QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: J.g_johnson on January 6, 2014, 03:23

Title: Fcc NaCl including 8 atoms
Post by: J.g_johnson on January 6, 2014, 03:23

when i use the ATK to construct a Fcc NaCl including 8 atoms, there is always existing the same mistake reminder:

{Back Engine Exception : Diagonalization error, overlap matrix not positive definite. This may be caused by atoms that are too close to each other or situated in equivalent positions, or (in the Extended Huckel model) a too low value of interaction_max_range
** Location of Exception : mathutils.cpp:687
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.}

So, i don`t know how to do with it. Please help me.
Thanks!

Title: Re: Fcc NaCl including 8 atoms
Post by: Shinji Usui on January 6, 2014, 04:02

Dear m.guo_johnson

I suppose you construct some incorrect structure for the fcc NaCl.
For example, the lattice vectors are too short.
Could you put your input file?

BR
Shinji

Title: Re: Fcc NaCl including 8 atoms
Post by: J.g_johnson on January 7, 2014, 07:36

Dear my friend,

   Thank you for your reply! The following is my input file.


# Set up lattice
lattice = FaceCenteredCubic(5.64056*Angstrom)

# Define elements
elements = [Sodium, Sodium, Sodium, Sodium, Chlorine, Chlorine, Chlorine, Chlorine]

# Define coordinates
fractional_coordinates = [[ 0. , 0. , 0. ],
                          [ 0. , 0. , 1.0],
                          [ 0. , 1.0, 0. ],
                          [ 1.0, 0. , 0. ],
                          [ 0.5, 0.5, 0.5],
                          [ -0.5, 0.5, 0.5],
                          [ 0.5, -0.5, 0.5],
                          [ 0.5, 0.5, -0.5]]

# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )

Looking forward to your reply!
Thanks again!

Title: Re: Fcc NaCl including 8 atoms
Post by: Shinji Usui on January 7, 2014, 07:55

Dear m.guo_johnson

Several atoms are occupying same coordinates.
You can check this by
Builder -> Select -> Close Neighbors
and click "Select" (see attached file).

Please check your configuration.

BR
Shinji

Title: Re: Fcc NaCl including 8 atoms
Post by: Umberto Martinez on January 7, 2014, 13:14

Correct. Also, notice that the primitive NaCl cell contains only two atoms in 0,0,0 and 0.5,  0.5,  0.5.
You will get this configuration after following the instruction of Shinji.

If you want to use the conventional (non-primitive) unit cell with 8 atoms instead, your script should look like:

Code

# Set up lattice
vector_a = [5.64056, 0.0, 0.0]*Angstrom
vector_b = [0.0, 5.64056, 0.0]*Angstrom
vector_c = [0.0, 0.0, 5.64056]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Sodium, Chlorine, Sodium, Chlorine, Sodium, Chlorine, Sodium,
            Chlorine]

# Define coordinates
fractional_coordinates = [[ 0. ,  0. ,  0. ],
                          [ 0.5,  0.5,  0.5],
                          [ 0.5,  0.5,  0. ],
                          [ 0. ,  0. ,  0.5],
                          [ 0.5,  0. ,  0.5],
                          [ 0. ,  0.5,  0. ],
                          [ 0. ,  0.5,  0.5],
                          [ 0.5,  0. ,  0. ]]

# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )

Title: Re: Fcc NaCl including 8 atoms
Post by: J.g_johnson on January 8, 2014, 06:51

Thank you, Shinji and  Umberto! That`s really help me a lot! This problem,you know, really makes me confused for several days! I feel so lucky to get both of your help! Well, think you, again!  :)