cclib-devel — Developer's mailing list

[cclib-devel] Possible collaboration

[Noel O'B. <bao...@gm...>]

Hello Stefano,

I've just come across your TheoChemPy project on SourceForge. It seems
that its functionality overlaps to some extent with cclib
(http://cclib.sf.net). It would be great if we would collaborate
somehow, for example, on common parsers.

Regards,
    Noel

Re: [cclib-devel] New parser for cclib

[Karol M. L. <kar...@gm...>]

Hi all,

 That's right, I don't have access to DGauss. Before this discussion I 
dodn't even know it existed, actually! I will look at it, and ask if 
anyone here is using it.

Cheers,
Karol

On Wednesday 29 October 2008, Noel O'Boyle wrote:
> Cher Jerome,
>
> I'm guessing by Karol's silence that he doesn't have access to
> DGauss either. We'll add the code into SVN, but I don't think it'll
> make it into a release unless we can get it to pass some tests.
> Would you be willing to run a series of test jobs?
>
> Regards,
>    Noel
>
> 2008/10/21 Adam Tenderholt <a-t...@st...>:
> > Jerome,
> >
> > Thanks for your contribution. I don't have access to DGauss, so I
> > won't be able to help maintain your parser. Noel, Karol: how bad
> > would it be to have an "unsupported" parser in the release?
> >
> > Adam
> >
> > On Oct 21, 2008, at 6:54 AM, Noel O'Boyle wrote:
> >> Cher Jerome,
> >>
> >> We certainly are interested. However, I just need to check with
> >> the others whether we are able to maintain it. That is, do any
> >> of us have access to this software (I don't)?
> >>
> >> If not, we may be in a strange situation as we will be unable to
> >> fix any bugs, etc. But first, let us check...
> >>
> >> Noel
> >>
> >> 2008/10/20 Jerome Kieffer <jer...@te...>:
> >>> Hello Noel,
> >>>
> >>> Are you interested in a new parser for cclib ?
> >>>
> >>> I need a parser for DGauss software, distributed by Fujitsu
> >>> http://www.cache.fujitsu.com/biomedcache/dgauss/index.shtml
> >>>
> >>> I tested the code both on windows and linux output of DGauss
> >>> and it seems to work. this code is derivated from the
> >>> orcaparser.py in cclib-0.9. You can re-distribute it under
> >>> LGPL.
> >>>
> >>> Cheers
> >>>
> >>> --
> >>> Jérôme KIEFFER
> >>> http://www.terre-adelie.org


-- 
written by Karol Langner
Thu Oct 30 15:05:29 CET 2008

Re: [cclib-devel] New parser for cclib

[Noel O'B. <bao...@gm...>]

Cher Jerome,

I'm guessing by Karol's silence that he doesn't have access to DGauss
either. We'll add the code into SVN, but I don't think it'll make it
into a release unless we can get it to pass some tests. Would you be
willing to run a series of test jobs?

Regards,
   Noel

2008/10/21 Adam Tenderholt <a-t...@st...>:
> Jerome,
>
> Thanks for your contribution. I don't have access to DGauss, so I won't be
> able to help maintain your parser. Noel, Karol: how bad would it be to have
> an "unsupported" parser in the release?
>
> Adam
>
> On Oct 21, 2008, at 6:54 AM, Noel O'Boyle wrote:
>
>> Cher Jerome,
>>
>> We certainly are interested. However, I just need to check with the
>> others whether we are able to maintain it. That is, do any of us have
>> access to this software (I don't)?
>>
>> If not, we may be in a strange situation as we will be unable to fix
>> any bugs, etc. But first, let us check...
>>
>> Noel
>>
>> 2008/10/20 Jerome Kieffer <jer...@te...>:
>>>
>>> Hello Noel,
>>>
>>> Are you interested in a new parser for cclib ?
>>>
>>> I need a parser for DGauss software, distributed by Fujitsu
>>> http://www.cache.fujitsu.com/biomedcache/dgauss/index.shtml
>>>
>>> I tested the code both on windows and linux output of DGauss and it
>>> seems to work. this code is derivated from the orcaparser.py in
>>> cclib-0.9. You can re-distribute it under LGPL.
>>>
>>> Cheers
>>>
>>> --
>>> Jérôme KIEFFER
>>> http://www.terre-adelie.org
>>>
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the
>> world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> cclib-devel mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
>

Re: [cclib-devel] New parser for cclib

[Adam T. <a-t...@st...>]

Jerome,

Thanks for your contribution. I don't have access to DGauss, so I  
won't be able to help maintain your parser. Noel, Karol: how bad would  
it be to have an "unsupported" parser in the release?

