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[Xavier Gonze <xavier.gonze@uclouvain.be>]

Dear David,

On 17 Nov 2009, at 01:08, David M. Wood wrote:

> Greetings all!
>
> I'm examining the 'bonding' of a (neutral) molecule to a ZnO Zn- 
> terminated surface (using a 5 bilayer slab geometry) and, in order  
> not to bias the orientation of the molecule, started force  
> relaxation [ionmov=3] (with the molecule 'above' the surface) with  
> the bottom atom of the molecule 10 bohr above the 'top' surface  
> atom.  To my horror, after 75 Broyden steps all I've seen is small  
> (about 0.1 bohr) oscillations about the z value where I started the  
> molecule. The molecule has *twisted* slightly in place around its  
> original axis.  With ionmov=7 (quenched Verlet molecular dynamics)  
> the same thing occurs.  I'm going to die of old age before these  
> calculations converge.  In some sense this (not my death) is  
> reassuring  since very different approaches to structural relaxation  
> exhibit the same (annoying) physics.
>
> I assume that the problem lies in intra-molecular forces far  
> exceeding the molecule-surface atom force at this distance, so that  
> the neutral molecule experiences only a weak torque due to an  
> (inhomogeneous) electric field.  Even a rigid rotation of the  
> molecule might then induce a long cascade of slight readjustment of  
> Cartesian coordinates that change the total energy very little and  
> very very slowly.

Exact

>  I found that optimizing isolated molecules (in a large-lattice- 
> constant cubic cell) was extremely easy by comparison.
>
> So, a several obvious questions:
>
> (0) Which mode of IONMOV is most resistant to being trapped in local  
> minima of the energy as a function, say, of the molecular orientation?
>
> (1) LARGE MAIN QUESTION: Is there a simple way within ABINIT to  
> freeze the RELATIVE coordinates of the atoms in a molecule and allow  
> the "rigid" molecule to rotate and move as a block in response to  
> external forces (in my case, due to the atoms in the slab).

To allow a block of atoms to be translated rigidly should be possible  
thanks to the use of the following input variables :
nconeq , natcon , iatcon and wtatcon .
Warning : this is likely powerful, but not very often used, so there  
might be problems ...

To allow to rotate rigidly is not implemented ...

Xavier
> (2) SMALL AUXILIARY QUESTION: Is there a general protocol for such  
> relaxations: e.g., first do a not-so-well converged relaxation  
> starting from no more than 'xxx' bohr from the surface, then do a  
> refinement once a plausible near-equilibrium geometry has been  
> found?  (Yes, xxx would obviously depend on nasty details: I should  
> estimate surface charges and hence the non-uniform electric field,  
> the molecule's dipole moment, and hence the non-uniform field force  
> and insist this exceed intra-atomic forces.)
>
> I'm using ABINIT 5.8.4 but believe my problems have little to do  
> with ABINIT per se.  Key parts of my input file:
>
> occopt 7
> tsmear 0.01
> ionmov 3
> toldff 1.d-6 #this is for ELECTRON SCF: 10x bigger than tolmxf:
> tolmxf 1.d-5 #somewhat finer than before (sep 15)
>
> Many thanks for any suggestions!
>
> DMW
>
>
> David M. Wood, Dept. of Physics, Colorado School of Mines, Golden,  
> CO 80401
> Phone: (303) 273-3853; Fax: (303) 273-3919