cclib-users — Help and support for cclib users

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

[Felix P. <fel...@un...>]

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  ]  1
end

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

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

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

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

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

[cclib-users] Releave v1.5.2

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

Hello,

Earlier today I released cclib v1.5.2, which includes two new writers
(Molden and WFX) and other Google Summer of Code work by Sagar Gaur.
Congrats!

There are also some new attributes and various bug fixes in this release.
Please see the release history on github (
https://github.com/cclib/cclib/releases/tag/v1.5.2) for details.

I moved most pending changes to v1.5.3, but it looks like this might be
released sometime soon if we wrap up more things. I think there is some
energy now to try harder to finish up existing PRs, and close or finalize
existing issues. Let's try to follow up. There are also some topics we're
discussing for a future backwards incompatible 2.x release. Stay tuned!

- Karol

Re: [cclib-users] Installing cclib-1.5 to local directory

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

Note that the various custom installation target options such as --prefix
and --install-base are mutually exclusive. All the detail can be found in
the docs: https://docs.python.org/2/install/#alternate-installation

On Fri, May 19, 2017 at 8:51 AM, Eric Berquist <er...@pi...> wrote:

> If you do
>
> python setup.py install --help
>
> there are a number of options for controlling the install location. The
> most commonly desired option is python setup.py install --home, which
> would install almost any Python library into ~/.local, which Python knows
> to check automatically for modules. I see there is also --install-base if
> you want it somewhere else.
>
> There is another option, where python setup.py build is used instead, and
> the code is compiled under cclib/build/, but you'll have to manually
> modify $PYTHONPATH.
>
> Eric
>
> On Fri, May 19, 2017 at 11:42 AM, Colin Lam <yh...@gm...> wrote:
>
>> Hello,
>>
>> This may be an obvious question, but how do I install cclib-1.5 to a
>> local directory on my home disk in a computing cluster running Linux? I do
>> not have root permission to run the install command "python setup.py
>> install" given on the tutorial page.
>>
>> Thanks,
>> Colin
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=
>> 01%7C01%7Cerb74%40pitt.edu%7C1e8131bdc4ed4f734a6c08d49ecdb7c
>> 3%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=nmO83GJkJOu5g
>> JWD4kziNF9Q59hgt4JNDVXrNKDSU%2Bc%3D&reserved=0
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://na01.safelinks.protection.outlook.com/?url=https%3A%
>> 2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcclib-
>> users&data=01%7C01%7Cerb74%40pitt.edu%7C1e8131bdc4ed4f734
>> a6c08d49ecdb7c3%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&
>> sdata=%2BOouRlLloaRqVtjMRjYn2FsYD3TONf1OTuSnzgEd%2FG0%3D&reserved=0
>>
>>
>
> ------------------------------------------------------------
> ------------------
> 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] Installing cclib-1.5 to local directory

[Eric B. <er...@pi...>]

If you do

python setup.py install --help

there are a number of options for controlling the install location. The
most commonly desired option is python setup.py install --home, which would
install almost any Python library into ~/.local, which Python knows to
check automatically for modules. I see there is also --install-base if you
want it somewhere else.

There is another option, where python setup.py build is used instead, and
the code is compiled under cclib/build/, but you'll have to manually modify
$PYTHONPATH.

Eric

On Fri, May 19, 2017 at 11:42 AM, Colin Lam <yh...@gm...> wrote:

> Hello,
>
> This may be an obvious question, but how do I install cclib-1.5 to a local
> directory on my home disk in a computing cluster running Linux? I do not
> have root permission to run the install command "python setup.py install"
> given on the tutorial page.
>
> Thanks,
> Colin
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! https://na01.safelinks.
> protection.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=01%7C01%
> 7Cerb74%40pitt.edu%7C1e8131bdc4ed4f734a6c08d49ecdb7c3%
> 7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=
> nmO83GJkJOu5gJWD4kziNF9Q59hgt4JNDVXrNKDSU%2Bc%3D&reserved=0
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.
> sourceforge.net%2Flists%2Flistinfo%2Fcclib-users&data=
> 01%7C01%7Cerb74%40pitt.edu%7C1e8131bdc4ed4f734a6c08d49ecdb7c3%
> 7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=%
> 2BOouRlLloaRqVtjMRjYn2FsYD3TONf1OTuSnzgEd%2FG0%3D&reserved=0
>
>

Re: [cclib-users] Installing cclib-1.5 to local directory

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

You can add the option --prefix=... to "python setup.py install" to install
under a specific directory. For pip this
is --install-option="--prefix=...". The directories you install to will
need to be in your path.

