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From: harsh s. <har...@gm...> - 2016-03-02 16:50:46
|
how to discuss gsoc 2016 ideas? I am applying for gsoc 2016. |
|
From: Karol L. <kar...@gm...> - 2016-03-02 15:05:57
|
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 > > |
|
From: Felix P. <fel...@un...> - 2016-03-02 13:47:59
|
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 |
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From: Karol L. <kar...@gm...> - 2016-03-01 20:50:40
|
Reposting here in case there is a student among cclib users and contributors that might be interested. ---------- Forwarded message ---------- From: Geoffrey Hutchison <ge...@pi...> Date: Tue, Mar 1, 2016 at 7:56 AM Subject: [BlueObelisk-discuss] Google Summer of Code To: BlueObelisk-Discuss <blu...@li...> OpenChemistry has been accepted into the Google Summer of Code for 2016 - including Open Babel, Avogadro, cclib and 3DMol.js https://summerofcode.withgoogle.com/organizations/6290185763422208/ http://wiki.openchemistry.org/GSoC_Ideas_2016 If you are a student and interested in doing open chemistry software development this summer (or know of someone who is), we're definitely interested in good proposal ideas. Looking forward to a summer of great science! Cheers, -Geoff ------------------------------------------------------------------------------ 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 _______________________________________________ Blueobelisk-discuss mailing list Blu...@li... https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss |
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From: Karol L. <kar...@gm...> - 2016-01-26 07:39:29
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Hi guys, I added convenience methods for the three formats we support in a pull request (https://github.com/cclib/cclib/pull/234). Karol On Thu, Jan 21, 2016 at 6:16 PM, Eric Berquist <er...@pi...> wrote: > Hi Supun, > > There isn't a writejson() method, but there is a write() method. What > isn't clear right now is that in addition to passing a filename with the > appropriate extension, you can get a string back using the outputtype > kwarg: > > data.write(outputtype='json') > > There's currently a bug though because the code tries to take the length > of a generator, so I'll have a patch up soon. > > Eric > > On Fri, Jan 15, 2016 at 2:55 PM, Supun Nakandala < > sup...@gm...> wrote: > >> >> Hi all, >> >> I am experimenting with cclib 1.3.1 version and when I try to get a dump >> of the data object in json format I get the following error I get the >> following error. >> >> >>> data.writejson() >> >> Traceback (most recent call last): >> >> File "<stdin>", line 1, in <module> >> >> AttributeError: 'ccData_optdone_bool' object has no attribute 'writejson' >> >> >> Any idea on what is going wrong here? >> >> >> Thank you >> >> >> ------------------------------------------------------------------------------ >> 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=267308311&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=267308311&iu=/4140 > _______________________________________________ > cclib-users mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-users > > |
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From: Eric B. <er...@pi...> - 2016-01-22 02:51:21
|
Hi Supun, There isn't a writejson() method, but there is a write() method. What isn't clear right now is that in addition to passing a filename with the appropriate extension, you can get a string back using the outputtype kwarg: data.write(outputtype='json') There's currently a bug though because the code tries to take the length of a generator, so I'll have a patch up soon. Eric On Fri, Jan 15, 2016 at 2:55 PM, Supun Nakandala <sup...@gm...> wrote: > > Hi all, > > I am experimenting with cclib 1.3.1 version and when I try to get a dump > of the data object in json format I get the following error I get the > following error. > > >>> data.writejson() > > Traceback (most recent call last): > > File "<stdin>", line 1, in <module> > > AttributeError: 'ccData_optdone_bool' object has no attribute 'writejson' > > > Any idea on what is going wrong here? > > > Thank you > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > _______________________________________________ > cclib-users mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-users > > |
|
From: Supun N. <sup...@gm...> - 2016-01-15 19:55:33
|
Hi all, I am experimenting with cclib 1.3.1 version and when I try to get a dump of the data object in json format I get the following error I get the following error. >>> data.writejson() Traceback (most recent call last): File "<stdin>", line 1, in <module> AttributeError: 'ccData_optdone_bool' object has no attribute 'writejson' Any idea on what is going wrong here? Thank you |
|
From: Karol L. <kar...@gm...> - 2015-09-09 19:27:19
|
Alexis,
The fix is now in the master branch on our github repository and will go
into the next relase (probably at the end of September).
Please let us know if you are releasing the test files you sent us into the
Public Domain.
Best,
Karol
On Sat, Sep 5, 2015 at 10:34 PM, Karol Langner <kar...@gm...>
wrote:
> Hi Alexis,
>
> Thanks for the files. Are you placing these in the Public Domain? Please
> let us know explicitly, in which case we can use it as a regression test.
>
> Changing the typo fixes the problem for me:
> ~$ ccget mocoeffs h2o.log
> Attempting to read h2o.log
> mocoeffs:
> [array([[-0.994216, -0.025847, 0. , 0. , -0.004164, 0.005584,
> 0.005584],
> [-0.233765, 0.844446, 0. , 0. , 0.122842, 0.155595,
> 0.155595],
> (...)
