cclib-users — Help and support for cclib users

Re: [cclib-users] Error when reading ORCA output file for AM1 calculations

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

Hi Julien,

It seems the print out is a bit different for semiempirical runs on ORCA, so I added
an appropriate addition to the parser that should take care of that. I also uploaded
one of your files as a regression, so that we will cover your test case in the future.

Please download the latest svn version of cclib and I think you will find that it will
parse your files now.

Cheers,
Karol

On Sep 04 2013, Julien Idé wrote:
> Hi Karol,
> 
> First of all thank you for your fast reply. Here are my output files and my
> python scripts which lead to this error.
> To run my script use the following command line:
> python CT3x3_ORCA.py PCB_1_222__PCB_1_122.out
> You can use these files in the public domain.
> 
> Cheers,
> 
> Julien
> 
> 
> 2013/9/3 Karol M. Langner <kar...@gm...>
> 
> > Hi Julien,
> >
> > First of all, hello and thanks for reporting your problem!
> >
> > It might be a simple difference in the formatting of the output that we
> > have
> > not covered in our parser. If you provide us with an example output file
> > that causes this problem, I am quite certain this could be fixed. We need
> > your
> > consent to use this file in the public domain.
> >
> > Cheers,
> > Karol
> >
> > On Sep 03 2013, Julien Idé wrote:
> > > Dear cclib staff,
> > >
> > > I am a new cclib user. I have already managed to read ORCA ouput files
> > for
> > > some DFT calculations to extract DFT orbitals and compute electronic
> > > couplings between molecular fragments (Using Numpy).
> > > I am now trying to do exactly the same calculation, using the same python
> > > script, for AM1 calculations. However, it seems that cclib cannot read
> > > properly the ORCA output file for AM1 calculations. I get the following
> > > error message:
> > >
> > > Traceback (most recent call last):
> > >   File "CT3x3_ORCA.py", line 45, in <module>
> > >     orcaData= orcaOut.parse()
> > >   File "/usr/lib/python2.6/site-packages/cclib/parser/logfileparser.py",
> > > line 221, in parse
> > >     self.extract(inputfile, line)
> > >   File "/usr/lib/python2.6/site-packages/cclib/parser/orcaparser.py",
> > line
> > > 274, in extract
> > >     self.aooverlaps = numpy.zeros( (self.nbasis, self.nbasis), "d")
> > > AttributeError: 'ORCA' object has no attribute 'nbasis'
> > >
> > > Could you please tell me what I am missing here. Why this script doesn't
> > > work for ORCA AM1  outputs while it was working properly for ORCA DFT
> > > outputs.
> > >
> > > Best regards,
> > >
> > > Julien
> >
> > >
> > ------------------------------------------------------------------------------
> > > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> > > Discover the easy way to master current and previous Microsoft
> > technologies
> > > and advance your career. Get an incredible 1,500+ hours of step-by-step
> > > tutorial videos with LearnDevNow. Subscribe today and save!
> > >
> > http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk
> >
> > > _______________________________________________
> > > cclib-users mailing list
> > > ccl...@li...
> > > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
> >
> > --
> > written by Karol M. Langner
> > Tue Sep  3 14:17:04 EDT 2013
> >







-- 
written by Karol M. Langner
Thu Sep  5 23:25:22 EDT 2013

Re: [cclib-users] Error when reading ORCA output file for AM1 calculations

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

Hi Julien,

First of all, hello and thanks for reporting your problem!

It might be a simple difference in the formatting of the output that we have
not covered in our parser. If you provide us with an example output file
that causes this problem, I am quite certain this could be fixed. We need your
consent to use this file in the public domain.

Cheers,
Karol

On Sep 03 2013, Julien Idé wrote:
> Dear cclib staff,
> 
> I am a new cclib user. I have already managed to read ORCA ouput files for
> some DFT calculations to extract DFT orbitals and compute electronic
> couplings between molecular fragments (Using Numpy).
> I am now trying to do exactly the same calculation, using the same python
> script, for AM1 calculations. However, it seems that cclib cannot read
> properly the ORCA output file for AM1 calculations. I get the following
> error message:
> 
> Traceback (most recent call last):
>   File "CT3x3_ORCA.py", line 45, in <module>
>     orcaData= orcaOut.parse()
>   File "/usr/lib/python2.6/site-packages/cclib/parser/logfileparser.py",
> line 221, in parse
>     self.extract(inputfile, line)
>   File "/usr/lib/python2.6/site-packages/cclib/parser/orcaparser.py", line
> 274, in extract
>     self.aooverlaps = numpy.zeros( (self.nbasis, self.nbasis), "d")
> AttributeError: 'ORCA' object has no attribute 'nbasis'
> 
> Could you please tell me what I am missing here. Why this script doesn't
> work for ORCA AM1  outputs while it was working properly for ORCA DFT
> outputs.
> 
> Best regards,
> 
> Julien

> ------------------------------------------------------------------------------
> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk

> _______________________________________________
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> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users


-- 
written by Karol M. Langner
Tue Sep  3 14:17:04 EDT 2013

[cclib-users] Error when reading ORCA output file for AM1 calculations

[Julien I. <jul...@gm...>]

Dear cclib staff,

I am a new cclib user. I have already managed to read ORCA ouput files for
some DFT calculations to extract DFT orbitals and compute electronic
couplings between molecular fragments (Using Numpy).
I am now trying to do exactly the same calculation, using the same python
script, for AM1 calculations. However, it seems that cclib cannot read
properly the ORCA output file for AM1 calculations. I get the following
error message:

Traceback (most recent call last):
  File "CT3x3_ORCA.py", line 45, in <module>
    orcaData= orcaOut.parse()
  File "/usr/lib/python2.6/site-packages/cclib/parser/logfileparser.py",
line 221, in parse
    self.extract(inputfile, line)
  File "/usr/lib/python2.6/site-packages/cclib/parser/orcaparser.py", line
274, in extract
    self.aooverlaps = numpy.zeros( (self.nbasis, self.nbasis), "d")
AttributeError: 'ORCA' object has no attribute 'nbasis'

Could you please tell me what I am missing here. Why this script doesn't
work for ORCA AM1  outputs while it was working properly for ORCA DFT
outputs.

Best regards,

Julien

Re: [cclib-users] Parsing error with DFT single point calculation output files when Guess=Indo is used

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

Hi Scott,

I thought you already knew, but our policy is "No file no fix".
Unfortunately Adam has already provided you with a workaround but this
won't benefit the other cclib users. I hope you'll reconsider.

