From khalifaiza at yahoo.fr  Tue Aug  6 22:50:45 2024
From: khalifaiza at yahoo.fr (Faiza Khali)
Date: Tue, 6 Aug 2024 20:50:45 +0000 (UTC)
Subject: [xcrysden] XCrysden installation
In-Reply-To: <0d6cec60-63aa-49a5-8533-e5dd1c760df1@gmail.com>
References: <1173152132.26653.1721946307849.ref@mail.yahoo.com>
	<1173152132.26653.1721946307849@mail.yahoo.com>
	<0d6cec60-63aa-49a5-8533-e5dd1c760df1@gmail.com>
Message-ID: <844817740.4627639.1722977445623@mail.yahoo.com>

Dear,Thank you for your message,Unfortunately, I can't know what kind of methods can i choose or I must test the two ones!!Best

 

    Le samedi 27 juillet 2024 ? 05:05:28 UTC+2, Gavin Abo <gabo13279 at gmail.com> a ?crit :  
 
  
As seen on the XCrySDen webpage at [1], there is two installation methods for Windows 10.? Are you using WSL or are you using Cygwin64?
 
 
[1] http://www.xcrysden.org/Download.html
 
 
Kind Regards,
 Gavin
 XCrySDen user
 
  On 7/25/2024 4:25 PM, Faiza Khali wrote:
  
 
 Dear all, 
  I hope that you are doing fine. 
  Please help me to install XCrysden on Windows, please I? need your help. Best Regards 
    *********************************** Dr. Faiza Bouamra ***********************************    _______________________________________________
XCrySDen mailing list
XCrySDen at democritos.it
http://www.democritos.it/mailman/listinfo/xcrysden
  
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From gabo13279 at gmail.com  Thu Aug  8 14:27:17 2024
From: gabo13279 at gmail.com (Gavin Abo)
Date: Thu, 8 Aug 2024 06:27:17 -0600
Subject: [xcrysden] XCrysden installation
In-Reply-To: <844817740.4627639.1722977445623@mail.yahoo.com>
References: <1173152132.26653.1721946307849.ref@mail.yahoo.com>
	<1173152132.26653.1721946307849@mail.yahoo.com>
	<0d6cec60-63aa-49a5-8533-e5dd1c760df1@gmail.com>
	<844817740.4627639.1722977445623@mail.yahoo.com>
Message-ID: <08f41d34-5ccc-49e0-837d-ab040d9fcd05@gmail.com>

You could try either method.? It's up to you which one you choose.

On 8/6/2024 2:50 PM, Faiza Khali wrote:
> Dear,
> Thank you for your message,
> Unfortunately, I can't know what kind of methods can i choose or I 
> must test the two ones!!
> Best
>
>
>
>
> Le samedi 27 juillet 2024 ? 05:05:28 UTC+2, Gavin Abo 
> <gabo13279 at gmail.com> a ?crit :
>
>
> As seen on the XCrySDen webpage at [1], there is two installation 
> methods for Windows 10.? Are you using WSL or are you using Cygwin64?
>
> [1] http://www.xcrysden.org/Download.html 
> <http://www.xcrysden.org/Download.html>
>
> Kind Regards,
>
> Gavin
> XCrySDen user
>
> On 7/25/2024 4:25 PM, Faiza Khali wrote:
> Dear all,
>
> I hope that you are doing fine.
>
> Please help me to install XCrysden on Windows, please I? need your help.
> Best Regards
>
> /***********************************/
> /Dr. Faiza Bouamra/
> /***********************************/
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
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From upanta at ucmerced.edu  Tue Aug 13 22:49:43 2024
From: upanta at ucmerced.edu (Uday Panta)
Date: Tue, 13 Aug 2024 20:49:43 +0000
Subject: [xcrysden] Load a state with isosurface expanded to whole structure
Message-ID: <d5d1e47e20e041c987c4a8ca52c046cfSJ0PR06MB69263E60A4734DAD53F380BFB1852@SJ0PR06MB6926.namprd06.prod.outlook.com>

Hi,
I'm trying to batch render hundreds of isosurfaces. I use a state file to a load specific angle and isovalue with --state along with --print to directly print to a png file. But I can't get the isosurface to load over the whole structure, instead it loads only on a unit cell. Even when I do not use --print, it loads the isosurface only on a unit cell and the "Isosurface/Property-plane Controls" dialog box appears with all the right options already selected. Expand isosurface is set to "to whole structure" as I want it to be. But I need to click on the "submit" button manually to see the effect on the whole structure. Is there a way I can automate this? Maybe edit something on the state file? I'm using version 1.6.2 on linux.

Best,
Uday
Dept. of Physics
University of California, Merced
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From delamora at unam.mx  Mon Aug 26 22:24:42 2024
From: delamora at unam.mx (delamora)
Date: Mon, 26 Aug 2024 20:24:42 +0000
Subject: [xcrysden] Running XCrySDen
Message-ID: <BY5PR06MB6676824148773BE1E25FE099CB8B2@BY5PR06MB6676.namprd06.prod.outlook.com>

I have Fedora Linux
I installed xcrysden-1.5.60-bin-semishared, but when I try to open it
"xcrysden"
it does not open, it gives the error;

/home/Programas/xcrysden-1.5.60-bin-semishared/bin/ftnunit: error while loading

How can I fix it

Yours

Pablo
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From gabo13279 at gmail.com  Tue Aug 27 06:35:32 2024
From: gabo13279 at gmail.com (Gavin Abo)
Date: Mon, 26 Aug 2024 22:35:32 -0600
Subject: [xcrysden] Running XCrySDen
In-Reply-To: <BY5PR06MB6676824148773BE1E25FE099CB8B2@BY5PR06MB6676.namprd06.prod.outlook.com>
References: <BY5PR06MB6676824148773BE1E25FE099CB8B2@BY5PR06MB6676.namprd06.prod.outlook.com>
Message-ID: <695b30bb-98d0-40d8-a5de-64d5b34aec3a@gmail.com>

The issue might be because the version of Fedora that you are using does 
not have the operating system library that it needs to load ftnunit.? 
Thus, the "error while loading" error.


What is the Fedora version?? The xcrysden-1.5.60-bin-semishared worked 
with around Fedora versions 25 to 27.


With Fedora 34, xcrysden 1.6.2 was used, but it had to be compiled.


The compile steps used were given the post at:


http://www.democritos.it/pipermail/xcrysden/2021-April/002050.html


At https://fedoraproject.org , I see that Fedora is now at version 40.? 
I've not tried?XCrySDen 1.6.2 with that version if that is what you are 
using.


With some other code packages, I have seen some GNU compiler 
compatibility issues encountered with newer Linux distributions that 
release with gcc/g++ version 13.? With Ubuntu 24.04 LTS that comes 
with?gcc/g++ version 13, though, I was able to fall back as a workaround 
(while waiting to see if the code developers would provide new versions 
with code changes for working with the newer compilers) for example by 
installing a g++ version 10 package using "sudo apt install g++-10".? 
Don't know yet if there are any issues compiling XCrySDen 1.6.2 with the 
latest gcc versions or if Fedora has a similar fall back package that 
can be installed like Ubuntu.


Kind Regards,

Gavin

XCrySDen user


On 8/26/2024 2:24 PM, delamora wrote:
> I have Fedora Linux
> I installed xcrysden-1.5.60-bin-semishared, but when I try to open it
> "xcrysden"
> it does not open, it gives the error;
>
> /home/Programas/xcrysden-1.5.60-bin-semishared/bin/ftnunit: error 
> while loading
>
> How can I fix it
>
> Yours
>
> Pablo
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From delamora at unam.mx  Tue Aug 27 06:56:32 2024
From: delamora at unam.mx (delamora)
Date: Tue, 27 Aug 2024 04:56:32 +0000
Subject: [xcrysden] Running XCrySDen
In-Reply-To: <695b30bb-98d0-40d8-a5de-64d5b34aec3a@gmail.com>
References: <BY5PR06MB6676824148773BE1E25FE099CB8B2@BY5PR06MB6676.namprd06.prod.outlook.com>
	<695b30bb-98d0-40d8-a5de-64d5b34aec3a@gmail.com>
Message-ID: <BY5PR06MB667622090C4D831CA3E65987CB942@BY5PR06MB6676.namprd06.prod.outlook.com>

Dear Gavin,
Thank for your reply, I will try it.
Yes, I have the Fedora 40
Pablo
________________________________
The issue might be because the version of Fedora that you are using does not have the operating system library that it needs to load ftnunit.  Thus, the "error while loading" error.


