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Re: [ESPResSo-users] stopping the simulation


From: Ulf Schiller
Subject: Re: [ESPResSo-users] stopping the simulation
Date: Wed, 11 Jul 2012 18:16:43 +0200
User-agent: Mozilla/5.0 (X11; Linux i686 on x86_64; rv:13.0) Gecko/20120614 Thunderbird/13.0.1

Hi Tarun,

you can try the following: Immediately after writing, load the configuration from the file it was just saved to. That should make sure that the order of the particles in the lists is consistent with the sequence of random numbers. Be sure to also set the random seed correctly, as Peter pointed out.

Cheers,
Ulf

On 07/11/2012 06:01 PM, Tarun Khanna wrote:
hi,

Thankyou for such an early reply and sorry for incomplete description of
the problem. Here I am including the script in which i am having the
problem mentioned.


set n_solute 250
set n_solvent 500
set density 0.006
set box_l [expr pow($n_part/$density,1./3.)]
setmd box_l $box_l $box_l $box_l
setmd periodic 1 1 1
for {set i 0} { $i < 250 } {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 2 mass 125
}
for {set i 250} { $i < 750 } {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 0.02
setmd skin 0.4
set temp 2.493
set gamma 1
thermostat langevin $temp $gamma

set sig 3.0
set eps 1.0
set cut [expr 2.5*$sig]
set shift [expr 0.25*$eps]
inter 0 0 lennard-jones $eps $sig $cut $shift 0
inter 1 0 lennard-jones $eps $sig $cut $shift 0
inter 1 1 lennard-jones $eps $sig $cut $shift 0
inter coulomb 2.3462 p3m tunev2 accuracy 1e-3

set inter_steps 50000
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 "analysis.data" "w"]
set n_part [expr ($n_solute + $n_solvent)]
for {set i 0} { $i < 6000 } {incr i} {
     puts "step $i ftime=[setmd time] energy=[analyze energy total]"
     puts "temp = [expr [analyze energy kinetic]/(1.5*[setmd n_part])]"
     integrate 1000

     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}
     blockfile $f write random
     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

This script i am stopping after every 1000 configurations and then
running it afterward with the input as the last configuration stored
instead of random configuration..

And i am using the configurations both for the calculation of dynamic as
well as static properties and hence the reproducibility of the
trajectory is important.


Thankyou

Tarun




--
Dr. Ulf D. Schiller                        Building 04.16, Room 3006
Institute of Complex Systems (ICS-2)       Phone:   +49 2461 61-6144
Forschungszentrum J├╝lich, Germany          Fax:     +49 2461 61-3180



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