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<p class="MsoNormal">Dear Sydney,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">With that said…<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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:
<a href="https://dalcorso.github.io/thermo_pw/">https://dalcorso.github.io/thermo_pw/</a>. 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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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: <a href="https://phonopy.github.io/phonopy/index.html">
https://phonopy.github.io/phonopy/index.html</a> , 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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hope that helps,<o:p></o:p></p>
<p class="MsoNormal">Steve<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">-- <o:p></o:p></p>
<div>
<p class="MsoNormal">Stephen Weitzner, PhD<o:p></o:p></p>
<p class="MsoNormal">Postdoctoral Research Scientist<o:p></o:p></p>
<p class="MsoNormal">Quantum Simulations Group<o:p></o:p></p>
<p class="MsoNormal">Lawrence Livermore National Laboratory<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">T : (925) 422-4449<o:p></o:p></p>
</div>
<p class="MsoNormal">E : weitzner1@llnl.gov<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">users <users-bounces@lists.quantum-espresso.org> on behalf of
</span><span style="font-size:12.0pt;font-family:"MS Gothic";color:black">劉芸瑄</span><span style="font-size:12.0pt;color:black"> <danosunny@gmail.com><br>
<b>Reply-To: </b>Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org><br>
<b>Date: </b>Monday, March 2, 2020 at 3:33 AM<br>
<b>To: </b>"users@lists.quantum-espresso.org" <users@lists.quantum-espresso.org><br>
<b>Subject: </b>Re: [QE-users] how to study adsorption energy (Sydney Liu)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal">Dear Steve <o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"> 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. <o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal">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 ) ?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="color:black;border:none windowtext 1.0pt;padding:0in">And , the </span><span style="border:none windowtext 1.0pt;padding:0in">convergence tests that you mentioned. Could you please explain specifically and in more detail ?</span><o:p></o:p></p>
</div>
<div style="border:none black 1.0pt;padding:0in 0in 0in 0in;background-color:rgba(0,0,0,0)">
<p class="MsoNormal"><span style="border:none windowtext 1.0pt;padding:0in">Thank you so much !!</span><o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"><<a href="mailto:users-request@lists.quantum-espresso.org" target="_blank">users-request@lists.quantum-espresso.org</a>><span style="font-family:"MS Gothic"">於</span> 2020<span style="font-family:"MS Gothic"">年</span>3<span style="font-family:"MS Gothic"">月</span>1<span style="font-family:"MS Gothic"">日</span>
<span style="font-family:"MS Gothic"">週日，下午</span>7:02<span style="font-family:"MS Gothic"">寫道：</span><o:p></o:p></p>
</div>
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Today's Topics:<br>
<br>
1. how to study adsorption energy (???)<br>
2. Compilation of QE v6.5 using libxc-4.3.4 (arini kar)<br>
3. Re: how to study adsorption energy (Weitzner, Stephen Eric)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sat, 29 Feb 2020 19:28:11 +0800<br>
From: ??? <<a href="mailto:danosunny@gmail.com" target="_blank">danosunny@gmail.com</a>><br>
To: "<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>"<br>
<<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: [QE-users] how to study adsorption energy<br>
Message-ID:<br>
<CAGj2qC=<a href="mailto:dXZY-8HNaWPZi7PyDzGqbuAfhcq8S1uP7_3QANDZJ2A@mail.gmail.com" target="_blank">dXZY-8HNaWPZi7PyDzGqbuAfhcq8S1uP7_3QANDZJ2A@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear all<br>
I am a beginner in QE. Here are my question about adsorption energy. ( ex<br>
H2O adsorb on Cu surface )<br>
<br>
I know that I have to optimize the structure of the adsorbent molecule<br>
and the surface respectively. And then optimize the adsorbent + surface<br>
system.<br>
<br>
Getting the adsorption energy by the equation<br>
<br>
Eads= E(Ad+surface)-[(Ead)+(Esurface)]<br>
<br>
<br>
But I am confused about the more specific step of how to use QE to study<br>
it.<br>
<br>
First , I think I have to build the surface with the molecule above it. I<br>
try to use the BURAI to build the slab but I fail to build the molecule<br>
above it. Because I can not built the molecule with accurate bond length or<br>
angle which just like the Gaussview can do .<br>
<br>
Alternatively, I hope to use VESTA to build the slab and then output the<br>
xyz file to Avogadro. And then build the more accurate molecule structure<br>
above the slab by Avogadro. After that, output the xyz file to BURAI to<br>
create the QE input file. Is that alright ? Or is there any software or<br>
method that is more easily to build the molecule + slab surface system ?<br>
<br>
Also, which part or parameter that I should be aware of ? I think there<br>
are still a lot to be concerned. Like the size of the slab, the distance<br>
between adsorbent and surface , the QE input file parameter, all of these<br>
could affect the convergence of the SCF and the accuracy of the energy. As<br>
a beginner, how to start studying the adsorption energy ?<br>
<br>