What is the Fedora version?  The xcrysden-1.5.60-bin-semishared worked with around Fedora versions 25 to 27.


With Fedora 34, xcrysden 1.6.2 was used, but it had to be compiled.


The compile steps used were given the post at:


http://www.democritos.it/pipermail/xcrysden/2021-April/002050.html


At https://fedoraproject.org , I see that Fedora is now at version 40.  I've not tried XCrySDen 1.6.2 with that version if that is what you are using.


With some other code packages, I have seen some GNU compiler compatibility issues encountered with newer Linux distributions that release with gcc/g++ version 13.  With Ubuntu 24.04 LTS that comes with gcc/g++ version 13, though, I was able to fall back as a workaround (while waiting to see if the code developers would provide new versions with code changes for working with the newer compilers) for example by installing a g++ version 10 package using "sudo apt install g++-10".  Don't know yet if there are any issues compiling XCrySDen 1.6.2 with the latest gcc versions or if Fedora has a similar fall back package that can be installed like Ubuntu.


Kind Regards,

Gavin

XCrySDen user


On 8/26/2024 2:24 PM, delamora wrote:
I have Fedora Linux
I installed xcrysden-1.5.60-bin-semishared, but when I try to open it
"xcrysden"
it does not open, it gives the error;

/home/Programas/xcrysden-1.5.60-bin-semishared/bin/ftnunit: error while loading

How can I fix it

Yours

Pablo
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From gabo13279 at gmail.com  Wed Aug 28 09:11:45 2024
From: gabo13279 at gmail.com (Gavin Abo)
Date: Wed, 28 Aug 2024 01:11:45 -0600
Subject: [xcrysden] Running XCrySDen
In-Reply-To: <BY5PR06MB667622090C4D831CA3E65987CB942@BY5PR06MB6676.namprd06.prod.outlook.com>
References: <BY5PR06MB6676824148773BE1E25FE099CB8B2@BY5PR06MB6676.namprd06.prod.outlook.com>
	<695b30bb-98d0-40d8-a5de-64d5b34aec3a@gmail.com>
	<BY5PR06MB667622090C4D831CA3E65987CB942@BY5PR06MB6676.namprd06.prod.outlook.com>
Message-ID: <e628d115-4c24-41c7-abc6-0ea4194817b1@gmail.com>

I tried it out.? It seems to work as seen in the screenshot at:


https://github.com/gsabo/xcrysden-Patches/blob/main/Fedora%2040%20XCrySDen%201.6.2.png


Apparently, Fedora 40 ships with gcc version 14:


username at fedora:~$ gfortran --version
GNU Fortran (GCC) 14.2.1 20240801 (Red Hat 14.2.1-1)
Copyright (C) 2024 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


Most of the Fedora 34 steps still applied to Fedora 40, but I had to 
make some adjustments in order to get it to work as follows.


Since you already have Fedora 40 installed, you can skip to step 8 below.


1. Went to: https://getfedora.org/en/workstation/download/
2. Downloaded Fedora Workstation 40:
Fedora-Workstation-Live-x86_64-40-1.14.iso
3. Downloaded Fedora Media Writer Windows:
FedoraMediaWriter-win32-latest.exe
4. Ran: FedoraMediaWriter-win32-latest.exe
 ?? a. Clicked "I Agree"
 ?? b. Clicked "Install"
 ?? c. Clicked "Next"
 ?? d. With "Run Fedora Media Writer" selected, clicked "Finish"
 ?? e. Selected "Select .iso file", then clicked "Next"
 ?? f. Clicked "Select..."
 ?? g. Selected "Fedora-Workstation-Live-x86_64-40-1.14.iso", then 
clicked "Open"
 ?? h. Selected USB Drive, then clicked "Write"
 ?? i. Click "Finish"
 ?? j. Closed the Fedora Media Write dialog (upper right x in window)
5. Booted from the USB stick
6. Installed Fedora 40
 ??? a. Selected "Start Fedora-Workstation-Live 40"
 ??? b. Clicked "Install Fedora..."
 ??? c. Selected English and clicked Continue
 ??? d. Clicked "Installation Destination"
 ??? e. Clicked Done
 ??? WARNING: The steps f-h will wipe everything for starting fresh with 
the drive.
 ??? f. Clicked "Reclaim space"
 ??? g. Clicked "Delete all"
 ??? h. Clicked "Reclaim space"
 ??? i. Clicked "Begin Installation"
 ??? j. Clicked "Finish Installation"
 ??? k. In Fedora Live, click on bar with power icon, click on power 
icon, click "Restart", click "Restart" button
7. Setup Fedora 40
 ??? a. Clicked "Start Setup"
 ??? b. Click Skip (or setup Wi-Fi)
 ??? c. Turn off "Location Services" and "Automatic Problem Reporting", 
then click Next
 ??? d. Click "Enable Third-Party Repositories", then click Next
 ??? e. Type a Full Name and Username and click Next
 ??? f. Type a password and click Next
 ??? g. Click "Start Using Fedora Linux"
 ??? h. For tour prompt, click "Skip"
8. Opened a terminal in Fedora 40 and performed the following:

username at fedora:~$ sudo yum install patch ImageMagick openbabel 
mesa-libGL-devel mesa-libGLU-devel tcl-devel tk-devel fftw-devel 
libXmu-devel gfortran
...
Is this ok [y/N]: y
...
username at fedora:~$ wget 
https://sourceforge.net/projects/togl/files/Togl/2.0/Togl2.0-src.tar.gz/download
...
username at fedora:~$ tar xvf download
...
username at fedora:~$ cd Togl2.0/
username at fedora:~/Togl2.0$? ./configure --with-tcl=/usr/lib64 
--with-tk=/usr/lib64 --enable-64bit
...


The Togl 2.0 failed due the gcc version 14 compiler as seen here:


username at fedora:~/Togl2.0$ make
gcc -DPACKAGE_NAME=\"Togl\" -DPACKAGE_TARNAME=\"togl\" 
-DPACKAGE_VERSION=\"2.0\" -DPACKAGE_STRING=\"Togl\ 2.0\" 
-DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 
-DHAVE_SYS_PARAM_H=1 -DUSE_THREAD_ALLOC=1 -D_REENTRANT=1 
-D_THREAD_SAFE=1 -DTCL_THREADS=1 -DMODULE_SCOPE=extern\ 
__attribute__\(\(__visibility__\(\"hidden\"\)\)\) 
-D_LARGEFILE64_SOURCE=1 -DTCL_WIDE_INT_IS_LONG=1 -DUSE_TCL_STUBS=1 
-DUSE_TK_STUBS=1 -DAUTOSTEREOD=\"\" -I"/usr/include/tcl-private/generic" 
-I"/usr/include/tcl-private/unix" -I"/usr/include/tk-private/generic" 
-I"/usr/include/tk-private/unix" 
-I"/usr/include/tk-private/generic/ttk"???? -pipe -m64 -O2 
-fomit-frame-pointer -Wall -Wno-implicit-int -fPIC? -c `echo togl.c` -o 
togl.o
togl.c: In function ?Togl_Init?:
togl.c:928:26: error: assignment to ?void (*)(struct Tk_Window_ *, 
Tk_ClassProcs *, void *)? from incompatible pointer type ?void 
(*)(struct Tk_Window_ *, const Tk_ClassProcs *, void *)? 
[-Wincompatible-pointer-types]
 ? 928 |???????? SetClassProcsPtr = tkStubsPtr->tk_SetClassProcs;
 ????? |????????????????????????? ^
make: *** [Makefile:357: togl.o] Error 1


However, I was able to patch it for continuing with the build:


username at fedora:~/Togl2.0$ wget 
https://raw.githubusercontent.com/gsabo/xcrysden-Patches/main/togl.patch

username at fedora:~/Togl2.0$ patch -b togl.c togl.patch
username at fedora:~/Togl2.0$ make

...

username at fedora:~/Togl2.0$ cd ..
username at fedora:~$ wget 
http://www.xcrysden.org/download/xcrysden-1.6.2.tar.gz
...
username at fedora:~$ tar xvf xcrysden-1.6.2.tar.gz
...
username at fedora:~$ cd xcrysden-1.6.2/
username at fedora:~/xcrysden-1.6.2$ cp system/Make.sys-semishared Make.sys
username at fedora:~/xcrysden-1.6.2$ wget 
https://raw.githubusercontent.com/gsabo/xcrysden-Patches/main/Make-fedora34.patch
...
username at fedora:~/xcrysden-1.6.2$ patch -b Make.sys Make-fedora34.patch
patching file Make.sys
username at fedora:~/xcrysden-1.6.2$ make all
...

