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Re: [ESPResSo-users] ESPResSo Lennard-Jones cut-off question


From: Florian Weik
Subject: Re: [ESPResSo-users] ESPResSo Lennard-Jones cut-off question
Date: Mon, 14 Jul 2014 14:18:32 +0200

Hello,
this is a bug. The problem vanishes if you set a skin (setmd skin 1.0). I will prepare a patch, the user should at least be warned about this.

Regards,
Florian


On Mon, Jul 14, 2014 at 12:17 PM, Karl Kue <address@hidden> wrote:
Dear all,

I was playing around with the "analyze energy" command when I found that it gave me zero energy for systems which I assumed was supposed to give non-zero energies. I tested a small script as follows:

setmd box_l 10 10 10
inter 0 0 lennard-jones 1.0 1.0 3.0
part 0 pos 0 0 0 type 0
part 1 pos 0 0 2.1 type 0
puts [analyze energy]
 
I was expecting a non-zero energy but it returns the following:

{ energy 0.0 } { kinetic 0.0 } { 0  0 nonbonded 0.0 } 

If I change the lennard-jones cut-off to 3.1, however, I get a non-zero energy; I get the following output

{ energy -0.041592730503778354 } { kinetic 0.0 } { 0  0 nonbonded -0.041592730503778354 } 

I dug up an old thread from 24 Aug 2007 and it says

For the future you can test your question more easily yourself with:
setmd box_l 10 10 10
part 0 pos 1 1 1 type 0
part 1 pos 1.5 1 1 type 1
inter 0 1 lennard-jones 2 2 1 1 0
analyze energy 
If this doesn't give you a nonzero energy, please bug me again!

This does not, in fact, give me a nonzero energy; it gives me a zero energy. I played around with the feature some more and I think that the Lennard-Jones cuts off at 1 less than the cut-off value specified (or r_cut - 1). Is this really the way the potential works or did I do something wrong? I tried this on different machines and they gave me the same results. I am using ESPresSo 3.2.0.

--
Kue, Karl Thomas Y.


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