> which are the values from the MOLECULAR ORBITALS block. I'm not sure why
> you were getting zeros.
>
> Anyway, I should be able to get a fix into github within a few days.
>
> Best,
> Karol
>
>
> On Tue, Sep 1, 2015 at 11:00 AM, Otero Calvi <ao...@is...> wrote:
>
>> Karol
>> Any file of gamess or firefly whenever you try to extract information
>> concerning the molecular orbitals section shows the related to eigenvector
>> section.
>> I send 3 files, h2o.log (firefly result), Orbitales.py (code to extract
>> molecular orbital information) and orbitales.out (information obtained with
>> Orbitales.py that correspond with the values of eigenvector and not with
>> the molecular orbital of the optimized structure)
>>
>> Thanks
>> Alexis
>>
>>
>> ------------------------------
>> *De: *"Karol Langner" <kar...@gm...>
>> *Para: *"Otero Calvi" <ao...@is...>
>> *CC: *"Adam Tenderholt" <ate...@gm...>,
>> ccl...@li...
>> *Enviados: *Martes, 1 de Septiembre 2015 11:55:17
>> *Asunto: *Re: [cclib-users] About gamessparser in cclib
>>
>>
>> Hi Alexis,
>>
>> Thanks for reporting this! It would be great if you could supply us with
>> an example output file exhibiting this problem. Is that possible?
>>
>> Best,
>> Karol
>>
>> On Tue, Sep 1, 2015 at 6:48 AM, Otero Calvi <ao...@is...> wrote:
>>
>>> Hi,
>>>
>>> I found an error in gamessparser, trying to extract the molecular
>>> orbital coefficients. In line 844 where says
>>> if line.find ("EIGENVECTORS") == 10 or line.find ("MOLECULAR OBRITALS")
>>> == 10:
>>> must be
>>> if line.find ("EIGENVECTORS") == 10 or line.find ("MOLECULAR ORBITALS")
>>> == 10:
>>>
>>> The error is in O B R I T A L S where should be O R B I T A L S ... I
>>> modified the code and wrote ORBITALS but does not work, when I try to find
>>> the coefficients is not possible, that is for example, mocoeffs is always
>>> zero.
>>>
>>> Thanks,
>>> Alexis
>>>
>>> Participe en la VIII Conferencia Internacional de Aprovechamiento de
>>> Recursos Minerales CINAREM-2015 En Moa, del 17 al 19 de noviembre de 2015
>>> http://www.ismm.edu.cu
>>> Email:ci...@is...
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> _______________________________________________
>>> cclib-users mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>
>>
>>
>>
>>
>> Participe en la VIII Conferencia Internacional de Aprovechamiento de
>> Recursos Minerales CINAREM-2015 En Moa
>>
>> Del 17 al 19 de noviembre de 2015
>> *www.ismm.edu.cu* <http://www.ismm.edu.cu>
>>
>> Email:ci...@is...
>>
>>
>
|
|
From: Karol L. <kar...@gm...> - 2015-09-06 05:34:33
|
Hi Alexis,
Thanks for the files. Are you placing these in the Public Domain? Please
let us know explicitly, in which case we can use it as a regression test.
Changing the typo fixes the problem for me:
~$ ccget mocoeffs h2o.log
Attempting to read h2o.log
mocoeffs:
[array([[-0.994216, -0.025847, 0. , 0. , -0.004164, 0.005584,
0.005584],
[-0.233765, 0.844446, 0. , 0. , 0.122842, 0.155595,
0.155595],
(...)
which are the values from the MOLECULAR ORBITALS block. I'm not sure why
you were getting zeros.
Anyway, I should be able to get a fix into github within a few days.
Best,
Karol
On Tue, Sep 1, 2015 at 11:00 AM, Otero Calvi <ao...@is...> wrote:
> Karol
> Any file of gamess or firefly whenever you try to extract information
> concerning the molecular orbitals section shows the related to eigenvector
> section.
> I send 3 files, h2o.log (firefly result), Orbitales.py (code to extract
> molecular orbital information) and orbitales.out (information obtained with
> Orbitales.py that correspond with the values of eigenvector and not with
> the molecular orbital of the optimized structure)
>
> Thanks
> Alexis
>
>
> ------------------------------
> *De: *"Karol Langner" <kar...@gm...>
> *Para: *"Otero Calvi" <ao...@is...>
> *CC: *"Adam Tenderholt" <ate...@gm...>,
> ccl...@li...
> *Enviados: *Martes, 1 de Septiembre 2015 11:55:17
> *Asunto: *Re: [cclib-users] About gamessparser in cclib
>
>
> Hi Alexis,
>
> Thanks for reporting this! It would be great if you could supply us with
> an example output file exhibiting this problem. Is that possible?
