<div><div><div dir="auto">Dear Steve </div></div><div dir="auto"> 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. </div><div style="background-color:rgba(0,0,0,0)!important;border-color:rgb(0,0,0)!important;color:rgb(0,0,0)!important"><div dir="auto">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 ) ?</div><div dir="auto" style="background-color:rgba(0,0,0,0)!important;border-color:rgb(0,0,0)!important;color:rgb(0,0,0)!important"><font style="border-color:rgb(0,0,0) rgb(0,0,0) rgb(0,0,0) rgb(204,204,204);color:rgb(0,0,0)">And , the </font><span style="border-color:rgb(0,0,0) rgb(0,0,0) rgb(0,0,0) rgb(204,204,204)">convergence tests that you mentioned. Could you please explain specifically and in more detail ?</span></div><div dir="auto" style="background-color:rgba(0,0,0,0);border-color:rgb(0,0,0)"><span style="border-color:rgb(0,0,0) rgb(0,0,0) rgb(0,0,0) rgb(204,204,204)">Thank you so much !!</span></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr"><<a href="mailto:users-request@lists.quantum-espresso.org" target="_blank">users-request@lists.quantum-espresso.org</a>>於 2020年3月1日 週日，下午7:02寫道：<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;padding-left:1ex;border-left-color:rgb(204,204,204)">Send users mailing list submissions to<br>
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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>
<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/" rel="noreferrer" 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" rel="noreferrer" 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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</blockquote></div></div>
</div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature">TOK TAIWAN CO.,LTD<br>Sydney Liu<br>E-mail : <a href="mailto:danosunny@gmail.com">danosunny@gmail.com</a><br></div>