Re: [ESPResSo-users] stopping the simulation

[Ulf Schiller]

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 Jülich, Germany          Fax:     +49 2461 61-3180

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