[Pw_forum] overlap of atoms

[elbuesta at icqmail.com]

I may be missing something, but when I opened your structure with the XCrysden there were many warning messages, including many messages of atoms overlapped. I don't have Jmole to re-check, but it seems to me that your structure is too much compressed.


Fabio Negreiros Ribeiro
Laboratorio de Fisica de Superficies da Universidade Federal de Minas Gerais, Brasil



-----Original Message-----
From: Payam Norouzzadeh <payam.norouzzadeh at gmail.com>
To: pw_forum at pwscf.org
Sent: Wed, Jun 16, 2010 5:29 pm
Subject: [Pw_forum] overlap of atoms


Hello Espresso users
I have checked the structure I want to relax it by Xcrysden and Jmole and there was no overlap between atoms but Espresso leave
an error message  like : overlap between atoms 1 and 5, 2 and 6 ,....
Could someone please have a look to my input file and let me know how can I fix it?


Best regards,Payam Norouzzadeh




 &CONTROL
                       title = Ba ,
                 calculation = 'relax' ,
                restart_mode = 'from_scratch' ,
                  wf_collect = .true. ,
                      outdir = '/lustre/work/pnorouzz/espresso/Ba/relax' ,
                      wfcdir = '/lustre/work/pnorouzz/espresso/Ba/relax' ,
                  pseudo_dir = '/lustre/work/pnorouzz/espresso/Ba/relax' ,
                          dt = 20 ,
 /
 &SYSTEM
                     ibrav =  3, 
                     celldm(1) = 11.6, 
                     nat = 54,
                     ntyp = 3,
                     ecutwfc = 50 ,
                     ecutrho = 500 ,
 /
 &ELECTRONS
                    conv_thr = 1.D-8 ,
                 mixing_beta = 0.5D0 ,
 /
 &IONS
                ion_dynamics = 'damp' ,
           pot_extrapolation = 'second_order' ,
           wfc_extrapolation = 'second_order' ,
                     upscale = 100 ,
 /
ATOMIC_SPECIES
   Ba   137.327    Ba.pw91-nsp-van.UPF
   Sn   118.710    Sn.pw91-n-van.UPF
   Ga   71.0843639 Ga.pw91-n-van.UPF 
ATOMIC_POSITIONS  
Ba 0.186   0.186   0.186
Ba  0.814   0.814   0.186
Ba 0.814   0.186   0.814
Ba  0.186   0.814   0.814
Ba 0.686   0.686   0.686
Ba  0.314   0.314   0.686
Ba 0.314   0.686   0.314
Ba  0.686   0.314   0.314
Sn 0   0   0
Sn  0.5 0.5 0.5
Sn   0.6348  0.6348  0.3652
Sn  0.3652  0.6348  0.6348
Sn    0.1348  0.1348  0.8652
Sn  0.8652  0.1348  0.1348
Sn    0.41596 0.41596 0.1441
Sn  0.58404 0.58404 0.1441
Sn  0.58404 0.41596 0.8559
Sn    0.41596 0.58404 0.8559
Sn  0.1441  0.41596 0.41596
Sn  0.8559  0.41596 0.58404
Sn   0.41596 0.1441  0.41596
Sn  0.58404 0.1441  0.58404
Sn  0.91596 0.91596 0.6441
Sn    0.08404 0.08404 0.6441
Sn  0.08404 0.91596 0.3559
Sn  0.91596 0.08404 0.3559
Sn    0.6441  0.91596 0.91596
Sn  0.3559  0.91596 0.08404
Sn  0.91596 0.6441  0.91596
Sn   0.08404 0.6441  0.08404
Sn  0.91596 0.3559  0.08404
Sn  0.08404 0.3559  0.91596
Sn   0   0.25    0.5
Sn  0   0.75    0.5
Sn   0.5 0   0.25
Sn  0.5 0   0.75
Sn  0   0.5 0.25
Sn  0   0.5 0.75
Ga  0.3652  0.3652  0.3652
Ga  0.6348  0.3652  0.6348
Ga    0.8652  0.8652  0.8652
Ga  0.1348  0.8652  0.1348
Ga    0.1441  0.58404 0.58404
Ga  0.8559  0.58404 0.41596
Ga  0.41596 0.8559  0.58404
Ga   0.58404 0.8559  0.41596
Ga  0.6441  0.08404 0.08404
Ga  0.3559  0.08404 0.91596
Ga   0.25    0.5 0
Ga  0.75    0.5 0
Ga 0.5 0.25    0
Ga  0.5 0.75    0
Ga 0.25    0   0.5
Ga  0.75    0   0.5
K_POINTS automatic 
4 4 4  0 0 0 

 
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