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

劉芸瑄 danosunny at gmail.com
Mon Mar 2 12:31:41 CET 2020 

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>於 2020年3月1日 週日，下午7:02寫道：

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>    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>
> To: "users at lists.quantum-espresso.org"
>         <users at lists.quantum-espresso.org>
> Subject: [QE-users]  how to study adsorption energy
> Message-ID:
>         <CAGj2qC=
> 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
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 2
> Date: Sat, 29 Feb 2020 20:03:09 +0530
> From: arini kar <arini.kar at gmail.com>
> To: 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>
> 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>
> To: Quantum ESPRESSO users Forum <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>
> 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> on behalf of ??? <
> danosunny at gmail.com>
> Reply-To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Date: Saturday, February 29, 2020 at 3:36 AM
> To: "users at lists.quantum-espresso.org" <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>
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-- 
TOK TAIWAN CO.,LTD
Sydney Liu
E-mail : danosunny at gmail.com
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