[Pw_forum] Question on environ

[Oliviero Andreussi]

Dear Dra. Verónica M. Sánchez,

The environ.in file seems fine to me, the way you set it up will 
correspond to no environment effects (vacuum), but I guess you will use 
the values in parenthesis for the real calculations in solution. If that 
is the case, you may want to try using only the dielectric part 
(env_static_permittivity=79) or the whole contributions (thus plus 
env_surface_tension = 50 and env_pressure = -0.35) which were fitted to 
reproduce non-electrostatic effects in solvation free energies of 
organic molecules. I am not sure why you didn't include env_pressure in 
your input file (if non-electrostatic is not important, then I would 
also skip the env_surface_tension part).

Having said this, assume_isolated = 'slabz' should work also for an 
isolated molecule, but will only remove periodicity along the z axis. 
Since the full calculation and the one on the surface alone are done 
with this correction I would say this is the most consistent way to go 
(but you could always double-check by increasing the cell size, just to 
be sure you don't have periodicity artifacts).

You are right that assume_isolated = 'pcc' will not work for non-cubic 
cells, and in general it is not necessary to use it, since makov-payne 
gives similar results and is cheaper.

Please, feel free to ask more questions (even directly to my email 
address) if you find any problem with running the calculation or with 
the code. BTW, the current release of Environ only works with QE-5.1.1 
and QE-5.1.2, not yet with the most recent release of QE-5.2. There will 
be a new release of Environ soon, that will be compatible (and have some 
new features, including the possibility to restart a calculation) soon.

Best,

Oliviero Andreussi

On 07/02/2015 04:44 PM, veronica sanchez wrote:
> Dear all,
>
> I am a young researcher working on adsorption of organic molecules 
> upon carbonate surface. I would like to evaluate the solvation effect 
> on it, so, in order to do that I would like to employ the SCCS 
> recently implemented on the QE.
>
> As far as I understand to add the solvent environment to the system 
> composed by the organic molecule adsorbed upon the surface, I have to 
> set up the environ.in <http://environ.in> as:
>
>  &ENVIRON
>    !
>    verbose = 0
>    environ_thr = 10 (system is big, an orthorhombic dimension, which 
> largest size is aroung 60 angstroms )
>    environ_type = 'input'
>    eps_mode = 'full'
>    tolrhopol = 1.D-11
>    mixrhopol = 0.6
>    env_static_permittivity = 1 (79 for water)
>    env_surface_tension = 0    (50 for water)
>    !
> /
>
> And we add the line:
> isolated_system='slabz'
> to the &SYSTEM section of the QE input file.
>
> Did I understand correctly? the environ.in <http://environ.in> is ok?
>
> If so, I would like to follow with the next question.
>
> As I was mention on the begging, I would like to calculate the 
> adsorption energy of this molecule in the solvent environment, 
> therefore I have to calculate two more systems: the surface and the 
> molecule. For the surface I understand that the same conditions have 
> to be applied (the same environ.in <http://environ.in> and the same 
> 'isolated_system' in the QE file). Now, for the isolated molecule I 
> understand we could use the same environ.in <http://environ.in> (just 
> changing the  environ_thr to 0.1 as was indicating for molecules), but 
> to maintain the same cell dimensions as for the surface case, it is 
> correct to use 'isolated_system'='slabz' in this case? Because 'pcc' 
> only applies for cubic systems, right?
>
> I hope my questions were exposed in an understandable way and I 
> apologize if my English is not fully correct.
>
> I would be grateful for any suggestion on how to proceed with this 
> calculation.
>
> Thanks,
>
> Regards
>
> -- 
> Dra. Verónica M. Sánchez
> CSC-CONICET
> Godoy Cruz 2390
> 1425 Ciudad de Buenos Aires
> Argentina
> Tel 54 11 4899 5500 ext 5616
>
>
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> Pw_forum at pwscf.org
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