feat: Fix muscle models

.gitignore

@@ -2,6 +2,7 @@
 *.pyc
 **/Output/*
 !**/Output/.gitkeep
+!Application/MocapExamples/Plug-in-gait_Simple_GMFoot/Output/LowerExtremity_BareFootWalk.anyset
 Docs/_build/*
 Docs/auto_examples/*
 Documentation/*

Application/Examples/FreePosture3SFoot/FreePostureFullBodyStatic3SFoot.Main.any

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+#include "../libdef.any"
+
+/** ----------------------------------------------------------------------------
+This model uses the full body model, i.e. most of the body parts available
+in the AAUHuman part of the Body directory. The model is grounded at the
+pelvis and the posture if the model is controlled through a mannequin.any 
+file by means of joint angles.
+
+This application is a really good starting point for new applications 
+involving the entire body.
+
+The model do not contain muscles and is only intended for running kinematic analysis
+
+The model has several configurations which can be changed in the file "Config.any"
+
+BodyModelSelection can be either "FullBodyModel"  or "FullBodySRHand" 
+FullBodyModel is a fullbody model
+FullBodyModelSRHand is a fullbody model with a detailed hand and shoulder rhythm
+
+CONFIGURATION2 can be either "FreePostureStatic" or "FreePostureMove"
+FreePostureStatic is a static model which do not move its joint angles are controlled in the "mannequin.any" file 
+FreePostureMove is a dynamic model controlled through angles which can be set in the "MannequinInterpolation.any" file
+
+
+---------------------------------------------------------------------------- */
+Main = {
+
+  // ----------------------------------------------------------
+  // Driver type settings
+  // ----------------------------------------------------------
+  #ifndef DriverSelection
+    #define DriverSelection "FreePostureStatic"
+  #endif
+
+  // ----------------------------------------------------------
+  // Body Model Configuration
+  // ----------------------------------------------------------
+  #include "Model/BodyModelConfiguration.any"
+  #define BM_FOOT_MODEL _FOOT_MODEL_NONE_
+  #define BM_JOINT_TYPE_ANKLE_RIGHT _JOINT_TYPE_USERDEFINED_
+  #define BM_JOINT_TYPE_ANKLE_LEFT _JOINT_TYPE_USERDEFINED_ 
+
+  // The Mannequin file specifies load-time positions for all the segments
+  // in the HumanModel. This is important for the model's ablity to resolve
+  // all the kinematic constraints when the model is analyzed.
+  // The mannequin file also drives those degrees of freedom of the human 
+  // model that are not governed by problem-specific drivers at run time.    
+
+  #if DriverSelection == "FreePostureStatic"
+    // use different initial positions for two configurations
+    #include "Model/Mannequin.any" 
+  #else //#if DriverSelection == "FreePostureMove"
+    // use different initial positions for two configurations
+    #include "Model/MannequinInterpolation.any" 
+  #endif
+
+  // Model of the human body to be used for the analysis  
+  #include "<ANYBODY_PATH_BODY>/HumanModel.any"
+
+  #ifndef SimplifiedContactMH
+  #define SimplifiedContactMH
+  #endif
+  #include "<ANYBODY_PATH_BODY>/Foot3S/3S_foot_model.any"
+
+  // The actual model where all components are assembled
+  AnyFolder Model={
+    /// Body model without default drivers
+    AnyFolder &BodyModel=.HumanModel.BodyModel;
+    /// Reference to the mannequin folder (used by drivers)
+    AnyFolder &Mannequin =.HumanModel.Mannequin;
+
+    #include "Model/Environment.any"   
+
+    /// Constraints and drivers
+    AnyFolder ModelEnvironmentConnection = {    
+     #if DriverSelection == "FreePostureStatic"
+         #include "Model/JointsAndDriversConstant.any"
+     #else //#if DriverSelection == "FreePostureMove"
+         #include "Model/JointsAndDriversInterpolation.any"
+     #endif
+    };
+
+  };
+
+  AnyBodyStudy Study = {
+    AnyFolder &Model = .Model;
+    tEnd = 1.0;
+    Gravity = {0.0, -9.81, 0.0};
+
+    #if DriverSelection=="FreePostureStatic"
+    nStep = 1;
+    #endif
+
+    #if DriverSelection=="FreePostureMove"
+    nStep = 150;
+    #endif   
+
+
+  }; // End of study
+
+  // Include an operation sequence to run all required steps of your application (see Operations tab)
+    #include "<ANYBODY_PATH_MODELUTILS>\Operations\RunAppSequence.any"
+
+}; //Main
+