Regards,
- Noel

On 9 April 2013 04:28, Scott McKechnie <js...@ca...> wrote:
> Thanks Adam, I used sed to replace the 'It=' with '###It=' and now all the
> files work (hundreds of files). In around one hundred of the files I was
> looking at, the expression 'Projected INDO guess.' occurs instead of 'It='
> and cclib handles these fine.
>
> I'm not sure about the publication of Gaussian output files, I'll send you a
> follow up e-mail about this.
>
> Scott
>
>
>
>
> On 8 April 2013 22:55, Adam Tenderholt <ate...@gm...> wrote:
>>
>> Hi Scott,
>>
>> It looks like cclib thinks your file is for an AM1 calculation due to the
>> INDO guess, and then gets stuck in that section of the parser code. For the
>> time being, a simple fix is to look for the line beginning with "It=", and
>> change it slightly (for instance, I added ### at the beginning).
>>
>> Thanks for alerting us to this issue. Are you willing to place the
>> guessIndo.out file in the Public Domain so that we can include it in our
>> regression tests?
>>
>> Adam
>>
>>
>>
>> On Mon, Apr 8, 2013 at 6:50 AM, Scott McKechnie <js...@ca...> wrote:
>>>
>>> Hi all,
>>>
>>> The parsing works fine for the single point calculation (DFT) with
>>> default settings but fails when Guess=Indo is used (this happens for a
>>> number of different runs where the only difference between the files is the
>>> change in the Guess). Any idea why this is? I've attached the two files.
>>>
>>> The error message is:
>>>
>>> Traceback (most recent call last):
>>>   File "Parse_g09_out_14.py", line 223, in <module>
>>>     data = open_file.parse()
>>>   File
>>> "/usr/local/lib/python2.7/site-packages/cclib/parser/logfileparser.py", line
>>> 221, in parse
>>>     self.extract(inputfile, line)
>>>   File
>>> "/usr/local/lib/python2.7/site-packages/cclib/parser/gaussianparser.py",
>>> line 274, in extract
>>>     line = inputfile.next()
>>> StopIteration
>>>
>>> Thanks,
>>>
>>> Scott
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Minimize network downtime and maximize team effectiveness.
>>> Reduce network management and security costs.Learn how to hire
>>> the most talented Cisco Certified professionals. Visit the
>>> Employer Resources Portal
>>> http://www.cisco.com/web/learning/employer_resources/index.html
>>> _______________________________________________
>>> cclib-users mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>
>>
>
>
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>

Re: [cclib-users] Parsing error with DFT single point calculation output files when Guess=Indo is used

[Scott M. <js...@ca...>]

Thanks Adam, I used sed to replace the 'It=' with '###It=' and now all the
files work (hundreds of files). In around one hundred of the files I was
looking at, the expression 'Projected INDO guess.' occurs instead of 'It='
and cclib handles these fine.

I'm not sure about the publication of Gaussian output files, I'll send you
a follow up e-mail about this.

Scott



On 8 April 2013 22:55, Adam Tenderholt <ate...@gm...> wrote:

> Hi Scott,
>
> It looks like cclib thinks your file is for an AM1 calculation due to the
> INDO guess, and then gets stuck in that section of the parser code. For the
> time being, a simple fix is to look for the line beginning with "It=", and
> change it slightly (for instance, I added ### at the beginning).
>
> Thanks for alerting us to this issue. Are you willing to place the
> guessIndo.out file in the Public Domain so that we can include it in our
> regression tests?
>
> Adam
>
>
>
> On Mon, Apr 8, 2013 at 6:50 AM, Scott McKechnie <js...@ca...> wrote:
>
>> Hi all,
>>
>> The parsing works fine for the single point calculation (DFT) with
>> default settings but fails when Guess=Indo is used (this happens for a
>> number of different runs where the only difference between the files is the
>> change in the Guess). Any idea why this is? I've attached the two files.
>>
>> The error message is:
>>
>> Traceback (most recent call last):
>>   File "Parse_g09_out_14.py", line 223, in <module>
>>     data = open_file.parse()
>>   File
>> "/usr/local/lib/python2.7/site-packages/cclib/parser/logfileparser.py",
>> line 221, in parse
>>     self.extract(inputfile, line)
>>   File
>> "/usr/local/lib/python2.7/site-packages/cclib/parser/gaussianparser.py",
>> line 274, in extract
>>     line = inputfile.next()
>> StopIteration
>>
>> Thanks,
>>
>> Scott
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Minimize network downtime and maximize team effectiveness.
>> Reduce network management and security costs.Learn how to hire
>> the most talented Cisco Certified professionals. Visit the
>> Employer Resources Portal
>> http://www.cisco.com/web/learning/employer_resources/index.html
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>
>

Re: [cclib-users] Parsing error with DFT single point calculation output files when Guess=Indo is used

[Adam T. <ate...@gm...>]

Hi Scott,

It looks like cclib thinks your file is for an AM1 calculation due to the
INDO guess, and then gets stuck in that section of the parser code. For the
time being, a simple fix is to look for the line beginning with "It=", and
change it slightly (for instance, I added ### at the beginning).

Thanks for alerting us to this issue. Are you willing to place the
guessIndo.out file in the Public Domain so that we can include it in our
regression tests?

Adam



On Mon, Apr 8, 2013 at 6:50 AM, Scott McKechnie <js...@ca...> wrote:

> Hi all,
>
> The parsing works fine for the single point calculation (DFT) with default
> settings but fails when Guess=Indo is used (this happens for a number of
> different runs where the only difference between the files is the change in
> the Guess). Any idea why this is? I've attached the two files.
>
> The error message is:
>
> Traceback (most recent call last):
>   File "Parse_g09_out_14.py", line 223, in <module>
>     data = open_file.parse()
>   File
> "/usr/local/lib/python2.7/site-packages/cclib/parser/logfileparser.py",
> line 221, in parse
>     self.extract(inputfile, line)
>   File
> "/usr/local/lib/python2.7/site-packages/cclib/parser/gaussianparser.py",
> line 274, in extract
>     line = inputfile.next()
> StopIteration
>
> Thanks,
>
> Scott
>
>
>
> ------------------------------------------------------------------------------
> Minimize network downtime and maximize team effectiveness.
> Reduce network management and security costs.Learn how to hire
> the most talented Cisco Certified professionals. Visit the
> Employer Resources Portal
> http://www.cisco.com/web/learning/employer_resources/index.html
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

Re: [cclib-users] bug in makebiopython?

