cclib-users Mailing List for cclib (Page 3)

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thanks, thats exactly what I was looking for. Thanks Felix. Wasn't aware 
about the ccget script.

Cheers, Johannes

Both ways work nicely. IIRC one of the reasons for creating ccData was to
make this kind of thing easier.

On Fri, May 13, 2016 at 2:08 AM, Noel O'Boyle <bao...@gm...> wrote:

> dir(object) is also an option.
>
> On 13 May 2016 at 10:06, Felix Plasser <fel...@un...> wrote:
> > I think this is what ccget does:
> >
> >             print("cclib can parse the following attributes from %s:" %
> > name)
> >             for attr in data._attrlist:
> >                 if hasattr(data, attr):
> >                     print("  %s" % attr)
> >
> > Is that what you need?
> >
> > -Felix
> >
> >
> > On 05/13/2016 09:33 AM, Johannes Wagner wrote:
> >
> > hey together,
> > quick question: Is there a possibility in cclib do get an overview of all
> > successful parsed attributes contained in the object? I actually thought
> > help(object) does it, but it shows just generic informations about which
> > attribute has which format.
> >
> > The logging I think should show that, but even setting
> >
> > object.logger.setLevel(logging.INFO)
> >
> > does only show warnings. Well setting to .DEBUG I get a log for every
> single
> > parsed value, but that’s overkill and also only shows while parsing, not
> > later on anymore when handling the object…
> >
> > Is there something in cclib that shows an overview over all parsed
> > attributes of the given log file?
> >
> >
> > On a side note, I think a 'using cclib' section a’la
> > http://cclib.sourceforge.net/wiki/index.php/Using_cclib should be
> > transferred to the http://cclib.github.io page. Thats completely
> missing in
> > the tutorial page, just install and read about parsed data notes, but no
> > documentation how to actually use cclib...
> >
> > Oh and btw, the link for the mailing list at the bottom of the cclib
> github
> > page (https://github.com/cclib/cclib) is a url that points to
> >
> >
> https://github.com/cclib/cclib/blob/master/ccl...@li...
> >
> > instead of
> >
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
> > maybe someone fixes this quick.
> >
> >
> > cheers, Johannes
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Mobile security can be enabling, not merely restricting. Employees who
> > bring their own devices (BYOD) to work are irked by the imposition of MDM
> > restrictions. Mobile Device Manager Plus allows you to control only the
> > apps on BYO-devices by containerizing them, leaving personal data
> untouched!
> > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> >
> >
> >
> > _______________________________________________
> > cclib-users mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
> >
> > --
> > Felix Plasser
> > Institute for Theoretical Chemistry
> > University of Vienna
> > Währingerstr. 17/404
> > 1090 Wien
> > fel...@un...
> > http://homepage.univie.ac.at/felix.plasser/
> > Tel.: +43-1-4277-52757
> >
> >
> >
> ------------------------------------------------------------------------------
> > Mobile security can be enabling, not merely restricting. Employees who
> > bring their own devices (BYOD) to work are irked by the imposition of MDM
> > restrictions. Mobile Device Manager Plus allows you to control only the
> > apps on BYO-devices by containerizing them, leaving personal data
> untouched!
> > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> > _______________________________________________
> > cclib-users mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data
> untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

dir(object) is also an option.

On 13 May 2016 at 10:06, Felix Plasser <fel...@un...> wrote:
> I think this is what ccget does:
>
>             print("cclib can parse the following attributes from %s:" %
> name)
>             for attr in data._attrlist:
>                 if hasattr(data, attr):
>                     print("  %s" % attr)
>
> Is that what you need?
>
> -Felix
>
>
> On 05/13/2016 09:33 AM, Johannes Wagner wrote:
>
> hey together,
> quick question: Is there a possibility in cclib do get an overview of all
> successful parsed attributes contained in the object? I actually thought
> help(object) does it, but it shows just generic informations about which
> attribute has which format.
>
> The logging I think should show that, but even setting
>
> object.logger.setLevel(logging.INFO)
>
> does only show warnings. Well setting to .DEBUG I get a log for every single
> parsed value, but that’s overkill and also only shows while parsing, not
> later on anymore when handling the object…
>
> Is there something in cclib that shows an overview over all parsed
> attributes of the given log file?
>
>
> On a side note, I think a 'using cclib' section a’la
> http://cclib.sourceforge.net/wiki/index.php/Using_cclib should be
> transferred to the http://cclib.github.io page. Thats completely missing in
> the tutorial page, just install and read about parsed data notes, but no
> documentation how to actually use cclib...
>
> Oh and btw, the link for the mailing list at the bottom of the cclib github
> page (https://github.com/cclib/cclib) is a url that points to
>
> https://github.com/cclib/cclib/blob/master/ccl...@li...
>
> instead of
>
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
> maybe someone fixes this quick.
>
>
> cheers, Johannes
>
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>
>
>
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>
> --
> Felix Plasser
> Institute for Theoretical Chemistry
> University of Vienna
> Währingerstr. 17/404
> 1090 Wien
> fel...@un...
> http://homepage.univie.ac.at/felix.plasser/
> Tel.: +43-1-4277-52757
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

I think this is what ccget does:

             print("cclib can parse the following attributes from %s:" % 
name)
             for attr in data._attrlist:
                 if hasattr(data, attr):
                     print("  %s" % attr)

Is that what you need?

-Felix

On 05/13/2016 09:33 AM, Johannes Wagner wrote:
> hey together,
> quick question: Is there a possibility in cclib do get an overview of 
> all successful parsed attributes contained in the object? I actually 
> thought help(object) does it, but it shows just generic informations 
> about which attribute has which format.
>
> The logging I think should show that, but even setting
>
> object.logger.setLevel(logging.INFO)
>
> does only show warnings. Well setting to .DEBUG I get a log for every 
> single parsed value, but that’s overkill and also only shows while 
> parsing, not later on anymore when handling the object…
>
> Is there something in cclib that shows an overview over all parsed 
> attributes of the given log file?
>
>
> On a side note, I think a 'using cclib' section a’la 
> http://cclib.sourceforge.net/wiki/index.php/Using_cclib should be 
> transferred to the http://cclib.github.io page. Thats completely 
> missing in the tutorial page, just install and read about parsed data 
> notes, but no documentation how to actually use cclib...
>
> Oh and btw, the link for the mailing list at the bottom of the cclib 
> github page (https://github.com/cclib/cclib) is a url that points to
>
> https://github.com/cclib/cclib/blob/master/ccl...@li...
>
> instead of
>
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
> maybe someone fixes this quick.
>
>
> cheers, Johannes
>
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>
>
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users

-- 
Felix Plasser
Institute for Theoretical Chemistry
University of Vienna
Währingerstr. 17/404
1090 Wien
fel...@un...
http://homepage.univie.ac.at/felix.plasser/
Tel.: +43-1-4277-52757

hey together,
quick question: Is there a possibility in cclib do get an overview of all successful parsed attributes contained in the object? I actually thought help(object) does it, but it shows just generic informations about which attribute has which format.

The logging I think should show that, but even setting 

object.logger.setLevel(logging.INFO)

does only show warnings. Well setting to .DEBUG I get a log for every single parsed value, but that’s overkill and also only shows while parsing, not later on anymore when handling the object…

Is there something in cclib that shows an overview over all parsed attributes of the given log file?

On a side note, I think a 'using cclib' section a’la http://cclib.sourceforge.net/wiki/index.php/Using_cclib <http://cclib.sourceforge.net/wiki/index.php/Using_cclib> should be transferred to the http://cclib.github.io <http://cclib.github.io/> page. Thats completely missing in the tutorial page, just install and read about parsed data notes, but no documentation how to actually use cclib...

Oh and btw, the link for the mailing list at the bottom of the cclib github page (https://github.com/cclib/cclib) is a url that points to

https://github.com/cclib/cclib/blob/master/ccl...@li... <https://github.com/cclib/cclib/blob/master/ccl...@li...>

instead of

https://lists.sourceforge.net/lists/listinfo/cclib-users <https://lists.sourceforge.net/lists/listinfo/cclib-users>

maybe someone fixes this quick.

cheers, Johannes

Hi Alexis,

Could you provide us with an example output file that causes this error?

