[Octopus-users] Parser Issue
Mark Lusk
mlusk at mines.edu
Wed Jan 9 13:14:12 WET 2008
Very helpful. I had already run the make install and so spec_ps_tm2 name
worked fine. Also,
Output = wfs
OutputWfsNumber = "1-4"
OutputHow = dx + axis_x + axis_y + axis_z
worked fine as the correct supplementary lines. I just did not recognize
the original as a problem with the markup translation.
Thanks Emily and Miguel,
Mark
Mark T. Lusk, Professor
Department of Physics
Colorado School of Mines
Golden, CO 80401
303-273-3675
http://www.mines.edu/Academic/physics/people/pages/lusk.html
-----Original Message-----
From: octopus-users-bounces at tddft.org
[mailto:octopus-users-bounces at tddft.org] On Behalf Of
octopus-users-request at tddft.org
Sent: Wednesday, January 09, 2008 5:00 AM
To: octopus-users at tddft.org
Subject: Octopus-users Digest, Vol 41, Issue 4
Send Octopus-users mailing list submissions to
octopus-users at tddft.org
To subscribe or unsubscribe via the World Wide Web, visit
http://www.tddft.org/mailman/listinfo/octopus-users
or, via email, send a message with subject or body 'help' to
octopus-users-request at tddft.org
You can reach the person managing the list at
octopus-users-owner at tddft.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Octopus-users digest..."
Today's Topics:
1. Parser Issue (Mark Lusk)
2. Re: Parser Issue (Emily)
3. Re: Parser Issue (Miguel Marques)
----------------------------------------------------------------------
Message: 1
Date: Tue, 8 Jan 2008 11:26:22 -0700
From: "Mark Lusk" <mlusk at mines.edu>
Subject: [Octopus-users] Parser Issue
To: <octopus-users at tddft.org>
Message-ID: <006a01c85223$f8bdcb20$c08f438a at solitude>
Content-Type: text/plain; charset="us-ascii"
Dear all,
I am working through some simple examples and am having problems using
standard Octopus variables. For instance, I have to use '100' to identify
the TM2 pseudo instead of writing 'spec_ps_psf':
%Species
'N' |14.0 | 100 | 7 | 1 | 0
%
Another example of the problem is that attempted use of the following line
{{Variable|Output|Output}} = wfs
gives the error message below:
Input error:
symbol 'variable' used before being defined
It seems as if the parser is somehow not working properly. Any advice would
be much appreciated.
Best,
Mark
Mark T. Lusk, Professor
Department of Physics
Colorado School of Mines
Golden, CO 80401
303-273-3675
http://www.mines.edu/Academic/physics/people/pages/lusk.html
------------------------------
Message: 2
Date: Tue, 08 Jan 2008 15:32:03 -0500
From: "Emily" <listemily at eml.cc>
Subject: Re: [Octopus-users] Parser Issue
To: "Mark Lusk" <mlusk at mines.edu>, "octopus users group"
<octopus-users at tddft.org>
Message-ID: <1199824323.4431.1230162387 at webmail.messagingengine.com>
Content-Type: text/plain; charset="ISO-8859-1"
Hi Mark,
Some of the examples in the user's guide are old, and do not use the
most current format for variable names, and this may be the source of
your problems.
To see the current names go to:
http://www.tddft.org/programs/octopus/doc/2.1.0/html/vars.php
and choose the "System" folder, then the "Species" folder. As you can
see, the number 100 at that particular place in the species block now
corresponds to:
spec_ps_tm2 (100): Troullier Martins pseudopotential, the
pseudopotential will be read from an .ascii or .vps file, either in the
working directory or in the OCTOPUS-HOME/share/PP/TM2 directory.
I suspect that "spec_ps_psf" is an old variable that's been renamed,
hopefully its been renamed to "spec_ps_tm2" if they both correspond to
100, but I don't know myself.
The correct format for telling octopus to output wavefunctions is:
Output = wfs
That thing in braces,{{Variable|Output|Output}} = wfs, I believe is some
sort of artefact of the wiki markup language. Its supposed to render
just as "Output" but also be a link to the page where you can read about
the variable.
