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Re: [ESPResSo-users] Correlations, MSD, plotting and python.

From: Peter Košovan
Subject: Re: [ESPResSo-users] Correlations, MSD, plotting and python.
Date: Mon, 22 Jun 2015 10:52:49 +0200

Hi Rohit,

I suppose you are correlating observable particle_positions, i.e. a vector of the form (x1, y1, z1, x2, y2, z2 ... xN, yN, zN), then the output of the correlation square_distance_componentwise is (msd_x1, msd_y1, msd_z1 ... msd_xN, msd_yN, msd_zN), i.e. a 3N-dimensional vector, which gives you an individual msd per each particle and direction. The post-processing is left for the user, as the observable/correlation concept is more general and allows for more complex information than the msd. If you want msd from these numbers, you need to add up all the individual particle-direction msd's.

I am not sure how much of these features is presently accessible from python, sorry.



On Sat, Jun 20, 2015 at 1:30 AM, Rohit Goswami <address@hidden> wrote:
On running the sample correlation.tcl , I was unable to understand the output format. From the user guide it mentions the output to be the time, the contributing particle number and the individual components of the correlation..
How would these individual components be interpreted as plottable MSD values? [In context of the msd files produced from the correlation.tcl file]

The data in question is in the following form

0.32 499984 0.0930939 0.093013 0.0939898 0.0939667 0.0916034 0.0915876

A more inefficient method involving the particle positions being substracted and squared directly gives easily plotted values in the form

3  9.7157884

[The second data set isn't related to correlation.tcl, its taken from the msd.tcl file in the docs produced for the first tutorial]

Any help would be greatly appreciated.

Additionally, are the core analysis techniques accessible from within the python interface?

Dr. Peter Košovan

Department 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
Tel. +420221951290
Fax +420224919752

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