Application/Examples/FreePosture3SFoot/Model/BodyModelConfiguration.any

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+#path __BM_PLUGIN_FILE__ "BodyModelConfiguration.any"
+#define BM_CONFIG_PLUGIN __BM_PLUGIN_FILE__
+
+// -----------------------------------------------------------------------------------
+// The BodyModel configuration can be modified using BodyModel GUI plugin
+// or by manually editing this file.
+//
+// Please see this this file for more information on the options:
+// #path HTML_DOC "<AMMR_PATH_DOC>/bm_config/index.html"
+// -----------------------------------------------------------------------------------
+
+// The model is without muscles
+#define BM_LEG_MUSCLES_RIGHT _MUSCLES_SIMPLE_
+#define BM_LEG_MUSCLES_LEFT _MUSCLES_SIMPLE_
+
+#define BM_ARM_MUSCLES_RIGHT OFF
+#define BM_ARM_MUSCLES_LEFT OFF
+
+#define BM_TRUNK_MUSCLES OFF
+
+
+// Remove default drivers
+#define BM_MANNEQUIN_DRIVER_DEFAULT OFF
+#define BM_ARM_LEFT ON
+#define BM_ARM_RIGHT ON

Application/Examples/FreePosture3SFoot/Model/Config.any

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+
+
+//FullBodyModel FullBodySRHand
+#ifndef BodyModelSelection  
+#define BodyModelSelection  "FullBodyModel"
+#endif
+
+//FreePostureStatic   FreePostureMove
+#ifndef DriverSelection  
+#define DriverSelection  "FreePostureMove"
+#endif
+
+
+
+#define ERRORMSG (ErrorMessage) AnyMessage MISSING_SELECTION = { TriggerPreProcess = On; Type = MSG_ErrorFatal; Message = ErrorMessage; };
+
+//Error messages to inform about selection possibilities
+#if BodyModelSelection  != "FullBodySRHand"   &   BodyModelSelection  != "FullBodyModel" 
+ERRORMSG ("In Config.any please select  BodyModelSelection to be either FullBodyModel or FullBodySRHand.")
+#define MISSING_SELECTION 
+#endif  
+
+#if DriverSelection  != "FreePostureMove"   &   DriverSelection  != "FreePostureStatic" 
+ERRORMSG ("In Config.any please select DriverSelection to be either FreePostureMove or FreePostureStatic")
+#define MISSING_SELECTION 
+#endif  
+

