Input Parameters¶

Checkpoint Parameters¶

The checkpoint parameters control how the simulation saves its state for both restart purposes and visualisation. These parameters are specified in the checkpoint_params namelist block in the input file.

&checkpoint_params
  checkpoint_freq = 1000
  snapshot_freq = 500
  keep_checkpoint = .false.
  checkpoint_prefix = "checkpoint"
  snapshot_prefix = "snapshot"
  snapshot_sp = .false.
  output_stride = 2, 2, 2
  output_fields = 'pressure', 'vorticity', 'qcriterion', 'species'
  restart_from_checkpoint = .false.
  restart_file = ""
/End

checkpoint_freq: Frequency (in timesteps) at which to save checkpoint files for simulation restart. Set to 0 to disable checkpointing.: Default: 0
snapshot_freq: Frequency (in timesteps) at which to save visualisation snapshot files. Set to 0 to disable snapshots.: Default: 0
keep_checkpoint: Controls whether to keep all checkpoint files (true) or only the most recent one (false).: Default: false
checkpoint_prefix: String prefix for checkpoint filenames. Each checkpoint will be named as <checkpoint_prefix>_XXXXXX.bp where XXXXXX is the timestep number.: Default: "checkpoint"
snapshot_prefix: String prefix for visualisation snapshot filenames. Each snapshot will be named as <snapshot_prefix>_XXXXXX.bp.: Default: "snapshot"

snapshot_sp: Boolean flag to save visualisation snapshots in single precision (float) instead of double precision (double). This reduces file size but may lose some precision. Default: false (double precision)

output_stride: Three-element array specifying the spatial stride (subsampling) in X, Y, and Z directions for visualisation snapshots. Using values greater than 1 reduces file size and increases I/O performance, but decreases visualisation resolution.: Default: [1, 1, 1]

output_fields: List of additional fields to include in visualisation snapshots. Velocity components (u, v, w) are always written. Supported field names:

'pressure' — Pressure field, interpolated from its native cell-centred grid to the vertex grid for ParaView compatibility. Not included in checkpoint files since it is recomputed from velocity.

'vorticity' — Vorticity magnitude \(|\omega| = \sqrt{\omega_x^2 + \omega_y^2 + \omega_z^2}\), computed from the full velocity gradient tensor.

'qcriterion' — Q-criterion \(Q = -\frac{1}{2} \sum_{ij} \frac{\partial u_i}{\partial x_j} \frac{\partial u_j}{\partial x_i}\), identifying vortical structures (positive Q indicates rotation-dominated regions).

'ibm' — Immersed boundary method mask field (ep1). Values are 1 in the fluid domain and 0 in the solid domain. Requires ibm_on = .true. in the input file.

'species' — All transported species fields. In the input file, set n_species = N with N > 0 and provide pr_species = ... in solver_params, then add 'species' to output_fields. Snapshots then include phi_1 through phi_N.

When both 'vorticity' and 'qcriterion' are requested, the velocity gradient tensor is computed only once. Default: (empty — only velocity is written)

restart_from_checkpoint: Boolean flag to restart the simulation from a checkpoint file.: Default: false
restart_file: Path to the checkpoint file for restarting the simulation. Required when restart_from_checkpoint is true.: Default: "" (empty string)

Technical Details¶

The checkpoint system uses ADIOS2 BP format for I/O which provides:

Efficient parallel I/O even on large HPC systems
Compression options to reduce storage requirements
Compatibility with visualisation tools (ParaView can directly read BP files)
Restart files contain full-resolution field data
Visualisation files can use strided (lower resolution) output for performance

To view snapshot files in ParaView, open the generated .bp files using the ADIOS2 reader plugin.

Statistics Parameters¶

The statistics parameters control the accumulation and output of time-averaged flow statistics. These parameters are specified in the stats_params namelist block in the input file.

&stats_params
  initstat = 0
  istatfreq = 1
  istatout = 0
  stats_prefix = "statistics"
/

initstat: Timestep at which to begin accumulating statistics. Statistics are not collected before this iteration. Set to 0 to disable statistics entirely.: Default: 0
istatfreq: Frequency (in timesteps) at which statistics are accumulated. A value of 1 means statistics are accumulated every timestep; a value of N means every N-th timestep.: Default: 1
istatout: Frequency (in timesteps) at which accumulated statistics are written to file. Set to 0 to disable output.: Default: 0
stats_prefix: String prefix for statistics output filenames.: Default: "statistics"

Output Fields¶

Statistics are written to separate ADIOS2 .bp files (e.g. statistics_001000.bp), independent of the snapshot system. The output contains:

Velocity statistics (always present):

umean, vmean, wmean — time-averaged velocity components
uprime, vprime, wprime — RMS velocity fluctuations: \(u' = \sqrt{\max(0,\, \overline{u^2} - \bar{u}^2)}\)
uvmean, uwmean, vwmean — Reynolds stresses: \(\langle u'v' \rangle = \overline{uv} - \bar{u}\bar{v}\)
sample_count — number of samples accumulated

Pressure statistics (when 'pressure' is in output_fields in checkpoint_params):

pmean — time-averaged pressure field

Scalar statistics (when n_species > 0 in solver_params):

phimean_N — time-averaged scalar field for species N
phiprime_N — RMS scalar fluctuation for species N

Accumulation uses Welford’s numerically stable online algorithm. Statistics always restart from scratch — they are not saved in checkpoint files.