[Pw_forum] Question on environ

[veronica sanchez]

Thank you very much for the answer and for the possibility to keep asking
about it.

I must say I made a mistake and I forgot the pressure on the environ.in. In
fact I would like to evaluate the difference considering all or just the
electrostatic part on the calculation.

I will also check more carefully the cell parameter along z direction
considering the lack of pbc on this direction.

Best,
Verónica

On Thu, Jul 2, 2015 at 12:22 PM, Oliviero Andreussi <
oliviero.andreussi at usi.ch> wrote:

>  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 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 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 and the same 'isolated_system' in the QE file). Now, for the
> isolated molecule I understand we could use the same 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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-- 
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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