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Re: [ESPResSo-users] stopping the simulation


From: Axel Arnold
Subject: Re: [ESPResSo-users] stopping the simulation
Date: Wed, 11 Jul 2012 19:55:21 +0200
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On Wednesday 11 July 2012, Ulf Schiller wrote:
> Hi Tarun,
> 
> you can try the following: Immediately after writing, load the
> configuration from the file it was just saved to.

Hi!

Actually, there is a command, invalidate_system, which does the same in 
memory.

> 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.

And to use the same number of processors, since the RNGs are per processor.

Axel

> 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


-- 
JP Dr. Axel Arnold      Tel: +49 711 685 67609
ICP, Universit├Ąt Stuttgart      Email: address@hidden
Pfaffenwaldring 27
70569 Stuttgart, Germany



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