cclib-users — Help and support for cclib users

[cclib-users] Mailing list moved to new home

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

Dear cclib users,

Please note that this mailing list has been moved to Google Groups:
https://groups.google.com/g/cclib

Yo can send future questions or reports directly to cc...@go...

Thanks,
cclib developers

[cclib-users] Release 1.7.1

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

Hello everyone,

It's my pleasure to let you know that we recently released v1.7.1 of cclib.
The main improvements this time around were one new parser (formatted
checkpoint files) and a few new attributes (related NMR chemical shielding
tensors).

You can find the release and all details at:
https://github.com/cclib/cclib/releases/tag/v1.7.1

Best regards,
cclib developers

[cclib-users] Release 1.7!

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

Hello everyone,

It's my pleasure to let you know that we recently released v1.7 of cclib.
The main change for this release (not the minor version change) is letting
go of Python2 support.

You can find the release and all details at:
https://github.com/cclib/cclib/releases/tag/v1.7

Best regards,
cclib developers

[cclib-users] Issues in for loops?

[Henry K. <doc...@gm...>]

Hi all,

I am trying to get the parser to move through a list of filenames stored in
a text file by simply adapting the provided example in the documentation
(see below). The text files are organized with a new line after each output
file.

with open('filenames.txt', 'r') as pfiles:
for line in pfiles:
data = cclib.io.ccread(line)
print(data.natom)

However, print(data.natom), returns:

AttributeError: 'NoneType' object has no attribute 'natom'


An analogous expression is not inundated with this issue and provides the
anticipated output (see below). I fail to see why this for loop would throw
off the read. Any help or input would be greatly appreciated.



filename = compound_condensate_5.out

data = cclib.io.ccread(filename)

data.natom.


Kind Regards,

Henry

[cclib-users] v1.7 and dropping Python2 support

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

Hello everyone,

We had a dev meeting recently and decided that we will accelerate our
sunsetting of support for Python2. We're going to drop Python2 in the
coming days in master, and plan to release v1.7 in about two weeks. This
will let us clean up the codebase and make future development easier.

If anyone has concerns about dropping Python2, please reach out to us.

Thank you,
cclib dev team

[cclib-users] cclib-v1.6.4 is now out!

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

Hello everyone,

I recently finalized the v1.6.4 release. Here are the links:
GitHub: https://github.com/cclib/cclib/releases/tag/v1.6.4
PyPI: https://pypi.org/project/cclib
Conda: https://anaconda.org/conda-forge/cclib

Thanks for all the work!

Karol

Re: [cclib-users] Fwd: Issue with moldenwriter

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

Hi David,

Sorry for the late reply. Are you able to contribute a logfile so that we
can reproduce this and keep it tested going forward?

Feel free to also move the discussion to a an issue on GitHub:
https://github.com/cclib/cclib/issues

Karol

On Sat, Aug 8, 2020 at 10:00 PM David Zigler <dfz...@gm...> wrote:

>
> Hi cclib Developers,
> I encountered an issue with ccwrite when the outputype is set to 'molden'
> or 'wfz'. The error and trace back are below. The issue appears to be with
> handling spin-unrestricted orbital sets. Open shell systems give the error,
> and closed shell systems generate only the alpha set, no beta. By checking
> the attributes, ccread appears to read and parse the files (gamess.log)
> perfectly. I've been able to write my own python script to use the ccread
> output to generate correctly formatted molden files, but it's not obvious
> to me why moldenwriter.py is passing the index error.
>
> ---------------------------------------------------------------------------
>
> IndexError                                Traceback (most recent call last)<ipython-input-50-a9f587f2ced0> in <module>     13             mldndest = join(root,mldndest)     14             gmslogObj = ccread(gmslogpath)---> 15             mldnObj = ccwrite(gmslogObj,'molden',mldndest)     16      17
> ~\.conda\envs\compchem\lib\site-packages\cclib\io\ccio.py in ccwrite(ccobj, outputtype, outputdest, indices, terse, returnstr, *args, **kwargs)    379                             indices=indices, terse=terse,    380                             *args, **kwargs)--> 381     output = outputobj.generate_repr()    382     383     # If outputdest isn't None, write the output to disk.
> ~\.conda\envs\compchem\lib\site-packages\cclib\io\moldenwriter.py in generate_repr(self)    209     210             molden_lines.append('[MO]')--> 211             molden_lines.extend(self._mo_from_ccdata())    212     213         # Omitting until issue #390 is resolved.
> ~\.conda\envs\compchem\lib\site-packages\cclib\io\moldenwriter.py in _mo_from_ccdata(self)    164         spin = 'Alpha'    165         for i in range(mult):--> 166             for j in range(len(moenergies[i])):    167                 if has_syms:    168                     lines.append(' Sym= %s' % syms[i][j])
> IndexError: list index out of range
>
> ```
>
> Sincerely,
> Dave
>
> David F. Zigler, Ph.D.
> Assistant Professor
> Department of Chemistry and Biochemistry
> California Polytechnic State University
> San Luis Obispo, CA
> dfz...@gm...
> Office:   805-756-2661
>
> https://github.com/cpdfzigler
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

[cclib-users] Fwd: Issue with moldenwriter

[David Z. <dfz...@gm...>]

Hi cclib Developers,
I encountered an issue with ccwrite when the outputype is set to 'molden'
or 'wfz'. The error and trace back are below. The issue appears to be with
handling spin-unrestricted orbital sets. Open shell systems give the error,
and closed shell systems generate only the alpha set, no beta. By checking
the attributes, ccread appears to read and parse the files (gamess.log)
perfectly. I've been able to write my own python script to use the ccread
output to generate correctly formatted molden files, but it's not obvious
to me why moldenwriter.py is passing the index error.