Note: username in commands below should be replaced with your user name.

username at fedora:~/xcrysden-1.6.2$ echo 'export 
XCRYSDEN_TOPDIR=/home/username/xcrysden-1.6.2'>>~/.bashrc
username at fedora:~/xcrysden-1.6.2$ echo 'export 
PATH=$PATH:$XCRYSDEN_TOPDIR'>>~/.bashrc
username at fedora:~/xcrysden-1.6.2$ echo 'export 
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/Togl2.0'>>~/.bashrc
username at fedora:~/xcrysden-1.6.2$ source ~/.bashrc


Best Regards,

Gavin

XCrySDen user


On 8/26/2024 10:56 PM, delamora wrote:
> Dear Gavin,
> Thank for your reply, I will try it.
> Yes, I have the Fedora 40
> Pablo
> ------------------------------------------------------------------------
> The issue might be because the version of Fedora that you are using 
> does not have the operating system library that it needs to load 
> ftnunit.? Thus, the "error while loading" error.
>
>
> What is the Fedora version?? The xcrysden-1.5.60-bin-semishared worked 
> with around Fedora versions 25 to 27.
>
>
> With Fedora 34, xcrysden 1.6.2 was used, but it had to be compiled.
>
>
> The compile steps used were given the post at:
>
>
> http://www.democritos.it/pipermail/xcrysden/2021-April/002050.html 
> <http://www.democritos.it/pipermail/xcrysden/2021-April/002050.html>
>
>
> At https://fedoraproject.org <https://fedoraproject.org>?, I see that 
> Fedora is now at version 40.? I've not tried?XCrySDen 1.6.2 with that 
> version if that is what you are using.
>
>
> With some other code packages, I have seen some GNU compiler 
> compatibility issues encountered with newer Linux distributions that 
> release with gcc/g++ version 13.? With Ubuntu 24.04 LTS that comes 
> with?gcc/g++ version 13, though, I was able to fall back as a 
> workaround (while waiting to see if the code developers would provide 
> new versions with code changes for working with the newer compilers) 
> for example by installing a g++ version 10 package using "sudo apt 
> install g++-10".? Don't know yet if there are any issues compiling 
> XCrySDen 1.6.2 with the latest gcc versions or if Fedora has a similar 
> fall back package that can be installed like Ubuntu.
>
>
> Kind Regards,
>
> Gavin
>
> XCrySDen user
>
>
> On 8/26/2024 2:24 PM, delamora wrote:
>
>     I have Fedora Linux
>     I installed xcrysden-1.5.60-bin-semishared, but when I try to open it
>     "xcrysden"
>     it does not open, it gives the error;
>
>     /home/Programas/xcrysden-1.5.60-bin-semishared/bin/ftnunit: error
>     while loading
>
>     How can I fix it
>
>     Yours
>
>     Pablo
>
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From delamora at unam.mx  Thu Aug 29 00:12:49 2024
From: delamora at unam.mx (delamora)
Date: Wed, 28 Aug 2024 22:12:49 +0000
Subject: [xcrysden] Running XCrySDen
In-Reply-To: <e628d115-4c24-41c7-abc6-0ea4194817b1@gmail.com>
References: <BY5PR06MB6676824148773BE1E25FE099CB8B2@BY5PR06MB6676.namprd06.prod.outlook.com>
	<695b30bb-98d0-40d8-a5de-64d5b34aec3a@gmail.com>
	<BY5PR06MB667622090C4D831CA3E65987CB942@BY5PR06MB6676.namprd06.prod.outlook.com>
	<e628d115-4c24-41c7-abc6-0ea4194817b1@gmail.com>
Message-ID: <BY5PR06MB66768D53E29181C3D8865B2DCB952@BY5PR06MB6676.namprd06.prod.outlook.com>

I tried to run xcrysden and I get;
******
Version: 1.6.2
******
XCRYSDEN_TOPDIR=/home/Programas/xcrysden-1.6.2
XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp

/home/Programas/xcrysden-1.6.2/xcrysden: line 275: /home/Programas/xcrysden-1.6.2/bin/xcrys: No such file or directory

Pablo

________________________________
De: xcrysden-bounces at democritos.it <xcrysden-bounces at democritos.it> en nombre de Gavin Abo <gabo13279 at gmail.com>
Enviado: mi?rcoles, 28 de agosto de 2024 01:11 a. m.
Para: xcrysden at democritos.it <xcrysden at democritos.it>
Asunto: Re: [xcrysden] Running XCrySDen


I tried it out.  It seems to work as seen in the screenshot at:


https://github.com/gsabo/xcrysden-Patches/blob/main/Fedora%2040%20XCrySDen%201.6.2.png


Apparently, Fedora 40 ships with gcc version 14:


username at fedora:~$ gfortran --version
GNU Fortran (GCC) 14.2.1 20240801 (Red Hat 14.2.1-1)
Copyright (C) 2024 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


Most of the Fedora 34 steps still applied to Fedora 40, but I had to make some adjustments in order to get it to work as follows.


Since you already have Fedora 40 installed, you can skip to step 8 below.


1. Went to: https://getfedora.org/en/workstation/download/
2. Downloaded Fedora Workstation 40:
Fedora-Workstation-Live-x86_64-40-1.14.iso
3. Downloaded Fedora Media Writer Windows:
FedoraMediaWriter-win32-latest.exe
4. Ran: FedoraMediaWriter-win32-latest.exe
   a. Clicked "I Agree"
   b. Clicked "Install"
   c. Clicked "Next"
   d. With "Run Fedora Media Writer" selected, clicked "Finish"
   e. Selected "Select .iso file", then clicked "Next"
   f. Clicked "Select..."
   g. Selected "Fedora-Workstation-Live-x86_64-40-1.14.iso", then clicked "Open"
   h. Selected USB Drive, then clicked "Write"
   i. Click "Finish"
   j. Closed the Fedora Media Write dialog (upper right x in window)
5. Booted from the USB stick
6. Installed Fedora 40
    a. Selected "Start Fedora-Workstation-Live 40"
    b. Clicked "Install Fedora..."
    c. Selected English and clicked Continue
    d. Clicked "Installation Destination"
    e. Clicked Done
    WARNING: The steps f-h will wipe everything for starting fresh with the drive.
    f. Clicked "Reclaim space"
    g. Clicked "Delete all"
    h. Clicked "Reclaim space"
    i. Clicked "Begin Installation"
    j. Clicked "Finish Installation"
    k. In Fedora Live, click on bar with power icon, click on power icon, click "Restart", click "Restart" button
7. Setup Fedora 40
    a. Clicked "Start Setup"
    b. Click Skip (or setup Wi-Fi)
    c. Turn off "Location Services" and "Automatic Problem Reporting", then click Next
    d. Click "Enable Third-Party Repositories", then click Next
    e. Type a Full Name and Username and click Next
    f. Type a password and click Next
    g. Click "Start Using Fedora Linux"
    h. For tour prompt, click "Skip"
8. Opened a terminal in Fedora 40 and performed the following:

username at fedora:~$ sudo yum install patch ImageMagick openbabel mesa-libGL-devel mesa-libGLU-devel tcl-devel tk-devel fftw-devel libXmu-devel gfortran
...
Is this ok [y/N]: y
...
username at fedora:~$ wget https://sourceforge.net/projects/togl/files/Togl/2.0/Togl2.0-src.tar.gz/download
...
username at fedora:~$ tar xvf download
...
username at fedora:~$ cd Togl2.0/
username at fedora:~/Togl2.0$<mailto:username at fedora:~/Togl2.0$>  ./configure --with-tcl=/usr/lib64 --with-tk=/usr/lib64 --enable-64bit
...


