cclib-devel — Developer's mailing list

[cclib-devel] New attribute vibanharms

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

Hi all,

Following an email by John Simmie to CCL.net, I've added support to
extract the  "X matrix of Anharmonic Constants (cm-1)" from a
FREQ=ANHARM job in Gaussian. I'm not quite sure what to call it, but
for the moment it's "vibanharms". I think there are also anharmonic
frequencies, so maybe it should instead be "vibanharmconsts".

- Noel

Re: [cclib-devel] Atommasses

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

On Wed, Mar 16, 2011 at 02:33:34PM +0000, Noel O'Boyle wrote:
> On 16 March 2011 13:45, Karol M. Langner <kar...@gm...> wrote:
> > On Wed, Mar 16, 2011 at 12:11:34PM +0000, Noel O'Boyle wrote:
> >> On 16 March 2011 09:37, Noel O'Boyle <bao...@gm...> wrote:
> >> > On 16 March 2011 09:36, Karol M. Langner <kar...@gm...> wrote:
> >> >> On Mon, Mar 14, 2011 at 11:53:20AM +0000, Noel O'Boyle wrote:
> >> >>> Hi Karol,
> >> >>>
> >> >>> I'm just updating the changelog for cclib-1.0.1 and I see that you
> >> >>> added a new attribute atommasses in r296. Can you update the wiki with
> >> >>> information on this?
> >> >>>
> >> >>> - Noel
> >> >>
> >> >> Sure. I can't seem to edit pages on the wiki. Does that have something to
> >> >> do with the recent software change?
> >> >
> >> > Probably - have you logged into SourceForge first, and then tried?
> >>
> >> It's looks like I needed to give you permissions - you're now an
> >> editor and admin. It seems that an account is only created when you
> >> visit the wiki for the first time. Then one of the wiki admins can
> >> give permissions to the account.
> >
> > Works now. I added atommasses to both 'parsed data' pages, as I understand it made
> > it into 1.0.1. The coverage is quite low among the parsers...
> 
> That's right. 1.0.1 is basically trunk.
> 
> A quick question: should every Gaussian calculation have atommasses set?

Generally, yes, if there are atoms then I think Gaussian will always print
a section with IAtWgt and AtmWgt. Althought there could be a special kind of calculation
that does not have explicit atoms, it would be beyond the current scope of cclib.

- Karol

Re: [cclib-devel] Atommasses

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

On 16 March 2011 13:45, Karol M. Langner <kar...@gm...> wrote:
> On Wed, Mar 16, 2011 at 12:11:34PM +0000, Noel O'Boyle wrote:
>> On 16 March 2011 09:37, Noel O'Boyle <bao...@gm...> wrote:
>> > On 16 March 2011 09:36, Karol M. Langner <kar...@gm...> wrote:
>> >> On Mon, Mar 14, 2011 at 11:53:20AM +0000, Noel O'Boyle wrote:
>> >>> Hi Karol,
>> >>>
>> >>> I'm just updating the changelog for cclib-1.0.1 and I see that you
>> >>> added a new attribute atommasses in r296. Can you update the wiki with
>> >>> information on this?
>> >>>
>> >>> - Noel
>> >>
>> >> Sure. I can't seem to edit pages on the wiki. Does that have something to
>> >> do with the recent software change?
>> >
>> > Probably - have you logged into SourceForge first, and then tried?
>>
>> It's looks like I needed to give you permissions - you're now an
>> editor and admin. It seems that an account is only created when you
>> visit the wiki for the first time. Then one of the wiki admins can
>> give permissions to the account.
>
> Works now. I added atommasses to both 'parsed data' pages, as I understand it made
> it into 1.0.1. The coverage is quite low among the parsers...

That's right. 1.0.1 is basically trunk.

A quick question: should every Gaussian calculation have atommasses set?

- Noel

Re: [cclib-devel] Atommasses

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

On Wed, Mar 16, 2011 at 12:11:34PM +0000, Noel O'Boyle wrote:
> On 16 March 2011 09:37, Noel O'Boyle <bao...@gm...> wrote:
> > On 16 March 2011 09:36, Karol M. Langner <kar...@gm...> wrote:
> >> On Mon, Mar 14, 2011 at 11:53:20AM +0000, Noel O'Boyle wrote:
> >>> Hi Karol,
> >>>
> >>> I'm just updating the changelog for cclib-1.0.1 and I see that you
> >>> added a new attribute atommasses in r296. Can you update the wiki with
> >>> information on this?
> >>>
> >>> - Noel
> >>
> >> Sure. I can't seem to edit pages on the wiki. Does that have something to
> >> do with the recent software change?
> >
> > Probably - have you logged into SourceForge first, and then tried?
> 
> It's looks like I needed to give you permissions - you're now an
> editor and admin. It seems that an account is only created when you
> visit the wiki for the first time. Then one of the wiki admins can
> give permissions to the account.