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

Thanks for letting us know, Ramon. We will correct this in the next release.

- Noel

On 7 March 2013 12:31, Ramon Crehuet <rc...@iq...> wrote:
> Dear cclib developers,
> I was trying to export my coordinates to Biopython and when using the
> makebiopython function, I got an error. After reading the Atom function in
> Biopython, I changed line 36 of cclib2biopython.py
> from:
> bioatoms.append(Atom(pt.element[atomno], coords, 0, 0, 0, 0, 0))
> to:
> bioatoms.append(Atom(pt.element[atomno], coords, 0, 1, ' ', ' ',
> pt.element[atomno]))
>
> Now it works. I am using Biopython version 1.60.
> Hope this helps,
> Ramon
>
>
> ------------------------------------------------------------------------------
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
> endpoint security space. For insight on selecting the right partner to
> tackle endpoint security challenges, access the full report.
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/cclib-users

[cclib-users] bug in makebiopython?

[Ramon C. <rc...@iq...>]

Dear cclib developers,
I was trying to export my coordinates to Biopython and when using the 
makebiopython function, I got an error. After reading the Atom function in 
Biopython, I changed line 36 of cclib2biopython.py
from:
bioatoms.append(Atom(pt.element[atomno], coords, 0, 0, 0, 0, 0))
to:
bioatoms.append(Atom(pt.element[atomno], coords, 0, 1, ' ', ' ', 
pt.element[atomno]))

Now it works. I am using Biopython version 1.60.
Hope this helps,
Ramon

[cclib-users] Possible bug in cclib2biopython.py

[Ramon C. <rc...@iq...>]

Dear cclib developers,
I was trying to export my coordinates to Biopython and when using the
makebiopython function, I got an error. After reading the Atom function in
Biopython, I changed line 36 of cclib2biopython.py
from:
bioatoms.append(Atom(pt.element[atomno], coords, 0, 0, 0, 0, 0))
to:
bioatoms.append(Atom(pt.element[atomno], coords, 0, 1, ' ', ' ',
pt.element[atomno]))

Now it works. I am using Biopython version 1.60.
Hope this helps,
Ramon

Re: [cclib-users] z-matrix in Gaussian

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

I don't know. Best to luck at the code. You may be able to rearrange the atoms.

- Noel

On 25 February 2013 23:27, Karol M. Langner <kar...@gm...> wrote:
> BTW, Noel, is there a way to specify the atom order in OB for internal coordinates?
>
> On Feb 19 2013, Noel O'Boyle wrote:
>> (Nice use of OpenBabel :-)
>>
>> Just to clarify, there is a difference between the z-matrix input
>> format and the internal coordinate format used by Gaussian during
>> geometry optimisations. The former is non-redundant while the latter
>> is redundant ("redundant internal coordinates"). I'm not sure which
>> you want.
>>
>> - Noel
>>
>> On 19 February 2013 22:02, Adam Tenderholt <ate...@gm...> wrote:
>> > Hi Yaron,
>> >
>> > cclib doesn't directly support parsing internal coordinates. However, you
>> > can use openbabel to save using an internal coordinate system:
>> >
>> >>>> from cclib.parser import ccopen
>> >>>> import openbabel
>> >>>> parser = ccopen("dvb_sp.log")
>> >>>> data = parser.parse()
>> >>>> from cclib.bridge import makeopenbabel
>> >>>> mol = makeopenbabel(data.atomcoords[0], data.atomnos)
>> >>>> obconv = openbabel.OBConversion()
>> >>>> obconv.SetInAndOutFormats("XYZ", "FH")
>> >>>> obconv.WriteFile(mol, "test.fh")
>> >
>> > --
>> > 20
>> > C   1
>> > C   1 1.421
>> > C   2 1.402  1 120.857
>> > C   3 1.422  2 121.354  1   0.0
>> > C   4 1.421  3 117.789  2   0.0
>> > H   2 1.098  1 119.765  3 180.0
>> > H   3 1.099  2 119.629  1 180.0
>> > H   5 1.098  4 119.765  3 180.0
>> > C   4 1.498  3 119.172  2 180.0
>> > C   9 1.344  4 126.593  3 180.0
>> > H  10 1.096  9 122.647  4   0.0
>> > H   9 1.100  4 114.434  3   0.0
>> > H  10 1.096  9 121.228  4 180.0
>> > C   1 1.498  2 123.039  3 180.0
>> > H  14 1.100  1 114.434  2 180.0
>> > C  14 1.344  1 126.593  2   0.0
>> > H  16 1.096 14 122.647  1   0.0
>> > H  16 1.096 14 121.228  1 180.0
>> > C   5 1.402  4 120.857  3   0.0
>> > H  19 1.099  5 119.629  4 180.0
>> > --
>> >
>> > You may also want to see the list of formats supported by openbabel in case
>> > you need something slightly different:
>> > http://openbabel.org/docs/2.3.1/FileFormats/Overview.html
>> >
>> > Hope this helps,
>> >
>> > Adam
>> >
>> >
>> >
>> > On Tue, Feb 19, 2013 at 10:48 AM, Yaron Pshetitsky
>> > <yar...@li...> wrote:
>> >>
>> >> Dear cclib community,
>> >> I'm trying to get the z-matrix (internal coordinates) from a Gaussian
>> >> output file using cclib.
>> >> I know that Gaussian do converts any internal or XYZ coordinates in the
>> >> input to it's format so one can get internal coordinates from it, even if
>> >> the input file was in cartesian coordinates.
>> >> Can cclib output the internal coordinates?
>> >>
>> >> Thanks very much,
>> >> Yaron
>> >>
>> >>
>> >> ------------------------------------------------------------------------------
>> >> Everyone hates slow websites. So do we.
>> >> Make your web apps faster with AppDynamics
>> >> Download AppDynamics Lite for free today:
>> >> http://p.sf.net/sfu/appdyn_d2d_feb
>> >> _______________________________________________
>> >> cclib-users mailing list
>> >> ccl...@li...
>> >> https://lists.sourceforge.net/lists/listinfo/cclib-users
>> >>
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Everyone hates slow websites. So do we.
>> > Make your web apps faster with AppDynamics
>> > Download AppDynamics Lite for free today:
>> > http://p.sf.net/sfu/appdyn_d2d_feb
>> > _______________________________________________
>> > cclib-users mailing list
>> > ccl...@li...
>> > https://lists.sourceforge.net/lists/listinfo/cclib-users
>> >
>>
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_feb
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
> --
> written by Karol M. Langner
> Tue Feb 26 00:27:13 CET 2013

Re: [cclib-users] z-matrix in Gaussian

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

BTW, Noel, is there a way to specify the atom order in OB for internal coordinates?