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

IndexError                                Traceback (most recent call
last)<ipython-input-50-a9f587f2ced0> in <module>     13
mldndest = join(root,mldndest)     14             gmslogObj =
ccread(gmslogpath)---> 15             mldnObj =
ccwrite(gmslogObj,'molden',mldndest)     16      17
~\.conda\envs\compchem\lib\site-packages\cclib\io\ccio.py in
ccwrite(ccobj, outputtype, outputdest, indices, terse, returnstr,
*args, **kwargs)    379                             indices=indices,
terse=terse,    380                             *args, **kwargs)-->
381     output = outputobj.generate_repr()    382     383     # If
outputdest isn't None, write the output to disk.
~\.conda\envs\compchem\lib\site-packages\cclib\io\moldenwriter.py in
generate_repr(self)    209     210
molden_lines.append('[MO]')--> 211
molden_lines.extend(self._mo_from_ccdata())    212     213         #
Omitting until issue #390 is resolved.
~\.conda\envs\compchem\lib\site-packages\cclib\io\moldenwriter.py in
_mo_from_ccdata(self)    164         spin = 'Alpha'    165         for
i in range(mult):--> 166             for j in
range(len(moenergies[i])):    167                 if has_syms:    168
                   lines.append(' Sym= %s' % syms[i][j])
IndexError: list index out of range

```

Sincerely,
Dave

David F. Zigler, Ph.D.
Assistant Professor
Department of Chemistry and Biochemistry
California Polytechnic State University
San Luis Obispo, CA
dfz...@gm...
Office:   805-756-2661

https://github.com/cpdfzigler

[cclib-users] cclib-v1.6.3 is now published!

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

Hello everyone,

I just finalized the v1.6.3 release:
https://github.com/cclib/cclib/releases/tag/v1.6.3. The new version is now
also available in pypi <https://pypi.org/project/cclib/> and conda
<https://anaconda.org/conda-forge/cclib>.

Thanks for all the work, and I think we'll do another release after the
summer when Minsik's GSOC project is finished.

Karol

[cclib-users] Release 1.6.2 is out

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

Hi everyone,

I just finalized the 1.6.2 release now:
https://github.com/cclib/cclib/releases/tag/v1.6.2

It's mostly bugfixes and such. For v1.6.3, I'd like to whittle down the
number of PRs and issues we have, some of which have been around for just
too long and are lingering and inactive. I'd also like to catch up a bit
with the documentation and dev guidelines, so it's clear how we contribute
and what others need to do if they want to contribute. With the project
more clean, hopefully it'll be easier to work towards a 2.x version with
some major changes, which I think are really needed after 10 years :)

Best,
Karol

[cclib-users] Version 1.6.1 is out!

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

Hi all,

I just finished up the v1.6.1 release:
https://github.com/cclib/cclib/releases/tag/v1.6.1

I also uploaded to PyPI, and I noticed it has been picked up by conda-forge
(https://github.com/conda-forge/cclib-feedstock/pull/1). So that's that.
Let me know if I missed something in the release process.

Thanks for all the work. And on to v1.6.2!

- Karol

[cclib-users] Version 1.6 is released!

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

Hello cclibers,

I just completed the v1.6 release on GitHub and PyPI. This is a minor
version increment (previous was v1.5.3), because we have some new parsers...

Speaking of which, this version includes most of the GSOC 2018 work done by
Kunal over the summer. We had a great time working with him, and I think he
was quite productive. As a result, cclib now has some degree of support for
both Molcas and Turbomole. Thanks Kunal!

Summary of changes since last version:
 - New parser: cclib can now parse Molcas files (Kunal Sharma)
 - New parser: cclib can now parse Turbomole files (Christopher Rowley,
Kunal Sharma)
 - New script: ccframe writes data table files from logfiles (Felipe
Schneider)
 - Support time attribute and BOMD output in Gaussian, NWChem, ORCA and
QChem
 - Support package version in metadata for most parsers
 - Many other minor improvements and bug fixes from Jonathon Vandezande,
Jaime Rodríguez-Guerra and others

I would also add that we now have documentation that automatically builds
and updates after each commit (and sources are alongside the code), thanks
to Eric Berquist's work. This is a very positive change in my mind, and I
hope the docs will continue improving in quality.

As always, the main place to coordinate future work is GitHub:
https://github.com/cclib/cclib

Best,
Karol

[cclib-users] Version 1.5.3 just release

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

Hi all,

I just published v1.5.3 in GitHub, merged it into master and uploaded to
PyPI. We'll now be working to fix as many additional things for v1.5.4 and
get that out before GSOC 2018 starts in May.

Best,
Karol

Re: [cclib-users] Interested in GSoC Mentorship

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

Hi Somesh,

In that case I suppose what we'd like to see in the application is what you
think the main goals of this project should be, and how you want to get
there. It's not immediately obvious how that paper builds into a
just-scraping project, but of course we're open to modifying the project or
even an entirely new idea, especially if it's connected to earlier research.

I would encourage you to try out cclib a bit in practice - try parsing some
logfiles, try looking for some online and parsing those. For scraping
itself, there are a lot of non-compchem tools out there that can be used,
and any demo code you can put together during the application period would
also be an advantage. There are also many compchem databases and
repositories already online, so it's also important how those would fit
into a crawler/scraper ecosystem.

I would also encourage you to look around at the other OpenChemistry
projects for a while, you might find some more projects that look
interesting to you.


On Tue, Feb 20, 2018 at 7:13 AM, Somesh Mohapatra <pik...@gm...>
wrote:

> Apart from enlisting, we can also go on similar lines as the following
> paper -
>
> https://www.nature.com/articles/s41524-017-0055-6
>
> This work is by the lab I am looking forward to join at MIT, so that makes
> the GSoC project a hands on experience prior to starting there.
>
> Somesh.
>
>
> On Feb 20, 2018 8:39 PM, "Somesh Mohapatra" <pik...@gm...> wrote:
>
> Hi Karol
>
> Yes, that is the one.
>
> Somesh.
>
>
> On Feb 20, 2018 8:36 PM, "Karol Langner" <kar...@gm...> wrote:
>
> Hi Somesh,
>
> Nice to hear from you. Which project is the "content enlisting project"?
> Do you mean the cclib web scraper?
>
> - Karol
>
> On Sun, Feb 18, 2018 at 2:09 AM, Somesh Mohapatra <pik...@gm...>
> wrote:
>
>> Dear Karol
>>
>> I have recently been accepted to MIT for PhD in Materials Science, and
>> looking forward to be a part of GSoC over the Summer of 2018. I have