Works now. I added atommasses to both 'parsed data' pages, as I understand it made
it into 1.0.1. The coverage is quite low among the parsers...

Also, I will try to make a more comprehensive update of these tables in the next
few days.

- Karol

Re: [cclib-devel] Atommasses

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

On 16 March 2011 09:37, Noel O'Boyle <bao...@gm...> wrote:
> On 16 March 2011 09:36, Karol M. Langner <kar...@gm...> wrote:
>> On Mon, Mar 14, 2011 at 11:53:20AM +0000, Noel O'Boyle wrote:
>>> Hi Karol,
>>>
>>> I'm just updating the changelog for cclib-1.0.1 and I see that you
>>> added a new attribute atommasses in r296. Can you update the wiki with
>>> information on this?
>>>
>>> - Noel
>>
>> Sure. I can't seem to edit pages on the wiki. Does that have something to
>> do with the recent software change?
>
> Probably - have you logged into SourceForge first, and then tried?

It's looks like I needed to give you permissions - you're now an
editor and admin. It seems that an account is only created when you
visit the wiki for the first time. Then one of the wiki admins can
give permissions to the account.

>> Cheers,
>> Karol
>>
>

Re: [cclib-devel] Atommasses

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

On 16 March 2011 09:36, Karol M. Langner <kar...@gm...> wrote:
> On Mon, Mar 14, 2011 at 11:53:20AM +0000, Noel O'Boyle wrote:
>> Hi Karol,
>>
>> I'm just updating the changelog for cclib-1.0.1 and I see that you
>> added a new attribute atommasses in r296. Can you update the wiki with
>> information on this?
>>
>> - Noel
>
> Sure. I can't seem to edit pages on the wiki. Does that have something to
> do with the recent software change?

Probably - have you logged into SourceForge first, and then tried?

> Cheers,
> Karol
>

Re: [cclib-devel] Atommasses

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

On Mon, Mar 14, 2011 at 11:53:20AM +0000, Noel O'Boyle wrote:
> Hi Karol,
> 
> I'm just updating the changelog for cclib-1.0.1 and I see that you
> added a new attribute atommasses in r296. Can you update the wiki with
> information on this?
> 
> - Noel

Sure. I can't seem to edit pages on the wiki. Does that have something to
do with the recent software change?

Cheers,
Karol

[cclib-devel] ANN: cclib 1.0.1

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

Hello all,

cclib 1.0.1 is now available for download from http://cclib.sf.net.
This is largely a bug fix release (thanks to everyone that reported
bugs or supplied patches). We've also taken the opportunity to
(finally!) add instructions on the command-line application 'ccget' to
our wiki, so check it out, as it's quite handy.

Thanks to everyone that cited the cclib paper in the past - we really
appreciate it. This paper was the 2nd most cited J Comp Chem paper in
2009.

Changes since cclib-1.0:

Features:
	* New attribute atommasses - atomic masses in Dalton
	* Added support for Gaussian geometry optimisations that change
	the number of linearly independent basis functions over the
	course of the calculation

Bugfixes:
	* Handle triplet PM3 calculations in Gaussian03 (Greg Magoon)
	* Some Gaussian09 calculations were missing atomnos (Marius Retegan)
	* Handle multiple pseudopotentials in Gaussian03 (Tiago Silva)
	* Handle Gaussian calculations with >999 basis functions
	* ADF versions > 2007 no longer print overlap info by default
	* Handle parsing Firefly calculations that fail
	* Fix parsing of ORCA calculation (Marius Retegan)

Regards,
   Noel (on behalf of the cclib dev team)

[cclib-devel] Atommasses

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

Hi Karol,

I'm just updating the changelog for cclib-1.0.1 and I see that you
added a new attribute atommasses in r296. Can you update the wiki with
information on this?

- Noel

Re: [cclib-devel] Basis set parsing

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

Sounds good - when you have it, send it in.

No Anaheim for me I'm afraid...

