[QE-users] how to study adsorption energy (Sydney Liu)

Weitzner, Stephen Eric weitzner1 at llnl.gov
Tue Mar 3 18:48:08 CET 2020 

Dear Sydney,

Just as an FYI (some developers may correct me here) I don’t think this forum is usually used for providing such instruction, more so for reporting issues and challenges with using and compiling the code.

With that said…

From what I understand, if you install python via the Anaconda distribution you should be able to install ASE fairly readily (I am not a windows user, so don’t take me at my word on this).

The output energy you get from pw.x is that of the electronic ground state energy of the system, hence why you need to perform a separate calculation to obtain the vibrational zero point energy and vibrational free energy of the adsorbate. There are tools in newer versions of Quantum ESPRESSO to streamline this process, such as Thermo PW developed by Andrea Dal Corso: https://dalcorso.github.io/thermo_pw/. I have not tried this yet, but there seems to be a lot of information out there on how to use the code and probably many answered questions about this code on this forum.

You can perform vibrational calculations using the Phonon code ph.x. You should freeze all atoms belonging to the slab atoms except the atoms belonging to the adsorbate. Or you can use a finite difference method to calculate vibrational modes such as the methods implemented in Phonopy: https://phonopy.github.io/phonopy/index.html , or you can implement your own finite difference code in Python. It’s quite easy to write a bare bones code to do this. Phonopy is more advanced and will take symmetry into consideration.

For the convergence tests, you should look up some of the many tutorials prepared by Quantum ESPRESSO developers that describe how to do these calculations and show examples. Beyond the tests that they describe in there, you should prepare similar tests for the vacuum spacing between slabs, as well as changing the number of layers and surface primitive cells in your slab. You should similarly try calculations using van der Waals functionals. Beyond that I can’t really say much without getting into overly detailed specifics of how to run the calculations, and I will leave that up to you.

Hope that helps,
Steve

--
Stephen Weitzner, PhD
Postdoctoral Research Scientist
Quantum Simulations Group
Lawrence Livermore National Laboratory

T : (925) 422-4449
E : weitzner1 at llnl.gov



From: users <users-bounces at lists.quantum-espresso.org> on behalf of 劉芸瑄 <danosunny at gmail.com>
Reply-To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Date: Monday, March 2, 2020 at 3:33 AM
To: "users at lists.quantum-espresso.org" <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] how to study adsorption energy (Sydney Liu)

Dear Steve
   Thank you for your advice.  Because the operation system I used is windows. So it seems to be a little complicated to install ASE. But I will try to install it anyway.
Also, I have some questions. like you said I have to perform vibrational calculations. I had calculation = relax in QE . Is the output energy including the correlation of thermal energy ( zero point energy ) ?
And , the convergence tests that you mentioned. Could you please explain specifically and in more detail ?
Thank you so much !!

<users-request at lists.quantum-espresso.org<mailto:users-request at lists.quantum-espresso.org>>於 2020年3月1日 週日，下午7:02寫道：
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Today's Topics:

   1.  how to study adsorption energy (???)
   2. Compilation of QE v6.5 using libxc-4.3.4 (arini kar)
   3. Re: how to study adsorption energy (Weitzner, Stephen Eric)


----------------------------------------------------------------------

Message: 1
Date: Sat, 29 Feb 2020 19:28:11 +0800
From: ??? <danosunny at gmail.com<mailto:danosunny at gmail.com>>
To: "users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>"
        <users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>>
Subject: [QE-users]  how to study adsorption energy
Message-ID:
        <CAGj2qC=dXZY-8HNaWPZi7PyDzGqbuAfhcq8S1uP7_3QANDZJ2A at mail.gmail.com<mailto:dXZY-8HNaWPZi7PyDzGqbuAfhcq8S1uP7_3QANDZJ2A at mail.gmail.com>>
Content-Type: text/plain; charset="utf-8"

Dear all
  I am a beginner in QE. Here are my question about adsorption energy. ( ex
H2O adsorb on Cu surface )

  I know that I have to optimize the structure of the adsorbent molecule
and the surface respectively. And then optimize the adsorbent + surface
system.

Getting the adsorption energy by the equation

Eads= E(Ad+surface)-[(Ead)+(Esurface)]


  But I am confused about the more specific step of how to use QE to study
it.

First , I think I have to build the surface with the molecule above it. I
try to use the BURAI to build the slab but I fail to build the molecule
above it. Because I can not built the molecule with accurate bond length or
angle which just like the Gaussview can do .

  Alternatively, I hope to use VESTA to build the slab and then output the
xyz file to Avogadro. And then build the more accurate molecule structure
above the slab by Avogadro. After that, output the xyz file to BURAI to
create the QE input file. Is that alright ? Or is there any software or
method that is more easily to build the molecule + slab surface system ?

  Also, which part or parameter that I should be aware of ? I think there
are still a lot to be concerned. Like the size of the slab, the distance
between adsorbent and surface , the QE input file parameter, all of these
could affect the convergence of the SCF and the accuracy of the energy. As
a beginner, how to start studying the adsorption energy ?

  I will really appreciate that if you could kindly teach me the more
specific instruction of adsorption energy calculation.

Thank you so much!