Application/Examples/FreePosture3SFoot/Model/ConstantDrivers/LeftArmDrivers.any

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+
+
+  // ************************************
+  // Drivers for the left arm
+  // ************************************
+
+
+  #if BM_ARM_LEFT & (BM_ARM_SHOULDER_RHYTHM == OFF)
+  //Sterno clavicular joint driver
+  AnyKinEqSimpleDriver SCDriverLeft ={
+    AnyKinMeasure& ref1 =...BodyModel.Interface.Left.SternoClavicularProtraction;
+    AnyKinMeasure& ref2 =...BodyModel.Interface.Left.SternoClavicularElevation;
+    DriverPos = pi/180*{
+      .JntPos.Left.SternoClavicularProtraction,
+      .JntPos.Left.SternoClavicularElevation
+    };
+    DriverVel = pi/180*{
+      .JntVel.Left.SternoClavicularProtraction,
+      .JntVel.Left.SternoClavicularElevation
+    };
+    Reaction.Type={Off,Off};
+  };
+  #endif
+
+  //Glenohumeral joint 
+  AnyKinEqSimpleDriver GHDriverLeft={
+    AnyKinMeasure& ref1 =...BodyModel.Interface.Left.GlenohumeralAbduction;
+    AnyKinMeasure& ref2 =...BodyModel.Interface.Left.GlenohumeralFlexion;
+    AnyKinMeasure& ref3 =...BodyModel.Interface.Left.GlenohumeralExternalRotation;
+
+     DriverPos=pi/180*{
+      .JntPos.Left.GlenohumeralAbduction,  //GH joint
+      .JntPos.Left.GlenohumeralFlexion,  //GH joint
+      .JntPos.Left.GlenohumeralExternalRotation  //GH joint
+     };
+     DriverVel = pi/180*{
+      .JntVel.Left.GlenohumeralAbduction,  //GH joint
+      .JntVel.Left.GlenohumeralFlexion,  //GH joint
+      .JntVel.Left.GlenohumeralExternalRotation  //GH joint
+     };    
+     Reaction.Type={Off,Off,Off};
+  };
+
+  //Elbow flexion driver  
+  AnyKinEqSimpleDriver ElbowFlexionDriverLeft={
+    AnyKinMeasureOrg  &Elbow =...BodyModel.Interface.Left.ElbowFlexion;
+    DriverPos=pi/180*{.JntPos.Left.ElbowFlexion};  
+    DriverVel = pi/180*{.JntVel.Left.ElbowFlexion};  
+    Reaction.Type={Off};
+  };
+
+  //Elbow pronation driver
+  AnyKinEqSimpleDriver ElbowPronationDriverLeft={
+    AnyKinMeasure& Elbow =...BodyModel.Interface.Left.ElbowPronation;
+    DriverPos = pi/180*{.JntPos.Left.ElbowPronation };  
+    DriverVel=pi/180*{.JntVel.Left.ElbowPronation };  
+    Reaction.Type={Off};
+  };
+
+  //Wrist driver 
+  AnyKinEqSimpleDriver WristDriverLeft ={
+    AnyKinMeasure& ref1 =...BodyModel.Interface.Left.WristFlexion;
+    AnyKinMeasure& ref2 =...BodyModel.Interface.Left.WristAbduction;
+    DriverPos = pi/180*{
+         .JntPos.Left.WristFlexion,
+         .JntPos.Left.WristAbduction
+       };
+
+    DriverVel = pi/180*{
+         .JntVel.Left.WristFlexion,
+         .JntVel.Left.WristAbduction};
+    Reaction.Type={Off,Off};
+  };

