Manual Introduction to the calculation of structure factors

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Important comment for Core-shell and Core shell cylinder and Unified tube. The volume definition for Core-shell objects is matter of discussion. Heated at times and I suspect that the appropriate answer depends on the case when and how the FF is used. Therefore from version 2. The options are: whole particle, core, and shell. Note: Unified tube is using as volume the volume of shell.

Temperature value

It is how it is defined at this time and it is meant for cases like Carbon nanotubes, when this is appropriate. For aspect rations smaller than 0. Following graphs are examples:. Since Irena version 2. Note, the bin star and end points are calcualted linearly even for log-binned data as half way distance:. Note that the bessel function oscillations are somewho smooth out. With wider bins in R these oscillations may disappear all together.

The code uses the following code to calculate form factor for cylinder. Note, that also this code is doing the same integration as integrated spheroid above see 2. Note, this form factor calculation also includes integration over the width of bin in radii same as integrated spheroid and cylinder. Note, that there is volume definition choice you need to do: Whole particle, core, or shell, as appropriate for given problem.

This volume definition is used for all volume calculations for this particle. Note, that to my surprise these calculations copied from NIST Form factors do not normalize correctly to 1 at low q. The reason is that the weighting is done by volume and contrast. If the diffusion in the matrix is not fast enough, the chemistry around the particle changes, which results in rho changing in the other direction. Therefore one can end with coreshell particle which has higher-then-solvent rho core surounded by lower-then-solvent rho shell or the other way.

With average rho same as matrix. Fro example of this type of precipitation see:.

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Imhoff, S. Journal of Applied Physics, Also, they probably need to be pretty close together. If this is not correct, the code would create negative shell thicknesses and abort. Do not do it, it is not very physical….


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Code uses regular coreshell form factor see above. For each size the shell thickness is calculated so the average rho of the particle matches the rho of the solvent. This form factor was requested by Dale Schaefer and I cannot very well guarantee its functionality…. Note, that parameters are : Param1 - radius of primary particle param2 - fractal dimension of the fractal particles.

Comment: Note, that this is not scaled correctly at all… I have no idea why - apparently this formula is either wrongly coded or plainly does not behave right. List of Model Parameters: R1 : core radius R2 : outer radius of the first shell R3 : outer radius of the second shell : scattering length density of the matrix.


  • Please note:!
  • 1. Introduction.
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  • Make sure your choice is appropriate. Cryst paper : J. The model is locally mono dispersed system, therefore locally one can use spheres Form factor combined with structure factor. Phi is simply fraction of Percus Yevic structure factor. The result is different than multiplying dilute system by Structure factor — that assumes that the distance for Structure factor is the same for all sizes.

    In this case the ratio of distance to size of particle is the same. We assume here that the phi is the same for all sizes. Suffise to say, that using this form factor with another structure factor is meaningless and garbage will be produced. This is form factor based on manuscript: T. Futterer, G. Vliegenthart, and P. The Form factor follows formula 3 of this manuscript.

    This may result in unexpected problems with absolute calibration. The reason for the two implementations is, that in usual implementation the shell thickness is fixed while the particle size has size distribution - but this is possible ONlY if core has distribution of sizes. This may be incorrect, as someone can have monodispersed cores, but distribution of shell thicknesses. Be warned, results will be difficult to present meaningfully!

    You are on your own…. Note the suspicious difference in calibrations. See note above about my suspicion on the problem here…. Janus CoreShell Micelle 1, fake the core shell with same contrast The difference in absolute intensity here is surely related to different assumptions on volume of particle. This is form factor or rectangular Parallelpiped, cuboid shape with side A x B x C and all angle 90 degrees.

    Since version 2. It seems they had to go to original manuscript and recreate the form factor from the German original, Mittelbach and Porod, Acta Phys. Unlike the R factors, the correlation coefficients do not depend on the overall scale factor between the observed and the calculated structure factors. The region of the unit cell that should be covered for a translation search with the above indicators does not normally correspond to the asymmetric unit of the space group.

    Because the molecule to be searched has a determined orientation, it can only reside in one of the asymmetric units in the unit cell. Lacking a knowledge as to which asymmetric unit the molecule is occupying, the entire unit cell would need to be searched. However, most space groups have alternative origins, which means the position of a molecule in the unit cell can only be determined to within certain sets of translations the Cheshire group.

    Structure factor

    Once the first molecule has been located, the origin is determined as well. The search for subsequent molecules will need to cover the entire unit cell. The orientations of the molecules have been determined beforehand with rotation searches e. Therefore, only the positional parameters of the molecules need to be varied. The structure factor equation can be written as a double summation first over the atoms in one asymmetric unit of the unit cell and then over all the asymmetric units,.

    The n th crystallographic symmetry operator is given by. For simplicity, consider the case where there is only one molecule in the asymmetric unit.

    Theory of Structure Factor

    In the translation search, the molecule will be placed at different positions in the unit cell,. Substituting x j in Eq. Therefore, the summation over the atoms in the structure factor calculation, a rather time-consuming process, need to be performed only once, for the molecule at a reference position x j 0.

    Subsequent structure factor calculation after translation of the molecule from the reference position is no longer dependent on the number of atoms present in the unit cell Eq. The reference position is usually chosen with the center of the molecule at 0, 0, 0.

    Teaching aims

    Then the translation vector that is determined from the translation searches will define the center of the molecule in the unit cell. Equation 7 can be generalized to allow for the presence of other molecules that are to remain stationary during the translation search,. This formulation is useful if there are more than one molecules in the asymmetric unit. The position of one of the molecules can be determined first and the model is then input as a stationary molecule for the search of the position of the next molecule.

    Besides the R factor and the correlation coefficient, another commonly-used translation search indicator is the correlation between the observed and the calculated Patterson maps. Rotation functions are based on the overlap of only a subset of the interatomic vectors in the Patterson map, i. The correct orientation and position of a molecular structure in the crystal unit cell should lead to the maximal overlap of both the self and the cross vectors, i.

    The calculated structure factor is a function of the translation vector x 0 Eq.