On Feb 19 2013, Noel O'Boyle wrote:
> (Nice use of OpenBabel :-)
> 
> Just to clarify, there is a difference between the z-matrix input
> format and the internal coordinate format used by Gaussian during
> geometry optimisations. The former is non-redundant while the latter
> is redundant ("redundant internal coordinates"). I'm not sure which
> you want.
> 
> - Noel
> 
> On 19 February 2013 22:02, Adam Tenderholt <ate...@gm...> wrote:
> > Hi Yaron,
> >
> > cclib doesn't directly support parsing internal coordinates. However, you
> > can use openbabel to save using an internal coordinate system:
> >
> >>>> from cclib.parser import ccopen
> >>>> import openbabel
> >>>> parser = ccopen("dvb_sp.log")
> >>>> data = parser.parse()
> >>>> from cclib.bridge import makeopenbabel
> >>>> mol = makeopenbabel(data.atomcoords[0], data.atomnos)
> >>>> obconv = openbabel.OBConversion()
> >>>> obconv.SetInAndOutFormats("XYZ", "FH")
> >>>> obconv.WriteFile(mol, "test.fh")
> >
> > --
> > 20
> > C   1
> > C   1 1.421
> > C   2 1.402  1 120.857
> > C   3 1.422  2 121.354  1   0.0
> > C   4 1.421  3 117.789  2   0.0
> > H   2 1.098  1 119.765  3 180.0
> > H   3 1.099  2 119.629  1 180.0
> > H   5 1.098  4 119.765  3 180.0
> > C   4 1.498  3 119.172  2 180.0
> > C   9 1.344  4 126.593  3 180.0
> > H  10 1.096  9 122.647  4   0.0
> > H   9 1.100  4 114.434  3   0.0
> > H  10 1.096  9 121.228  4 180.0
> > C   1 1.498  2 123.039  3 180.0
> > H  14 1.100  1 114.434  2 180.0
> > C  14 1.344  1 126.593  2   0.0
> > H  16 1.096 14 122.647  1   0.0
> > H  16 1.096 14 121.228  1 180.0
> > C   5 1.402  4 120.857  3   0.0
> > H  19 1.099  5 119.629  4 180.0
> > --
> >
> > You may also want to see the list of formats supported by openbabel in case
> > you need something slightly different:
> > http://openbabel.org/docs/2.3.1/FileFormats/Overview.html
> >
> > Hope this helps,
> >
> > Adam
> >
> >
> >
> > On Tue, Feb 19, 2013 at 10:48 AM, Yaron Pshetitsky
> > <yar...@li...> wrote:
> >>
> >> Dear cclib community,
> >> I'm trying to get the z-matrix (internal coordinates) from a Gaussian
> >> output file using cclib.
> >> I know that Gaussian do converts any internal or XYZ coordinates in the
> >> input to it's format so one can get internal coordinates from it, even if
> >> the input file was in cartesian coordinates.
> >> Can cclib output the internal coordinates?
> >>
> >> Thanks very much,
> >> Yaron
> >>
> >>
> >> ------------------------------------------------------------------------------
> >> Everyone hates slow websites. So do we.
> >> Make your web apps faster with AppDynamics
> >> Download AppDynamics Lite for free today:
> >> http://p.sf.net/sfu/appdyn_d2d_feb
> >> _______________________________________________
> >> cclib-users mailing list
> >> ccl...@li...
> >> https://lists.sourceforge.net/lists/listinfo/cclib-users
> >>
> >
> >
> > ------------------------------------------------------------------------------
> > Everyone hates slow websites. So do we.
> > Make your web apps faster with AppDynamics
> > Download AppDynamics Lite for free today:
> > http://p.sf.net/sfu/appdyn_d2d_feb
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> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
> 
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
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-- 
written by Karol M. Langner
Tue Feb 26 00:27:13 CET 2013

Re: [cclib-users] Orca 2.9.0 error

[Adam T. <ate...@gm...>]

Hi Melchor,

Sorry for the delay. I've finally looked into your parse error. The problem
is the output from the SCF convergence. For instance, it your file, it is:

--------------
SCF ITERATIONS
--------------
               ***  Starting incremental Fock matrix formation  ***

                         ----------------------------
                         !        ITERATION     0   !
                         ----------------------------
   Total Energy        :    -377.995940441385 Eh
   Energy Change       :    -377.995940441385 Eh
   MAX-DP              :       0.104636203272
   RMS-DP              :       0.004511416837
   Actual Damping      :       0.7000
   Actual Level Shift  :       0.2500 Eh
   Int. Num. El.       :    43.99928165 (UP=   21.99964083 DN=
21.99964083)
   Exchange            :   -34.30375363
   Correlation         :    -2.02696332


                         ----------------------------
                         !        ITERATION     1   !
                         ----------------------------
   Total Energy        :    -378.158637308210 Eh
   Energy Change       :      -0.162696866825 Eh
   MAX-DP              :       0.056981704567
   RMS-DP              :       0.002392614971
   Actual Damping      :       0.7000
   Actual Level Shift  :       0.2500 Eh
   Int. Num. El.       :    43.99902992 (UP=   21.99951496 DN=
21.99951496)
   Exchange            :   -34.01830967
   Correlation         :    -2.01718102

However, cclib is expecting the following:

--------------
SCF ITERATIONS
--------------
ITER       Energy         Delta-E        Max-DP      RMS-DP      [F,P]
Damp
               ***  Starting incremental Fock matrix formation  ***
  0   -381.9867779344   0.000000000000 0.05707535  0.00425410  0.0807540
0.7000
  1   -382.0079986969  -0.021220762511 0.02895905  0.00220039  0.0411442
0.7000

I tried to make sense of your input file, but I don't have any experience
with MRCI calculations with ORCA. Do you know if there was some option that
caused the SCF convergence to be printed differently? Or is this how the
convergence for all MRCI calculations is printed?

Also, are you willing to place your logfile in the public domain? We would
like to include it with our other regression files.