>> earlier worked on Computational Materials Science and simulations for my
>> projects (Resume, attached), and then on Bioinformatics and Computational
>> Biology.
>>
>> I am looking forward to hone my coding skills and contribute to the
>> Computational Chemistry content enlisting project. I am open to
>> understanding other projects as well, if you see that based on my skillset,
>> I would be a better fit in another work.
>>
>> Looking forward to discuss more on the possibilities!
>>
>> Somesh Mohapatra
>> Graduate Student (Fall 18)
>> Department of Materials Science and Engineering
>> Massachusetts Institute of Technology
>> Contact - +91 7060 33 45 66
>> E-Mail - pik...@gm...
>> Website - someshmohapatra.in
>> ᐧ
>>
>
>
>
>

[cclib-users] Fwd: [Avogadro Discussion] [General Discussion] Avogadro Part of Google Summer of Code 2018

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

Great to see OpenChemistry participating again. Like last year, cclib is
part of it and we have a number of great project ideas for cclib ready for
students!

---------- Forwarded message ----------
From: Geoff Hutchison <no...@ma...>
Date: Mon, Feb 12, 2018 at 11:12 AM
Subject: [Avogadro Discussion] [General Discussion] Avogadro Part of Google
Summer of Code 2018
To: kar...@gm...


ghutchis <https://discuss.avogadro.cc/u/ghutchis>
February 12

As in the last 2 years, Avogadro is thrilled to be part of Google Summer of
Code 2018 as part of Open Chemistry:
https://summerofcode.withgoogle.com/organizations/6513013473935360/

We’re looking for some great students and great ideas… Some are listed
here, but new ideas are also welcome (including from the community - i.e.,
*you*)
http://wiki.openchemistry.org/GSoC_Ideas_2018

Got a good idea you’d like to see in Avogadro?
------------------------------

Visit Topic
<https://discuss.avogadro.cc/t/avogadro-part-of-google-summer-of-code-2018/2622/1>
or reply to this email to respond.

To unsubscribe from these emails, click here
<https://discuss.avogadro.cc/email/unsubscribe/9dad6296cea49a4bce9469e0dfab7eed39f52b7bc320fe1636dd7856979168d0>
.

[cclib-users] cclib applying for Google Summer of Code

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

Hello,

Like last year, cclib is working with Open Chemistry to apply for the
Google Summer of Code 2018. If you're interested in participating or have
some ideas for fun student projects, please let us know.

Re: [cclib-users] Problem with the parser when going from 1.3 --> 1.5

[Martin R. <mar...@gm...>]

Alright, thanks Adam.

Then I am sorry to bother you with this request for clarification:

I was under the impression that cclib per default considers the last sets
of energies if there are multiple sepparate jobs in a file. For instance,
if several scf calculations have proceeded in a geometry optimization run,
that it is the last set that is parsed.

If inputfile is a file with several jobs in it, such as my N2 example, or
any general opt+freq run, and I write

data = ccopen(inputfile)

data = data.parse()

energies_alpha=data.moenergies[0]


Then the size of the array data.moenergies is one. There is only one set of
orbital energies, and those are the one of the last successful calculation,
no?


Thanks again,

Martin



On Tue, Dec 5, 2017 at 1:02 AM, Adam Tenderholt <ate...@gm...>
wrote:

> Hi Martin,
>
> Eric looked at your files, and says that there appear to be multiple jobs
> in a single file: https://github.com/cclib/cclib/issues/453. Generally,
> it's best to run things as separate jobs. Let us know if we're missing
> something, or if you have any other questions or problems.
>
> Best regards,
>
> Adam
>
>
> On Wed, Nov 29, 2017 at 6:57 AM Adam Tenderholt <ate...@gm...>
> wrote:
>
>> Thanks for sharing the files. I've created an issue on Github:
>> https://github.com/cclib/cclib/issues/453.
>>
>>
>> On Wed, Nov 29, 2017 at 6:49 AM Martin Rahm <mar...@gm...>
>> wrote:
>>
>>> Hi Adam,
>>>
>>> I resolved most of my problems. A few peculiarities remain, likely
>>> minor:
>>>
>>> N2 with ORCA runs OK, but results in the following warnings (not seen in
>>> some other orca output):
>>>
>>> [ORCA ['./X-analysis_pyt3.py', 'N2.out'] WARNING] The geotargets
>>> attribute should not exist yet. There is a problem in the parser.
>>>
>>> [ORCA ['./X-analysis_pyt3.py', 'N2.out'] WARNING] The geotargets
>>> attribute should not exist yet. There is a problem in the parser.
>>>
>>> [ORCA ['./X-analysis_pyt3.py', 'N2.out'] WARNING] Modes corresponding to
>>> rotations/translations may be non-zero.
>>>
>>>
>>> NCNO2 with ORCA runs OK, but results in the following warnings (not seen
>>> in some other orca output):
>>>
>>> [ORCA ['./X-analysis_pyt3_v2.py', 'NCNO2-12.out'] WARNING] Attribute
>>> atomnos changed value ([7, 6, 6, 8, 8] -> [7, 6, 7, 8, 8])
>>>
>>> [ORCA ['./X-analysis_pyt3_v2.py', 'NCNO2-12.out'] WARNING] The
>>> geotargets attribute should not exist yet. There is a problem in the parser.
>>>
>>>
>>> I do not think these affect my script output, but would still like to
>>> know what they refer to.. Have you seen this before? The two output files
>>> are attached, along with the script (remove .txt and unzip).
>>>
>>> Thanks for the help, and, as always, for cclib.
>>>
>>>
>>> Best regards,
>>>
>>> Martin
>>>
>>> On Wed, Nov 29, 2017 at 3:40 PM, Adam Tenderholt <ate...@gm...>
>>> wrote:
>>>
>>>> Yes, keep us posted if the new version works for you. Also, I think we
>>>> push releases to PyPI so you should be able to install easily with pip.
>>>>
>>>>
>>>> On Wed, Nov 29, 2017 at 1:40 AM Martin Rahm <mar...@gm...>
>>>> wrote:
>>>>
>>>>> My bad, Google didn't show me https://github.com/cclib/cclib/releases
>>>>> at first.
>>>>>
>>>>> I will try, and get back to you.
>>>>>
>>>>> You might want to update the other webpage though, and maybe remove
>>>>> the older http://cclib.sourceforge.net/wiki/index.php/Main_Page
>>>>>
>>>>> Thanks,
>>>>> Martin
>>>>>
>>>>> On Wed, Nov 29, 2017 at 10:31 AM, Martin Rahm <mar...@gm...>
>>>>> wrote:
>>>>>
>>>>>> Hi Adam,
>>>>>>
>>>>>> I am using 1.5, which I thought was the latest (according to
>>>>>> https://cclib.github.io/how_to_install.html)
>>>>>>
>>>>>> The source code of the newest release of cclib (version 1.5) is
>>>>>> distributed as:
>>>>>>
>>>>>>    - A .tar.gz file: https://github.com/
>>>>>>    cclib/cclib/releases/download/v1.5/cclib-1.5.post1.tar.gz
>>>>>>    <https://github.com/cclib/cclib/releases/download/v1.5/cclib-1.5.post1.tar.gz>
>>>>>>
>>>>>> Where can the even newer versions be found?
>>>>>>
>>>>>> Best,
>>>>>> Martin
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, Nov 28, 2017 at 6:32 PM, Adam Tenderholt <
>>>>>> ate...@gm...> wrote:
>>>>>>
>>>>>>> Are you using 1.5? Or one of the newer releases like 1.5.2? If
>>>>>>> you're still having problems with the latest release, are you able to share
>>>>>>> your file for some debugging?
>>>>>>>
>>>>>>> On Tue, Nov 28, 2017 at 12:11 AM Martin Rahm <mar...@gm...>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi cclib-lovers,
