[ESPResSo] RE: tuning parameters?

[Limbach, Hans Joerg, LAUSANNE, NRC-FS]

Hi to all,

P3M tuning is a tool for people who know how P3M works and how its error 
depends on the parameters. Before using you should read the following papers 
(as given in the developers guide in 
http://espressowiki.mpip-mainz.mpg.de/espresso/dg/html/p3m_8h.html):

P.P. Ewald, Die Berechnung optischer und elektrostatischer Gitterpotentiale, 
Ann. Phys. (64) 253-287, 1921 
R. W. Hockney and J. W. Eastwood, Computer Simulation Using Particles, IOP, 
London, 1988 
M. Deserno and C. Holm, How to mesh up {E}wald sums. I. + II., J. Chem. Phys. 
(109) 7678, 1998; (109) 7694, 1998 
M. Deserno, C. Holm and H. J. Limbach, How to mesh up {E}wald sums. , in 
Molecular Dynamics on Parallel Computers, Ed. R. Esser et al., World 
Scientific, Singapore, 2000 
M. Deserno, Counterion condensation for rigid linear polyelectrolytes, 
PhdThesis, Universit{\"a}t Mainz, 2000 

I have added the corresponding information to the user guide.

Regards,
Hanjo

> -----Original Message-----
> From: Christopher Jesudason [mailto:address@hidden 
> Sent: lundi, 27. août 2007 15:43
> To: Limbach,Hans Joerg,LAUSANNE,NRC-FS
> Cc: espresso
> Subject: RE: tuning parameters? 
> 
> Dear friends,
> Some of my coworkers have expressed   skepticism
> concerning the results obtained here because of the positive 
> electrostatic  energies for the
> polyelectrolyte system, and   the tuning parameters
> have been questioned. I could not find precise details of the 
> tuning process but this is what I did: I need confirmation 
> from you that the procedure is correct since the exact steps 
> are not to be found in the
> manual:
> Step1 :
> When I placed this snippet in my program just before exiting 
> 
> puts "[inter coulomb 1.0 p3m tune accuracy 1.e-6 r_cut 0 mesh 
> 0 cao 0 ]"
> #Defining electrostatics just before warm-up inter coulomb 
> 1.00  p3m tune accuracy 1.e-6  r_cut 0 mesh 0 cao 0 I got the 
> following output:
> System: box_l = 200.0, # charged part = 300 Sum[q_i^2] = 
> 300.0 Range for p3m.r_cut_iL: [0.0176078431373-0.498]
> Range for p3m.mesh:     [8-16]
> Range for p3m.cao:      [1-7]
> 
> set mesh cao r_cut_iL     alpha_L      err         
> ks_err     rs_err     time [ms]
> 1   16   4   4.98000e-01  5.22317e+00  7.31462e-07 
> 7.071e-07  1.872e-07  10      
> 2   16   5   3.31333e-01  7.96784e+00  9.40345e-07 
> 7.071e-07  6.199e-07  8       
> 
> Tune results of 2 trials:
> 2   16   5   3.31333e-01  7.96784e+00  9.40345e-07 
> 7.071e-07  6.199e-07  8       
> => inter coulomb 1 p3m 66.2667 16 5 0.0398392
> 9.40345e-07
> I noticed that r_cut_iL is not the same as the r_cut defined 
> in the standard declaration below and ditto the alpha_L is 
> not the same as the alpha in the standard declaration below:
> inter coulomb $p3m_bjerrum p3m $p3m_r_cut $p3m_mesh $p3m_cao 
> $p3m_alpha $p3m_accuracy where I assigned p3m_bjerrum=1, 
> p3m_r_cut=66.2667
> p3m_mesh=16 p3m_cao=5 p3m_alpha=0.0398392 p3m_accuracy=
> 9.40345e-07
>  Is this the correct procedure? For the same system at 
> different temperatures I made use of the same parameters.
> In particular, how is r_cut_iL     alpha_L      err   
>       ks_err     rs_err relater to r_cut and alpha 
> and the error that is put into the parameter list above ? I 
> could not find any documentation on this.
> Any tips would be welcome.
> Chris 
> 
> During the tuning  process I got
> --- "Limbach,Hans Joerg,LAUSANNE,NRC-FS"
> <address@hidden> wrote:
> 
> > Dear Christopher,
> > 
> > The last return value is the lj force cap radius.
> > This is indeed not documented. It is the radius at which 
> the force of 
> > the given lj interaction is equal to the force that you 
> have set with 
> > inter ljforcecap.
> > Regards,
> > Hanjo
> > 
> > 
> > > -----Original Message-----
> > > From: Christopher Jesudason
> > [mailto:address@hidden
> > > Sent: vendredi, 24. août 2007 19:12
> > > To: Limbach,Hans Joerg,LAUSANNE,NRC-FS
> > > Subject: Fwd: RE: what is the 6th parameter in the
> > LJ list
> > > when the inter command is given? 
> > > 
> > > 
> > > --- Christopher Jesudason <address@hidden>
> > > wrote:
> > > 
> > > > Date: Fri, 24 Aug 2007 08:28:26 -0700 (PDT)
> > > > From: Christopher Jesudason
> > <address@hidden>
> > > > Subject: RE: what is the 6th parameter in the LJ
> > list when
> > > the inter
> > > > command is given?
> > > > To: ESPResSo users' mailing list
> > > > <address@hidden>
> > > > 
> > > > Dear Hanjo,
> > > > thanks for your email. I need to carry out
> > further tests
> > > but there is
> > > > a technical question where I could not get any
> > information from the
> > > > manual. When I used the inter command I got a
> > list with an
> > > entry like
> > > > {1
> > > > 2 lennard-jones 1.0 1.0 1.12246 0.25 0.0
> > > > 1.00946218967
> > > > }  where a standard repulsive hard-c0re was
> > given what is the 6th
> > > > parameter with value 1.00946218967? ; in the
> > manual only 5
> > > parameters
> > > > are listed and I used these.
> > > > chris
> > > > --- "Limbach, Hans Joerg, LAUSANNE, NRC-FS"
> > > > <address@hidden> wrote:
> > > > 
> > > > 
> > > > 
> > > > 
> > > >        
> > > >
> > >
> >
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