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

劉芸瑄 danosunny at gmail.com
Fri Mar 6 17:27:11 CET 2020 

Dear Steve
  Sorry for the late reply.
Thank you so much for the explanation.
I will try everything you mentioned.
They are definitely useful !!

<users-request at lists.quantum-espresso.org>於 2020年3月4日 週三，下午7:02寫道：

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> Today's Topics:
>
>    1. Re: Generation of Pseudo-potentials with core-holes for
>       Xspectra calculation (Soumyadeep)
>    2. recommended math libraries, ELPA and XCONFIGURE (Michal Krompiec)
>    3. Transparent atoms with Xcrysden (Antoine Jay)
>    4. Re: how to study adsorption energy (Sydney Liu)
>       (Weitzner, Stephen Eric)
>    5. Location of Fermi level in spin polarised XAS in xspectra
>       (Sonu Kumar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 03 Mar 2020 17:51:11 +0530
> From: Soumyadeep <soumyadeep at rrcat.gov.in>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] Generation of Pseudo-potentials with
>         core-holes for Xspectra calculation
> Message-ID: <d158531a70fd9b1a1692b94d871d4773 at rrcat.gov.in>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Thanks for the answers.
>
> On 03-03-2020 16:01, Lorenzo Paulatto wrote:
> >>  ? (i) How to generate core-excited pseudopotentials starting from
> >> scratch/PP available in Psilibrary?
> >
> > You take a reference pseudopotential from pslibrary, at the beginning
> > of the file you usually find the input used to generate it with ld1.x
> > You take this input and modify the all-electron configuration,
> > removing one electron from the core. You will also have to specify the
> > valence charge by hand, please check the ld1 manual (INPUT_LD1.html)
> >
> According to you I have to set the parameter zval? If yes then how to
> set it for K-edge XANES calculation with core 1s core hole?
>
>
> >>
> >>  ?(ii) Is it necessary to use PAW PP for XANES calculation or GGA-PBE
> >> will be enough for metallic systems?
> >
> > PAW and GGA are not mutually exclusives. I'm not sure that XANES works
> > with PAW though.
> >
> >>
> >> (iii) Now upf2plotcore.sh is obsolete. Instead of that extract_core.x
> >> is advised to use. But How to make .wfc like output file using it? No
> >> examples are given.
> >
> > I think there is a new version in QE 6.5 that works
> >
> extract_core.x gives all the core states individually not like
> upf2plotcore.sh output which gave .wfc file. This problem can be solved
> by manually putting all the stuffs in single input file. upf2plotcore.sh
> is not working in QE-6.5
>
>
> > cheers
> >
> >>
> >>  ? please help.
> >>
> >> With many thanks and best regards
> >> Soumyadeep
> >> -------------------------------------------------------------------
> >> Soumyadeep Ghosh,
> >> Senior Research Fellow,
> >> Homi Bhabha National Institute (HBNI),
> >> Raja Ramanna Centre for Advanced Technology, Indore, India-452013
> >> Mob: (+91)9424664553
> >> User Lab: 0731244-2580
> >> Email: soumyadeepghosh35 at gmail.com, soumyadeep at rrcat.gov.in
> >> -------------------------------------------------------------------
> >> _______________________________________________
> >> Quantum ESPRESSO is supported by MaX
> >> (www.max-centre.eu/quantum-espresso)
> >> users mailing list users at lists.quantum-espresso.org
> >> https://lists.quantum-espresso.org/mailman/listinfo/users
>
> with best regards
> Soumyadeep
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 3 Mar 2020 12:48:55 +0000
> From: Michal Krompiec <michal.krompiec at gmail.com>
> To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
> Subject: [QE-users] recommended math libraries, ELPA and XCONFIGURE
> Message-ID:
>         <
> CAOWoSSNrTsZD1Jb6FbsSivjGUH7xbmsmnEH2XtyeSwGRSA_DgQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello,
> What is the recommended math library to link to, for highest
> performance, on a Intel-based HPC? Is it still ELPA (2017? 2019?),
> built with the XCONFIGURE scripts?
> Does anyone have experience with building QE+ELPA with gcc using
> XCONFIGURE scripts?
> Thanks in advance,
>
> Michal Krompiec
>
> Merck KGaA, Darmstadt, Germany and University of Southampton, UK
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 03 Mar 2020 14:39:46 +0100
> From: "Antoine Jay" <ajay at laas.fr>
> To: "Quantum ESPRESSO users Forum" <users at lists.quantum-espresso.org>
> Subject: [QE-users] Transparent atoms with Xcrysden
> Message-ID: <69f9-5e5e5e00-1f-53b57780 at 127473636>
> Content-Type: text/plain; charset="utf-8"
>
>
> Dear all,
>
> Do you know if it is possible to change the transparency of atoms with
> Xcrsyden?
>
> Thank you very much
>
> Antoine Jay
> LAAS CNRS
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> Message: 4
> Date: Tue, 3 Mar 2020 17:48:08 +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 (Sydney Liu)
> Message-ID: <9242EF59-9039-4CBF-83FB-D93B4D1C1133 at llnl.gov>
> Content-Type: text/plain; charset="utf-8"
>
> 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 ??? <
> 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>>? 2020?3?1? ?????7:02???
> Send users mailing list submissions to
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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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> Message: 5
> Date: Wed, 4 Mar 2020 12:05:35 +0900
> From: Sonu Kumar <1009ukumar at gmail.com>
> To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
> Subject: [QE-users] Location of Fermi level in spin polarised XAS in
>         xspectra
> Message-ID:
>         <
> CAHePdfCVPGnKOy3AM-yoacHCRgdQ5jry_co-AdisXwq1eAoJHQ at mail.gmail.com>
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>
> Dear QE users and experts,
>
> Xspecta assumes one common reference energy level to calculate the total
> absorption cross-section in DFT+U calculations, which I can understand.
>
> However, it separately calculates both spin channel contributions to the
> absorption cross-section; does it take different reference levels to
> calculate the absorption cross-sections for these channels? If not, could
> you suggest some references to understand it or give hints?
>
> With best regards,
> kumar
>
>
>
> *With kind regards,*
>
> *S Kumar |  PhD.*
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E-mail : danosunny at gmail.com
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