Karol

On Fri, May 6, 2016 at 9:55 AM, Alexis Otero Calvi <ao...@is...>
wrote:

> Hi all
>
> I tried to use cclib to extract information of Gamess log files, but have
> met with the following
>
> Traceback (most recent call last):
>   File "/usr/local/bin/ccget", line 180, in <module>
>     ccget()
>   File "/usr/local/bin/ccget", line 153, in ccget
>     data = ccread(filename, **kwargs)
>   File "/usr/local/lib/python2.7/dist-packages/cclib/parser/ccio.py", line
> 107, in ccread
>     return log.parse()
>   File
> "/usr/local/lib/python2.7/dist-packages/cclib/parser/logfileparser.py",
> line 309, in parse
>     self.extract(inputfile, line)
>   File
> "/usr/local/lib/python2.7/dist-packages/cclib/parser/gamessparser.py", line
> 968, in extract
>     self.mocoeffs[0][base+j, i] = float(coeffs[j * 11:(j + 1) * 11])
> ValueError: could not convert string to float: B
>
> How I can solve it?
>
> cclib version 1.4
>
>
> Instituto Superior Minero Metalúrgico de Moa Dr. Antonio Núñez Jiménez
> 40 años al servicio de la docencia, la investigación y la innovación
> tecnológica
>
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications
> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

Hi all

I tried to use cclib to extract information of Gamess log files, but have met with the following

Traceback (most recent call last):
  File "/usr/local/bin/ccget", line 180, in <module>
    ccget()
  File "/usr/local/bin/ccget", line 153, in ccget
    data = ccread(filename, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/cclib/parser/ccio.py", line 107, in ccread
    return log.parse()
  File "/usr/local/lib/python2.7/dist-packages/cclib/parser/logfileparser.py", line 309, in parse
    self.extract(inputfile, line)
  File "/usr/local/lib/python2.7/dist-packages/cclib/parser/gamessparser.py", line 968, in extract
    self.mocoeffs[0][base+j, i] = float(coeffs[j * 11:(j + 1) * 11])
ValueError: could not convert string to float: B

How I can solve it?

cclib version 1.4

Instituto Superior Minero Metalúrgico de Moa Dr. Antonio Núñez Jiménez
40 años al servicio de la docencia, la investigación y la innovación tecnológica

If it fixes something, I would say push it back to us. Simple fixes are
great, because they're easy to evaluate.

We don't plan to support Python2.6 generally, but is you create a bug and
provide the exact version and error message, I can take a look.

On Wed, May 4, 2016 at 2:06 AM, Felix Plasser <fel...@un...>
wrote:

> Hi, thank you for your responses!
>
> My problems only exist for python2.6 (which is the default on our CentOS
> system). But python2.7 works. So that is ok!
>
> I'll adjust the README and add the cclib paper to the list of references.
>
> So far I just made a tiny change in adfparser.py to parse atombasis
>
> https://github.com/felixplasser/cclib/commit/de40471b2d38dec73d020045144d4b15af72eb8e
> I don't know of how much general interest this is. I guess I'll wait until
> I have some more serious code before I do a pull request.
>
> -Felix
>
> On 05/03/2016 04:18 PM, Karol Langner wrote:
>
> 1. Eric is correct - and please submit a bug if something doesn't work in
> Py2. I think we generally want to support everything between 2.7 and 3.x.
>
> 2. Feel free to do anything within the LGPL. Consider donating code back
> to cclib if it's of general interest.
>
> On Tue, May 3, 2016 at 6:49 AM, Eric Berquist <er...@pi...> wrote:
>
>> Hi Felix,
>>
>> 1. cclib should be fully backwards-compatible with Python 2.7. It might
>> be compatible with earlier versions, but we don't test for it. Can you post
>> the error you're getting?
>>
>> 2. Yes, that sounds correct. I also think that if you have a README file,
>> it should mention that you use cclib and contain a link to our website:
>> http://cclib.github.io/
>>
>> Eric
>>
>> On Tue, May 3, 2016 at 3:24 AM, Felix Plasser <fel...@un...
>> > wrote:
>>
>>> Hello,
>>>
>>> Could I just ask two quick questions:
>>>
>>> First, what is the philosophy of cclib with respect to backward
>>> compatibility with python 2? When I try to run it with python 2, I have
>>> to deactivate molproparser manually. Is there any other way to run cclib
>>> with python 2 or is that just not a priority?
>>>
>>> Second, since cclib is distributed as LGPL, I am allowed distribute it
>>> with my own code ( http://theodore-qc.sourceforge.net/ ), right? I just
>>> have to supply the full source and LICENSE file of cclib.
>>>
>>> Thanks!
>>> Felix
>>>
>>> --
>>> Felix Plasser
>>> Institute for Theoretical Chemistry
>>> University of Vienna
>>> Währingerstr. 17/404
>>> 1090 Wien
>>> fel...@un...
>>> http://homepage.univie.ac.at/felix.plasser/
>>> Tel.: +43-1-4277-52757
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Find and fix application performance issues faster with Applications
>>> Manager
>>> Applications Manager provides deep performance insights into multiple
>>> tiers of
>>> your business applications. It resolves application problems quickly and
>>> reduces your MTTR. Get your free trial!
>>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>>> _______________________________________________
>>> cclib-users mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Find and fix application performance issues faster with Applications
>> Manager
>> Applications Manager provides deep performance insights into multiple
>> tiers of
>> your business applications. It resolves application problems quickly and
>> reduces your MTTR. Get your free trial!
>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>
>
> --
> Felix Plasser
> Institute for Theoretical Chemistry
> University of Vienna
> Währingerstr. 17/404
> 1090 Wie...@un...http://homepage.univie.ac.at/felix.plasser/
> Tel.: +43-1-4277-52757
>
>

Hi, thank you for your responses!

My problems only exist for python2.6 (which is the default on our CentOS 
system). But python2.7 works. So that is ok!

I'll adjust the README and add the cclib paper to the list of references.

So far I just made a tiny change in adfparser.py to parse atombasis
https://github.com/felixplasser/cclib/commit/de40471b2d38dec73d020045144d4b15af72eb8e
I don't know of how much general interest this is. I guess I'll wait 
until I have some more serious code before I do a pull request.

-Felix

On 05/03/2016 04:18 PM, Karol Langner wrote:
> 1. Eric is correct - and please submit a bug if something doesn't work 
> in Py2. I think we generally want to support everything between 2.7 
> and 3.x.
>
> 2. Feel free to do anything within the LGPL. Consider donating code 
> back to cclib if it's of general interest.
>
> On Tue, May 3, 2016 at 6:49 AM, Eric Berquist <er...@pi... 
> <mailto:er...@pi...>> wrote:
>
>     Hi Felix,
>
>     1. cclib should be fully backwards-compatible with Python 2.7. It
>     might be compatible with earlier versions, but we don't test for
>     it. Can you post the error you're getting?
>
>     2. Yes, that sounds correct. I also think that if you have a
>     README file, it should mention that you use cclib and contain a
>     link to our website: http://cclib.github.io/
>
>     Eric
>
>     On Tue, May 3, 2016 at 3:24 AM, Felix Plasser
>     <fel...@un... <mailto:fel...@un...>>
>     wrote:
>
>         Hello,
>
>         Could I just ask two quick questions:
>
>         First, what is the philosophy of cclib with respect to backward
>         compatibility with python 2? When I try to run it with python
>         2, I have
>         to deactivate molproparser manually. Is there any other way to
>         run cclib
>         with python 2 or is that just not a priority?
>
>         Second, since cclib is distributed as LGPL, I am allowed
>         distribute it
>         with my own code ( http://theodore-qc.sourceforge.net/ ),
>         right? I just
>         have to supply the full source and LICENSE file of cclib.
>
>         Thanks!
>         Felix
>
>         --
>         Felix Plasser
>         Institute for Theoretical Chemistry
>         University of Vienna
>         Währingerstr. 17/404
>         1090 Wien
>         fel...@un... <mailto:fel...@un...>
>         http://homepage.univie.ac.at/felix.plasser/
>         Tel.: +43-1-4277-52757 <tel:%2B43-1-4277-52757>
>
>
>         ------------------------------------------------------------------------------
>         Find and fix application performance issues faster with
>         Applications Manager
>         Applications Manager provides deep performance insights into
>         multiple tiers of
>         your business applications. It resolves application problems
>         quickly and
>         reduces your MTTR. Get your free trial!
>         https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>         _______________________________________________
>         cclib-users mailing list
>         ccl...@li...
>         <mailto:ccl...@li...>
>         https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>
>
>     ------------------------------------------------------------------------------
>     Find and fix application performance issues faster with
>     Applications Manager
>     Applications Manager provides deep performance insights into
>     multiple tiers of
>     your business applications. It resolves application problems
>     quickly and
>     reduces your MTTR. Get your free trial!
>     https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>     _______________________________________________
>     cclib-users mailing list
>     ccl...@li...
>     <mailto:ccl...@li...>
>     https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

-- 
Felix Plasser
Institute for Theoretical Chemistry
University of Vienna
Währingerstr. 17/404
1090 Wien
fel...@un...
http://homepage.univie.ac.at/felix.plasser/
Tel.: +43-1-4277-52757

1. Eric is correct - and please submit a bug if something doesn't work in
Py2. I think we generally want to support everything between 2.7 and 3.x.

