In the following link, the atomic position of different space groups has been shown.
http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list
http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list?gnum=71
For a first principle calculation, I need to know the atomic position of a compound. I found the crystal space group (e.g. Immm (Pearson number:71)). But for adding atoms in materials studio, I don't know how I should find the atomic position.
I really appreciate if you help me to find out how to use this website. What should be replaced by x, y, z?
Best wishes,
Hi Ahmad:
I suggest you to use ATOMS program.http://cars9.uchicago.edu/cgi-bin/atoms/atoms.cgi
. You can get the atomic positions in the cartesian coordinate by this program if you have the crystal parameters or the cif file.
You need to know the space group, unic cell parameters, and fractionla cooridnates of each elements in the crystal.
May be you already found the solution. but I wanted to give my suggestion even if it is very late.
The space group description only describes the arrangement of symmetry operators and give a general list of positions following from this unique arrangement. It is nothing else like a construction plan you have to follow if you enter real atomic positions. Therefore we have finally only 230 space group types which are given as standard descriptions (or construction plans) in International Tables for Crystallography. On the other hand we have thousands of structures described by one and the same construction plan. This mean, the knowledge about the symmetry-equivalent positions doesn't help you at all (except if you have special positions without any degree of freedom like 0, 0.5, 0.5). You need to know the content of the asymmetric unit. Commonly, structure crystallographers have some idea which structure could be very close and use this as initial data for refinement. But again: the list of symmetry-equivalent positions doesn't help you at all.
Which compound is this? How do you know the spacegroup? Have tried to find for this or similar structure in crystallographic databases?
Let's suppose for Mg7Zn3. You know, it is my general problem, for many of intermetallic and compounds, it is not very difficult to find out the space group by googling or searching in databases, but I don't know how I can find their atomic position. For example for Mg7Zn3 (IMMM), or Ca2Mg6Zn3 (P63/mmc).
Best wishes,
The best way is to find the actual atomic coordinates in a crystallographic database (like ICSD, CSD or COD), or listed in a paper which describes the structure of the compound of interest.
I cannot find Mg7Zn3 and Ca2Mg6Zn3 in the ICSD database. You need to find publications which report these structures and list the unit cell constants, atomic coordinates and occupancies.
Good luck!
Thank you dear tomasz.
So do you have any idea that how the people in their publications can find the atomic positions? Using XRD and refinement? or is there any other way?
Best
In ICSD (104901) is a phase with space group Immm Mg~51 Zn~20 having lattice parameters of 14.083, 14.486, and 14.025, i.e. practically pseudo-tetragonal or even close to cubic metric. Is this perhaps your phase Mg7Zn3? Unfortunately Ca-Mg-Zn phase is indeed not liste there.
In doi: http://dx.doi.org/10.1016/j.corsci.2012.07.015 they are also discussing Mg51Zn20 and Ca2Mg6Zn3.
Dear Sir,
Thank you so much, as you said the crystal of Mg7Zn3 is same as Mg51Zn20.
For the case of Ca2Mg6Zn3 I found the following article.
DOI: 10.1017/S1431927602010413
But the simulation is so lasting long. But the simulation takes so long.
Best regards
Hi Ahmad:
I suggest you to use ATOMS program.http://cars9.uchicago.edu/cgi-bin/atoms/atoms.cgi
. You can get the atomic positions in the cartesian coordinate by this program if you have the crystal parameters or the cif file.
You need to know the space group, unic cell parameters, and fractionla cooridnates of each elements in the crystal.
May be you already found the solution. but I wanted to give my suggestion even if it is very late.
@ Yimin Mijiti, thank you for the site, it was indeed helpful. The other problem is getting the occupancy and the B factor. Do you have any more idea how I can get it for a given compound?
You can catch up the CIF file, it has all the atom positions.
For this purpose, you should do the following work:
1- read book "International Table for Crystallography"
2- The best way for a new material is to do the single crystal diffraction by yourself.
3- If the compound is known, you can check the literature and usually (if it has been refined from single crystal data) the paper that contains it gives the atomic positions, lattice parameters, space group etc.
good,
The best place to find out the atomic position is the Crystallography Open Database.
i am facing similar problem . making a model for licoo2. online the model is avaible in cif format but i am not sure how they have derived the atomic coordinates using the symmetry. i know the positions of the 3 basis atoms but how can i make the unit cell using the symmetry of r3m space grou
Ahmad Bahmani can you let me know how your problem was solved. jazakallah
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