Muons : The muon is tested for isolation against all the Clusters.
In Athena-Atlfast the job is set to run in the AtlfastDoNotTouch.txt file with electron, then photon, then muon isolation, so muons are never tested for Isolation against isolated-electrons or isolated-photons associated clusters. In Fortran-Atlfast, the order is electron, muon then photon isolation, so the muon is tested for isolation against isolated-photons associated clusters. The Athena-Atlfast job can be configured to run the same as the Fortran-Atlfast by changing the order of the algorithms in the AtlfastDoNotTouch.txt.
4) The Fortran-Atlfast has the value for Barrel-Forewad eta transition hardwired into the JetSmearer as 3.0. It is set to the GlobalEventDataMaker.BarrelForwadrEta value in Athena-Atlfast (3.2 as default).
Extensions
1) By default both Athena-Atlfast and Fortran-Atlfast calculate all the clusters and thus Jets as massless. Athena-Atlfast has an option (ClusterMaker.MasslessJets = false/true) which if set to false means that the Clusterss will be calculated as purely the sum of cells four-momenta, and thus they and the Jets will not be massless. (see here for more information.)
A Note on the Grid Edge Problems
It was found that when comparing Athena-Atlfast and Fortran-Atlfast on an event by event basis subtle differences were seen. This was due to probelms in the ClusterMaking. The Calorimeter grid was made up by 0.1 by 0.1 cells and the clustering algorithm had a cone of 0.400. It looks for any cells lying even slightly within a cone of this radius. It was common that the cone edge would fall on the boundry between cells. As a computer cannot have an infinately accurate number, the cone edge never fell exactly on a cell boundry, but just slightly over to one side. It was found that sometimes the cone edge would be just inside a cell in the Athena-Atlfast and just outside in the Fortran-Atlfast or vice-versa. This problem was solved by making the cone radius 0.401 and then the cone edge should never fall on a cell boundary.