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Re: [ESPResSo-users] referring to stored configs separately

From: Axel Arnold
Subject: Re: [ESPResSo-users] referring to stored configs separately
Date: Tue, 26 Mar 2013 13:27:03 +0100
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There is another option, which I normally use. Rather than using the writing of analysis configs, which was mainly meant for writing analysis test cases. More flexible is, to write out the particle configurations using "blockfile write particles", which also allows you to specify which properties you need (just {pos} would be the equivalent of analyze append). Using "blockfile read auto", you can easily traverse over a file written like that, since it always returns the type of the last read block. So, if you get "particles"", a new configuration was loaded that you can analyze, and you can store all properties you wish - velocities, forces,...

N.B., there is a brief introduction in the UG (I believe) how you can easily inject arbitrary block types. By that, you can even save derived values that you compute at run time, or just make a block {config 42} to get the number of the current configuration. scripts/blockfile_support.tcl contains the reading functions for the basic blocks, that might be already enough to understand how it works.


On 03/26/2013 08:18 AM, Koen Nickmans wrote:
Hi all,

I have two questions which I think should be easy to answer!

1. When a lennard-jones potential is shifted so that the potential is equal at a cutoff radius, how does espresso handle the calculation of forces around the cutoff point? I cannot find where this is discussed.

2. During my simulation I store configurations at regular intervals using the analyze append command, and write them with the blockfile command. In a next script I retrieve the configurations with blockfile $file read auto. How can I now refer to each stored configuration separately? What I would like is:

for i number of configs {
access config i
calculate property

It's the 'access config i' that I'm looking for.

As always, thanks for your help!

Koen Nickmans
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JP Dr. Axel Arnold
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