Re: [ESPResSo-users] Correlation

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: espressomd-users-bounces+markus.wink=address@hidden [mailto:espressomd-users-bounces+markus.wink=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

From:	Peter Košovan
Subject:	Re: [ESPResSo-users] Correlation
Date:	Thu, 24 Apr 2014 09:32:34 +0200