[Pw_forum] CPO-27-Zn scf not converge

[Lori 91]

Dear Paolo 
Thanks to help me now I have understood thanks a lot.
But can you tell why my structure is not correctly visualized from xcrysden or jice??
Thanks a lot again 
Dearly
Lorenzo 

Inviato da iPhone

> Il giorno 30 mag 2016, alle ore 22:42, Paolo Giannozzi <p.giannozzi at gmail.com> ha scritto:
> 
> The cell you report is Hexagonal and is defined by two parameters, a
> and c. Space group 148 has a trigonal (R) lattice, defined by
> parameter a and alpha = angle between two vectors. You should figure
> out which alpha for the trigonal lattice corresponds to your hexagonal
> cell, then you provide in input a (in A) and cosab=cos(alpha); or,
> equivalently, celldm(1)=a (in a.u.) and celldm(4)=cos(alpha). See
> here: http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idm6425376
> for definition of lattices in PW, here for the two descriptions of
> space group 148:
> http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list?gnum=148&grha=rhombohedral
> http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list?gnum=148&grha=hexagonal
> Hard to say if your atomic positions are correct, but chemical formula
> Zn_6 C_24 O_18 H_6 looks strange to me
> 
> Paolo
> 
>> On Mon, May 30, 2016 at 7:42 PM, Lorenzo Donà <lorechimica91 at hotmail.it> wrote:
>> Dear Paolo thanks for your replay and to help me
>> this is an hexagonal space group there are 54 atoms in the cell and it is
>> correct.
>> Space group R-3 with 9 atoms in the asymmetric unit cell with this cell
>> parameters for my system:
>> 26.22563    26.22563     6.95529    90.00000    90.00000   120.00000
>> But when i open the output with xcrysden for this system i found only atoms
>> without connectivity.
>> This appears only for system like hexagonal or other system where i must put
>> coasb or cosbc etc…. in the input.
>> can you tell me where my input is wrong???
>> this is my input:
>> 
>> &control
>> 
>>    pseudo_dir='/home/utente/Scaricati/espresso-5.4.0/pseudo/'
>> 
>>    wf_collect = .true.,
>> 
>>    verbosity= high,
>> 
>> /
>> 
>> &system
>> 
>>    a= 25.226, cosab= 0.5, space_group = 148,
>> 
>>    nat=  9, ntyp= 4,
>> 
>>    ecutwfc =15.0,
>> 
>>   occupations='smearing', smearing='marzari-vanderbilt', degauss=0.07
>> 
>>   input_dft= PBE,
>> 
>> /
>> 
>> &electrons
>> 
>>    mixing_mode='TF'
>> 
>>    diagonalization='cg'
>> 
>>    mixing_beta = 0.1
>> 
>>    conv_thr= 1.0e-7
>> 
>>    electron_maxstep=500,
>> 
>> /
>> 
>> ATOMIC_SPECIES
>> 
>> Zn 65.409 Zn.pbe-van.UPF
>> 
>> C 12.010  C.pbe-van_ak.UPF
>> 
>> O 16.00   O.pbe-van_ak.UPF
>> 
>> H 1.00    H.pbe-van_ak.UPF
>> 
>> ATOMIC_POSITIONS crystal_sg
>> 
>>  C   7.127430447398E-02 -2.455696438145E-01  7.991093030472E-02
>> 
>>  C   1.197468901477E-01 -2.066445045066E-01  2.152449225957E-01
>> 
>>  C   2.117353032357E-01 -1.117780631842E-01  2.553368090727E-01
>> 
>>  C   1.646071563067E-01 -1.528403540257E-01  1.440875844425E-01
>> 
>>  H   1.629458066146E-01 -1.419696182443E-01 -4.760745519579E-03
>> 
>> Zn  -1.943259345214E-02  2.834354147594E-01  3.060064447988E-01
>> 
>>  O   7.229455751443E-02 -2.290060932141E-01 -9.085450716092E-02
>> 
>>  O   3.018234203718E-02 -2.947952345384E-01  1.422041978763E-01
>> 
>>  O   2.519030126218E-01 -6.097111538485E-02  1.721974260943E-01
>> 
>> K_POINTS gamma
>> 
>> 
>> thanks a lot very very to help me.
>> dearly
>> lorenzo
>> 
>> Il giorno 30 mag 2016, alle ore 18:51, Paolo Giannozzi
>> <p.giannozzi at gmail.com> ha scritto:
>> 
>> You must provide what is needed: the space group number specifies the
>> lattice and the allowed atomic sites and symmetries, so you have to
>> specify
>> - the lattice parameter(s) for your lattice: either celldm, or a,b,c,
>> as described in the input documentation;
>> - the occupied sites, with the free parameter(s) (if any) of each site
>> (also described in the documentation of the input).
>> You find the information you need for your group in the Bilbao
>> Crystallographic server. If it is group 148, it can be described
>> either as hexagonal or as rhombohedra (see also option "rhombohedral":
>> I think hexagonal has 3 times the atoms of rhombohedral, so you should
>> use the latter)
>> 
>> Paolo
>> 
>> On Mon, May 30, 2016 at 5:50 PM, Lori 91 <lorechimica91 at hotmail.it> wrote:
>> 
>> Dear Paolo in the input must I put a and cosab or not with space group
>> keyword??
>> 
>> Inviato da iPhone
>> 
>> Il giorno 30 mag 2016, alle ore 14:31, Paolo Giannozzi
