commit for version 1.9; adapt MatrixContainer and FEM module to scipy…

… csr_matrix; add verlet integrator; fix issues and bugs - see issues list in docu

README.rst

@@ -39,14 +39,14 @@ Exudyn
 
 **A flexible multibody dynamics systems simulation code with Python and C++**
 
-Exudyn version = 1.8.52.dev1 (Jones)
+Exudyn version = 1.9.0 (Krall)
 
 +  **University of Innsbruck**, Department of Mechatronics, Innsbruck, Austria
 
 If you like using Exudyn, please add a *star* on github and follow us on 
 `Twitter @RExudyn <https://twitter.com/RExudyn>`_ !
 
-+  **Update on Exudyn V1.8.52**: newer examples use ``exudyn.graphics`` instead of ``GraphicsData`` functions. The old models are backwards-compatible, but the updated examples and test models require version 1.8.52 or newer! Install with ``pip install exudyn --pre -U``
++  **Update on Exudyn V1.9.0**: newer examples use ``exudyn.graphics`` instead of ``GraphicsData`` functions. The old models are backwards-compatible, but the new updated examples and test models require version 1.8.52 or newer! FEM now uses internally in mass and stiffness matrices the scipy sparse csr matrices, check also your models for that!
 
 +  **NOTE**: for pure installation, use **pip install exudyn** (see further description below)
 +  *free, open source* and with plenty of *documentation* and *examples*
@@ -73,7 +73,9 @@ If you like using Exudyn, please add a *star* on github and follow us on
 
 |pic1| |pic2| |pic3| |pic4| |pic5| |pic6|
 
-Johannes Gerstmayr. Exudyn -- A C++ based Python package for flexible multibody systems. Multibody System Dynamics, 2023. `https://doi.org/10.1007/s11044-023-09937-1 <https://doi.org/10.1007/s11044-023-09937-1>`_
+How to cite:
+
++ Johannes Gerstmayr. Exudyn -- A C++ based Python package for flexible multibody systems. Multibody System Dynamics, Vol. 60, pp. 533-561, 2024. `https://doi.org/10.1007/s11044-023-09937-1 <https://doi.org/10.1007/s11044-023-09937-1>`_
 
 Due to limitations for complex formulas, images and references in .rst files, some (small) details are only available in theDoc.pdf, see the `github page of Exudyn <https://github.com/jgerstmayr/EXUDYN/blob/master/docs/theDoc/theDoc.pdf>`_! There may also be some conversion errors in the auto-generated html pages.
 

conf.py

@@ -186,6 +186,7 @@ def ProcessTokens(self,text):
             'tkappa': r'{\boldsymbol{\kappa}}',
             'tkappaDot': r'{\boldsymbol{\dot \kappa}}',
             'tphi': r'{\boldsymbol{\phi}}',
+            'boldVarPhi': r'{\boldsymbol{\varphi}}',
             'tPhi': r'{\boldsymbol{\Phi}}',
             'ttheta': r'{\boldsymbol{\theta}}',
             'tTheta': r'{\boldsymbol{\Theta}}',

docs/RST/Examples/ROSMobileManipulator.rst

@@ -203,7 +203,7 @@ You can view and download this file on Github: `ROSMobileManipulator.py <https:/
                        }  
            
        #################### Build mobile robot and add it to existing mbs
-       mobileRobotBackDic = mobile.mobileRobot2MBS(mbs, mobileRobot, markerGround)
+       mobileRobotBackDic = mobile.MobileRobot2MBS(mbs, mobileRobot, markerGround)
        mbs.variables['mobileRobotBackDic'] = mobileRobotBackDic # to be able to use all variables in all functions (make it global useable)
        # add mbs.variable for ROS sensor
        mbs.variables['nodeNumber'] = mobileRobotBackDic['nPlatformList'][0] # just needed if nodeNumber is used for sensor information 
@@ -461,7 +461,7 @@ You can view and download this file on Github: `ROSMobileManipulator.py <https:/
                    print('finished Statemachine. ')
                
                # platform kinematics calculation 
-               w = platformKinematics.getWheelVelocities(vel)
+               w = platformKinematics.GetWheelVelocities(vel)
    
                if TArm != None: 
                    lastTraj = mbs.variables['trajectory'][-1]

docs/RST/Examples/basicTutorial2024.rst

@@ -33,7 +33,7 @@ You can view and download this file on Github: `basicTutorial2024.py <https://gi
                                drawSize=0.2,
                                color=graphics.color.red)
    
-   oSD = mbs.CreateSpringDamper(bodyList=[oGround, oMass],
+   oSD = mbs.CreateSpringDamper(bodyNumbers=[oGround, oMass],
                                 stiffness=500,
                                 damping=10,
                                 drawSize=0.1)

docs/RST/Examples/bicycleIftommBenchmark.rst

@@ -152,69 +152,70 @@ You can view and download this file on Github: `bicycleIftommBenchmark.py <https
                                              VObjectGround(graphicsDataUserFunction=UFgraphics)))
    #add rigid bodies
    #rear wheel
-   [nR,bR]=AddRigidBody(mainSys = mbs, 
-                        inertia = inertiaR, 
-                        rotationMatrix = RotationMatrixZ(pi*0.5), #rotate 90° around z
-                        nodeType = exu.NodeType.RotationEulerParameters, 
-                        position = P1,
-                        velocity=[vX0,omegaX0*P1[2]*sZ,0],
-                        # velocity=[0,0,0],
-                        angularVelocity=[omegaX0,omegaRy0,0], #local rotation axis is now x
-                        gravity = g, 
-                        graphicsDataList = [graphicsR])
+   resultR = mbs.CreateRigidBody(
+       referencePosition = P1,  
+       referenceRotationMatrix = RotationMatrixZ(np.pi*0.5),
+       initialVelocity = [vX0, omegaX0*P1[2]*sZ, 0],  
+       initialAngularVelocity = [omegaX0, omegaRy0, 0],
+       inertia = inertiaR,
+       gravity = g,
+       graphicsDataList = [graphicsR],
+       returnDict = True)
+   
+   nR, bR = resultR['nodeNumber'], resultR['bodyNumber']
    