However, I would suggest looking into virtualenv or even better
virtualenvwrapper (https://virtualenvwrapper.readthedocs.io) which make
working with multiple installations/version a breeze.

On Fri, May 19, 2017 at 8:42 AM, Colin Lam <yh...@gm...> wrote:

> Hello,
>
> This may be an obvious question, but how do I install cclib-1.5 to a local
> directory on my home disk in a computing cluster running Linux? I do not
> have root permission to run the install command "python setup.py install"
> given on the tutorial page.
>
> Thanks,
> Colin
>
> ------------------------------------------------------------
> ------------------
> 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] Installing cclib-1.5 to local directory

[Colin L. <yh...@gm...>]

Hello,

This may be an obvious question, but how do I install cclib-1.5 to a local
directory on my home disk in a computing cluster running Linux? I do not
have root permission to run the install command "python setup.py install"
given on the tutorial page.

Thanks,
Colin

[cclib-users] Release v1.5.1

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

Hi everyone,

I just released cclib v1.5.1, which includes two new attributes and other
minor changes and fixes. Thanks for all the hard work that went into this.
It's been another few months, and this is a good way to have a clean start
for GSOC 2017 (looking forward to Sagar's work over the summer).

I moved a lot of the pending issues to v1.5.2, which I'd like to release
during the summer if there are enough changes.

Best,
Karol

Re: [cclib-users] Windows 8.1 Install Issue

[Eric B. <er...@pi...>]

In my limited experience with Python on Windows, it is probably easiest to
use a prepackaged distribution such as Continuum's Anaconda or Miniconda (
https://conda.io/miniconda.html) or Enthought's Canopy (
https://www.enthought.com/products/canopy/), where they have gone through
the trouble of building packages like NumPy or SciPy that require C or
Fortran compilation.

I mention this because our documentation is out of date; there is no more
pre-built NumPy binary installer for Windows, so it would have to be
compiled (see https://www.scipy.org/scipylib/download.html).

But, the first thing to try is pip install numpy, since it looks like they
provide pre-built packages in the new Python format. pip should be
available on your PATH from the Python install.

Eric

On Mon, Apr 10, 2017 at 10:59 AM, Tim Hockswender <tim...@gm...>
wrote:

> How does one install numpy-1.91 for use with cclib?
>
> I have python 3.4 and it’s in the PATH.
>
> The install directions for numpy leave out the reference to the installer
> and imply a build with a fortran compiler.
>
>
>
> Tim
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=
> 01%7C01%7Cerb74%40pitt.edu%7C110a4aaf471d488570de08d48022405
> 4%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=7J4APgeb8K9Yn
> vdya%2BgZV0ffM6jshB%2B%2BC%2FvySecdc9Q%3D&reserved=0
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://na01.safelinks.protection.outlook.com/?url=https%3A%
> 2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcclib-
> users&data=01%7C01%7Cerb74%40pitt.edu%7C110a4aaf471d48857
> 0de08d480224054%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&
> sdata=Fja0amMYC%2F2VTyeyZfBSkoqla34gb%2FYMAIXLkoFecSw%3D&reserved=0
>
>

[cclib-users] Windows 8.1 Install Issue

[Tim H. <tim...@gm...>]

How does one install numpy-1.91 for use with cclib?

I have python 3.4 and it's in the PATH.

The install directions for numpy leave out the reference to the installer
and imply a build with a fortran compiler.