>
> Best,
> Karol
>
> On Tue, Sep 1, 2015 at 6:48 AM, Otero Calvi <ao...@is...> wrote:
>
>> Hi,
>>
>> I found an error in gamessparser, trying to extract the molecular orbital
>> coefficients. In line 844 where says
>> if line.find ("EIGENVECTORS") == 10 or line.find ("MOLECULAR OBRITALS")
>> == 10:
>> must be
>> if line.find ("EIGENVECTORS") == 10 or line.find ("MOLECULAR ORBITALS")
>> == 10:
>>
>> The error is in O B R I T A L S where should be O R B I T A L S ... I
>> modified the code and wrote ORBITALS but does not work, when I try to find
>> the coefficients is not possible, that is for example, mocoeffs is always
>> zero.
>>
>> Thanks,
>> Alexis
>>
>> Participe en la VIII Conferencia Internacional de Aprovechamiento de
>> Recursos Minerales CINAREM-2015 En Moa, del 17 al 19 de noviembre de 2015
>> http://www.ismm.edu.cu
>> Email:ci...@is...
>>
>>
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>
>
>
>
> Participe en la VIII Conferencia Internacional de Aprovechamiento de
> Recursos Minerales CINAREM-2015 En Moa
>
> Del 17 al 19 de noviembre de 2015
> *www.ismm.edu.cu* <http://www.ismm.edu.cu>
>
> Email:ci...@is...
>
>
|
|
From: Karol L. <kar...@gm...> - 2015-09-01 15:55:24
|
Hi Alexis,
Thanks for reporting this! It would be great if you could supply us with an
example output file exhibiting this problem. Is that possible?
Best,
Karol
On Tue, Sep 1, 2015 at 6:48 AM, Otero Calvi <ao...@is...> wrote:
> Hi,
>
> I found an error in gamessparser, trying to extract the molecular orbital
> coefficients. In line 844 where says
> if line.find ("EIGENVECTORS") == 10 or line.find ("MOLECULAR OBRITALS") ==
> 10:
> must be
> if line.find ("EIGENVECTORS") == 10 or line.find ("MOLECULAR ORBITALS") ==
> 10:
>
> The error is in O B R I T A L S where should be O R B I T A L S ... I
> modified the code and wrote ORBITALS but does not work, when I try to find
> the coefficients is not possible, that is for example, mocoeffs is always
> zero.
>
> Thanks,
> Alexis
>
> Participe en la VIII Conferencia Internacional de Aprovechamiento de
> Recursos Minerales CINAREM-2015 En Moa, del 17 al 19 de noviembre de 2015
> http://www.ismm.edu.cu
> Email:ci...@is...
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
|
|
From: Otero C. <ao...@is...> - 2015-09-01 14:06:25
|
Hi,
I found an error in gamessparser, trying to extract the molecular orbital coefficients. In line 844 where says
if line.find ("EIGENVECTORS") == 10 or line.find ("MOLECULAR OBRITALS") == 10:
must be
if line.find ("EIGENVECTORS") == 10 or line.find ("MOLECULAR ORBITALS") == 10:
The error is in O B R I T A L S where should be O R B I T A L S ... I modified the code and wrote ORBITALS but does not work, when I try to find the coefficients is not possible, that is for example, mocoeffs is always zero.
Thanks,
Alexis
Participe en la VIII Conferencia Internacional de Aprovechamiento de Recursos Minerales CINAREM-2015 En Moa, del 17 al 19 de noviembre de 2015
http://www.ismm.edu.cu
Email:ci...@is...
|
|
From: Eric B. <er...@pi...> - 2015-06-23 13:39:12
|
Yes, this is the way I run cclib most often. You make a sandboxed virtual environment: virtualenv --system-site-packages /path/to/my/virtualenv With Python 2, it's called virtualenv, for Python 3, it's called pyvenv. I've added the --system-site-packages flag incase you want to use the system's version of NumPy or other packages. Otherwise, you'll have to reinstall them all. Then, you activate it, so all the software you install will go in there: source /path/to/my/virtualenv/bin/activate The other methods brought up here also work well. Eric On Mon, Jun 22, 2015 at 7:07 PM, Adam Tenderholt <ate...@gm...> wrote: > Hi Will, > > I think that virtualenv ( > http://docs.python-guide.org/en/latest/dev/virtualenvs/) may be of use to > you. If I recall correctly, once the virtual env is enabled/setup, any > packages are installed to a custom directory. This should let you bypass > the root access. > > Best regards, > > Adam > > > On Fri, Jun 19, 2015 at 11:34 AM, Will Kennerly < > the...@ya...> wrote: > >> I would like to use cclib on a (linux) computer that I do not have root >> access on. I can certainly unpack the source code archive and use "python >> setup.py build", and then "python setup.py install", the latter of which of >> course fails. >> >> Is there a particular path in the cclib subdirectory in my $HOME that I >> can add to $PYTHONPATH or use in sys.path.append() so that the cclib module >> can be imported as if it was installed by the normal method? >> >> Thank you, >> Will >> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> cclib-users mailing list >> ccl...@li... >> https://lists.sourceforge.net/lists/listinfo/cclib-users >> >> > > > ------------------------------------------------------------------------------ > Monitor 25 network devices or servers for free with OpManager! > OpManager is web-based network management software that monitors > network devices and physical & virtual servers, alerts via email & sms > for fault. Monitor 25 devices for free with no restriction. Download now > http://ad.doubleclick.net/ddm/clk/292181274;119417398;o > _______________________________________________ > cclib-users mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-users > > |
