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atomic coordinates
Date: 2017/09/28 15:03
Name: Mojtaba   <mj.mahmoudzadeh@shahroodut.ac.ir>

hi everyone,
i am new to openmx, i am using openmx 3.8.
i could not understood How do I find values for atomic coordinates?
for compound like Cs2InSbBr6, with cubic structure and Fm-3m space group, What atoms coordinate do I consider in input file?
so i need your help. could you mail me your guidance please?
thank you very much.
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Re: atomic coordinates ( No.1 )
Date: 2017/09/28 17:38
Name: Yung Ting Lee  <ytlee@issp.u-tokyo.ac.jp>

Dear Mojtaba,

(1) You can find atomic coordinates in the output files, such as *.out, *.md (for all steps), or *.md2 (for final step). You can check these files.

In the case of H2O:

------------------------------
***********************************************************
***********************************************************
xyz-coordinates (Ang) and forces (Hartree/Bohr)
***********************************************************
***********************************************************

<coordinates.forces
3
1 O 0.00000 -0.04620 -0.00000 -0.000000019859 -0.000075930198 0.000000011443
2 H 0.76305 0.55408 0.00000 0.000000385290 0.000001769369 -0.000000000303
3 H -0.76304 0.55408 -0.00000 -0.000000403544 0.000001801657 0.000000007802
coordinates.forces>

***********************************************************
***********************************************************
Fractional coordinates of the final structure
***********************************************************
***********************************************************

1 O 0.00000033333572 0.99482137453576 0.99999998657738
2 H 0.07697498381304 0.06210504389136 0.00000001297287
3 H 0.92302564276244 0.06210497169846 0.99999980320498
------------------------------

(2) The user's manual of OpenMX (version:3.8) can be found and downloaded from OpenMX website.

http://www.openmx-square.org/openmx_man3.8/openmx.html


(3) In this manual, it gives examples for users to understand basic structure of the OpenMX input file easily.

An example: methane molecule ( http://www.openmx-square.org/openmx_man3.8/node23.html )

------------------------------
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C 0.000000 0.000000 0.000000 2.0 2.0
2 H -0.889981 -0.629312 0.000000 0.5 0.5
3 H 0.000000 0.629312 -0.889981 0.5 0.5
4 H 0.000000 0.629312 0.889981 0.5 0.5
5 H 0.889981 -0.629312 0.000000 0.5 0.5
Atoms.SpeciesAndCoordinates>
------------------------------

The unit of atomic coordinates is angstrom in this case.
If you want to use fractional coordinates, just change "Ang" to "frac".


In addition, in the "work" folder, there are many kinds of examples for users' references to construct their own input files.

Best regards,
Yung Ting Lee.
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