>>>>>>>>
>>>>>>>> I've recently updated from 1.3 to 1.5, and I'm seeing some
>>>>>>>> peculiarities with the basic parsing. Maybe this has been explained
>>>>>>>> somewhere, and if so I apologize. I have been unable to find an answer on
>>>>>>>> my own, and hope you can help. I'm running a Linux environment with Python
>>>>>>>> 3.6 (I used to run 2.7.5 so that might have affected things as well).
>>>>>>>>
>>>>>>>> from cclib.parser import ccopen
>>>>>>>>
>>>>>>>> seem to have been replaced by
>>>>>>>>
>>>>>>>> from cclib.io import ccopen
>>>>>>>>
>>>>>>>>
>>>>>>>> so the basic guide shown https://cclib.github.io/methods.html doesn't
>>>>>>>> seem to be right anymore.
>>>>>>>>
>>>>>>>>
>>>>>>>> ccopen doesn't seem to function as it used to.
>>>>>>>>
>>>>>>>> data = ccopen("file.out") results in the following error:
>>>>>>>>
>>>>>>>>
>>>>>>>> File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/io/ccio.py",
>>>>>>>> line 190, in ccopen
>>>>>>>>
>>>>>>>>     inputfile.seek(0, 0)
>>>>>>>>
>>>>>>>> AttributeError: 'FileInput' object has no attribute 'seek'
>>>>>>>>
>>>>>>>> This led me to use the (new?) functions:
>>>>>>>>
>>>>>>>> from cclib.parser import Gaussian ORCA
>>>>>>>>
>>>>>>>>
>>>>>>>> when calling
>>>>>>>>
>>>>>>>> data = ORCA("inputfile.out")
>>>>>>>>
>>>>>>>>
>>>>>>>> This seems to work, albeit sometimes with the following omnious
>>>>>>>> error messages:
>>>>>>>>
>>>>>>>> [ORCA ['./script.py', 'file.out'] WARNING] Attribute atomnos
>>>>>>>> changed value ([7, 6, 6, 8, 8] -> [7, 6, 7, 8, 8])
>>>>>>>>
>>>>>>>> [ORCA ['./script.py', 'file.out'] WARNING] The geotargets attribute
>>>>>>>> should not exist yet. There is a problem in the parser.
>>>>>>>>
>>>>>>>>
>>>>>>>> when instead calling
>>>>>>>>
>>>>>>>> data = Gaussian("file.out")
>>>>>>>>
>>>>>>>>
>>>>>>>> it proceeds to crash at the next line, which is
>>>>>>>>
>>>>>>>> data = data.parse()
>>>>>>>>
>>>>>>>>
>>>>>>>> Traceback (most recent call last):
>>>>>>>>
>>>>>>>>   File "./script.py", line 87, in <module>
>>>>>>>>
>>>>>>>>     data = data.parse()
>>>>>>>>
>>>>>>>>   File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-
>>>>>>>> packages/cclib/parser/logfileparser.py", line 301, in parse
>>>>>>>>
>>>>>>>>     self.extract(inputfile, line)
>>>>>>>>
>>>>>>>>   File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-
>>>>>>>> packages/cclib/parser/gaussianparser.py", line 163, in extract
>>>>>>>>
>>>>>>>>     line = inputfile.next()
>>>>>>>>
>>>>>>>> AttributeError: 'FileInput' object has no attribute 'next'
>>>>>>>>
>>>>>>>>
>>>>>>>> So, to sum up, my questions are:
>>>>>>>>
>>>>>>>>
>>>>>>>> 1.  Can cclib no longer automatically determine which output it is
>>>>>>>> trying to parse (ccopen could do this, and there was nothing fancy with the
>>>>>>>> output files I tried)?
>>>>>>>>
>>>>>>>>
>>>>>>>> 2. Do the the errors shown for the ORCA parser imply a real problem
>>>>>>>>
>>>>>>>>
>>>>>>>> 3. How do I get the Gaussian parser to run?
>>>>>>>>
>>>>>>>>
>>>>>>>> Many thanks,
>>>>>>>>
>>>>>>>>
>>>>>>>> Martin
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------
>>>>>>>> ------------------
>>>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>>>>>>>> _________________________________________
>>>>>>>> cclib-users mailing list
>>>>>>>> ccl...@li...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>

Re: [cclib-users] Problem with the parser when going from 1.3 --> 1.5

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

Hi Martin,

Eric looked at your files, and says that there appear to be multiple jobs
in a single file: https://github.com/cclib/cclib/issues/453. Generally,
it's best to run things as separate jobs. Let us know if we're missing
something, or if you have any other questions or problems.

Best regards,

Adam


On Wed, Nov 29, 2017 at 6:57 AM Adam Tenderholt <ate...@gm...>
wrote:

> Thanks for sharing the files. I've created an issue on Github:
> https://github.com/cclib/cclib/issues/453.
>
>
> On Wed, Nov 29, 2017 at 6:49 AM Martin Rahm <mar...@gm...> wrote:
>
>> Hi Adam,
>>
>> I resolved most of my problems. A few peculiarities remain, likely minor:
>>
>> N2 with ORCA runs OK, but results in the following warnings (not seen in
>> some other orca output):
>>
>> [ORCA ['./X-analysis_pyt3.py', 'N2.out'] WARNING] The geotargets
>> attribute should not exist yet. There is a problem in the parser.
>>
>> [ORCA ['./X-analysis_pyt3.py', 'N2.out'] WARNING] The geotargets
>> attribute should not exist yet. There is a problem in the parser.
>>
>> [ORCA ['./X-analysis_pyt3.py', 'N2.out'] WARNING] Modes corresponding to
>> rotations/translations may be non-zero.
>>
>>
>> NCNO2 with ORCA runs OK, but results in the following warnings (not seen
>> in some other orca output):
>>
>> [ORCA ['./X-analysis_pyt3_v2.py', 'NCNO2-12.out'] WARNING] Attribute
>> atomnos changed value ([7, 6, 6, 8, 8] -> [7, 6, 7, 8, 8])
>>
>> [ORCA ['./X-analysis_pyt3_v2.py', 'NCNO2-12.out'] WARNING] The geotargets
>> attribute should not exist yet. There is a problem in the parser.
>>
>>
>> I do not think these affect my script output, but would still like to
>> know what they refer to.. Have you seen this before? The two output files
>> are attached, along with the script (remove .txt and unzip).
>>
>> Thanks for the help, and, as always, for cclib.
>>
>>
>> Best regards,
>>
>> Martin
>>
>> On Wed, Nov 29, 2017 at 3:40 PM, Adam Tenderholt <ate...@gm...>
>> wrote:
>>
>>> Yes, keep us posted if the new version works for you. Also, I think we
>>> push releases to PyPI so you should be able to install easily with pip.
>>>
>>>
>>> On Wed, Nov 29, 2017 at 1:40 AM Martin Rahm <mar...@gm...>
>>> wrote:
>>>
>>>> My bad, Google didn't show me https://github.com/cclib/cclib/releases
>>>> at first.
>>>>
>>>> I will try, and get back to you.
>>>>
>>>> You might want to update the other webpage though, and maybe remove the
>>>> older http://cclib.sourceforge.net/wiki/index.php/Main_Page
>>>>
>>>> Thanks,
>>>> Martin
>>>>
>>>> On Wed, Nov 29, 2017 at 10:31 AM, Martin Rahm <mar...@gm...>
>>>> wrote:
>>>>
>>>>> Hi Adam,
>>>>>
>>>>> I am using 1.5, which I thought was the latest (according to
>>>>> https://cclib.github.io/how_to_install.html)
>>>>>
>>>>> The source code of the newest release of cclib (version 1.5) is
>>>>> distributed as:
>>>>>
>>>>>    - A .tar.gz file:
>>>>>    https://github.com/cclib/cclib/releases/download/v1.5/cclib-1.5.post1.tar.gz
>>>>>
>>>>> Where can the even newer versions be found?
>>>>>
>>>>> Best,
>>>>> Martin
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Nov 28, 2017 at 6:32 PM, Adam Tenderholt <
>>>>> ate...@gm...> wrote:
>>>>>
>>>>>> Are you using 1.5? Or one of the newer releases like 1.5.2? If you're
>>>>>> still having problems with the latest release, are you able to share your
>>>>>> file for some debugging?
>>>>>>
>>>>>> On Tue, Nov 28, 2017 at 12:11 AM Martin Rahm <mar...@gm...>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi cclib-lovers,
>>>>>>>