2. Feel free to do anything within the LGPL. Consider donating code back to
cclib if it's of general interest.

On Tue, May 3, 2016 at 6:49 AM, Eric Berquist <er...@pi...> wrote:

> Hi Felix,
>
> 1. cclib should be fully backwards-compatible with Python 2.7. It might be
> compatible with earlier versions, but we don't test for it. Can you post
> the error you're getting?
>
> 2. Yes, that sounds correct. I also think that if you have a README file,
> it should mention that you use cclib and contain a link to our website:
> http://cclib.github.io/
>
> Eric
>
> On Tue, May 3, 2016 at 3:24 AM, Felix Plasser <fel...@un...>
> wrote:
>
>> Hello,
>>
>> Could I just ask two quick questions:
>>
>> First, what is the philosophy of cclib with respect to backward
>> compatibility with python 2? When I try to run it with python 2, I have
>> to deactivate molproparser manually. Is there any other way to run cclib
>> with python 2 or is that just not a priority?
>>
>> Second, since cclib is distributed as LGPL, I am allowed distribute it
>> with my own code ( http://theodore-qc.sourceforge.net/ ), right? I just
>> have to supply the full source and LICENSE file of cclib.
>>
>> Thanks!
>> Felix
>>
>> --
>> Felix Plasser
>> Institute for Theoretical Chemistry
>> University of Vienna
>> Währingerstr. 17/404
>> 1090 Wien
>> fel...@un...
>> http://homepage.univie.ac.at/felix.plasser/
>> Tel.: +43-1-4277-52757
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Find and fix application performance issues faster with Applications
>> Manager
>> Applications Manager provides deep performance insights into multiple
>> tiers of
>> your business applications. It resolves application problems quickly and
>> reduces your MTTR. Get your free trial!
>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>
>
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications
> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

Hi Felix,

1. cclib should be fully backwards-compatible with Python 2.7. It might be
compatible with earlier versions, but we don't test for it. Can you post
the error you're getting?

2. Yes, that sounds correct. I also think that if you have a README file,
it should mention that you use cclib and contain a link to our website:
http://cclib.github.io/

Eric

On Tue, May 3, 2016 at 3:24 AM, Felix Plasser <fel...@un...>
wrote:

> Hello,
>
> Could I just ask two quick questions:
>
> First, what is the philosophy of cclib with respect to backward
> compatibility with python 2? When I try to run it with python 2, I have
> to deactivate molproparser manually. Is there any other way to run cclib
> with python 2 or is that just not a priority?
>
> Second, since cclib is distributed as LGPL, I am allowed distribute it
> with my own code ( http://theodore-qc.sourceforge.net/ ), right? I just
> have to supply the full source and LICENSE file of cclib.
>
> Thanks!
> Felix
>
> --
> Felix Plasser
> Institute for Theoretical Chemistry
> University of Vienna
> Währingerstr. 17/404
> 1090 Wien
> fel...@un...
> http://homepage.univie.ac.at/felix.plasser/
> Tel.: +43-1-4277-52757
>
>
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications
> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
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> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

Hello,

Could I just ask two quick questions:

First, what is the philosophy of cclib with respect to backward 
compatibility with python 2? When I try to run it with python 2, I have 
to deactivate molproparser manually. Is there any other way to run cclib 
with python 2 or is that just not a priority?

Second, since cclib is distributed as LGPL, I am allowed distribute it 
with my own code ( http://theodore-qc.sourceforge.net/ ), right? I just 
have to supply the full source and LICENSE file of cclib.

Thanks!
Felix

-- 
Felix Plasser
Institute for Theoretical Chemistry
University of Vienna
Währingerstr. 17/404
1090 Wien
fel...@un...
http://homepage.univie.ac.at/felix.plasser/
Tel.: +43-1-4277-52757

Hello cclib users and devs,

On behalf of the cclib development team, we are pleased to announce the
release of cclib 1.4, which is now available for download from
http://cclib.github.io. This is a major update to version 1.3.1 that
includes new parsers and attributes, as well as many bug fixes and small
improvements.

cclib is an open source library, written in Python, for parsing and
interpreting the results of computational chemistry packages. It currently
parses output files from ADF, DALTON, Firefly, GAMESS (US), GAMESS-UK,
Gaussian, Jaguar, Molpro, NWChem, ORCA, Psi and QChem.

Among other data, cclib extracts:
    * coordinates and energies
    * information about geometry optimization
    * atomic orbital information
    * molecular orbital information
    * information on vibrational modes
    * the results of a TD-DFT calculation
    * charges and mutlipole moments
(For a complete list see http://cclib.github.io/data.html).

cclib also provides some calculation methods for interpreting the
electronic properties of molecules using analyses such as:
    * Mulliken and Lowdin population analyses
    * Overlap population analysis
    * Calculation of Mayer's bond orders.
(For a complete list see http://cclib.github.io/methods.html).

For information on how to use cclib, see
    http://cclib.github.io/tutorial.html

If you need help, find a bug, want new features or have any questions,
please send an email to our mailing list:
    https://lists.sourceforge.net/lists/listinfo/cclib-users

If your published work uses cclib, please support its development by citing
the following article:
    N. M. O'Boyle, A. L. Tenderholt, K. M. Langner, cclib: a library for
package-independent computational chemistry algorithms, J. Comp. Chem. 29
(5), 839-845 (2008)
You can also specifically reference this version of cclib as:
    Eric Berquist, Karol M. Langner, Noel M. O'Boyle, and Adam L.
Tenderholt. Release of cclib version 1.4. 2016.
http://dx.doi.org/10.5281/zenodo.50324

Regards,
The cclib development team

———

Summary of changes since cclib 1.3.1:
    * New parser: cclib can now parse DALTON files
    * New parser: cclib can now parse ORCA files
    * New attribute optstatus for status during geometry optimizations and
scans
    * Improvements to the unit test and regression suites
    * Support for Python 3.5
    * Many bugfixes and patches thanks to Sagar Gaur, mwykes, Martin Peeks
and others

Great! If the tests pass, then we can be quite certain it works correctly.

On Fri, Mar 4, 2016 at 9:25 AM, Felix Plasser <fel...@un...>
wrote:

