[QE-users] [EXT] Environ and 2D slab pp.x potential

Wed Jul 29 20:08:59 CEST 2020

Dear Oliviero,

Thank you very much for your kind replies and very useful information!
I'd like to add a last question.
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:

 WARNING: Unphysical forces due to core electrons are non-negligible

I was not able to find any documentation about this warning and therefore I
don't know how to deal with it.
Thank you very much for your patience!
All the best,

Antonio

--
Department of Physics "Aldo Moro"
University of Bari

Il giorno mar 28 lug 2020 alle ore 01:56 Andreussi, Oliviero <
Oliviero.Andreussi at unt.edu> ha scritto:

> Hi Mauro,
>
> 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.
>
> 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.
>
> I hope this helps,
>
> Oliviero
>
> Oliviero Andreussi
> --
> Assistant Professor
> Department of Physics
> University of North Texas
> Email: oliviero.andreussi at unt.edu <oliviero.andreussi at unt.edu>
> Phone: +1-(940)-369-5316
> Skype: olivieroandreussi
> Web: https://www.materialab.org
>
> On Jul 25, 2020, at 12:36 AM, Mauro Sgroi <maurofrancesco.sgroi at gmail.com>
> wrote:
>
> Dear Oliviero,
> 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?
>
> Thanks a lot and best regards,
> Mauro Sgroi.
>
> Il giorno mer 22 lug 2020 alle ore 17:36 Andreussi, Oliviero <
> Oliviero.Andreussi at unt.edu> ha scritto:
>
>> 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).
>> Best,
>>
>> Oliviero
>>
>> On Jul 22, 2020, at 9:53 AM, Antonio Crepaldi <
>> antonio.crepaldi.lanza at gmail.com> wrote:
>>
>> Dear Oliviero,
>>
>> Thank you very much for your detailed explanation!
>> 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.
>> Thank you again.
>> Best,
>>
>> Antonio
>>
>> Il giorno mar 21 lug 2020 alle ore 17:54 Andreussi, Oliviero <
>> Oliviero.Andreussi at unt.edu> ha scritto:
>>
>>> 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.
>>>
>>> I hope this helps,
>>>
>>> Best,
>>>
>>> Oliviero
>>>
>>> On Jul 21, 2020, at 10:47 AM, Andreussi, Oliviero <
>>> Oliviero.Andreussi at unt.edu> wrote:
>>>
>>> Dear Antonio,
>>>
>>> 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.
>>>
>>> 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.
>>>
>>> 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.
>>> quantum-environ-users
>>> <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>
>>>  (https://groups.google.com/forum/?hl=en#!forum/quantum-environ-users
>>> <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>
>>> )
>>>
>>> Best,
>>>
>>> Oliviero
>>>
>>> Oliviero Andreussi
>>> --
>>> Assistant Professor
>>> Department of Physics
>>> University of North Texas
>>> Email: oliviero.andreussi at unt.edu <oliviero.andreussi at unt.edu>
>>> Phone: +1-(940)-369-5316
>>> Skype: olivieroandreussi
>>> Web: https://www.materialab.org
>>> <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>
>>>
>>> On Jul 21, 2020, at 8:42 AM, Antonio Crepaldi <
>>> antonio.crepaldi.lanza at gmail.com> wrote:
>>>
>>> Dear QE users and developers,
>>>
>>> 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.
>>> Here is my environ input
>>>
>>> &ENVIRON
>>>>    verbose = 0
>>>>    environ_thr = 1.d0
>>>>    environ_type = 'input'
>>>>    env_electrostatic = .true.
>>>>    env_static_permittivity = 80
>>>>    env_surface_tension = 0.D0
>>>>    env_pressure = 0.D0
>>>>    env_external_charges = 2
>>>> /
>>>> &BOUNDARY
>>>>    solvent_mode = 'full'
>>>> /
>>>> &ELECTROSTATIC
>>>>    pbc_correction = 'parabolic'
>>>>    pbc_dim = 2
>>>>    pbc_axis = 3
>>>>    tol = 5.D-13
>>>>    !inner_tol = 5.D-18
>>>> /
>>>> EXTERNAL_CHARGES (bohr)
>>>> 2. 0.0 0.0 -14.29 1.0 2 3
>>>> 2. 0.0 0.0  14.29 1.0 2 3
>>>
>>>
>>>  Thank you very much for your help.
>>> Best,
>>>
>>> Antonio Crepaldi-Lanza
>>>
>>> --
>>> Department of Physics "Aldo Moro"
>>> University of Bari
>>> _______________________________________________
>>> Quantum ESPRESSO is supported by MaX (
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