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Re: [ESPResSo-users] Correlation
From: |
Stefan Kesselheim |
Subject: |
Re: [ESPResSo-users] Correlation |
Date: |
Thu, 24 Apr 2014 16:25:01 +0200 |
Hi,
a small extra remark: Observables are n-dimensional vectors.
particle_velocities contains 3N components, where N is the particle number. You
specified probably all particles of you polymer.
The correlation operation scalar_product calculates the scalar product of the
observable at two different times. The result is scalar. Thus what your thing
calculates is
C(tau) = < \sum_{i=0}{N-1} v_{x,i}(t) v_{x,i}(t+tau) + v_{y,i}(t)
v_{y,i}(t+tau) + v_{z,i}(t) v_{z,i}(t+tau) >_t
If you want to calculate the center-of-mass VACF, you should use the
com_velocity observable.
Cheers
Stefan
On Apr 24, 2014, at 9:32 AM, Peter Košovan <address@hidden> wrote:
> Hi Roya,
>
> Regarding your point 2:
>
> See user guide, sec. 9.2.5:
> Output format
>
> The output looks as follows:
>
> tau1 n_samples C1 C2 ... Cn
> tau2 n_samples C1 C2 ... Cn
>
> Where each line corresponds to a given value of tau, n_samples is the number
> of samples
> which contributed to the correlation at this level and Ci are the individual
> components
> of the correlation.
>
> From your output, I guess that you have just a single particle, not a
> polymer.
>
> Note that vacf relaxes raher fast, while a reasonably long polymer relaxes
> much much ... much slower. To get an idea about polymer relaxation times,
> it's better to autocorrelate Re or Rg.
>
> How to obtain the autocorrelation time concerns elementary data analysis, not
> the usage of Espresso. I would fit the output with the autocorrelation
> function with an appropriate function, or try to integrate it.
> A*exp(-tau/tau_corr) often works well, but not for vacf which is an
> oscillating function. Mind that the error of the autocorrelation grows
> steeply with tau, so the result at higher tau is often mere garbage and you
> need to exclude it from your analysis.
>
> Regards,
>
> peter
>
>
> 2014-04-24 9:00 GMT+02:00 Wink, Markus <address@hidden>:
> Dear Roya,
>
>
>
> concerning your questions:
>
> 1. When you write time=[setmd time], what is the time that it gives you?
> What is its unit?
>
> ESPResSo does not predefine any system of units. In a simulation you convert
> your parameters into MD units. This means that a timestep can correspond to
> any “physical-timestep”, depending on how you have chosen your setup. More
> information on “units in ESPResSo” can be found in the user’s manual.
>
>
>
> 3. I want to add Lattice Boltzman to my simulation and I need to see some
> sample codes about it or some projects on it. It really helps me since LB is
> complicated for me.
>
> In the repository of Espresso, you will find an example of a
> lattice-boltzmann implementation (“object_in_fluid.tcl”). That, at least for
> me, is of great help to get an deeper understanding of the LB algorithm and
> implementation.
>
>
>
> I hope that helps a bit (sorry, for the second question I don’t have an
> answer since I have never used it).
>
> @ ESPResSo-experts: don’t hesitate to correct me, if anything is wrong in my
> answers!
>
>
>
> Greetings
>
>
>
> Markus
>
>
>
>
>
> Von: address@hidden [mailto:address@hidden Im Auftrag von roya moghaddasi
> Gesendet: Mittwoch, 23. April 2014 16:56
> An: address@hidden
> Betreff: [ESPResSo-users] Correlation
>
>
>
> Hello everybody,
>
> I have three questions:
>
> 1. When you write time=[setmd time], what is the time that it gives you?
> What is its unit?
>
> 2. I have some polymers in my system and I want to calculate its velocity
> autocorreletion in order to find the decay time or the time my system
> relaxes, so I write the following:
>
> set vel [observable new particle_velocities type [list 0]]
>
> set vacf1 [correlation new obs1 $vel corr_operation scalar_product tau_max 1
> dt $time_step]
>
> correlation $vacf1 write_to_file "vacf1.dat"
>
> What it gives me in vasf1.dat is some lines like:
>
> 0 579900 11953.9
> 0.005 579899 11906.2
> 0.01 579898 11793.8
> 0.015 579897 11647.8
>
> I don't know the meaning of each column. Of course I read the Espresso manual
> about it but I need more explanation, and I want to know how to find the
> decay time by these information.
>
> 3. I want to add Lattice Boltzman to my simulation and I need to see some
> sample codes about it or some projects on it. It really helps me since LB is
> complicated for me.
>
> I would appreciate if someone can help me.
>
> Thank you very much.
>
> Roya
>
>
>
>
>
>
> --
> Dr. Peter Košovan
>
> Departmtent of Physical and Macromolecular Chemistry
> Faculty of Science, Charles University in Prague, Czech Republic
>
> Katedra fyzikální a makromolekulární chemie
> Přírodovědecká fakulta Univerzity Karlovy v Praze
>
> www.natur.cuni.cz/chemistry/fyzchem/
> Tel. +420221951290
> Fax +420224919752
>
> Pokud je tento e-mail součástí obchodního jednání, Přírodovědecká fakulta
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