Adam

On Oct 21, 2008, at 6:54 AM, Noel O'Boyle wrote:

> Cher Jerome,
>
> We certainly are interested. However, I just need to check with the
> others whether we are able to maintain it. That is, do any of us have
> access to this software (I don't)?
>
> If not, we may be in a strange situation as we will be unable to fix
> any bugs, etc. But first, let us check...
>
> Noel
>
> 2008/10/20 Jerome Kieffer <jer...@te...>:
>> Hello Noel,
>>
>> Are you interested in a new parser for cclib ?
>>
>> I need a parser for DGauss software, distributed by Fujitsu
>> http://www.cache.fujitsu.com/biomedcache/dgauss/index.shtml
>>
>> I tested the code both on windows and linux output of DGauss and it
>> seems to work. this code is derivated from the orcaparser.py in
>> cclib-0.9. You can re-distribute it under LGPL.
>>
>> Cheers
>>
>> --
>> Jérôme KIEFFER
>> http://www.terre-adelie.org
>>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's  
> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in  
> the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel

Re: [cclib-devel] New parser for cclib

[Noel O'B. <bao...@gm...>]

Cher Jerome,

We certainly are interested. However, I just need to check with the
others whether we are able to maintain it. That is, do any of us have
access to this software (I don't)?

If not, we may be in a strange situation as we will be unable to fix
any bugs, etc. But first, let us check...

Noel

2008/10/20 Jerome Kieffer <jer...@te...>:
> Hello Noel,
>
> Are you interested in a new parser for cclib ?
>
> I need a parser for DGauss software, distributed by Fujitsu
> http://www.cache.fujitsu.com/biomedcache/dgauss/index.shtml
>
> I tested the code both on windows and linux output of DGauss and it
> seems to work. this code is derivated from the orcaparser.py in
> cclib-0.9. You can re-distribute it under LGPL.
>
> Cheers
>
> --
> Jérôme KIEFFER
> http://www.terre-adelie.org
>

[cclib-devel] Fwd: New parser for cclib

[Noel O'B. <bao...@gm...>]

---------- Forwarded message ----------
From: Jerome Kieffer <jer...@te...>
Date: 2008/10/20
Subject: New parser for cclib
To: bao...@gm...


Hello Noel,

Are you interested in a new parser for cclib ?

I need a parser for DGauss software, distributed by Fujitsu
http://www.cache.fujitsu.com/biomedcache/dgauss/index.shtml

I tested the code both on windows and linux output of DGauss and it
seems to work. this code is derivated from the orcaparser.py in
cclib-0.9. You can re-distribute it under LGPL.

Cheers

--
Jérôme KIEFFER
http://www.terre-adelie.org

Re: [cclib-devel] Gaussian PBC

[Noel O'B. <bao...@gm...>]

Hmmm...here's the text of an email I sent to a user back in May. It's
basically the same problem and the same solution:

==========
The problem is that GaussSum is confused over the number of atoms: 11
or 8? The correct answer is 8, but there are also 3 translation
vectors. The avoid the error, please replace the line in
gausssianparser.py that says
"assert self.natom == natom"
with
"pass"

If this works, please check all of the data carefully. It is possible
that there will be some other error because I have not looked at a PBC
file before this.
==========

This is just a workaround, but if you could try this out, could you
let me know how it goes. What sort of information do you extract from
PBC calculations in general? I would like to make sure that such
information is extracted correctly before releasing a fix to this.

I've added neoprene.zip to our test suite, so that we will remember to
fix this before the next release.

Noel

2008/9/22 Nuno A. G. Bandeira <nun...@is...>:
> Hi!
>>
>> Regarding PBC, I think it is an easy fix (although I could be wrong).
>> I have a feeling this has been fixed in SVN or that I have a test file
>> somewhere. Just in case, can you send us a small test file (public
>> domain and zipped please) that I can look at...?
>>
>
> I think the problem is the coordinate read out which isn't parsed correctly.
>
> Anyway here's one example from the manual.
>
>
>
> --
> Nuno A. G. Bandeira, AMRSC  Graduate researcher and molecular sculptor
> Inorganic and Theoretical Chemistry Group, Faculty of Science University of
> Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal
> http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student @ IST,Lisbon
> --
>
>

Re: [cclib-devel] Choices about Mediawiki

[Noel O'B. <bao...@gm...>]

Our wiki seems to be back up to normal. Editing works, etc. In fact,
it seems a lot faster now. Yay!

