E4yBch9dOZZ=NcVZtYT+wciTkxUgBLzVj2YHHfwvK7g@mail.gmail.com>

You may want to read the past posts about the issues with Wayland. For
example at:

http://www.democritos.it/pipermail/xcrysden/2021-April/002056.html

I did not report it to the list previously, but the reason Wayland might
have worked for me might have been because it was using VirtualBox's video
driver and not the video driver for my graphics card.  So if running
xcryden on Fedora 34 in VirtualBox on a Linux or Windows machine is not an
issue, that may be an alternate solution rather than using Xorg instead of
Wayland.

On Fri, Jun 18, 2021, 1:35 AM Carlo Federico Pauletti <carlofedep at gmail.com>
wrote:

> Good morning,
>
> I would like to run XCrysDen on Fedora34. I downloaded and extracted the
> compiled package in my home directory but as soon as I execute:
>
> ./xcrysden
>
> I get this error:
>
> /home/carlofedep/xcrysden-1.6.2-bin-shared/bin/xcrys: error while
> loading shared libraries: libTogl.so.2: cannot open shared object file:
> No such file or directory.
>
> I tried to look for it via:
>
> sudo dnf install libTogl.so.2
>
> but it does not work. May I receive some help in solving this issue?
>
> Thanks a lot,
>
> Federico
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.democritos.it/pipermail/xcrysden/attachments/20210618/e9d77952/attachment.htm