|
From: Noel O'B. <bao...@gm...> - 2015-06-23 10:23:30
|
python setup.py install --prefix=mylocalfolder, then set PYTHONPATH. On 23 June 2015 at 00:07, Adam Tenderholt <ate...@gm...> wrote: > Hi Will, > > I think that virtualenv > (http://docs.python-guide.org/en/latest/dev/virtualenvs/) may be of use to > you. If I recall correctly, once the virtual env is enabled/setup, any > packages are installed to a custom directory. This should let you bypass the > root access. > > Best regards, > > Adam > > > On Fri, Jun 19, 2015 at 11:34 AM, Will Kennerly > <the...@ya...> wrote: >> >> I would like to use cclib on a (linux) computer that I do not have root >> access on. I can certainly unpack the source code archive and use "python >> setup.py build", and then "python setup.py install", the latter of which of >> course fails. >> >> Is there a particular path in the cclib subdirectory in my $HOME that I >> can add to $PYTHONPATH or use in sys.path.append() so that the cclib module >> can be imported as if it was installed by the normal method? >> >> Thank you, >> Will >> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> cclib-users mailing list >> ccl...@li... >> https://lists.sourceforge.net/lists/listinfo/cclib-users >> > > > ------------------------------------------------------------------------------ > Monitor 25 network devices or servers for free with OpManager! > OpManager is web-based network management software that monitors > network devices and physical & virtual servers, alerts via email & sms > for fault. Monitor 25 devices for free with no restriction. Download now > http://ad.doubleclick.net/ddm/clk/292181274;119417398;o > _______________________________________________ > cclib-users mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-users > |
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From: Felix P. <fel...@un...> - 2015-06-23 09:43:18
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Hi, actually what I did was to simply set the PYTHONPATH: Konsole output export PYTHONPATH=$HOME/programs/cclib/cclib-1.3/build/lib.linux-x86_64-2.7:$PYTHONPATH That seemed to work ... Cheers, Felix On 2015-06-19 20:34, Will Kennerly wrote: > I would like to use cclib on a (linux) computer that I do not have > root access on. I can certainly unpack the source code archive and > use "python setup.py build", and then "python setup.py install", the > latter of which of course fails. > > Is there a particular path in the cclib subdirectory in my $HOME that > I can add to $PYTHONPATH or use in sys.path.append() so that the cclib > module can be imported as if it was installed by the normal method? > > Thank you, > Will > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > cclib-users mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-users |
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From: Adam T. <ate...@gm...> - 2015-06-22 23:08:06
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Hi Will, I think that virtualenv ( http://docs.python-guide.org/en/latest/dev/virtualenvs/) may be of use to you. If I recall correctly, once the virtual env is enabled/setup, any packages are installed to a custom directory. This should let you bypass the root access. Best regards, Adam On Fri, Jun 19, 2015 at 11:34 AM, Will Kennerly < the...@ya...> wrote: > I would like to use cclib on a (linux) computer that I do not have root > access on. I can certainly unpack the source code archive and use "python > setup.py build", and then "python setup.py install", the latter of which of > course fails. > > Is there a particular path in the cclib subdirectory in my $HOME that I > can add to $PYTHONPATH or use in sys.path.append() so that the cclib module > can be imported as if it was installed by the normal method? > > Thank you, > Will > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > cclib-users mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-users > > |
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From: Will K. <the...@ya...> - 2015-06-19 18:37:36
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I would like to use cclib on a (linux) computer that I do not have root access on. I can certainly unpack the source code archive and use "python setup.py build", and then "python setup.py install", the latter of which of course fails. Is there a particular path in the cclib subdirectory in my $HOME that I can add to $PYTHONPATH or use in sys.path.append() so that the cclib module can be imported as if it was installed by the normal method? Thank you, Will |
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From: Karol L. <kar...@gm...> - 2015-05-06 18:52:16
