gmane.science.chemistry.zeobuilder.user

querries

Abu Naser — 2012-06-20T08:03:53

Hi All Users,

I am very new to zeolite structures. I wish to build ZSM-5 from information 
provided in the link (http://izasc.ethz.ch/fmi/xsl/IZA-SC/ftc_fw.xsl?-db=Atlas_main&-lay=web&STC=MFI&-find).
Could please advise me where to start to achieve my goal? 

With regards,

Abu

Re: installation problem

Jaber Jahanbin Sardroodi — 2011-05-12T13:52:22

Hi,
Did you have installed molmod python module? The error message tells
molmod.unit module does not exist on your system. install it using "python
setup.py build; python setup.py install (latter with sudo probabily!).
by!

On Tue, May 10, 2011 at 1:52 PM, bhaskar bora <bhaskargreen-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org>wrote:

installation problem

bhaskar bora — 2011-05-10T09:22:51

Dear users and developers,

I am having some problem in invoking zeobuilder. The installation seems to
be completed. When I invoke zeobuilder as a normal user in my terminal it
shows the following errors

Traceback (most recent call last):
  File "/usr/bin/zeobuilder", line 69, in <module>
    Application(init_fn)
  File "/usr/lib/python2.7/site-packages/zeobuilder/application.py", line
38, in __init__
    self.initialize_config()
  File "/usr/lib/python2.7/site-packages/zeobuilder/application.py", line
56, in initialize_config
    from zeobuilder.config import Configuration
  File "/usr/lib/python2.7/site-packages/zeobuilder/config.py", line 26, in
<module>
    from zeobuilder.conversion import measures, units_by_measure
  File "/usr/lib/python2.7/site-packages/zeobuilder/conversion.py", line 23,
in <module>
    import molmod.units
ImportError: No module named molmod.units

Could you kindly suggest how to sort it out. My machine has fedora as OS.

kind regards
Bhaskar

Re: problem with zeobuilder execution

Esteban Vöhringer Martinez — 2011-01-11T14:31:47

Both files contain the same information.
I added the line and also a message to see if the function is called but
after new installation of zeobuilder my message is not printed and I get
the usual error. So I think this function is executed.

Sorry to bother you with all this and thanks for your help.


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Zeobuilder-users mailing list
Zeobuilder-users< at >molmod.UGent.be
https://molmod.ugent.be/code/wiki/

Re: problem with zeobuilder execution

Toon Verstraelen — 2011-01-11T14:18:15

Hi Esteban,

I do not immediately see the error. There may be some confusion between

/usr/local/lib/python2.6/dist-packages/zeobuilder/datadir.txt

and

/usr/local/lib/python2.6/site-packages/zeobuilder/datadir.txt

Your machine may be using the latter instead of the former I mentioned 
earlier. Could you try the following: add

         print result


after line 51 in lib/__init__.py?
(make sure the line starts with eight spaces)

Then reinstall zeobuilder, execute zeobuilder and send back the printed 
line.

cheers,

Toon

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https://molmod.ugent.be/code/wiki/

Re: problem with zeobuilder execution

Esteban Vöhringer Martinez — 2011-01-11T14:03:11

YES
Attached you find the output of the compilation and installation of the
molmod, iterative, conscan and zeobuilder. I couldn't find an error.

Bye Esteban


removed `/usr/local/lib/python2.6/site-packages/conscan/__init__.py'
removed `/usr/local/lib/python2.6/site-packages/conscan/triangle.pyc'
removed `/usr/local/lib/python2.6/site-packages/conscan/triangle.py'
removed `/usr/local/lib/python2.6/site-packages/conscan/interface.pyc'
removed `/usr/local/lib/python2.6/site-packages/conscan/interface.py'
removed `/usr/local/lib/python2.6/site-packages/conscan/pair.pyc'
removed `/usr/local/lib/python2.6/site-packages/conscan/base.py'
removed `/usr/local/lib/python2.6/site-packages/conscan/pair.py'
removed `/usr/local/lib/python2.6/site-packages/conscan/base.pyc'
removed `/usr/local/lib/python2.6/site-packages/conscan/__init__.pyc'
removed directory: `/usr/local/lib/python2.6/site-packages/conscan'
running install
running build
running build_py
creating build
creating build/lib.linux-i686-2.6
creating build/lib

Re: problem with zeobuilder execution

Toon Verstraelen — 2011-01-11T13:35:21

Does the directory /usr/local/share/zeobuilder exist on your machine?

Could you sent the complete screen output of the install procedure. That 
probably contains a clue.

cheers,

Toon

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Re: problem with zeobuilder execution

Esteban Vöhringer Martinez — 2011-01-11T13:28:32

but
latest
archiving 
'/share/zeobuilder' 
data 
Hi

Thank you a lot for the quick answer. I'm now registered and this answer
should also go to the mailing list.

Actually the file you mentioned was not existing. I created it and
wrote /usr/local as you said but I get the same error after excecution.

