Dear Elio
> Thanks for reply. I can see where you are coming from. I did put "crystal" > because those coordinates are the "fractional" coordinates given by > the "Crystal builder". Isn't crystal (in terms of the primitive cells) in QE > equivalent to fractional? In *crystal* (as well as *fractional*) coordinates 0.10168*=*1.10168 the two atoms are not shifted by 1 A. They are shifted by 1 lattice vector so that they *fold on the same position in the unit cell and overlap*. If you want to replicate a unit cell in crystal coordinates along a given direction you should double the corresponding lattice parameter and divide by 2 the corresponding crystal coordinates. HTH Giuseppe On Tuesday, January 12, 2016 12:22:54 AM Elio Physics wrote: > Dear Henry, > > Thanks for reply. I can see where you are coming from. I did put "crystal" > because those coordinates are the "fractional" coordinates given by > the "Crystal builder". Isn't crystal (in terms of the primitive cells) in QE > equivalent to fractional? > > Thanks > > ________________________________________ > From: pw_forum-boun...@pwscf.org <pw_forum-boun...@pwscf.org> on behalf of > Henry J Seeley <hsee...@uoregon.edu> > Sent: Monday, January 11, 2016 10:13 PM > To: PWSCF Forum > Subject: Re: [Pw_forum] Atomic positions for Black Phosphorus calculations > > You have set your atomic coordinates to the crystal coordinates: > > ATOMIC_POSITIONS >>>crystal<<< > P -0.89832 0.89832 0.91944 > P -0.39832 0.39832 0.58056 > P -0.10168 0.10168 0.08056 > P 0.10168 0.89832 0.91944 > P -0.10168 1.10168 0.08056 > P -0.60168 0.60168 0.41944 > P -0.39832 1.39832 0.58056 > P 0.39832 0.60168 0.41944 > > You're positioning your atoms with reference to your lattice constant, > with 0.0 begin on one end of a lattice vector and 1.0 on the other end. > Atoms #2&7 and #3&5 differ by 1 lattice vector in the 2nd column, and > are therefor in the same position. If you wanted units of angstroms, > replace "crystal" with "angtrom" after ATOMIC_POSITIONS. > > Check out the pw.x input guide: > http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html > > > Hope this helps, > Hank Seeley > University of Oregon, Chemistry > > On 2016/01/11 16:03, Elio Physics wrote: > > Thanks for your help once again. I do not have XCrysDen and I have > > been having problems installing it. This is weird as with Crystal > > builder the atoms were well separated and different. One more thing: > > Where can I find the ccorect coordinates? any idea how to form the > > atomic positions? > > > > Thanks > > > > ------------------------- > > > > FROM: pw_forum-boun...@pwscf.org <pw_forum-boun...@pwscf.org> on > > behalf of Duc-Long NGUYEN <longnguyen...@gmail.com> > > SENT: Monday, January 11, 2016 9:53 PM > > TO: PWSCF Forum > > SUBJECT: Re: [Pw_forum] Atomic positions for Black Phosphorus > > calculations > > > > Hi, > > > > You could use xcrysden to check your input. > > This is the result with your input: > > Number of Atoms: 8 > > Number of Frames: 12 > > WARNING: Atom 1 and atom 3 overlap !!! Atom 3 deleted !!! > > WARNING: Atom 2 and atom 7 overlap !!! Atom 7 deleted !!! > > WARNING: Atom 4 and atom 8 overlap !!! Atom 8 deleted !!! > > WARNING: Atom 5 and atom 6 overlap !!! Atom 6 deleted !!! > > That was also why pwscf showed that error. > > > > Duc-Long > > > > On 1/12/2016 7:46 AM, Elio Physics wrote: > >> Dear Duc-Long, > >> > >> thanks for your response. I do not think they have the same > >> coordinate. The "y" coordinate of one is 0.10168 while that of the > >> 2nd is 1.10168, that is a difference of 1 ang. > >> > >> Elio > >> > >> ------------------------- > >> > >> FROM: pw_forum-boun...@pwscf.org <pw_forum-boun...@pwscf.org> on > >> behalf of Duc-Long NGUYEN <longnguyen...