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Re: [ESPResSo-users] Control Temperature in version 3.2


From: Axel Arnold
Subject: Re: [ESPResSo-users] Control Temperature in version 3.2
Date: Tue, 14 May 2013 22:41:01 +0200
User-agent: Mozilla/5.0 (X11; Linux i686; rv:17.0) Gecko/20130330 Thunderbird/17.0.5

On 05/14/2013 08:36 PM, Salvador H-V wrote:
However, in my script I am not making assumptions about the number degrees of freedom.

I just obtain the system temperature with:
set temp [expr [analyze energy kinetic]/(0.5*$np)]

Hmm, but that means you assume 1 DOF per particle, if np is the number of particles. That should give you a factor 3 too high temperature, 1.5 would be correct for 3 DOFs. Or 3 with ROTATION on, but ROTATION_PER_PARTICLE off. And if you use RATTLE to constrain some distances, these constraints need to be subtract from the number of DOFs...

What I found is that only when I turn off the Rotation, Rotational_Inertia, Rotation_Per_Particle and Virtual_Sites I get

puts "The degrees of freedom is [degrees_of_freedom] " = 3!

Yes, that is since the other features require rotation, and degrees_of_freedom checks if any rotation-related feature is on.

If I understand well, if some of the virtual_sites features are activated, then rotation feature is automatically activated, then

% [code_info]
invalid command name "ESPResSo-3.2.0
{ Compilation status { FFTW } { CONSTRAINTS } { BOND_ANGLE_HARMONIC } { GAUSSIAN } { COMFIXED } { HERTZIAN } { PARTIAL_PERIODIC } { LENNARD_JONES } { VIRTUAL_SITES_RELATIVE } { EXTERNAL_FORCES } { TABULATED } { ROTATION } { SOFT_SPHERE } { VIRTUAL_SITES_NO_VELOCITY } { LENNARD_JONES_GENERIC } { BOND_VIRTUAL } }"
% [degrees_of_freedom]
invalid command name "6"

That is correct, since rotation is on, so the particles have 6 DOFs. However, if ROTATION_PER_PARTICLE is on, that is no longer necessarily true, but depends on the particle. Only for particles, that have rotational properties, the number of DOFs should be 6, but then, that cannot be reflected by degrees_of_freedom. Might be the best to just dump the function, since it cannot give meaningful results anymore.

Axel

--
JP Dr. Axel Arnold
ICP, Universit├Ąt Stuttgart
Pfaffenwaldring 27
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609




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