>>>>>>> I've recently updated from 1.3 to 1.5, and I'm seeing some
>>>>>>> peculiarities with the basic parsing. Maybe this has been explained
>>>>>>> somewhere, and if so I apologize. I have been unable to find an answer on
>>>>>>> my own, and hope you can help. I'm running a Linux environment with Python
>>>>>>> 3.6 (I used to run 2.7.5 so that might have affected things as well).
>>>>>>>
>>>>>>> from cclib.parser import ccopen
>>>>>>>
>>>>>>> seem to have been replaced by
>>>>>>>
>>>>>>> from cclib.io import ccopen
>>>>>>>
>>>>>>>
>>>>>>> so the basic guide shown https://cclib.github.io/methods.html doesn't
>>>>>>> seem to be right anymore.
>>>>>>>
>>>>>>>
>>>>>>> ccopen doesn't seem to function as it used to.
>>>>>>>
>>>>>>> data = ccopen("file.out") results in the following error:
>>>>>>>
>>>>>>>
>>>>>>> File
>>>>>>> "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/io/ccio.py",
>>>>>>> line 190, in ccopen
>>>>>>>
>>>>>>>     inputfile.seek(0, 0)
>>>>>>>
>>>>>>> AttributeError: 'FileInput' object has no attribute 'seek'
>>>>>>>
>>>>>>> This led me to use the (new?) functions:
>>>>>>>
>>>>>>> from cclib.parser import Gaussian ORCA
>>>>>>>
>>>>>>>
>>>>>>> when calling
>>>>>>>
>>>>>>> data = ORCA("inputfile.out")
>>>>>>>
>>>>>>>
>>>>>>> This seems to work, albeit sometimes with the following omnious
>>>>>>> error messages:
>>>>>>>
>>>>>>> [ORCA ['./script.py', 'file.out'] WARNING] Attribute atomnos changed
>>>>>>> value ([7, 6, 6, 8, 8] -> [7, 6, 7, 8, 8])
>>>>>>>
>>>>>>> [ORCA ['./script.py', 'file.out'] WARNING] The geotargets attribute
>>>>>>> should not exist yet. There is a problem in the parser.
>>>>>>>
>>>>>>>
>>>>>>> when instead calling
>>>>>>>
>>>>>>> data = Gaussian("file.out")
>>>>>>>
>>>>>>>
>>>>>>> it proceeds to crash at the next line, which is
>>>>>>>
>>>>>>> data = data.parse()
>>>>>>>
>>>>>>>
>>>>>>> Traceback (most recent call last):
>>>>>>>
>>>>>>>   File "./script.py", line 87, in <module>
>>>>>>>
>>>>>>>     data = data.parse()
>>>>>>>
>>>>>>>   File
>>>>>>> "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/parser/logfileparser.py",
>>>>>>> line 301, in parse
>>>>>>>
>>>>>>>     self.extract(inputfile, line)
>>>>>>>
>>>>>>>   File
>>>>>>> "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/parser/gaussianparser.py",
>>>>>>> line 163, in extract
>>>>>>>
>>>>>>>     line = inputfile.next()
>>>>>>>
>>>>>>> AttributeError: 'FileInput' object has no attribute 'next'
>>>>>>>
>>>>>>>
>>>>>>> So, to sum up, my questions are:
>>>>>>>
>>>>>>>
>>>>>>> 1.  Can cclib no longer automatically determine which output it is
>>>>>>> trying to parse (ccopen could do this, and there was nothing fancy with the
>>>>>>> output files I tried)?
>>>>>>>
>>>>>>>
>>>>>>> 2. Do the the errors shown for the ORCA parser imply a real problem
>>>>>>>
>>>>>>>
>>>>>>> 3. How do I get the Gaussian parser to run?
>>>>>>>
>>>>>>>
>>>>>>> Many thanks,
>>>>>>>
>>>>>>>
>>>>>>> Martin
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>> _______________________________________________
>>>>>>> cclib-users mailing list
>>>>>>> ccl...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>>>>
>>>>>>
>>>>>
>>>>
>>

Re: [cclib-users] Problem with the parser when going from 1.3 --> 1.5

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

Thanks for sharing the files. I've created an issue on Github:
https://github.com/cclib/cclib/issues/453.


On Wed, Nov 29, 2017 at 6:49 AM Martin Rahm <mar...@gm...> wrote:

> Hi Adam,
>
> I resolved most of my problems. A few peculiarities remain, likely minor:
>
> N2 with ORCA runs OK, but results in the following warnings (not seen in
> some other orca output):
>
> [ORCA ['./X-analysis_pyt3.py', 'N2.out'] WARNING] The geotargets attribute
> should not exist yet. There is a problem in the parser.
>
> [ORCA ['./X-analysis_pyt3.py', 'N2.out'] WARNING] The geotargets attribute
> should not exist yet. There is a problem in the parser.
>
> [ORCA ['./X-analysis_pyt3.py', 'N2.out'] WARNING] Modes corresponding to
> rotations/translations may be non-zero.
>
>
> NCNO2 with ORCA runs OK, but results in the following warnings (not seen
> in some other orca output):
>
> [ORCA ['./X-analysis_pyt3_v2.py', 'NCNO2-12.out'] WARNING] Attribute
> atomnos changed value ([7, 6, 6, 8, 8] -> [7, 6, 7, 8, 8])
>
> [ORCA ['./X-analysis_pyt3_v2.py', 'NCNO2-12.out'] WARNING] The geotargets
> attribute should not exist yet. There is a problem in the parser.
>
>
> I do not think these affect my script output, but would still like to know
> what they refer to.. Have you seen this before? The two output files are
> attached, along with the script (remove .txt and unzip).
>
> Thanks for the help, and, as always, for cclib.
>
>
> Best regards,
>
> Martin
>
> On Wed, Nov 29, 2017 at 3:40 PM, Adam Tenderholt <ate...@gm...>
> wrote:
>
>> Yes, keep us posted if the new version works for you. Also, I think we
>> push releases to PyPI so you should be able to install easily with pip.
>>
>>
>> On Wed, Nov 29, 2017 at 1:40 AM Martin Rahm <mar...@gm...>
>> wrote:
>>
>>> My bad, Google didn't show me https://github.com/cclib/cclib/releases
>>> at first.
>>>
>>> I will try, and get back to you.
>>>
>>> You might want to update the other webpage though, and maybe remove the
>>> older http://cclib.sourceforge.net/wiki/index.php/Main_Page
>>>
>>> Thanks,
>>> Martin
>>>
>>> On Wed, Nov 29, 2017 at 10:31 AM, Martin Rahm <mar...@gm...>
>>> wrote:
>>>
>>>> Hi Adam,
>>>>
>>>> I am using 1.5, which I thought was the latest (according to
>>>> https://cclib.github.io/how_to_install.html)
>>>>
>>>> The source code of the newest release of cclib (version 1.5) is
>>>> distributed as:
>>>>
>>>>    - A .tar.gz file:
>>>>    https://github.com/cclib/cclib/releases/download/v1.5/cclib-1.5.post1.tar.gz
>>>>
>>>> Where can the even newer versions be found?
>>>>
>>>> Best,
>>>> Martin
>>>>
>>>>
>>>>
>>>> On Tue, Nov 28, 2017 at 6:32 PM, Adam Tenderholt <ate...@gm...
>>>> > wrote:
>>>>
>>>>> Are you using 1.5? Or one of the newer releases like 1.5.2? If you're
>>>>> still having problems with the latest release, are you able to share your
>>>>> file for some debugging?
>>>>>
>>>>> On Tue, Nov 28, 2017 at 12:11 AM Martin Rahm <mar...@gm...>
>>>>> wrote:
>>>>>
>>>>>> Hi cclib-lovers,
>>>>>>
>>>>>> I've recently updated from 1.3 to 1.5, and I'm seeing some
>>>>>> peculiarities with the basic parsing. Maybe this has been explained
>>>>>> somewhere, and if so I apologize. I have been unable to find an answer on
>>>>>> my own, and hope you can help. I'm running a Linux environment with Python
>>>>>> 3.6 (I used to run 2.7.5 so that might have affected things as well).
>>>>>>
>>>>>> from cclib.parser import ccopen
>>>>>>
>>>>>> seem to have been replaced by
>>>>>>
>>>>>> from cclib.io import ccopen
>>>>>>
>>>>>>
>>>>>> so the basic guide shown https://cclib.github.io/methods.html doesn't
>>>>>> seem to be right anymore.
>>>>>>
>>>>>>
>>>>>> ccopen doesn't seem to function as it used to.
>>>>>>
>>>>>> data = ccopen("file.out") results in the following error:
>>>>>>
>>>>>>
>>>>>> File
>>>>>> "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/io/ccio.py",
>>>>>> line 190, in ccopen
>>>>>>
>>>>>>     inputfile.seek(0, 0)
>>>>>>
>>>>>> AttributeError: 'FileInput' object has no attribute 'seek'
>>>>>>
>>>>>> This led me to use the (new?) functions:
>>>>>>
>>>>>> from cclib.parser import Gaussian ORCA
>>>>>>
>>>>>>
>>>>>> when calling
>>>>>>
>>>>>> data = ORCA("inputfile.out")
>>>>>>
>>>>>>
>>>>>> This seems to work, albeit sometimes with the following omnious error
>>>>>> messages:
>>>>>>
>>>>>> [ORCA ['./script.py', 'file.out'] WARNING] Attribute atomnos changed
>>>>>> value ([7, 6, 6, 8, 8] -> [7, 6, 7, 8, 8])
>>>>>>
>>>>>> [ORCA ['./script.py', 'file.out'] WARNING] The geotargets attribute
>>>>>> should not exist yet. There is a problem in the parser.
>>>>>>
>>>>>>
>>>>>> when instead calling
>>>>>>
>>>>>> data = Gaussian("file.out")
>>>>>>
>>>>>>
>>>>>> it proceeds to crash at the next line, which is
>>>>>>
>>>>>> data = data.parse()
>>>>>>
>>>>>>
>>>>>> Traceback (most recent call last):
>>>>>>
>>>>>>   File "./script.py", line 87, in <module>
>>>>>>
>>>>>>     data = data.parse()
>>>>>>
>>>>>>   File
>>>>>> "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/parser/logfileparser.py",
>>>>>> line 301, in parse
>>>>>>
>>>>>>     self.extract(inputfile, line)
>>>>>>
>>>>>>   File
>>>>>> "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/parser/gaussianparser.py",
>>>>>> line 163, in extract
>>>>>>
>>>>>>     line = inputfile.next()
>>>>>>
>>>>>> AttributeError: 'FileInput' object has no attribute 'next'
>>>>>>
>>>>>>
>>>>>> So, to sum up, my questions are:
>>>>>>
>>>>>>
>>>>>> 1.  Can cclib no longer automatically determine which output it is
>>>>>> trying to parse (ccopen could do this, and there was nothing fancy with the
>>>>>> output files I tried)?
>>>>>>
>>>>>>
>>>>>> 2. Do the the errors shown for the ORCA parser imply a real problem
>>>>>>
>>>>>>
>>>>>> 3. How do I get the Gaussian parser to run?
>>>>>>
>>>>>>
>>>>>> Many thanks,
>>>>>>
>>>>>>
>>>>>> Martin
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>> _______________________________________________
>>>>>> cclib-users mailing list
>>>>>> ccl...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>>>
>>>>>
>>>>
>>>
>

Re: [cclib-users] Problem with the parser when going from 1.3 --> 1.5

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

Yes, keep us posted if the new version works for you. Also, I think we push
releases to PyPI so you should be able to install easily with pip.


On Wed, Nov 29, 2017 at 1:40 AM Martin Rahm <mar...@gm...> wrote:

> My bad, Google didn't show me https://github.com/cclib/cclib/releases at
> first.
>
> I will try, and get back to you.
>
> You might want to update the other webpage though, and maybe remove the
> older http://cclib.sourceforge.net/wiki/index.php/Main_Page
>
> Thanks,
> Martin
>
> On Wed, Nov 29, 2017 at 10:31 AM, Martin Rahm <mar...@gm...>
> wrote:
>
>> Hi Adam,
>>
>> I am using 1.5, which I thought was the latest (according to
>> https://cclib.github.io/how_to_install.html)
>>
>> The source code of the newest release of cclib (version 1.5) is
>> distributed as:
>>
>>    - A .tar.gz file:
>>    https://github.com/cclib/cclib/releases/download/v1.5/cclib-1.5.post1.tar.gz
>>
>> Where can the even newer versions be found?
>>
>> Best,
>> Martin
>>
>>
>>
>> On Tue, Nov 28, 2017 at 6:32 PM, Adam Tenderholt <ate...@gm...>
>> wrote:
>>
>>> Are you using 1.5? Or one of the newer releases like 1.5.2? If you're
>>> still having problems with the latest release, are you able to share your
>>> file for some debugging?
>>>
>>> On Tue, Nov 28, 2017 at 12:11 AM Martin Rahm <mar...@gm...>
>>> wrote:
>>>
>>>> Hi cclib-lovers,
>>>>
>>>> I've recently updated from 1.3 to 1.5, and I'm seeing some
>>>> peculiarities with the basic parsing. Maybe this has been explained
>>>> somewhere, and if so I apologize. I have been unable to find an answer on
>>>> my own, and hope you can help. I'm running a Linux environment with Python
>>>> 3.6 (I used to run 2.7.5 so that might have affected things as well).
>>>>
>>>> from cclib.parser import ccopen
>>>>
>>>> seem to have been replaced by
>>>>
>>>> from cclib.io import ccopen
>>>>
>>>>
>>>> so the basic guide shown https://cclib.github.io/methods.html doesn't
>>>> seem to be right anymore.
>>>>
>>>>
>>>> ccopen doesn't seem to function as it used to.
>>>>
>>>> data = ccopen("file.out") results in the following error:
>>>>
>>>>
>>>> File
>>>> "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/io/ccio.py",
>>>> line 190, in ccopen
>>>>
>>>>     inputfile.seek(0, 0)
>>>>
>>>> AttributeError: 'FileInput' object has no attribute 'seek'
>>>>
>>>> This led me to use the (new?) functions:
>>>>
>>>> from cclib.parser import Gaussian ORCA
>>>>
>>>>
>>>> when calling
>>>>
>>>> data = ORCA("inputfile.out")
>>>>
>>>>
>>>> This seems to work, albeit sometimes with the following omnious error
>>>> messages:
>>>>
>>>> [ORCA ['./script.py', 'file.out'] WARNING] Attribute atomnos changed
>>>> value ([7, 6, 6, 8, 8] -> [7, 6, 7, 8, 8])
>>>>
>>>> [ORCA ['./script.py', 'file.out'] WARNING] The geotargets attribute
>>>> should not exist yet. There is a problem in the parser.
>>>>
>>>>
>>>> when instead calling
>>>>
>>>> data = Gaussian("file.out")
>>>>
>>>>
>>>> it proceeds to crash at the next line, which is
>>>>
>>>> data = data.parse()
>>>>
>>>>
>>>> Traceback (most recent call last):
>>>>
>>>>   File "./script.py", line 87, in <module>
>>>>
>>>>     data = data.parse()
>>>>
>>>>   File
>>>> "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/parser/logfileparser.py",
>>>> line 301, in parse
>>>>
>>>>     self.extract(inputfile, line)
>>>>
>>>>   File
>>>> "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/parser/gaussianparser.py",
>>>> line 163, in extract
>>>>
>>>>     line = inputfile.next()
>>>>
>>>> AttributeError: 'FileInput' object has no attribute 'next'
>>>>
>>>>
>>>> So, to sum up, my questions are:
>>>>
>>>>
>>>> 1.  Can cclib no longer automatically determine which output it is
>>>> trying to parse (ccopen could do this, and there was nothing fancy with the
>>>> output files I tried)?
>>>>
>>>>
>>>> 2. Do the the errors shown for the ORCA parser imply a real problem
>>>>
>>>>
>>>> 3. How do I get the Gaussian parser to run?
>>>>
>>>>
>>>> Many thanks,
>>>>
>>>>
>>>> Martin
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> cclib-users mailing list
>>>> ccl...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>
>>>
>>
>

Re: [cclib-users] Problem with the parser when going from 1.3 --> 1.5

[Martin R. <mar...@gm...>]

My bad, Google didn't show me https://github.com/cclib/cclib/releases at
first.

I will try, and get back to you.

You might want to update the other webpage though, and maybe remove the
older http://cclib.sourceforge.net/wiki/index.php/Main_Page

Thanks,
Martin

On Wed, Nov 29, 2017 at 10:31 AM, Martin Rahm <mar...@gm...> wrote:

> Hi Adam,
>
