Usage & Workflow

Running rbsolve consists of an initialization phase and the main time-stepping loop. This document walks through setting up a run, configuring NetCDF4 output, and managing long simulations via restarts.

1. Generating Initial Conditions

Before the code can step forward in time, it requires an initial state. This corresponds to step 0.

First, ensure param.h, config.h, and param_namelist correctly match your desired grid and physics. Then run:

./inicond

  • This binary reads the current configuration.

  • It sets the initial velocity field (typically to a rest state or a small seed).

  • It perturbs the temperature field slightly to break symmetry and kickstart convection.

  • It outputs a single baseline file. In NetCDF mode, this creates rb_0000000.nc, which contains only step 0.

2. Running the Simulation

Once step 0 exists, you can execute the main simulation binary:

./rb

rb automatically detects the current timestamp from rb_0000000.nc and integrates forward up to the absolute timestep defined by ttot in param_namelist.

NetCDF Output Staggering

If NETCDF_OUTPUT is enabled (highly recommended), the code performs automatic file rotation to prevent monolithic data structures.

Assuming nsnc = 1000 and nsave = 250: * rb_0000000.nc: Generated by inicond. Contains step 0. * rb_0000000.nc: Generated continuously by rb. Collects steps 250, 500, 750. * rb_0001000.nc: Seamlessly opened when the code crosses step 1000. Collects steps 1000, 1250, 1500, 1750. * rb_0002000.nc: Opened when crossing step 2000. And so on.

3. Restarts

To continue a simulation that has reached its ttot limit, or to recover a crashed run:

  1. Open param_namelist.

  2. Increase the absolute target ttot to your new desired final step.

  3. Simply execute ./rb again.

The code will automatically: * Identify the highest fully-written chunk. * Perform a “read-all” command, extracting the exact physical state (u, v, w, t) and converting it back into the pseudo-spectral arrays. * Continue time-stepping exactly as if the run had never stopped.

Data Analysis

Data saved by the NetCDF routine uses physical space (x, z, y, time). Because it transforms and standardizes the coordinate formats automatically, users can immediately view the results using community tools like ncview or Python’s xarray.

import xarray as xr
import matplotlib.pyplot as plt

ds = xr.open_dataset('rb_0001000.nc')
ds.t.isel(time=-1, y=64).plot()
plt.title("Mid-plane Temperature")
plt.show()