From tone.kokalj at ijs.si  Mon Aug  1 13:16:38 2022
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 01 Aug 2022 13:16:38 +0200
Subject: [xcrysden] Error: while executing exec sh optcoor
In-Reply-To: <SA0PR17MB4345240D407CFF114F143FF994969@SA0PR17MB4345.namprd17.prod.outlook.com>
References: <SA0PR17MB4345240D407CFF114F143FF994969@SA0PR17MB4345.namprd17.prod.outlook.com>
Message-ID: <5df5672b947fc9374a5e957f8e90a6f3de636a45.camel@ijs.si>

Dear Markus,

To provide any help or hints on your problem, you will need to provide
more information: at least the pertinent pw.x output file and the
operating system you are using.

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

On Thu, 2022-07-28 at 14:58 +0000, markus.becker85 at outlook.de wrote:
> Hello,
> 
> get this error message when trying to open the optimized ccordinates
> of a Quantum Espresso pw output-file:
> 
> Error: while executing exec sh .../xcrysden-1.6.2-bin-
> shared/scripts/pwo2xsf.sh --optcoor ....
> 
> I am using the newest version 1.6.2 and my QE version is quite new,
> i.e. 7.0. I found in some forum compatibility problems and update
> suggestions, however, I already use the newest version of xcrysden.?
> Maybe someone has an idea on this.
> 
> Best regards
> Markus
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden


From markus.becker85 at outlook.de  Mon Aug  1 19:38:19 2022
From: markus.becker85 at outlook.de (markus.becker85 at outlook.de)
Date: Mon, 1 Aug 2022 17:38:19 +0000
Subject: [xcrysden] Error: while executing exec sh optcoor
In-Reply-To: <5df5672b947fc9374a5e957f8e90a6f3de636a45.camel@ijs.si>
References: <SA0PR17MB4345240D407CFF114F143FF994969@SA0PR17MB4345.namprd17.prod.outlook.com>
	<5df5672b947fc9374a5e957f8e90a6f3de636a45.camel@ijs.si>
Message-ID: <MW4PR17MB4339A64267D526DA70678BCA949A9@MW4PR17MB4339.namprd17.prod.outlook.com>

Dear Tone,

Thanks for your reply. Attached you find the QE output-file. Maybe is it due to the usage of the Environ addon? I use QE and Environ with the Cygwin interface for Win10. It is based on the example01 from Environ "h2o_vacuum" and I performed the calculation with my own system settings. It seems that the run was successful.

Kind regards
Markus
________________________________
Von: xcrysden-bounces at democritos.it <xcrysden-bounces at democritos.it> im Auftrag von Tone Kokalj <tone.kokalj at ijs.si>
Gesendet: Montag, 1. August 2022 13:16
An: xcrysden at democritos.it <xcrysden at democritos.it>
Betreff: Re: [xcrysden] Error: while executing exec sh optcoor

Dear Markus,

To provide any help or hints on your problem, you will need to provide
more information: at least the pertinent pw.x output file and the
operating system you are using.

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

On Thu, 2022-07-28 at 14:58 +0000, markus.becker85 at outlook.de wrote:
> Hello,
>
> get this error message when trying to open the optimized ccordinates
> of a Quantum Espresso pw output-file:
>
> Error: while executing exec sh .../xcrysden-1.6.2-bin-
> shared/scripts/pwo2xsf.sh --optcoor ....
>
> I am using the newest version 1.6.2 and my QE version is quite new,
> i.e. 7.0. I found in some forum compatibility problems and update
> suggestions, however, I already use the newest version of xcrysden.
> Maybe someone has an idea on this.
>
> Best regards
> Markus
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden

_______________________________________________
XCrySDen mailing list
XCrySDen at democritos.it
http://www.democritos.it/mailman/listinfo/xcrysden
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From tone.kokalj at ijs.si  Tue Aug  2 09:25:15 2022
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 02 Aug 2022 09:25:15 +0200
Subject: [xcrysden] Error: while executing exec sh optcoor
In-Reply-To: <MW4PR17MB4339A64267D526DA70678BCA949A9@MW4PR17MB4339.namprd17.prod.outlook.com>
References: <SA0PR17MB4345240D407CFF114F143FF994969@SA0PR17MB4345.namprd17.prod.outlook.com>
	<5df5672b947fc9374a5e957f8e90a6f3de636a45.camel@ijs.si>
	<MW4PR17MB4339A64267D526DA70678BCA949A9@MW4PR17MB4339.namprd17.prod.outlook.com>
Message-ID: <64aa30cbee6f3fcbe4b4a907454e15dcaccfff32.camel@ijs.si>

Dear Marcus,

Your pw.x output works OK on my side, hence I suspect the problem may
be the cygwin version of xcrysden (I do not have the access to any
cygwin machine at the moment, hence I cannot test it). 