> Hi, I double checked this and it looks like gbasis is parsed correctly. If
> I do the same calculation with Orca and Gaussian, then I get the same
> results with
> ccget orca.out gbasis
> and
> ccget gaussian.log gbasis
> So everything looks fine and I get the same canonical result.
>
> The thing that confused me initially is that Orca uses a different order
> for the p-functions - and because of that things looked differently. But
> this is already parsed correctly by cclib:
> ccget orca.out aonames
> [ ..., u'C1_1PZ', u'C1_1PX', u'C1_1PY', ...]
> And I will just have to reorder the MO-coefficients accordingly for my
> purposes.
>
> As I see it, everything looks fine, and I'll send the pull request.
>
> By the way, getting the correct ordering of the basis functions would also
> be a challenge for the Molden writer. My own little tool cc2molden.py
> https://sourceforge.net/p/theodore-qc/code/ci/master/tree/bin/cc2molden.py
> failed because of this ordering. And that is what confused me ...
>
> -Felix
>
>
> On 03/04/2016 03:06 PM, Karol Langner wrote:
>
> I think we want to parse the canonical gbasis before any normalization,
> because that's transferable. In any case, we want it to be the same for all
> programs. Is there an easy way to unnormalize?
> On Mar 4, 2016 1:49 AM, "Felix Plasser" <fel...@un...>
> wrote:
>
>> Hi Karol and Eric,
>>
>> I do have the parser now
>>
>> https://github.com/felixplasser/cclib/commit/0f8e6db49910aedb92a1cad5e0ba384a3fc0efaa?diff=unified
>>
>> This parses gbasis as it is printed out in the standard output. The
>> problem is that internally ORCA changes the normalization factors, and then
>> this gbasis is no longer consistent with the MO-coefficients. For example
>> when I run orca_2mkl, it tells me
>> "The basis set has NOT been un-normalized for printing"
>> And then I get the un-normalized coefficients that are used internally
>> and that are consistent with mocoeffs. But they are not the same
>> coefficients printed in the output file.
>>
>> For my specific application gbasis works they way it is parsed now. But I
>> do not really know what gbasis is supposed to be: the input coefficients,
>> or the coefficients used internally.
>>
>> About Molden format: it would just parse a few attributes, mainly atmnos,
>> atomcoords, gbasis, and mocoeffs
>> But the important point here would be that gbasis and mocoeffs are
>> consistent and well-defined (assuming that the molden file was created
>> properly)
>>
>> Felix
>>
>> On 03/03/2016 09:35 PM, Eric Berquist wrote:
>>
>> Hi Felix and Karol,
>>
>> If a pull request is made, I guarantee I'll take a look at it, since I'm
>> trying to be more active in the project.
>>
>> We don't have a Molden parser yet, though I started a Molden writer for
>> cclib, and have something standalone that attempts to clean up the Molden
>> output produced by a few different programs, since Molden itself seemed
>> pretty picky about the section ordering:
>> https://github.com/berquist/scripts/blob/master/fix_molden.py
>>
>> Eric
>>
>> On Thu, Mar 3, 2016 at 3:25 PM, Karol Langner <kar...@gm...>
>> wrote:
>>
>>> Yes, pull requests are definitely the way to go. Turnaround time varies
>>> with how busy people are.
>>>
>>> Parsing molden files is possible, just requires some work. However, I'm
>>> not sure what kind of coverage of cclib attribute one could get from those
>>> files. Are they text format or binary?
>>>
>>> On Thu, Mar 3, 2016 at 3:01 AM, Felix Plasser <
>>> fel...@un...> wrote:
>>>
>>>> Ok, sounds good. I will try to set it up. And then I'll send a
>>>> pull-request via github, if that's the way to do it ...
>>>>
>>>> By the way, another thing I am thinking about is that cclib would be
>>>> able to parse files in Molden format. That would be a nice way to get:
>>>> atmonos, atomcoords, gbasis, and mocoeffs in a standardized way.
>>>>
>>>> Cheers,
>>>> Felix
>>>>
>>>> On 03/03/2016 06:54 AM, Karol Langner wrote:
>>>>
>>>> Hi Felix,
>>>>
>>>> If you look at the table showing coverage of attributes (
>>>> http://cclib.github.io/data.html#details-of-current-implementation)
>>>> you'll see there's a T/D for gbasis/ORCA. That's automatically generated
>>>> from the code, and as you've observed there is no parsing code for that yet
>>>> :) apparently I put that note there to not forget.
>>>>
>>>> If you implement this, please do contribute it to cclib. I probably
>>>> won't get around to it anytime soon.
>>>>
>>>> Cheers,
>>>> Karol
>>>>
>>>>
>>>> On Wed, Mar 2, 2016 at 7:05 AM, Karol Langner <kar...@gm...>
>>>> wrote:
>>>>
>>>>> Hi Felix,
>>>>>
>>>>> It might be lingering in a branch or pull request. Let me check and
>>>>> get back to you.
>>>>>
>>>>> Karol
>>>>> On Mar 2, 2016 6:57 AM, "Felix Plasser" <fel...@un...>
>>>>> wrote:
>>>>>
>>>>>> Hi, I am just testing cclib for a new project of ours.
>>>>>>
>>>>>> What I was wondering is: Is it possible to get the gbasis attribute
>>>>>> from Orca? In the "parsed data notes" it says the it should work if I
>>>>>> include the line
>>>>>> Print[ P_Basis ] 2 in the output block
>>>>>>
>>>>>> Indeed, that will print out the basis coefficients and exponents (see
>>>>>> the attached orca.out file), but the gbasis attribute is not parsed. I
>>>>>> checked the newest source from github and it looks like the file
>>>>>> orcaparser.py does not contain the word gbasis anywhere. So I assume this
>>>>>> is not parsed?
>>>>>>
>>>>>> I guess it will not be too much trouble for me to add the
>>>>>> functionality. I just wanted to check if this is already there before I
>>>>>> would try to implement it myself.
>>>>>>
>>>>>> Thank you,
>>>>>> Felix
>>>>>>
>>>>>> --
>>>>>> Felix Plasser
>>>>>> Institute for Theoretical Chemistry
>>>>>> University of Vienna
>>>>>> Währingerstr. 17/404
>>>>>> 1090 Wien
>>>>>> fel...@un...
>>>>>> http://homepage.univie.ac.at/felix.plasser/
>>>>>> Tel.: +43-1-4277-52757
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>>>>> _______________________________________________
>>>>>> cclib-users mailing list
>>>>>> ccl...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>>>
>>>>>>
>>>>
>>>> --
>>>> Felix Plasser
>>>> Institute for Theoretical Chemistry
>>>> University of Vienna
>>>> Währingerstr. 17/404
>>>> 1090 Wie...@un...http://homepage.univie.ac.at/felix.plasser/
>>>> Tel.: +43-1-4277-52757
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>> Monitor end-to-end web transactions and take corrective actions now
>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>>> _______________________________________________
>>>> cclib-users mailing list
>>>> ccl...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>> _______________________________________________
>>> cclib-users mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>
>>>
>>
>> --
>> Felix Plasser
>> Institute for Theoretical Chemistry
>> University of Vienna
>> Währingerstr. 17/404
>> 1090 Wie...@un...http://homepage.univie.ac.at/felix.plasser/
>> Tel.: +43-1-4277-52757
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>
> --
> Felix Plasser
> Institute for Theoretical Chemistry
> University of Vienna
> Währingerstr. 17/404
> 1090 Wie...@un...http://homepage.univie.ac.at/felix.plasser/
> Tel.: +43-1-4277-52757
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

Hi, I double checked this and it looks like gbasis is parsed correctly. 
If I do the same calculation with Orca and Gaussian, then I get the same 
results with
ccget orca.out gbasis
and
ccget gaussian.log gbasis
So everything looks fine and I get the same canonical result.

The thing that confused me initially is that Orca uses a different order 
for the p-functions - and because of that things looked differently. But 
this is already parsed correctly by cclib:
ccget orca.out aonames
[ ..., u'C1_1PZ', u'C1_1PX', u'C1_1PY', ...]
And I will just have to reorder the MO-coefficients accordingly for my 
purposes.

As I see it, everything looks fine, and I'll send the pull request.

By the way, getting the correct ordering of the basis functions would 
also be a challenge for the Molden writer. My own little tool cc2molden.py
https://sourceforge.net/p/theodore-qc/code/ci/master/tree/bin/cc2molden.py
failed because of this ordering. And that is what confused me ...