The Togl 2.0 failed due the gcc version 14 compiler as seen here:


username at fedora:~/Togl2.0$<mailto:username at fedora:~/Togl2.0$> make
gcc -DPACKAGE_NAME=\"Togl\" -DPACKAGE_TARNAME=\"togl\" -DPACKAGE_VERSION=\"2.0\" -DPACKAGE_STRING=\"Togl\ 2.0\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_SYS_PARAM_H=1 -DUSE_THREAD_ALLOC=1 -D_REENTRANT=1 -D_THREAD_SAFE=1 -DTCL_THREADS=1 -DMODULE_SCOPE=extern\ __attribute__\(\(__visibility__\(\"hidden\"\)\)\) -D_LARGEFILE64_SOURCE=1 -DTCL_WIDE_INT_IS_LONG=1 -DUSE_TCL_STUBS=1 -DUSE_TK_STUBS=1 -DAUTOSTEREOD=\"\"  -I"/usr/include/tcl-private/generic" -I"/usr/include/tcl-private/unix" -I"/usr/include/tk-private/generic" -I"/usr/include/tk-private/unix" -I"/usr/include/tk-private/generic/ttk"     -pipe -m64 -O2 -fomit-frame-pointer -Wall -Wno-implicit-int -fPIC  -c `echo togl.c` -o togl.o
togl.c: In function ?Togl_Init?:
togl.c:928:26: error: assignment to ?void (*)(struct Tk_Window_ *, Tk_ClassProcs *, void *)? from incompatible pointer type ?void (*)(struct Tk_Window_ *, const Tk_ClassProcs *, void *)? [-Wincompatible-pointer-types]
  928 |         SetClassProcsPtr = tkStubsPtr->tk_SetClassProcs;
      |                          ^
make: *** [Makefile:357: togl.o] Error 1


However, I was able to patch it for continuing with the build:


username at fedora:~/Togl2.0$<mailto:username at fedora:~/Togl2.0$> wget https://raw.githubusercontent.com/gsabo/xcrysden-Patches/main/togl.patch

username at fedora:~/Togl2.0$<mailto:username at fedora:~/Togl2.0$> patch -b togl.c togl.patch
username at fedora:~/Togl2.0$<mailto:username at fedora:~/Togl2.0$> make

...

username at fedora:~/Togl2.0$<mailto:username at fedora:~/Togl2.0$> cd ..
username at fedora:~$ wget http://www.xcrysden.org/download/xcrysden-1.6.2.tar.gz
...
username at fedora:~$ tar xvf xcrysden-1.6.2.tar.gz
...
username at fedora:~$ cd xcrysden-1.6.2/
username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> cp system/Make.sys-semishared Make.sys
username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> wget https://raw.githubusercontent.com/gsabo/xcrysden-Patches/main/Make-fedora34.patch
...
username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> patch -b Make.sys Make-fedora34.patch
patching file Make.sys
username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> make all
...

Note: username in commands below should be replaced with your user name.

username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> echo 'export XCRYSDEN_TOPDIR=/home/username/xcrysden-1.6.2'>>~/.bashrc
username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> echo 'export PATH=$PATH:$XCRYSDEN_TOPDIR'>>~/.bashrc
username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/Togl2.0'>>~/.bashrc
username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> source ~/.bashrc


Best Regards,

Gavin

XCrySDen user


On 8/26/2024 10:56 PM, delamora wrote:
Dear Gavin,
Thank for your reply, I will try it.
Yes, I have the Fedora 40
Pablo
________________________________
The issue might be because the version of Fedora that you are using does not have the operating system library that it needs to load ftnunit.  Thus, the "error while loading" error.


What is the Fedora version?  The xcrysden-1.5.60-bin-semishared worked with around Fedora versions 25 to 27.


With Fedora 34, xcrysden 1.6.2 was used, but it had to be compiled.


The compile steps used were given the post at:


http://www.democritos.it/pipermail/xcrysden/2021-April/002050.html


At https://fedoraproject.org , I see that Fedora is now at version 40.  I've not tried XCrySDen 1.6.2 with that version if that is what you are using.


With some other code packages, I have seen some GNU compiler compatibility issues encountered with newer Linux distributions that release with gcc/g++ version 13.  With Ubuntu 24.04 LTS that comes with gcc/g++ version 13, though, I was able to fall back as a workaround (while waiting to see if the code developers would provide new versions with code changes for working with the newer compilers) for example by installing a g++ version 10 package using "sudo apt install g++-10".  Don't know yet if there are any issues compiling XCrySDen 1.6.2 with the latest gcc versions or if Fedora has a similar fall back package that can be installed like Ubuntu.


Kind Regards,

Gavin

XCrySDen user


On 8/26/2024 2:24 PM, delamora wrote:
I have Fedora Linux
I installed xcrysden-1.5.60-bin-semishared, but when I try to open it
"xcrysden"
it does not open, it gives the error;

/home/Programas/xcrysden-1.5.60-bin-semishared/bin/ftnunit: error while loading

How can I fix it

Yours

Pablo
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From delamora at unam.mx  Thu Aug 29 00:59:01 2024
From: delamora at unam.mx (delamora)
Date: Wed, 28 Aug 2024 22:59:01 +0000
Subject: [xcrysden] Running XCrySDen
In-Reply-To: <BY5PR06MB66768D53E29181C3D8865B2DCB952@BY5PR06MB6676.namprd06.prod.outlook.com>
References: <BY5PR06MB6676824148773BE1E25FE099CB8B2@BY5PR06MB6676.namprd06.prod.outlook.com>
	<695b30bb-98d0-40d8-a5de-64d5b34aec3a@gmail.com>
	<BY5PR06MB667622090C4D831CA3E65987CB942@BY5PR06MB6676.namprd06.prod.outlook.com>
	<e628d115-4c24-41c7-abc6-0ea4194817b1@gmail.com>
	<BY5PR06MB66768D53E29181C3D8865B2DCB952@BY5PR06MB6676.namprd06.prod.outlook.com>
Message-ID: <BY5PR06MB6676A6F015FAB75FBC2EDF2BCB952@BY5PR06MB6676.namprd06.prod.outlook.com>

I got the
xcrysden-1.6.2-bin-shared
then I ran
xcrysden
and I got
-------------
[ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.
        Code available from http://www.xcrysden.org/.

XCRYSD[ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.
        Code available from http://www.xcrysden.org/.

XCRYSDEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared
XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp

/home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading shared libraries: libtk8.6.so: cannot open shared object file: No such file or directoryEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared
XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp

/home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading shared libraries: libtk8.6.so: cannot open shared object file: No such file or directory
------------------------------
In the xcrysden page it says;
  *
  *   Linux x86_64 binary packages (64bit):

  *   Shared: xcrysden-1.6.2-linux_x86_64-shared.tar.gz<http://www.xcrysden.org/download/xcrysden-1.6.2-linux_x86_64-shared.tar.gz>
     *   Requires: libtk8.6.so, libtcl8.6.so, libTogl.so.2, libGLU.so.1, libGL.so.1, libfftw3.so.3, libXmu.so.6, libX11.so.6, libgfortran.so.5, ..

