<div dir="ltr"><span style="font-size:12.8000001907349px">Thank you very much for the answer and for the possibility to keep asking about it.</span><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">I must say I made a mistake and I forgot the pressure on the <a href="http://environ.in/" target="_blank">environ.in</a>. In fact I would like to evaluate the difference considering all or just the electrostatic part on the calculation.</div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">I will also check more carefully the cell parameter along z direction considering the lack of pbc on this direction.</div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">Best,</div><div style="font-size:12.8000001907349px">Verónica</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jul 2, 2015 at 12:22 PM, Oliviero Andreussi <span dir="ltr"><<a href="mailto:oliviero.andreussi@usi.ch" target="_blank">oliviero.andreussi@usi.ch</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Dear Dra. Verónica M. Sánchez,<br>
<br>
The <a href="http://environ.in" target="_blank">environ.in</a> 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). <br>
<br>
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). <br>
<br>
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. <br>
<br>
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. <br>
<br>
Best,<br>
<br>
Oliviero Andreussi<div><div class="h5"><br>
<br>
<div>On 07/02/2015 04:44 PM, veronica
sanchez wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<div dir="ltr">Dear all,
<div><br>
</div>
<div style="text-align:left">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. </div>
<div style="text-align:left"><br>
</div>
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 <a href="http://environ.in" target="_blank">environ.in</a> as:<br>
<br>
<span> &ENVIRON</span><span> </span><br>
!<br>
verbose = 0<br>
environ_thr = 10 (system is big, an orthorhombic dimension,
which largest size is aroung 60 angstroms ) <br>
environ_type = 'input'<br>
eps_mode = 'full'<br>
tolrhopol = 1.D-11<br>
mixrhopol = 0.6<br>
env_static_permittivity = 1 (79 for water)<br>
env_surface_tension = 0 (50 for water)<br>
!
<div>/</div>
<div><br>
And we add the line: </div>
<div>
<div>isolated_system='slabz'</div>
<div>to the &SYSTEM section of the QE input file.<br>
</div>
<div><br>
</div>
<div>Did I understand correctly? the <a href="http://environ.in" target="_blank">environ.in</a>
is ok?</div>
<div><br>
</div>
<div>If so, I would like to follow with the next question. </div>
<div><br>
</div>
<div>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 <a href="http://environ.in" target="_blank">environ.in</a>
and the same 'isolated_system' in the QE file). Now, for the
isolated molecule I understand we could use the same <a href="http://environ.in" target="_blank">environ.in</a>
(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?</div>
<div><br>
</div>
<div>I hope my questions were exposed in an understandable way
and I apologize if my English is not fully correct.</div>
<div><br>
</div>
<div>I would be grateful for any suggestion on how to proceed
with this calculation.</div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>-- <br>
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div style="font-size:small">Dra. Verónica M.
Sánchez</div>
<div style="font-size:small">CSC-CONICET</div>
<div style="font-size:small">Godoy Cruz 2390</div>
<div style="font-size:small">1425 Ciudad de Buenos
Aires</div>
<div style="font-size:small">Argentina</div>
<div style="font-size:small">Tel 54 11 4899 5500 ext
5616</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
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