Application/Examples/FreePosture3SFoot/Model/ConstantDrivers/LeftHandDrivers.any

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+
+
+  // ************************************
+  // Drivers for the left fingers
+  // ************************************
+
+  //finger1
+  AnyKinEqSimpleDriver CMC1FlexionL={
+    AnyKinMeasure& ref =.RefHM.Interface.Left.CMCFlexion;
+    DriverPos= {.JntPos.Right.Finger1.CMCFlexion}*pi/180;  
+    DriverVel={0};
+  };
+
+  AnyKinEqSimpleDriver CMC1AbductionL={
+    AnyKinMeasure& ref =.RefHM.Interface.Left.CMCAbduction;
+    DriverPos={.JntPos.Right.Finger1.CMCDeviation}*pi/180;  
+    DriverVel={0};
+  };
+
+
+
+  AnyKinEqSimpleDriver MCP1FlexionL={
+    AnyKinMeasure&ref= .RefHM.Interface.Left.MCPFlexion;
+    DriverPos={.JntPos.Right.Finger1.MCPFlexion}*pi/180;
+    DriverVel={0};
+  };
+  AnyKinEqSimpleDriver MCP1AbductionL={
+    AnyKinMeasure&ref= .RefHM.Interface.Left.MCPAbduction;
+    DriverPos={.JntPos.Right.Finger1.MCPDeviation}*pi/180;
+    DriverVel={0};
+  };
+
+  AnyKinEqSimpleDriver DIP1L={
+    AnyKinMeasure&ref= .RefHM.Interface.Left.DIP;
+    DriverPos={.JntPos.Right.Finger1.DIPFlexion}*pi/180;  
+    DriverVel={0};
+  };
+
+  // finger2
+//    AnyKinEqSimpleDriver CMC2={
+//      AnyUniversalJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger2.Jnt.CMC;
+//      DriverPos={0,0};  
+//      DriverVel={0,0};
+//    };
+  AnyKinEqSimpleDriver MCP2L={
+    AnyRevoluteJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger2.Jnt.MCP;
+    DriverPos={.JntPos.Left.Finger2.MCPFlexion}*pi/180;  
+    DriverVel={0};
+  };  
+  AnyKinEqSimpleDriver PIP2L={
+    AnyRevoluteJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger2.Jnt.PIP;
+    DriverPos={.JntPos.Left.Finger2.PIPFlexion}*pi/180;  
+    DriverVel={0};
+  };
+    AnyKinEqSimpleDriver DIP2L={
+      AnyRevoluteJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger2.Jnt.DIP;
+      DriverPos={.JntPos.Left.Finger2.DIPFlexion}*pi/180;  
+      DriverVel={0};
+    };
+
+
+
+  // finger3
+//    AnyKinEqSimpleDriver CMC3={
+//      AnyUniversalJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger3.Jnt.CMC;
+//      DriverPos={0,0};  
+//      DriverVel={0,0};
+//    };
+  AnyKinEqSimpleDriver MCP3L={
+    AnyRevoluteJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger3.Jnt.MCP;
+    DriverPos={.JntPos.Left.Finger3.MCPFlexion}*pi/180;  
+    DriverVel={0};
+  };  
+  AnyKinEqSimpleDriver PIP3L={
+    AnyRevoluteJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger3.Jnt.PIP;
+    DriverPos={.JntPos.Left.Finger3.PIPFlexion}*pi/180;  
+    DriverVel={0};
+  };
+    AnyKinEqSimpleDriver DIP3L={
+      AnyRevoluteJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger3.Jnt.DIP;
+      DriverPos={.JntPos.Left.Finger3.DIPFlexion}*pi/180;  
+      DriverVel={0};
+    };
+
+
+  //finger4
+//    AnyKinEqSimpleDriver CMC4={
+//      AnyUniversalJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger4.Jnt.CMC;
+//      DriverPos={0,0}*pi/180;  
+//      DriverVel={0,0};
+//    };
+  AnyKinEqSimpleDriver MCP4L={
+    AnyRevoluteJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger4.Jnt.MCP;
+    DriverPos={.JntPos.Left.Finger4.MCPFlexion}*pi/180;  
+    DriverVel={0};
+  };  
+  AnyKinEqSimpleDriver PIP4L={
+    AnyRevoluteJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger4.Jnt.PIP;
+    DriverPos={.JntPos.Left.Finger4.PIPFlexion}*pi/180;  
+    DriverVel={0};
+  };
+    AnyKinEqSimpleDriver DIP4L={
+      AnyRevoluteJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger4.Jnt.DIP;
+      DriverPos={.JntPos.Left.Finger4.DIPFlexion}*pi/180;  
+      DriverVel={0};
+    };
+
+
+  // finger5
+//    AnyKinEqSimpleDriver CMC5={
+//      AnyUniversalJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger5.Jnt.CMC;
+//      DriverPos={0,0};  
+//      DriverVel={0,0};
+//    };
+  AnyKinEqSimpleDriver MCP5L={
+    AnyRevoluteJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger5.Jnt.MCP;
+    DriverPos={.JntPos.Left.Finger5.MCPFlexion}*pi/180;  
+    DriverVel={0};
+  };  
+  AnyKinEqSimpleDriver PIP5L={
+    AnyRevoluteJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger5.Jnt.PIP;
+    DriverPos={.JntPos.Left.Finger5.PIPFlexion}*pi/180;  
+    DriverVel={0};
+  };
+    AnyKinEqSimpleDriver DIP5L={
+      AnyRevoluteJoint &ref=  .RefHM.Left.ShoulderArm.Seg.Hand.Finger5.Jnt.DIP;
+      DriverPos={.JntPos.Left.Finger5.DIPFlexion}*pi/180;  
+      DriverVel={0};
+    };
+
+
+