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Hi Jos, Can you provide us with the output file? If you can, we will be more than happy to fix the issue. Cheers, Karol On Wed, May 6, 2015 at 9:45 AM, Jos Teunissen <jlt...@gm...> wrote: > Dear Reader, > > When i want to parse a Gaussian output consisting of multiple steps I get > an AssertionError. Do you have any suggestions? or do i really have to > split the file first? > > Kind regards, > Jos > > The job: > %chk=hclsto.chk > # am1/sto-3g opt > > Title Card Required > > 0 1 > H 0.0 0.0 0.0 > Cl 0.0 0.0 1.1 > > --link1-- > %chk=hclsto.chk > # geom=check mp2/6-31G > > plus > > 1 2 > > > > > ------------------------------------------------------------------------------ > One dashboard for servers and applications across Physical-Virtual-Cloud > Widest out-of-the-box monitoring support with 50+ applications > Performance metrics, stats and reports that give you Actionable Insights > Deep dive visibility with transaction tracing using APM Insight. > http://ad.doubleclick.net/ddm/clk/290420510;117567292;y > _______________________________________________ > cclib-users mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-users > > |
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From: Jos T. <jlt...@gm...> - 2015-05-06 13:45:07
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Dear Reader, When i want to parse a Gaussian output consisting of multiple steps I get an AssertionError. Do you have any suggestions? or do i really have to split the file first? Kind regards, Jos The job: %chk=hclsto.chk # am1/sto-3g opt Title Card Required 0 1 H 0.0 0.0 0.0 Cl 0.0 0.0 1.1 --link1-- %chk=hclsto.chk # geom=check mp2/6-31G plus 1 2 |
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From: Felix P. <pl...@un...> - 2014-12-03 13:51:52
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Hi Karol, I am not really a TDDFT person either, so I can't say much about the physics of the Y vectors. But I think writing them into etsecs as virtual->occupied entries makes sense. Then it is clear what they are and any user of cclib can decide for themselves if and how to process them. Best, Felix On 03/12/14 02:02, Karol Langner wrote: > Hi Felix, > > I have given this some investigation and replied at length on github > where I created an issue: https://github.com/cclib/cclib/issues/154 > > In short, I see no reason to omit the Y vectors (deexcitations). They > can be parsed and stored in cclib's etsecs attribute without > modification as a virtual->occupied (de)excitation. Is there any > reason to get rid of them? > > Best, > Karol > > > On Fri, Nov 14, 2014 at 11:31 AM, Felix Plasser > <pl...@un... <mailto:pl...@un...>> wrote: > > Hi Karol, > > Sure I am happy to release these input and output files into the > public domain. Do I have to do anything special about that? > > For parsing you can also look at the corresponding code from TheoDORE: > https://sourceforge.net/p/theodore-qc/code/ci/master/tree/lib/file_parser.py#l435 > > The question in the case of RPA/TDDFT is what to do with the Y > vectors. I am just discarding them, since they are small anyway. > Otherwise you'd either have to add them, subtract them, or switch > the occupied and virtual indices to put them as a de-excitation. I > don't know ... > > Felix > > Am 14.11.2014 13:55, schrieb Karol Langner: >> Hi Felix, >> >> If you release your file into the public domain, we will be happy >> to include the file into our regression suite (and fix it, of >> course). >> >> Karol >> >> On Fri, Nov 14, 2014 at 5:45 AM, Felix Plasser >> <pl...@un... <mailto:pl...@un...>> wrote: >> >> Hi, >> >> I just wanted to let you know that cclib fails if you try to >> parse a >> TDDFT/RPA (rather than TDDFT/TDA) file produced by Q-Chem >> with cclib. >> >> Input file: >> >> $rem >> method = b3lyp >> basis = sto-3g >> cis_n_roots = 5 >> cis_ampl_print 1 >> rpa = true >> $end >> >> $molecule >> 0 1 >> C 0.27867948 -1.36683162 0.00000000 >> C 1.32303041 -0.44173575 0.00000000 >> C 1.04434506 0.92484978 0.00000000 >> C -0.27867948 1.36683162 0.00000000 >> C -1.32303041 0.44173575 0.00000000 >> C -1.04434506 -0.92484978 0.00000000 >> H 2.36595443 -0.79037726 0.00000000 >> H 1.86746094 1.65407997 0.00000000 >> H -2.36595443 0.79037726 0.00000000 >> H -1.86746094 -1.65407997 0.00000000 >> C -0.58659169 2.87589931 0.00000000 >> C 0.36350188 3.80076420 0.00000000 >> H -1.65647768 3.12394312 0.00000000 >> H 0.14429560 4.87693235 0.00000000 >> H 1.43338788 3.55272039 0.00000000 >> C 0.58659169 -2.87589931 0.00000000 >> C -0.36350188 -3.80076420 0.00000000 >> H 1.65647768 -3.12394312 0.00000000 >> H -0.14429560 -4.87693235 0.00000000 >> H -1.43338788 -3.55272039 0.00000000 >> $end >> >> output file: >> https://ccuw.iwr.uni-heidelberg.de/UnsereWolke/public.php?service=files&t=6647292656910525f1902c5014518886 >> >> The program apparently fails when it tries to parse lines of >> the type >> X: D( 12) --> V( 13) amplitude = 0.0162 >> The difference is that in the RPA case, it has to be >> specified whether >> one talks about the X or Y vector >> >> Cheers, >> Felix >> >> -- >> Felix Plasser >> Interdisciplinary Center for Scientific Computing >> Ruprecht-Karls-University >> Im Neuenheimer Feld 368 >> 69120 Heidelberg >> Mobile: +49-151-651 27211 <tel:%2B49-151-651%2027211> >> E-mail: pl...