cclib-devel

[cclib-devel] PyVib2

[Maxim F. <Max...@un...>]

       Dear developers of cclib,

    I have started a Python project, called PyVib2 
http://pyvib2.sourceforge.net/ , which probably could be interesting for 
you.

   
    With best regards,
    Maxim Fedorovsky.

Re: [cclib-devel] PyVib2

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

On 24/02/07, Maxim Fedorovsky <Max...@un...> wrote:
>        Dear developers of cclib,
>
>     I have started a Python project, called PyVib2
> http://pyvib2.sourceforge.net/ , which probably could be interesting for
> you.

Indeed it is. Very impressive, although I must admit that I wasn't
able to open any files due to an error with VTK on Windows (see end of
message for the text, but I think that this error has nothing to do
with pyvib2).

However, I can see it's a very useful program. As I said to you in an
earlier email, we would be very interested in integrating cclib and
pyvib2. From our point of view, this would basically involve
extracting some extra information from the output files of the
different programs with your guidance. By the way, some nice features
of cclib that you may not be aware of are automatic detection of the
appropriate parser for a particular file, and the ability to handle
.gz, .tar, .zip, and .bz2 files.

What do you think?

Regards,
    Noel

Error message follows:
>>>>>>>>>>>>>>>>>>>>>>>>>>
couldn't load library "vtkRenderingPythonTkWidgets.dll": this library
or a dependent library could not be found in library path

Traceback :
  File "C:\Python24\Lib\site-packages\pyviblib\gui\main.py", line 378,
in __open_file
    self.__append_molecule(mol, parser)
  File "C:\Python24\Lib\site-packages\pyviblib\gui\main.py", line 285,
in __append_molecule
    check_command=self.__update_GUI)
  File "C:\Python24\Lib\site-packages\pyviblib\gui\widgets.py", line
6013, in __init__
    BaseWidget.__init__(self, **kw)
  File "C:\Python24\Lib\site-packages\pyviblib\gui\widgets.py", line
127, in __init__
    self._constructGUI()
  File "C:\Python24\Lib\site-packages\pyviblib\gui\widgets.py", line
6043, in _constructGUI
    self._varsdict['renderWidget'] = MoleculeRenderWidget(self, **kw)
  File "C:\Python24\Lib\site-packages\pyviblib\gui\widgets.py", line
324, in __init__
    vtktkrw.vtkTkRenderWidget.__init__(self, master,
  File "C:\Python24\lib\site-packages\vtk_python\vtk\tk\vtkTkRenderWidget.py",
line 84, in __init__
    vtkLoadPythonTkWidgets(master.tk)
  File "C:\Python24\lib\site-packages\vtk_python\vtk\tk\vtkLoadPythonTkWidgets.py",
line 63, in vtkLoadPythonTkWidgets
    interp.call('load', filename)

VTK don't provide a binary with the Python interface, so I got it from:
    http://mayavi.sourceforge.net/dwnld/vtk/win32/

Re: [cclib-devel] PyVib2

[Maxim F. <Max...@un...>]

Noel O'Boyle schrieb:
> On 24/02/07, Maxim Fedorovsky <Max...@un...> wrote:
>>        Dear developers of cclib,
>>
>>     I have started a Python project, called PyVib2
>> http://pyvib2.sourceforge.net/ , which probably could be interesting for
>> you.
>
> Indeed it is. Very impressive, although I must admit that I wasn't
> able to open any files due to an error with VTK on Windows (see end of
> message for the text, but I think that this error has nothing to do
> with pyvib2).
>
> However, I can see it's a very useful program. As I said to you in an
> earlier email, we would be very interested in integrating cclib and
> pyvib2. From our point of view, this would basically involve
> extracting some extra information from the output files of the
> different programs with your guidance.
Thank you) I think we could make some work together in order to avoid 
the double overhead :)

However, if I understood it correctly, you want to provide the user with 
an universal suite of parsers for extracting a big set of properties 
from the main computational packages. Our primary goal is to facilitate 
the interpretation of results. As you have probably seen, we are working 
mainly with Gaussian and DALTON. I'am planning to spend time in 
programming new parsers (e.g. for Turbomole and ADF) if it would help 
the user to use the functionalities of PyVib2 and if someone would 
*really* need it.

> By the way, some nice features
> of cclib that you may not be aware of are automatic detection of the
> appropriate parser for a particular file, and the ability to handle
> .gz, .tar, .zip, and .bz2 files.
>
> What do you think?
You mean that cclib looks inside a file to determine its type ? It is 
nice. My simple pyviblib.io.parsers.ParserFactory.create_parser() just 
analyzes the extension.

> couldn't load library "vtkRenderingPythonTkWidgets.dll": this library
> or a dependent library could not be found in library path
>
> VTK don't provide a binary with the Python interface, so I got it from:
>    http://mayavi.sourceforge.net/dwnld/vtk/win32/
>

Unfortunately, the installation of VTK under Windows is not so painless 
as under Linux :( I have compiled VTK from the source with Microsoft 
Visual Studio 6.0. Under a Debian-based Linux "apt-get install 
python-vtk" would do the job perfectly.


With best regards,
Maxim Fedorovsky.

