Repeated writing objects to files

With the current master branch, one example does not run because writing to file is attemptied for second time:

$ python -W ignore ../scripts/run_model.py -f atoms.vm
File exists error: vre-language/examples/atoms.vm:36:1 --> water to file 'water.yaml' <--
[Errno 17] File exists: 'water.yaml'

Only in instant and deferred mode.