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Re: [ESPResSo-users] Espressomd-users Digest, Vol 35, Issue 3


From: Stefan Kesselheim
Subject: Re: [ESPResSo-users] Espressomd-users Digest, Vol 35, Issue 3
Date: Thu, 12 Sep 2013 08:35:45 +0200

Dear Uday,
I tried your script with less particles and without electrostatics, and reduced 
the number of steps (on my poor small laptop). The output is below, and looks 
perfect.
You behaviour looks as if your time-step was too large: We usually apply t=0.01 
for temperature 1 and mass 1. Your thermal velocity is larger by a factor of 
2.493, and hence I'd try a time step of 0.01/2.493, which is around 0.004.
What you observe is typical for an almost stable integration scheme: Most of 
the time everything looks OK, the kinetic energy is reasonable (not 1e100 or 
so) but eventually one particle bumps to badly into another and is strongly 
accelerated, not to incredibly large speeds, however. I assume you noticed your 
temperature of 1226.6668964027733. At that point something really bad had 
happened.
I hope that helps.
Cheers and good luck
Stefan

t=0.0 E=280.938469643488 T=1.1017194887979922
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
t=6.000000000000005 E=596.9042548544768 T=2.340800999429321
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
t=12.000000000000233 E=604.8727054826621 T=2.3720498254222044
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
t=18.00000000000046 E=657.2053785866518 T=2.577275994457458
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
t=24.000000000000686 E=722.55426540435 T=2.833546138840588
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
t=30.000000000000913 E=578.1727244966031 T=2.2673440176337376
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
t=36.00000000000114 E=671.9191506686635 T=2.6349770614457393
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
t=42.000000000001364 E=669.5787129698989 T=2.6257988743917604
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
t=48.00000000000159 E=643.4494161337196 T=2.5233310436616456
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
t=54.00000000000182 E=656.1849249589054 T=2.573274215525119
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
t=60.000000000002046 E=662.0536959631918 T=2.5962890037772226
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
t=66.00000000000227 E=573.1894861992037 T=2.2478019066635437
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
t=72.0000000000025 E=626.788313224326 T=2.457993385193435
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
t=78.00000000000273 E=604.2511991405424 T=2.369612545649186
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
t=84.00000000000296 E=618.0628582264868 T=2.4237759146136737
WARNING: "inter ljforcecap" is deprecated and will be removed in some further 
version. Use "inter forcecap" instead.
^Cbackground_errors 0 {000 caught signal 2} 


On Sep 11, 2013, at 9:55 PM, padidela uday <address@hidden> wrote:

> Hello Georg Rempfer
> 
> This is my simulation script.
> 
> 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
> }
> 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 
> # 1 TIMESTEP = 6E-14
> setmd skin 0.4
> set temp 2.493
> # 300K
> set gamma 0.4
> thermostat langevin $temp $gamma
> 
> # WCA POTENTIAL
> #radius of solute=16nm and radius of solvent=1.0nm
> set sig 1.0
> set eps 1.0
> set cut [expr 1.22426*$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 $shift 0  
> 
> inter coulomb 0.718 p3m tunev2 accuracy 1e-3
> # p3m VARIABLES LIKE NO. OF MESH POINTS,CHARGE ASSIGNMENT ORDER ETC. ARE 
> CALCULATED BY THE FUNCTION TUNEV2
> 
> set inter_steps 100000
> for {set cap 30} {$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 < 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}
>     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
> 
> 
> And my equilibration steps goes like this
> 
> 
> t=0.0 E=5020.1630531796645 T=1.018479456496
> t=599.999999998393 E=18220.59709794523 T=5.810625670095469
> t=1199.9999999989084 E=15816.115978703594 T=5.256242903696039
> t=1800.0000000074576 E=34210.471905675084 T=9.991591589316466
> t=2400.0000000026675 E=36777.37784842733 T=10.675911375103668
> t=2999.9999999884794 E=42742.20641527184 T=11.999132235697983
> t=3599.9999999742913 E=26673.72159004423 T=7.974431903864867
> t=4199.999999967986 E=4779348.10622052 T=1226.6668964027733
> t=4799.999999999272 E=57093.543095210924 T=15.791968482255356
> 
> Thanks
> 
> Uday
> 
> 
> On Wed, Sep 11, 2013 at 9:30 PM, <address@hidden> wrote:
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> Today's Topics:
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>    1. [Espresso] Langevin thermostat (padidela uday)
>    2. Re: [Espresso] Langevin thermostat (Georg Rempfer)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 11 Sep 2013 15:43:04 +0530
> From: padidela uday <address@hidden>
> To: address@hidden
> Subject: [ESPResSo-users] [Espresso] Langevin thermostat
> Message-ID:
>         <address@hidden>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear All,
> 
> I am simulating a charged colloidal system using WCA potential.
> 
> Charge -25:1
> Size 16:1 nm
> Box length 200
> No of particles are 2600 (100:2500)
> Timestep:0.006
> Skin : 0.4
> Temp 2.492 (300k)
> Gamma 1.0
> 
> But the temperature of my system is not maintained to the set value of temp.
> The system gets fluctuated with this gamma value.
> What would be the ideal gamma value to be used for larger system?
> 
> 
> 
> With regards
> 
> 
> Uday
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> ------------------------------
> 
> Message: 2
> Date: Wed, 11 Sep 2013 12:24:58 +0200
> From: Georg Rempfer <address@hidden>
> To: "address@hidden" <address@hidden>
> Subject: Re: [ESPResSo-users] [Espresso] Langevin thermostat
> Message-ID:
>         <address@hidden>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hello Padidela,
> 
> please provide a simulation script, otherwise we can only provide you
> with wild guesses. My wild guess would be that you don't substract the
> center of mass motion from your particles, to calculate the
> temperature.
> 
> Regards,
> Georg Rempfer
> 
> 2013/9/11 padidela uday <address@hidden>:
> > Dear All,
> >
> > I am simulating a charged colloidal system using WCA potential.
> >
> > Charge -25:1
> > Size 16:1 nm
> > Box length 200
> > No of particles are 2600 (100:2500)
> > Timestep:0.006
> > Skin : 0.4
> > Temp 2.492 (300k)
> > Gamma 1.0
> >
> > But the temperature of my system is not maintained to the set value of temp.
> > The system gets fluctuated with this gamma value.
> > What would be the ideal gamma value to be used for larger system?
> >
> >
> >
> > With regards
> >
> >
> > Uday
> >
> >
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
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> 
> 
> End of Espressomd-users Digest, Vol 35, Issue 3
> ***********************************************
> 
> 
> 
> -- 
> UDAY KUMAR PADIDELA
> SRF (CSIR) Department Of Chemistry,
> BITS Pilani, Goa,
> Mobile: +91-9890869615
>  
>              
> 




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