pyvib2-users — Common discussions on PyVib2

[Pyvib2-users] VTK package

[Jose A. <ja...@gm...>]

I'm having trouble installing this package...

How can i do It on Windows 10 or If It more easy in Linux...in what flavour?

Thanks

[Pyvib2-users] Question about extracting VCD spectra

[Matthew M. <mm...@sc...>]

Hi,

I am wondering if it is possible to extract the VCD spectrum of a 
molecule as a list of (x,y) values or something similar, once it is 
displayed in PyVib? i.e. to plot the VCD spectrum in another plotting 
software.

I am using PyVib2 1.1 right now, if that is important.

Thank you, and thanks for creating this program!

Matt

[Pyvib2-users] Can not read the .fch file

[Xiaojun Li <xj...@ya...>]

Hi,
I want to open the .fch file, but they are many errors, the calculations were performed by window Gaissian 09 program. Some errors are shown:
Traceback :
  File "pyviblib\gui\main.pyc", line 367, in __open_file
  File "pyviblib\io\parsers.pyc", line 180, in create_parser
  File "pyviblib\io\parsers.pyc", line 490, in __init__
  File "pyviblib\io\parsers.pyc", line 97, in __init__
  File "pyviblib\io\parsers.pyc", line 580, in _parse
  File "pyviblib\io\parsers.pyc", line 875, in __read_number
Additionally, i tried also to open the example .fch with IR/VCD, no dialog with isotopes is invoked automatically, so only show the sturcture, no frequency analysis.
How to change or update these errors? Or can i get a updated version, thanks.

Best regards,
Xiaojun

[Pyvib2-users] update for gaussian 09

[Li, G. <G....@tu...>]

Dear pyvib2 developer,

It is a very nice program for vibration analysis.
But I notice that the latest version only match the Gaussian 03 frequency-dependent output format, but Gaussian 09. If the developer also consider updating pyvib2 to be fitting the G09 output, it would be amazing.

Cheers, gli

Re: [Pyvib2-users] non-supported packages

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

        Dear Jose,

    To be honest, I do not clearly understand what is wrong with the 
flexible approach to implement a parser class for each data type 
supported by the program. Apropos, this approach is widely used, in 
particular in OpenBabel.

    If you are interested in how to implement such a class and if you 
are familiar with Python, then please refer to 
http://pyvib2.sourceforge.net/doc/pydoc/pyviblib.io.parsers.html as well 
as to the source code pyviblib/io/parsers.py. In short, one has to 
inherit from AbstractFileParser, override a couple of protected methods 
and set properly certain protected attributes of the parent class.


    With best regards,
    Maxim Fedorovsky.
> Hello
>
> The software I intend to use to perform some calculations, 
> GAMESSUK, isn't supported by PyVib2. I wonder if there's some way 
> to make PyVib2 to read plain text data files where the relevant 
> matrices (Hessian, analytical second derivaties, etc...) and 
> geometry would be especified. This way PyVib2 would support 
> virtually every computational package with no need to write a new 
> parser for each of them--the parsing would be done 'by hand' by the 
> user.
>
> I believe this probably is trivial to implement, but I lack the 
> required knowledge to sort all the bits out. Any hints as to how to 
> proceed to trick PyVib2 into accepting manually created input files 
> (instead of the results of the built-in parsers) would be most welcome.
>
> Thanks
>
> Jose
>
>
>
>   

[Pyvib2-users] non-supported packages

[Jose R. <j.c...@re...>]

Hello

The software I intend to use to perform some calculations, 
GAMESSUK, isn't supported by PyVib2. I wonder if there's some way 
to make PyVib2 to read plain text data files where the relevant 
matrices (Hessian, analytical second derivaties, etc...) and 
geometry would be especified. This way PyVib2 would support 
virtually every computational package with no need to write a new 
parser for each of them--the parsing would be done 'by hand' by the 
user.

I believe this probably is trivial to implement, but I lack the 
required knowledge to sort all the bits out. Any hints as to how to 
proceed to trick PyVib2 into accepting manually created input files 
(instead of the results of the built-in parsers) would be most welcome.

Thanks

Jose



-- 
Jose Rodriguez
PhD student
School of Chemistry
University of Reading
Whiteknights, PO BOX 217
Reading, Berkshire
RG6 6AH