Parallel H5MD Output

H5MD is a format specification on top of the HDF5 file format.

Dump Simulation

Dumping a simulation with espressopp.io.DumpH5MDParallel

dump_h5md_parallel = espressopp.io.DumpH5MDParallel(system, 'dump.h5')
dump_h5md_parallel.dump()

ATTENTION

Only V=const (NVT, NVE) simulation are dumped correctly since we do not save box dimensions at every simulation step.

Configuration

  • dump* controls which properties are saved to file.

  • *Dataset controls the dataset name within the file of the corresponding property.

Restore Simulation

Restoring a simulation with espressopp.io.RestoreH5MDParallel

system.storage.removeAllParticles()
restore_h5md_parallel = espressopp.io.RestoreH5MDParallel(system, 'dump.h5')
restore_h5md_parallel.restore()
system.storage.decompose()
ATTENTION

  • No checks for duplicates are performed nor is the particle storage cleared before inserting new particles. You might want to remove all particles from the simulation before calling restore.

  • Particles are inserted equally among the processes without obeying subdomains. You have to call decompose to ensure particles are located on the correct process after restoration.

Configuration

  • restore* controls which properties are loaded from file.

  • *Dataset controls the dataset name within the file of the corresponding property.