 

Tim

[cclib-users] Problem with ADF output

[Felix P. <fel...@un...>]

Dear cclib team,

I wanted to forward you an ADF output file from a TheoDORE user. It 
seems that this file is not properly parsed by cclib. Using the newest 
cclib version from github and python3:

ccget etoscs 166-tddft-0.31-new.out

Attempting to read 166-tddft-0.31-new.out
Traceback (most recent call last):
   File 
"/user/plasserf/programs/cclib/GIT-standalone/src/scripts/ccget", line 
180, in <module>
     ccget()
   File 
"/user/plasserf/programs/cclib/GIT-standalone/src/scripts/ccget", line 
153, in ccget
     data = ccread(filename, **kwargs)
   File 
"/user/plasserf/programs/cclib/GIT-standalone/build/lib/cclib/parser/ccio.py", 
line 107, in ccread
     return log.parse()
   File 
"/user/plasserf/programs/cclib/GIT-standalone/build/lib/cclib/parser/logfileparser.py", 
line 309, in parse
     self.extract(inputfile, line)
   File 
"/user/plasserf/programs/cclib/GIT-standalone/build/lib/cclib/parser/adfparser.py", 
line 141, in extract
     line = inputfile.next()
   File 
"/user/plasserf/programs/cclib/GIT-standalone/build/lib/cclib/parser/logfileparser.py", 
line 101, in next
     line = next(self.src)
StopIteration

I looked at the code. The problematic part seems to be in adfparser.py

         # In ADF 2014.01, there are (INPUT FILE) messages, so we need 
to use just
         # the lines that start with 'Create' and run until the title or 
something
         # else we are sure is is the calculation proper. It would be 
good to combine
         # this with the previous block, if possible.
         if line[:6] == "Create":
             while line[:5] != "title":
                 line = inputfile.next()

This loop runs until the end of the file.

The ADF output file can be downloaded here:

https://sourceforge.net/p/theodore-qc/discussion/bugs_questions/thread/6b353080/8710/attachment/adf.tgz

Thanks,
Felix

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

Re: [cclib-users] Projects for GSoC 2017

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

Hi Sagar,

All the ideas are listed at http://wiki.openchemistry.org/GSoC_Ideas_2017.
Please take a look, also at the other libraries involved.

- Karol

On Mon, Feb 27, 2017 at 10:45 AM, Sagar Gaur <gau...@gm...> wrote:

> Hi,
>
> What are the projects available in cclib for GSoC 2017?
> I had previously made a (tiny) contribution to the project
> https://github.com/cclib/cclib/issues/248 and would like to help more.
>
> Thanks,
> Sagar
>
> ------------------------------------------------------------
> ------------------
> 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] Projects for GSoC 2017

[Sagar G. <gau...@gm...>]

Hi,

What are the projects available in cclib for GSoC 2017?
I had previously made a (tiny) contribution to the project
https://github.com/cclib/cclib/issues/248 and would like to help more.

Thanks,
Sagar

Re: [cclib-users] Outdated wiki problem readjson

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

Hi Marvin,

Sorry about that - these pages are terribly outdated. I'll try to make that
clearer on the wiki, or better maybe just take the wiki down.

Please refer to cclib.github.io for up to date docs.

Let us know if you have any other problems.

- Karol


On Thu, Feb 2, 2017 at 1:32 AM, Marvin GMX <ma...@gm...> wrote:

> Hello,
>
>
>
> This wiki I found seems not to work with 1.5
>
> http://cclib.sourceforge.net/wiki/index.php/Using_cclib#
> How_to_store_the_information_extracted_from_a_log_file
>
>
>
> # In program 1
>
> mydata.writejson("output.txt")
>
>
>
> # In program 2
>
> from cclib.data import readjson
>
> mydata = readjson(filename="output.txt")
>
> # The readjson function can also accept text...
>
> # mydata = readjson(text='{"atomnos": [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6]}')
>
>
>
>
>
> This does not work with 1.5
>
> I already changed some things, but the last line doesn’t work.
>
>
>
>   mydata = csreadjson(filename="output.txt")
>
> NameError: name 'csreadjson' is not defined
>
>
>
> Can someone please tell me what I have to change?
>
>
>
> data.writejson("output.txt")
>
> from cclib.parser import data
>
> from cclib.io import cjsonreader
>
> mydata = *csreadjson*(filename="output.txt")
>
>
>
> Thanks!
>
>
>
> Regards
>
> Marvin
>
> ------------------------------------------------------------
> ------------------
> 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] Outdated wiki problem readjson

[Marvin G. <ma...@gm...>]

Hello,

 

This wiki I found seems not to work with 1.5

http://cclib.sourceforge.net/wiki/index.php/Using_cclib#How_to_store_the_inf
ormation_extracted_from_a_log_file

 

# In program 1

mydata.writejson("output.txt")

 

# In program 2

from cclib.data import readjson

mydata = readjson(filename="output.txt")

# The readjson function can also accept text...

# mydata = readjson(text='{"atomnos": [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6]}')

 

 

This does not work with 1.5

I already changed some things, but the last line doesn't work. 