-Felix

On 03/04/2016 03:06 PM, Karol Langner wrote:
>
> I think we want to parse the canonical gbasis before any 
> normalization, because that's transferable. In any case, we want it to 
> be the same for all programs. Is there an easy way to unnormalize?
>
> On Mar 4, 2016 1:49 AM, "Felix Plasser" <fel...@un... 
> <mailto:fel...@un...>> wrote:
>
>     Hi Karol and Eric,
>
>     I do have the parser now
>     https://github.com/felixplasser/cclib/commit/0f8e6db49910aedb92a1cad5e0ba384a3fc0efaa?diff=unified
>
>     This parses gbasis as it is printed out in the standard output.
>     The problem is that internally ORCA changes the normalization
>     factors, and then this gbasis is no longer consistent with the
>     MO-coefficients. For example when I run orca_2mkl, it tells me
>     "The basis set has NOT been un-normalized for printing"
>     And then I get the un-normalized coefficients that are used
>     internally and that are consistent with mocoeffs. But they are not
>     the same coefficients printed in the output file.
>
>     For my specific application gbasis works they way it is parsed
>     now. But I do not really know what gbasis is supposed to be: the
>     input coefficients, or the coefficients used internally.
>
>     About Molden format: it would just parse a few attributes, mainly
>     atmnos, atomcoords, gbasis, and mocoeffs
>     But the important point here would be that gbasis and mocoeffs are
>     consistent and well-defined (assuming that the molden file was
>     created properly)
>
>     Felix
>
>     On 03/03/2016 09:35 PM, Eric Berquist wrote:
>>     Hi Felix and Karol,
>>
>>     If a pull request is made, I guarantee I'll take a look at it,
>>     since I'm trying to be more active in the project.
>>
>>     We don't have a Molden parser yet, though I started a Molden
>>     writer for cclib, and have something standalone that attempts to
>>     clean up the Molden output produced by a few different programs,
>>     since Molden itself seemed pretty picky about the section
>>     ordering:
>>     https://github.com/berquist/scripts/blob/master/fix_molden.py
>>
>>     Eric
>>
>>     On Thu, Mar 3, 2016 at 3:25 PM, Karol Langner
>>     <kar...@gm... <mailto:kar...@gm...>> wrote:
>>
>>         Yes, pull requests are definitely the way to go. Turnaround
>>         time varies with how busy people are.
>>
>>         Parsing molden files is possible, just requires some work.
>>         However, I'm not sure what kind of coverage of cclib
>>         attribute one could get from those files. Are they text
>>         format or binary?
>>
>>         On Thu, Mar 3, 2016 at 3:01 AM, Felix Plasser
>>         <fel...@un...
>>         <mailto:fel...@un...>> wrote:
>>
>>             Ok, sounds good. I will try to set it up. And then I'll
>>             send a pull-request via github, if that's the way to do
>>             it ...
>>
>>             By the way, another thing I am thinking about is that
>>             cclib would be able to parse files in Molden format. That
>>             would be a nice way to get: atmonos, atomcoords, gbasis,
>>             and mocoeffs in a standardized way.
>>
>>             Cheers,
>>             Felix
>>
>>             On 03/03/2016 06:54 AM, Karol Langner wrote:
>>>             Hi Felix,
>>>
>>>             If you look at the table showing coverage of attributes
>>>             (http://cclib.github.io/data.html#details-of-current-implementation)
>>>             you'll see there's a T/D for gbasis/ORCA. That's
>>>             automatically generated from the code, and as you've
>>>             observed there is no parsing code for that yet :)
>>>             apparently I put that note there to not forget.
>>>
>>>             If you implement this, please do contribute it to cclib.
>>>             I probably won't get around to it anytime soon.
>>>
>>>             Cheers,
>>>             Karol
>>>
>>>
>>>             On Wed, Mar 2, 2016 at 7:05 AM, Karol Langner
>>>             <kar...@gm...
>>>             <mailto:kar...@gm...>> wrote:
>>>
>>>                 Hi Felix,
>>>
>>>                 It might be lingering in a branch or pull request.
>>>                 Let me check and get back to you.
>>>
>>>                 Karol
>>>
>>>                 On Mar 2, 2016 6:57 AM, "Felix Plasser"
>>>                 <fel...@un...
>>>                 <mailto:fel...@un...>> wrote:
>>>
>>>                     Hi, I am just testing cclib for a new project of
>>>                     ours.
>>>
>>>                     What I was wondering is: Is it possible to get
>>>                     the gbasis attribute from Orca? In the "parsed
>>>                     data notes" it says the it should work if I
>>>                     include the line
>>>                     Print[ P_Basis ] 2 in the output block
>>>
>>>                     Indeed, that will print out the basis
>>>                     coefficients and exponents (see the attached
>>>                     orca.out file), but the gbasis attribute is not
>>>                     parsed. I checked the newest source from github
>>>                     and it looks like the file orcaparser.py does
>>>                     not contain the word gbasis anywhere. So I
>>>                     assume this is not parsed?
>>>
>>>                     I guess it will not be too much trouble for me
>>>                     to add the functionality. I just wanted to check
>>>                     if this is already there before I would try to
>>>                     implement it myself.
>>>
>>>                     Thank you,
>>>                     Felix
>>>
>>>                     -- 
>>>                     Felix Plasser
>>>                     Institute for Theoretical Chemistry
>>>                     University of Vienna
>>>                     Währingerstr. 17/404
>>>                     1090 Wien
>>>                     fel...@un...
>>>                     <mailto:fel...@un...>
>>>                     http://homepage.univie.ac.at/felix.plasser/
>>>                     Tel.: +43-1-4277-52757 <tel:%2B43-1-4277-52757>
>>>
>>>
>>>                     ------------------------------------------------------------------------------
>>>                     Site24x7 APM Insight: Get Deep Visibility into
>>>                     Application Performance
>>>                     APM + Mobile APM + RUM: Monitor 3 App instances
>>>                     at just $35/Month
>>>                     Monitor end-to-end web transactions and take
>>>                     corrective actions now
>>>                     Troubleshoot faster and improve end-user
>>>                     experience. Signup Now!
>>>                     http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>>                     _______________________________________________
>>>                     cclib-users mailing list
>>>                     ccl...@li...
>>>                     <mailto:ccl...@li...>
>>>                     https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>
>>>
>>
>>             -- 
>>             Felix Plasser
>>             Institute for Theoretical Chemistry
>>             University of Vienna
>>             Währingerstr. 17/404
>>             1090 Wien
>>             fel...@un...  <mailto:fel...@un...>
>>             http://homepage.univie.ac.at/felix.plasser/
>>             Tel.: +43-1-4277-52757
>>
>>
>>             ------------------------------------------------------------------------------
>>             Site24x7 APM Insight: Get Deep Visibility into
>>             Application Performance
>>             APM + Mobile APM + RUM: Monitor 3 App instances at just
>>             $35/Month
>>             Monitor end-to-end web transactions and take corrective
>>             actions now
>>             Troubleshoot faster and improve end-user experience.
>>             Signup Now!
>>             http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>             _______________________________________________
>>             cclib-users mailing list
>>             ccl...@li...
>>             <mailto:ccl...@li...>
>>             https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>
>>
>>         ------------------------------------------------------------------------------
>>         Site24x7 APM Insight: Get Deep Visibility into Application
>>         Performance
>>         APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>         Monitor end-to-end web transactions and take corrective
>>         actions now
>>         Troubleshoot faster and improve end-user experience. Signup Now!
>>         http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>         _______________________________________________
>>         cclib-users mailing list
>>         ccl...@li...
>>         <mailto:ccl...@li...>
>>         https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>
>
>     -- 
>     Felix Plasser
>     Institute for Theoretical Chemistry
>     University of Vienna
>     Währingerstr. 17/404
>     1090 Wien
>     fel...@un...  <mailto:fel...@un...>
>     http://homepage.univie.ac.at/felix.plasser/
>     Tel.: +43-1-4277-52757
>
>
>     ------------------------------------------------------------------------------
>     Site24x7 APM Insight: Get Deep Visibility into Application Performance
>     APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>     Monitor end-to-end web transactions and take corrective actions now
>     Troubleshoot faster and improve end-user experience. Signup Now!
>     http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>     _______________________________________________
>     cclib-users mailing list
>     ccl...@li...
>     <mailto:ccl...@li...>
>     https://lists.sourceforge.net/lists/listinfo/cclib-users
>

-- 
Felix Plasser
Institute for Theoretical Chemistry
University of Vienna
Währingerstr. 17/404
1090 Wien
fel...@un...
http://homepage.univie.ac.at/felix.plasser/
Tel.: +43-1-4277-52757

I think we want to parse the canonical gbasis before any normalization,
because that's transferable. In any case, we want it to be the same for all
programs. Is there an easy way to unnormalize?
On Mar 4, 2016 1:49 AM, "Felix Plasser" <fel...@un...> wrote:

> Hi Karol and Eric,
>
> I do have the parser now
>
> https://github.com/felixplasser/cclib/commit/0f8e6db49910aedb92a1cad5e0ba384a3fc0efaa?diff=unified
>
> This parses gbasis as it is printed out in the standard output. The
> problem is that internally ORCA changes the normalization factors, and then
> this gbasis is no longer consistent with the MO-coefficients. For example
> when I run orca_2mkl, it tells me
> "The basis set has NOT been un-normalized for printing"
> And then I get the un-normalized coefficients that are used internally and
> that are consistent with mocoeffs. But they are not the same coefficients
> printed in the output file.
>
> For my specific application gbasis works they way it is parsed now. But I
> do not really know what gbasis is supposed to be: the input coefficients,
> or the coefficients used internally.
>
> About Molden format: it would just parse a few attributes, mainly atmnos,
> atomcoords, gbasis, and mocoeffs
> But the important point here would be that gbasis and mocoeffs are
> consistent and well-defined (assuming that the molden file was created
> properly)
>
> Felix
>
> On 03/03/2016 09:35 PM, Eric Berquist wrote:
>
> Hi Felix and Karol,
>
> If a pull request is made, I guarantee I'll take a look at it, since I'm
> trying to be more active in the project.
>
> We don't have a Molden parser yet, though I started a Molden writer for
> cclib, and have something standalone that attempts to clean up the Molden
> output produced by a few different programs, since Molden itself seemed
> pretty picky about the section ordering:
> https://github.com/berquist/scripts/blob/master/fix_molden.py
>
> Eric
>
> On Thu, Mar 3, 2016 at 3:25 PM, Karol Langner <kar...@gm...>
> wrote:
>
>> Yes, pull requests are definitely the way to go. Turnaround time varies
>> with how busy people are.
>>
>> Parsing molden files is possible, just requires some work. However, I'm
>> not sure what kind of coverage of cclib attribute one could get from those
>> files. Are they text format or binary?
>>
>> On Thu, Mar 3, 2016 at 3:01 AM, Felix Plasser <fel...@un...
>> > wrote:
>>
>>> Ok, sounds good. I will try to set it up. And then I'll send a
>>> pull-request via github, if that's the way to do it ...
>>>
>>> By the way, another thing I am thinking about is that cclib would be
>>> able to parse files in Molden format. That would be a nice way to get:
>>> atmonos, atomcoords, gbasis, and mocoeffs in a standardized way.
>>>
>>> Cheers,
>>> Felix
>>>
>>> On 03/03/2016 06:54 AM, Karol Langner wrote:
>>>
>>> Hi Felix,
>>>
>>> If you look at the table showing coverage of attributes (
>>> http://cclib.github.io/data.html#details-of-current-implementation)
>>> you'll see there's a T/D for gbasis/ORCA. That's automatically generated
>>> from the code, and as you've observed there is no parsing code for that yet
>>> :) apparently I put that note there to not forget.
>>>
>>> If you implement this, please do contribute it to cclib. I probably
>>> won't get around to it anytime soon.
>>>
>>> Cheers,
>>> Karol
>>>
>>>
>>> On Wed, Mar 2, 2016 at 7:05 AM, Karol Langner <kar...@gm...>
>>> wrote:
>>>
>>>> Hi Felix,
>>>>
>>>> It might be lingering in a branch or pull request. Let me check and get
>>>> back to you.
>>>>
>>>> Karol
>>>> On Mar 2, 2016 6:57 AM, "Felix Plasser" <fel...@un...>
>>>> wrote:
>>>>
>>>>> Hi, I am just testing cclib for a new project of ours.
>>>>>
>>>>> What I was wondering is: Is it possible to get the gbasis attribute
>>>>> from Orca? In the "parsed data notes" it says the it should work if I
>>>>> include the line
>>>>> Print[ P_Basis ] 2 in the output block
>>>>>
>>>>> Indeed, that will print out the basis coefficients and exponents (see
>>>>> the attached orca.out file), but the gbasis attribute is not parsed. I
>>>>> checked the newest source from github and it looks like the file
>>>>> orcaparser.py does not contain the word gbasis anywhere. So I assume this
>>>>> is not parsed?
>>>>>
>>>>> I guess it will not be too much trouble for me to add the
>>>>> functionality. I just wanted to check if this is already there before I
>>>>> would try to implement it myself.
>>>>>
>>>>> Thank you,
>>>>> Felix
>>>>>
>>>>> --
>>>>> Felix Plasser
>>>>> Institute for Theoretical Chemistry
>>>>> University of Vienna
>>>>> Währingerstr. 17/404
>>>>> 1090 Wien
>>>>> fel...@un...
>>>>> http://homepage.univie.ac.at/felix.plasser/
>>>>> Tel.: +43-1-4277-52757
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>>>> _______________________________________________
>>>>> cclib-users mailing list
>>>>> ccl...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>>
>>>>>
>>>
>>> --
>>> Felix Plasser
>>> Institute for Theoretical Chemistry
>>> University of Vienna
>>> Währingerstr. 17/404
>>> 1090 Wie...@un...http://homepage.univie.ac.at/felix.plasser/
>>> Tel.: +43-1-4277-52757
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>> _______________________________________________
>>> cclib-users mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>
>
> --
> Felix Plasser
> Institute for Theoretical Chemistry
> University of Vienna
> Währingerstr. 17/404
> 1090 Wie...@un...http://homepage.univie.ac.at/felix.plasser/
> Tel.: +43-1-4277-52757
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

