A cif file represents a unit cell with minimum energy. My question is, in the start of any ab initio calculation for unit cell generated from the cif file, why we are advised to optimize cell parameters and atomic coordinates both. Can't we just optimize atomic coordinates or perform single point calculation?
Lattice constants are strongly depending on a set of parameters used in your ab initio calculation (kspacing, ecut and so on). So, you should optimize unit cell from cif with using of your parameters.
Also, don't forget about Pulay stress phenomena https://www.vasp.at/wiki/index.php/Energy_vs_volume_Volume_relaxations_and_Pulay_stress
To eliminate Pulay errors the lattice optimization (ISIF = 4) must be performed at constant volume for several contracted and expanded cells (5 - 7 points). https://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/create_vasp_calculation.ipynb
Mr. Singh,
The problem lies in determining the accurate position of the protons experimentally by means of single crystal X-ray diffraction measurements, which does not represent a trivial task even using high resolution crystallographic data. There is a deviation in the position of the protons within 0.01 to 0.02 Å.
The electron density of the protons in the molecules within the framework of the unit cell can be very delocalized. The same is true for the electron density of the metal ion of complexes of Ag(I)-ion.
In the latter cases, a strong electron localization we have found only in a pi-complex of the silver ion [2].
Please, consider the experimental electron density maps of high resolution single crystal X-ray diffraction data of metal-organics in our works [1,2].
Simply speaking, a spherical electron density with maximum of the electronic density at the centre of the sphere is observed only in pi-complexes. The coordination of the metal ions to the ligands can lead to a significant deviation in spherical electron density, which affects on the accuracy of the determined atomic position in the final cif.
[1] Polyhedron, 137 (2017) 256-264
On the nature of the coordination bonding of metal–organics for ions with the d10 electronic configuration – Experimental and theoretical analyses
Bojidarka Ivanova, Michael Spiteller
[2] Inorganica Chimica Acta, 471 (2018) 219-222
Cation-π-complex of Ag(I) ion with 1H-indole-5-carboxylic acid – Structural analysis and energetics of the M–L bonds
Bojidarka Ivanova, Michael Spiteller
Thank you A.O. Boev and Bojidarka Ivanova for the response. Your answers is very helpful.
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