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General Questions and Answers / Re: optimisation of geometry of large molecular junction
« on: January 18, 2012, 16:53 »
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General Questions and Answers / Re: optimisation of geometry of large molecular junction
« on: January 17, 2012, 18:06 »
how to change the dangling bond using vnl.
I have tried with 5 layers also there is same problem.
how can i convert 4 layers to 5 layers in builder please tell if u are talking about custom builder then i know, otherwise please tell me
I have tried with 5 layers also there is same problem.
how can i convert 4 layers to 5 layers in builder please tell if u are talking about custom builder then i know, otherwise please tell me
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General Questions and Answers / Re: optimisation of geometry of large molecular junction
« on: January 16, 2012, 19:12 »
Thanx for the reply
I am a new user so I dont know how to keep Z constant. in other words i didnt understand your solution.
secondly my molecule contain Oxygen can I still do non consistent calculations.
Please tell me the procedure to solve this problem.
Like in steps or in script format.
I am a new user so I dont know how to keep Z constant. in other words i didnt understand your solution.
secondly my molecule contain Oxygen can I still do non consistent calculations.
Please tell me the procedure to solve this problem.
Like in steps or in script format.
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General Questions and Answers / optimisation of geometry of large molecular junction
« on: January 16, 2012, 08:46 »
HI.........
I am a new user of VNL. I trying to use this from past 8 months. I am working on molecular junctions. My central molecules are Quite large like 40- 200 atoms. I am confused that how many layers of electrodes to be attached for Different types of molecules. i.e what is the relation between no of atoms in the molecule with the no. of layers of electrodes.
Like when I am trying for molecule with 46 atoms.
1. I have attached 5 layers on each side, then it give error that no. of atoms are not equal on both sides of electrodes. But they are same in script.
2. If I put less no layers then molecule breaks.
3. If i take 8 layers then total no. of molecules is very large and it will not converge easily.
These are problems with such a small system of 46 atoms.
then what about larger molecules like 129 atoms
for this I have put 11 layers on each side still it gives same error.
I don't know what to do.
please help me if anyone knows...
I am attaching XYZ file, inp file and error messages with this post
I am a new user of VNL. I trying to use this from past 8 months. I am working on molecular junctions. My central molecules are Quite large like 40- 200 atoms. I am confused that how many layers of electrodes to be attached for Different types of molecules. i.e what is the relation between no of atoms in the molecule with the no. of layers of electrodes.
Like when I am trying for molecule with 46 atoms.
1. I have attached 5 layers on each side, then it give error that no. of atoms are not equal on both sides of electrodes. But they are same in script.
2. If I put less no layers then molecule breaks.
3. If i take 8 layers then total no. of molecules is very large and it will not converge easily.
These are problems with such a small system of 46 atoms.
then what about larger molecules like 129 atoms
for this I have put 11 layers on each side still it gives same error.
I don't know what to do.
please help me if anyone knows...
I am attaching XYZ file, inp file and error messages with this post
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