[Pw_forum] error two atoms overlap

2012-03-27 Thread GAO Zhe 
Since your system is simple cubic, and your first and second atoms position are 
(0,0,0) and (-1,0,0), which are both at the vertex position of a cubic, thus 
the 1st and 2nd atoms at exactly same position (please think about the 
translation in crystal). Actually, in you input file, atom 1~4 aimed the same 
position.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-03-27 06:33:35,"mohamed makhyoun"  wrote:

| Dear All:

By running the given input file for pw.x I get the error:



 from check_atoms : error # 1
 atoms #   1 and #   2 overlap!

Although I checked the input by XCRYSDEN visualization program and nothing is 
wrong.
 I appreciate any help.

Best Regard

Mohamed
###

&CONTROL
 calculation = 'scf' ,
 prefix='cu3nbs4'
restart_mode = 'from_scratch' ,
  outdir = '$TMP_DIR/' ,
  pseudo_dir = '/home/mohamed/espresso/exec/pseudo' ,
  verbosity = 'default' ,

 /
 &SYSTEM
   ibrav=1
   celldm(1)= 10.397 ,
   nat = 20,
ntyp = 3,
 ecutwfc = 60. ,
 nbnd=90,
 /
 &ELECTRONS
  conv_thr=1.0D-8 ,
 /
ATOMIC_SPECIES
   Nb  92.9064   Nb.pbe-sR-sc-us.UPF
   Cu  63.546Cu.pbe-sR-us.UPF
S   32.06 S.pbe-van-bm.UPF
 ATOMIC_POSITIONS crystal
Nb   0.0  0.0  0.0
Nb  -1.0  0.0  0.0
Nb   0.0  0.0 -1.0
Nb   1.0  0.0  0.0
Cu   0.5  0.0  0.0
Cu   0.0  0.0 -0.5
Cu  -0.5  0.0  0.0
Cu   0.0 -0.5  0.0
Cu   0.0  0.5  0.0
Cu   0.0  0.0  0.5
S0.242599953  0.242599953  0.242599953
S0.242599953 -0.242599953 -0.242599953
S   -0.242599953  0.242599953 -0.242599953
S   -0.242599953 -0.242599953  0.242599953
S   -0.757400047  0.242599953  0.242599953
S0.242599953  0.242599953 -0.757400047
S   -0.757400047 -0.242599953 -0.242599953
S0.757400047  0.242599953 -0.242599953
S   -0.242599953 -0.242599953 -0.757400047
S0.757400047 -0.242599953  0.242599953
K_POINTS gamma


|
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[Pw_forum] error two atoms overlap

2012-03-26 Thread Axel Kohlmeyer 
On Mon, Mar 26, 2012 at 6:33 PM, mohamed makhyoun wrote:

> Dear All:
>
> By running the given input file for pw.x I get the error:
>
>
> 
>  from check_atoms : error # 1
>  atoms #   1 and #   2 overlap!
> 
> Although I checked the input by XCRYSDEN visualization program and nothing
> is wrong.
>  I appreciate any help.
>

there is a lot wrong.

on a crystal lattice positions

0.0 0.0 0.0

and

-1.0 0.0 0.0

are indeed the same,
just shifted by an entire cell.
your structure should have
only one Nb atom.

axel.



>
> Best Regard
>
> Mohamed
> ###
>
> &CONTROL
>  calculation = 'scf' ,
>  prefix='cu3nbs4'
> restart_mode = 'from_scratch' ,
>   outdir = '$TMP_DIR/' ,
>   pseudo_dir = '/home/mohamed/espresso/exec/pseudo' ,
>   verbosity = 'default' ,
>
>  /
>  &SYSTEM
>ibrav=1
>celldm(1)= 10.397 ,
>nat = 20,
> ntyp = 3,
>  ecutwfc = 60. ,
>  nbnd=90,
>  /
>  &ELECTRONS
>   conv_thr=1.0D-8 ,
>  /
> ATOMIC_SPECIES
>Nb  92.9064   Nb.pbe-sR-sc-us.UPF
>Cu  63.546Cu.pbe-sR-us.UPF
> S   32.06 S.pbe-van-bm.UPF
>  ATOMIC_POSITIONS crystal
> Nb   0.0  0.0  0.0
> Nb  -1.0  0.0  0.0
> Nb   0.0  0.0 -1.0
> Nb   1.0  0.0  0.0
> Cu   0.5  0.0  0.0
> Cu   0.0  0.0 -0.5
> Cu  -0.5  0.0  0.0
> Cu   0.0 -0.5  0.0
> Cu   0.0  0.5  0.0
> Cu   0.0  0.0  0.5
> S0.242599953  0.242599953  0.242599953
> S0.242599953 -0.242599953 -0.242599953
> S   -0.242599953  0.242599953 -0.242599953
> S   -0.242599953 -0.242599953  0.242599953
> S   -0.757400047  0.242599953  0.242599953
> S0.242599953  0.242599953 -0.757400047
> S   -0.757400047 -0.242599953 -0.242599953
> S0.757400047  0.242599953 -0.242599953
> S   -0.242599953 -0.242599953 -0.757400047
> S0.757400047 -0.242599953  0.242599953
> K_POINTS gamma
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com  http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.
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[Pw_forum] error two atoms overlap

2012-03-26 Thread mohamed makhyoun 
Dear All: 

By running the given input file for pw.x I get the error:



 from check_atoms : error # 1
 atoms #?? 1 and #?? 2 overlap!

Although I checked the input by XCRYSDEN visualization program and nothing is 
wrong.
?I appreciate any help.

Best Regard

Mohamed
###

&CONTROL
 calculation = 'scf' ,
 prefix='cu3nbs4'
??? restart_mode = 'from_scratch' ,
? outdir = '$TMP_DIR/' ,
? pseudo_dir = '/home/mohamed/espresso/exec/pseudo' ,
? verbosity = 'default' ,

?/
?&SYSTEM
?? ibrav=1
?? celldm(1)= 10.397 ,
?? nat = 20,
??? ntyp = 3,
 ecutwfc = 60. ,
 nbnd=90,
?/
?&ELECTRONS
? conv_thr=1.0D-8 ,
?/
ATOMIC_SPECIES
?? Nb? 92.9064?? Nb.pbe-sR-sc-us.UPF
?? Cu? 63.546??? Cu.pbe-sR-us.UPF
??? S?? 32.06 S.pbe-van-bm.UPF
?ATOMIC_POSITIONS crystal
Nb?? 0.0? 0.0? 0.0
Nb? -1.0? 0.0? 0.0
Nb?? 0.0? 0.0 -1.0
Nb?? 1.0? 0.0? 0.0
Cu?? 0.5? 0.0? 0.0
Cu?? 0.0? 0.0 -0.5
Cu? -0.5? 0.0? 0.0
Cu?? 0.0 -0.5? 0.0
Cu?? 0.0? 0.5? 0.0
Cu?? 0.0? 0.0? 0.5
S??? 0.242599953? 0.242599953? 0.242599953
S??? 0.242599953 -0.242599953 -0.242599953
S?? -0.242599953? 0.242599953 -0.242599953
S?? -0.242599953 -0.242599953? 0.242599953
S?? -0.757400047? 0.242599953? 0.242599953
S??? 0.242599953? 0.242599953 -0.757400047
S?? -0.757400047 -0.242599953 -0.242599953
S??? 0.757400047? 0.242599953 -0.242599953
S?? -0.242599953 -0.242599953 -0.757400047
S??? 0.757400047 -0.242599953? 0.242599953
K_POINTS gamma


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