Noel

2008/9/27 Noel O'Boyle <bao...@gm...>:
> 2008/9/24 Adam Tenderholt <a-t...@st...>:
>> I guess I don't understand what changed on sourceforge. Were we in charge of
>> actually setting up the wiki (and its software) before,
> Yes. We set one up in our project web space.
>
>> and now they provide
>> that for us?
> Yes. They now have three hosted applications which we can opt into.
> These are hosted by SF, not in our project web space.
>
>> But we can still keep our current (old) wiki?
> It looks like we can. Basically, they've gone thru a whole upgrade,
> moved directories around, renamed the sql servers, so I needed to
> update some of the config files, etc. (and I'm still not done). It
> looks like this is the best option for the moment, as they don't allow
> import into the hosted mediawiki.
>
>> Adam
>>
>> On Sep 24, 2008, at 4:12 AM, Noel O'Boyle wrote:
>>
>>> Actually, I've tried to renable our current wiki and I have gotten 80%
>>> of the way. Currently, the website is back up, but editing is not
>>> possible. I think they've renamed the databases so I need to change
>>> some settings. That's a job for another day...
>>>
>>> Noel
>>>
>>> 2008/9/24 Noel O'Boyle <bao...@gm...>:
>>>>
>>>> Hello all,
>>>>
>>>> I've been looking at the hosted MW (MediaWiki) on SF as we need to do
>>>> something about our own MW. Unfortunately, it is currently not
>>>> possible to import a database into the hosted MW, nor is it possible
>>>> to use Special:Import to import the text directly. While the former is
>>>> unlikely to be possible for a while (apparently it's on the To Do
>>>> list), the latter is described as Urgent in a recent Feature Request
>>>>
>>>> (http://sourceforge.net/tracker/?func=detail&aid=2107929&group_id=1&atid=200001).
>>>>
>>>> The hosted MW is at apps.sf.net/mediawiki/cclib.
>>>>
>>>> Right now, I can copy and paste the contents of our old wiiki into the
>>>> hosted MW. This is boring tedious work but it shouldn't take too long.
>>>> On the downside, we lose our wiki history. Does anyone care about
>>>> this? I don't think our history is worth that much and am happy to go
>>>> ahead and never have to worry about maintaining a MW in future.
>>>>
>>>> Thoughts?
>>>>
>>>> Noel
>>>>
>>>
>>> -------------------------------------------------------------------------
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win great
>>> prizes
>>> Grand prize is a trip for two to an Open Source event anywhere in the
>>> world
>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>> _______________________________________________
>>> cclib-devel mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>
>>
>

Re: [cclib-devel] Choices about Mediawiki

[Noel O'B. <bao...@gm...>]

2008/9/24 Adam Tenderholt <a-t...@st...>:
> I guess I don't understand what changed on sourceforge. Were we in charge of
> actually setting up the wiki (and its software) before,
Yes. We set one up in our project web space.

> and now they provide
> that for us?
Yes. They now have three hosted applications which we can opt into.
These are hosted by SF, not in our project web space.

> But we can still keep our current (old) wiki?
It looks like we can. Basically, they've gone thru a whole upgrade,
moved directories around, renamed the sql servers, so I needed to
update some of the config files, etc. (and I'm still not done). It
looks like this is the best option for the moment, as they don't allow
import into the hosted mediawiki.

> Adam
>
> On Sep 24, 2008, at 4:12 AM, Noel O'Boyle wrote:
>
>> Actually, I've tried to renable our current wiki and I have gotten 80%
>> of the way. Currently, the website is back up, but editing is not
>> possible. I think they've renamed the databases so I need to change
>> some settings. That's a job for another day...
>>
>> Noel
>>
>> 2008/9/24 Noel O'Boyle <bao...@gm...>:
>>>
>>> Hello all,
>>>
>>> I've been looking at the hosted MW (MediaWiki) on SF as we need to do
>>> something about our own MW. Unfortunately, it is currently not
>>> possible to import a database into the hosted MW, nor is it possible
>>> to use Special:Import to import the text directly. While the former is
>>> unlikely to be possible for a while (apparently it's on the To Do
>>> list), the latter is described as Urgent in a recent Feature Request
>>>
>>> (http://sourceforge.net/tracker/?func=detail&aid=2107929&group_id=1&atid=200001).
>>>
>>> The hosted MW is at apps.sf.net/mediawiki/cclib.
>>>
>>> Right now, I can copy and paste the contents of our old wiiki into the
>>> hosted MW. This is boring tedious work but it shouldn't take too long.
>>> On the downside, we lose our wiki history. Does anyone care about
>>> this? I don't think our history is worth that much and am happy to go
>>> ahead and never have to worry about maintaining a MW in future.
>>>
>>> Thoughts?
>>>
>>> Noel
>>>
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the
>> world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> cclib-devel mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
>

Re: [cclib-devel] Choices about Mediawiki

[Adam T. <a-t...@st...>]

I guess I don't understand what changed on sourceforge. Were we in  
charge of actually setting up the wiki (and its software) before, and  
now they provide that for us? But we can still keep our current (old)  
wiki?

