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Common errors in PhysiCell and their solutions

Common PhysiCell Rules Errors

1. Error adding rule for phagocytose dead cell

Error message:

Warning! Attempted to add behavior phagocytose dead cell which is not in the dictionary.
Either fix your model or add the missing behavior to the simulation.

Background: In PhysiCell v1.14.0, phagocytosis of dead cells became death-model specific. Previously, any dead cell would be phagocytosed at the rate dead_phagocytosis_rate. Now, there are three phagocytosis rates:

New Rate Name	New Rule Name	Description
apoptotic_phagocytosis_rate	phagocytose apoptotic cell	Rate of phagocytosing apoptotic cell
necrotic_phagocytosis_rate	phagocytose necrotic cell	Rate of phagocytosing necrotic cell
other_dead_phagocytosis_rate	phagocytose other dead cell	Rate of phagocytosing dead cells using a user-defined death model

Solution: To produce phagocytosis results guaranteed identical to simulations run in pre-v1.14.0 PhysiCell, replace the one rule targeting phagocytose dead cell with three rules targeting phagocytose apoptotic cell, phatocytose necrotic cell, and phagocytose other dead cell. Alternatively, if not all these death models are used in the model, only include the relevant rules.

2. Error using rules version="2.0".

Error message:

**Error: Version < 3 no longer supported.

Background: In PhysiCell v1.14.0, several changes were made to the rules language prompting a change to the rules version. Phagoctyosis changed (see above) and the meaning of damage_rate also changed from indicating the rate of damage being dealt to another cell (v2.0) to the rate of damage accumulation by the cell (v3.0).

Solution: Update the configuration file so that the version attribute for the ruleset element is set to "3.0":

<cell_rules>
    <rulesets>
        <ruleset protocol="CBHG" version="3.0" format="csv" enabled="true">
            <folder>./config</folder>
            <filename>rules.csv</filename>
        </ruleset>
    </rulesets>
    <settings />
</cell_rules>

Common Miscellaneous PhysiCell Errors

1. random_seed not found in User Parameters.

Error message:

ERROR : Unknown parameter random_seed ! Quitting.

Background: In PhysiCell v1.14.0, the random_seed can be specified within the <options> element of the configuration file. The purpose is to make it more flexible to allow for the user to set the random seed by the system clock to allow for batches of different simulations. While including in user_parameters is still acceptable, this is now discouraged. However, custom.cpp taken from pre-v1.14.0 projects will likely call SeedRandom(parameters.ints("random_seed")); without first checking the existence of random_seed within user_parameters.

Solution: Find the call to SeedRandom(parameters.ints("random_seed")); in the project-specific code. This is almost certainly in create_cell_types( void ) at the top of custom.cpp. Either remove this call or replace with

if (parameters.ints.find_index("random_seed") != -1)
{
    SeedRandom(parameters.ints("random_seed"));
}

It is recommended to remove it and instead include random_seed in <options>:

<options>
...
    <random_seed>0</random_seed>
</options>

OR to use the system clock:

<options>
...
    <random_seed>system_clock</random_seed>
</options>