For automatic mesh generation, a Default Initialization node is automatically created in the Initial Conditions tree. This is used to describe all regions not otherwise specified in separate region initializations.
There are two strategies for defining initial conditions in cases using automatic-mesh generation:
The Initial Conditions icon bar offers the option: Secondary
Region from Material Point 
, which can be used to define a new region that will be initialized
differently from the default initialization. The new region can be a cylinder, an engine
manifold, or an engine port. Creating a new Initialization will add an item to the Initial
Conditions tree and open an Editor panel to configure the initial conditions of that region.
For a Secondary Region Initialization, the location of the region is defined by the location of
a region material point (See Mesh Controls for Automatic Meshing.) The material point sits inside the
watertight surface, and touches a cell inside the secondary region. Once a secondary region is
created, then the Initialization order must be correctly set.
Initialization order indicates which region should be used in the assigning of properties in newly created cells. The order should generally follow the direction of the flow. For example, when new cells are created by the movement of an intake valve, those cells should be initialized from the intake port, and not from the cylinder, such that the initialization order of the intake port should be lower than the Initialization order of the cylinder. Similarly, the Initialization order of the cylinder should be lower than the Initialization order of the exhaust port.
Initialization order for a four-stroke engine:
Initialization order for two-stroke engine with side ports that are uncovered by the piston motion:
In the unusual case that no stationary location exists that stays inside the watertight surface throughout the entire simulation, the material point location can be set to translate along with a moving boundary surface. Use the Translate Material Point with Boundary Motion option on the Initial Conditions panel to specify the boundary that should have paired movement with the material point.
The Initial Conditions icon bar offers the option: Secondary
Region from Subvolume 
, which can be used to define a new region that will be initialized
differently from the default initialization. This strategy allows selection of one or more
user-defined sub-volumes to initialize to the same state. In an engine simulation, it is
typically used to define a subchamber or prechamber attached to an engine cylinder. Using this
strategy requires the creation of user-defined sub-volumes under the Geometry node. See Sub-Volumes for more information about sub-volumes and how to
specify them.
Note: Strategy 2, Let User-defined Volumes Separate Regions, should not be used to define engine port or manifold regions, as it can lead to incorrect region IDs for cells near the port/cylinder interface. These errors are difficult to notice and cause problems in the calculations.
As with other initialization strategies, any cells not explicitly identified by the region definition will receive the default initial conditions. Region IDs are valid in either Strategy 1 or Strategy 2 for defining initial conditions
When you create a subvolume, the "regions" are defined through the initialization items, that is, the first initialization item listed on the Workflow tree receives region ID = 1, the second initialization item is given region ID = 2, and so on.
You can accept the default RegionType or assign another type to the subvolume:
Cylinder / Primary: Cylinder corresponds to reciprocating engine cases and Primary corresponds to non-engine cases. Note that a cylinder region is expected to be adjacent to at least one slider-crank moving boundary. From the modeling perspective, chemistry (both gas-phase and particle chemistry), spark ignition, and flame propagation are calculated in this type of region; from the output-reporting perspective, parameters reported in most of the CSV files are averaged over a cylinder/primary region. These files include thermo.csv, dynamic.csv, speciesmass.csv, molefraction.csv, massfraction.csv, chemsolver.csv, flame.csv, particle.csv, particle_size_distribution.csv.
Other: In this type of region, chemistry, spark ignition, and flame propagation are not modeled, from the modeling perspective. From the output-reporting perspective, parameters reported in the CSV files (listed above) do not consider these regions.
Subchamber: A subchamber region is a region constantly connected to a cylinder/primary region and it is typically created based on a subvolume. From the modeling point of view, chemistry, spark ignition, and flame propagation are allowed to happen in this type of region. From the output-reporting perspective, a subchamber region is considered as part of the cylinder/primary region to which it is connected when the spatially averaged parameters are calculated for the aforementioned CSV files. For example, when a subvolume connected to a cylinder is defined as a subchamber, the volume of this subchamber will be included in the in-cylinder volume reported in thermo.csv for this cylinder. This subchamber region type is useful when you want to give different initial conditions to a subchamber and the cylinder connected to it. To monitor spatially averaged parameters in a subchamber, consider using a subvolume-based monitor probe.