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fix bug in recreate_sim_state #437

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fix bug in recreate_sim_state #437

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68 changes: 39 additions & 29 deletions modules/PhysiCell_MultiCellDS.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1645,11 +1645,15 @@ int recreate_sim_state(std::string filename, Microenvironment& M,

// cell cycle
// e.g., phenotype.cycle.model().find_phase_index( PhysiCell_constants::quiescent )
int phase_index = pCell->phenotype.cycle.model().find_phase_index(current_phase_code);
if (debug_print)
int phase_index = -1;
if (create_cells)
{
std::cout << "------ cycle:\n";
std::cout << " --- phase_index =" << phase_index << std::endl;
phase_index = pCell->phenotype.cycle.model().find_phase_index(current_phase_code);
if (debug_print)
{
std::cout << "------ cycle:\n";
std::cout << " --- phase_index =" << phase_index << std::endl;
}
}

fread(&dTemp, sizeof(double), 1, fp);
Expand Down Expand Up @@ -2140,21 +2144,24 @@ int recreate_sim_state(std::string filename, Microenvironment& M,
if (debug_print)
{ std::cout << "custom var: " << pair.first << " = " << dTemp << std::endl; }

// find the variable
// int n = pCD->custom_data.find_variable_index( name );
int idx_var = pCell->custom_data.find_variable_index( pair.first );
// if it exists, overwrite
if( idx_var > -1 )
{
// pCell->custom_data.variables[idx_var].value = pair.second;
pCell->custom_data.variables[idx_var].value = dTemp;
if (debug_print)
{ std::cout << " ---- pCell->custom_data[" << pair.first << "] = " <<pCell->custom_data[pair.first] << std::endl; }
}
else
if (create_cells)
{
std::cout << __FUNCTION__ << " Error: got an invalid custom data var name: " << pair.first << " . Exiting! " << std::endl;
std::exit(-1);
// find the variable
// int n = pCD->custom_data.find_variable_index( name );
int idx_var = pCell->custom_data.find_variable_index( pair.first );
// if it exists, overwrite
if( idx_var > -1 )
{
// pCell->custom_data.variables[idx_var].value = pair.second;
pCell->custom_data.variables[idx_var].value = dTemp;
if (debug_print)
{ std::cout << " ---- pCell->custom_data[" << pair.first << "] = " <<pCell->custom_data[pair.first] << std::endl; }
}
else
{
std::cout << __FUNCTION__ << " Error: got an invalid custom data var name: " << pair.first << " . Exiting! " << std::endl;
std::exit(-1);
}
}
}

Expand All @@ -2167,18 +2174,21 @@ int recreate_sim_state(std::string filename, Microenvironment& M,
if (debug_print)
{ std::cout << "custom vector var: " << pair.first << "[" << jj << "] = " << dTemp << std::endl; }

// find the variable
// int n = pCD->custom_data.find_variable_index( name );
int idx_var = pCell->custom_data.find_vector_variable_index( pair.first );
// if it exists, overwrite
if( idx_var > -1 )
{
pCell->custom_data.vector_variables[idx_var].value[jj] = pair.second;
}
else
if (create_cells)
{
std::cout << __FUNCTION__ << " Error: got an invalid custom data vector name: " << pair.first << " . Exiting! " << std::endl;
std::exit(-1);
// find the variable
// int n = pCD->custom_data.find_variable_index( name );
int idx_var = pCell->custom_data.find_vector_variable_index( pair.first );
// if it exists, overwrite
if( idx_var > -1 )
{
pCell->custom_data.vector_variables[idx_var].value[jj] = pair.second;
}
else
{
std::cout << __FUNCTION__ << " Error: got an invalid custom data vector name: " << pair.first << " . Exiting! " << std::endl;
std::exit(-1);
}
Comment on lines +2181 to +2191

@drbergman drbergman Sep 22, 2026

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could lift the checks for this out of the for block over the vector entries.

@rheiland rheiland Sep 22, 2026

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All I know is that my test for wanting to see debug prints, but not create cells, resulted in a segfault and these "fixes" avoided that. I'm OK with your logic so long as there are tests included to confirm it. I only discovered the segfault when I was wrapping the "resume" functionality for the Python API, which now works.

}
}
}
Expand Down
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