>> <p.giannozzi at gmail.com> ha scritto:
>> 
>> You need to know the space group number and the Wyckoff positions of
>> your crystal. Don't specify "ibrav", set "nat" to the number of
>> inequivalent sites, list those inequivalent sites ufter
>> ATOMIC_POSITIONS crystal_sg as explained in the documentation
>> 
>> 
>> Paolo
>> 
>> On Mon, May 30, 2016 at 12:43 PM, Lori 91 <lorechimica91 at hotmail.it> wrote:
>> Someone can help me to use correctly crystal_sg and space group number
>> because I found a connectivity problem for CPO-27Zn??
>> Thanks a lot
>> 
>> Inviato da iPhone
>> 
>> Il giorno 30 mag 2016, alle ore 12:37, Lori 91 <lorechimica91 at hotmail.it> ha
>> scritto:
>> 
>> 
>> 
>> Inviato da iPhone
>> 
>> (Inizio messaggio inoltrato)
>> 
>> Da: Lori 91 <lorechimica91 at hotmail.it>
>> Data: 30 maggio 2016 11:23:46 CEST
>> A: Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
>> Oggetto: Re: [Pw_forum] CPO-27-Zn scf not converge
>> 
>> Someone can help me to use correctly crystal_sg and space group number
>> because I found a connectivity problem for CPO-27Zn??
>> Thanks a lot
>> 
>> Inviato da iPhone
>> 
>> Il giorno 30 mag 2016, alle ore 11:02, Giuseppe Mattioli
>> <giuseppe.mattioli at ism.cnr.it> ha scritto:
>> 
>> 
>> 
>> Dear Lorenzo
>> 
>> Sorry, I'm not familiar with the new crystal_sg coordinates, but it seems to
>> me that there is something strange in the structure. I suggest that you
>> 
>> "fill the unit cell" with all the equivalent atoms (Avogadro or Vesta can do
>> it for you) and check the results to be sure that you are calculating
>> 
>> exactly what you want. If pw.x fills the unit cell and write the resulting
>> alat coordinates of all atoms (as usual), then you may directly check them
>> 
>> with xcrysden. You might try to run the job with the full structure and
>> simple "crystal" coordinates. Maybe something goes wrong when the code try
>> to
>> 
>> fill the unit cell in the crystal_sg case. Anyway I suppose that there is no
>> computational gain in using the crystal_sg coordinates ("no free lunch"
>> 
>> :-)).
>> 
>> HTH
>> 
>> Giuseppe
>> 
>> 
>> 
>> On Sunday, May 29, 2016 09:11:49 PM Lorenzo Donà wrote:
>> 
>> Dear all can you help me or give me some tips to make scf convergence on
>> this calculation:
>> 
>> 
>> &control
>> 
>> pseudo_dir='/home/utente/Scaricati/espresso-5.4.0/pseudo/'
>> 
>> outdir = './',
>> 
>> wf_collect = .true.,
>> 
>> verbosity= high,
>> 
>> /
>> 
>> &system
>> 
>> ibrav=  5,
>> 
>> a= 25.226, cosab= 0.5,  space_group = 148,
>> 
>> nat=  9, ntyp= 4,
>> 
>> ecutwfc =15.0,
>> 
>> occupations='fixed', smearing='gauss',
>> 
>> input_dft= PBE,
>> 
>> /
>> 
>> &electrons
>> 
>> mixing_mode='plain'
>> 
>> diagonalization='david'
>> 
>> mixing_beta = 0.01
>> 
>> conv_thr= 1.0e-4
>> 
>> electron_maxstep=500,
>> 
>> /
>> 
>> ATOMIC_SPECIES
>> 
>> Zn 65.409 Zn.pbe-van.UPF
>> 
>> C 12.010  C.pbe-van_ak.UPF
>> 
>> O 16.00   O.pbe-van_ak.UPF
>> 
>> H 1.00    H.pbe-van_ak.UPF
>> 
>> ATOMIC_POSITIONS crystal_sg
>> 
>> C   7.127430447398E-02 -2.455696438145E-01  7.991093030472E-02
>> 
>> C   1.197468901477E-01 -2.066445045066E-01  2.152449225957E-01
>> 
>> C   2.117353032357E-01 -1.117780631842E-01  2.553368090727E-01
>> 
>> C   1.646071563067E-01 -1.528403540257E-01  1.440875844425E-01
>> 
>> H   1.629458066146E-01 -1.419696182443E-01 -4.760745519579E-03
>> 
>> Zn  -1.943259345214E-02  2.834354147594E-01  3.060064447988E-01
>> 
>> O   7.229455751443E-02 -2.290060932141E-01 -9.085450716092E-02
>> 
>> O   3.018234203718E-02 -2.947952345384E-01  1.422041978763E-01
>> 
>> O   2.519030126218E-01 -6.097111538485E-02  1.721974260943E-01
>> 
>> K_POINTS gamma
>> 
>> 
>> Thanks a lot to help me
>> 
>> 
>> dearly
>> 
>> 
>> lorenzo
>> 
>> 
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>> 
>> Giuseppe Mattioli
>> 
>> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
>> 
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>> 
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>> 
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>> 
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>> 
>> --
>> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
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>> 
>> --
>> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>> 
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> 
> 
> -- 
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
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