Adam

On Sep 24, 2008, at 4:12 AM, Noel O'Boyle wrote:

> Actually, I've tried to renable our current wiki and I have gotten 80%
> of the way. Currently, the website is back up, but editing is not
> possible. I think they've renamed the databases so I need to change
> some settings. That's a job for another day...
>
> Noel
>
> 2008/9/24 Noel O'Boyle <bao...@gm...>:
>> Hello all,
>>
>> I've been looking at the hosted MW (MediaWiki) on SF as we need to do
>> something about our own MW. Unfortunately, it is currently not
>> possible to import a database into the hosted MW, nor is it possible
>> to use Special:Import to import the text directly. While the former  
>> is
>> unlikely to be possible for a while (apparently it's on the To Do
>> list), the latter is described as Urgent in a recent Feature Request
>> (http://sourceforge.net/tracker/?func=detail&aid=2107929&group_id=1&atid=200001 
>> ).
>>
>> The hosted MW is at apps.sf.net/mediawiki/cclib.
>>
>> Right now, I can copy and paste the contents of our old wiiki into  
>> the
>> hosted MW. This is boring tedious work but it shouldn't take too  
>> long.
>> On the downside, we lose our wiki history. Does anyone care about
>> this? I don't think our history is worth that much and am happy to go
>> ahead and never have to worry about maintaining a MW in future.
>>
>> Thoughts?
>>
>> Noel
>>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's  
> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in  
> the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel

Re: [cclib-devel] Fwd: Gaussian PBC

[Adam T. <a-t...@st...>]

> Also, Mayer bond orders are twice as much as they should  be in
> Gaussian outputs.
> You can confirm that with any Gaussian run. Somehow along the way
> cclib overmultiplies the values by two.

Yeah, I'm aware of this, although I'm pretty sure it's only affects  
restricted calculations. Can you confirm that this is your case?

Adam

Re: [cclib-devel] Choices about Mediawiki

[Noel O'B. <bao...@gm...>]

Actually, I've tried to renable our current wiki and I have gotten 80%
of the way. Currently, the website is back up, but editing is not
possible. I think they've renamed the databases so I need to change
some settings. That's a job for another day...

Noel

2008/9/24 Noel O'Boyle <bao...@gm...>:
> Hello all,
>
> I've been looking at the hosted MW (MediaWiki) on SF as we need to do
> something about our own MW. Unfortunately, it is currently not
> possible to import a database into the hosted MW, nor is it possible
> to use Special:Import to import the text directly. While the former is
> unlikely to be possible for a while (apparently it's on the To Do
> list), the latter is described as Urgent in a recent Feature Request
> (http://sourceforge.net/tracker/?func=detail&aid=2107929&group_id=1&atid=200001).
>
> The hosted MW is at apps.sf.net/mediawiki/cclib.
>
> Right now, I can copy and paste the contents of our old wiiki into the
> hosted MW. This is boring tedious work but it shouldn't take too long.
> On the downside, we lose our wiki history. Does anyone care about
> this? I don't think our history is worth that much and am happy to go
> ahead and never have to worry about maintaining a MW in future.
>
> Thoughts?
>
> Noel
>

[cclib-devel] Choices about Mediawiki

[Noel O'B. <bao...@gm...>]

Hello all,

I've been looking at the hosted MW (MediaWiki) on SF as we need to do
something about our own MW. Unfortunately, it is currently not
possible to import a database into the hosted MW, nor is it possible
to use Special:Import to import the text directly. While the former is
unlikely to be possible for a while (apparently it's on the To Do
list), the latter is described as Urgent in a recent Feature Request
(http://sourceforge.net/tracker/?func=detail&aid=2107929&group_id=1&atid=200001).

The hosted MW is at apps.sf.net/mediawiki/cclib.

Right now, I can copy and paste the contents of our old wiiki into the
hosted MW. This is boring tedious work but it shouldn't take too long.
On the downside, we lose our wiki history. Does anyone care about
this? I don't think our history is worth that much and am happy to go
ahead and never have to worry about maintaining a MW in future.

Thoughts?

