{
  "manifest": {
    "$BASE_DIR": ".",
    "$OUTPUT_DIR": "$BASE_DIR/output_xstim",
    "$COMPONENT_DIR": "$BASE_DIR/../bio_components",
    "$STIM_DIR": "$BASE_DIR/../bio_components/stimulations",
    "$NETWORK_DIR": "$BASE_DIR/network"
  },

  "run": {
    "tstop": 4000.0,
    "dt": 0.1,
    "dL": 20.0,
    "spike_threshold": -15,
    "nsteps_block": 10000
  },

  "target_simulator":"NEURON",

  "conditions": {
    "celsius": 34.0,
    "v_init": -80
  },

  "inputs": {
    "Extracellular_Stim": {
      "input_type": "lfp",
      "node_set": "all",
      "module": "xstim",
      "positions_file": "$STIM_DIR/485058595_0000.csv",
      "mesh_files_dir": "$STIM_DIR",
      "waveform": {
        "shape": "sin",
        "del": 1000.0,
        "amp": 0.100,
        "dur": 2000.0,
        "freq": 8.0
      }
    }
  },

  "output":{
    "log_file": "log.txt",
    "output_dir": "$OUTPUT_DIR",
    "spikes_file": "spikes.h5",
    "spikes_file_csv": "spikes.csv",
    "spikes_sort_order": "time"
  },

  "node_sets": {
    "biophys_cells": {
      "model_type": "biophysical"
    }
  },

  "reports": {
    "calcium_concentration": {
      "cells": "biophys_cells",
      "variable_name": "cai",
      "module": "membrane_report",
      "file_name": "cai_report.h5",
      "sections": "soma",
      "enabled": true
    },

    "membrane_potential": {
      "cells": "biophys_cells",
      "variable_name": "v",
      "module": "membrane_report",
      "file_name": "v_report.h5",
      "sections": "soma",
      "enabled": true
    },

    "extracellular": {
      "cells": "biophys_cells",
      "variable_name": "e_extracellular",
      "module": "membrane_report",
      "file_name": "e_report.h5",
      "sections": "soma",
      "enabled": true
    },

    "im": {
      "cells": "biophys_cells",
      "variable_name": "i_membrane",
      "module": "membrane_report",
      "file_name": "i_report.h5",
      "sections": "soma",
      "enabled": true
    },

    "vext": {
      "cells": "biophys_cells",
      "variable_name": "vext",
      "module": "membrane_report",
      "file_name": "vext_report.h5",
      "sections": "soma",
      "transform": "first_element",
      "enabled": true
    },

    "ecp": {
      "cells": "biophys_cells",
      "variable_name": "v",
      "module": "extracellular",
      "electrode_positions": "$COMPONENT_DIR/recXelectrodes/linear_electrode.csv",
      "file_name": "ecp.h5",
      "electrode_channels": "soma",
      "contributions_dir": "ecp_contributions",
      "enabled": true
    }
  },

  "components": {
    "morphologies_dir": "$COMPONENT_DIR/morphologies",
    "synaptic_models_dir": "$COMPONENT_DIR/synaptic_models",
    "mechanisms_dir":"$COMPONENT_DIR/mechanisms",
    "biophysical_neuron_models_dir": "$COMPONENT_DIR/biophysical_neuron_templates/ctdb"
  },

  "networks": {
    "nodes": [
      {
        "nodes_file": "$NETWORK_DIR/bio_nodes.h5",
        "node_types_file": "$NETWORK_DIR/bio_node_types.csv"
      }
    ]
  }
}
