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bdm.json
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{
"bdm::OptimizationParam": {
"_typename": "bdm::OptimizationParam",
"algorithm": "",
"max_iterations": 100,
"params": [],
"repetition": 1
},
"bdm::Param": {
"_typename": "bdm::Param",
"backup_file": "",
"backup_interval": 1800,
"bound_space": 1,
"cache_neighbors": false,
"calculate_gradients": false,
"compute_target": "cpu",
"debug_numa": false,
"detect_static_agents": false,
"diffusion_boundary_condition": "closed",
"diffusion_method": "euler",
"environment": "uniform_grid",
"execution_order": 0,
"export_visualization": true,
"insitu_visualization": false,
"mapped_data_array_mode": 0,
"max_bound": 1300,
"mem_mgr_aligned_pages_shift": 5,
"mem_mgr_growth_rate": 1.1,
"mem_mgr_max_mem_per_thread_factor": 1,
"min_bound": -1300,
"minimize_memory_while_rebalancing": true,
"nanoflann_depth": 10,
"numerical_ode_solver": 1,
"opencl_debug": false,
"output_dir": "output",
"plot_memory_layout": false,
"preferred_gpu": -1,
"progress_bar_time_unit": "min",
"random_seed": 4357,
"remove_output_dir_contents": false,
"restore_file": "",
"root_visualization": false,
"scheduling_batch_size": 1000,
"show_simulation_step": 0,
"simulation_max_displacement": 3,
"simulation_time_step": 30,
"statistics": true,
"thread_safety_mechanism": 1,
"unibn_bucketsize": 16,
"unschedule_default_operations": [],
"use_bdm_mem_mgr": true,
"use_progress_bar": true,
"visualization_compress_pv_files": true,
"visualization_engine": "paraview",
"visualization_export_generate_pvsm": true,
"visualize_agents": {
"TumorCell": [
"cell_state_",
"diameter_",
"radius_"
],
"Vessel": [],
"_typename": "map<string,set<string> >"
},
"visualize_diffusion": [
{
"_typename": "bdm::Param::VisualizeDiffusion",
"concentration": true,
"gradient": false,
"name": "VEGF"
},
{
"_typename": "bdm::Param::VisualizeDiffusion",
"concentration": true,
"gradient": false,
"name": "Nutrients"
},
{
"_typename": "bdm::Param::VisualizeDiffusion",
"concentration": true,
"gradient": false,
"name": "DOX"
},
{
"_typename": "bdm::Param::VisualizeDiffusion",
"concentration": true,
"gradient": false,
"name": "TRA"
}
]
},
"bdm::SimParam": {
"_typename": "bdm::SimParam",
"action_radius_factor": 1.214,
"adhesion_scale_parameter": 0.0489,
"alpha_Q_D_N": 6.8e-06,
"alpha_Q_SG2_N": 0.000821666666666667,
"alpha_Q_SG2_TRA": 30,
"alpha_SG2_D_DOX": 0.001,
"alpha_SG2_SG2_DOX": 0.1,
"apical_growth_gradient_weight": 0.3,
"apical_growth_old_weight": 0.5,
"apical_growth_quotient_threshold": 0.001,
"apical_growth_random_weight": 0.2,
"apical_growth_speed": 0.033,
"base_rate_H_D": 0.00001,
"boundary_condition_dox": 0,
"boundary_condition_nutrients": 0,
"boundary_condition_tra": 0,
"boundary_condition_vegf": 0,
"cell_nuclear_radius": 5.296,
"cell_radius": 9.953,
"decay_rate_dox": 0.0002,
"decay_rate_nutrients": 1e-05,
"decay_rate_tra": 0,
"decay_rate_vegf": 1e-05,
"default_vessel_length": 30,
"diffusion_dox": 0.7083,
"diffusion_nutrients": 0.833333333333333,
"diffusion_resolution_dox": 200,
"diffusion_resolution_nutrients": 200,
"diffusion_resolution_tra": 200,
"diffusion_resolution_vegf": 200,
"diffusion_tra": 0.09,
"diffusion_vegf": 0.175,
"dox_consumption_rate_tcell": -0,
"dox_supply_rate_vessel": 0.005,
"duration_apoptosis": 516,
"duration_cell_cycle": 1080,
"duration_growth_phase": 540,
"filled_volume": 0.64,
"force_calculation_frequency": 6,
"gamma_Q_D_N": 0.000408333333333333,
"hypoxic_threshold": 0.09,
"initial_concentration_dox": 0,
"initial_concentration_nutrients": 0.0,
"initial_concentration_tra": 0,
"initial_concentration_vegf": 0,
"k_Q_D_N": 50,
"keep_dead_cells": true,
"max_speed": 10,
"min_dist_to_bifurcation": 80,
"min_dist_to_tip_cell": 150,
"num_cells": 1000,
"nutrient_consumption_rate_tcell": -1.76,
"nutrient_supply_rate_vessel": 0.003,
"random_vessel_exponent": 1,
"random_vessel_frequency_mean": 3.1415,
"random_vessel_frequency_std": 4,
"random_vessel_max_deviation": 0.2,
"random_vessel_num_modes": 10,
"repulsive_scale_parameter": 10,
"sprouting_rate": 0.001,
"threshold_Q_D_N": 0.000538,
"threshold_Q_SG2_N": 0.0538,
"threshold_SG2_D_DOX": 0.001,
"threshold_SG2_SG2_DOX": 0.001,
"tip_cell_finder_update_frequency": 1,
"total_sim_time": 100000,
"tra_consumption_rate_tcell": -0.036,
"tra_supply_rate_vessel": 0.1,
"vegf_consumption_rate_vessel": -4,
"vegf_grad_threshold_apical_growth": 1e-05,
"vegf_supply_rate_tcell": 100,
"vegf_threshold_sprouting": 0.001,
"verify_continuum_values": false,
"viscosity": 2,
"visualization_interval": 1000,
"zeta_H_D_DOX": 100,
"zeta_H_D_TRA": 0.0,
"zeta_H_D_TRA_DOX": 0,
"zeta_Q_D_DOX": 100,
"zeta_Q_D_TRA": 0,
"zeta_Q_D_TRA_DOX": 0
},
"bdm::neuroscience::Param": {
"_typename": "bdm::neuroscience::Param",
"neurite_default_actual_length": 1,
"neurite_default_adherence": 0.1,
"neurite_default_density": 1,
"neurite_default_diameter": 1,
"neurite_default_spring_constant": 10,
"neurite_default_tension": 0,
"neurite_max_length": 15,
"neurite_min_length": 2,
"neurite_minimial_bifurcation_length": 0
}
}