Implement writing to same H5MD files on multiple steps

[J-Hizzle]

At the moment, one can only save a single microstate in an H5MD file at a time. For further statistical analysis, it would be convenient to have the entire trajectory stored to the same file.

The dump-function in DumpH5MDParallel.hpp:36 will then probably need the time step at which the data is supposed to be stored as input.

[XzzX]

We need to change how the files are opened (currently existing content is deleted) and add the time step as you suggested. I think opening and closing the file every time a new time step is stored is acceptable. Do you want to call it frequently? Opening and closing makes sure the data is written to disc - good in case the program crashes. However, performance is probably worse than keeping the file open all time.

[J-Hizzle]

Do you want to call it frequently?

Yes, I expect I will need to call it around every 1000 steps and at the same time when all the observables are calculated.

Opening and closing makes sure the data is written to disc - good in case the program crashes. However, performance is probably worse than keeping the file open all time.

In Gromacs, there is a checkpoint parameter which sets the number of steps after which everything is saved. I think this would also make sense here: Have the file open all the time for performance and store the data frequently and then, once a checkpoint is reached, close and open again. Would that be possible?