-------------------------
so I searched for these packages and I got

dnf search libtk8.6.so libtcl8.6.so libTogl.so.2 libGLU.so.1 libGL.so.1 libfftw3.so.3 libXmu.so.6 libX11.so.6 libgfortran.so.5
?ltima comprobaci?n de caducidad de metadatos hecha hace 2:37:04, el mi? 28 ago 2024 13:17:04.
No se encontraron coincidencias.
(=>there were no coincidences)

Saludos

Pablo
________________________________
De: delamora <delamora at unam.mx>
Enviado: mi?rcoles, 28 de agosto de 2024 04:12 p. m.
Para: XCrySDen mailing list <xcrysden at democritos.it>
Asunto: Re: [xcrysden] Running XCrySDen

I tried to run xcrysden and I get;
******
Version: 1.6.2
******
XCRYSDEN_TOPDIR=/home/Programas/xcrysden-1.6.2
XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp

/home/Programas/xcrysden-1.6.2/xcrysden: line 275: /home/Programas/xcrysden-1.6.2/bin/xcrys: No such file or directory

Pablo

________________________________
De: xcrysden-bounces at democritos.it <xcrysden-bounces at democritos.it> en nombre de Gavin Abo <gabo13279 at gmail.com>
Enviado: mi?rcoles, 28 de agosto de 2024 01:11 a. m.
Para: xcrysden at democritos.it <xcrysden at democritos.it>
Asunto: Re: [xcrysden] Running XCrySDen


I tried it out.  It seems to work as seen in the screenshot at:


https://github.com/gsabo/xcrysden-Patches/blob/main/Fedora%2040%20XCrySDen%201.6.2.png


Apparently, Fedora 40 ships with gcc version 14:


username at fedora:~$ gfortran --version
GNU Fortran (GCC) 14.2.1 20240801 (Red Hat 14.2.1-1)
Copyright (C) 2024 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


Most of the Fedora 34 steps still applied to Fedora 40, but I had to make some adjustments in order to get it to work as follows.


Since you already have Fedora 40 installed, you can skip to step 8 below.


1. Went to: https://getfedora.org/en/workstation/download/
2. Downloaded Fedora Workstation 40:
Fedora-Workstation-Live-x86_64-40-1.14.iso
3. Downloaded Fedora Media Writer Windows:
FedoraMediaWriter-win32-latest.exe
4. Ran: FedoraMediaWriter-win32-latest.exe
   a. Clicked "I Agree"
   b. Clicked "Install"
   c. Clicked "Next"
   d. With "Run Fedora Media Writer" selected, clicked "Finish"
   e. Selected "Select .iso file", then clicked "Next"
   f. Clicked "Select..."
   g. Selected "Fedora-Workstation-Live-x86_64-40-1.14.iso", then clicked "Open"
   h. Selected USB Drive, then clicked "Write"
   i. Click "Finish"
   j. Closed the Fedora Media Write dialog (upper right x in window)
5. Booted from the USB stick
6. Installed Fedora 40
    a. Selected "Start Fedora-Workstation-Live 40"
    b. Clicked "Install Fedora..."
    c. Selected English and clicked Continue
    d. Clicked "Installation Destination"
    e. Clicked Done
    WARNING: The steps f-h will wipe everything for starting fresh with the drive.
    f. Clicked "Reclaim space"
    g. Clicked "Delete all"
    h. Clicked "Reclaim space"
    i. Clicked "Begin Installation"
    j. Clicked "Finish Installation"
    k. In Fedora Live, click on bar with power icon, click on power icon, click "Restart", click "Restart" button
7. Setup Fedora 40
    a. Clicked "Start Setup"
    b. Click Skip (or setup Wi-Fi)
    c. Turn off "Location Services" and "Automatic Problem Reporting", then click Next
    d. Click "Enable Third-Party Repositories", then click Next
    e. Type a Full Name and Username and click Next
    f. Type a password and click Next
    g. Click "Start Using Fedora Linux"
    h. For tour prompt, click "Skip"
8. Opened a terminal in Fedora 40 and performed the following:

username at fedora:~$ sudo yum install patch ImageMagick openbabel mesa-libGL-devel mesa-libGLU-devel tcl-devel tk-devel fftw-devel libXmu-devel gfortran
...
Is this ok [y/N]: y
...
username at fedora:~$ wget https://sourceforge.net/projects/togl/files/Togl/2.0/Togl2.0-src.tar.gz/download
...
username at fedora:~$ tar xvf download
...
username at fedora:~$ cd Togl2.0/
username at fedora:~/Togl2.0$<mailto:username at fedora:~/Togl2.0$>  ./configure --with-tcl=/usr/lib64 --with-tk=/usr/lib64 --enable-64bit
...


The Togl 2.0 failed due the gcc version 14 compiler as seen here:


username at fedora:~/Togl2.0$<mailto:username at fedora:~/Togl2.0$> make
gcc -DPACKAGE_NAME=\"Togl\" -DPACKAGE_TARNAME=\"togl\" -DPACKAGE_VERSION=\"2.0\" -DPACKAGE_STRING=\"Togl\ 2.0\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_SYS_PARAM_H=1 -DUSE_THREAD_ALLOC=1 -D_REENTRANT=1 -D_THREAD_SAFE=1 -DTCL_THREADS=1 -DMODULE_SCOPE=extern\ __attribute__\(\(__visibility__\(\"hidden\"\)\)\) -D_LARGEFILE64_SOURCE=1 -DTCL_WIDE_INT_IS_LONG=1 -DUSE_TCL_STUBS=1 -DUSE_TK_STUBS=1 -DAUTOSTEREOD=\"\"  -I"/usr/include/tcl-private/generic" -I"/usr/include/tcl-private/unix" -I"/usr/include/tk-private/generic" -I"/usr/include/tk-private/unix" -I"/usr/include/tk-private/generic/ttk"     -pipe -m64 -O2 -fomit-frame-pointer -Wall -Wno-implicit-int -fPIC  -c `echo togl.c` -o togl.o
togl.c: In function ?Togl_Init?:
togl.c:928:26: error: assignment to ?void (*)(struct Tk_Window_ *, Tk_ClassProcs *, void *)? from incompatible pointer type ?void (*)(struct Tk_Window_ *, const Tk_ClassProcs *, void *)? [-Wincompatible-pointer-types]
  928 |         SetClassProcsPtr = tkStubsPtr->tk_SetClassProcs;
      |                          ^
make: *** [Makefile:357: togl.o] Error 1


However, I was able to patch it for continuing with the build:


username at fedora:~/Togl2.0$<mailto:username at fedora:~/Togl2.0$> wget https://raw.githubusercontent.com/gsabo/xcrysden-Patches/main/togl.patch

username at fedora:~/Togl2.0$<mailto:username at fedora:~/Togl2.0$> patch -b togl.c togl.patch
username at fedora:~/Togl2.0$<mailto:username at fedora:~/Togl2.0$> make

...

username at fedora:~/Togl2.0$<mailto:username at fedora:~/Togl2.0$> cd ..
username at fedora:~$ wget http://www.xcrysden.org/download/xcrysden-1.6.2.tar.gz
...
username at fedora:~$ tar xvf xcrysden-1.6.2.tar.gz
...
username at fedora:~$ cd xcrysden-1.6.2/
username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> cp system/Make.sys-semishared Make.sys
username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> wget https://raw.githubusercontent.com/gsabo/xcrysden-Patches/main/Make-fedora34.patch
...
username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> patch -b Make.sys Make-fedora34.patch
patching file Make.sys
username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> make all
...

Note: username in commands below should be replaced with your user name.

username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> echo 'export XCRYSDEN_TOPDIR=/home/username/xcrysden-1.6.2'>>~/.bashrc
username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> echo 'export PATH=$PATH:$XCRYSDEN_TOPDIR'>>~/.bashrc
username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/Togl2.0'>>~/.bashrc
username at fedora:~/xcrysden-1.6.2$<mailto:username at fedora:~/xcrysden-1.6.2$> source ~/.bashrc


Best Regards,

Gavin

XCrySDen user


On 8/26/2024 10:56 PM, delamora wrote:
Dear Gavin,
Thank for your reply, I will try it.
Yes, I have the Fedora 40
Pablo
________________________________
The issue might be because the version of Fedora that you are using does not have the operating system library that it needs to load ftnunit.  Thus, the "error while loading" error.


What is the Fedora version?  The xcrysden-1.5.60-bin-semishared worked with around Fedora versions 25 to 27.


With Fedora 34, xcrysden 1.6.2 was used, but it had to be compiled.


The compile steps used were given the post at:


http://www.democritos.it/pipermail/xcrysden/2021-April/002050.html


At https://fedoraproject.org , I see that Fedora is now at version 40.  I've not tried XCrySDen 1.6.2 with that version if that is what you are using.


