[Pw_forum] Fwd: au111 surface
Filipe Camargo Dalmatti Alves Lima
flima at if.usp.br
Mon Apr 21 15:33:42 CEST 2014
Just my opinion: you should use ASE (Atomic Simulation Environment) to
build the surface for you.
https://wiki.fysik.dtu.dk/ase/
Documentation for surfaces:
https://wiki.fysik.dtu.dk/ase/ase/surface.html#module-ase.lattice.surface
This is the easiest method I have ever found to build a surface and it is
script friendly.
I also recommend you give a look on this article:
http://iopscience.iop.org/0953-8984/19/30/305018
It might be worth.
Regards,
Filipe
On Mon, Apr 21, 2014 at 9:20 AM, raha khalili <khadije.khalili at gmail.com>wrote:
> Dear David
>
> Very thanks for your suggestion. I downloaded avogadro-1.1.1.
> First I have installed cmake and gt4.8. But I get this error when
> installing:
>
> steps as INSTALL file in avogadro directory:
>
> cd avogadro-1.1.1
> mkdir build
> cd build
> cmake ../
>
> -- The C compiler identification is GNU 4.7.2
> -- The CXX compiler identification is GNU 4.7.2
> -- Check for working C compiler: /usr/lib64/ccache/cc
> -- Check for working C compiler: /usr/lib64/ccache/cc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Check for working CXX compiler: /usr/lib64/ccache/c++
> -- Check for working CXX compiler: /usr/lib64/ccache/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- The build type is Release
> -- Performing Test HAVE_NO_RTTI
> -- Performing Test HAVE_NO_RTTI - Success
> -- Performing Test HAVE_RTTI
> -- Performing Test HAVE_RTTI - Success
> -- Performing Test HAVE_GCC_VISIBILITY
> -- Performing Test HAVE_GCC_VISIBILITY - Success
> -- Performing Test COMPILES_WITHOUT_FPERMISSIVE
> -- Performing Test COMPILES_WITHOUT_FPERMISSIVE - Failed
> CMake Error at /usr/share/cmake/Modules/FindQt4.cmake:1368 (message):
> Found unsuitable Qt version "" from NOTFOUND, this code requires Qt 4.x
> Call Stack (most recent call first):
> CMakeLists.txt:226 (find_package)
>
> Could you tell me please what the problem is?
>
> Best Regards
> Raha
>
>
>
> On Sun, Apr 20, 2014 at 9:16 PM, David Foster <davidfoster751 at yahoo.com>wrote:
>
>> Dear Raha
>> You can use Avogadro for constructing it. The code is free. In addition,
>> you can search the web to find its cif file and use it in Avogadro, if you
>> don't want to do it by hand.
>>
>>
>>
>>
>> Regards
>>
>> David Foster
>>
>> Ph.D. Student of Chemistry
>>
>> --------------------------------------------
>> On Sat, 4/19/14, raha khalili <khadije.khalili at gmail.com> wrote:
>>
>> Subject: [Pw_forum] Fwd: au111 surface
>> To: "PWSCF Forum" <pw_forum at pwscf.org>
>> Date: Saturday, April 19, 2014, 3:45 AM
>>
>> Dear QE users
>>
>> I want to construct Au111 surfaces. But my
>> output file seems to be incorrect. Could you help me for
>> it?
>>
>> Input:&control
>> calculation = 'relax'
>> restart_mode='from_scratch',
>> prefix='au', tprnfor =
>> .true. pseudo_dir =
>> '/home/khalili/espresso-5.0.2/pseudo',
>>
>> outdir='./' / &system
>> ibrav= 0, celldm(1)=6.0, celldm(2)=1,
>> celldm(3)=0.222460766, nat= 13, ntyp=
>> 1, noncolin=.true.,
>> lspinorb=.true.,
>> starting_magnetization(1)=0.0,
>> ecutwfc = 27.0, ecutrho =
>> 391.0,
>> occupations='smearing',
>> smearing='fd',
>> degauss=0.001
>> / &electrons
>> diagonalization='david'
>> electron_maxstep = 500, mixing_mode =
>> 'plain' mixing_beta =
>> 0.7 conv_thr = 1.0d-6
>> /&ions
>> ion_dynamics =
>> 'bfgs'/ATOMIC_SPECIES Au
>> 196.966
>> Au.rel-pz-dn-rrkjus_psl.0.1.UPFATOMIC_POSITIONS Au
>> 2.949785413 3.672551581 0.719332431
>> Au 2.742687251 2.865572222
>> 0.719332431Au 3.563230179 3.098796549
>> 0.719332431Au 3.356132017
>> 2.291817190 0.719332431Au 3.534436578
>> 1.470557957 0.051950134
>> Au 3.732270300 2.268356755
>> 0.051950134Au 3.928237209 3.069472551
>> 0.051950134Au 2.912648680
>> 2.043258658 0.051950134Au 3.119592323
>> 2.850332820 0.051950134
>> Au 3.343806277 3.659523280
>> 0.051950134Au 2.299120168 2.617060049
>> 0.051950134Au 2.523263349
>> 3.426298953 0.051950134Au 2.730361511
>> 4.233278312 0.051950134
>> CELL_PARAMETERS6.0 0.0 0.00.0 6.0
>> 0.00.0 0.0 1.334764594K_POINTS
>> {Automatic} 1 1 4 1 1 1
>> output:
>> ATOMIC_POSITIONS (alat)Au
>> 2.937386209 3.582923161 0.719330203Au
>> 2.593545725 2.740963547 0.719333040Au
>> 3.670168686 3.044796914 0.719331555Au
>> 3.326200204 2.202685361 0.719334648
>> Au 3.478788201 1.670372948
>> 0.051951374Au 3.865644556 2.412608619
>> 0.051953914Au 4.175978091
>> 3.185452798 0.051947555Au 2.759515725
>> 2.097309245 0.051954205
>> Au 3.133871517 2.883011335
>> 0.051949504Au 3.504225226 3.675472063
>> 0.051948273Au 2.091449270
>> 2.593809644 0.051950705Au 2.407897276
>> 3.365285757 0.051948060
>> Au 2.790900569 4.112185484
>> 0.051947893End final
>> coordinates
>> Any help will be appreciated. --
>>
>> Khadije KhaliliPh.D
>> Student of Solid-State PhysicsDepartment of
>> PhysicsUniversity of
>> MazandaranBabolsar, Irankh.khalili at stu.umz.ac.ir
>>
>>
>>
>> -----Inline Attachment Follows-----
>>
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>
>
>
> --
> Khadije Khalili
> Ph.D Student of Solid-State Physics
> Department of Physics
> University of Mazandaran
> Babolsar, Iran
> kh.khalili at stu.umz.ac.ir
>
>
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--
_________________________________________
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of São Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones: (11) 3091-6881 (USP)
(11) 97408-2755 (Vivo)
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