Thanks,

Adam




On Thu, Feb 21, 2013 at 1:48 AM, msmqbm <ms...@ci...> wrote:

> Dear cclib developers,
> When trying to parse an Orca 2.9.0 output file I get the following error:
>
> >>> import cclib
> >>> f1= cclib.parser.ORCA("DAT6600.**out")
> >>> data1= f1.parse()
> [ORCA DAT6600.out INFO] Creating attribute atomcoords[]
> [ORCA DAT6600.out INFO] Creating attribute atomnos[]
> [ORCA DAT6600.out INFO] Creating attribute natom: 9
> [ORCA DAT6600.out INFO] Creating attribute nbasis: 90
> [ORCA DAT6600.out INFO] Creating attribute charge: 0
> [ORCA DAT6600.out INFO] Creating attribute mult: 1
> [ORCA DAT6600.out INFO] Creating attribute scfvalues[]
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/lib/python2.7/dist-**packages/cclib/parser/**logfileparser.py",
> line 221, in parse
>     self.extract(inputfile, line)
>   File "/usr/lib/python2.7/dist-**packages/cclib/parser/**orcaparser.py",
> line 90, in extract
>     assert line[1] == "Energy"
> AssertionError
>
> I'm using cclib version 1.1 (the latest one). I attach the file
> DAT6600.out.
>
> Is there a solution to this?
>
> Thanks in advance,
>
> --
> Melchor Sánchez
> PhD candidate
> Institute of Advanced Chemistry of Catalonia
> http://www.iqac.csic.es/qteor
> IQAC - CSIC
> Tel. +34 934006100 ext: 1307
> Jordi Girona 18-26
> 08034 Barcelona (Spain)
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

[cclib-users] Orca 2.9.0 error

[msmqbm <ms...@ci...>]

Dear cclib developers,
When trying to parse an Orca 2.9.0 output file I get the following error:

 >>> import cclib
 >>> f1= cclib.parser.ORCA("DAT6600.out")
 >>> data1= f1.parse()
[ORCA DAT6600.out INFO] Creating attribute atomcoords[]
[ORCA DAT6600.out INFO] Creating attribute atomnos[]
[ORCA DAT6600.out INFO] Creating attribute natom: 9
[ORCA DAT6600.out INFO] Creating attribute nbasis: 90
[ORCA DAT6600.out INFO] Creating attribute charge: 0
[ORCA DAT6600.out INFO] Creating attribute mult: 1
[ORCA DAT6600.out INFO] Creating attribute scfvalues[]
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
   File 
"/usr/lib/python2.7/dist-packages/cclib/parser/logfileparser.py", line 
221, in parse
     self.extract(inputfile, line)
   File "/usr/lib/python2.7/dist-packages/cclib/parser/orcaparser.py", 
line 90, in extract
     assert line[1] == "Energy"
AssertionError

I'm using cclib version 1.1 (the latest one). I attach the file 
DAT6600.out.

Is there a solution to this?

Thanks in advance,

-- 
Melchor Sánchez
PhD candidate
Institute of Advanced Chemistry of Catalonia
http://www.iqac.csic.es/qteor
IQAC - CSIC
Tel. +34 934006100 ext: 1307
Jordi Girona 18-26
08034 Barcelona (Spain)

Re: [cclib-users] z-matrix in Gaussian

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

(Nice use of OpenBabel :-)

Just to clarify, there is a difference between the z-matrix input
format and the internal coordinate format used by Gaussian during
geometry optimisations. The former is non-redundant while the latter
is redundant ("redundant internal coordinates"). I'm not sure which
you want.

- Noel

On 19 February 2013 22:02, Adam Tenderholt <ate...@gm...> wrote:
> Hi Yaron,
>
> cclib doesn't directly support parsing internal coordinates. However, you
> can use openbabel to save using an internal coordinate system:
>
>>>> from cclib.parser import ccopen
>>>> import openbabel
>>>> parser = ccopen("dvb_sp.log")
>>>> data = parser.parse()
>>>> from cclib.bridge import makeopenbabel
>>>> mol = makeopenbabel(data.atomcoords[0], data.atomnos)
>>>> obconv = openbabel.OBConversion()
>>>> obconv.SetInAndOutFormats("XYZ", "FH")
>>>> obconv.WriteFile(mol, "test.fh")
>
> --
> 20
> C   1
> C   1 1.421
> C   2 1.402  1 120.857
> C   3 1.422  2 121.354  1   0.0
> C   4 1.421  3 117.789  2   0.0
> H   2 1.098  1 119.765  3 180.0
> H   3 1.099  2 119.629  1 180.0
> H   5 1.098  4 119.765  3 180.0
> C   4 1.498  3 119.172  2 180.0
> C   9 1.344  4 126.593  3 180.0
> H  10 1.096  9 122.647  4   0.0
> H   9 1.100  4 114.434  3   0.0
> H  10 1.096  9 121.228  4 180.0
> C   1 1.498  2 123.039  3 180.0
> H  14 1.100  1 114.434  2 180.0
> C  14 1.344  1 126.593  2   0.0
> H  16 1.096 14 122.647  1   0.0
> H  16 1.096 14 121.228  1 180.0
> C   5 1.402  4 120.857  3   0.0
> H  19 1.099  5 119.629  4 180.0
> --
>
> You may also want to see the list of formats supported by openbabel in case
> you need something slightly different:
> http://openbabel.org/docs/2.3.1/FileFormats/Overview.html
>
> Hope this helps,
>
> Adam
>
>
>
> On Tue, Feb 19, 2013 at 10:48 AM, Yaron Pshetitsky
> <yar...@li...> wrote:
>>
>> Dear cclib community,
>> I'm trying to get the z-matrix (internal coordinates) from a Gaussian
>> output file using cclib.
>> I know that Gaussian do converts any internal or XYZ coordinates in the
>> input to it's format so one can get internal coordinates from it, even if
>> the input file was in cartesian coordinates.
>> Can cclib output the internal coordinates?
>>
>> Thanks very much,
>> Yaron
>>
>>
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_feb
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

Re: [cclib-users] z-matrix in Gaussian

[Adam T. <ate...@gm...>]

Hi Yaron,

cclib doesn't directly support parsing internal coordinates. However, you
can use openbabel to save using an internal coordinate system:

>>> from cclib.parser import ccopen
>>> import openbabel
>>> parser = ccopen("dvb_sp.log")
>>> data = parser.parse()
>>> from cclib.bridge import makeopenbabel
>>> mol = makeopenbabel(data.atomcoords[0], data.atomnos)
>>> obconv = openbabel.OBConversion()
>>> obconv.SetInAndOutFormats("XYZ", "FH")
>>> obconv.WriteFile(mol, "test.fh")