Noel

[cclib-devel] Fwd: Gaussian PBC

[Noel O'B. <bao...@gm...>]

---------- Forwarded message ----------
From: Nuno A. G. Bandeira <nun...@is...>
Date: 2008/9/22
Subject: Re: [cclib-devel] Gaussian PBC
To: Noel O'Boyle <bao...@gm...>


Hi!
>
> Regarding PBC, I think it is an easy fix (although I could be wrong).
> I have a feeling this has been fixed in SVN or that I have a test file
> somewhere. Just in case, can you send us a small test file (public
> domain and zipped please) that I can look at...?
>

I think the problem is the coordinate read out which isn't parsed correctly.

Anyway here's one example from the manual.



--
Nuno A. G. Bandeira, AMRSC  Graduate researcher and molecular sculptor
Inorganic and Theoretical Chemistry Group, Faculty of Science
University of Lisbon - C8 building, Campo Grande, 1749-016
Lisbon,Portugal
http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student @ IST,Lisbon
--

[cclib-devel] Fwd: Gaussian PBC

[Noel O'B. <bao...@gm...>]

---------- Forwarded message ----------
From: Nuno A. G. Bandeira <nun...@is...>
Date: 2008/9/23
Subject: Re: [cclib-devel] Gaussian PBC
To: Noel O'Boyle <bao...@gm...>



Also, Mayer bond orders are twice as much as they should  be in
Gaussian outputs.
You can confirm that with any Gaussian run. Somehow along the way
cclib overmultiplies the values by two.

Best,
Nuno

--
Nuno A. G. Bandeira, AMRSC  Graduate researcher and molecular sculptor
Inorganic and Theoretical Chemistry Group, Faculty of Science
University of Lisbon - C8 building, Campo Grande, 1749-016
Lisbon,Portugal
http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student @ IST,Lisbon
--

Re: [cclib-devel] cclib website

[Adam T. <a-t...@st...>]

The website used to be at cclib.sourceforge.net. Unfortunately, it's  
now saying that we don't have permission to access the wiki  
subdirectory. Noel, do you know anything about this?

Adam

On Sep 23, 2008, at 10:35 AM, Nuno A. G. Bandeira wrote:

> Strange error message from the cclib website
>
> An error has been encountered in accessing this page.
>
> 1. Server: www.cclib.sourceforge.net
> 2. URL path: /
> 3. Error notes: NONE
> 4. Error type: 404
> 5. Request method: GET
> 6. Request query string: NONE
> 7. Time: 2008-09-23 17:33:12 UTC (1222191192)
>
> Reporting this problem: The problem you have encountered is with a  
> project web site hosted by SourceForge.net. This issue should be  
> reported to the SourceForge.net-hosted project (not to  
> SourceForge.net).
>
> If this is a severe or recurring/persistent problem, please do one  
> of the following, and provide the error text (numbered 1 through 7,  
> above):
>
> 	• Contact the project via their designated support resources.
> 	• Contact the project administrators of this project via email (see  
> the upper right-hand corner of the Project Summary page for their  
> usernames) at use...@us...
> If you are a member of the project that maintains this web content,  
> please refer to the Site Documentation regarding the project web  
> service for further assistance
>
>
>
> -- 
> Nuno A. G. Bandeira, AMRSC
> Graduate researcher and molecular sculptor
> Inorganic and Theoretical Chemistry Group,
> Faculty of Science
> University of Lisbon - C8 building, Campo Grande,
> 1749-016 Lisbon,Portugal
> http://cqb.fc.ul.pt/intheochem/nuno.html
> Doctoral student @ IST,Lisbon
> --
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's  
> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in  
> the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/_______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel

[cclib-devel] cclib website

[Nuno A. G. B. <nun...@is...>]