You may try to use the pwo2xsf.sh filter directly from the terminal to
see what you get, i.e., try these:

$XCRYSDEN_TOPDIR/scripts/pwo2xsf.sh -ic h2o_vacuum_direct.out
$XCRYSDEN_TOPDIR/scripts/pwo2xsf.sh -oc h2o_vacuum_direct.out
$XCRYSDEN_TOPDIR/scripts/pwo2xsf.sh -a h2o_vacuum_direct.out

where $XCRYSDEN_TOPDIR is the location of your xcrysden installation.
What do you get?

As an alternative to Cygwin, you may consider to use WSL on Windows
(default is Ubuntu and then you can use Ubuntu version of xcrysden).

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

On Mon, 2022-08-01 at 17:38 +0000, markus.becker85 at outlook.de wrote:
> Dear Tone,
> 
> Thanks for your reply. Attached you find the QE output-file. Maybe is
> it due to the usage of the Environ addon? I use QE and Environ with
> the Cygwin interface for Win10. It is based on the example01 from
> Environ "h2o_vacuum" and I performed the calculation with my own
> system settings. It seems that the run was successful.
> 
> Kind regards
> Markus
> Von: xcrysden-bounces at democritos.it <xcrysden-bounces at democritos.it>
> im Auftrag von Tone Kokalj <tone.kokalj at ijs.si>
> Gesendet: Montag, 1. August 2022 13:16
> An: xcrysden at democritos.it <xcrysden at democritos.it>
> Betreff: Re: [xcrysden] Error: while executing exec sh optcoor?
> Dear Markus,
> 
> To provide any help or hints on your problem, you will need to
> provide
> more information: at least the pertinent pw.x output file and the
> operating system you are using.
> 
> Best regards, Tone
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden


From markus.becker85 at outlook.de  Mon Aug 15 13:14:11 2022
From: markus.becker85 at outlook.de (markus.becker85 at outlook.de)
Date: Mon, 15 Aug 2022 11:14:11 +0000
Subject: [xcrysden] Error: while executing exec sh optcoor
In-Reply-To: <64aa30cbee6f3fcbe4b4a907454e15dcaccfff32.camel@ijs.si>
References: <SA0PR17MB4345240D407CFF114F143FF994969@SA0PR17MB4345.namprd17.prod.outlook.com>
	<5df5672b947fc9374a5e957f8e90a6f3de636a45.camel@ijs.si>
	<MW4PR17MB4339A64267D526DA70678BCA949A9@MW4PR17MB4339.namprd17.prod.outlook.com>
	<64aa30cbee6f3fcbe4b4a907454e15dcaccfff32.camel@ijs.si>
Message-ID: <MW4PR17MB433959771D8D84FAB742E64794689@MW4PR17MB4339.namprd17.prod.outlook.com>

Dear Tone,

In between I tried the first command and get this data:

Markus at Notebook-17Zoll ~/xcrysden-1.6.2-bin-shared/scripts

$ ./pwo2xsf.sh -ic h2o_vacuum_direct.out

./pwo2xsf.sh: line 95: bc: command not found
 DIM-GROUP
 3   1
 PRIMVEC
  10.5835441718     0.0000000000     0.0000000000
   0.0000000000    10.5835441718     0.0000000000
   0.0000000000     0.0000000000    10.5835441718

 PRIMCOORD
 3 1
 O       6.2389992893     6.3765853635     6.0855378988       0.0028084200    -0.0147293400    -0.0000000700
 H       7.1174334555     5.9373682804     6.0855378988      -0.0139018600     0.0049228800     0.0000000300
 H       5.5881113227     5.6410290436     6.0855378988       0.0110934400     0.0098064600     0.0000000400

It seems, pwo2xsf.sh gets something Does this look okay? But then still the question, why the error appears.

Kind regards
Markus
________________________________
Von: xcrysden-bounces at democritos.it <xcrysden-bounces at democritos.it> im Auftrag von Tone Kokalj <tone.kokalj at ijs.si>
Gesendet: Dienstag, 2. August 2022 09:25
An: xcrysden at democritos.it <xcrysden at democritos.it>
Betreff: Re: [xcrysden] Error: while executing exec sh optcoor

Dear Marcus,

Your pw.x output works OK on my side, hence I suspect the problem may
be the cygwin version of xcrysden (I do not have the access to any
cygwin machine at the moment, hence I cannot test it).

You may try to use the pwo2xsf.sh filter directly from the terminal to
see what you get, i.e., try these:

$XCRYSDEN_TOPDIR/scripts/pwo2xsf.sh -ic h2o_vacuum_direct.out
$XCRYSDEN_TOPDIR/scripts/pwo2xsf.sh -oc h2o_vacuum_direct.out
$XCRYSDEN_TOPDIR/scripts/pwo2xsf.sh -a h2o_vacuum_direct.out

where $XCRYSDEN_TOPDIR is the location of your xcrysden installation.
What do you get?

As an alternative to Cygwin, you may consider to use WSL on Windows
(default is Ubuntu and then you can use Ubuntu version of xcrysden).