 

  mydata = csreadjson(filename="output.txt")

NameError: name 'csreadjson' is not defined

 

Can someone please tell me what I have to change?

 

data.writejson("output.txt")

from cclib.parser import data

from cclib.io import cjsonreader

mydata = csreadjson(filename="output.txt")

 

Thanks!

 

Regards

Marvin

[cclib-users] email address

[Bo Hu <jan...@gm...>]

jan...@gm...
-- 
Department of Chemistry
Fujian Provincial Key Lab of Theoretical and Computational Chemistry (FTCC)
State Key Lab of Physical Chemistry of Solid Surfaces (PCOSS)
College of Chemistry & Chemical Engineering
Xiamen University, Fujian 361005 P.R.C.
Tel: +18205989067 QQ:1620132067
E-mail: jan...@gm...//jan...@st...

[cclib-users] Release v1.5

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

Hello everyone,

I just released cclib v1.5, which includes CJSON read/write functionality
(yay GSOC!), a new parser for MOPAC and various minor features and bug
fixes. Please see the changelog
<https://github.com/cclib/cclib/blob/master/CHANGELOG> for details.

There are a number of things to follow up on and add to this release, so I
anticipate v1.5.1 sometime later this year. If you have time to spare,
please take a look at the dozens of issues waiting to be resolved on GitHub
<https://github.com/cclib/cclib/issues> and dig in.

The core dev team has also grown with this release - welcome Geoff
Hutchison (known as @ghutchis <https://github.com/ghutchis> on GitHub).
Geoff will probably be most active in the area of integrating cclib with
Avogadro.

Best,
Karol

[cclib-users] Release v1.4.1

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

Hi everyone,

I just released cclib v1.4.1, which includes a number of fixes and some
preliminary features for v1.5.

I don't think there's enough time to release v1.4.2 so I've simply pushed
back all remaining issues to v1.5. I set the release date for August 14th,
which is right before GSOC end this year. Ideally, we'd get all of
Sanjeed's CJSON contributions in that release, as well as the planned CSX
writer support.

Best,
Karol

Re: [cclib-users] How to compute Mulliken atomic spin densities using cclib.method.mpa.MPA ?

[Eric B. <er...@pi...>]

Hi Jiaguo,

Thanks for pointing this out. I'll make sure that this is available for
Mulliken, Lowdin, and CSPA.

Eric

On Sat, Jun 11, 2016 at 7:43 PM, Jiaguo Yu <jia...@ya...> wrote:

> Dear cclib users,
>
>   The Mulliken atomic spin densities can be obtained after the following
> change :D
>
> diff -r cclib-master/src/cclib/method/mpa.py
> cclib-master-original/src/cclib/method/mpa.py
> 115c115,117
> <
> ---
> >
> >         alpha = numpy.zeros([size], "d")
> >         beta = numpy.zeros([size], "d")
> 121a124,127
> >                 if spin == 0:
> >                     alpha = numpy.add(alpha, temp)
> >                 elif spin == 1:
> >                     beta = numpy.add(beta, temp)
> 124a131,134
> >         else:
> >             self.logger.info("Creating fragspins: array[1]")
> >             self.fragspins = numpy.zeros([size], "d")
> >             self.fragspins = numpy.subtract(alpha, beta)
>
> Best regards,
> Jiaguo Yu
>
>
> 11.06.2016, 18:30, "Jiaguo Yu" <jia...@ya...>:
> > Dear cclib users,
> >
> >     From
> https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fcclib.github.io%2fmethods.html&data=01%7c01%7cerb74%40pitt.edu%7c325b1a801f4849abf72a08d3926b65f3%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=p4FcUHGrHpAoYKHErSfLpUbLt26%2fYhDDgMRXMejrH2o%3d, cclib
> can perform Mulliken population analysis (MPA) and store the results
> in aoresults, fragresults and fragcharges. The fragcharges can be used to
> compute Mulliken atomic charges. Nonetheless, how can one compute Mulliken
> atomic spin densities (for example, from fragresults) ?
> >
> >     The blunt snippet below shows that "alpha" and "beta" variables
> contains almost the same values...
> >
> > sum_alpha = 0.0
> > sum_beta = 0.0
> > for i in range(len(m.fragcharges)):
> > alpha = 0.0
> > beta = 0.0
> > for j in range(len(m.fragresults[0])):
> > alpha += m.fragresults[0][j][i]
> > beta += m.fragresults[1][j][i]
> > sum_alpha += alpha
> > sum_beta += beta
> > print("sum_alpha=%10.5f, sum_beta=%10.5f, alpha=%10.5f, beta=%10.5f" %
> (sum_alpha, sum_beta, alpha, beta))
> >
> > Best regards,
> > Jiaguo Yu
> > ,
> >
> >
> ------------------------------------------------------------------------------
> > What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> > patterns at an interface-level. Reveals which users, apps, and protocols
> are
> > consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> > J-Flow, sFlow and other flows. Make informed decisions using capacity
> > planning reports.
> https://na01.safelinks.protection.outlook.com/?url=https%3a%2f%2fad.doubleclick.net%2fddm%2fclk%2f305295220%3b132659582%3be&data=01%7c01%7cerb74%40pitt.edu%7c325b1a801f4849abf72a08d3926b65f3%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=%2ffHADUXpf%2bAA5rLrJkOlFMDvP1O7nQkNHoo79KXtTBU%3d
> > ,
> >
> > _______________________________________________
> > cclib-users mailing list
> > ccl...@li...
> >
> https://na01.safelinks.protection.outlook.com/?url=https%3a%2f%2flists.sourceforge.net%2flists%2flistinfo%2fcclib-users&data=01%7c01%7cerb74%40pitt.edu%7c325b1a801f4849abf72a08d3926b65f3%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=olFk0%2bErPRTwiaEklgMMd3xE4c4jl1b8%2bw40aVVxLi8%3d
>
>
> ------------------------------------------------------------------------------
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and protocols
> are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning reports.
> https://na01.safelinks.protection.outlook.com/?url=https%3a%2f%2fad.doubleclick.net%2fddm%2fclk%2f305295220%3b132659582%3be&data=01%7c01%7cerb74%40pitt.edu%7c325b1a801f4849abf72a08d3926b65f3%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=%2ffHADUXpf%2bAA5rLrJkOlFMDvP1O7nQkNHoo79KXtTBU%3d
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
>
> https://na01.safelinks.protection.outlook.com/?url=https%3a%2f%2flists.sourceforge.net%2flists%2flistinfo%2fcclib-users&data=01%7c01%7cerb74%40pitt.edu%7c325b1a801f4849abf72a08d3926b65f3%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=olFk0%2bErPRTwiaEklgMMd3xE4c4jl1b8%2bw40aVVxLi8%3d
>

Re: [cclib-users] How to compute Mulliken atomic spin densities using cclib.method.mpa.MPA ?

[Jiaguo Yu <jia...@ya...>]

Dear cclib users,

  The Mulliken atomic spin densities can be obtained after the following change :D

diff -r cclib-master/src/cclib/method/mpa.py cclib-master-original/src/cclib/method/mpa.py
115c115,117
<         
---
> 
>         alpha = numpy.zeros([size], "d")
>         beta = numpy.zeros([size], "d")
121a124,127
>                 if spin == 0:
>                     alpha = numpy.add(alpha, temp)
>                 elif spin == 1:
>                     beta = numpy.add(beta, temp)
124a131,134
>         else:
>             self.logger.info("Creating fragspins: array[1]")
>             self.fragspins = numpy.zeros([size], "d")
>             self.fragspins = numpy.subtract(alpha, beta)

Best regards,
Jiaguo Yu


11.06.2016, 18:30, "Jiaguo Yu" <jia...@ya...>:
> Dear cclib users,
>
>     From http://cclib.github.io/methods.html, cclib can perform Mulliken population analysis (MPA) and store the results in aoresults, fragresults and fragcharges. The fragcharges can be used to compute Mulliken atomic charges. Nonetheless, how can one compute Mulliken atomic spin densities (for example, from fragresults) ?
>
>     The blunt snippet below shows that "alpha" and "beta" variables contains almost the same values...
>
> sum_alpha = 0.0
> sum_beta = 0.0
> for i in range(len(m.fragcharges)):
> alpha = 0.0
> beta = 0.0
> for j in range(len(m.fragresults[0])):
> alpha += m.fragresults[0][j][i]
> beta += m.fragresults[1][j][i]
> sum_alpha += alpha
> sum_beta += beta
> print("sum_alpha=%10.5f, sum_beta=%10.5f, alpha=%10.5f, beta=%10.5f" % (sum_alpha, sum_beta, alpha, beta))
>
> Best regards,
> Jiaguo Yu
> ,
>
> ------------------------------------------------------------------------------
> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
> patterns at an interface-level. Reveals which users, apps, and protocols are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
> ,
>
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users

