vnl file is larger, how to read it?

[renren123123]

recently we calculated a model with about 200 atoms, we can get its voltage drop file, however, it is about 150MB, so it doesn't read on my computer(4G memory),it shows the memory is not enough! how
to deal with  it?Thank you very much!!!

[Anders Blom]

VNL can use a lot of memory sometimes... One way to minimize the memory usage is to not use the Result Browser, but drag the VNL file directly onto the Nanoscope, directly after starting VNL up. Does that help for your system?

(I hope you are using VNL 2008.02 or 10? Earlier versions had memory leaks...)

[renren123123]

However, I directly drop the vnl file to nanoscope, it display not enough memory! my system is windowXP, I dont know how to install in linux?

[Anders Blom]

I'm not sure the memory issue is different in Linux... Unfortunately it seems this is a real bug in VNL

[Nordland]

I have seen the behavior on linux as well, so I think it is a bug :| - however usually I use 3rd part plotting tools like GNUplot since it is easy to read-of values etc
from a dedicated plotting tool! I hope that a new version of VNL would support this....

[Anders Blom]

There are a couple of solutions I can propose to this troublesome situation.

1) You can export the 3D grid to a file which can be imported and read by another software, like Matlab. Detailed instructions are available in another post on this forum.

2) Perhaps you can consider if you really need to visualize the voltage drop in 3D? Perhaps the real information you are looking for can be obtained by integrating the data in the XY plane and just plot how the voltage drops along the Z axis?

[renren123123]

Thank you for your advice! however, I dont know how to extract data from VNL file such as VoltageDrop.vnl which is larger about 150MB?

[Nordland]

Hey!

I justed tried to hack something together for you - it will not solve all your problems but it will export data to standard out.

[renren123123]

THANK YOU VERY MUCH!
I modify the name of VNL, and run it on my computer, however, it displays :
Traceback (most recent call last):
File "save_my_data_from_vnl.py",line 15,in ?
t['Real Space Effective Potential-Real Space Effective Potential Voltage Drop']
KeyError:''Real Space Effective Potential-Real Space Effective Potential Voltage Drop'
How to deal with it? Thanks a lot!!!

[Nordland]

I fixed a small bug - and updated the script, please try it again.

[renren123123]

I can see your updated script, Can you attach it here?
thank you very much!

[Nordland]

I attached it to this post.

[renren123123]

I have run it however it display the same error! this time I correct the name of my vnl file is "voltage_drop.vnl" , and run it .

[Nordland]

Try inserting the following into the script and tell me what it writes:
print t.keys()

So the it will look such that:

t = samples[0].properties({"calculated_with_NL":None})
print t.keys()
d = t['Real Space Effective Potential-Real Space Effective Potential Voltage Drop']

[renren123123]

 
I run it adding a line, however, it remains