> I am using 1.5, which I thought was the latest (according to
> https://cclib.github.io/how_to_install.html)
>
> The source code of the newest release of cclib (version 1.5) is
> distributed as:
>
>    - A .tar.gz file: https://github.com/cclib/cclib/releases/download/
>    v1.5/cclib-1.5.post1.tar.gz
>
> Where can the even newer versions be found?
>
> Best,
> Martin
>
>
>
> On Tue, Nov 28, 2017 at 6:32 PM, Adam Tenderholt <ate...@gm...>
> wrote:
>
>> Are you using 1.5? Or one of the newer releases like 1.5.2? If you're
>> still having problems with the latest release, are you able to share your
>> file for some debugging?
>>
>> On Tue, Nov 28, 2017 at 12:11 AM Martin Rahm <mar...@gm...>
>> wrote:
>>
>>> Hi cclib-lovers,
>>>
>>> I've recently updated from 1.3 to 1.5, and I'm seeing some peculiarities
>>> with the basic parsing. Maybe this has been explained somewhere, and if so
>>> I apologize. I have been unable to find an answer on my own, and hope you
>>> can help. I'm running a Linux environment with Python 3.6 (I used to run
>>> 2.7.5 so that might have affected things as well).
>>>
>>> from cclib.parser import ccopen
>>>
>>> seem to have been replaced by
>>>
>>> from cclib.io import ccopen
>>>
>>>
>>> so the basic guide shown https://cclib.github.io/methods.html doesn't
>>> seem to be right anymore.
>>>
>>>
>>> ccopen doesn't seem to function as it used to.
>>>
>>> data = ccopen("file.out") results in the following error:
>>>
>>>
>>> File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/io/ccio.py",
>>> line 190, in ccopen
>>>
>>>     inputfile.seek(0, 0)
>>>
>>> AttributeError: 'FileInput' object has no attribute 'seek'
>>>
>>> This led me to use the (new?) functions:
>>>
>>> from cclib.parser import Gaussian ORCA
>>>
>>>
>>> when calling
>>>
>>> data = ORCA("inputfile.out")
>>>
>>>
>>> This seems to work, albeit sometimes with the following omnious error
>>> messages:
>>>
>>> [ORCA ['./script.py', 'file.out'] WARNING] Attribute atomnos changed
>>> value ([7, 6, 6, 8, 8] -> [7, 6, 7, 8, 8])
>>>
>>> [ORCA ['./script.py', 'file.out'] WARNING] The geotargets attribute
>>> should not exist yet. There is a problem in the parser.
>>>
>>>
>>> when instead calling
>>>
>>> data = Gaussian("file.out")
>>>
>>>
>>> it proceeds to crash at the next line, which is
>>>
>>> data = data.parse()
>>>
>>>
>>> Traceback (most recent call last):
>>>
>>>   File "./script.py", line 87, in <module>
>>>
>>>     data = data.parse()
>>>
>>>   File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages
>>> /cclib/parser/logfileparser.py", line 301, in parse
>>>
>>>     self.extract(inputfile, line)
>>>
>>>   File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages
>>> /cclib/parser/gaussianparser.py", line 163, in extract
>>>
>>>     line = inputfile.next()
>>>
>>> AttributeError: 'FileInput' object has no attribute 'next'
>>>
>>>
>>> So, to sum up, my questions are:
>>>
>>>
>>> 1.  Can cclib no longer automatically determine which output it is
>>> trying to parse (ccopen could do this, and there was nothing fancy with the
>>> output files I tried)?
>>>
>>>
>>> 2. Do the the errors shown for the ORCA parser imply a real problem
>>>
>>>
>>> 3. How do I get the Gaussian parser to run?
>>>
>>>
>>> Many thanks,
>>>
>>>
>>> Martin
>>>
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>>> _________________________________________
>>> cclib-users mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>
>>
>

Re: [cclib-users] Problem with the parser when going from 1.3 --> 1.5

[Martin R. <mar...@gm...>]

Hi Adam,

I am using 1.5, which I thought was the latest (according to
https://cclib.github.io/how_to_install.html)

The source code of the newest release of cclib (version 1.5) is distributed
as:

   - A .tar.gz file:
   https://github.com/cclib/cclib/releases/download/v1.5/cclib-1.5.post1.tar.gz

Where can the even newer versions be found?

Best,
Martin



On Tue, Nov 28, 2017 at 6:32 PM, Adam Tenderholt <ate...@gm...>
wrote:

> Are you using 1.5? Or one of the newer releases like 1.5.2? If you're
> still having problems with the latest release, are you able to share your
> file for some debugging?
>
> On Tue, Nov 28, 2017 at 12:11 AM Martin Rahm <mar...@gm...>
> wrote:
>
>> Hi cclib-lovers,
>>
>> I've recently updated from 1.3 to 1.5, and I'm seeing some peculiarities
>> with the basic parsing. Maybe this has been explained somewhere, and if so
>> I apologize. I have been unable to find an answer on my own, and hope you
>> can help. I'm running a Linux environment with Python 3.6 (I used to run
>> 2.7.5 so that might have affected things as well).
>>
>> from cclib.parser import ccopen
>>
>> seem to have been replaced by
>>
>> from cclib.io import ccopen
>>
>>
>> so the basic guide shown https://cclib.github.io/methods.html doesn't
>> seem to be right anymore.
>>
>>
>> ccopen doesn't seem to function as it used to.
>>
>> data = ccopen("file.out") results in the following error:
>>
>>
>> File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/io/ccio.py",
>> line 190, in ccopen
>>
>>     inputfile.seek(0, 0)
>>
>> AttributeError: 'FileInput' object has no attribute 'seek'
>>
>> This led me to use the (new?) functions:
>>
>> from cclib.parser import Gaussian ORCA
>>
>>
>> when calling
>>
>> data = ORCA("inputfile.out")
>>
>>
>> This seems to work, albeit sometimes with the following omnious error
>> messages:
>>
>> [ORCA ['./script.py', 'file.out'] WARNING] Attribute atomnos changed
>> value ([7, 6, 6, 8, 8] -> [7, 6, 7, 8, 8])
>>
>> [ORCA ['./script.py', 'file.out'] WARNING] The geotargets attribute
>> should not exist yet. There is a problem in the parser.
>>
>>
>> when instead calling
>>
>> data = Gaussian("file.out")
>>
>>
>> it proceeds to crash at the next line, which is
>>
>> data = data.parse()
>>
>>
>> Traceback (most recent call last):
>>
>>   File "./script.py", line 87, in <module>
>>
>>     data = data.parse()
>>
>>   File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-
>> packages/cclib/parser/logfileparser.py", line 301, in parse
>>
>>     self.extract(inputfile, line)
>>
>>   File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-
>> packages/cclib/parser/gaussianparser.py", line 163, in extract
>>
>>     line = inputfile.next()
>>
>> AttributeError: 'FileInput' object has no attribute 'next'
>>
>>
>> So, to sum up, my questions are:
>>
>>
>> 1.  Can cclib no longer automatically determine which output it is trying
>> to parse (ccopen could do this, and there was nothing fancy with the output
>> files I tried)?
>>
>>
>> 2. Do the the errors shown for the ORCA parser imply a real problem
>>
>>
>> 3. How do I get the Gaussian parser to run?
>>
>>
>> Many thanks,
>>
>>
>> Martin
>>
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>> _________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>

Re: [cclib-users] Problem with the parser when going from 1.3 --> 1.5

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

Are you using 1.5? Or one of the newer releases like 1.5.2? If you're still