Bye and thanks for the help,

Esteban


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Re: Run zeobuilder Problems

Toon Verstraelen — 2011-01-11T10:16:29

It does no harm. You can ignore it.

cheers,

Toon

Re: Run zeobuilder Problems

Hernan Ahumada — 2011-01-11T10:13:47

Hi again

I followed the instructions in the instalationguide but when I try to
install cd molmod*; ./install.sh. The display show me the next error

rm: cannot remove `molmod/extmodule.c': No such file or directory

Thanks for all

Hernan


2011/1/6 Toon Verstraelen <Toon.Verstraelen-Cru1EgDzd7c< at >public.gmane.org>

Re: problem with zeobuilder execution

Toon Verstraelen — 2011-01-11T08:00:22


Hi Esteban,

Could you subscribe to the mailinglist? It is a great way of archiving 
this discussion so that others may benefit from it.

For some reason the location of the 'share' directory is not correct. 
Could you send the content of the following file:

/usr/local/lib/python2.6/dist-packages/zeobuilder/datadir.txt

It should countain a directory name. If you append '/share/zeobuilder' 
to that directory, you should get the directory that contains the data 
files of zeobuilder, including the icons. Could you check if this is 
indeed the case?

cheers,

Toon

Re: Run zeobuilder Problems

Toon Verstraelen — 2011-01-06T07:28:38

Hi Hernan,

Can you try the following (after uninstalling the deb files):

http://molmod.ugent.be/code/wiki/Zeobuilder/InstallationGuide/GenericLinux

I recommend that you use the latest development version.

cheers,

Toon

Run zeobuilder Problems

Hernan Ahumada — 2011-01-05T11:58:31

Hi All
My Name is Hernan Ahumada, and  I am installing zeobuilder for ubuntu
maverick.

I have installed the deb files for ubuntu. I downloaded from
https://molmod.ugent.be/code/wiki/Download and It was all OK. When execute
zeobuilder the display send the following error.
Thanks for all

Hernan Ahumada
Best Wishes

Traceback (most recent call last):
  File "/usr/bin/zeobuilder", line 69, in <module>
    Application(init_fn)
  File "/usr/lib/pymodules/python2.6/zeobuilder/application.py", line 41, in
__init__
    self.initialize_gui()
  File "/usr/lib/pymodules/python2.6/zeobuilder/application.py", line 82, in
initialize_gui
    self.vis_backend = VisBackendOpenGL(self.scene, self.camera)
  File "/usr/lib/pymodules/python2.6/zeobuilder/gui/visual/vis_backends.py",
line 195, in __init__
    VisBackend.__init__(self, scene, camera)
TypeError: object.__init__() takes no parameters

Re: Zeobuilder error

Toon Verstraelen — 2010-09-29T12:40:54

Hi Shu,

Sorry for the late reply. I've been swamped lately because the TAMkin 
tutorial. The log shows what is going wrong. It is a bug in version 0.003, 
which is fixed in the latest development release. Could you try to install the 
latests development release? The installation is explained at the bottom of 
this page:

http://molmod.ugent.be/code/wiki/Zeobuilder/InstallationGuide/GenericLinux

under the section "Latest development version".

cheers,

Toon

Re: Zeobuilder error

Toon Verstraelen — 2010-09-13T10:08:31

 > Hi!
 >
 > I have installed zeobuilder without any problem. At the last step when I
 > want to run zeobuilder, a message appear:
 > Type error: object _init_( ) takes no parameter.
 >
 > How should I fix this?
 >
 > Regards,
 > Shu
 >

Hi Shu,

I'm sending the reply to the zeobuilder-users-kLNAkSzVt5omCttN7JqJIg< at >public.gmane.org as this list is 
more appropriate for these questions.

I've never seen the error before, so I'm going to ask for a bit more 
information that can help me to figure out what is going wrong. I guess this 
an error occurring during the import phase, so I'd like you to try the 
following: run Python interactively and enter the following import statements.

import numpy
import gtk
import gtk.gtkgl
import OpenGL.GL
import OpenGL.GLU
import OpenGL.GLUT
import molmod
import conscan
import iterative
import zeobuilder

When you run this in a terminal, it will look like this:

toon< at >zeug ~> python
Python 2.6.5 (r265:79063, Apr 16 2010, 13:57:41)
[GCC 4.4.3] on linux2
Type "help", "copyright",

Re: Zeolite framework

Toon Verstraelen — 2010-08-20T09:26:08

Hi Shu,

I've prepared some structures with Zeobuider that you may find interesting, including the 
84T cluster. Just a few things to take into account when you make zeolite clusters for ONIOM:

- Avoid Q1 T atoms. (with three terminations)
- Minimize the number of Q2 T atoms. (with two terminations)
- Make sure your active site and the guest molecules are well-embedded by the crystal 
surrounding, i.e. keep some margin between the termination and the active site with guest 
molecules.
- Terminate with H atoms bonded to Si atoms. Avoid hydroxyls.
- Take a look at the work of Lesthaeghe et al for more details.

Before you do anything with the attached structures, they need some more work:

- The Si-H bond are probably too long. Optimize the positions of the H atoms first, 
keeping all other atoms fixed in space.
- In all subsequent optimizations, keep the positions of the H-atoms fixed and let the 
others move freely. The first thing you probably want to do is the optimization of the 
empty framework, keeping