In my opinion, the index selection part in the "KDNet_Batch" in "kdnet.py" may be wrong. The offset addition part of variable "sel" makes that the order in "sel" can not match the real points' order in "x".
The mistake can be fixed by change
"sel = Variable(sel + (torch.arange(0,dim) * 3).repeat(batchsize,1).long()).view(-1,1)"
into
"sel = Variable(sel * dim + torch.arange(0,dim).repeat(batchsize,1).long()).view(-1,1)"