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From: padidela uday
Subject: [ESPResSo-users] QUERY on TIME STEPS
Date: Tue, 12 Nov 2013 23:15:33 +0530


As Equilibration time steps and production steps are important in simulation.
My first query is:

How should i find out that my system has equilibrated after certain timesteps and how can i know
that these timesteps are enough for a system to get equilibrated?

My second query is:
I would like to know whether this script tells about the production time steps?
If it is so then how can i calculate them?
If this script doesn't give idea about production time steps then how can i include production steps?

set n_solute 100
set n_solvent 2500
set box_l 200
setmd box_l $box_l $box_l $box_l
setmd periodic 1 1 1
for {set i 0} { $i < 100 } {incr i} {
    set posx [expr $box_l*[t_random]]
    set posy [expr $box_l*[t_random]]
    set posz [expr $box_l*[t_random]]
    set vx [gauss_random]
    set vy [gauss_random]
    set vz [gauss_random]
    part $i pos $posx $posy $posz type 0 v $vx $vy $vz q -25 mass 1
set density 1.0
for {set i 100} { $i < 2600 } {incr i} {
    set posx [expr $box_l*[t_random]]
    set posy [expr $box_l*[t_random]]
    set posz [expr $box_l*[t_random]]
    set vx [gauss_random]
    set vy [gauss_random]
    set vz [gauss_random]
    part $i pos $posx $posy $posz type 1 v $vx $vy $vz q 1 mass 1

setmd time_step 0.006
setmd skin 0.4
set temp 2.493
set gamma 1
thermostat langevin $temp $gamma

set sig 1.0
set eps 1.0
set cut [expr 1.2246*$sig]
set shift [expr 0.25*$eps]
inter 0 0 lennard-jones $eps $sig $cut $shift
inter 1 0 lennard-jones $eps $sig $cut $shift
inter 1 1 lennard-jones $eps $sig $cut $shift

inter coulomb 0.718 p3m tunev2 accuracy 1e-3

set inter_steps 100000
for {set cap 20} {$cap < 200} {incr cap 10} {
    set temp [expr [analyze energy kinetic]/(1.5*[setmd n_part ])]
    puts "t=[setmd time] E=[analyze energy total] T=$temp"
    inter ljforcecap $cap;
    integrate $inter_steps
inter ljforcecap 0

set g [open "" "w"]
set n_part [expr ($n_solute + $n_solvent)]
for {set i 0} { $i < 3350 } {incr i} {
    puts "step $i ftime=[setmd time] energy=[analyze energy total]"
    puts "temp = [expr [analyze energy kinetic]/(1.5*[setmd n_part])]"
    integrate 300

    set f [open "config_$i" "w"]
    blockfile $f write tclvariable {box_l density}
    blockfile $f write variable box_l
    blockfile $f write particles {id pos type v f q mass}
    set temp [expr [analyze energy kinetic]/(1.5*[setmd n_part ])]
    puts $f " \ { energy [analyze energy total] $temp}"
    puts $g " [analyze energy kinetic] [analyze pressure total] [analyze energy total] $temp"

    close $f
close $g

Thank you,

With regards


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