[cclib-users] How to compute Mulliken atomic spin densities using cclib.method.mpa.MPA ?

[Jiaguo Yu <jia...@ya...>]

<div>Dear cclib users,</div><div> </div><div>    From <a href="http://cclib.github.io/methods.html," target="_blank">http://cclib.github.io/methods.html,</a> cclib can perform Mulliken population analysis (MPA) and store the results in aoresults, fragresults and fragcharges. The fragcharges can be used to compute Mulliken atomic charges. Nonetheless, how can one compute Mulliken atomic spin densities (for example, from fragresults) ?</div><div> </div><div>    The blunt snippet below shows that "alpha" and "beta" variables contains almost the same values...</div><div><pre>sum_alpha = 0.0<br />sum_beta = 0.0<br />for i in range(len(m.fragcharges)):<br />    alpha = 0.0<br />    beta = 0.0<br />    for j in range(len(m.fragresults[0])):<br />        alpha += m.fragresults[0][j][i]<br />        beta += m.fragresults[1][j][i]<br />    sum_alpha += alpha<br />    sum_beta += beta<br />    print("sum_alpha=%10.5f, sum_beta=%10.5f, alpha=%10.5f, beta=%10.5f" % (sum_alpha, sum_beta, alpha, beta))</pre></div><div> </div><div>Best regards,</div><div>Jiaguo Yu</div>

Re: [cclib-users] Contritbuting

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

Hi Ramon,

We don't really have any precedent for parding dynamics / MD trajectories.
I think for the time being it would be sufficient to add your file as a
regression and make cclib work for that case (assuming you're OK with
releasing a file for such use).

Best,
Karol


On Wed, Jun 1, 2016 at 4:10 AM, Ramon Crehuet <rc...@iq...> wrote:

> Dear Karol,
> Thanks for your help. I've now integrated the code to read Gaussian BOMD
> in my cclib git repo. I haven't yet prepared any test file, because I'm not
> sure what the policy is or how it works (but of course I've tested it works
> with my files). Should I do a pull request or should I include the tests
> first? For the later I'm afraid I need some advice...
> All the best,
> Ramon
>
>
>
> On 27/05/16 19:44, Karol Langner wrote:
>
> Hi Ramon,
>
> Of course, all contributions are very welcome and appreciated. Probably
> the best way to move forward is just to try to fit your code into cclib and
> open a pull request. It is also better (well, easier to review) to submit
> small changes separately, if it is possible to break down your code into
> independent fragments.
>
> Please take a look at cclib.github.io, although some of the things may be
> outdated and developer docs are not very detailed. Sorry about that!
>
> Best,
> Karol
>
>
> On Fri, May 27, 2016 at 5:55 AM, Ramon Crehuet <rc...@iq...>
> wrote:
>
>> Dear cclib developers,
>> I've been using cclib as a user for a long time and great sucess. My last
>> use
>> concerned readling BOMD trajectories from Gaussian. Because of the
>> peculiarities
>> of these calculations, cclib does not perform optimally, so I finally
>> wrote my
>> own parser.
>> Is there anybody working on implementing this in cclib? If not, could I
>> contribute with my code? If so, how should I proceed? (Guide for
>> developpers,
>> coding style, tests to prepare, create a github pull request?)
>> All the best,
>> Ramon
>>
>> --
>> Ramon Crehuet
>> Cientific Titular (Assistant Professor)
>> Institute of Advanced Chemistry of Catalonia
>> IQAC - CSIC
>> http://www.iqac.csic.es/qteor
>> https://twitter.com/rcrehuet
>> http://ramoncrehuet.wordpress.com/
>> Tel. +34 934006116
>> Jordi Girona 18-26
>> 08034 Barcelona (Spain)
>>
>>
>>
>> ------------------------------------------------------------------------------
>> What NetFlow Analyzer can do for you? Monitors network bandwidth and
>> traffic
>> patterns at an interface-level. Reveals which users, apps, and protocols
>> are
>> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
>> J-Flow, sFlow and other flows. Make informed decisions using capacity
>> planning reports.
>> https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>
>
> --
> Ramon Crehuet
> Cientific Titular (Assistant Professor)
> Institute of Advanced Chemistry of Catalonia
> IQAC - CSIChttp://www.iqac.csic.es/qteor https://twitter.com/rcrehuethttp://ramoncrehuet.wordpress.com/
> Tel. +34 934006116
> Jordi Girona 18-26
> 08034 Barcelona (Spain)
>
>

