Hi all! I'm working with reading from a .gsd trajectory in order to do CG mapping. I followed along with the example notebooks, but I get an issue when I try to apply the mapping and output the mapped particle positions. Attached is a MWE with two requisite .gsd files and a jupyter notebook. In the final cell of the notebook, if youcan manually feed in the correct [16., 16., 16.] for box_size, but in the examples I was following, it is fed in as htf.box_size(box). However, if we print that out we can see that the third box dimension is coming out as zero, which causes nans to show up for the mapped particle positions.
Hi @RainierBarrett thanks for pointing this out! I believe this line needs to be corrected to match the box doc. @hgandhi2411 or @geemi725 can one of you set-up a PR for this?
Hi all! I'm working with reading from a .gsd trajectory in order to do CG mapping. I followed along with the example notebooks, but I get an issue when I try to apply the mapping and output the mapped particle positions. Attached is a MWE with two requisite .gsd files and a jupyter notebook. In the final cell of the notebook, if youcan manually feed in the correct
[16., 16., 16.]
forbox_size
, but in the examples I was following, it is fed in ashtf.box_size(box)
. However, if we print that out we can see that the third box dimension is coming out as zero, which causesnan
s to show up for the mapped particle positions.box-size-mwe.zip