Hi Karol and Eric,

I do have the parser now
https://github.com/felixplasser/cclib/commit/0f8e6db49910aedb92a1cad5e0ba384a3fc0efaa?diff=unified

This parses gbasis as it is printed out in the standard output. The 
problem is that internally ORCA changes the normalization factors, and 
then this gbasis is no longer consistent with the MO-coefficients. For 
example when I run orca_2mkl, it tells me
"The basis set has NOT been un-normalized for printing"
And then I get the un-normalized coefficients that are used internally 
and that are consistent with mocoeffs. But they are not the same 
coefficients printed in the output file.

For my specific application gbasis works they way it is parsed now. But 
I do not really know what gbasis is supposed to be: the input 
coefficients, or the coefficients used internally.

About Molden format: it would just parse a few attributes, mainly 
atmnos, atomcoords, gbasis, and mocoeffs
But the important point here would be that gbasis and mocoeffs are 
consistent and well-defined (assuming that the molden file was created 
properly)

Felix

On 03/03/2016 09:35 PM, Eric Berquist wrote:
> Hi Felix and Karol,
>
> If a pull request is made, I guarantee I'll take a look at it, since 
> I'm trying to be more active in the project.
>
> We don't have a Molden parser yet, though I started a Molden writer 
> for cclib, and have something standalone that attempts to clean up the 
> Molden output produced by a few different programs, since Molden 
> itself seemed pretty picky about the section ordering: 
> https://github.com/berquist/scripts/blob/master/fix_molden.py
>
> Eric
>
> On Thu, Mar 3, 2016 at 3:25 PM, Karol Langner <kar...@gm... 
> <mailto:kar...@gm...>> wrote:
>
>     Yes, pull requests are definitely the way to go. Turnaround time
>     varies with how busy people are.
>
>     Parsing molden files is possible, just requires some work.
>     However, I'm not sure what kind of coverage of cclib attribute one
>     could get from those files. Are they text format or binary?
>
>     On Thu, Mar 3, 2016 at 3:01 AM, Felix Plasser
>     <fel...@un... <mailto:fel...@un...>>
>     wrote:
>
>         Ok, sounds good. I will try to set it up. And then I'll send a
>         pull-request via github, if that's the way to do it ...
>
>         By the way, another thing I am thinking about is that cclib
>         would be able to parse files in Molden format. That would be a
>         nice way to get: atmonos, atomcoords, gbasis, and mocoeffs in
>         a standardized way.
>
>         Cheers,
>         Felix
>
>         On 03/03/2016 06:54 AM, Karol Langner wrote:
>>         Hi Felix,
>>
>>         If you look at the table showing coverage of attributes
>>         (http://cclib.github.io/data.html#details-of-current-implementation)
>>         you'll see there's a T/D for gbasis/ORCA. That's
>>         automatically generated from the code, and as you've observed
>>         there is no parsing code for that yet :) apparently I put
>>         that note there to not forget.
>>
>>         If you implement this, please do contribute it to cclib. I
>>         probably won't get around to it anytime soon.
>>
>>         Cheers,
>>         Karol
>>
>>
>>         On Wed, Mar 2, 2016 at 7:05 AM, Karol Langner
>>         <kar...@gm... <mailto:kar...@gm...>> wrote:
>>
>>             Hi Felix,
>>
>>             It might be lingering in a branch or pull request. Let me
>>             check and get back to you.
>>
>>             Karol
>>
>>             On Mar 2, 2016 6:57 AM, "Felix Plasser"
>>             <fel...@un...
>>             <mailto:fel...@un...>> wrote:
>>
>>                 Hi, I am just testing cclib for a new project of ours.
>>
>>                 What I was wondering is: Is it possible to get the
>>                 gbasis attribute from Orca? In the "parsed data
>>                 notes" it says the it should work if I include the line
>>                 Print[ P_Basis ] 2 in the output block
>>
>>                 Indeed, that will print out the basis coefficients
>>                 and exponents (see the attached orca.out file), but
>>                 the gbasis attribute is not parsed. I checked the
>>                 newest source from github and it looks like the file
>>                 orcaparser.py does not contain the word gbasis
>>                 anywhere. So I assume this is not parsed?
>>
>>                 I guess it will not be too much trouble for me to add
>>                 the functionality. I just wanted to check if this is
>>                 already there before I would try to implement it myself.
>>
>>                 Thank you,
>>                 Felix
>>
>>                 -- 
>>                 Felix Plasser
>>                 Institute for Theoretical Chemistry
>>                 University of Vienna
>>                 Währingerstr. 17/404
>>                 1090 Wien
>>                 fel...@un...
>>                 <mailto:fel...@un...>
>>                 http://homepage.univie.ac.at/felix.plasser/
>>                 Tel.: +43-1-4277-52757 <tel:%2B43-1-4277-52757>
>>
>>
>>                 ------------------------------------------------------------------------------
>>                 Site24x7 APM Insight: Get Deep Visibility into
>>                 Application Performance
>>                 APM + Mobile APM + RUM: Monitor 3 App instances at
>>                 just $35/Month
>>                 Monitor end-to-end web transactions and take
>>                 corrective actions now
>>                 Troubleshoot faster and improve end-user experience.
>>                 Signup Now!
>>                 http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>                 _______________________________________________
>>                 cclib-users mailing list
>>                 ccl...@li...
>>                 <mailto:ccl...@li...>
>>                 https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>
>
>         -- 
>         Felix Plasser
>         Institute for Theoretical Chemistry
>         University of Vienna
>         Währingerstr. 17/404
>         1090 Wien
>         fel...@un...  <mailto:fel...@un...>
>         http://homepage.univie.ac.at/felix.plasser/
>         Tel.: +43-1-4277-52757
>
>
>         ------------------------------------------------------------------------------
>         Site24x7 APM Insight: Get Deep Visibility into Application
>         Performance
>         APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>         Monitor end-to-end web transactions and take corrective
>         actions now
>         Troubleshoot faster and improve end-user experience. Signup Now!
>         http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>         _______________________________________________
>         cclib-users mailing list
>         ccl...@li...
>         <mailto:ccl...@li...>
>         https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>
>
>     ------------------------------------------------------------------------------
>     Site24x7 APM Insight: Get Deep Visibility into Application Performance
>     APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>     Monitor end-to-end web transactions and take corrective actions now
>     Troubleshoot faster and improve end-user experience. Signup Now!
>     http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>     _______________________________________________
>     cclib-users mailing list
>     ccl...@li...
>     <mailto:ccl...@li...>
>     https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

-- 
Felix Plasser
Institute for Theoretical Chemistry
University of Vienna
Währingerstr. 17/404
1090 Wien
fel...@un...
http://homepage.univie.ac.at/felix.plasser/
Tel.: +43-1-4277-52757

Hi Eric,

That's great. I will have more time for cclib now than in the past year,
but it can still be sketchy at times.