Re: [cclib-users] Contritbuting

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

<html>
  <head>
    <meta content="text/html; charset=utf-8" http-equiv="Content-Type">
  </head>
  <body text="#000000" bgcolor="#FFFFFF">
    Dear Karol,<br>
    Thanks for your help. I've now integrated the code to read Gaussian
    BOMD in my cclib git repo. I haven't yet prepared any test file,
    because I'm not sure what the policy is or how it works (but of
    course I've tested it works with my files). Should I do a pull
    request or should I include the tests first? For the later I'm
    afraid I need some advice...<br>
    All the best,<br>
    Ramon<br>
    <br>
    <br>
    <div class="moz-cite-prefix">On 27/05/16 19:44, Karol Langner wrote:<br>
    </div>
    <blockquote
cite="mid:CAG...@ma..."
      type="cite">
      <div dir="ltr">Hi Ramon,
        <div><br>
        </div>
        <div>Of course, all contributions are very welcome and
          appreciated. Probably the best way to move forward is just to
          try to fit your code into cclib and open a pull request. It is
          also better (well, easier to review) to submit small changes
          separately, if it is possible to break down your code into
          independent fragments.</div>
        <div><br>
        </div>
        <div>Please take a look at <a moz-do-not-send="true"
            href="http://cclib.github.io">cclib.github.io</a>, although
          some of the things may be outdated and developer docs are not
          very detailed. Sorry about that!</div>
        <div><br>
        </div>
        <div>Best,</div>
        <div>Karol</div>
        <div><br>
        </div>
      </div>
      <div class="gmail_extra"><br>
        <div class="gmail_quote">On Fri, May 27, 2016 at 5:55 AM, Ramon
          Crehuet <span dir="ltr">&lt;<a moz-do-not-send="true"
              href="mailto:rc...@iq..." target="_blank">rc...@iq...</a>&gt;</span>
          wrote:<br>
          <blockquote class="gmail_quote" style="margin:0 0 0
            .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear cclib
            developers,<br>
            I've been using cclib as a user for a long time and great
            sucess. My last use<br>
            concerned readling BOMD trajectories from Gaussian. Because
            of the peculiarities<br>
            of these calculations, cclib does not perform optimally, so
            I finally wrote my<br>
            own parser.<br>
            Is there anybody working on implementing this in cclib? If
            not, could I<br>
            contribute with my code? If so, how should I proceed? (Guide
            for developpers,<br>
            coding style, tests to prepare, create a github pull
            request?)<br>
            All the best,<br>
            Ramon<br>
            <br>
            --<br>
            Ramon Crehuet<br>
            Cientific Titular (Assistant Professor)<br>
            Institute of Advanced Chemistry of Catalonia<br>
            IQAC - CSIC<br>
            <a moz-do-not-send="true"
              href="http://www.iqac.csic.es/qteor" rel="noreferrer"
              target="_blank">http://www.iqac.csic.es/qteor</a><br>
            <a moz-do-not-send="true"
              href="https://twitter.com/rcrehuet" rel="noreferrer"
              target="_blank">https://twitter.com/rcrehuet</a><br>
            <a moz-do-not-send="true"
              href="http://ramoncrehuet.wordpress.com/" rel="noreferrer"
              target="_blank">http://ramoncrehuet.wordpress.com/</a><br>
            Tel. <a moz-do-not-send="true" href="tel:%2B34%20934006116"
              value="+34934006116">+34 934006116</a><br>
            Jordi Girona 18-26<br>
            08034 Barcelona (Spain)<br>
            <br>
            <br>
------------------------------------------------------------------------------<br>
            What NetFlow Analyzer can do for you? Monitors network
            bandwidth and traffic<br>
            patterns at an interface-level. Reveals which users, apps,
            and protocols are<br>
            consuming the most bandwidth. Provides multi-vendor support
            for NetFlow,<br>
            J-Flow, sFlow and other flows. Make informed decisions using
            capacity<br>
            planning reports. <a moz-do-not-send="true"
              href="https://ad.doubleclick.net/ddm/clk/305295220;132659582;e"
              rel="noreferrer" target="_blank">https://ad.doubleclick.net/ddm/clk/305295220;132659582;e</a><br>
            _______________________________________________<br>
            cclib-users mailing list<br>
            <a moz-do-not-send="true"
              href="mailto:ccl...@li...">ccl...@li...</a><br>
            <a moz-do-not-send="true"
              href="https://lists.sourceforge.net/lists/listinfo/cclib-users"
              rel="noreferrer" target="_blank">https://lists.sourceforge.net/lists/listinfo/cclib-users</a><br>
          </blockquote>
        </div>
        <br>
      </div>
    </blockquote>
    <br>
    <pre class="moz-signature" cols="80">-- 
Ramon Crehuet
Cientific Titular (Assistant Professor)
Institute of Advanced Chemistry of Catalonia 
IQAC - CSIC
<a class="moz-txt-link-freetext" href="http://www.iqac.csic.es/qteor">http://www.iqac.csic.es/qteor</a> 
<a class="moz-txt-link-freetext" href="https://twitter.com/rcrehuet">https://twitter.com/rcrehuet</a>
<a class="moz-txt-link-freetext" href="http://ramoncrehuet.wordpress.com/">http://ramoncrehuet.wordpress.com/</a>
Tel. +34 934006116
Jordi Girona 18-26
08034 Barcelona (Spain) </pre>
  </body>
</html>

