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[ESPResSo] Basic Questions

From: Salvador Herrera Velarde
Subject: [ESPResSo] Basic Questions
Date: Tue, 17 Mar 2009 19:46:48 -0400

Dear All,
I have some basic questions about ESPResSO that I couldn't figure out the answer.

I am writing some basic scritps for 3D colloids (beads) that interact via the repulsive part of
Yukawa potential (Debye-Huckel in ESPResSO). Righ now, I can calculate the radial distribution function, the structure factor and the MSD.

a) First, I want to study structural and dynamical properties of these systems in 2D.
What I did to simulate a two-dimensional was:  
#   --- The simulation Box is periodic in both  directions
setmd periodic 1 1 0
#   --- Simulation Box
setmd box_l $bl $bl $bl
& during the cycle to place the particles inside the simulation box:
part $i pos $posx $posy $posz type 0 q $zeff fix 0 0 1
so, my question is: Is this the best way to model a 2Dim system in ESPResSO ?
Should I do something similar for 1D?

b) Also, I am interested in binary mixtures of Yukawa colloids. However, I don't know how to specify the interactions for mixtures in ESPResSO. For potentials like Lennard-Jones you can specify the type of the particles:  inter type1 type2 lennard-jones...
but... how I can do the same for the Debye-Huckel potential ?
It is possible to specify different Bjerrum lengths for the species?

c) Finally, I am using the example provided in the user's guide to calculate the average of the gr and Sq. But (sometimes) when I stored many files configurations (to improve the statistics), I have some problems when I tried to calculate the averages of the gr & Sq. The result during the average is the next:

missing operand at address@hidden
in _expression_ "0 + address@hidden"
    (parsing _expression_ "0 + ")
    invoked from within
"expr $ai + $bi"
    (procedure "vecadd" line 3)
    invoked from within
"vecadd $avg_rdf $rdflist"
    ("for" body line 34)
    invoked from within
"for {set i 1 } { $i <= $nfiles } { incr i }  {
   set filename Pos$i
   set f [open "$filename" "r" ]
   while { [blockfile $f read auto] != "eof" } {..."
    (file "Debye-H.tcl" line 463)

Could you help me to handle these issues?

Thanks a lot,

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