With some other code packages, I have seen some GNU compiler compatibility issues encountered with newer Linux distributions that release with gcc/g++ version 13.  With Ubuntu 24.04 LTS that comes with gcc/g++ version 13, though, I was able to fall back as a workaround (while waiting to see if the code developers would provide new versions with code changes for working with the newer compilers) for example by installing a g++ version 10 package using "sudo apt install g++-10".  Don't know yet if there are any issues compiling XCrySDen 1.6.2 with the latest gcc versions or if Fedora has a similar fall back package that can be installed like Ubuntu.


Kind Regards,

Gavin

XCrySDen user


On 8/26/2024 2:24 PM, delamora wrote:
I have Fedora Linux
I installed xcrysden-1.5.60-bin-semishared, but when I try to open it
"xcrysden"
it does not open, it gives the error;

/home/Programas/xcrysden-1.5.60-bin-semishared/bin/ftnunit: error while loading

How can I fix it

Yours

Pablo
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From gabo13279 at gmail.com  Thu Aug 29 04:16:57 2024
From: gabo13279 at gmail.com (Gavin Abo)
Date: Wed, 28 Aug 2024 20:16:57 -0600
Subject: [xcrysden] Running XCrySDen
In-Reply-To: <BY5PR06MB6676A6F015FAB75FBC2EDF2BCB952@BY5PR06MB6676.namprd06.prod.outlook.com>
References: <BY5PR06MB6676824148773BE1E25FE099CB8B2@BY5PR06MB6676.namprd06.prod.outlook.com>
	<695b30bb-98d0-40d8-a5de-64d5b34aec3a@gmail.com>
	<BY5PR06MB667622090C4D831CA3E65987CB942@BY5PR06MB6676.namprd06.prod.outlook.com>
	<e628d115-4c24-41c7-abc6-0ea4194817b1@gmail.com>
	<BY5PR06MB66768D53E29181C3D8865B2DCB952@BY5PR06MB6676.namprd06.prod.outlook.com>
	<BY5PR06MB6676A6F015FAB75FBC2EDF2BCB952@BY5PR06MB6676.namprd06.prod.outlook.com>
Message-ID: <052b52f0-1dba-47c4-b2bc-19c22dc8a3e3@gmail.com>

I see that you have the error "libtk8.6.so: cannot open shared object 
file: No such file or directory".


 From the message, it looks like XCrySDen cannot find the libtk8.6.so file.


That file should be in your /lib64 directory:


username at fedora:~$ ls -l /lib64/libtk8.6.so
-rwxr-xr-x. 1 root root 1343528 Jan 26? 2024 /lib64/libtk8.6.so


If it isn't, the package for it might not be installed.


In Fedora 40, it was likely installed by the command:


sudo yum install tk-devel


Kind Regards,

Gavin

XCrySDen user


On 8/28/2024 4:59 PM, delamora wrote:
> I got the
> xcrysden-1.6.2-bin-shared
> then I ran
> xcrysden
> and I got
> -------------
> [ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.
> ? ? ? ? Code available from http://www.xcrysden.org/.
>
> XCRYSD[ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.
> ? ? ? ? Code available from http://www.xcrysden.org/.
>
> XCRYSDEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared
> XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp
>
> /home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while 
> loading shared libraries: libtk8.6.so: cannot open shared object file: 
> No such file or 
> directoryEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared
> XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp
>
> /home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while 
> loading shared libraries: libtk8.6.so: cannot open shared object file: 
> No such file or directory
> ------------------------------
> In the xcrysden page it says;
>#
>
> # */Linux x86_64/*/?binary packages (64bit):/
>
>   * Shared: xcrysden-1.6.2-linux_x86_64-shared.tar.gz
>     <http://www.xcrysden.org/download/xcrysden-1.6.2-linux_x86_64-shared.tar.gz>
>       o Requires: libtk8.6.so, libtcl8.6.so, libTogl.so.2,
>         libGLU.so.1, libGL.so.1, libfftw3.so.3, libXmu.so.6,
>         libX11.so.6, libgfortran.so.5, ..
>
> -------------------------
> so I searched for these packages and I got
>
> dnf search libtk8.6.so libtcl8.6.so libTogl.so.2 libGLU.so.1 
> libGL.so.1 libfftw3.so.3 libXmu.so.6 libX11.so.6 libgfortran.so.5
> ?ltima comprobaci?n de caducidad de metadatos hecha hace 2:37:04, el 
> mi? 28 ago 2024 13:17:04.
> No se encontraron coincidencias.
> (=>there were no coincidences)
>
> Saludos
>
> Pablo
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From delamora at unam.mx  Thu Aug 29 18:37:40 2024
From: delamora at unam.mx (delamora)
Date: Thu, 29 Aug 2024 16:37:40 +0000
Subject: [xcrysden] Running XCrySDen
In-Reply-To: <052b52f0-1dba-47c4-b2bc-19c22dc8a3e3@gmail.com>
References: <BY5PR06MB6676824148773BE1E25FE099CB8B2@BY5PR06MB6676.namprd06.prod.outlook.com>
	<695b30bb-98d0-40d8-a5de-64d5b34aec3a@gmail.com>
	<BY5PR06MB667622090C4D831CA3E65987CB942@BY5PR06MB6676.namprd06.prod.outlook.com>
	<e628d115-4c24-41c7-abc6-0ea4194817b1@gmail.com>
	<BY5PR06MB66768D53E29181C3D8865B2DCB952@BY5PR06MB6676.namprd06.prod.outlook.com>
	<BY5PR06MB6676A6F015FAB75FBC2EDF2BCB952@BY5PR06MB6676.namprd06.prod.outlook.com>
	<052b52f0-1dba-47c4-b2bc-19c22dc8a3e3@gmail.com>
Message-ID: <BY5PR06MB667609773C2282D58C4EB11ACB962@BY5PR06MB6676.namprd06.prod.outlook.com>

I found it;
----
# find / -name *libtk8.6*
/opt/intel/oneapi/intelpython/python3.9/pkgs/tk-8.6.10-hbc83047_0/lib/libtk8.6.so
/opt/intel/oneapi/intelpython/python3.9/envs/2022.0.2/lib/libtk8.6.so
/opt/intel/oneapi/intelpython/python3.9/lib/libtk8.6.so
----
but xcrysden does not find it

Pablo
________________________________
De: xcrysden-bounces at democritos.it <xcrysden-bounces at democritos.it> en nombre de Gavin Abo <gabo13279 at gmail.com>
Enviado: mi?rcoles, 28 de agosto de 2024 08:16 p. m.
Para: xcrysden at democritos.it <xcrysden at democritos.it>
Asunto: Re: [xcrysden] Running XCrySDen


I see that you have the error "libtk8.6.so: cannot open shared object file: No such file or directory".



From gabo13279 at gmail.com  Fri Aug 30 05:50:53 2024
From: gabo13279 at gmail.com (Gavin Abo)
Date: Thu, 29 Aug 2024 21:50:53 -0600
Subject: [xcrysden] Running XCrySDen
In-Reply-To: <BY5PR06MB667609773C2282D58C4EB11ACB962@BY5PR06MB6676.namprd06.prod.outlook.com>
References: <BY5PR06MB6676824148773BE1E25FE099CB8B2@BY5PR06MB6676.namprd06.prod.outlook.com>
	<695b30bb-98d0-40d8-a5de-64d5b34aec3a@gmail.com>
	<BY5PR06MB667622090C4D831CA3E65987CB942@BY5PR06MB6676.namprd06.prod.outlook.com>
	<e628d115-4c24-41c7-abc6-0ea4194817b1@gmail.com>
	<BY5PR06MB66768D53E29181C3D8865B2DCB952@BY5PR06MB6676.namprd06.prod.outlook.com>
	<BY5PR06MB6676A6F015FAB75FBC2EDF2BCB952@BY5PR06MB6676.namprd06.prod.outlook.com>
	<052b52f0-1dba-47c4-b2bc-19c22dc8a3e3@gmail.com>
	<BY5PR06MB667609773C2282D58C4EB11ACB962@BY5PR06MB6676.namprd06.prod.outlook.com>
Message-ID: <db69e186-0341-43e1-b1fd-4ddc1205621f@gmail.com>

XCrySDen 1.6.2 works with Fedora 40 when libtk8.6.so from the operating 
system tk-devel package is used.


