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: [email protected] <[email protected]> on > behalf of Duc-Long NGUYEN <[email protected]> > 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: [email protected] <[email protected]> on >> behalf of Duc-Long NGUYEN <[email protected]> >> 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 >>> [email protected] >>> 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 >> [email protected] >> http://pwscf.org/mailman/listinfo/pw_forum > > > _______________________________________________ > 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