Good luck,
Emily
----- Original message -----
From: "Mark Lusk" <mlusk at mines.edu>
To: octopus-users at tddft.org
Date: Tue, 8 Jan 2008 11:26:22 -0700
Subject: [Octopus-users] Parser Issue
Dear all,
I am working through some simple examples and am having problems using
standard Octopus variables. For instance, I have to use '100' to
identify
the TM2 pseudo instead of writing 'spec_ps_psf':
%Species
'N' |14.0 | 100 | 7 | 1 | 0
%
Another example of the problem is that attempted use of the following
line
{{Variable|Output|Output}} = wfs
gives the error message below:
Input error:
symbol 'variable' used before being defined
It seems as if the parser is somehow not working properly. Any advice
would
be much appreciated.
Best,
Mark
Mark T. Lusk, Professor
Department of Physics
Colorado School of Mines
Golden, CO 80401
303-273-3675
http://www.mines.edu/Academic/physics/people/pages/lusk.html
_______________________________________________
Octopus-users mailing list
Octopus-users at tddft.org
http://www.tddft.org/mailman/listinfo/octopus-users
------------------------------
Message: 3
Date: Wed, 09 Jan 2008 09:10:36 +0100
From: Miguel Marques <Miguel.Marques at tddft.org>
Subject: Re: [Octopus-users] Parser Issue
To: octopus users group <octopus-users at tddft.org>
Cc: Mark Lusk <mlusk at mines.edu>
Message-ID: <4784817C.405 at tddft.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Mark,
Emily is right in what she says, but I believe that there is an extra
issue: did you "make install" octopus? The problem is that the
definition of the variables (like spec_ps_tm2) is in a file that is
installed when you "make install". So, if you do not install, octopus
can not find the file, and the variables in the input are unknown. If
you really can not "make install", for whatever reason, there is a
workaround, which is to define the system variable OCTOPUS_SHARE with
the location of the share directory of octopus.
Hope this helped,
Miguel
Emily wrote:
> Hi Mark,
>
> Some of the examples in the user's guide are old, and do not use the
> most current format for variable names, and this may be the source of
> your problems.
>
> To see the current names go to:
> http://www.tddft.org/programs/octopus/doc/2.1.0/html/vars.php
> and choose the "System" folder, then the "Species" folder. As you can
> see, the number 100 at that particular place in the species block now
> corresponds to:
> spec_ps_tm2 (100): Troullier Martins pseudopotential, the
> pseudopotential will be read from an .ascii or .vps file, either in the
> working directory or in the OCTOPUS-HOME/share/PP/TM2 directory.
>
> I suspect that "spec_ps_psf" is an old variable that's been renamed,
> hopefully its been renamed to "spec_ps_tm2" if they both correspond to
> 100, but I don't know myself.
>
>
> The correct format for telling octopus to output wavefunctions is:
> Output = wfs
>
> That thing in braces,{{Variable|Output|Output}} = wfs, I believe is some
> sort of artefact of the wiki markup language. Its supposed to render
> just as "Output" but also be a link to the page where you can read about
> the variable.
>
> Good luck,
> Emily
>
> ----- Original message -----
> From: "Mark Lusk" <mlusk at mines.edu>
> To: octopus-users at tddft.org
> Date: Tue, 8 Jan 2008 11:26:22 -0700
> Subject: [Octopus-users] Parser Issue
>
> Dear all,
>
> I am working through some simple examples and am having problems using
> standard Octopus variables. For instance, I have to use '100' to
> identify
> the TM2 pseudo instead of writing 'spec_ps_psf':
>
> %Species
> 'N' |14.0 | 100 | 7 | 1 | 0
> %
>
> Another example of the problem is that attempted use of the following
> line
>
> {{Variable|Output|Output}} = wfs
>
> gives the error message below:
>
> Input error:
> symbol 'variable' used before being defined
>
> It seems as if the parser is somehow not working properly. Any advice
> would
> be much appreciated.
>
> Best,
>
> Mark
>
> Mark T. Lusk, Professor
> Department of Physics
> Colorado School of Mines
> Golden, CO 80401
> 303-273-3675
> http://www.mines.edu/Academic/physics/people/pages/lusk.html
>
>
> _______________________________________________
> Octopus-users mailing list
> Octopus-users at tddft.org
> http://www.tddft.org/mailman/listinfo/octopus-users
> _______________________________________________
> Octopus-users mailing list
> Octopus-users at tddft.org
> http://www.tddft.org/mailman/listinfo/octopus-users
>
>
------------------------------
_______________________________________________
Octopus-users mailing list
Octopus-users at tddft.org
http://www.tddft.org/mailman/listinfo/octopus-users
End of Octopus-users Digest, Vol 41, Issue 4
********************************************
More information about the Octopus-users
mailing list