Re: [cclib-users] Contritbuting

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

Hi Ramon,

Of course, all contributions are very welcome and appreciated. Probably the
best way to move forward is just to try to fit your code into cclib and
open a pull request. It is also better (well, easier to review) to submit
small changes separately, if it is possible to break down your code into
independent fragments.

Please take a look at cclib.github.io, although some of the things may be
outdated and developer docs are not very detailed. Sorry about that!

Best,
Karol


On Fri, May 27, 2016 at 5:55 AM, Ramon Crehuet <rc...@iq...> wrote:

> Dear cclib developers,
> I've been using cclib as a user for a long time and great sucess. My last
> use
> concerned readling BOMD trajectories from Gaussian. Because of the
> peculiarities
> of these calculations, cclib does not perform optimally, so I finally
> wrote my
> own parser.
> Is there anybody working on implementing this in cclib? If not, could I
> contribute with my code? If so, how should I proceed? (Guide for
> developpers,
> coding style, tests to prepare, create a github pull request?)
> All the best,
> Ramon
>
> --
> Ramon Crehuet
> Cientific Titular (Assistant Professor)
> Institute of Advanced Chemistry of Catalonia
> IQAC - CSIC
> http://www.iqac.csic.es/qteor
> https://twitter.com/rcrehuet
> http://ramoncrehuet.wordpress.com/
> Tel. +34 934006116
> Jordi Girona 18-26
> 08034 Barcelona (Spain)
>
>
>
> ------------------------------------------------------------------------------
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and protocols
> are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

[cclib-users] Contritbuting

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

Dear cclib developers,
I've been using cclib as a user for a long time and great sucess. My last use 
concerned readling BOMD trajectories from Gaussian. Because of the peculiarities 
of these calculations, cclib does not perform optimally, so I finally wrote my 
own parser.
Is there anybody working on implementing this in cclib? If not, could I 
contribute with my code? If so, how should I proceed? (Guide for developpers, 
coding style, tests to prepare, create a github pull request?)
All the best,
Ramon

-- 
Ramon Crehuet
Cientific Titular (Assistant Professor)
Institute of Advanced Chemistry of Catalonia
IQAC - CSIC
http://www.iqac.csic.es/qteor
https://twitter.com/rcrehuet
http://ramoncrehuet.wordpress.com/
Tel. +34 934006116
Jordi Girona 18-26
08034 Barcelona (Spain)