Best regards

Sydney Liu
--
TOK TAIWAN CO.,LTD
Sydney Liu
E-mail : danosunny at gmail.com<mailto:danosunny at gmail.com>
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Message: 2
Date: Sat, 29 Feb 2020 20:03:09 +0530
From: arini kar <arini.kar at gmail.com<mailto:arini.kar at gmail.com>>
To: users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
Subject: [QE-users] Compilation of QE v6.5 using libxc-4.3.4
Message-ID:
        <CAKidL+A94gt=0HHRHTxfb3T+hF04jh0QZxvK80K-9TxRynoTOQ at mail.gmail.com<mailto:0HHRHTxfb3T%2BhF04jh0QZxvK80K-9TxRynoTOQ at mail.gmail.com>>
Content-Type: text/plain; charset="utf-8"

Dear users,
I am currently using quantum espresso v6.5. I have been trying to add
libxc-4.3.4 using the following command:
configure --with-libxc --with-libxc-prefix=... --with-libxc-include=....
and QE configures successfully.
However, while making pw.x the following error occurs:

../../Modules/libqemod.a(funct.o): In function
`__funct_MOD_set_dft_from_name':
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined
reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'
collect2: error: ld returned 1 exit status
Makefile:256: recipe for target 'pw.x' failed
make[2]: *** [pw.x] Error 1
make[2]: Leaving directory '/home/arini/Downloads/QE/q-e-qe-6.5/PW/src'
Makefile:9: recipe for target 'pw' failed
make[1]: *** [pw] Error 1
make[1]: Leaving directory '/home/arini/Downloads/QE/q-e-qe-6.5/PW'
Makefile:74: recipe for target 'pw' failed
make: *** [pw] Error 1

I am not able to find a solution to the problem. I request you to help me
with suggestions and possible corrections to overcome the error.

Regards
Arini Kar
PhD scholar
Indian Institute of Technology Bombay
India
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Message: 3
Date: Sat, 29 Feb 2020 17:16:32 +0000
From: "Weitzner, Stephen Eric" <weitzner1 at llnl.gov<mailto:weitzner1 at llnl.gov>>
To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>>
Subject: Re: [QE-users] how to study adsorption energy
Message-ID: <BC29D1DD-53C6-4043-BC85-9412921FAE93 at llnl.gov<mailto:BC29D1DD-53C6-4043-BC85-9412921FAE93 at llnl.gov>>
Content-Type: text/plain; charset="utf-8"

Dear Sydney,

You may want to take a look at the Python-based Atomic Simulation Environment (ASE) (https://wiki.fysik.dtu.dk/ase/). You can build simple adsorbate systems using its python interface and directly generate a PWscf input file from a simple Python script.

Your expression for the binding energy is correct. You should perform vibrational calculations for the adsorbate bound to the surface and for the isolated molecule in vacuum to include at the very least zero point energy corrections. You can also use ASE to compute enthalpic and entropic corrections using its thermochemistry tools (https://wiki.fysik.dtu.dk/ase/ase/thermochemistry/thermochemistry.html) to generate finite temperature free energies (if this is what you are after).

You should perform convergence tests to see what properties are important for your application, because it depends on what it is you are trying to calculate. You should try these calculations with and without van der Waals corrections, change the slab cross-sectional area (only if you are trying to eliminate lateral adsorbate-adsorbate interactions), and try several vacuum heights in addition to the usual convergence tests you should perform. Be aware that you may have a dipole across your supercell if your slab is not symmetric. You may need to include dipole corrections.

Hope that helps.
Steve

--
Stephen Weitzner, PhD
Postdoctoral Research Scientist
Quantum Simulations Group
Lawrence Livermore National Laboratory

From: users <users-bounces at lists.quantum-espresso.org<mailto:users-bounces at lists.quantum-espresso.org>> on behalf of ??? <danosunny at gmail.com<mailto:danosunny at gmail.com>>
Reply-To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>>
Date: Saturday, February 29, 2020 at 3:36 AM
To: "users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>" <users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>>
Subject: [QE-users] how to study adsorption energy

Dear all
  I am a beginner in QE. Here are my question about adsorption energy. ( ex H2O adsorb on Cu surface )

  I know that I have to optimize the structure of the adsorbent molecule and the surface respectively. And then optimize the adsorbent + surface system.

Getting the adsorption energy by the equation

Eads= E(Ad+surface)-[(Ead)+(Esurface)]



  But I am confused about the more specific step of how to use QE to study it.

First , I think I have to build the surface with the molecule above it. I try to use the BURAI to build the slab but I fail to build the molecule above it. Because I can not built the molecule with accurate bond length or angle which just like the Gaussview can do .

  Alternatively, I hope to use VESTA to build the slab and then output the xyz file to Avogadro. And then build the more accurate molecule structure above the slab by Avogadro. After that, output the xyz file to BURAI to create the QE input file. Is that alright ? Or is there any software or method that is more easily to build the molecule + slab surface system ?

  Also, which part or parameter that I should be aware of ? I think there are still a lot to be concerned. Like the size of the slab, the distance between adsorbent and surface , the QE input file parameter, all of these could affect the convergence of the SCF and the accuracy of the energy. As a beginner, how to start studying the adsorption energy ?

  I will really appreciate that if you could kindly teach me the more specific instruction of adsorption energy calculation.

Thank you so much!



Best regards

Sydney Liu
--
TOK TAIWAN CO.,LTD
Sydney Liu
E-mail : danosunny at gmail.com<mailto:danosunny at gmail.com><mailto:danosunny at gmail.com<mailto:danosunny at gmail.com>>
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TOK TAIWAN CO.,LTD
Sydney Liu
E-mail : danosunny at gmail.com<mailto:danosunny at gmail.com>
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