I've not tried libtk8.6.so from Intel's OneAPI.? That library file 
likely was compiled with the Intel compiler. So, it might be that the 
file has different function declarations than that produced by GCC.? 
That might explain why you would need the?libtk8.6.so from the operating 
system package that was compiled with GCC for being able to use 
xcrysden-1.6.2-linux_x86_64-shared.tar.gz.


Thus, if you wanted to use 
/opt/intel/oneapi/intelpython/python3.9/lib/libtk8.6.so (instead of 
/lib64/libtk8.6.so), it is likely that you would need to compile 
XCrySDen using xcrysden-1.6.2.tar.gz and you would need to modify 
Make.sys yourself to use the OneAPI compiler.? Since that is probably a 
more difficult approach, I would recommend using the operating system 
version of libtk8.6.so instead.


For that, at [1], the webpage shows the Fedora 40 operating system 
tk-devel package. The tk-devel package when installed puts libtk.so 
(i.e., libtk8.6.so) also in the directory:


/usr/lib64/


With Fedora 40, when I checked that directory, the libtk8.6.so was there:


username at fedora:~$ ls -l /usr/lib64/libtk*
-rwxr-xr-x. 1 root root 1343528 Jan 26? 2024 /usr/lib64/libtk8.6.so
lrwxrwxrwx. 1 root root????? 11 Jan 26? 2024 /usr/lib64/libtk.so -> 
libtk8.6.so
-rwxr-xr-x. 1 root root??? 6640 Jan 26? 2024 /usr/lib64/libtkstub8.6.a


When the tk-devel package has been successfully installed, the terminal 
should show the same or similar terminal display of:


username at fedora:~$ sudo yum install tk-devel
[sudo] password for username:
Last metadata expiration check: 0:27:44 ago on Thu 29 Aug 2024 09:16:34 
PM MDT.
Package tk-devel-1:8.6.13-3.fc40.x86_64 is already installed.
Dependencies resolved.
Nothing to do.
Complete!


[1] https://packages.fedoraproject.org/pkgs/tk/tk-devel/fedora-40.html


Kind Regards,

Gavin

XCrySDen user


On 8/29/2024 10:37 AM, delamora wrote:
> I found it;
> ----
> # find / -name *libtk8.6*
> /opt/intel/oneapi/intelpython/python3.9/pkgs/tk-8.6.10-hbc83047_0/lib/libtk8.6.so
> /opt/intel/oneapi/intelpython/python3.9/envs/2022.0.2/lib/libtk8.6.so
> /opt/intel/oneapi/intelpython/python3.9/lib/libtk8.6.so
> ----
> but xcrysden does not find it
>
> Pablo
> ------------------------------------------------------------------------
> *De:* xcrysden-bounces at democritos.it <xcrysden-bounces at democritos.it> 
> en nombre de Gavin Abo <gabo13279 at gmail.com>
> *Enviado:*?mi?rcoles, 28 de agosto de 2024 08:16 p. m.
> *Para:* xcrysden at democritos.it <xcrysden at democritos.it>
> *Asunto:*?Re: [xcrysden] Running XCrySDen
>
> I see that you have the error "libtk8.6.so: cannot open shared object 
> file: No such file or directory".
>
>
> From the message, it looks like XCrySDen cannot find the libtk8.6.so file.
>
>
> That file should be in your /lib64 directory:
>
>
> username at fedora:~$ ls -l /lib64/libtk8.6.so
> -rwxr-xr-x. 1 root root 1343528 Jan 26? 2024 /lib64/libtk8.6.so
>
>
> If it isn't, the package for it might not be installed.
>
>
> In Fedora 40, it was likely installed by the command:
>
>
> sudo yum install tk-devel
>
>
> Kind Regards,
>
> Gavin
>
> XCrySDen user
>
>
> On 8/28/2024 4:59 PM, delamora wrote:
>
>     I got the
>     xcrysden-1.6.2-bin-shared
>     then I ran
>     xcrysden
>     and I got
>     -------------
>     [ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.
>     ? ? ? ? Code available from http://www.xcrysden.org/
>     <http://www.xcrysden.org/>.
>
>     XCRYSD[ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp.
>     176-179, 1999.
>     ? ? ? ? Code available from http://www.xcrysden.org/
>     <http://www.xcrysden.org/>.
>
>     XCRYSDEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared
>     XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp
>
>     /home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while
>     loading shared libraries: libtk8.6.so: cannot open shared object
>     file: No such file or
>     directoryEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared
>     XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp
>
>     /home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while
>     loading shared libraries: libtk8.6.so: cannot open shared object
>     file: No such file or directory
>     ------------------------------
>     In the xcrysden page it says;
>  #
>
>   # */Linux x86_64/*/?binary packages (64bit):/
>
>       * Shared: xcrysden-1.6.2-linux_x86_64-shared.tar.gz
>         <http://www.xcrysden.org/download/xcrysden-1.6.2-linux_x86_64-shared.tar.gz>
>           o Requires: libtk8.6.so, libtcl8.6.so, libTogl.so.2,
>             libGLU.so.1, libGL.so.1, libfftw3.so.3, libXmu.so.6,
>             libX11.so.6, libgfortran.so.5, ..
>
>     -------------------------
>     so I searched for these packages and I got
>
>     dnf search libtk8.6.so libtcl8.6.so libTogl.so.2 libGLU.so.1
>     libGL.so.1 libfftw3.so.3 libXmu.so.6 libX11.so.6 libgfortran.so.5
>     ?ltima comprobaci?n de caducidad de metadatos hecha hace 2:37:04,
>     el mi? 28 ago 2024 13:17:04.
>     No se encontraron coincidencias.
>     (=>there were no coincidences)
>
>     Saludos
>
>     Pablo
>
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From delamora at unam.mx  Fri Aug 30 19:58:34 2024
From: delamora at unam.mx (delamora)
Date: Fri, 30 Aug 2024 17:58:34 +0000
Subject: [xcrysden] Running XCrySDen
In-Reply-To: <db69e186-0341-43e1-b1fd-4ddc1205621f@gmail.com>
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	<695b30bb-98d0-40d8-a5de-64d5b34aec3a@gmail.com>
	<BY5PR06MB667622090C4D831CA3E65987CB942@BY5PR06MB6676.namprd06.prod.outlook.com>
	<e628d115-4c24-41c7-abc6-0ea4194817b1@gmail.com>
	<BY5PR06MB66768D53E29181C3D8865B2DCB952@BY5PR06MB6676.namprd06.prod.outlook.com>
	<BY5PR06MB6676A6F015FAB75FBC2EDF2BCB952@BY5PR06MB6676.namprd06.prod.outlook.com>
	<052b52f0-1dba-47c4-b2bc-19c22dc8a3e3@gmail.com>
	<BY5PR06MB667609773C2282D58C4EB11ACB962@BY5PR06MB6676.namprd06.prod.outlook.com>
	<db69e186-0341-43e1-b1fd-4ddc1205621f@gmail.com>
Message-ID: <BY5PR06MB66767AF7E697D1219D8603AACB972@BY5PR06MB6676.namprd06.prod.outlook.com>

Estimado Gavin,

Running xcrysden, now it opens, but it gives this error;

./ftnunit: error while loading shared libraries: libgfortran.so.5: cannot open shared object file: No such file or directory

