Simulation Configuration

Runtime config

There are several runtime parameters can be changed before execution for specific usage.

Name	Type	Description
BIOMC_LIB_UDF	String	Path to .so model
BIOMC_TEAM_SIZE	integer	deprecated: controll team size of Kokkos league policy
BIOMC_LEAGUE_SIZE		deprecated: controll league size of Kokkos league policy
BIOMC_MC_REMOVE_RATIO_THRESHOLD	float	Maximum percentage of inactive particle
BIOMC_MC_MINIMUM_REMOVAL	integer	minimum number of inactive particle
BIOMC_MC_BUFFER_RATIO	float	ratio containersize/buffersize
BIOMC_MC_ALLOC_FACTOR	float	Container preallocation factor
BIOMC_MC_SHRINK_RATIO	float	max ratio new_size / old_size before reduce preallocated memory

CI

Scalar initialisation

There are different ways to initialize the initial concentration, but one simple method is to generate a .h5 file using the tools/init.py script.

A template fonction to add to this script is

def init_my_case():
    n_compartment=500
    n_species=4
    liquid_phase = np.zeros((n_compartment,n_species))
    gas_phase = np.zeros((n_compartment,n_species)) # Not mandatory if only liquid 
 
    gas_phase[:,0]=0 # g/l
    gas_phase[:,1]=0.21 #g/l
 
    liquid_phase[:,0]=5 # g/l
    liquid_phase[:,1]=0 # g/l
 
    make_initial_concentration("./cma_data/my-case-init.h5",liquid_phase,gas_phase)

Config

Running the simulation directly through the command line with arguments passed to the executable is not recommended due to the complexity involved. Instead, the preferred approach is to use the runner Python script and provide a specific case descriptor file. Below is a template for the case descriptor file, which should be in XML format:

<?xml version="1.0" encoding="UTF-8"?>
<!-- One file can contain multiple cases within this tag -->
<cases>
    <!-- 'name' refers to the case name to be given to the runner script -->
    <control name="my-case">
        <!-- Path to the root of the CMA case (don’t forget the leading '/') -->
        <!-- The 'recursive' parameter must be used for multi-flow map cases -->
        <cma_case_path recursive="true">/path/to/cma_case/</cma_case_path>
        
        <!-- Simulation time in seconds -->
        <final_time>10</final_time>
        
        <!-- Total number of particles to simulate (will be automatically balanced if using MPI) -->
        <number_particle>50000</number_particle>
        
        <!-- Simulation time step in seconds-->
        <!-- If 'n_compartment' > 1, leave the value as 0 to automatically determine the step size  -->
        <delta_time>0</delta_time>
        
        <!-- Name of the results folder -->
        <results_file_name>debug</results_file_name>
        
        <!-- Number of results to be saved in the HDF5 file -->
        <number_exported_result>100</number_exported_result>
        
        <!-- Model name; if not specified, the default model will be used -->
        <model_name>_</model_name>
        
        <!-- Scalar initializer file -->
        <initialiser_path>./cma_data/my-case-init.h5</initialiser_path>
    </control>
</cases>