[Pw_forum] (no subject)
Giovanni Cantele
giovanni.cantele at spin.cnr.it
Thu Nov 19 09:50:51 CET 2015
> On 18 Nov 2015, at 22:55, tomy tunde <rskadeniji at yahoo.com> wrote:
>
> Dear Giovanni,
> I appreciated your corrections you made for me on what i send.
> Sir, i have used visualization software with xcrysden at 2x2x2
in which way? I have just opened the input file you have provided in attachment and XcrysDen, after displaying the structure,
gives the following messages:
WARNING: Atom 1 and atom 4 overlap !!! Atom 4 deleted !!!
WARNING: Atom 1 and atom 7 overlap !!! Atom 7 deleted !!!
WARNING: Atom 1 and atom 8 overlap !!! Atom 8 deleted !!!
WARNING: Atom 1 and atom 11 overlap !!! Atom 11 deleted !!!
WARNING: Atom 1 and atom 14 overlap !!! Atom 14 deleted !!!
WARNING: Atom 1 and atom 15 overlap !!! Atom 15 deleted !!!
WARNING: Atom 1 and atom 16 overlap !!! Atom 16 deleted !!!
WARNING: Atom 1 and atom 17 overlap !!! Atom 17 deleted !!!
WARNING: Atom 1 and atom 18 overlap !!! Atom 18 deleted !!!
WARNING: Atom 1 and atom 21 overlap !!! Atom 21 deleted !!!
….
….
Moreover, if you click on the “translational asymmetric unit” button, that displays the atoms in the primitive unit cell (that is, just those positions you provide in the input), you get the attached image, from which it is clear that while you replicated the positions in a 2x2x2 unit cell, you forgot to provide the corresponding unit cell dimensions (there are atoms out the cell boundaries).
Example (same as I already pointed out in the previous message):
Atom 1
Mg 0.0000000000 0.0000000000 0.0000000000
Atom 4
Mg 0.0000000000 0.0000000000 3.5724606980
Their positions differ by the vector (0., 0., 3.572 A). But the unit cell vector along the c-axis has coordinates (0, 0, c) with c=1.155*5.845*0.529177 A = 3.572 A. Therefore, the positions of atoms 1 and 4 are periodic replicas of each other!!!! The pw.x error message just clearly says that you put two different atoms in the same or equivalent positions, which means that your input is wrong. You must update the cell size and be sure that what you have built is the correct 2x2x2 supercell.
> but i changed the pseudopotential of Mg
Why? By changing the pseudo potential you’ll never cure an error associated to atomic positions!!!!
Giovanni
> but it gave me error as shown bel %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> task # 0
> from check_atoms : error # 1
> atoms # 1 and # 4 overlap!
> Sir i need further assistance for it with my new scf and xsf file attach
> &control
> calculation = 'scf'
> restart_mode='from_scratch'
> prefix='MgB2',
> pseudo_dir = '/home/adeniji/espresso-5.0/pseudo/',
> outdir='./'
> /
> &system
> ibrav=4,
> celldm(1)=5.845,
> celldm(3)=1.155,
> nat=43,
> ntyp=2,
> ecutwfc =45.0,
> ecutrho = 450.0,
> occupations= 'smearing',
> degauss= 0.03,
> smearing= 'cold',
> /
> &electrons
> mixing_beta = 0.7
> conv_thr = 1.0d-12
> /
> ATOMIC_SPECIES
> Mg 24.31 Mg.pbe-sp-rrkjus.UPF
> B 10.81 B.pbe-n-rrkjus.UPF
> ATOMIC_POSITIONS {ANGSTROM}
> Mg 0.0000000000 0.0000000000 0.0000000000
> B -0.0000000000 1.7857663930 1.7661255920
> B 1.5465197830 0.8928986620 1.7661255920
> Mg 0.0000000000 0.0000000000 3.5724606980
> B -0.0000000000 1.7857663930 5.3385862900
> B 1.5465197830 0.8928986620 5.3385862900
> Mg 0.0000000000 0.0000000000 7.1449213960
> Mg -1.5465197830 2.6786508380 0.0000000000
> B -1.5465197830 4.4644172310 1.7661255920
> B -0.0000000000 3.5715495000 1.7661255920
> Mg -1.5465197830 2.6786508380 3.5724606980
> B -1.5465197830 4.4644172310 5.3385862900
> B -0.0000000000 3.5715495000 5.3385862900
> Mg -1.5465197830 2.6786508380 7.1449213960
> Mg -3.0930395660 5.3573016760 0.0000000000
> Mg -3.0930395660 5.3573016760 3.5724606980
> Mg -3.0930395660 5.3573016760 7.1449213960
> Mg 3.0930395650 0.0000000000 0.0000000000
> B 3.0930395650 1.7857663930 1.7661255920
> B 4.6395593480 0.8928986620 1.7661255920
> Mg 3.0930395650 0.0000000000 3.5724606980
> B 3.0930395650 1.7857663930 5.3385862900
> B 4.6395593480 0.8928986620 5.3385862900
> Mg 3.0930395650 0.0000000000 7.1449213960
> Mg 1.5465197820 2.6786508380 0.0000000000
> B 1.5465197820 4.4644172310 1.7661255920
> B 3.0930395650 3.5715495000 1.7661255920
> Mg 1.5465197820 2.6786508380 3.5724606980
> B 1.5465197820 4.4644172310 5.3385862900
> B 3.0930395650 3.5715495000 5.3385862900
> Mg 1.5465197820 2.6786508380 7.1449213960
> Mg -0.0000000010 5.3573016760 0.0000000000
> Mg -0.0000000010 5.3573016760 3.5724606980
> Mg -0.0000000010 5.3573016760 7.1449213960
> Mg 6.1860791300 0.0000000000 0.0000000000
> Mg 6.1860791300 0.0000000000 3.5724606980
> Mg 6.1860791300 0.0000000000 7.1449213960
> Mg 4.6395593470 2.6786508380 0.0000000000
> Mg 4.6395593470 2.6786508380 3.5724606980
> Mg 4.6395593470 2.6786508380 7.1449213960
> Mg 3.0930395640 5.3573016760 0.0000000000
> Mg 3.0930395640 5.3573016760 3.5724606980
> Mg 3.0930395640 5.3573016760 7.1449213960
> K_POINTS {automatic}
> 12 12 6 0 0 0
> Thanks your assistance
> ADENIJI RASAKI IDOWU
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--
Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cantele at spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74
ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
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