@un... >> <mailto:pl...@un...> >> http://www.iwr.uni-heidelberg.de/groups/compchem/personal/felix_plasser >> >> >> ------------------------------------------------------------------------------ >> Comprehensive Server Monitoring with Site24x7. >> Monitor 10 servers for $9/Month. >> Get alerted through email, SMS, voice calls or mobile push >> notifications. >> Take corrective actions from your mobile device. >> http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk >> _______________________________________________ >> cclib-users mailing list >> ccl...@li... >> <mailto:ccl...@li...> >> https://lists.sourceforge.net/lists/listinfo/cclib-users >> >> > -- Felix Plasser Interdisciplinary Center for Scientific Computing Ruprecht-Karls-University Im Neuenheimer Feld 368 69120 Heidelberg Mobile: +49-151-651 27211 E-mail: pl...@un... http://www.iwr.uni-heidelberg.de/groups/compchem/personal/felix_plasser |
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From: Karol L. <kar...@gm...> - 2014-12-03 01:02:22
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Hi Felix, I have given this some investigation and replied at length on github where I created an issue: https://github.com/cclib/cclib/issues/154 In short, I see no reason to omit the Y vectors (deexcitations). They can be parsed and stored in cclib's etsecs attribute without modification as a virtual->occupied (de)excitation. Is there any reason to get rid of them? Best, Karol On Fri, Nov 14, 2014 at 11:31 AM, Felix Plasser <pl...@un...> wrote: > Hi Karol, > > Sure I am happy to release these input and output files into the public > domain. Do I have to do anything special about that? > > For parsing you can also look at the corresponding code from TheoDORE: > > https://sourceforge.net/p/theodore-qc/code/ci/master/tree/lib/file_parser.py#l435 > > The question in the case of RPA/TDDFT is what to do with the Y vectors. I > am just discarding them, since they are small anyway. Otherwise you'd > either have to add them, subtract them, or switch the occupied and virtual > indices to put them as a de-excitation. I don't know ... > > Felix > > Am 14.11.2014 13:55, schrieb Karol Langner: > > Hi Felix, > > If you release your file into the public domain, we will be happy to > include the file into our regression suite (and fix it, of course). > > Karol > > On Fri, Nov 14, 2014 at 5:45 AM, Felix Plasser <pl...@un...> > wrote: > >> Hi, >> >> I just wanted to let you know that cclib fails if you try to parse a >> TDDFT/RPA (rather than TDDFT/TDA) file produced by Q-Chem with cclib. >> >> Input file: >> >> $rem >> method = b3lyp >> basis = sto-3g >> cis_n_roots = 5 >> cis_ampl_print 1 >> rpa = true >> $end >> >> $molecule >> 0 1 >> C 0.27867948 -1.36683162 0.00000000 >> C 1.32303041 -0.44173575 0.00000000 >> C 1.04434506 0.92484978 0.00000000 >> C -0.27867948 1.36683162 0.00000000 >> C -1.32303041 0.44173575 0.00000000 >> C -1.04434506 -0.92484978 0.00000000 >> H 2.36595443 -0.79037726 0.00000000 >> H 1.86746094 1.65407997 0.00000000 >> H -2.36595443 0.79037726 0.00000000 >> H -1.86746094 -1.65407997 0.00000000 >> C -0.58659169 2.87589931 0.00000000 >> C 0.36350188 3.80076420 0.00000000 >> H -1.65647768 3.12394312 0.00000000 >> H 0.14429560 4.87693235 0.00000000 >> H 1.43338788 3.55272039 0.00000000 >> C 0.58659169 -2.87589931 0.00000000 >> C -0.36350188 -3.80076420 0.00000000 >> H 1.65647768 -3.12394312 0.00000000 >> H -0.14429560 -4.87693235 0.00000000 >> H -1.43338788 -3.55272039 0.00000000 >> $end >> >> output file: >> >> https://ccuw.iwr.uni-heidelberg.de/UnsereWolke/public.php?service=files&t=6647292656910525f1902c5014518886 >> >> The program apparently fails when it tries to parse lines of the type >> X: D( 12) --> V( 13) amplitude = 0.0162 >> The difference is that in the RPA case, it has to be specified whether >> one talks about the X or Y vector >> >> Cheers, >> Felix >> >> -- >> Felix Plasser >> Interdisciplinary Center for Scientific Computing >> Ruprecht-Karls-University >> Im Neuenheimer Feld 368 >> 69120 Heidelberg >> Mobile: +49-151-651 27211 >> E-mail: pl...@un... >> http://www.iwr.uni-heidelberg.de/groups/compchem/personal/felix_plasser >> >> >> >> ------------------------------------------------------------------------------ >> Comprehensive Server Monitoring with Site24x7. >> Monitor 10 servers for $9/Month. >> Get alerted through email, SMS, voice calls or mobile push notifications. >> Take corrective actions from your mobile device. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk >> _______________________________________________ >> cclib-users mailing list >> ccl...@li... >> https://lists.sourceforge.net/lists/listinfo/cclib-users >> > > |