- Noel

On 9 March 2011 17:04, Benjamin Stein <bs...@un...> wrote:
> Hi all,
>
> Sorry for the long silence, but I've more or less got the basis set parsing sorted out (at least in ORCA, but the foundations are there for everything). I'll try and get a cleaned up bit of code out next week (spring break, plenty of time for once...).
>
> Also, is anyone else planning on being at the ACS conference in Anaheim at the end of the month?
>
> Best,
> Ben Stein
> ------------------------------------------------------------------------------
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> A question and answer guide to determining the best fit
> for your organization - today and in the future.
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>

[cclib-devel] Basis set parsing

[Benjamin S. <bs...@un...>]

Hi all,

Sorry for the long silence, but I've more or less got the basis set parsing sorted out (at least in ORCA, but the foundations are there for everything). I'll try and get a cleaned up bit of code out next week (spring break, plenty of time for once...).

Also, is anyone else planning on being at the ACS conference in Anaheim at the end of the month?

Best,
Ben Stein

[cclib-devel] New release

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

Hi all,

I aim to make a new release, cclib-1.0.1 or so, in the next few days...

- Noel

[cclib-devel] [ cclib-Bugs-3184890 ] ORCA doesn't parse scf energy

[SourceForge.net <no...@so...>]

Bugs item #3184890, was opened at 2011-02-17 15:24
Message generated for change (Tracker Item Submitted) made by 
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3184890&group_id=161285

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: Parsers
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: mretegan ()
Assigned to: Nobody/Anonymous (nobody)
Summary: ORCA doesn't parse scf energy

Initial Comment:
If you include solvent effects via COSMO interface, the parser fails to parse the scfenergies, since the printing changes in the output.
Attached you will find a patch and a test case, both released under public domain.

Also I've tried to induce a particular situation in this computation. If you limit orca to a specific number of scf cycles, it does not print the total energy after the scf has finished if this is not converged. As far as I can tell everithing else gets printed (energy change, density change etc).


----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3184890&group_id=161285

Re: [cclib-devel] Wiki

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

> Ok, the wiki is now at
> https://sourceforge.net/apps/mediawiki/cclib/index.php?title=Main_Page.
>
> I was unable to reactivate the old wiki. In fact, to get the pages out
> I had to export the MySQL, import into another mediawiki I set up on
> my own server, and then export the pages (Special:Export) from there
> as XML to import into Sourceforge's Mediawiki (this does not allow SQL
> import). It took a little while and had me pulling my hair out at
> times. It's probably a bit messed up (e.g. no LaTeX extension I'm
> afraid for example).
>
> I didn't delete anything from the server (myself!), and haven't yet
> redirected cclib.sf.net to the new address. There should be some image
> files somewhere on the server (I think?) but I haven't dug around too
> much yet...

Ok - I've updated all the redirections. There's no other images to
migrate, actually - the only image on the wiki is the cclib logo. I've
changed <tex> to <math> and the Latex equations render fine, so that's
sorted. The last thing to check is whether you guys can edit the wiki.
You should log into sourceforge first, and then try editing a wiki
page. If there's a problem, I'll need to click around a bit more...

- Noel

Re: [cclib-devel] Wiki

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

On 10 February 2011 11:02, Noel O'Boyle <bao...@gm...> wrote:
> On 10 February 2011 10:57, Karol M. Langner <kar...@gm...> wrote:
>> On Thursday 10 February 2011 10:14:23 Noel O'Boyle wrote:
>>> Hi all,
>>>
>>> SourceForge have just changed everything on their server, so the wiki
>>> is down. I'll sort it out by and by...
>>>
>>> - Noel
>>
>> Noel,
>>
>>  I see on the BO mailing list you want to move to the SCF-provided wiki. If
>> that works, will you do the same for cclib?
>
> It probably makes sense to do that too. Unfortunately, the SF wiki
> puts a huge banner at the top of the page, which is really annoying.

Ok, the wiki is now at
https://sourceforge.net/apps/mediawiki/cclib/index.php?title=Main_Page.

I was unable to reactivate the old wiki. In fact, to get the pages out
I had to export the MySQL, import into another mediawiki I set up on
my own server, and then export the pages (Special:Export) from there
as XML to import into Sourceforge's Mediawiki (this does not allow SQL
import). It took a little while and had me pulling my hair out at
times. It's probably a bit messed up (e.g. no LaTeX extension I'm
afraid for example).

I didn't delete anything from the server (myself!), and haven't yet
redirected cclib.sf.net to the new address. There should be some image
files somewhere on the server (I think?) but I haven't dug around too
much yet...

- Noel

Re: [cclib-devel] Wiki

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

On 10 February 2011 10:57, Karol M. Langner <kar...@gm...> wrote:
> On Thursday 10 February 2011 10:14:23 Noel O'Boyle wrote:
>> Hi all,
>>
>> SourceForge have just changed everything on their server, so the wiki
>> is down. I'll sort it out by and by...
>>
>> - Noel
>
> Noel,
>
>  I see on the BO mailing list you want to move to the SCF-provided wiki. If
> that works, will you do the same for cclib?