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
  <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Strange error message from the cclib website<br>
<p><br>
</p>
<p>An error has been encountered in accessing this page. </p>
<p>1. <b>Server:</b> <a class="moz-txt-link-abbreviated" href="http://www.cclib.sourceforge.net">www.cclib.sourceforge.net</a><br>
2. <b>URL path:</b> /<br>
3. <b>Error notes:</b> NONE<br>
4. <b>Error type:</b> 404<br>
5. <b>Request method:</b> GET<br>
6. <b>Request query string:</b> NONE<br>
7. <b>Time:</b> 2008-09-23 17:33:12 UTC (1222191192)
</p>
<p><b>Reporting this problem:</b> The problem you have encountered is
with a project web site hosted by SourceForge.net. <b>This issue
should be reported to the SourceForge.net-hosted project</b> (not to
SourceForge.net). </p>
<p><i>If this is a severe or recurring/persistent problem,</i> please
do one of the following, and provide the error text (numbered 1 through
7, above): </p>
<ol>
  <li>Contact the project via their <a
 href="http://sourceforge.net/support/prweb-lookup.php?host=www.cclib.sourceforge.net&amp;support=1">designated
support resources</a>. </li>
  <li>Contact the project administrators of this project via email (see
the upper right-hand corner of the <a
 href="http://sourceforge.net/support/prweb-lookup.php?host=www.cclib.sourceforge.net">Project
Summary page</a> for their usernames) at <i>user-name</i>@users.sourceforge.net</li>
</ol>
<p>If you are a member of the project that maintains this web content,
please refer to the <a href="https://sourceforge.net/docs/E07/">Site
Documentation regarding the project web service</a> for further
assistance</p>
<br>
<br>
<pre class="moz-signature" cols="72">-- 
Nuno A. G. Bandeira, AMRSC  
Graduate researcher and molecular sculptor
Inorganic and Theoretical Chemistry Group, 
Faculty of Science 
University of Lisbon - C8 building, Campo Grande, 
1749-016 Lisbon,Portugal
<a class="moz-txt-link-freetext" href="http://cqb.fc.ul.pt/intheochem/nuno.html">http://cqb.fc.ul.pt/intheochem/nuno.html</a> 
Doctoral student @ IST,Lisbon
--</pre>
</body>
</html>

Re: [cclib-devel] Gaussian PBC

[Noel O'B. <bao...@gm...>]

Hello Nuno,

The cclib website is down as sourceforge have just had a major update
of their web hosting system (for the first time ever!). We are going
to sort this out soon but it is not a quick fix.

Regarding PBC, I think it is an easy fix (although I could be wrong).
I have a feeling this has been fixed in SVN or that I have a test file
somewhere. Just in case, can you send us a small test file (public
domain and zipped please) that I can look at...?

Noel

2008/9/22 Nuno A. G. Bandeira <nun...@is...>:
> Hello,
>
> It seems that cclib is not equiped to handle periodic boundary condition
> runs. Is it on your to do list aytime soon ?
>
> Also the main website for cclib is down. Any reason for that ?
>
> Cheers,
> Nuno
>
> --
> Nuno A. G. Bandeira, AMRSC
> Graduate researcher and molecular sculptor
> Inorganic and Theoretical Chemistry Group,
> Faculty of Science
> University of Lisbon - C8 building, Campo Grande,
> 1749-016 Lisbon,Portugal
> http://cqb.fc.ul.pt/intheochem/nuno.html
> Doctoral student @ IST,Lisbon
> --
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
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> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>

[cclib-devel] Gaussian PBC

[Nuno A. G. B. <nun...@is...>]

Hello,

It seems that cclib is not equiped to handle periodic boundary condition 
runs. Is it on your to do list aytime soon ?

Also the main website for cclib is down. Any reason for that ?

Cheers,
Nuno

-- 
Nuno A. G. Bandeira, AMRSC  
Graduate researcher and molecular sculptor
Inorganic and Theoretical Chemistry Group, 
Faculty of Science 
University of Lisbon - C8 building, Campo Grande, 
1749-016 Lisbon,Portugal
http://cqb.fc.ul.pt/intheochem/nuno.html 
Doctoral student @ IST,Lisbon
--

[cclib-devel] SourceForge now hosts MediaWiki

[Noel O'B. <bao...@gm...>]

SF has just announced that projects can opt-in and have MediaWiki.
This means less support by us, and presumably a more up-to-date
MediaWiki installation.

Noel

[cclib-devel] Fwd: [Gausssum-help] GaussSum - GAMESS log file fails to load

[Noel O'B. <bao...@gm...>]