--
20
C   1
C   1 1.421
C   2 1.402  1 120.857
C   3 1.422  2 121.354  1   0.0
C   4 1.421  3 117.789  2   0.0
H   2 1.098  1 119.765  3 180.0
H   3 1.099  2 119.629  1 180.0
H   5 1.098  4 119.765  3 180.0
C   4 1.498  3 119.172  2 180.0
C   9 1.344  4 126.593  3 180.0
H  10 1.096  9 122.647  4   0.0
H   9 1.100  4 114.434  3   0.0
H  10 1.096  9 121.228  4 180.0
C   1 1.498  2 123.039  3 180.0
H  14 1.100  1 114.434  2 180.0
C  14 1.344  1 126.593  2   0.0
H  16 1.096 14 122.647  1   0.0
H  16 1.096 14 121.228  1 180.0
C   5 1.402  4 120.857  3   0.0
H  19 1.099  5 119.629  4 180.0
--

You may also want to see the list of formats supported by openbabel in case
you need something slightly different:
http://openbabel.org/docs/2.3.1/FileFormats/Overview.html

Hope this helps,

Adam



On Tue, Feb 19, 2013 at 10:48 AM, Yaron Pshetitsky <
yar...@li...> wrote:

> Dear cclib community,
> I'm trying to get the z-matrix (internal coordinates) from a Gaussian
> output file using cclib.
> I know that Gaussian do converts any internal or XYZ coordinates in the
> input to it's format so one can get internal coordinates from it, even if
> the input file was in cartesian coordinates.
> *Can cclib output the internal coordinates?*
>
> Thanks very much,
> Yaron
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

[cclib-users] z-matrix in Gaussian

[Yaron P. <yar...@li...>]

Dear cclib community,
I'm trying to get the z-matrix (internal coordinates) from a Gaussian output file using cclib.
I know that Gaussian do converts any internal or XYZ coordinates in the input to it's format so one can get internal coordinates from it, even if the input file was in cartesian coordinates.
Can cclib output the internal coordinates?

Thanks very much,
Yaron

[cclib-users] cclib 1.1 is released

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

Hello all,

cclib 1.1 is now available for download from http://cclib.sf.net (or
directly at https://sourceforge.net/projects/cclib/files/cclib/cclib-1.1/).
This contains a number of new features as well as several improvements
to the parsers. All users are recommended to upgrade to version 1.1.

Note that this will be the last release in the Python 2 series, as we
plan to move to Python 3.

Changes since cclib-1.0.1:

Features:
    * Add progress info for all parsers
    * Support ONIOM calculations in Gaussian (Karen Hemelsoet)
    * New attribute atomcharges extracts Mulliken and Lowdin atomic
    charges if present
    * New attribute atomspins extracts Mulliken and Lowdin atomic spin
    densities if present
    * New thermodynamic attributes: freeenergy, temperature, enthalpy
    (Edward Holland)
    * Extract PES information: scanenergies, scancoords, scanparm,
scannames (Edward Holland)

Bugfixes:
    * Handle coupled cluster energies in Gaussian 09 (Björn Dahlgren)
    * Vibrational displacement vectors missing for Gaussian 09 (Björn
    Dahlgren)
    * Fix problem parsing vibrational frequencies in some GAMESS-US files
    * Fix missing final scfenergy in ADF geometry optimisations
    * Fix missing final scfenergy for ORCA where a specific number of SCF
    cycles has been specified
    * ORCA scfenergies not parsed if COSMO solvent effects included
    * Allow spin unrestricted calculations to use the fragment MO overlaps
    correctly for the MPA and CDA calculations
    * Handle Gaussian MO energies that are printed as a row of asterisks
    (Jerome Kieffer)
    * Add more explicit license notices, and allow LGPL versions after 2.1
    * Support Firefly calculations where nmo != nbasis (Pavel Solntsev)
    * Fix problem parsing vibrational frequency information in recent
    GAMESS (US) files (Chengju Wang)
    * Apply patch from Chengju Wang to handle GAMESS calculations with more
    than 99 atoms
    * Handle Gaussian files with more than 99 atoms having pseudopotentials
    (Björn Baumeier)

Regards,
   Noel, Adam, Karol

Re: [cclib-users] Extract Mulliken atomic charges and spin densities

[Mikolaj F. <mik...@gm...>]

Hi Karol,

it works - thanks a lot!!

All the best,
mfx

On 10/06/2012 08:31 PM, Karol M. Langner wrote:
> Mikolaj,
>
> The current development code should parse this information correctly for
> ORCA, and present it in a dictionary with Mulliken and Lowdin values.
>
> For example:
> $ ccget atomcharges atomspins job.out.gz
> Attempting to parse job.out.gz
> atomcharges:
> {'lowdin':
> array([ 0.109834, -0.48075 ,  0.144867,  0.219485, -0.045542, -0.111878,
>          0.113258,  0.152248, -0.500877,  0.412007, -0.043762,  0.127572,
>         -0.528491,  0.383448, -0.114098,  0.10012 ,  0.121108, -0.437476,
>          0.378927]),
> 'mulliken':
> array([ 0.126447, -0.613018,  0.189146,  0.320041, -0.068218, -0.009025,
>   ...
> atomspins:
> {'lowdin': array([  2.48200000e-03,  -4.93200000e-03,   1.46740000e-02,
>   ... you get the idea ...
>
> Cheers,
> Karol
>
> On Oct 04 2012, Mikolaj Feliks wrote:
>>
>> Dear cclib users,
>>
>> cclib makes a really great job of calculating atomic properties, for
>> example atomic charges or spin densities.
>>
>> However, I was wondering whether those properties could also be
>> extracted from existing output files, since they are calculated by
>> default by most of the quantum chemical programs. For cclib to
>> perform a population analysis, the output file should contain an
>> overlap matrix and eigenvectors and it considerably grows in size.
>> But the values I want to calculate are already in the file and it
>> would make more sense to simply extract them from there.
>>
>> I am particularly interested in extracting/parsing Mulliken atomic
>> charges and spin densities from ORCA output files. Is there a chance
>> for such a feature to be implemented in cclib in the nearest future?
>> I enclose a sample file.
>>
>> Cheers, mfx
>>
>
>
>> ------------------------------------------------------------------------------
>> Don't let slow site performance ruin your business. Deploy New Relic APM
>> Deploy New Relic app performance management and know exactly
>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>> http://p.sf.net/sfu/newrelic-dev2dev
>
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

Re: [cclib-users] Extract Mulliken atomic charges and spin densities

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

Mikolaj,

The current development code should parse this information correctly for
ORCA, and present it in a dictionary with Mulliken and Lowdin values.

