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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 |
User-agent: |
KMail/1.13.6 (Linux/2.6.38-15-generic; KDE/4.6.5; x86_64; ; ) |
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, Universität Stuttgart Email: address@hidden
Pfaffenwaldring 27
70569 Stuttgart, Germany