Atletico Madrid have missed many opportunities at the same time, being eliminated from the CL competition and losing many points in La Liga matches and so I think the mentality and confidence of Atletico Madrid players has decreased drastically because of that and makes it difficult for them to compete again.
Now Barcelona and Real Madrid will compete for the La Liga title, not to put Atletico Madrid aside but realistically at this time, at the end of the season Atletico Madrid's performance has actually slumped and there is no guarantee that they will recover after a series of bad results like they have now.
Personally, I think Atletico Madrid kicked themselves out of the title race, they were in the title race during their game Vs Barcelona, they needed few minutes to hold on after going 2 goals up but they gave it away and surrendered everything after that loss. I feel for them though but as it stands even Barcelona will not give up that top spot to Real Madrid that's right behind them not to talk of Atletico Madrid.