For example:
$ ccget atomcharges atomspins job.out.gz 
Attempting to parse job.out.gz
atomcharges:
{'lowdin':
array([ 0.109834, -0.48075 ,  0.144867,  0.219485, -0.045542, -0.111878,
        0.113258,  0.152248, -0.500877,  0.412007, -0.043762,  0.127572,
       -0.528491,  0.383448, -0.114098,  0.10012 ,  0.121108, -0.437476,
        0.378927]),
'mulliken':
array([ 0.126447, -0.613018,  0.189146,  0.320041, -0.068218, -0.009025,
 ...
atomspins:
{'lowdin': array([  2.48200000e-03,  -4.93200000e-03,   1.46740000e-02,
 ... you get the idea ...

Cheers,
Karol

On Oct 04 2012, Mikolaj Feliks wrote:
> 
> Dear cclib users,
> 
> cclib makes a really great job of calculating atomic properties, for
> example atomic charges or spin densities.
> 
> However, I was wondering whether those properties could also be
> extracted from existing output files, since they are calculated by
> default by most of the quantum chemical programs. For cclib to
> perform a population analysis, the output file should contain an
> overlap matrix and eigenvectors and it considerably grows in size.
> But the values I want to calculate are already in the file and it
> would make more sense to simply extract them from there.
> 
> I am particularly interested in extracting/parsing Mulliken atomic
> charges and spin densities from ORCA output files. Is there a chance
> for such a feature to be implemented in cclib in the nearest future?
> I enclose a sample file.
> 
> Cheers, mfx
> 


> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev

> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users


-- 
written by Karol M. Langner
Sat Oct  6 20:25:47 CEST 2012

Re: [cclib-users] Extract Mulliken atomic charges and spin densities

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

Hi,

OK, thanks!

This is perhaps a good thing to add, since it is not always trivial to
recalculate a population analysis for methods other than RHF, and the
overlaps/coefficients are sometimes simply not there.

As far as the implementation is concerned, there is a problem. Namely,
aotmic partial charges and spin densities are arbitrary, that is, they
can be defined in many varieties -- Mulliken, Loewden, etc. We can't
assume that the parsed charge/spin densities are any one of these.

So, Noel, Adam... what do you think? We can't have na attribute for
every type of population analysis parsed. I see two options:
1) use a dictionary, with keys like 'Mulliken', 'Loewdin'
2) use a list of tuples consisting of a string and an array of charges

Any other ideas?

- Karol

On Oct 05 2012, Mikolaj Feliks wrote:
> 
> Hi Karol,
> 
> I see no problem making this file public. Go ahead!
> 
> Cheers, mfx
> 
> 
> On 10/05/12 18:50, Karol M. Langner wrote:
> > Mikolaj,
> >
> > Are making this sample file public domain? If so, we can then include in
> > our test suite.
> >
> > Thanks,
> > Karol
> >
> > On Oct 04 2012, Mikolaj Feliks wrote:
> >>
> >> Dear cclib users,
> >>
> >> cclib makes a really great job of calculating atomic properties, for
> >> example atomic charges or spin densities.
> >>
> >> However, I was wondering whether those properties could also be
> >> extracted from existing output files, since they are calculated by
> >> default by most of the quantum chemical programs. For cclib to
> >> perform a population analysis, the output file should contain an
> >> overlap matrix and eigenvectors and it considerably grows in size.
> >> But the values I want to calculate are already in the file and it
> >> would make more sense to simply extract them from there.
> >>
> >> I am particularly interested in extracting/parsing Mulliken atomic
> >> charges and spin densities from ORCA output files. Is there a chance
> >> for such a feature to be implemented in cclib in the nearest future?
> >> I enclose a sample file.
> >>
> >> Cheers, mfx
> >>
> >
> >
> >> ------------------------------------------------------------------------------
> >> Don't let slow site performance ruin your business. Deploy New Relic APM
> >> Deploy New Relic app performance management and know exactly
> >> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> >> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> >> http://p.sf.net/sfu/newrelic-dev2dev
> >
> >> _______________________________________________
> >> cclib-users mailing list
> >> ccl...@li...
> >> https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
> >
> 
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users

-- 
written by Karol M. Langner
Fri Oct  5 19:17:52 CEST 2012

Re: [cclib-users] Extract Mulliken atomic charges and spin densities

[Mikolaj F. <mik...@gm...>]

Hi Karol,

I see no problem making this file public. Go ahead!

Cheers, mfx


On 10/05/12 18:50, Karol M. Langner wrote:
> Mikolaj,
>
> Are making this sample file public domain? If so, we can then include in
> our test suite.
>
> Thanks,
> Karol
>
> On Oct 04 2012, Mikolaj Feliks wrote:
>>
>> Dear cclib users,
>>
>> cclib makes a really great job of calculating atomic properties, for
>> example atomic charges or spin densities.
>>
>> However, I was wondering whether those properties could also be
>> extracted from existing output files, since they are calculated by
>> default by most of the quantum chemical programs. For cclib to
>> perform a population analysis, the output file should contain an
>> overlap matrix and eigenvectors and it considerably grows in size.
>> But the values I want to calculate are already in the file and it
>> would make more sense to simply extract them from there.
>>
>> I am particularly interested in extracting/parsing Mulliken atomic
>> charges and spin densities from ORCA output files. Is there a chance
>> for such a feature to be implemented in cclib in the nearest future?
>> I enclose a sample file.
>>
>> Cheers, mfx
>>
>
>
>> ------------------------------------------------------------------------------
>> Don't let slow site performance ruin your business. Deploy New Relic APM
>> Deploy New Relic app performance management and know exactly
>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>> http://p.sf.net/sfu/newrelic-dev2dev
>
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

Re: [cclib-users] Extract Mulliken atomic charges and spin densities

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

Mikolaj,

Are making this sample file public domain? If so, we can then include in
our test suite.

