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dm.json
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dm.json
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{"mcell": {"initialization": {"warnings": {"degenerate_polygons": "WARNING", "missing_surface_orientation": "ERROR", "high_probability_threshold": "1", "high_reaction_probability": "IGNORED", "useless_volume_orientation": "WARNING", "missed_reaction_threshold": "0.001", "lifetime_too_short": "WARNING", "lifetime_threshold": "50", "all_warnings": "INDIVIDUAL", "negative_diffusion_constant": "WARNING", "missed_reactions": "WARNING", "negative_reaction_rate": "WARNING"}, "time_step": "1e-6", "space_step": "", "interaction_radius": "", "iterations": "5", "data_model_version": "DM_2014_10_24_1638", "surface_grid_density": "10000", "notifications": {"file_output_report": false, "varying_probability_report": true, "diffusion_constant_report": "BRIEF", "iteration_report": true, "box_triangulation_report": false, "probability_report": "ON", "probability_report_threshold": "0", "partition_location_report": false, "all_notifications": "INDIVIDUAL", "release_event_report": true, "final_summary": true, "molecule_collision_report": false, "progress_report": true}, "time_step_max": "", "vacancy_search_distance": "", "radial_directions": "", "partitions": {"recursion_flag": false, "x_start": "-1", "y_end": "1", "y_start": "-1", "x_end": "1", "data_model_version": "DM_2014_10_24_1638", "z_step": "0.02", "z_start": "-1", "z_end": "1", "x_step": "0.02", "y_step": "0.02", "include": false}, "radial_subdivisions": "", "center_molecules_on_grid": false, "microscopic_reversibility": "OFF", "accurate_3d_reactions": true}, "release_sites": {"release_site_list": [{"name": "rx", "pattern": "", "quantity": "1", "data_model_version": "DM_2015_11_11_1717", "points_list": [], "shape": "CUBIC", "stddev": "0", "quantity_type": "NUMBER_TO_RELEASE", "release_probability": "1", "location_z": "0", "molecule": "x", "object_expr": "", "location_x": ".5", "site_diameter": "0", "location_y": "0", "orient": "'"}, {"name": "ry", "pattern": "", "quantity": "2", "data_model_version": "DM_2015_11_11_1717", 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"define_molecules": {"molecule_list": [{"custom_space_step": "", "export_viz": false, "display": {"glyph": "Letter", "letter": "X", "emit": 0.0, "scale": 5.0, "color": [0.8000000715255737, 0.2649356424808502, 0.0]}, "mol_type": "3D", "data_model_version": "DM_2016_01_13_1930", "target_only": false, "custom_time_step": "", "mol_name": "x", "diffusion_constant": "1e-6", "mol_bngl_label": "", "maximum_step_length": ""}, {"custom_space_step": "", "export_viz": false, "display": {"glyph": "Letter", "letter": "Y", "emit": 0.0, "scale": 5.0, "color": [0.0, 0.8000000715255737, 0.007358146831393242]}, "mol_type": "3D", "data_model_version": "DM_2016_01_13_1930", "target_only": false, "custom_time_step": "", "mol_name": "y", "diffusion_constant": "2e-6", "mol_bngl_label": "", "maximum_step_length": ""}, {"custom_space_step": "", "export_viz": false, "display": {"glyph": "Letter", "letter": "Z", "emit": 0.0, "scale": 5.0, "color": [0.8000000715255737, 0.0, 0.4008074700832367]}, "mol_type": "3D", "data_model_version": "DM_2016_01_13_1930", "target_only": false, "custom_time_step": "", "mol_name": "z", "diffusion_constant": "3e-6", "mol_bngl_label": "", "maximum_step_length": ""}, {"custom_space_step": "", "export_viz": false, "display": {"glyph": "Letter", "letter": "P", "emit": 0.0, "scale": 3.0, "color": [1.0, 1.0, 1.0]}, "mol_type": "3D", "data_model_version": "DM_2016_01_13_1930", "target_only": false, "custom_time_step": "", "mol_name": "Sim", "diffusion_constant": "1e-6", "mol_bngl_label": "", "maximum_step_length": ""}], "data_model_version": "DM_2014_10_24_1638"}, "reaction_data_output": {"reaction_output_list": [], "plot_legend": "0", "rxn_step": "", "combine_seeds": true, "plot_layout": " plot ", "mol_colors": false, "data_model_version": "DM_2014_10_24_1638"}}}