I have intel fortran in

pablo at fedora:/home/Programas/xcrysden-1.6.2-bin-shared$ locate libgfortran
/opt/intel/oneapi/intelpython/python3.9/pkgs/_openmp_mutex-4.5-1_gnu/info/recipe/parent/install-libgfortran.sh
/opt/intel/oneapi/intelpython/python3.9/pkgs/libgcc-ng-9.3.0-h5101ec6_17/info/recipe/parent/install-libgfortran.sh
/opt/intel/oneapi/intelpython/python3.9/pkgs/libgomp-9.3.0-h5101ec6_17/info/recipe/parent/install-libgfortran.sh
/opt/intel/oneapi/intelpython/python3.9/pkgs/libstdcxx-ng-9.3.0-hd4cf53a_17/info/recipe/parent/install-libgfortran.sh
/var/lib/flatpak/runtime/org.fedoraproject.KDE6Platform/x86_64/f40/286405d778e073e4e01d75c42074307b13cfec2e00913baf6d552d8e7c584670/files/lib64/libgfortran.so.5
/var/lib/flatpak/runtime/org.fedoraproject.KDE6Platform/x86_64/f40/286405d778e073e4e01d75c42074307b13cfec2e00913baf6d552d8e7c584670/files/lib64/libgfortran.so.5.0.0

how to link intel fortran with xcrysden

Pablo
________________________________
De: xcrysden-bounces at democritos.it <xcrysden-bounces at democritos.it> en nombre de Gavin Abo <gabo13279 at gmail.com>
Enviado: jueves, 29 de agosto de 2024 09:50 p. m.
Para: xcrysden at democritos.it <xcrysden at democritos.it>
Asunto: Re: [xcrysden] Running XCrySDen


XCrySDen 1.6.2 works with Fedora 40 when libtk8.6.so from the operating system tk-devel package is used.


I've not tried libtk8.6.so from Intel's OneAPI.  That library file likely was compiled with the Intel compiler. So, it might be that the file has different function declarations than that produced by GCC.  That might explain why you would need the libtk8.6.so from the operating system package that was compiled with GCC for being able to use xcrysden-1.6.2-linux_x86_64-shared.tar.gz.


Thus, if you wanted to use /opt/intel/oneapi/intelpython/python3.9/lib/libtk8.6.so (instead of /lib64/libtk8.6.so), it is likely that you would need to compile XCrySDen using xcrysden-1.6.2.tar.gz and you would need to modify Make.sys yourself to use the OneAPI compiler.  Since that is probably a more difficult approach, I would recommend using the operating system version of libtk8.6.so instead.


For that, at [1], the webpage shows the Fedora 40 operating system tk-devel package. The tk-devel package when installed puts libtk.so (i.e., libtk8.6.so) also in the directory:


/usr/lib64/


With Fedora 40, when I checked that directory, the libtk8.6.so was there:


username at fedora:~$ ls -l /usr/lib64/libtk*
-rwxr-xr-x. 1 root root 1343528 Jan 26  2024 /usr/lib64/libtk8.6.so
lrwxrwxrwx. 1 root root      11 Jan 26  2024 /usr/lib64/libtk.so -> libtk8.6.so
-rwxr-xr-x. 1 root root    6640 Jan 26  2024 /usr/lib64/libtkstub8.6.a


When the tk-devel package has been successfully installed, the terminal should show the same or similar terminal display of:


username at fedora:~$ sudo yum install tk-devel
[sudo] password for username:
Last metadata expiration check: 0:27:44 ago on Thu 29 Aug 2024 09:16:34 PM MDT.
Package tk-devel-1:8.6.13-3.fc40.x86_64 is already installed.
Dependencies resolved.
Nothing to do.
Complete!


[1] https://packages.fedoraproject.org/pkgs/tk/tk-devel/fedora-40.html


Kind Regards,

Gavin

XCrySDen user


On 8/29/2024 10:37 AM, delamora wrote:
I found it;
----
# find / -name *libtk8.6*
/opt/intel/oneapi/intelpython/python3.9/pkgs/tk-8.6.10-hbc83047_0/lib/libtk8.6.so
/opt/intel/oneapi/intelpython/python3.9/envs/2022.0.2/lib/libtk8.6.so
/opt/intel/oneapi/intelpython/python3.9/lib/libtk8.6.so
----
but xcrysden does not find it

Pablo
________________________________
De: xcrysden-bounces at democritos.it<mailto:xcrysden-bounces at democritos.it> <xcrysden-bounces at democritos.it><mailto:xcrysden-bounces at democritos.it> en nombre de Gavin Abo <gabo13279 at gmail.com><mailto:gabo13279 at gmail.com>
Enviado: mi?rcoles, 28 de agosto de 2024 08:16 p. m.
Para: xcrysden at democritos.it<mailto:xcrysden at democritos.it> <xcrysden at democritos.it><mailto:xcrysden at democritos.it>
Asunto: Re: [xcrysden] Running XCrySDen


I see that you have the error "libtk8.6.so: cannot open shared object file: No such file or directory".



From gabo13279 at gmail.com  Sat Aug 31 02:10:57 2024
From: gabo13279 at gmail.com (Gavin Abo)
Date: Fri, 30 Aug 2024 18:10:57 -0600
Subject: [xcrysden] Running XCrySDen
In-Reply-To: <db69e186-0341-43e1-b1fd-4ddc1205621f@gmail.com>
References: <BY5PR06MB6676824148773BE1E25FE099CB8B2@BY5PR06MB6676.namprd06.prod.outlook.com>
	<695b30bb-98d0-40d8-a5de-64d5b34aec3a@gmail.com>
	<BY5PR06MB667622090C4D831CA3E65987CB942@BY5PR06MB6676.namprd06.prod.outlook.com>
	<e628d115-4c24-41c7-abc6-0ea4194817b1@gmail.com>
	<BY5PR06MB66768D53E29181C3D8865B2DCB952@BY5PR06MB6676.namprd06.prod.outlook.com>
	<BY5PR06MB6676A6F015FAB75FBC2EDF2BCB952@BY5PR06MB6676.namprd06.prod.outlook.com>
	<052b52f0-1dba-47c4-b2bc-19c22dc8a3e3@gmail.com>
	<BY5PR06MB667609773C2282D58C4EB11ACB962@BY5PR06MB6676.namprd06.prod.outlook.com>
	<db69e186-0341-43e1-b1fd-4ddc1205621f@gmail.com>
Message-ID: <eba03903-c351-4012-a408-4c8648ec4dbd@gmail.com>

In a previous post [1], there was a terminal command on a single line:


sudo yum install patch ImageMagick openbabel mesa-libGL-devel 
mesa-libGLU-devel tcl-devel tk-devel fftw-devel libXmu-devel gfortran


Maybe you missed entering all or parts of that command.? The 
libgfortran.so.5 should be provided by the gfortran package in that command.


[1] http://www.democritos.it/pipermail/xcrysden/2024-August/002139.html


Kind Regards,

Gavin

XCrySDen user


> On 8/30/2024, delamora wrote:
>> Estimado Gavin,
>>
>> Running xcrysden, now it opens, but it gives this error;
>>
>> ./ftnunit: error while loading shared libraries: libgfortran.so.5: 
>> cannot open shared object file: No such file or directory
>>
>> I have intel fortran in
>>
>> pablo at fedora:/home/Programas/xcrysden-1.6.2-bin-shared$ locate 
>> libgfortran
>> /opt/intel/oneapi/intelpython/python3.9/pkgs/_openmp_mutex-4.5-1_gnu/info/recipe/parent/install-libgfortran.sh
>> /opt/intel/oneapi/intelpython/python3.9/pkgs/libgcc-ng-9.3.0-h5101ec6_17/info/recipe/parent/install-libgfortran.sh
>> /opt/intel/oneapi/intelpython/python3.9/pkgs/libgomp-9.3.0-h5101ec6_17/info/recipe/parent/install-libgfortran.sh
>> /opt/intel/oneapi/intelpython/python3.9/pkgs/libstdcxx-ng-9.3.0-hd4cf53a_17/info/recipe/parent/install-libgfortran.sh
>> /var/lib/flatpak/runtime/org.fedoraproject.KDE6Platform/x86_64/f40/286405d778e073e4e01d75c42074307b13cfec2e00913baf6d552d8e7c584670/files/lib64/libgfortran.so.5
>> /var/lib/flatpak/runtime/org.fedoraproject.KDE6Platform/x86_64/f40/286405d778e073e4e01d75c42074307b13cfec2e00913baf6d552d8e7c584670/files/lib64/libgfortran.so.5.0.0
>>
>> how to link intel fortran with xcrysden
>>
>> Pabl30o
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