Thanks,
Karol

On Oct 04 2012, Mikolaj Feliks wrote:
> 
> Dear cclib users,
> 
> cclib makes a really great job of calculating atomic properties, for
> example atomic charges or spin densities.
> 
> However, I was wondering whether those properties could also be
> extracted from existing output files, since they are calculated by
> default by most of the quantum chemical programs. For cclib to
> perform a population analysis, the output file should contain an
> overlap matrix and eigenvectors and it considerably grows in size.
> But the values I want to calculate are already in the file and it
> would make more sense to simply extract them from there.
> 
> I am particularly interested in extracting/parsing Mulliken atomic
> charges and spin densities from ORCA output files. Is there a chance
> for such a feature to be implemented in cclib in the nearest future?
> I enclose a sample file.
> 
> Cheers, mfx
> 


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-- 
written by Karol M. Langner
Fri Oct  5 18:49:22 CEST 2012

[cclib-users] Extract Mulliken atomic charges and spin densities

[Mikolaj F. <mik...@gm...>]

Dear cclib users,

cclib makes a really great job of calculating atomic properties, for 
example atomic charges or spin densities.

However, I was wondering whether those properties could also be 
extracted from existing output files, since they are calculated by 
default by most of the quantum chemical programs. For cclib to perform a 
population analysis, the output file should contain an overlap matrix 
and eigenvectors and it considerably grows in size. But the values I 
want to calculate are already in the file and it would make more sense 
to simply extract them from there.

I am particularly interested in extracting/parsing Mulliken atomic 
charges and spin densities from ORCA output files. Is there a chance for 
such a feature to be implemented in cclib in the nearest future? I 
enclose a sample file.

Cheers, mfx

Re: [cclib-users] cclib-users Digest, Vol 34, Issue 1

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

Hi Yishen,

Thanks for the patch. Do you want us to incorporate it into the trunk?

Best,
Karol

On May 14 2012, Yishen Miao wrote:
> Hi Ed,
> 
> Thanks for your reply! I checked out the source from svn and the parser works fine. I attached a patch for adding ZPE and fixing a typo ("enthaply" :-p ). I tested it on my computer. I will work on adding translational entropy, rotational entropy and etc. on my local repo.
> 
> Best,
> Yishen Miao
> 
> PS: Also thanks for Adam's reply.
> 
> On May 14, 2012, at 12:11 , Edward Holland wrote:
> 
> > Hi Yishen,
> > 
> > Its only in a very recent patch we have added any support for thermochemistry data. Currently it only supports gaussian and only collects free energy, enthalpy, entropy and temperature, although it would be fairly easy to patch to also collect ZPE if people feel thats important.
> > If you want to collect thermochem data you will need to checkout a development version from the SVN hosted on source forge.
> > 
> > Yours
> > 
> > Ed Holland
> > 
> > On 14 May 2012, at 13:04, ccl...@li... wrote:
> > 
> >> Send cclib-users mailing list submissions to
> >> 	ccl...@li...
> >> 
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> 	https://lists.sourceforge.net/lists/listinfo/cclib-users
> >> or, via email, send a message with subject or body 'help' to
> >> 	ccl...@li...
> >> 
> >> You can reach the person managing the list at
> >> 	ccl...@li...
> >> 
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of cclib-users digest..."
> >> Today's Topics:
> >> 
> >>   1. [Question] Finding Thermchemistry Data (Yishen Miao)
> >> 
> >> From: Yishen Miao <mys...@gm...>
> >> Subject: [cclib-users] [Question] Finding Thermchemistry Data
> >> Date: 14 May 2012 08:39:52 GMT+01:00
> >> To: ccl...@li...
> >> 
> >> 
> >> Hello everyone,
> >> 
> >> I am trying to use cclib to parsing logs from Gaussian 09. However, after running mydata = myfile.parse() , I find I am not able to find thermchemistry data like zero-point energy from mydata's attributes. Could you please tell me how to find those data?
> >> 
> >> Thanks!
> >> Yishen Miao
> >> 
> >> 
> >> 
> >> 
> >> 
> >> ------------------------------------------------------------------------------
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> >> threat landscape has changed and how IT managers can respond. Discussions 
> >> will include endpoint security, mobile security and the latest in malware 
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> >> https://lists.sourceforge.net/lists/listinfo/cclib-users
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-- 
written by Karol M. Langner
Wed Jun 13 12:22:25 CEST 2012

Re: [cclib-users] cclib-users Digest, Vol 34, Issue 1

[Yishen M. <mys...@gm...>]

Hi Ed,

Thanks for your reply! I checked out the source from svn and the parser works fine. I attached a patch for adding ZPE and fixing a typo ("enthaply" :-p ). I tested it on my computer. I will work on adding translational entropy, rotational entropy and etc. on my local repo.

Best,
Yishen Miao

PS: Also thanks for Adam's reply.

On May 14, 2012, at 12:11 , Edward Holland wrote:

> Hi Yishen,
> 
> Its only in a very recent patch we have added any support for thermochemistry data. Currently it only supports gaussian and only collects free energy, enthalpy, entropy and temperature, although it would be fairly easy to patch to also collect ZPE if people feel thats important.
> If you want to collect thermochem data you will need to checkout a development version from the SVN hosted on source forge.
> 
> Yours
> 
> Ed Holland
> 
> On 14 May 2012, at 13:04, ccl...@li... wrote:
> 
>> Send cclib-users mailing list submissions to
>> 	ccl...@li...
>> 
>> To subscribe or unsubscribe via the World Wide Web, visit
>> 	https://lists.sourceforge.net/lists/listinfo/cclib-users
>> or, via email, send a message with subject or body 'help' to
>> 	ccl...@li...
>> 
>> You can reach the person managing the list at
>> 	ccl...@li...
>> 
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of cclib-users digest..."
>> Today's Topics:
>> 
>>   1. [Question] Finding Thermchemistry Data (Yishen Miao)
>> 
>> From: Yishen Miao <mys...@gm...>
>> Subject: [cclib-users] [Question] Finding Thermchemistry Data
>> Date: 14 May 2012 08:39:52 GMT+01:00
>> To: ccl...@li...
>> 
>> 
>> Hello everyone,
>> 
>> I am trying to use cclib to parsing logs from Gaussian 09. However, after running mydata = myfile.parse() , I find I am not able to find thermchemistry data like zero-point energy from mydata's attributes. Could you please tell me how to find those data?
>> 
>> Thanks!
>> Yishen Miao
>> 
>> 
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and 
>> threat landscape has changed and how IT managers can respond. Discussions 
>> will include endpoint security, mobile security and the latest in malware 
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users