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 > <[email protected]> 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 <[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 _______________________________________________ Pw_forum mailing list [email protected] http://pwscf.org/mailman/listinfo/pw_forum
