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[ESPResSo] Extracting Values of Quantities Calculated during Simulation

From: Lorenzo Isella
Subject: [ESPResSo] Extracting Values of Quantities Calculated during Simulation
Date: Mon, 19 Nov 2007 12:44:46 +0100

Dear All,
I have a couple of questions about how to save and manipulate the
output of a simulation with Espresso.
Despite the manual, I have not been able to do what I have in mind.
Apologies if it was already clear enough there, but I have been stuck
for quite a while.
1) Say that you saved the configuration of your system in a blockfile
using a command like:

set f [open "config_$i" "w"]
blockfile $f write tclvariable {box_l density}
blockfile $f write variable box_l
blockfile $f write particles {pos}
close $f

for i labeling the time during your simulation.
Then you read the corresponding blockfile using:
set f [open "config_$j" "r"]
while { [blockfile $f read auto] != "eof" } {}
close $f

After reading the blockfile, I can use e.g. Espresso builtin functions
to get a radius of gyration using one of its ready-to-use statistical
Now,  what if you want to calculate some statistics about the position
of your particles along the x axis?
In other words, how do you access that info which is not a hard-coded
function in Espresso?
2)It is similar to the previous question: what if I just want to save
the particle positions (x,y,z) as a N by 3 plain matrix to read it and
post-process it with other tools which do not like the blockfile

In general, as you can see, I have troubles in accessing "directly"
some of the quantities which are internally calculated by Espresso.
Many thanks


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