I will really appreciate that if you could kindly teach me the more<br>
specific instruction of adsorption energy calculation.<br>
<br>
Thank you so much!<br>
<br>
<br>
Best regards<br>
<br>
Sydney Liu<br>
-- <br>
TOK TAIWAN CO.,LTD<br>
Sydney Liu<br>
E-mail : <a href="mailto:danosunny@gmail.com" target="_blank">danosunny@gmail.com</a><br>
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<br>
Message: 2<br>
Date: Sat, 29 Feb 2020 20:03:09 +0530<br>
From: arini kar <<a href="mailto:arini.kar@gmail.com" target="_blank">arini.kar@gmail.com</a>><br>
To: <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
Subject: [QE-users] Compilation of QE v6.5 using libxc-4.3.4<br>
Message-ID:<br>
<CAKidL+A94gt=<a href="mailto:0HHRHTxfb3T%2BhF04jh0QZxvK80K-9TxRynoTOQ@mail.gmail.com" target="_blank">0HHRHTxfb3T+hF04jh0QZxvK80K-9TxRynoTOQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear users,<br>
I am currently using quantum espresso v6.5. I have been trying to add<br>
libxc-4.3.4 using the following command:<br>
configure --with-libxc --with-libxc-prefix=... --with-libxc-include=....<br>
and QE configures successfully.<br>
However, while making pw.x the following error occurs:<br>
<br>
../../Modules/libqemod.a(funct.o): In function<br>
`__funct_MOD_set_dft_from_name':<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'<br>
/home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined<br>
reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'<br>
collect2: error: ld returned 1 exit status<br>
Makefile:256: recipe for target 'pw.x' failed<br>
make[2]: *** [pw.x] Error 1<br>
make[2]: Leaving directory '/home/arini/Downloads/QE/q-e-qe-6.5/PW/src'<br>
Makefile:9: recipe for target 'pw' failed<br>
make[1]: *** [pw] Error 1<br>
make[1]: Leaving directory '/home/arini/Downloads/QE/q-e-qe-6.5/PW'<br>
Makefile:74: recipe for target 'pw' failed<br>
make: *** [pw] Error 1<br>
<br>
I am not able to find a solution to the problem. I request you to help me<br>
with suggestions and possible corrections to overcome the error.<br>
<br>
Regards<br>
Arini Kar<br>
PhD scholar<br>
Indian Institute of Technology Bombay<br>
India<br>
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------------------------------<br>
<br>
Message: 3<br>
Date: Sat, 29 Feb 2020 17:16:32 +0000<br>
From: "Weitzner, Stephen Eric" <<a href="mailto:weitzner1@llnl.gov" target="_blank">weitzner1@llnl.gov</a>><br>
To: Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: Re: [QE-users] how to study adsorption energy<br>
Message-ID: <<a href="mailto:BC29D1DD-53C6-4043-BC85-9412921FAE93@llnl.gov" target="_blank">BC29D1DD-53C6-4043-BC85-9412921FAE93@llnl.gov</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Sydney,<br>
<br>
You may want to take a look at the Python-based Atomic Simulation Environment (ASE) (<a href="https://wiki.fysik.dtu.dk/ase/" target="_blank">https://wiki.fysik.dtu.dk/ase/</a>). You can build simple adsorbate systems using its python interface and directly
generate a PWscf input file from a simple Python script.<br>
<br>
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 (<a href="https://wiki.fysik.dtu.dk/ase/ase/thermochemistry/thermochemistry.html" target="_blank">https://wiki.fysik.dtu.dk/ase/ase/thermochemistry/thermochemistry.html</a>) to generate
finite temperature free energies (if this is what you are after).<br>
<br>
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.<br>
<br>
Hope that helps.<br>
Steve<br>
<br>
--<br>
Stephen Weitzner, PhD<br>
Postdoctoral Research Scientist<br>
Quantum Simulations Group<br>
Lawrence Livermore National Laboratory<br>
<br>
From: users <<a href="mailto:users-bounces@lists.quantum-espresso.org" target="_blank">users-bounces@lists.quantum-espresso.org</a>> on behalf of ??? <<a href="mailto:danosunny@gmail.com" target="_blank">danosunny@gmail.com</a>><br>
Reply-To: Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Date: Saturday, February 29, 2020 at 3:36 AM<br>
To: "<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>" <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
Subject: [QE-users] how to study adsorption energy<br>
<br>
Dear all<br>
I am a beginner in QE. Here are my question about adsorption energy. ( ex H2O adsorb on Cu surface )<br>
<br>
I know that I have to optimize the structure of the adsorbent molecule and the surface respectively. And then optimize the adsorbent + surface system.<br>
<br>
Getting the adsorption energy by the equation<br>
<br>
Eads= E(Ad+surface)-[(Ead)+(Esurface)]<br>
<br>
<br>
<br>
But I am confused about the more specific step of how to use QE to study it.<br>
<br>
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 .<br>
<br>
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 ?<br>
<br>
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 ?<br>
<br>
I will really appreciate that if you could kindly teach me the more specific instruction of adsorption energy calculation.<br>
<br>
Thank you so much!<br>
<br>
<br>
<br>
Best regards<br>
<br>
Sydney Liu<br>
--<br>
TOK TAIWAN CO.,LTD<br>
Sydney Liu<br>
E-mail : <a href="mailto:danosunny@gmail.com" target="_blank">danosunny@gmail.com</a><mailto:<a href="mailto:danosunny@gmail.com" target="_blank">danosunny@gmail.com</a>><br>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal">TOK TAIWAN CO.,LTD<br>
Sydney Liu<br>
E-mail : <a href="mailto:danosunny@gmail.com">danosunny@gmail.com</a><o:p></o:p></p>
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