2008/7/25 Bill Gunn <bil...@gm...>:
> I William Gunn am the copyright owner of the GAMESS output file
> zolm_dft3a.log and I place it in the public domain.
>
> If you need anything more than this, filling a standard form etc, let me
> know.
>
>
> On 25/07/2008, Noel O'Boyle <bao...@gm...> wrote:
>>
>> Hello Bill,
>>
>> The cclib parser appears to be having problems, but I can see how to
>> fix it. However, for practical reasons, we (at cclib) have a policy of
>> only fixing bugs for cases where we have a public domain log file.
>> So...I would appreciate if you could either (a) place the file you
>> sent me into the public domain, or (b) send me an alternative public
>> domain log file exhibiting the problem.
>>
>> It should be possible also to work around it in the short term. I'll
>> need to think about this a bit first.
>>
>> Regards,
>>   Noel
>>
>> 2008/7/25 Bill Gunn <bil...@gm...>:
>> > Noel,
>> >
>> > Here it is.
>> >
>> > 2008/7/24 Noel O'Boyle <bao...@gm...>:
>> >>
>> >> Hello Bill,
>> >>
>> >> Can you zip the output file and send it to me directly at this address?
>> >>
>> >> Noel
>> >>
>> >> 2008/7/24 Bill Gunn <bil...@gm...>:
>> >> > A GAMESS output log file with HESSIAN enabled that I generated for a
>> >> > medium
>> >> > sized organic molecule fails to load in GaussSum.  The error reported
>> >> > is
>> >> > "cclib has problems parsing...".
>> >> >
>> >> > The file loads both MO's and frequencies in wxMacMolPlt and
>> >> > Jmol.  The
>> >> > output from a similar input deck with $DATA for ethene was handled
>> >> > without
>> >> > problem by GaussSum.  So it seems like the file is OK.
>> >> >
>> >> > Your mailer baulked at the 2.4 MB log file I attempted to send you as
>> >> > an
>> >> > attachment so below is the text of the input deck to give you an idea
>> >> > of
>> >> > the
>> >> > size of the molecule I was running
>> >> >
>> >> > !   File created by the GAMESS Input Deck Generator Plugin for
>> >> > Avogadro
>> >> > !   Edited by Bill
>> >> >  $BASIS GBASIS=N31 NGAUSS=6 $END
>> >> >  $GUESS=MOREAD $END
>> >> >  $CONTRL SCFTYP=RHF RUNTYP=HESSIAN DFTTYP=BLYP $END
>> >> >  $VIB $END
>> >> >  $SYSTEM TIMLIM=14400 MEMORY=20000000 $END
>> >> >  $SCF DIRSCF=.TRUE. $END
>> >> >  $FORCE METHOD=SEMINUM VIBSIZ=0.010000 VIBANL=.TRUE. $END
>> >> >
>> >> >
>> >> >  $DATA
>> >> >
>> >> > C1
>> >> > C     6.0    -2.14672     2.26626    -2.95665
>> >> > N     7.0    -0.80323     1.86578    -3.43302
>> >> > C     6.0     0.10561     3.02777    -3.57695
>> >> > C     6.0    -0.17129     0.79907    -2.60156
>> >> > C     6.0    -0.98629    -0.49296    -2.58115
>> >> > C     6.0    -0.19359    -1.57992    -1.96583
>> >> > C     6.0     0.52687    -2.55972    -2.62045
>> >> > N     7.0     1.09342    -3.42775    -1.66150
>> >> > C     6.0     0.80568    -2.92341    -0.37771
>> >> > C     6.0    -0.03095    -1.78875    -0.54829
>> >> > C     6.0    -0.49899    -1.09423     0.57313
>> >> > C     6.0    -0.11170    -1.52690     1.82946
>> >> > C     6.0     0.71583    -2.66412     1.98378
>> >> > C     6.0     1.18495    -3.37020     0.89684
>> >> > C     6.0    -0.53652    -0.76636     3.04632
>> >> > C     6.0     0.60786     0.11462     3.55021
>> >> > C     6.0     0.25212     0.92000     4.81852
>> >> > O     8.0     0.67628     2.27256     4.60055
>> >> > C     6.0     1.12613     2.41547     3.31026
>> >> > O     8.0     1.58568     3.47760     2.95026
>> >> > N     7.0     0.93858     1.20654     2.59114
>> >> > H     1.0    -2.49801     3.13859    -3.52289
>> >> > H     1.0    -2.84890     1.44146    -3.13704
>> >> > H     1.0    -2.17688     2.51812    -1.88543
>> >> > H     1.0     0.30566     3.54284    -2.62461
>> >> > H     1.0    -0.33529     3.75106    -4.27464
>> >> > H     1.0     1.06389     2.69147    -3.99448
>> >> > H     1.0     0.82674     0.59817    -3.04125
>> >> > H     1.0     0.00536     1.14725    -1.55956
>> >> > H     1.0    -1.91998    -0.35434    -1.99720
>> >> > H     1.0    -1.29785    -0.78003    -3.60409
>> >> > H     1.0     0.65853    -2.70597    -3.69358
>> >> > H     1.0     1.79592    -4.09423    -1.85071
>> >> > H     1.0    -1.14884    -0.22192     0.43848
>> >> > H     1.0     0.99105    -2.97835     2.99770
>> >> > H     1.0     1.84111    -4.23678     1.01943
>> >> > H     1.0    -0.82750    -1.47126     3.85118
>> >> > H     1.0    -1.44348    -0.16310     2.83554
>> >> > H     1.0     1.50561    -0.53193     3.72104
>> >> > H     1.0    -0.83023     0.94914     5.03269
>> >> > H     1.0     0.78018     0.57471     5.72077
>> >> > H     1.0     1.41321     1.01375     1.74127
>> >> >  $END
>> >> >
>> >> >
>> >> >
>> >> > -------------------------------------------------------------------------
>> >> > This SF.Net email is sponsored by the Moblin Your Move Developer's
>> >> > challenge
>> >> > Build the coolest Linux based applications with Moblin SDK & win
>> >> > great
>> >> > prizes
>> >> > Grand prize is a trip for two to an Open Source event anywhere in the
>> >> > world
>> >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> >> > _______________________________________________
>> >> > Gausssum-help mailing list
>> >> > Gau...@li...
>> >> > https://lists.sourceforge.net/lists/listinfo/gausssum-help
>> >> >
>> >> >
>> >
>> >
>
>