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From: Felix P. <pl...@un...> - 2014-11-14 16:32:22
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Hi Karol, Sure I am happy to release these input and output files into the public domain. Do I have to do anything special about that? For parsing you can also look at the corresponding code from TheoDORE: https://sourceforge.net/p/theodore-qc/code/ci/master/tree/lib/file_parser.py#l435 The question in the case of RPA/TDDFT is what to do with the Y vectors. I am just discarding them, since they are small anyway. Otherwise you'd either have to add them, subtract them, or switch the occupied and virtual indices to put them as a de-excitation. I don't know ... Felix Am 14.11.2014 13:55, schrieb Karol Langner: > Hi Felix, > > If you release your file into the public domain, we will be happy to > include the file into our regression suite (and fix it, of course). > > Karol > > On Fri, Nov 14, 2014 at 5:45 AM, Felix Plasser > <pl...@un... <mailto:pl...@un...>> wrote: > > Hi, > > I just wanted to let you know that cclib fails if you try to parse a > TDDFT/RPA (rather than TDDFT/TDA) file produced by Q-Chem with cclib. > > Input file: > > $rem > method = b3lyp > basis = sto-3g > cis_n_roots = 5 > cis_ampl_print 1 > rpa = true > $end > > $molecule > 0 1 > C 0.27867948 -1.36683162 0.00000000 > C 1.32303041 -0.44173575 0.00000000 > C 1.04434506 0.92484978 0.00000000 > C -0.27867948 1.36683162 0.00000000 > C -1.32303041 0.44173575 0.00000000 > C -1.04434506 -0.92484978 0.00000000 > H 2.36595443 -0.79037726 0.00000000 > H 1.86746094 1.65407997 0.00000000 > H -2.36595443 0.79037726 0.00000000 > H -1.86746094 -1.65407997 0.00000000 > C -0.58659169 2.87589931 0.00000000 > C 0.36350188 3.80076420 0.00000000 > H -1.65647768 3.12394312 0.00000000 > H 0.14429560 4.87693235 0.00000000 > H 1.43338788 3.55272039 0.00000000 > C 0.58659169 -2.87589931 0.00000000 > C -0.36350188 -3.80076420 0.00000000 > H 1.65647768 -3.12394312 0.00000000 > H -0.14429560 -4.87693235 0.00000000 > H -1.43338788 -3.55272039 0.00000000 > $end > > output file: > https://ccuw.iwr.uni-heidelberg.de/UnsereWolke/public.php?service=files&t=6647292656910525f1902c5014518886 > <https://ccuw.iwr.uni-heidelberg.de/UnsereWolke/public.php?service=files&t=6647292656910525f1902c5014518886> > > The program apparently fails when it tries to parse lines of the type > X: D( 12) --> V( 13) amplitude = 0.0162 > The difference is that in the RPA case, it has to be specified whether > one talks about the X or Y vector > > Cheers, > Felix > > -- > Felix Plasser > Interdisciplinary Center for Scientific Computing > Ruprecht-Karls-University > Im Neuenheimer Feld 368 > 69120 Heidelberg > Mobile: +49-151-651 27211 > E-mail: pl...@un... <mailto:pl...@un...> > http://www.iwr.uni-heidelberg.de/groups/compchem/personal/felix_plasser > > > ------------------------------------------------------------------------------ > Comprehensive Server Monitoring with Site24x7. > Monitor 10 servers for $9/Month. > Get alerted through email, SMS, voice calls or mobile push > notifications. > Take corrective actions from your mobile device. > http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk > <http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk> > _______________________________________________ > cclib-users mailing list > ccl...@li... > <mailto:ccl...@li...> > https://lists.sourceforge.net/lists/listinfo/cclib-users > > |
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From: Karol L. <kar...@gm...> - 2014-11-14 12:56:03
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Hi Felix, If you release your file into the public domain, we will be happy to include the file into our regression suite (and fix it, of course). Karol On Fri, Nov 14, 2014 at 5:45 AM, Felix Plasser <pl...@un...> wrote: > Hi, > > I just wanted to let you know that cclib fails if you try to parse a > TDDFT/RPA (rather than TDDFT/TDA) file produced by Q-Chem with cclib. > > Input file: > > $rem > method = b3lyp > basis = sto-3g > cis_n_roots = 5 > cis_ampl_print 1 > rpa = true > $end > > $molecule > 0 1 > C 0.27867948 -1.36683162 0.00000000 > C 1.32303041 -0.44173575 0.00000000 > C 1.04434506 0.92484978 0.00000000 > C -0.27867948 1.36683162 0.00000000 > C -1.32303041 0.44173575 0.00000000 > C -1.04434506 -0.92484978 0.00000000 > H 2.36595443 -0.79037726 0.00000000 > H 1.86746094 1.65407997 0.00000000 > H -2.36595443 0.79037726 0.00000000 > H -1.86746094 -1.65407997 0.00000000 > C -0.58659169 2.87589931 0.00000000 > C 0.36350188 3.80076420 0.00000000 > H -1.65647768 3.12394312 0.00000000 > H 0.14429560 4.87693235 0.00000000 > H 1.43338788 3.55272039 0.00000000 > C 0.58659169 -2.87589931 0.00000000 > C -0.36350188 -3.80076420 0.00000000 > H 1.65647768 -3.12394312 0.00000000 > H -0.14429560 -4.87693235 0.00000000 > H -1.43338788 -3.55272039 0.00000000 > $end > > output file: > > https://ccuw.iwr.uni-heidelberg.de/UnsereWolke/public.php?service=files&t=6647292656910525f1902c5014518886 > > The program apparently fails when it tries to parse lines of the type > X: D( 12) --> V( 13) amplitude = 0.0162 > The difference is that in the RPA case, it has to be specified whether > one talks about the X or Y vector > > Cheers, > Felix > > -- > Felix Plasser > Interdisciplinary Center for Scientific Computing > Ruprecht-Karls-University > Im Neuenheimer Feld 368 > 69120 Heidelberg > Mobile: +49-151-651 27211 > E-mail: pl...