It probably makes sense to do that too. Unfortunately, the SF wiki
puts a huge banner at the top of the page, which is really annoying.

> - Karol
>
> --
> written by Karol M. Langner
> Thu Feb 10 11:57:04 CET 2011
>

Re: [cclib-devel] Wiki

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

On Thursday 10 February 2011 10:14:23 Noel O'Boyle wrote:
> Hi all,
>
> SourceForge have just changed everything on their server, so the wiki
> is down. I'll sort it out by and by...
>
> - Noel

Noel,

 I see on the BO mailing list you want to move to the SCF-provided wiki. If 
that works, will you do the same for cclib?

- Karol

-- 
written by Karol M. Langner
Thu Feb 10 11:57:04 CET 2011

[cclib-devel] Wiki

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

Hi all,

SourceForge have just changed everything on their server, so the wiki
is down. I'll sort it out by and by...

- Noel

[cclib-devel] [ cclib-Bugs-3168810 ] Problem parsing Gaussian ONIOM

[SourceForge.net <no...@so...>]

Bugs item #3168810, was opened at 2011-01-31 17:11
Message generated for change (Comment added) made by baoilleach
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3168810&group_id=161285

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Noel O'Boyle (baoilleach)
Assigned to: Nobody/Anonymous (nobody)
Summary: Problem parsing Gaussian ONIOM

Initial Comment:
This came from a GaussSum user ((kar...@ug...). I didn't see a quick fix so I'm posting here to avoid forgetting about it...

The attached ONIOM file fails to parse correctly.

----------------------------------------------------------------------

>Comment By: Noel O'Boyle (baoilleach)
Date: 2011-02-01 12:11

Message:
Yes - that's it.

----------------------------------------------------------------------

Comment By: Adam Tenderholt (atenderholt)
Date: 2011-01-31 21:27

Message:
What is the parsing error? I'm getting the following error, which seems
easy-ish to fix:

---
Attempting to parse ortho_prod_freq.log
Traceback (most recent call last):
  File "/usr/local/bin/ccget", line 99, in <module>
    main()
  File "/usr/local/bin/ccget", line 81, in main
    data = log.parse()
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/cclib/parser/logfileparser.py",
line 221, in parse
    self.extract(inputfile, line)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/cclib/parser/gaussianparser.py",
line 866, in extract
    mocoeffs = [numpy.zeros((self.nmo, self.nbasis), "d")]
AttributeError: 'Gaussian' object has no attribute 'nmo'
---



----------------------------------------------------------------------

Comment By: Noel O'Boyle (baoilleach)
Date: 2011-01-31 17:15

Message:
File too large to attach. Please find it at
http://www.redbrick.dcu.ie/~noel/tmp/ortho_prod_freq.zip. I can confirm
that it was placed in the public domain (by the bug reporter).

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3168810&group_id=161285

[cclib-devel] [ cclib-Bugs-3168810 ] Problem parsing Gaussian ONIOM

[SourceForge.net <no...@so...>]

Bugs item #3168810, was opened at 2011-01-31 09:11
Message generated for change (Comment added) made by atenderholt
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3168810&group_id=161285

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Noel O'Boyle (baoilleach)
Assigned to: Nobody/Anonymous (nobody)
Summary: Problem parsing Gaussian ONIOM

Initial Comment:
This came from a GaussSum user ((kar...@ug...). I didn't see a quick fix so I'm posting here to avoid forgetting about it...

The attached ONIOM file fails to parse correctly.

----------------------------------------------------------------------

>Comment By: Adam Tenderholt (atenderholt)
Date: 2011-01-31 13:27

Message:
What is the parsing error? I'm getting the following error, which seems
easy-ish to fix:

---
Attempting to parse ortho_prod_freq.log
Traceback (most recent call last):
  File "/usr/local/bin/ccget", line 99, in <module>
    main()
  File "/usr/local/bin/ccget", line 81, in main
    data = log.parse()
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/cclib/parser/logfileparser.py",
line 221, in parse
    self.extract(inputfile, line)
  File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/cclib/parser/gaussianparser.py",
line 866, in extract
    mocoeffs = [numpy.zeros((self.nmo, self.nbasis), "d")]
AttributeError: 'Gaussian' object has no attribute 'nmo'
---



----------------------------------------------------------------------

Comment By: Noel O'Boyle (baoilleach)
Date: 2011-01-31 09:15

Message:
File too large to attach. Please find it at
http://www.redbrick.dcu.ie/~noel/tmp/ortho_prod_freq.zip. I can confirm
that it was placed in the public domain (by the bug reporter).

