Structure Factor for Microgels

Hello matsci community,

I try to produce a structure factor with ovito that looks similar to this:[email protected]/a-Experimental-scattering-data-for-PNIPA-microgels-obtained-by-SLS-and-SAXS-collapsed.ppm

The system that I use was created with the same insilico synthesis protocoll so it should have a similar structur factor (as on the right side of the linked picture). Is consists of about 40 thousand beads, connected with fixed springs to form a network structure. The equilibrium distance between neighbouring beads is about 1.0 and the diameter of the micogel sphere is about

This is the result for a fft grid space of about 0.5 (method from Spatial correlation function — OVITO User Manual 3.7.6 documentation). I can not go much lower or ovito crashes due some memory allocation error after using about 96 percent of my memory. I also tried to vary the cutoff radius (3 to 35) and the number of neighbor bins (50 to 50000) with almost the same result. Direct summation did not seem to make a difference as well.

Is it possible to get the task done with ovito? is there another postprocessing tool to calculate the structure factor of such a system. As far as I read the fourier transformation for bigger systems seems to work with gpu acceleration. Does anyone have some insights on this topic?

I think this might be related to this discussion about the existing limit on the number of FFT grid cells.


What is the size of simulation box around the beads? Is the box much larger than the structure or is it tightly fit?

I can take a look at this problem to see which resolution can be achieved with OVITO and whether there is room for further improvement. Would you mind sharing your simulation data with us?