Re: [cclib-devel] normal modes and vibdisps

[Noel O'B. <bao...@gm...>]

2008/7/22 Adam Tenderholt <a-t...@st...>:
> What are the differences between normal modes and cartesian
> displacement vectors? I think Gaussian uses the latter, while ADF and
> ORCA use the former.

Isn't it just that the normal mode is the actual thing which is being
represented by a cartesian displacement vector? Perhaps if you look at
the normal modes of water for Gaussian, ADF and ORCA, it will make
things clearer?

> ADF doesn't use mass-weighted normal modes while
> ORCA does use mass-weighted NMs. Do we need to change the way our
> parsers are thinking about vibdisps?

I've been looking back at an earlier conversation with Mehdi who was
interested in the hessian. He said that mass-unweighted is preferred
as then you can use it to calculate the normal modes for different
isotopes and so on. I have a feeling that it's not possible to change
MW NM to UMW NM. If so, this may mean that we should have two
attributes instead of just one vibdisps.

> Adam
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
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>

[cclib-devel] normal modes and vibdisps

[Adam T. <a-t...@st...>]

What are the differences between normal modes and cartesian  
displacement vectors? I think Gaussian uses the latter, while ADF and  
ORCA use the former. ADF doesn't use mass-weighted normal modes while  
ORCA does use mass-weighted NMs. Do we need to change the way our  
parsers are thinking about vibdisps?

Adam

Re: [cclib-devel] adf and td-dft

[Noel O'B. <bao...@gm...>]

(duplicate) You need to edit test\testdata

2008/7/21 Adam Tenderholt <a-t...@st...>:
> I've updated the adfparser in trunk to handle (restricted) TD calcs.
>
> I wasn't able to get testTD.py working by just adding an appropriate class.
> What else do I need to do?
>
> Adam
>
> On Jul 20, 2008, at 11:00 AM, Noel O'Boyle wrote:
>
>> 2008/7/18 Adam Tenderholt <a-t...@st...>:
>>>
>>> I'm looking to support parsing TD-DFT calcs in ADF, but we still need
>>> to create a TD test file (dvb_td). Are there a certain number of
>>> excitations that should be in this file? Are we handling both triplet
>>> (spin-forbidden) and singlet (spin-allowed) excited states?
>>
>> Looking at testTD.py, there's either 5 or 10 excitations. For programs
>> that calculate triplet and singlet excitations separately, there are
>> separate tests.
>>
>> We also have tests for unrestricted calculations, in testTDun.py.
>>
>>> Adam
>>>
>>>
>>> -------------------------------------------------------------------------
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win great
>>> prizes
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>>> world
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>>>
>>
>> -------------------------------------------------------------------------
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>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
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>> world
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>> _______________________________________________
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>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
>

Re: [cclib-devel] adf and td-dft

[Adam T. <a-t...@st...>]

I've updated the adfparser in trunk to handle (restricted) TD calcs.

I wasn't able to get testTD.py working by just adding an appropriate  
class. What else do I need to do?

Adam

On Jul 20, 2008, at 11:00 AM, Noel O'Boyle wrote:

> 2008/7/18 Adam Tenderholt <a-t...@st...>:
>> I'm looking to support parsing TD-DFT calcs in ADF, but we still need
>> to create a TD test file (dvb_td). Are there a certain number of
>> excitations that should be in this file? Are we handling both triplet
>> (spin-forbidden) and singlet (spin-allowed) excited states?
>
> Looking at testTD.py, there's either 5 or 10 excitations. For programs
> that calculate triplet and singlet excitations separately, there are
> separate tests.
>
> We also have tests for unrestricted calculations, in testTDun.py.
>
>> Adam
>>
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's  
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win  
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in  
>> the world
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>> _______________________________________________
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>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>
>
> -------------------------------------------------------------------------
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> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
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