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3168810&group_id=161285

[cclib-devel] [ cclib-Bugs-3168810 ] Problem parsing Gaussian ONIOM

[SourceForge.net <no...@so...>]

Bugs item #3168810, was opened at 2011-01-31 17:11
Message generated for change (Tracker Item Submitted) made by baoilleach
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3168810&group_id=161285

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Noel O'Boyle (baoilleach)
Assigned to: Nobody/Anonymous (nobody)
Summary: Problem parsing Gaussian ONIOM

Initial Comment:
This came from a GaussSum user ((kar...@ug...). I didn't see a quick fix so I'm posting here to avoid forgetting about it...

The attached ONIOM file fails to parse correctly.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3168810&group_id=161285

Re: [cclib-devel] Basis set handling improvements

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

On 19 January 2011 17:20, Benjamin Stein <bs...@un...> wrote:
> Adam and Noel,
>
> Thanks for the great feedback!
>
> I'll poke around in avogadro (we'll see how rusty my C++ is...) and see how they store the data. I think it's critically important for the data to be accessible as possible; if the basis set is locked up in some gruesome data construct, it likely will never see the light of day. This is probably going to be one of the harder bits to do properly.
>
> As an aside, I had read something once about the idea of integrating cclib into avogadro (on avogadro's wiki?), but I don't know if anything ever became of that.

That was me...at
http://baoilleach.blogspot.com/2010/04/plug-cclib-into-avogadro.html.

It worked to a good extent. For example, it was possible to create an
Avogadro Molecule from an OBMol although it had to be done by hand.
Similarly, one could imagine creating an IR spectrum or whatever, once
Avogadro gets around to supporting those.

> Ben

Re: [cclib-devel] Basis set handling improvements

[Benjamin S. <bs...@un...>]

Adam and Noel,

Thanks for the great feedback! 

I'll poke around in avogadro (we'll see how rusty my C++ is...) and see how they store the data. I think it's critically important for the data to be accessible as possible; if the basis set is locked up in some gruesome data construct, it likely will never see the light of day. This is probably going to be one of the harder bits to do properly.

As an aside, I had read something once about the idea of integrating cclib into avogadro (on avogadro's wiki?), but I don't know if anything ever became of that. 

Ben

On Jan 19, 2011, at 5:05 AM, ccl...@li... wrote:

> Send cclib-devel mailing list submissions to
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> 
> 
> Today's Topics:
> 
>   1. Re: Basis set handling improvements (Noel O'Boyle)
>   2. Re: Basis set handling improvements (Karol M. Langner)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 18 Jan 2011 15:55:58 +0000
> From: "Noel O'Boyle" <bao...@gm...>
> Subject: Re: [cclib-devel] Basis set handling improvements
> To: Adam Tenderholt <ate...@gm...>
> Cc: cclib-dev List <ccl...@li...>
> Message-ID:
> 	<AANLkTimAep3oTbnQajmkf5yjgC3_9R1ib2iW=12...@ma...>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Sounds great. You might want to coordinate with Avogadro here, as they
> already have code in the dev version (it's in C++ of course) to do
> something similar. This would save you some work. Also you can see
> what data structure they are using.
> 
> - Noel
> 
> On 17 January 2011 18:36, Adam Tenderholt <ate...@gm...> wrote:
>> Hey Ben (and everyone else),
>> 
>> It's great that you're thinking about undertaking such an interesting
>> addition to cclib. It's definitely something that I wanted to get
>> around to working on, but I've just been plenty busy with research and
>> such. Anyhow, I have a couple of thoughts about your approach.
>> 
>> You should try to put the basis sets in a format that makes it easy to
>> eventually convert to the densities that may be of some interest. Can
>> this be done with matrix operations in numpy?
>> 
>> There's also the promise of OpenCL. This might not help in the
>> short-term since I don't think that there are drivers that take
>> advantage of GPUs (my laptop for instance can only work with the CPU),
>> but it seems like a good long-term approach. One of my former
>> colleagues has written a Mac application that renders orbitals from
>> Gaussian calculations on the fly. I don't really know what his plans
>> are for his program, but I don't think he plans on developing it
>> commercially. If you're interested, I can see what he thinks and put
>> you two in contact.
>> 
>> Adam
>> 
>> 
>> On Sun, Jan 16, 2011 at 12:10 PM, Benjamin Stein <bs...@un...> wrote:
>>> Hello, and I hope everyones holidays were nice and relaxing!
>>> 
>>> I've been thinking about improving the basis set handling in cclib which, as I'm sure everyone knows, looks to be a bit of an undertaking. My eventual goal is to have the handling robust enough to provide methods to generate cube (or whichever format) files of orbitals, densities, etc.
>>> 
>>> Personally, my motivation (aside from learning how basis sets are handled in various packages) is to play around with orbital transformations, and being able to plot them would be beyond useful. In addition, this would open up doors to possibly visualizing time-dependent results (such as density differences and transition densities).
>>> 
>>> I'm attacking the problem using a bottom up sort of approach, by working out how to store the basis set information at the primitive gaussian (or slater, I'm trying to be agnostic) level. So far I've sketched out a few simple classes (bear with me, I'm new to this OO stuff).
>>> 
>>> 
>>> Some thoughts:
>>> 
>>> Have each atom possess a list of shells. Each shell is composed of primitive functions, each with a contraction coefficient and exponent. This part seems easy-ish; I think I've figured out the parsing of ORCA's basis set output. I haven't looked at Gaussian in a while, but I remember it being reasonable. As long as a package has an option to print out the basis set in some sort of sane format, we should be OK.
>>> 
>>> A tricky bit is how to handle the 2l+1 m_l components of each shell. None of the packages I've looked at so far have documented the m_l ordering. We can always ask the developers if need be, and I think I've figured it out for ORCA by looking at the output.
>>> 
>>> 
>>> I've attached some code I put together (I haven't tested any of it, just thinking out loud), but I'm not sure if attachments work on the mailing list. If not I'll just pop it up on dropbox or something.
>>> 
>>> Best,
>>> Ben
>>> 
>>> 
>>> 
>>> Benjamin Stein
>>> University of New Mexico
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> Protect Your Site and Customers from Malware Attacks
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>>> malware threats, the impact they can have on your business, and how you
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>>> 
>>> 
>> 
>> ------------------------------------------------------------------------------
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> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 18 Jan 2011 22:04:16 +0100
> From: "Karol M. Langner" <kar...@gm...>
> Subject: Re: [cclib-devel] Basis set handling improvements
> To: ccl...@li...
> Cc: Adam Tenderholt <ate...@gm...>,	Noel O'Boyle
> 	<bao...@gm...>
> Message-ID: <201...@gm...>
> Content-Type: text/plain;  charset="iso-8859-1"
> 
> I was just going to mention Avogadro, too. I think Marcus there is 
> separating part of the cube-generating code into a standalone library.
> 
> On Tuesday 18 January 2011 16:55:58 Noel O'Boyle wrote:
>> Sounds great. You might want to coordinate with Avogadro here, as
>> they already have code in the dev version (it's in C++ of course) to
>> do something similar. This would save you some work. Also you can
>> see what data structure they are using.
>> 
>> - Noel
>> 
>> On 17 January 2011 18:36, Adam Tenderholt <ate...@gm...> 
> wrote:
>>> Hey Ben (and everyone else),
>>> 
>>> It's great that you're thinking about undertaking such an
>>> interesting addition to cclib. It's definitely something that I
>>> wanted to get around to working on, but I've just been plenty busy
>>> with research and such. Anyhow, I have a couple of thoughts about
>>> your approach.
>>> 
>>> You should try to put the basis sets in a format that makes it
>>> easy to eventually convert to the densities that may be of some
>>> interest. Can this be done with matrix operations in numpy?
>>> 
>>> There's also the promise of OpenCL. This might not help in the
>>> short-term since I don't think that there are drivers that take
>>> advantage of GPUs (my laptop for instance can only work with the
>>> CPU), but it seems like a good long-term approach. One of my
>>> former colleagues has written a Mac application that renders
>>> orbitals from Gaussian calculations on the fly. I don't really
>>> know what his plans are for his program, but I don't think he
>>> plans on developing it commercially. If you're interested, I can
>>> see what he thinks and put you two in contact.
>>> 
>>> Adam
>>> 
>>> On Sun, Jan 16, 2011 at 12:10 PM, Benjamin Stein <bs...@un...> 
> wrote:
>>>> Hello, and I hope everyones holidays were nice and relaxing!
>>>> 
>>>> I've been thinking about improving the basis set handling in
>>>> cclib which, as I'm sure everyone knows, looks to be a bit of an
>>>> undertaking. My eventual goal is to have the handling robust
>>>> enough to provide methods to generate cube (or whichever format)
>>>> files of orbitals, densities, etc.
>>>> 
>>>> Personally, my motivation (aside from learning how basis sets are
>>>> handled in various packages) is to play around with orbital
>>>> transformations, and being able to plot them would be beyond
>>>> useful. In addition, this would open up doors to possibly
>>>> visualizing time-dependent results (such as density differences
>>>> and transition densities).
>>>> 
>>>> I'm attacking the problem using a bottom up sort of approach, by
>>>> working out how to store the basis set information at the
>>>> primitive gaussian (or slater, I'm trying to be agnostic) level.
>>>> So far I've sketched out a few simple classes (bear with me, I'm
>>>> new to this OO stuff).
>>>> 
>>>> 
>>>> Some thoughts:
>>>> 
>>>> Have each atom possess a list of shells. Each shell is composed
>>>> of primitive functions, each with a contraction coefficient and
>>>> exponent. This part seems easy-ish; I think I've figured out the
>>>> parsing of ORCA's basis set output. I haven't looked at Gaussian
>>>> in a while, but I remember it being reasonable. As long as a
>>>> package has an option to print out the basis set in some sort of
>>>> sane format, we should be OK.
>>>> 
>>>> A tricky bit is how to handle the 2l+1 m_l components of each
>>>> shell. None of the packages I've looked at so far have documented
>>>> the m_l ordering. We can always ask the developers if need be,
>>>> and I think I've figured it out for ORCA by looking at the
>>>> output.
>>>> 
>>>> 
>>>> I've attached some code I put together (I haven't tested any of
>>>> it, just thinking out loud), but I'm not sure if attachments work
>>>> on the mailing list. If not I'll just pop it up on dropbox or
>>>> something.
>>>> 
>>>> Best,
>>>> Ben
> 
> -- 
> written by Karol Langner
> Tue Jan 18 22:04:15 CET 2011
> 
> 
> 
> ------------------------------
> 
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand 
> malware threats, the impact they can have on your business, and how you 
> can protect your company and customers by using code signing.
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> 
> ------------------------------
> 
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel
> 
> 
> End of cclib-devel Digest, Vol 48, Issue 7
> ******************************************

