Topics

61

Installation and License Questions / FAQ: libg2c.so.0: cannot open shared object file: No such file or directory

« on: December 11, 2008, 15:56 »

One of the most common error messages when trying to start VNL/ATK is

'Not available', 'libg2c.so.0: cannot open shared object file: No such file or directory'

Quite obviously, this is because the library libg2c is missing. In many cases it is straightforward to install this library from the relevant package/software/update manager (look for libg2c, libf2c or g77), but one needs to pay some attention to which version to install, especially on 64-bit platforms, since VNL is a 32-bit application and therefore needs the corresponding 32-bit g2c library.

Some more detailed advice on specific platform will appear in further posts on this thread!

In general, a good resource for locating missing libraries to download is http://rpm.pbone.net/ (click "Search", then go to "Advanced Search" to be able to select distribution, otherwise you usually get way too many results in the search).

62

Installation and License Questions / FAQ: Cannot restore segment prot after reloc: Permission denied

« on: December 11, 2008, 15:41 »

When launching VNL after installing it, you may experience the following kind of error message:

QT ('Not available', '/home/user/vnl-2008.10.0/lib/python2.4/site-packages/qtext.so: cannot restore segment prot after reloc: Permission denied')

This can also occur for ATK, in which case the error message will point to the file lib/python2.4/_PyATK.so.

The cause of this error are the new kernel security extensions from the SELinux project which are enabled in some newer Linux distributions, to allow finer-grained control over system security and shared library loading. The solution is to register the relevant libraries in the security module to allow them to be relocated in memory.

For VNL:

Code

chcon -t texrel_shlib_t lib/python2.4/site-packages/qtext.so

For ATK:

Code

chcon -t texrel_shlib_t lib/python2.4/_PyATK.so

Don't forget that there is a local ATK installation inside the VNL installation too, which needs to be registered separately.

63

Installation and License Questions / FAQ: Unable to resolve GL/GLX symbols (and/or Xmu symbols)

« on: December 11, 2008, 15:24 »

It is quite common, on several different different Linux distributions, to encounter the following error message when you launch VNL after installing it:

Unable to resolve GL/GLX symbols - please check your GL library installation.

The solution is relatively simple.

Locate the library libGL.so. To do this, give the command (as root, in /)

Code

find -iname libGL.so*

Most likely this returns something like

./usr/lib64/libGL.so.1
./usr/lib64/libGL.so.1.2
./usr/lib/libGL.so.1
./usr/lib/libGL.so.1.2

What we need to do, is link VNL to the 32-bit libGL.so.1 library.

Go to the lib directory in the VNL installation, and give the command

Code

ln -s /usr/lib/libGL.so.1 libGL.so

In many cases, this will not be sufficient to resolve the problem entirely, however. When you again try to launch VNL, you may now instead get the error message

Unable to resolve Xmu symbols - please check your Xmu library installation.

The solution is similar. Locate the library libXmu.so by giving the command (as root, in /)

Code

find -iname libXmu.so*

Most likely this returns something like

./usr/lib64/libXmu.so.6.2.0
./usr/lib64/libXmu.so.6
./usr/lib/libXmu.so.6.2.0
./usr/lib/libXmu.so.6

What we need to do, is link VNL to the 32-bit libXmu.so.6 library.

Go to the lib directory in the VNL installation, and give the command (if a link/file libXmu.so already exists in this folder, remove it first)

Code

ln -s /usr/lib/libXmu.so.6 libXmu.so

64

Links to Resources and Publications / Papers from 2008

« on: December 11, 2008, 12:40 »

We are currently collecting article references from 2008 for inclusion on the QuantumWise web site. A few are already up - showing really exciting applications of ATK on topics which look not only like superb basic research, but even device-oriented in many cases:

• Molecular rectification in porphyrin dimer
• Spin-dependent electron transport in metallic carbon nanotubes
• Current-induced forces in conducting and semiconducting carbon nanotubes
• Ferrocene dimers for molecular wire applications
• Designing nanogadgets by interconnecting carbon nanotubes with zinc layers
• Electron transport through carbon nanotube in intramolecular heterojunctions with peptide linkages
• Conductance of benzene clusters in the Pi-stack direction
• Excess-silver-induced brigde formation in a silver sulfide atomic switch
• Interface electronic structures of zinc oxide and metals

Check them out at http://quantumwise.com/publications/scientific-publications!

If you have published an article with ATK, please make it known in the Forum (we would love it if you also included the abstract in the post!) or send us an email (contact details on the web site).

65

Scripts, Tutorials and Applications / Exporting XYZ files from VNL and ATK

« on: December 5, 2008, 23:43 »

A recent post (http://quantumwise.com/forum/index.php?topic=4.0) asked about importing XYZ files into VNL. Here is a way to export XYZ files from VNL! It is not possible as a direct function in the program, but it is relatively simple anyway, by using just a few lines of NanoLanguage code.

1. Open an editor (it can be the Script Editor in VNL) and make a NanoLanguage script that contains the following code:

Code

from ATK.KohnSham import *

def printXYZFile (configuration):
    elements = configuration.elements()
    coordinates = configuration.cartesianCoordinates()
    print len(elements)
    print 'From VNL'
    for elem,coords in zip(elements,coordinates):
        print elem.symbol(),
        for i in coords:
            print i.inUnitsOf(Angstrom),
        print

2. If you are using Windows, you first need to make a new directory called site-packages in the directory atk\lib in the VNL installation.

On Linux, this directory already exists, but is located in atk\lib\python2.4.

3. Save the file in the directory site-packages. Call it xyzexport.py for instance.

4. Now, assume we have a molecule in VNL, built e.g. in the Molecular Builder. Drag the molecule from the Molecular Builder to the Script Editor (make sure the editor is empty, in case you used it to create the script above). The corresponding NanoLanguage code will be shown in the editor. Now add these two lines at the bottom of the script:

Code

from xyzexport import printXYZFile
printXYZFile(molecule_configuration)

5. Drop the script on the Job Manager, and behold - an XYZ listing of the molecule will be printed in the Log Window. From there, you can just copy/paste the lines and save them as an XYZ file. (To copy lines from the Log Window, mark them and press Ctrl-C!)

In the future, whenever you want to export an XYZ file, you just follow steps 4 and 5 each time.

A ready file xyzexport.py is attached for convenience, you can copy it into the site-packages directory.

• Note that this trick is generally useful. Any Python files that are placed in site-packages can be imported directly in NanoLanguage scripts that are executed in the Job Manager.
  
• In order to make the same script available also in NanoLanguage scripts executed with ATK, you just copy the same file to the same directory in the ATK installation.