Note: A solution has been found, see below.
I am trying to create an SVG graph of nodes with D3, with "expandable nodes." That is, when one clicks on a node, its siblings are added to the graph (or more precisely: its siblings in the graph data are added to the graph visualization.)
The visualization uses a d3 force simulation (using D3 v5). When a node (an SVG circle) is clicked, the simulation is stopped (in case it was still running, to make sure there is no new node with no coordinates added in the middle of a run,) the corresponding nodes and links are added to the corresponding arrays,