Benjamin Stein
University of New Mexico

Re: [cclib-devel] Basis set handling improvements

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

I was just going to mention Avogadro, too. I think Marcus there is 
separating part of the cube-generating code into a standalone library.

On Tuesday 18 January 2011 16:55:58 Noel O'Boyle wrote:
> Sounds great. You might want to coordinate with Avogadro here, as
> they already have code in the dev version (it's in C++ of course) to
> do something similar. This would save you some work. Also you can
> see what data structure they are using.
>
> - Noel
>
> On 17 January 2011 18:36, Adam Tenderholt <ate...@gm...> 
wrote:
> > Hey Ben (and everyone else),
> >
> > It's great that you're thinking about undertaking such an
> > interesting addition to cclib. It's definitely something that I
> > wanted to get around to working on, but I've just been plenty busy
> > with research and such. Anyhow, I have a couple of thoughts about
> > your approach.
> >
> > You should try to put the basis sets in a format that makes it
> > easy to eventually convert to the densities that may be of some
> > interest. Can this be done with matrix operations in numpy?
> >
> > There's also the promise of OpenCL. This might not help in the
> > short-term since I don't think that there are drivers that take
> > advantage of GPUs (my laptop for instance can only work with the
> > CPU), but it seems like a good long-term approach. One of my
> > former colleagues has written a Mac application that renders
> > orbitals from Gaussian calculations on the fly. I don't really
> > know what his plans are for his program, but I don't think he
> > plans on developing it commercially. If you're interested, I can
> > see what he thinks and put you two in contact.
> >
> > Adam
> >
> > On Sun, Jan 16, 2011 at 12:10 PM, Benjamin Stein <bs...@un...> 
wrote:
> >> Hello, and I hope everyones holidays were nice and relaxing!
> >>
> >> I've been thinking about improving the basis set handling in
> >> cclib which, as I'm sure everyone knows, looks to be a bit of an
> >> undertaking. My eventual goal is to have the handling robust
> >> enough to provide methods to generate cube (or whichever format)
> >> files of orbitals, densities, etc.
> >>
> >> Personally, my motivation (aside from learning how basis sets are
> >> handled in various packages) is to play around with orbital
> >> transformations, and being able to plot them would be beyond
> >> useful. In addition, this would open up doors to possibly
> >> visualizing time-dependent results (such as density differences
> >> and transition densities).
> >>
> >> I'm attacking the problem using a bottom up sort of approach, by
> >> working out how to store the basis set information at the
> >> primitive gaussian (or slater, I'm trying to be agnostic) level.
> >> So far I've sketched out a few simple classes (bear with me, I'm
> >> new to this OO stuff).
> >>
> >>
> >> Some thoughts:
> >>
> >> Have each atom possess a list of shells. Each shell is composed
> >> of primitive functions, each with a contraction coefficient and
> >> exponent. This part seems easy-ish; I think I've figured out the
> >> parsing of ORCA's basis set output. I haven't looked at Gaussian
> >> in a while, but I remember it being reasonable. As long as a
> >> package has an option to print out the basis set in some sort of
> >> sane format, we should be OK.
> >>
> >> A tricky bit is how to handle the 2l+1 m_l components of each
> >> shell. None of the packages I've looked at so far have documented
> >> the m_l ordering. We can always ask the developers if need be,
> >> and I think I've figured it out for ORCA by looking at the
> >> output.
> >>
> >>
> >> I've attached some code I put together (I haven't tested any of
> >> it, just thinking out loud), but I'm not sure if attachments work
> >> on the mailing list. If not I'll just pop it up on dropbox or
> >> something.
> >>
> >> Best,
> >> Ben