Re: [cclib-devel] PyVib2

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

On 25/02/07, Maxim Fedorovsky <Max...@un...> wrote:
> Noel O'Boyle schrieb:
> > On 24/02/07, Maxim Fedorovsky <Max...@un...> wrote:
> >>        Dear developers of cclib,
> >>
> >>     I have started a Python project, called PyVib2
> >> http://pyvib2.sourceforge.net/ , which probably could be interesting for
> >> you.
> >
> > Indeed it is. Very impressive, although I must admit that I wasn't
> > able to open any files due to an error with VTK on Windows (see end of
> > message for the text, but I think that this error has nothing to do
> > with pyvib2).
> >
> > However, I can see it's a very useful program. As I said to you in an
> > earlier email, we would be very interested in integrating cclib and
> > pyvib2. From our point of view, this would basically involve
> > extracting some extra information from the output files of the
> > different programs with your guidance.
> Thank you) I think we could make some work together in order to avoid
> the double overhead :)

That would be great.

> However, if I understood it correctly, you want to provide the user with
> an universal suite of parsers for extracting a big set of properties
> from the main computational packages. Our primary goal is to facilitate
> the interpretation of results.
Yes, exactly.

> As you have probably seen, we are working
> mainly with Gaussian and DALTON. I'am planning to spend time in
> programming new parsers (e.g. for Turbomole and ADF) if it would help
> the user to use the functionalities of PyVib2 and if someone would
> *really* need it.
We don't currently support DALTON or Turbomole (simply because we
don't have access to these programs), but we do have parsers for ADF,
Gaussian, GAMESS, GAMESS-UK and (soon) Jaguar. We also have parsers
for Molpro and Molcas at various stages of development.

In the short term, we are likely to be busy as we are close to a new
release, but after that we can start adding whatever new attributes
you are interested in.

> > By the way, some nice features
> > of cclib that you may not be aware of are automatic detection of the
> > appropriate parser for a particular file, and the ability to handle
> > .gz, .tar, .zip, and .bz2 files.
> >
> > What do you think?
> You mean that cclib looks inside a file to determine its type ? It is
> nice.
Exactly, it makes things a lot easier when using cclib in applications
as the user doesn't have to choose the name of the program, or rely on
extensions.

> > couldn't load library "vtkRenderingPythonTkWidgets.dll": this library
> > or a dependent library could not be found in library path
> >
> > VTK don't provide a binary with the Python interface, so I got it from:
> >    http://mayavi.sourceforge.net/dwnld/vtk/win32/
> >
>
> Unfortunately, the installation of VTK under Windows is not so painless
> as under Linux :( I have compiled VTK from the source with Microsoft
> Visual Studio 6.0. Under a Debian-based Linux "apt-get install
> python-vtk" would do the job perfectly.
Yes, I used to have Debian too. Maybe I can install it with VMWare or
something. Would it be possible for you to use py2exe to create a
massive binary for Windows users?

Regards,
   Noel

Re: [cclib-devel] PyVib2

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

Dear Max,

  It has been some time since PyVib was discussed on the cclib list, but I 
stumbled onto this today:
http://www3.interscience.wiley.com/cgi-bin/abstract/114279037/ABSTRACT

 What is the relation between PyVib and PyVib2? Is Mohamed Zerara in the same 
research group as you?

Cheers,
Karol

On Saturday 24 February 2007 18:30, Maxim Fedorovsky wrote:
>        Dear developers of cclib,
>
>     I have started a Python project, called PyVib2
> http://pyvib2.sourceforge.net/ , which probably could be interesting for
> you.
>
>
>     With best regards,
>     Maxim Fedorovsky.

-- 
written by Karol Langner
Mon Sep  3 10:45:25 EDT 2007

Re: [cclib-devel] PyVib2

[Maxim F. <Max...@un...>]

       Dear Karol,

    Mohamed Zerara was a postdoc in our working group. At the time being 
he does work with us anymore. He has written pyVib and I supposed to 
extend it with new developments. But as I started, it became evident 
that it is much more easier to make an own program with an own 
infrastructure to do the job. So PyVib2 came into world.

    A significant difference between pyVib and PyVib2 is the following : 
the former does not have anything new from the scientific point of view, 
since it implements the existing things already done in a Matlab program 
called VOAVIEW of Gerard Zuber and Jacques Haesler. VOAVIEW was done 
already before I and Zerara entered the working group of Prof. Hug. In 
its turn, PyVib2 provides the possibility to compare force fields via 
their normal modes, which is a new development. Furthermore, in a next 
version, a new (currently top-secret) technique for VROA will become 
available -) I hope I clarified the question ;)


    With best regards,
    Maxim Fedorovsky.
> Dear Max,
>
>   It has been some time since PyVib was discussed on the cclib list, but I 
> stumbled onto this today:
> http://www3.interscience.wiley.com/cgi-bin/abstract/114279037/ABSTRACT
>
>  What is the relation between PyVib and PyVib2? Is Mohamed Zerara in the same 
> research group as you?
>
> Cheers,
> Karol
>
> On Saturday 24 February 2007 18:30, Maxim Fedorovsky wrote:
>   
>>        Dear developers of cclib,
>>
>>     I have started a Python project, called PyVib2
>> http://pyvib2.sourceforge.net/ , which probably could be interesting for
>> you.
>>
>>
>>     With best regards,
>>     Maxim Fedorovsky.
>>     
>
>