Support string activation_function_type and nested activation_function_values in JSON

Co-authored-by: aabrown100-git <71424733+aabrown100-git@users.noreply.github.com>

Author: Copilot

docs/pages/activation_functions.md

@@ -38,6 +38,26 @@ where `t_contract = max(0, t - t_active)`
 }
 ```
 
+Or with explicit activation function specification:
+```json
+{
+  "type": "ChamberElastanceInductor",
+  "name": "ventricle",
+  "values": {
+    "Emax": 1.057,
+    "Emin": 0.091,
+    "Vrd": 26.1,
+    "Vrs": 18.0,
+    "Impedance": 0.000351787,
+    "activation_function_type": "half_cosine",
+    "activation_function_values": {
+      "t_active": 0.2,
+      "t_twitch": 0.3
+    }
+  }
+}
+```
+
 ### 2. Piecewise Cosine Activation (Type 1)
 
 The default activation function for `LinearElastanceChamber` (formerly `PiecewiseCosineChamber`). It models separate contraction and relaxation phases:
@@ -63,10 +83,13 @@ The default activation function for `LinearElastanceChamber` (formerly `Piecewis
     "Emax": 199.95,
     "Epass": 260.59,
     "Vrest": 26.24,
-    "contract_start": 0.025,
-    "relax_start": 0.08625,
-    "contract_duration": 0.06125,
-    "relax_duration": 0.18375
+    "activation_function_type": "piecewise_cosine",
+    "activation_function_values": {
+      "contract_start": 0.025,
+      "relax_start": 0.08625,
+      "contract_duration": 0.06125,
+      "relax_duration": 0.18375
+    }
   }
 }
 ```
@@ -107,23 +130,49 @@ C is a normalization constant ensuring maximum activation is 1.
     "Vrd": 26.1,
     "Vrs": 18.0,
     "Impedance": 0.000351787,
-    "activation_type": 2,
-    "t_shift": 0.15,
-    "tau_1": 0.25,
-    "tau_2": 0.35,
-    "m1": 1.5,
-    "m2": 10.0
+    "activation_function_type": "two_hill",
+    "activation_function_values": {
+      "t_shift": 0.15,
+      "tau_1": 0.25,
+      "tau_2": 0.35,
+      "m1": 1.5,
+      "m2": 10.0
+    }
   }
 }
 ```
 
 ## Switching Between Activation Functions
 
-To use a specific activation function, add the `activation_type` parameter to your chamber configuration:
+To use a specific activation function, add the `activation_function_type` parameter to your chamber configuration:
+
+- `activation_function_type: "half_cosine"` - Half Cosine (default for ChamberElastanceInductor)
+- `activation_function_type: "piecewise_cosine"` - Piecewise Cosine (default for LinearElastanceChamber)  
+- `activation_function_type: "two_hill"` - Two Hill
+
+Group the activation function-specific parameters under `activation_function_values` as a nested dictionary.
+
+## Backward Compatibility
+
+For backward compatibility, the old flat format is also supported:
+
+```json
+{
+  "type": "ChamberElastanceInductor",
+  "name": "ventricle",
+  "values": {
+    "Emax": 1.057,
+    "Emin": 0.091,
+    "Vrd": 26.1,
+    "Vrs": 18.0,
+    "t_active": 0.2,
+    "t_twitch": 0.3,
+    "Impedance": 0.000351787
+  }
+}
+```
 
-- `activation_type: 0` - Half Cosine (default for ChamberElastanceInductor)
-- `activation_type: 1` - Piecewise Cosine (default for LinearElastanceChamber)
-- `activation_type: 2` - Two Hill
+This format will continue to work, with the activation function determined by which parameters are provided.
 
 ## Elastance Calculation
 
@@ -148,6 +197,7 @@ The two-hill activation function is described in:
 ## Backward Compatibility
 
 Existing configuration files will continue to work without modification:
-- `ChamberElastanceInductor` defaults to half cosine activation (type 0)
-- `LinearElastanceChamber` defaults to piecewise cosine activation (type 1)
-- `PiecewiseCosineChamber` is maintained as an alias to `LinearElastanceChamber` for backward compatibility
+- `ChamberElastanceInductor` defaults to half cosine activation when `t_active` and `t_twitch` are provided
+- `LinearElastanceChamber` defaults to piecewise cosine activation when contraction/relaxation parameters are provided  
+- The old numeric `activation_type` parameter (0, 1, 2) is still supported but deprecated in favor of the string format