-- 
written by Karol Langner
Tue Jan 18 22:04:15 CET 2011

Re: [cclib-devel] Basis set handling improvements

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

Sounds great. You might want to coordinate with Avogadro here, as they
already have code in the dev version (it's in C++ of course) to do
something similar. This would save you some work. Also you can see
what data structure they are using.

- Noel

On 17 January 2011 18:36, Adam Tenderholt <ate...@gm...> wrote:
> Hey Ben (and everyone else),
>
> It's great that you're thinking about undertaking such an interesting
> addition to cclib. It's definitely something that I wanted to get
> around to working on, but I've just been plenty busy with research and
> such. Anyhow, I have a couple of thoughts about your approach.
>
> You should try to put the basis sets in a format that makes it easy to
> eventually convert to the densities that may be of some interest. Can
> this be done with matrix operations in numpy?
>
> There's also the promise of OpenCL. This might not help in the
> short-term since I don't think that there are drivers that take
> advantage of GPUs (my laptop for instance can only work with the CPU),
> but it seems like a good long-term approach. One of my former
> colleagues has written a Mac application that renders orbitals from
> Gaussian calculations on the fly. I don't really know what his plans
> are for his program, but I don't think he plans on developing it
> commercially. If you're interested, I can see what he thinks and put
> you two in contact.
>
> Adam
>
>
> On Sun, Jan 16, 2011 at 12:10 PM, Benjamin Stein <bs...@un...> wrote:
>> Hello, and I hope everyones holidays were nice and relaxing!
>>
>> I've been thinking about improving the basis set handling in cclib which, as I'm sure everyone knows, looks to be a bit of an undertaking. My eventual goal is to have the handling robust enough to provide methods to generate cube (or whichever format) files of orbitals, densities, etc.
>>
>> Personally, my motivation (aside from learning how basis sets are handled in various packages) is to play around with orbital transformations, and being able to plot them would be beyond useful. In addition, this would open up doors to possibly visualizing time-dependent results (such as density differences and transition densities).
>>
>> I'm attacking the problem using a bottom up sort of approach, by working out how to store the basis set information at the primitive gaussian (or slater, I'm trying to be agnostic) level. So far I've sketched out a few simple classes (bear with me, I'm new to this OO stuff).
>>
>>
>> Some thoughts:
>>
>> Have each atom possess a list of shells. Each shell is composed of primitive functions, each with a contraction coefficient and exponent. This part seems easy-ish; I think I've figured out the parsing of ORCA's basis set output. I haven't looked at Gaussian in a while, but I remember it being reasonable. As long as a package has an option to print out the basis set in some sort of sane format, we should be OK.
>>
>> A tricky bit is how to handle the 2l+1 m_l components of each shell. None of the packages I've looked at so far have documented the m_l ordering. We can always ask the developers if need be, and I think I've figured it out for ORCA by looking at the output.
>>
>>
>> I've attached some code I put together (I haven't tested any of it, just thinking out loud), but I'm not sure if attachments work on the mailing list. If not I'll just pop it up on dropbox or something.
>>
>> Best,
>> Ben
>>
>>
>>
>> Benjamin Stein
>> University of New Mexico
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Protect Your Site and Customers from Malware Attacks
>> Learn about various malware tactics and how to avoid them. Understand
>> malware threats, the impact they can have on your business, and how you
>> can protect your company and customers by using code signing.
>> http://p.sf.net/sfu/oracle-sfdevnl
>> _______________________________________________
>> cclib-devel mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>
>>
>
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand
> malware threats, the impact they can have on your business, and how you
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
> _______________________________________________
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