Karol

On Thu, Mar 3, 2016 at 12:35 PM, Eric Berquist <er...@pi...> wrote:

> Hi Felix and Karol,
>
> If a pull request is made, I guarantee I'll take a look at it, since I'm
> trying to be more active in the project.
>
> We don't have a Molden parser yet, though I started a Molden writer for
> cclib, and have something standalone that attempts to clean up the Molden
> output produced by a few different programs, since Molden itself seemed
> pretty picky about the section ordering:
> https://github.com/berquist/scripts/blob/master/fix_molden.py
>
> Eric
>
> On Thu, Mar 3, 2016 at 3:25 PM, Karol Langner <kar...@gm...>
> wrote:
>
>> Yes, pull requests are definitely the way to go. Turnaround time varies
>> with how busy people are.
>>
>> Parsing molden files is possible, just requires some work. However, I'm
>> not sure what kind of coverage of cclib attribute one could get from those
>> files. Are they text format or binary?
>>
>> On Thu, Mar 3, 2016 at 3:01 AM, Felix Plasser <fel...@un...
>> > wrote:
>>
>>> Ok, sounds good. I will try to set it up. And then I'll send a
>>> pull-request via github, if that's the way to do it ...
>>>
>>> By the way, another thing I am thinking about is that cclib would be
>>> able to parse files in Molden format. That would be a nice way to get:
>>> atmonos, atomcoords, gbasis, and mocoeffs in a standardized way.
>>>
>>> Cheers,
>>> Felix
>>>
>>> On 03/03/2016 06:54 AM, Karol Langner wrote:
>>>
>>> Hi Felix,
>>>
>>> If you look at the table showing coverage of attributes (
>>> http://cclib.github.io/data.html#details-of-current-implementation)
>>> you'll see there's a T/D for gbasis/ORCA. That's automatically generated
>>> from the code, and as you've observed there is no parsing code for that yet
>>> :) apparently I put that note there to not forget.
>>>
>>> If you implement this, please do contribute it to cclib. I probably
>>> won't get around to it anytime soon.
>>>
>>> Cheers,
>>> Karol
>>>
>>>
>>> On Wed, Mar 2, 2016 at 7:05 AM, Karol Langner <kar...@gm...>
>>> wrote:
>>>
>>>> Hi Felix,
>>>>
>>>> It might be lingering in a branch or pull request. Let me check and get
>>>> back to you.
>>>>
>>>> Karol
>>>> On Mar 2, 2016 6:57 AM, "Felix Plasser" <fel...@un...>
>>>> wrote:
>>>>
>>>>> Hi, I am just testing cclib for a new project of ours.
>>>>>
>>>>> What I was wondering is: Is it possible to get the gbasis attribute
>>>>> from Orca? In the "parsed data notes" it says the it should work if I
>>>>> include the line
>>>>> Print[ P_Basis ] 2 in the output block
>>>>>
>>>>> Indeed, that will print out the basis coefficients and exponents (see
>>>>> the attached orca.out file), but the gbasis attribute is not parsed. I
>>>>> checked the newest source from github and it looks like the file
>>>>> orcaparser.py does not contain the word gbasis anywhere. So I assume this
>>>>> is not parsed?
>>>>>
>>>>> I guess it will not be too much trouble for me to add the
>>>>> functionality. I just wanted to check if this is already there before I
>>>>> would try to implement it myself.
>>>>>
>>>>> Thank you,
>>>>> Felix
>>>>>
>>>>> --
>>>>> Felix Plasser
>>>>> Institute for Theoretical Chemistry
>>>>> University of Vienna
>>>>> Währingerstr. 17/404
>>>>> 1090 Wien
>>>>> fel...@un...
>>>>> http://homepage.univie.ac.at/felix.plasser/
>>>>> Tel.: +43-1-4277-52757
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>>>> _______________________________________________
>>>>> cclib-users mailing list
>>>>> ccl...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>>
>>>>>
>>>
>>> --
>>> Felix Plasser
>>> Institute for Theoretical Chemistry
>>> University of Vienna
>>> Währingerstr. 17/404
>>> 1090 Wie...@un...http://homepage.univie.ac.at/felix.plasser/
>>> Tel.: +43-1-4277-52757
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>> _______________________________________________
>>> cclib-users mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>
>

Hi Felix and Karol,

If a pull request is made, I guarantee I'll take a look at it, since I'm
trying to be more active in the project.

We don't have a Molden parser yet, though I started a Molden writer for
cclib, and have something standalone that attempts to clean up the Molden
output produced by a few different programs, since Molden itself seemed
pretty picky about the section ordering:
https://github.com/berquist/scripts/blob/master/fix_molden.py

Eric

On Thu, Mar 3, 2016 at 3:25 PM, Karol Langner <kar...@gm...>
wrote:

> Yes, pull requests are definitely the way to go. Turnaround time varies
> with how busy people are.
>
> Parsing molden files is possible, just requires some work. However, I'm
> not sure what kind of coverage of cclib attribute one could get from those
> files. Are they text format or binary?
>
> On Thu, Mar 3, 2016 at 3:01 AM, Felix Plasser <fel...@un...>
> wrote:
>
>> Ok, sounds good. I will try to set it up. And then I'll send a
>> pull-request via github, if that's the way to do it ...
>>
>> By the way, another thing I am thinking about is that cclib would be able
>> to parse files in Molden format. That would be a nice way to get: atmonos,
>> atomcoords, gbasis, and mocoeffs in a standardized way.
>>
>> Cheers,
>> Felix
>>
>> On 03/03/2016 06:54 AM, Karol Langner wrote:
>>
>> Hi Felix,
>>
>> If you look at the table showing coverage of attributes (
>> http://cclib.github.io/data.html#details-of-current-implementation)
>> you'll see there's a T/D for gbasis/ORCA. That's automatically generated
>> from the code, and as you've observed there is no parsing code for that yet
>> :) apparently I put that note there to not forget.
>>
>> If you implement this, please do contribute it to cclib. I probably won't
>> get around to it anytime soon.
>>
>> Cheers,
>> Karol
>>
>>
>> On Wed, Mar 2, 2016 at 7:05 AM, Karol Langner <kar...@gm...>
>> wrote:
>>
>>> Hi Felix,
>>>
>>> It might be lingering in a branch or pull request. Let me check and get
>>> back to you.
>>>
>>> Karol
>>> On Mar 2, 2016 6:57 AM, "Felix Plasser" <fel...@un...>
>>> wrote:
>>>
>>>> Hi, I am just testing cclib for a new project of ours.
>>>>
>>>> What I was wondering is: Is it possible to get the gbasis attribute
>>>> from Orca? In the "parsed data notes" it says the it should work if I
>>>> include the line
>>>> Print[ P_Basis ] 2 in the output block
>>>>
>>>> Indeed, that will print out the basis coefficients and exponents (see
>>>> the attached orca.out file), but the gbasis attribute is not parsed. I
>>>> checked the newest source from github and it looks like the file
>>>> orcaparser.py does not contain the word gbasis anywhere. So I assume this
>>>> is not parsed?
>>>>
>>>> I guess it will not be too much trouble for me to add the
>>>> functionality. I just wanted to check if this is already there before I
>>>> would try to implement it myself.
>>>>
>>>> Thank you,
>>>> Felix
>>>>
>>>> --
>>>> Felix Plasser
>>>> Institute for Theoretical Chemistry
>>>> University of Vienna
>>>> Währingerstr. 17/404
>>>> 1090 Wien
>>>> fel...@un...
>>>> http://homepage.univie.ac.at/felix.plasser/
>>>> Tel.: +43-1-4277-52757
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>> Monitor end-to-end web transactions and take corrective actions now
>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>>> _______________________________________________
>>>> cclib-users mailing list
>>>> ccl...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>
>>>>
>>
>> --
>> Felix Plasser
>> Institute for Theoretical Chemistry
>> University of Vienna
>> Währingerstr. 17/404
>> 1090 Wie...@un...http://homepage.univie.ac.at/felix.plasser/
>> Tel.: +43-1-4277-52757
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

Yes, pull requests are definitely the way to go. Turnaround time varies
with how busy people are.

Parsing molden files is possible, just requires some work. However, I'm not
sure what kind of coverage of cclib attribute one could get from those
files. Are they text format or binary?