+- Parameters can be specified at the top level without using `activation_function_values` for backward compatibility

src/solve/SimulationParameters.cpp

@@ -544,7 +544,48 @@ void create_chambers(
     const auto& chamber_config = JsonWrapper(config, component, "name", i);
     std::string chamber_type = chamber_config["type"];
     std::string chamber_name = chamber_config["name"];
-    generate_block(model, chamber_config["values"], chamber_type, chamber_name);
+    
+    // Create a mutable copy of the values to handle activation function parameters
+    nlohmann::json chamber_values = chamber_config["values"];
+    
+    // Check if activation function type is specified as a string
+    if (chamber_values.contains("activation_function_type") && 
+        chamber_values["activation_function_type"].is_string()) {
+      std::string act_type_str = chamber_values["activation_function_type"];
+      
+      // Map string to numeric value
+      int act_type_num = 0;  // Default to half_cosine
+      if (act_type_str == "half_cosine") {
+        act_type_num = 0;
+      } else if (act_type_str == "piecewise_cosine") {
+        act_type_num = 1;
+      } else if (act_type_str == "two_hill") {
+        act_type_num = 2;
+      } else {
+        throw std::runtime_error("Unknown activation_function_type: " + act_type_str +
+                                 " in chamber " + chamber_name);
+      }
+      
+      // Replace string with numeric value
+      chamber_values["activation_type"] = act_type_num;
+      chamber_values.erase("activation_function_type");
+    }
+    
+    // Check if activation function values are specified in nested dict
+    if (chamber_values.contains("activation_function_values") &&
+        chamber_values["activation_function_values"].is_object()) {
+      const auto& act_values = chamber_values["activation_function_values"];
+      
+      // Flatten the nested dictionary - move all parameters to top level
+      for (auto& [key, value] : act_values.items()) {
+        chamber_values[key] = value;
+      }
+      
+      // Remove the nested dict
+      chamber_values.erase("activation_function_values");
+    }
+    
+    generate_block(model, chamber_values, chamber_type, chamber_name);
     DEBUG_MSG("Created chamber " << chamber_name);
   }
 }

tests/cases/chamber_two_hill_activation.json

@@ -102,12 +102,14 @@
         "Vrd": 26.1,
         "Vrs": 18.0,
         "Impedance": 0.000351787,
-        "activation_type": 2,
-        "t_shift": 0.15,
-        "tau_1": 0.25,
-        "tau_2": 0.35,
-        "m1": 1.5,
-        "m2": 10.0
+        "activation_function_type": "two_hill",
+        "activation_function_values": {
+          "t_shift": 0.15,
+          "tau_1": 0.25,
+          "tau_2": 0.35,
+          "m1": 1.5,
+          "m2": 10.0
+        }
       }
     }
   ],

tests/cases/linear_chamber_two_hill_activation.json

@@ -70,12 +70,14 @@
         "Emax": 199.95,
         "Epass": 89.80375933024839,
         "Vrest": 41.680015938842274,
-        "activation_type": 2,
-        "t_shift": 0.025,
-        "tau_1": 0.06,
-        "tau_2": 0.15,
-        "m1": 2.0,
-        "m2": 8.0
+        "activation_function_type": "two_hill",
+        "activation_function_values": {
+          "t_shift": 0.025,
+          "tau_1": 0.06,
+          "tau_2": 0.15,
+          "m1": 2.0,
+          "m2": 8.0
+        }
       }
     },
     {
@@ -85,12 +87,14 @@
         "Emax": 1662.0158240056528,
         "Epass": 40.85565535747109,
         "Vrest": 72.05452710344869,
-        "activation_type": 2,
-        "t_shift": 0.207,
-        "tau_1": 0.08,
-        "tau_2": 0.22,
-        "m1": 2.5,
-        "m2": 12.0
+        "activation_function_type": "two_hill",
+        "activation_function_values": {
+          "t_shift": 0.207,
+          "tau_1": 0.08,
+          "tau_2": 0.22,
+          "m1": 2.5,
+          "m2": 12.0
+        }
       }
     }
   ],