@un... > http://www.iwr.uni-heidelberg.de/groups/compchem/personal/felix_plasser > > > > ------------------------------------------------------------------------------ > Comprehensive Server Monitoring with Site24x7. > Monitor 10 servers for $9/Month. > Get alerted through email, SMS, voice calls or mobile push notifications. > Take corrective actions from your mobile device. > > http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk > _______________________________________________ > cclib-users mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-users > |
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From: Felix P. <pl...@un...> - 2014-11-14 10:46:25
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Hi, I just wanted to let you know that cclib fails if you try to parse a TDDFT/RPA (rather than TDDFT/TDA) file produced by Q-Chem with cclib. Input file: $rem method = b3lyp basis = sto-3g cis_n_roots = 5 cis_ampl_print 1 rpa = true $end $molecule 0 1 C 0.27867948 -1.36683162 0.00000000 C 1.32303041 -0.44173575 0.00000000 C 1.04434506 0.92484978 0.00000000 C -0.27867948 1.36683162 0.00000000 C -1.32303041 0.44173575 0.00000000 C -1.04434506 -0.92484978 0.00000000 H 2.36595443 -0.79037726 0.00000000 H 1.86746094 1.65407997 0.00000000 H -2.36595443 0.79037726 0.00000000 H -1.86746094 -1.65407997 0.00000000 C -0.58659169 2.87589931 0.00000000 C 0.36350188 3.80076420 0.00000000 H -1.65647768 3.12394312 0.00000000 H 0.14429560 4.87693235 0.00000000 H 1.43338788 3.55272039 0.00000000 C 0.58659169 -2.87589931 0.00000000 C -0.36350188 -3.80076420 0.00000000 H 1.65647768 -3.12394312 0.00000000 H -0.14429560 -4.87693235 0.00000000 H -1.43338788 -3.55272039 0.00000000 $end output file: https://ccuw.iwr.uni-heidelberg.de/UnsereWolke/public.php?service=files&t=6647292656910525f1902c5014518886 The program apparently fails when it tries to parse lines of the type X: D( 12) --> V( 13) amplitude = 0.0162 The difference is that in the RPA case, it has to be specified whether one talks about the X or Y vector Cheers, Felix -- Felix Plasser Interdisciplinary Center for Scientific Computing Ruprecht-Karls-University Im Neuenheimer Feld 368 69120 Heidelberg Mobile: +49-151-651 27211 E-mail: pl...@un... http://www.iwr.uni-heidelberg.de/groups/compchem/personal/felix_plasser |
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From: Adam T. <ate...@gm...> - 2014-11-01 16:28:12
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On behalf of the cclib development team, we are pleased to announce the release of cclib 1.3, which is now available for download from http://cclib.github.io. This version includes three new parsers (for NWchem, Psi and QChem), as well as a number of bug fixes and improvements (see below). 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, 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 the newest stable version of cclib as: Eric Berquist, Karol M. Langner, Noel M. O'Boyle, and Adam L. Tenderholt. Release of cclib version 1.3. 2014. http://dx.doi.org/10.5281/zenodo.12496. Regards, The cclib development team ——— Major changes since cclib 1.2: * New parser: cclib can now parse NWChem files * New parser: cclib can now parse Psi (versions 3 and 4) files * New parser: cclib can now parse QChem files (by Eric Berquist) * New method Nuclear, currently calculates nuclear repulsion energy * Replace PC-GAMESS tests with Firefly versions * Many bugfixes, thanks to Martin Rahm, Russell Johnson, Matt Ernst and others |
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From: Karol L. <kar...@gm...> - 2014-10-30 00:05:15
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Good to hear from you, Martin. Do you mean the file with the LZ value analysis? That is the one I put in our regression some time ago: https://raw.githubusercontent.com/cclib/cclib-data/master/GAMESS/GAMESS-US2013/N-UHF.out It should parse correctly in the upcoming release (v1.3) which is due Friday. We fixed it a while back: https://github.com/cclib/cclib/issues/130 Best regards, Karol On Wed, Oct 29, 2014 at 6:09 PM, Martin Rahm <mar...@gm...> wrote: > Hi, > > I think I brought this up earlier, and that it was concluded a bug. Has it > been fixed, and if so will it be included in the next version? > > print data.moenergies[1] > > IndexError: list index out of range > > > Thanks, > > Martin > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > cclib-users mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-users > > |
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