having problems with the latest release, are you able to share your file
for some debugging?

On Tue, Nov 28, 2017 at 12:11 AM Martin Rahm <mar...@gm...> wrote:

> Hi cclib-lovers,
>
> I've recently updated from 1.3 to 1.5, and I'm seeing some peculiarities
> with the basic parsing. Maybe this has been explained somewhere, and if so
> I apologize. I have been unable to find an answer on my own, and hope you
> can help. I'm running a Linux environment with Python 3.6 (I used to run
> 2.7.5 so that might have affected things as well).
>
> from cclib.parser import ccopen
>
> seem to have been replaced by
>
> from cclib.io import ccopen
>
>
> so the basic guide shown https://cclib.github.io/methods.html doesn't
> seem to be right anymore.
>
>
> ccopen doesn't seem to function as it used to.
>
> data = ccopen("file.out") results in the following error:
>
>
> File
> "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/io/ccio.py",
> line 190, in ccopen
>
>     inputfile.seek(0, 0)
>
> AttributeError: 'FileInput' object has no attribute 'seek'
>
> This led me to use the (new?) functions:
>
> from cclib.parser import Gaussian ORCA
>
>
> when calling
>
> data = ORCA("inputfile.out")
>
>
> This seems to work, albeit sometimes with the following omnious error
> messages:
>
> [ORCA ['./script.py', 'file.out'] WARNING] Attribute atomnos changed value
> ([7, 6, 6, 8, 8] -> [7, 6, 7, 8, 8])
>
> [ORCA ['./script.py', 'file.out'] WARNING] The geotargets attribute should
> not exist yet. There is a problem in the parser.
>
>
> when instead calling
>
> data = Gaussian("file.out")
>
>
> it proceeds to crash at the next line, which is
>
> data = data.parse()
>
>
> Traceback (most recent call last):
>
>   File "./script.py", line 87, in <module>
>
>     data = data.parse()
>
>   File
> "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/parser/logfileparser.py",
> line 301, in parse
>
>     self.extract(inputfile, line)
>
>   File
> "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/parser/gaussianparser.py",
> line 163, in extract
>
>     line = inputfile.next()
>
> AttributeError: 'FileInput' object has no attribute 'next'
>
>
> So, to sum up, my questions are:
>
>
> 1.  Can cclib no longer automatically determine which output it is trying
> to parse (ccopen could do this, and there was nothing fancy with the output
> files I tried)?
>
>
> 2. Do the the errors shown for the ORCA parser imply a real problem
>
>
> 3. How do I get the Gaussian parser to run?
>
>
> Many thanks,
>
>
> Martin
>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

[cclib-users] Problem with the parser when going from 1.3 --> 1.5

[Martin R. <mar...@gm...>]

Hi cclib-lovers,

I've recently updated from 1.3 to 1.5, and I'm seeing some peculiarities
with the basic parsing. Maybe this has been explained somewhere, and if so
I apologize. I have been unable to find an answer on my own, and hope you
can help. I'm running a Linux environment with Python 3.6 (I used to run
2.7.5 so that might have affected things as well).

from cclib.parser import ccopen

seem to have been replaced by

from cclib.io import ccopen


so the basic guide shown https://cclib.github.io/methods.html doesn't seem
to be right anymore.


ccopen doesn't seem to function as it used to.

data = ccopen("file.out") results in the following error:


File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-packages/cclib/io/ccio.py",
line 190, in ccopen

    inputfile.seek(0, 0)

AttributeError: 'FileInput' object has no attribute 'seek'

This led me to use the (new?) functions:

from cclib.parser import Gaussian ORCA


when calling

data = ORCA("inputfile.out")


This seems to work, albeit sometimes with the following omnious error
messages:

[ORCA ['./script.py', 'file.out'] WARNING] Attribute atomnos changed value
([7, 6, 6, 8, 8] -> [7, 6, 7, 8, 8])

[ORCA ['./script.py', 'file.out'] WARNING] The geotargets attribute should
not exist yet. There is a problem in the parser.


when instead calling

data = Gaussian("file.out")


it proceeds to crash at the next line, which is

data = data.parse()


Traceback (most recent call last):

  File "./script.py", line 87, in <module>

    data = data.parse()

  File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-
packages/cclib/parser/logfileparser.py", line 301, in parse

    self.extract(inputfile, line)

  File "/c3se/users/rahmma/Hebbe/.local/lib/python3.6/site-
packages/cclib/parser/gaussianparser.py", line 163, in extract

    line = inputfile.next()

AttributeError: 'FileInput' object has no attribute 'next'


So, to sum up, my questions are:


1.  Can cclib no longer automatically determine which output it is trying
to parse (ccopen could do this, and there was nothing fancy with the output
files I tried)?


2. Do the the errors shown for the ORCA parser imply a real problem


3. How do I get the Gaussian parser to run?


Many thanks,


Martin

Re: [cclib-users] "Missing overlap matrix" from ORCA calculation

[Felipe S. <sch...@gm...>]

Felix,

Thanks, it's solved!

Felipe

On Fri, 27 Oct 2017 at 12:32 Felix Plasser <fel...@un...>
wrote:

> Hi Felipe,
>
> If you want the full cclib/ORCA experience you should add the lines:
>
> %output
>  PrintLevel Normal
>  Print[ P_MOs ] 1
>  Print[ P_Overlap ] 1end
>
> see also:
> https://sourceforge.net/p/theodore-qc/wiki/Program%20specific%20information/#orca-tddft
>
> -Felix
>
> On 10/27/2017 04:25 PM, Felipe Schneider wrote:
>
> Hi everyone,
>
> I'm writing a simple code to build MO diagrams from two fragments and a
> molecule and, for the fragments-to-molecule projections, I'll need the AO
> overlaps. For that I want to use cclib.
>
> Now, the following python code works for me:
>
>     from cclib.method import CSPA
>     from cclib.parser import ORCA
>
>     p = ORCA("H2.out")
>     d = p.parse()
>
>     m = CSPA(d)
>     m.calculate()
>
> But the following doesn't:
>
>     from cclib.method import MBO
>     from cclib.parser import ORCA
>
>     p = ORCA("H2.out")
>     d = p.parse()
>
>     m = MBO(d)
>     m.calculate()
>
> It throws a `Missing overlap matrix` error. Below is the input used for
> the calculation:
>
>     ! B3LYP D3 Opt TightOpt Freq def2-TZVP LargePrint
>     ! Grid5 RIJCOSX def2/J
>
>     *xyz 0 1
>      H         -0.38000        0.00000        0.00000
>      H          0.38000        0.00000        0.00000
>     *
>     %pal
>      nprocs 4
>     end
>
> I'm using `cclib` version 1.5.2 and ORCA 4.0.1.2.
> So, my question is *how can I get the AO overlap matrix from ORCA using
> cclib*?
>
> All the best,
> Felipe
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> _______________________________________________
> cclib-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>
> --
> Felix Plasser
> Institute for Theoretical Chemistry
> University of Vienna
> Währingerstr. 17/404
> 1090 Wie...@un...http://homepage.univie.ac.at/felix.plasser/
> Tel.: +43-1-4277-52757
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>