Dear siesta user,
I made the supercell of one of the test file of siesta package BaTiO3
(a=4.006 Ang) . And when I visulize its xyz file it gives me the right
structure of Batio3 with right angle and bond length . Then I choose one of
the cubic cell from the supercell to make the cubic structure of it, when
I choose fractional coordinate of that cell it gives me the structure with
reduced bond length and when used scaled coordinate it gives structure
with increased bond length. and when I used NotScaledCartesian cordinates
siesta will show me the error
error atoms too close rij = ooo ang
cholesky factorisation in rdiag
stop from the node zero :0
this the output of supercell generated siesta:
==============================
Begin MD step = 1
==============================
outcoor: Atomic coordinates (fractional):
0.00000000 0.00000000 0.00000000 1 1 Ba
0.25000000 0.25000000 0.25000000 2 2 Ti
0.00000000 0.25000000 0.25000000 3 3 O
0.25000000 0.00000000 0.25000000 3 4 O
0.25000000 0.25000000 0.00000000 3 5 O
0.50000000 0.00000000 0.00000000 1 6 Ba
0.75000000 0.25000000 0.25000000 2 7 Ti
0.50000000 0.25000000 0.25000000 3 8 O
0.75000000 0.00000000 0.25000000 3 9 O
0.75000000 0.25000000 0.00000000 3 10 O
0.00000000 0.50000000 0.00000000 1 11 Ba
0.25000000 0.75000000 0.25000000 2 12 Ti
0.00000000 0.75000000 0.25000000 3 13 O
0.25000000 0.50000000 0.25000000 3 14 O
0.25000000 0.75000000 0.00000000 3 15 O
0.50000000 0.50000000 0.00000000 1 16 Ba
0.75000000 0.75000000 0.25000000 2 17 Ti
0.50000000 0.75000000 0.25000000 3 18 O
0.75000000 0.50000000 0.25000000 3 19 O
0.75000000 0.75000000 0.00000000 3 20 O
0.00000000 0.00000000 0.50000000 1 21 Ba
0.25000000 0.25000000 0.75000000 2 22 Ti
0.00000000 0.25000000 0.75000000 3 23 O
0.25000000 0.00000000 0.75000000 3 24 O
0.25000000 0.25000000 0.50000000 3 25 O
0.50000000 0.00000000 0.50000000 1 26 Ba
0.75000000 0.25000000 0.75000000 2 27 Ti
0.50000000 0.25000000 0.75000000 3 28 O
0.75000000 0.00000000 0.75000000 3 29 O
0.75000000 0.25000000 0.50000000 3 30 O
0.00000000 0.50000000 0.50000000 1 31 Ba
0.25000000 0.75000000 0.75000000 2 32 Ti
0.00000000 0.75000000 0.75000000 3 33 O
0.25000000 0.50000000 0.75000000 3 34 O
0.25000000 0.75000000 0.50000000 3 35 O
0.50000000 0.50000000 0.50000000 1 36 Ba
0.75000000 0.75000000 0.75000000 2 37 Ti
0.50000000 0.75000000 0.75000000 3 38 O
0.75000000 0.50000000 0.75000000 3 39 O
0.75000000 0.75000000 0.50000000 3 40 O
superc: Internal auxiliary supercell: 4 x 4 x 4 = 64
superc: Number of atoms, orbitals, and projectors: 2560 36864 45056
outcell: Unit cell vectors (Ang):
8.011740 0.000000 0.000000
0.000000 8.011740 0.000000
0.000000 0.000000 8.011740
outcell: Cell vector modules (Ang) : 8.011740 8.011740 8.011740
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 514.2573
and this the xyz file
40
Ba 0.000000 0.000000 -0.000000
Ti 2.002935 2.002935 2.002935
O 0.000000 2.002935 2.002935
O 2.002935 0.000000 2.002935
O 2.002935 2.002935 0.000000
Ba 4.005870 0.000000 0.000000
Ti 6.008805 2.002935 2.002935
O 4.005870 2.002935 2.002935
O 6.008805 0.000000 2.002935
O 6.008805 2.002935 0.000000
Ba 0.000000 4.005870 0.000000
Ti 2.002935 6.008805 2.002935
O 0.000000 6.008805 2.002935
O 2.002935 4.005870 2.002935
O 2.002935 6.008805 0.000000
Ba 4.005870 4.005870 0.000000
Ti 6.008805 6.008805 2.002935
O 4.005870 6.008805 2.002935
O 6.008805 4.005870 2.002935
O 6.008805 6.008805 0.000000
Ba 0.000000 0.000000 4.005870
Ti 2.002935 2.002935 6.008805
O 0.000000 2.002935 6.008805
O 2.002935 0.000000 6.008805
O 2.002935 2.002935 4.005870
Ba 4.005870 0.000000 4.005870
Ti 6.008805 2.002935 6.008805
O 4.005870 2.002935 6.008805
O 6.008805 0.000000 6.008805
O 6.008805 2.002935 4.005870
Ba 0.000000 4.005870 4.005870
Ti 2.002935 6.008805 6.008805
O -0.000000 6.008805 6.008805
O 2.002935 4.005870 6.008805
O 2.002935 6.008805 4.005870
Ba 4.005870 4.005870 4.005870
Ti 6.008805 6.008805 6.008805
O 4.005870 6.008805 6.008805
O 6.008805 4.005870 6.008805
O 6.008805 6.008805 4.005870
I select atomic cordinates from these files.Please help me out from this
problem because same problem occurs in my other structure also. I shall be
really thankful to siesta users.
regards
swati
