Dear Steve Sorry for the late reply. Thank you so much for the explanation. I will try everything you mentioned. They are definitely useful !!
<[email protected]>於 2020年3月4日 週三，下午7:02寫道： > Send users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.quantum-espresso.org/mailman/listinfo/users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of users digest..." > > > 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 <[email protected]> > To: Quantum ESPRESSO users Forum <[email protected]> > Subject: Re: [QE-users] Generation of Pseudo-potentials with > core-holes for Xspectra calculation > Message-ID: <[email protected]> > 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 (iii) Now upf2plotcore.sh is obsolete.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: [email protected], [email protected] > >> ------------------------------------------------------------------- > >> _______________________________________________ > >> Quantum ESPRESSO is supported by MaX > >> (www.max-centre.eu/quantum-espresso) > >> users mailing list [email protected] > >> 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 <[email protected]> > To: Quantum Espresso users Forum <[email protected]> > Subject: [QE-users] recommended math libraries, ELPA and XCONFIGURE > Message-ID: > < > caowossnrtszd1jb6fbssivjguh7xbmsmneh2xtyeswgrsa_...@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" <[email protected]> > To: "Quantum ESPRESSO users Forum" <[email protected]> > Subject: [QE-users] Transparent atoms with Xcrysden > Message-ID: <69f9-5e5e5e00-1f-53b57780@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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20200303/7e3bfa5a/attachment-0001.html > > > > ------------------------------ > > Message: 4 > Date: Tue, 3 Mar 2020 17:48:08 +0000 > From: "Weitzner, Stephen Eric" <[email protected]> > To: Quantum ESPRESSO users Forum <[email protected]> > Subject: Re: [QE-users] how to study adsorption energy (Sydney Liu) > Message-ID: <[email protected]> > 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 : [email protected] > > > > From: users <[email protected]> on behalf of ??? < > [email protected]> > Reply-To: Quantum ESPRESSO users Forum <[email protected]> > Date: Monday, March 2, 2020 at 3:33 AM > To: "[email protected]" <[email protected]> > 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 !! > > <[email protected]<mailto: > [email protected]>>? 2020?3?1? ?????7:02??? > Send users mailing list submissions to > [email protected]<mailto: > [email protected]> > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.quantum-espresso.org/mailman/listinfo/users > or, via email, send a message with subject or body 'help' to > [email protected]<mailto: > [email protected]> > > You can reach the person managing the list at > [email protected]<mailto: > [email protected]> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of users digest..." > > > 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: ??? <[email protected]<mailto:[email protected]>> > To: "[email protected]<mailto: > [email protected]>" > <[email protected]<mailto: > [email protected]>> > Subject: [QE-users] how to study adsorption energy > Message-ID: > <CAGj2qC= > [email protected]<mailto: > [email protected]>> > 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 : [email protected]<mailto:[email protected]> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20200229/2ce01270/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Sat, 29 Feb 2020 20:03:09 +0530 > From: arini kar <[email protected]<mailto:[email protected]>> > To: [email protected]<mailto: > [email protected]> > Subject: [QE-users] Compilation of QE v6.5 using libxc-4.3.4 > Message-ID: > <CAKidL+A94gt= > [email protected]<mailto: > 0hhrhtxfb3t%[email protected]>> > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20200229/8eea0c66/attachment-0001.html > > > > ------------------------------ > > Message: 3 > Date: Sat, 29 Feb 2020 17:16:32 +0000 > From: "Weitzner, Stephen Eric" <[email protected]<mailto: > [email protected]>> > To: Quantum ESPRESSO users Forum <[email protected]<mailto: > [email protected]>> > Subject: Re: [QE-users] how to study adsorption energy > Message-ID: <[email protected]<mailto: > [email protected]>> > 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 <[email protected]<mailto: > [email protected]>> on behalf of ??? < > [email protected]<mailto:[email protected]>> > Reply-To: Quantum ESPRESSO users Forum <[email protected] > <mailto:[email protected]>> > Date: Saturday, February 29, 2020 at 3:36 AM > To: "[email protected]<mailto: > [email protected]>" <[email protected] > <mailto:[email protected]>> > 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 : [email protected]<mailto:[email protected]><mailto: > [email protected]<mailto:[email protected]>> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20200229/447c7061/attachment-0001.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > users mailing list > [email protected]<mailto:[email protected]> > https://lists.quantum-espresso.org/mailman/listinfo/users > > ------------------------------ > > End of users Digest, Vol 152, Issue 1 > ************************************* > -- > TOK TAIWAN CO.,LTD > Sydney Liu > E-mail : [email protected]<mailto:[email protected]> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20200303/921eeb41/attachment-0001.html > > > > ------------------------------ > > Message: 5 > Date: Wed, 4 Mar 2020 12:05:35 +0900 > From: Sonu Kumar <[email protected]> > To: Quantum Espresso users Forum <[email protected]> > Subject: [QE-users] Location of Fermi level in spin polarised XAS in > xspectra > Message-ID: > < > cahepdfcvpgnkoy3am-yoachcrgdq5jry_co-adisxwq1eao...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > 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.* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20200304/05b61f9c/attachment-0001.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > users mailing list > [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users > > ------------------------------ > > End of users Digest, Vol 152, Issue 4 > ************************************* > -- TOK TAIWAN CO.,LTD Sydney Liu E-mail : [email protected]
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