[CPMD-list] Where to find more examples?

[Axel Kohlmeyer]

On Thu, 18 Mar 2004 13:13:52 -0800 (PST)  Weiqiao Deng wrote:

> Dear Axel,
> 
> 
> Many thanks for your message.
> I have one more question. 32-bulk water is a neutral system. If we have
> extra OH- or H+ in the system, we set the charge as -1 or +1 for whole
> system? Do we have a way to set the particle extra H's charge as +1?
> Thanks.

you can only set the charge for the whole system
(CHARGE keyword, &SYSTEM section). cpmd uses that
information in combination with the (effective)
charges of the atoms from the pseudopotential files
to compute the total number of electrons in the system.

the actual charge distribution
will be calculated, when you do the wavefunction
optimization. please note that the keyword ATOMIC CHARGES
(&ATOMS section) is only used to calculate the initial 
guess for the electron structure and has no effect on
the total number of electrons.

you may also have a look at
<http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/files/xyz2cpmd.pl>
which might be helpful to contruct the &ATOMS and &SYSTEM section
of for your simulations if you feed it an xyz-file with your pre-equlibrated
restart. you may have to adapt it for your choice of pseudopotentials.

axel

> 
> Weiqiao
> 
> 
> On Thu, 18 Mar 2004, Axel Kohlmeyer wrote:
> 
> > On Wed, 17 Mar 2004, Weiqiao Deng wrote:
> > 
> > WD> Dear list,
> > WD> 
> > WD> I am a beginner to use CPMD and hope to find more examples to repeat and
> > WD> learn CPMD simulation.
> > WD> 
> > WD> Here is the special example I am interested at repeating. Anyone has that
> > WD> input file of that example? Thanks in advance.
> > WD>  
> > WD> Tuckerman ME, Marx D, Parrinello M
> > WD> The nature and transport mechanism of hydrated hydroxide ions in aqueous
> > WD> solution NATURE 417 (6892): 925-929 JUN 27 2002
> > 
> > dear weiqiao,
> > 
> > there is a 32-bulk water example in the cpmd-test archive,
> > using MT pseudopotentials, you could use that as a starting point.
> > 
> > i suggest you first equilibrate a suitable configuration with
> > a classical MD simulation (i found the SPC/E water potential 
> > seems to yield structures, that are very close to the 
> > CP-MD structures with the BLYP functional). this way you
> > would have a comparatively short equilibration time
> > for the CP-MD run (compared to, e.g. removing a hydrogen
> > atom from a bulk water system). 
> > 
> > btw: don't forget to set the charge or you 
> > will get very surprising results. <g>
> > 
> > good luck,
> > 	axel.
> > 
> > WD> 
> > WD> Weiqiao
> > WD> 
> > WD> _______________________________________________
> > WD> CPMD-list mailing list
> > WD> CPMD-list at cpmd.org
> > WD> http://www.cpmd.org/mailman/listinfo/cpmd-list
> > WD> 
> > WD> 
> > 
> > 
> 

--

=======================================================================
Axel Kohlmeyer      e-mail:  axel.kohlmeyer at theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                   http://www.theochem.ruhr-uni-bochum.de
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.