@gmail.com> > >> SENT: Monday, January 11, 2016 9:38 PM > >> TO: PWSCF Forum > >> SUBJECT: Re: [Pw_forum] Atomic positions for Black Phosphorus > >> calculations > >> > >> Dear Elio, > >> > >> ATOMIC_POSITIONS crystal > >> P -0.89832 0.89832 0.91944 > >> P -0.39832 0.39832 0.58056 > >> P -0.10168 0.10168 0.08056 > >> P 0.10168 0.89832 0.91944 > >> P -0.10168 1.10168 0.08056 > >> P -0.60168 0.60168 0.41944 > >> P -0.39832 1.39832 0.58056 > >> P 0.39832 0.60168 0.41944 These two atom positions have the same > >> coordinate. This could be the problem. > >> > >> Duc-Long > >> > >> On 1/12/2016 6:44 AM, Elio Physics wrote: > >>> Dear all, > >>> > >>> I am trying to perform some calculations on Black Phosphorus (BP). > >>> To get the atomic positions I used the Crystal Builder, where I > >>> have chosen the lattice type to be base centered orthorhombic. > >>> The "builder" produced a set of cartesian and fractional (in > >>> terms of the primitive cell vectors) . I have used the fractional > >>> ones and I have also used ibrav=0 with the CELL_PARAMETERS defined > >>> as in the builder (a/2, -b/2, 0), (a/2, b/2,0), (0,0,c). However I > > > >>> have got the following error: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > >>> from check_atoms : error # 1 > >>> atoms # 1 and # 4 overlap! > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > >>> Doing the same calculation with ibrav=8 and using the coordinates > >>> produced by the Crystal builder for a simple orthorhombic does not > >>> produce any errors. Can anyone please tell me what is wrong with > >>> atoms (1) and (4). Is BP simple or base centered > >>> orthorhombic..Where can I find the coorect atomic position of bulk > >>> BP? The scf input is below: > >>> > >>> &CONTROL > >>> prefix='bp', > >>> calculation='scf', > >>> restart_mode='from_scratch', > >>> wf_collect=.true., > >>> forc_conv_thr=1.D-4 > >>> etot_conv_thr=1.D-5 > >>> tstress=.true., > >>> tprnfor=.true., > >>> pseudo_dir ='/home_cluster/fis718/elio/espresso-4.1.3/pseudo', > >>> > >>> outdir='/home_cluster/fis718/elio/espresso-4.1.3/BP/OUT' > >>> / > >>> &SYSTEM > >>> ibrav=0,celldm(1)=6.26179,nat=8, ntyp= 1, ecutwfc=10, > >>> ecutrho=40, occupations='smearing', london=.true., smearing='mp', > >>> degauss=0.035,nbnd=32 > >>> / > >>> &ELECTRONS > >>> conv_thr=1.D-8, > >>> mixing_beta=0.1 > >>> / > >>> &IONS > >>> ion_dynamics='bfgs' > >>> / > >>> &CELL > >>> cell_dynamics='bfgs' > >>> press=0.0 > >>> / > >>> ATOMIC_SPECIES > >>> P 30.97376 P.pbe-n-van.UPF > >>> ATOMIC_POSITIONS crystal > >>> P -0.89832 0.89832 0.91944 > >>> P -0.39832 0.39832 0.58056 > >>> P -0.10168 0.10168 0.08056 > >>> P 0.10168 0.89832 0.91944 > >>> P -0.10168 1.10168 0.08056 > >>> P -0.60168 0.60168 0.41944 > >>> P -0.39832 1.39832 0.58056 > >>> P 0.39832 0.60168 0.41944 > >>> > >>> K_POINTS automatic > >>> 2 2 2 0 0 0 > >>> > >>> CELL_PARAMETERS alat > >>> 0.5000 -1.58106 0.0000 > >>> 0.500 1.58106 0.0000 > >>> 0.0000 0.00000 4.3763 > >>> > >>> thanks > >>> > >>> Elio Arbid > >>> University of Nottingham > >>> UK > >>> > >>> _______________________________________________ > >>> Pw_forum mailing list > >>> Pw_forum@pwscf.org > >>> http://pwscf.org/mailman/listinfo/pw_forum > >> > >> -- > >> Duc-Long Nguyen > >> Graduate Student, Molecular Science and Technology Program, TIGP > >> Institute of Atomic and Molecular Sciences, > >> Academia Sinica, Taipei 106, Taiwan > >> Phone +886 979279073 > >> > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum@pwscf.org > >> http://pwscf.org/mailman/listinfo/pw_forum > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum@pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > _______________________________________________ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > _______________________________________________ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ******************************************************** - Article premier - Les hommes naissent et demeurent libres et égaux en droits. 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