<div dir="ltr"><div dir="ltr"><div dir="ltr">Dear Oliviero,<div><br></div><div>Thank you very much for your kind replies and very useful information!</div><div>I'd like to add a last question.</div><div>I'm computing energies of molecules adsorbed on a metal slab using environ with the electrolyte setup. When a H atom is present in the molecule I often get this message:</div><div><br></div> WARNING: Unphysical forces due to core electrons are non-negligible </div><div dir="ltr"><br></div><div>I was not able to find any documentation about this warning and therefore I don't know how to deal with it. </div><div>Thank you very much for your patience!</div><div>All the best,</div><div><br></div><div>Antonio</div><div><br></div><div><br></div><div><div>--</div><div>Department of Physics "Aldo Moro"</div><div>University of Bari</div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Il giorno mar 28 lug 2020 alle ore 01:56 Andreussi, Oliviero <<a href="mailto:Oliviero.Andreussi@unt.edu">Oliviero.Andreussi@unt.edu</a>> ha scritto:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div style="word-wrap:break-word;line-break:after-white-space">
Hi Mauro,
<div><br>
</div>
<div>Sorry for the delay. I am afraid other electrostatic models implemented in QE cannot be coupled with Environ electrostatics, including dielectric solvent. The only exception is for the Martyna-Tuckerman correction for PBCs, which is compatible
with Environ. Apart from this, 2d coulomb, ESM, QM/MM, and other tools of QE that affect the electrostatics of the environment are not accounted for in Environ, and vice-versa. </div>
<div><br>
</div>
<div>If you want to use non-electrostatic embeddings in environ (surface term, volume term, confinement), this should work fine with ESM as well and with other QE options. </div>
<div><br>
</div>
<div>I hope this helps,</div>
<div><br>
</div>
<div>Oliviero</div>
<div><br>
<div>
<div dir="auto" style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;word-wrap:break-word;line-break:after-white-space">
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Oliviero Andreussi<br>
--<br>
Assistant Professor<br>
Department of Physics<br>
University of North Texas<br>
<a href="mailto:oliviero.andreussi@unt.edu" target="_blank">Email: oliviero.andreussi@unt.edu</a> </div>
<div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
Phone: +1-(940)-369-5316<br>
Skype: olivieroandreussi<br>
Web: <a href="https://www.materialab.org" target="_blank">https://www.materialab.org</a></div>
</div>
</div>
</div>
</div>
<div><br>
<blockquote type="cite">
<div>On Jul 25, 2020, at 12:36 AM, Mauro Sgroi <<a href="mailto:maurofrancesco.sgroi@gmail.com" target="_blank">maurofrancesco.sgroi@gmail.com</a>> wrote:</div>
<br>
<div>
<div dir="ltr">Dear Oliviero,
<div>a question related to this discussion: if I use Environ just to add the solvent effect and ESM for the electrostatic, how should I evaluate the electrostatic potential at the center of the vacuum region? Should I use pp.x? Or also in that case
environ generate the cube files with the correct potential?</div>
<div><br>
</div>
<div>Thanks a lot and best regards,</div>
<div>Mauro Sgroi.</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Il giorno mer 22 lug 2020 alle ore 17:36 Andreussi, Oliviero <<a href="mailto:Oliviero.Andreussi@unt.edu" target="_blank">Oliviero.Andreussi@unt.edu</a>> ha scritto:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div>I am sorry, I may not be familiar with the terminology. You want to run a simulation with constant applied potential? Do you plan to do a molecular dynamics simulation or just total energy/geometry relaxations?
With Environ you can perform simulations with constant electrode charge, which can be converted into a constant potential simulations. These simulations could include a reasonable description of the solvent interface, as well as a reasonable description of
the electrochemical diffuse layer. You could vary the charge in the substrate (i.e. tot_charge in the pw input file) so as to obtain the potential drop that you want, or if you are interested in computing interfacial energies as a function of different potentials,
you could use an approach based on Legendre transforms such as the one described in N. Hörmann et al, J. Chem. Phys. 150, 041730 (2019).
<div>Best,</div>
<div><br>
</div>
<div>Oliviero<br>
<div>
<div><br>
<blockquote type="cite">
<div>On Jul 22, 2020, at 9:53 AM, Antonio Crepaldi <<a href="mailto:antonio.crepaldi.lanza@gmail.com" target="_blank">antonio.crepaldi.lanza@gmail.com</a>> wrote:</div>
<br>
<div>
<div dir="ltr">Dear Oliviero,
<div><br>
</div>
<div>Thank you very much for your detailed explanation!</div>
<div>I would just like to ask you if it is possible to make a constant mu calculation with environ. I've read in the manual that this requires ESM, but I don't know if this is compatible with the environ setup.</div>
<div>Thank you again.</div>
<div>Best,</div>
<div><br>
</div>
<div>Antonio</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Il giorno mar 21 lug 2020 alle ore 17:54 Andreussi, Oliviero <<a href="mailto:Oliviero.Andreussi@unt.edu" target="_blank">Oliviero.Andreussi@unt.edu</a>> ha scritto:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div>I am sorry my answer can be misleading. The wave function and the density also depend on the environment, but the point is that PP does not recompute them, it just reads them from the saved wfc files and plot
them. PP instead needs to recompute the potentials to plot them and this is where the missing environ makes the results meaningless.
