Crystallographic input for a structure having screw axis and co-ordinates shifted by certain amount
Dear Members, I would like to know, *Q1)* If there is a screw axis in the system, like the anatase phase of TiO2, whose space group is I41/amd, how should I enter that in the atoms for feff calculation. Kindly tell me which is the correct way. When I entered 141(the space group number) and I41/amd, both generated separate set of atomic positions. The older version of artemis, now the new one(latest version), both generates different set of atomic position with the same crystallographic input, i.e if I enter 141(or I41/amd) in place of space group and run atoms, it generates two different set of co-ordinates in Artemis 0.8.012 and in Demeter 0.9.18. Ideally this should be same. *Q2)* And when co-ordinates is shifted by certain amount, do we have to enter that in the shift vector as well as while defining the (x y z) of a particular site. Or I should just enter the shift vector and define the co-ordinates at its usual position ( I feel this one is correct). For example in anatase crystal structure the co-ordinates are shifted by (0,0.25,-0.125). So, the inputs can be For shift vector 0,0.25,-0.125 and in place of sites Ti(core) x=0, y=0, z= 0 and O (scatterer) x= 0, y=0, z=0.20806 (Or) shift vector 0,0,0 and in place of sites Ti(core) x=0, y=0.25, z= -0.125 and O (scatterer) x= 0, y=0.25, z=0.08160 Ideally both should give the same result. But it gives different set of atomic positions. Even the same input in different version of artemis is yielding different results(in Artemis 0.8.012 and in Demeter 0.9.18) . I am confused about how atoms work in artemis. I request you to elucidate the correct method. Warm wishes Madhusmita India
Madhusmita, Regarding the first question, I am not clear what the problem is. I grabbed the crystal data for anatase from Matt's website: http://cars9.uchicago.edu/atomsdb/TiO2-ana.inp and imported it into Artemis. I certainly don't know what the interatomic distances for anatase should be off the top of my head, but what Atoms produced from that input data certainly seems reasonable. If you think there is a problem, you are going to need to explain it in a way that I can reproduce easily on my own computer. Regarding the second question, the vector specified in the box labeled "Shift vector" will be added to each site *before* any calculation is made. B On 06/12/2014 01:45 AM, madhusmita sahoo wrote:
Dear Members,
I would like to know,
*Q1)* If there is a screw axis in the system, like the anatase phase of TiO2, whose space group is I41/amd, how should I enter that in the atoms for feff calculation. Kindly tell me which is the correct way.
When I entered 141(the space group number) and I41/amd, both generated separate set of atomic positions.
The older version of artemis, now the new one(latest version), both generates different set of atomic position with the same crystallographic input, i.e if I enter 141(or I41/amd) in place of space group and run atoms, it generates two different set of co-ordinates in Artemis 0.8.012 and in Demeter 0.9.18. Ideally this should be same.
*Q2)* And when co-ordinates is shifted by certain amount, do we have to enter that in the shift vector as well as while defining the (x y z) of a particular site. Or I should just enter the shift vector and define the co-ordinates at its usual position ( I feel this one is correct).
For example in anatase crystal structure the co-ordinates are shifted by (0,0.25,-0.125).
So, the inputs can be
For shift vector 0,0.25,-0.125 and in place of sites Ti(core) x=0, y=0, z= 0 and O (scatterer) x= 0, y=0, z=0.20806
(Or) shift vector 0,0,0 and in place of sites Ti(core) x=0, y=0.25, z= -0.125 and O (scatterer) x= 0, y=0.25, z=0.08160 Ideally
both should give the same result. But it gives different set of atomic positions.
Even the same input in different version of artemis is yielding different results(in Artemis 0.8.012 and in Demeter 0.9.18) .
I am confused about how atoms work in artemis. I request you to elucidate the correct method.
Warm wishes
Madhusmita
India
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