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 <[email protected]> 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 > <[email protected]> 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 <[email protected]> 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 > <[email protected]> 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 <[email protected]> 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 <[email protected]> ha > scritto: > > > > Inviato da iPhone > > (Inizio messaggio inoltrato) > > Da: Lori 91 <[email protected]> > Data: 30 maggio 2016 11:23:46 CEST > A: Giuseppe Mattioli <[email protected]> > 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 > <[email protected]> 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 > > > ******************************************************** > > - Article premier - Les hommes naissent et demeurent > > libres et égaux en droits. Les distinctions sociales > > ne peuvent être fondées que sur l'utilité commune > > - Article 2 - Le but de toute association politique > > est la conservation des droits naturels et > > imprescriptibles de l'homme. Ces droits sont la liberté, > > la propriété, la sûreté et la résistance à l'oppression. > > ******************************************************** > > > Giuseppe Mattioli > > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > > v. Salaria Km 29,300 - C.P. 10 > > I 00015 - Monterotondo Stazione (RM), Italy > > Tel + 39 06 90672342 - Fax +39 06 90672316 > > E-mail: <[email protected]> > > http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ > > ResearcherID: F-6308-2012 > > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > > > > > -- > 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 > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > > > > > -- > 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 > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum -- 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 _______________________________________________ Pw_forum mailing list [email protected] http://pwscf.org/mailman/listinfo/pw_forum
