CellSim3D/inp.json at master · SoftSimu/CellSim3D · GitHub

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{
    "core": {
        "MaxNoofC180s": 10000,
        "particle_mass": 0.04,
        "repulsion_range": 0.2,
        "attraction_range": 0.3,
        "repulsion_strength": 100.0,
        "attraction_strength": 0.5,
        "Youngs_mod": 1000,
        "stiffFactor1": 1.0,
        "viscotic_damping": 1,
        "internal_damping": 100.0,
        "gamma_visc": 1.0,
        "division_Vol": 2.9,
        //"division_Vol": 2.0,
        "random_z_offset?": 0,
        "z_offset": 0,
        "div_time_steps": 50000,
        "time_interval": 0.0001,
        "Restart": 0,
        "trajWriteInt": 1000,
        "non_div_time_steps": 50000,
        "trajFileName": "inp.xyz",
        "binaryOutput": 1,
        "maxPressure": 65.0,
        "minPressure": 50.0,
        "growth_rate": 0.002,
        "checkSphericity": 1,
        "constrainAngles": 1,
        "doAdaptive_dt": 0,
        "dt_max": 1e-4,
        "dt_tol": 1e-8,
        "phase_count": 2000000000,
        "write_cont_force": 1,
        "forces_file": "inp.csv",
        "correct_com" : 0
    },
    "counting": {
        "countCells": 0,
        "mit-index_file_name": "inp.dat",
        "count_only_internal_cells?": 0,
        "radius_cutoff": 0.6,
        "overwrite_mit_ind_file?": 0,
        "cell_count_int": 1000
    },

    "population": {
        "doPopModel": 0,
        "totalFood": 5000.0,
        "regular_consumption": 2.0,
        "division_consumption": 10.0,
        "death_release_food": 10.0,
        "haylimit": 10,
        "cellLifeTime": 20000
    },

    "walls": { // deprecated, use box params
        "useWalls": 0,
        "perpAxis": "z",
        "dAxis": 1.1,
        "wallLen": 10.0,
        "wallWidth": 10.0,
        "threshDist": 0.01
    },

    "divParams":{
        "useDivPlaneBasis": 0,
        "divPlaneBasisX": 0,
        "divPlaneBasisY": 0,
        "divPlaneBasisZ": 1
    },

    "stiffnessParams":{
        "useDifferentStiffnesses": 0,
        "softStiffFactor": 0.8,
        "numberOfSofterCells": 0,
        "fractionOfSofterCells": 0.3,
        "duringGrowth": 1,
        "daughtSameStiffness": 1,
        "closenessToCenter": 0,
        "startAtPop": 2000,
        "chooseRandomCellIndices": 0,
        "recalc_r0": 0
    },

    "boxParams":{
        "useRigidSimulationBox": 1,
        "usePBCs": 0, // unavailable
        "pbcAx": "x", // unavailable
        "boxLength": 6.0, // deprecated
        "box_len_x": 500.0,
        "box_len_y": 500.0,
        "box_len_z": 2.0,
        "flatbox": 1,
        "dom_len": 1.5,
        "rand_pos": 0
    },

    "rand_params":{
        "add_rands": 0,
        "rand_seed": -1, // use time if < 0
        "rand_dist": 0, /*
                          0 - uniform (default)
                          Others to be impimented
                        */
        "rand_scale_factor": 0.001
    }
}