The parseOneExpression_fromString
call in your example fails because you can't really expect to be able to find an atom name in the module
object (which represents only your model and knows nothing about any solutions of that model). Once you obtain a solution, you can add all atom and skolem names to the module object, and then you will be able to parse expressions containing atoms names.
module = CompUtil.parseEverything_fromFile(...);
solution = A4SolutionReader.read(module.getAllReachableSigs(), ...);
for(ExprVar a:solution.getAllAtoms()) { module.addGlobal(a.label, a); }
for(ExprVar a:solution.getAllSkolems()) { module.addGlobal(a.label, a); }