[QE-users] how to study adsorption energy (Sydney Liu)
Sebastian Gsänger
sebastian.gsaenger at gmail.com
Mon Mar 2 16:06:56 CET 2020
Dear Sidney,
i hope it's okay to self-advertise here:
I've created a graphical editor that tries to combine the ease-of-use of
avogadro with more intuitive treatment of periodic calculations:
https://github.com/sgsaenger/vipster/releases
It's still in beta, but supports most features of PWScf and runs on Windows.
Hope it can be of use to you.
Regards,
Sebastian Gsänger
Am 02.03.2020 um 12:38 schrieb 劉芸瑄:
> Dear Chris
> Thank you for your advice. Because the operation system I used is
> windows. So it seems to be a little complicated to install ASE or
> molsimplify. But I will try to install them anyway. If anyone had
> installed them on windows before. Could you please share the tip with
> me ? I would really appreciate it!!
> Thank you so much!!
>
> Best regards
> Sydney Liu
>
> <users-request at lists.quantum-espresso.org
> <mailto:users-request at lists.quantum-espresso.org>>於 2020年3月2日
> 週一，下午7:02寫道：
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> Today's Topics:
>
> 1. Re: Compilation of QE v6.5 using libxc-4.3.4 (Fabrizio Ferrari)
> 2. Re: how to study adsorption energy (Christoph Wolf)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 1 Mar 2020 12:34:11 +0100
> From: Fabrizio Ferrari <ferrariruffino.fz at gmail.com
> <mailto:ferrariruffino.fz at gmail.com>>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org
> <mailto:users at lists.quantum-espresso.org>>
> Subject: Re: [QE-users] Compilation of QE v6.5 using libxc-4.3.4
> Message-ID:
> <CAL7fUk5MaH3y70PKhK7cmQjKAiM3wYM3eq_Oss4xgejTdBx=CA at mail.gmail.com
> <mailto:CA at mail.gmail.com>>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Arini,
> apparently the lxcf03 flag is missing (it is needed in v6.5). You
> should
> add it to LD_LIBS in the make.inc file. If it still does not
> compile, I
> suggest you to link 'maually' libxc only after the configuration:
> - run configure without any libxc flag
> - go to the make.inc file and, by following the comments inside,
> add the
> needed flags to DFLAGS, IFLAGS and LD_LIBS.
> Just one note: if you are planning to use GGA functionals with libxc I
> suggest you to use the develop version of QE (downloadable from
> GitLab)
> since there is a factor 2 correction in one of the terms of the
> potential
> that has been only recently added.
> Best regards,
> Fabrizio
>
>
>
>
> On Sat, Feb 29, 2020 at 3:33 PM arini kar <arini.kar at gmail.com
> <mailto:arini.kar at gmail.com>> wrote:
>
> > 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
> > _______________________________________________
> > Quantum ESPRESSO is supported by MaX
> (www.max-centre.eu/quantum-espresso
> <http://www.max-centre.eu/quantum-espresso>)
> > users mailing list users at lists.quantum-espresso.org
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> ------------------------------
>
> Message: 2
> Date: Sun, 1 Mar 2020 22:09:34 +0900
> From: Christoph Wolf <wolf.christoph at qns.science>
> 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:
>
> <CAMC_G_52NoZXvtEw6BUCu0dLkh5utnmf2ygP1mesUT94_cBkiw at mail.gmail.com
> <mailto:CAMC_G_52NoZXvtEw6BUCu0dLkh5utnmf2ygP1mesUT94_cBkiw at mail.gmail.com>>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Sydney,
>
> the following tools are very convenient to build surface slabs with
> adsorbates as you described:
>
> http://hjkgrp.mit.edu/content/molsimplify-tutorial-2-slab-builder
> https://wiki.fysik.dtu.dk/ase/
>
>
> If you want to do it more "manually" you can of course also use
> Avogadro,
> VESTA, or simply a text editor if you have a lot of time ;)
>
> HTH!
> Chris
>
>
>
> --
> Postdoctoral Researcher
> Center for Quantum Nanoscience, Institute for Basic Science
> Ewha Womans University, Seoul, South Korea
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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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