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

On Mon, 2022-08-01 at 17:38 +0000, markus.becker85 at outlook.de wrote:
> Dear Tone,
>
> Thanks for your reply. Attached you find the QE output-file. Maybe is
> it due to the usage of the Environ addon? I use QE and Environ with
> the Cygwin interface for Win10. It is based on the example01 from
> Environ "h2o_vacuum" and I performed the calculation with my own
> system settings. It seems that the run was successful.
>
> Kind regards
> Markus
> Von: xcrysden-bounces at democritos.it <xcrysden-bounces at democritos.it>
> im Auftrag von Tone Kokalj <tone.kokalj at ijs.si>
> Gesendet: Montag, 1. August 2022 13:16
> An: xcrysden at democritos.it <xcrysden at democritos.it>
> Betreff: Re: [xcrysden] Error: while executing exec sh optcoor
> Dear Markus,
>
> To provide any help or hints on your problem, you will need to
> provide
> more information: at least the pertinent pw.x output file and the
> operating system you are using.
>
> Best regards, Tone
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden

_______________________________________________
XCrySDen mailing list
XCrySDen at democritos.it
http://www.democritos.it/mailman/listinfo/xcrysden
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From tone.kokalj at ijs.si  Wed Aug 17 17:04:19 2022
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Wed, 17 Aug 2022 17:04:19 +0200
Subject: [xcrysden] Error: while executing exec sh optcoor
In-Reply-To: <MW4PR17MB433959771D8D84FAB742E64794689@MW4PR17MB4339.namprd17.prod.outlook.com>
References: <SA0PR17MB4345240D407CFF114F143FF994969@SA0PR17MB4345.namprd17.prod.outlook.com>
	<5df5672b947fc9374a5e957f8e90a6f3de636a45.camel@ijs.si>
	<MW4PR17MB4339A64267D526DA70678BCA949A9@MW4PR17MB4339.namprd17.prod.outlook.com>
	<64aa30cbee6f3fcbe4b4a907454e15dcaccfff32.camel@ijs.si>
	<MW4PR17MB433959771D8D84FAB742E64794689@MW4PR17MB4339.namprd17.prod.outlook.com>
Message-ID: <e6d1012bf54989717187a5f9dc30d12ac8e17ff9.camel@ijs.si>

On Mon, 2022-08-15 at 11:14 +0000, markus.becker85 at outlook.de wrote:
> Dear Tone,
> 
> In between I tried the first command and get this data:
> 
> Markus at Notebook-17Zoll ~/xcrysden-1.6.2-bin-shared/scripts
> 
> $ ./pwo2xsf.sh -ic h2o_vacuum_direct.out
> 
> ./pwo2xsf.sh: line 95: bc: command not found

This implies that you are missing the "bc" package. The list of cygwin
packages that xcrysden needs is listed at the top of the README.cygwin
file, located in the xcrysden's root directory. Try to install them and
check if this makes a difference.

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





From markus.becker85 at outlook.de  Fri Aug 19 13:51:17 2022
From: markus.becker85 at outlook.de (markus.becker85 at outlook.de)
Date: Fri, 19 Aug 2022 11:51:17 +0000
Subject: [xcrysden] Error: while executing exec sh optcoor
In-Reply-To: <e6d1012bf54989717187a5f9dc30d12ac8e17ff9.camel@ijs.si>
References: <SA0PR17MB4345240D407CFF114F143FF994969@SA0PR17MB4345.namprd17.prod.outlook.com>
	<5df5672b947fc9374a5e957f8e90a6f3de636a45.camel@ijs.si>
	<MW4PR17MB4339A64267D526DA70678BCA949A9@MW4PR17MB4339.namprd17.prod.outlook.com>
	<64aa30cbee6f3fcbe4b4a907454e15dcaccfff32.camel@ijs.si>
	<MW4PR17MB433959771D8D84FAB742E64794689@MW4PR17MB4339.namprd17.prod.outlook.com>
	<e6d1012bf54989717187a5f9dc30d12ac8e17ff9.camel@ijs.si>
Message-ID: <MW4PR17MB43390A76FBEFC4F796C2D529946C9@MW4PR17MB4339.namprd17.prod.outlook.com>

Dear Tone,

Thanks for the tip. Indded, it was the missing "bc" package for Cygwin. I installed it and it works now. Very good, thanks for your support!

Kind regards
Markus
________________________________
Von: xcrysden-bounces at democritos.it <xcrysden-bounces at democritos.it> im Auftrag von Tone Kokalj <tone.kokalj at ijs.si>
Gesendet: Mittwoch, 17. August 2022 17:04
An: xcrysden at democritos.it <xcrysden at democritos.it>
Betreff: Re: [xcrysden] Error: while executing exec sh optcoor

On Mon, 2022-08-15 at 11:14 +0000, markus.becker85 at outlook.de wrote:
> Dear Tone,
>
> In between I tried the first command and get this data:
>
> Markus at Notebook-17Zoll ~/xcrysden-1.6.2-bin-shared/scripts
>
> $ ./pwo2xsf.sh -ic h2o_vacuum_direct.out
>
> ./pwo2xsf.sh: line 95: bc: command not found

This implies that you are missing the "bc" package. The list of cygwin
packages that xcrysden needs is listed at the top of the README.cygwin
file, located in the xcrysden's root directory. Try to install them and
check if this makes a difference.

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




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