Loss and gain of region in ATAC seq I would like to calculate what is the number of region which is lost or gained between two condition,such as Stem cell vs Leukemic stemcell, atac seq data. 

How do I get the information after peak calling such as what tools should i be using ?

As shown in the paper figure 1c I would like to do the same. How do i calculate the gain and loss of peak relative to a condition 
paper
What you are looking for is "Differential accessibility analysis", you are using ATAC-seq, hence "accessibility". You will need to "call" and then "normalize" "count"(*) peaks, after these, you can use DESeq2 or edgeR for the "differential" part.

Here is a nice Nextflow workflow that addresses all of the steps of a differential accessibility analysis of ATAC-Seq data.

* featureCounts can be used the identify peaks, see this and this.