Re: [ESPResSo-users] Correlation

[Stefan Kesselheim]

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 
> Univerzity Karlovy v Praze:
> a) si vyhrazuje právo jednání kdykoliv ukončit a to i bez uvedení důvodu,
> b) stanovuje, že smlouva musí mít písemnou formu,
> c) vylučuje přijetí nabídky s dodatkem či odchylkou,
> d) stanovuje, že smlouva je uzavřena teprve výslovným dosažením shody na 
> všech náležitostech smlouvy.