<div><br>
</div>
<div>I hope this helps,</div>
<div><br>
</div>
<div>Best,</div>
<div><br>
</div>
<div>Oliviero<br>
<div><br>
<blockquote type="cite">
<div>On Jul 21, 2020, at 10:47 AM, Andreussi, Oliviero <<a href="mailto:Oliviero.Andreussi@unt.edu" target="_blank">Oliviero.Andreussi@unt.edu</a>> wrote:</div>
<br>
<div>
<div>Dear Antonio,
<div><br>
</div>
<div>Thanks for reporting this issue and for trying Environ for your simulations. I am afraid the documentation of Environ needs to be improved on the point that you report, as this is not the first time I see this question. </div>
<div><br>
</div>
<div>Environ is not coupled with the PP code. If PP is used to plot quantities that do not depend on the environment, such as the wavefunction, the density, etc., it should work fine. However, you cannot use PP to plot quantities that depend on the
environment, namely the electrostatic potential. For this purpose, you can turn on the verbosity of Environ using the verbose keyword. If you set verbose = 2 (or higher) you should get some .cube files that you can use to visualize properties of the simulation
cell, in particular the electrostatic potential. Cubefiles are read by many programs and can be processed relatively easily with scripts.</div>
<div><br>
</div>
<div>Don’t hesitate to let me know if you have any problem with running Environ. You may also consider joining the google group created to support Environ users, there are not too many discussions right now, but it would be nice to build a collection
of known problems, solutions and suggestions. <a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgroups.google.com%2Fforum%2F%3Fhl%3Den%23!forum%2Fquantum-environ-users&data=02%7C01%7Coliviero.andreussi%40unt.edu%7Cd4155ba2162b42ab3b0a08d8305cc406%7C70de199207c6480fa318a1afcba03983%7C0%7C0%7C637312522282845646&sdata=S7qH%2BxxTde3GuAMqLFkFGq4EDDsadHw2HUQfw60iupY%3D&reserved=0" target="_blank">quantum-environ-users</a> (<a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgroups.google.com%2Fforum%2F%3Fhl%3Den%23!forum%2Fquantum-environ-users&data=02%7C01%7Coliviero.andreussi%40unt.edu%7Cd4155ba2162b42ab3b0a08d8305cc406%7C70de199207c6480fa318a1afcba03983%7C0%7C0%7C637312522282845646&sdata=S7qH%2BxxTde3GuAMqLFkFGq4EDDsadHw2HUQfw60iupY%3D&reserved=0" target="_blank">https://groups.google.com/forum/?hl=en#!forum/quantum-environ-users</a>)</div>
<div><br>
</div>
<div>Best,</div>
<div><br>
</div>
<div>Oliviero</div>
<div><br>
</div>
<div>
<div>
<div dir="auto" style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<div dir="auto" style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
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Oliviero Andreussi<br>
--<br>
Assistant Professor<br>
Department of Physics<br>
University of North Texas<br>
<a href="mailto:oliviero.andreussi@unt.edu" target="_blank">Email: oliviero.andreussi@unt.edu</a> </div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
Phone: +1-(940)-369-5316<br>
Skype: olivieroandreussi<br>
Web: <a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.materialab.org%2F&data=02%7C01%7Coliviero.andreussi%40unt.edu%7Cd4155ba2162b42ab3b0a08d8305cc406%7C70de199207c6480fa318a1afcba03983%7C0%7C0%7C637312522282855641&sdata=cuyGGey9yT4C%2FQmK9Tne%2FbaG5nYHUpuNn04ELU1ZD3M%3D&reserved=0" target="_blank">https://www.materialab.org</a></div>
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<div><br>
<blockquote type="cite">
<div>On Jul 21, 2020, at 8:42 AM, Antonio Crepaldi <<a href="mailto:antonio.crepaldi.lanza@gmail.com" target="_blank">antonio.crepaldi.lanza@gmail.com</a>> wrote:</div>
<br>
<div>
<div dir="ltr">
<div dir="ltr">Dear QE users and developers,
<div><br>
</div>
<div>I'm currently trying to simulate a charged 2D slab embedded in water. I'm using two planar countercharges as explained in Example 5 of Environ. The computation does not have any convergence problem, however, when I plot the total electrostatic
potential (plot_num=11 in pp.x) I do not get a flat potential in the vacuum region screened by the countercharges. I would expect to find a flat potential in that region and be able to use it as a reference for further calculations.</div>
<div>Here is my environ input</div>
<div><br>
</div>
<div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
&ENVIRON<br>
verbose = 0<br>
environ_thr = 1.d0<br>
environ_type = 'input'<br>
env_electrostatic = .true.<br>
env_static_permittivity = 80<br>
env_surface_tension = 0.D0<br>
env_pressure = 0.D0<br>
env_external_charges = 2<br>
/<br>
&BOUNDARY<br>
solvent_mode = 'full'<br>
/<br>
&ELECTROSTATIC<br>
pbc_correction = 'parabolic'<br>
pbc_dim = 2<br>
pbc_axis = 3<br>
tol = 5.D-13<br>
!inner_tol = 5.D-18<br>
/<br>
EXTERNAL_CHARGES (bohr)<br>
2. 0.0 0.0 -14.29 1.0 2 3<br>
2. 0.0 0.0 14.29 1.0 2 3</blockquote>
<div><br>
</div>
<div> Thank you very much for your help.</div>
</div>
<div>Best,</div>
<div><br>
</div>
<div>Antonio Crepaldi-Lanza</div>
<div><br>
</div>
<div>--</div>
<div>Department of Physics "Aldo Moro"</div>
<div>University of Bari</div>
</div>
</div>
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