On Thu, Mar 3, 2016 at 3:01 AM, Felix Plasser <fel...@un...>
wrote:

> Ok, sounds good. I will try to set it up. And then I'll send a
> pull-request via github, if that's the way to do it ...
>
> By the way, another thing I am thinking about is that cclib would be able
> to parse files in Molden format. That would be a nice way to get: atmonos,
> atomcoords, gbasis, and mocoeffs in a standardized way.
>
> Cheers,
> Felix
>
> On 03/03/2016 06:54 AM, Karol Langner wrote:
>
> Hi Felix,
>
> If you look at the table showing coverage of attributes (
> http://cclib.github.io/data.html#details-of-current-implementation)
> you'll see there's a T/D for gbasis/ORCA. That's automatically generated
> from the code, and as you've observed there is no parsing code for that yet
> :) apparently I put that note there to not forget.
>
> If you implement this, please do contribute it to cclib. I probably won't
> get around to it anytime soon.
>
> Cheers,
> Karol
>
>
> On Wed, Mar 2, 2016 at 7:05 AM, Karol Langner <kar...@gm...>
> wrote:
>
>> Hi Felix,
>>
>> It might be lingering in a branch or pull request. Let me check and get
>> back to you.
>>
>> Karol
>> On Mar 2, 2016 6:57 AM, "Felix Plasser" <fel...@un...>
>> wrote:
>>
>>> Hi, I am just testing cclib for a new project of ours.
>>>
>>> What I was wondering is: Is it possible to get the gbasis attribute from
>>> Orca? In the "parsed data notes" it says the it should work if I include
>>> the line
>>> Print[ P_Basis ] 2 in the output block
>>>
>>> Indeed, that will print out the basis coefficients and exponents (see
>>> the attached orca.out file), but the gbasis attribute is not parsed. I
>>> checked the newest source from github and it looks like the file
>>> orcaparser.py does not contain the word gbasis anywhere. So I assume this
>>> is not parsed?
>>>
>>> I guess it will not be too much trouble for me to add the functionality.
>>> I just wanted to check if this is already there before I would try to
>>> implement it myself.
>>>
>>> Thank you,
>>> Felix
>>>
>>> --
>>> Felix Plasser
>>> Institute for Theoretical Chemistry
>>> University of Vienna
>>> Währingerstr. 17/404
>>> 1090 Wien
>>> fel...@un...
>>> http://homepage.univie.ac.at/felix.plasser/
>>> Tel.: +43-1-4277-52757
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>> _______________________________________________
>>> cclib-users mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>
>>>
>
> --
> Felix Plasser
> Institute for Theoretical Chemistry
> University of Vienna
> Währingerstr. 17/404
> 1090 Wie...@un...http://homepage.univie.ac.at/felix.plasser/
> Tel.: +43-1-4277-52757
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

Ok, sounds good. I will try to set it up. And then I'll send a 
pull-request via github, if that's the way to do it ...

By the way, another thing I am thinking about is that cclib would be 
able to parse files in Molden format. That would be a nice way to get: 
atmonos, atomcoords, gbasis, and mocoeffs in a standardized way.

Cheers,
Felix

On 03/03/2016 06:54 AM, Karol Langner wrote:
> Hi Felix,
>
> If you look at the table showing coverage of attributes 
> (http://cclib.github.io/data.html#details-of-current-implementation) 
> you'll see there's a T/D for gbasis/ORCA. That's automatically 
> generated from the code, and as you've observed there is no parsing 
> code for that yet :) apparently I put that note there to not forget.
>
> If you implement this, please do contribute it to cclib. I probably 
> won't get around to it anytime soon.
>
> Cheers,
> Karol
>
>
> On Wed, Mar 2, 2016 at 7:05 AM, Karol Langner <kar...@gm... 
> <mailto:kar...@gm...>> wrote:
>
>     Hi Felix,
>
>     It might be lingering in a branch or pull request. Let me check
>     and get back to you.
>
>     Karol
>
>     On Mar 2, 2016 6:57 AM, "Felix Plasser"
>     <fel...@un... <mailto:fel...@un...>>
>     wrote:
>
>         Hi, I am just testing cclib for a new project of ours.
>
>         What I was wondering is: Is it possible to get the gbasis
>         attribute from Orca? In the "parsed data notes" it says the it
>         should work if I include the line
>         Print[ P_Basis ] 2 in the output block
>
>         Indeed, that will print out the basis coefficients and
>         exponents (see the attached orca.out file), but the gbasis
>         attribute is not parsed. I checked the newest source from
>         github and it looks like the file orcaparser.py does not
>         contain the word gbasis anywhere. So I assume this is not parsed?
>
>         I guess it will not be too much trouble for me to add the
>         functionality. I just wanted to check if this is already there
>         before I would try to implement it myself.
>
>         Thank you,
>         Felix
>
>         -- 
>         Felix Plasser
>         Institute for Theoretical Chemistry
>         University of Vienna
>         Währingerstr. 17/404
>         1090 Wien
>         fel...@un... <mailto:fel...@un...>
>         http://homepage.univie.ac.at/felix.plasser/
>         Tel.: +43-1-4277-52757 <tel:%2B43-1-4277-52757>
>
>
>         ------------------------------------------------------------------------------
>         Site24x7 APM Insight: Get Deep Visibility into Application
>         Performance
>         APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>         Monitor end-to-end web transactions and take corrective
>         actions now
>         Troubleshoot faster and improve end-user experience. Signup Now!
>         http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>         _______________________________________________
>         cclib-users mailing list
>         ccl...@li...
>         <mailto:ccl...@li...>
>         https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

-- 
Felix Plasser
Institute for Theoretical Chemistry
University of Vienna
Währingerstr. 17/404
1090 Wien
fel...@un...
http://homepage.univie.ac.at/felix.plasser/
Tel.: +43-1-4277-52757

Hi Felix,

If you look at the table showing coverage of attributes (
http://cclib.github.io/data.html#details-of-current-implementation) you'll
see there's a T/D for gbasis/ORCA. That's automatically generated from the
code, and as you've observed there is no parsing code for that yet :)
apparently I put that note there to not forget.

If you implement this, please do contribute it to cclib. I probably won't
get around to it anytime soon.

Cheers,
Karol

On Wed, Mar 2, 2016 at 7:05 AM, Karol Langner <kar...@gm...>
wrote:

> Hi Felix,
>
> It might be lingering in a branch or pull request. Let me check and get
> back to you.
>
> Karol
> On Mar 2, 2016 6:57 AM, "Felix Plasser" <fel...@un...>
> wrote:
>
>> Hi, I am just testing cclib for a new project of ours.
>>
>> What I was wondering is: Is it possible to get the gbasis attribute from
>> Orca? In the "parsed data notes" it says the it should work if I include
>> the line
>> Print[ P_Basis ] 2 in the output block
>>
>> Indeed, that will print out the basis coefficients and exponents (see the
>> attached orca.out file), but the gbasis attribute is not parsed. I checked
>> the newest source from github and it looks like the file orcaparser.py does
>> not contain the word gbasis anywhere. So I assume this is not parsed?
>>
>> I guess it will not be too much trouble for me to add the functionality.
>> I just wanted to check if this is already there before I would try to
>> implement it myself.
>>
>> Thank you,
>> Felix
>>
>> --
>> Felix Plasser
>> Institute for Theoretical Chemistry
>> University of Vienna
>> Währingerstr. 17/404
>> 1090 Wien
>> fel...@un...
>> http://homepage.univie.ac.at/felix.plasser/
>> Tel.: +43-1-4277-52757
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>

See the details here: https://summerofcode.withgoogle.com/

On Wed, Mar 2, 2016 at 9:08 AM, Karol Langner <kar...@gm...>
wrote:

> The student application period starts March 14th. Until then we can
> organize and discuss ideas.
>
> On Wed, Mar 2, 2016 at 8:56 AM, Noel O'Boyle <bao...@gm...> wrote:
>
>> I was wondering what the students are expected to do also? I'd like to
>> post something on my blog about the whole thing but am a bit confused.
>>
>> - Noel
>>
>> On 2 March 2016 at 16:50, harsh savasil <har...@gm...>
>> wrote:
>> > how to discuss gsoc 2016 ideas?
>> > I am applying for gsoc 2016.
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> > Monitor end-to-end web transactions and take corrective actions now
>> > Troubleshoot faster and improve end-user experience. Signup Now!
>> > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> > _______________________________________________
>> > cclib-users mailing list
>> > ccl...@li...
>> > https://lists.sourceforge.net/lists/listinfo/cclib-users
>> >
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>
>

The student application period starts March 14th. Until then we can
organize and discuss ideas.

On Wed, Mar 2, 2016 at 8:56 AM, Noel O'Boyle <bao...@gm...> wrote:

> I was wondering what the students are expected to do also? I'd like to
> post something on my blog about the whole thing but am a bit confused.
>
> - Noel
>
> On 2 March 2016 at 16:50, harsh savasil <har...@gm...>
> wrote:
> > how to discuss gsoc 2016 ideas?
> > I am applying for gsoc 2016.
> >
> >
> ------------------------------------------------------------------------------
> > Site24x7 APM Insight: Get Deep Visibility into Application Performance
> > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> > Monitor end-to-end web transactions and take corrective actions now
> > Troubleshoot faster and improve end-user experience. Signup Now!
> > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> > _______________________________________________
> > cclib-users mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

I was wondering what the students are expected to do also? I'd like to
post something on my blog about the whole thing but am a bit confused.

- Noel

On 2 March 2016 at 16:50, harsh savasil <har...@gm...> wrote:
> how to discuss gsoc 2016 ideas?
> I am applying for gsoc 2016.
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

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