Add interface file

deleteme.txt

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+rate_secretion_immunostimulatory_factor = 10
+saturation_density_immunostimulatory_factor = 1
+oncoprotein_mean = 1
+oncoprotein_standard_deviation = 0.25
+oxygen_saturation_for_proliferation = 38
+oxygen_limit_for_proliferation = 10
+oxygen_limit_for_necrosis = 5
+oxygen_limit_for_necrosis_maximum = 2.5
+time_lysis = 86400
+kDivisionRate = 0.000452833
+maximum_necrosis_rate = 0.00277778
+default_oxygen_consumption_tumor_cell = 10
+default_volume_new_tumor_cell = 2494
+default_volume_nucleus_tumor_cell = 540
+default_fraction_fluid_tumor_cell = 0.75
+average_time_transformation_random_rate = 38.6
+standard_deviation_transformation_random_rate = 3.7
+adhesion_time = 60
+oncoprotein_limit = 0.5
+oncoprotein_saturation = 2
+oncoprotein_difference = 1.5
+kVolumeRelaxarionRateAliveCytoplasm = 0.00216667
+kVolumeRelaxarionRateAliveNucleus = 0.00366667
+kVolumeRelaxarionRateAliveFluid = 0.0216667
+kVolumeRelaxarionRateCytoplasmNecroticSwelling = 5.33333e-05
+kVolumeRelaxarionRateNucleusNecroticSwelling = 0.000216667
+kVolumeRelaxarionRateFluidNecroticSwelling = 0.000833333
+kVolumeRelaxarionRateCytoplasmNecroticLysed = 5.33333e-05
+kVolumeRelaxarionRateNucleusNecroticLysed = 0.000216667
+kVolumeRelaxarionRateFluidNecroticLysed = 0.000833333
+threshold_cancer_cell_type1 = 1.5
+threshold_cancer_cell_type2 = 1
+threshold_cancer_cell_type3 = 0.5
+threshold_cancer_cell_type4 = 0
+seed = 1
+output_performance_statistics = 1
+dt_substances = 0.01
+dt_mechanics = 0.1
+dt_cycle = 6
+dt_step = 0.1
+steps_per_cell_cycle = 60
+output_csv_interval = 7200
+total_minutes_to_simulate = 43200
+kEpsilon = 1e-10
+kEpsilonDistance = 1e-05
+bounded_space_length = 1000
+initial_tumor_radius = 150
+kTwicePi = 6.28319
+kVolumeRelaxarionRateCytoplasmApoptotic = 0.0166667
+kVolumeRelaxarionRateNucleusApoptotic = 0.00583333
+kVolumeRelaxarionRateFluidApoptotic = 0
+time_apoptosis = 516
+reduction_consumption_dead_cells = 0.1
+kHalf = 2
+resolution_grid_substances = 50
+voxel_volume = 8000
+diffusion_coefficient_oxygen = 100000
+decay_constant_oxygen = 0.1
+diffusion_coefficient_immunostimulatory_factor = 1000
+decay_constant_immunostimulatory_factor = 0.016
+oxygen_reference_level = 38
+initial_oxygen_level = 38
+oxygen_saturation = 30
+cell_repulsion_between_tumor_tumor = 10
+cell_repulsion_between_cart_cart = 50
+cell_repulsion_between_cart_tumor = 50
+cell_repulsion_between_tumor_cart = 10
+max_relative_adhesion_distance = 1.25
+cell_adhesion_between_tumor_tumor = 0.4
+cell_adhesion_between_cart_cart = 0
+cell_adhesion_between_cart_tumor = 0
+cell_adhesion_between_tumor_cart = 0
+dnew = 0.15
+dold = -0.05
+length_box_mechanics = 22
+squared_max_distance_neighbors_force = 446.552
+kTimeTooLarge = 1e+100
+kMinutesInAnHour = 60
+kHoursInADay = 24
+average_maximum_time_untill_apoptosis_cart = 86400
+default_oxygen_consumption_cart = 1
+default_volume_new_cart_cell = 2494
+kDefaultVolumeNucleusCarTCell = 540
+kDefaultFractionFluidCarTCell = 0.75
+kill_rate_cart = 0.06667
+adhesion_rate_cart = 0.013
+max_adhesion_distance_cart = 18
+min_adhesion_distance_cart = 14
+minimum_distance_from_tumor_to_spawn_cart = 50
+persistence_time_cart = 10
+migration_bias_cart = 0.5
+migration_speed_cart = 5
+elastic_constant_cart = 0.01
+treatment: 
+  Day 0: 3957 CAR-T cells
+  Day 8: 3957 CAR-T cells
+migration_one_minus_bias_cart = 0.5
+motility_probability_cart = 0.01
+probability_escape_from_cart = 0.00166667
+steps_in_one_day = 14400
+squared_max_adhesion_distance_cart = 324
+difference_cart_adhesion_distances = 4
+radius_tumor_cell = 8.41271
+radius_cart_cell = 8.41271
+max_squared_distance_cart_moving_towards_tumor_cell = 317.746

params.json

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+{
+  "seed": 1,
+  "output_performance_statistics": true,
+  "total_minutes_to_simulate": 43200,
+  "initial_tumor_radius": 150.0,
+  "bounded_space_length": 1000,
+  "treatment": {
+    "0": 3957,
+    "8": 3957
+  }
+}