    mbs.variables['nTrackNode'] = nR #node to be tracked
    
    #front wheel
-   [nF,bF]=AddRigidBody(mainSys = mbs, 
-                        inertia = inertiaF, 
-                        rotationMatrix = RotationMatrixZ(pi*0.5),
-                        nodeType = exu.NodeType.RotationEulerParameters, 
-                        position = P3,
-                        velocity=[vX0,omegaX0*P3[2]*sZ,0],
-                        # velocity=[0,0,0],
-                        angularVelocity=[omegaX0 ,omegaFy0,0],
-                        gravity = g, 
-                        graphicsDataList = [graphicsF])
+   resultF = mbs.CreateRigidBody(
+       referencePosition = P3,
+       referenceRotationMatrix = RotationMatrixZ(pi*0.5),
+       initialVelocity = [vX0, omegaX0*P3[2]*sZ, 0],
+       initialAngularVelocity = [omegaX0, omegaFy0, 0],
+       inertia = inertiaF,
+       gravity = g,
+       nodeType = exu.NodeType.RotationEulerParameters,
+       graphicsDataList = [graphicsF],
+       returnDict = True
+   )
+   nF, bF = resultF['nodeNumber'], resultF['bodyNumber']
    
    #read body
-   [nB,bB]=AddRigidBody(mainSys = mbs, 
-                        inertia = inertiaB, 
-                        nodeType = exu.NodeType.RotationEulerParameters, 
-                        position = bCOM,
-                        velocity=[vX0,omegaX0*bCOM[2]*sZ,0],
-                        # velocity=[0,0,0],
-                        angularVelocity=[omegaX0,0,0],
-                        gravity = g, 
-                        graphicsDataList = [graphicsB,graphicsB2])
+   resultB = mbs.CreateRigidBody(
+       referencePosition = bCOM,
+       initialVelocity = [vX0, omegaX0*bCOM[2]*sZ, 0],
+       initialAngularVelocity = [omegaX0, 0, 0],
+       inertia = inertiaB,
+       gravity = g,
+       nodeType = exu.NodeType.RotationEulerParameters,
+       graphicsDataList = [graphicsB, graphicsB2],
+       returnDict = True
+   )
+   nB, bB = resultB['nodeNumber'], resultB['bodyNumber']
    
    #handle
-   [nH,bH]=AddRigidBody(mainSys = mbs, 
-                        inertia = inertiaH, 
-                        nodeType = exu.NodeType.RotationEulerParameters, 
-                        position = hCOM,
-                        velocity=[vX0,omegaX0*hCOM[2]*sZ,0],
-                        # velocity=[0,0,0],
-                        angularVelocity=[omegaX0,0,0],
-                        gravity = g, 
-                        graphicsDataList = [graphicsH])
+   resultH = mbs.CreateRigidBody(
+       referencePosition = hCOM,
+       initialVelocity = [vX0, omegaX0*hCOM[2]*sZ, 0],
+       initialAngularVelocity = [omegaX0, 0, 0],
+       inertia = inertiaH,
+       gravity = g,
+       nodeType = exu.NodeType.RotationEulerParameters,
+       graphicsDataList = [graphicsH],
+       returnDict = True
+   )
+   nH, bH = resultH['nodeNumber'], resultH['bodyNumber']
    
    
    #%%++++++++++++++++++++++++++++++++++++++++++++++++
    #ground body and marker
-   gGround = graphics.CheckerBoard(point=[0,0,0], size=200, nTiles=64)
-   oGround = mbs.AddObject(ObjectGround(visualization=VObjectGround(graphicsData=[gGround])))
+   gGround = graphics.CheckerBoard(point=[0,0,0], size=50, nTiles=64)
+   oGround = mbs.CreateGround(graphicsDataList=[gGround])
    markerGround = mbs.AddMarker(MarkerBodyRigid(bodyNumber=oGround, localPosition=[0,0,0]))
    
    markerR = mbs.AddMarker(MarkerBodyRigid(bodyNumber=bR, localPosition=[0,0,0]))
    markerF = mbs.AddMarker(MarkerBodyRigid(bodyNumber=bF, localPosition=[0,0,0]))
-   
    markerB1 = mbs.AddMarker(MarkerBodyRigid(bodyNumber=bB, localPosition=P1-bCOM))
-   markerB2 = mbs.AddMarker(MarkerBodyRigid(bodyNumber=bB, localPosition=P2-bCOM))
-   
-   markerH3 = mbs.AddMarker(MarkerBodyRigid(bodyNumber=bH, localPosition=P3-hCOM))
-   markerH2 = mbs.AddMarker(MarkerBodyRigid(bodyNumber=bH, localPosition=P2-hCOM))
-   
    
    sMarkerR = mbs.AddSensor(SensorMarker(markerNumber=markerR, outputVariableType=exu.OutputVariableType.Position))
    sMarkerB1= mbs.AddSensor(SensorMarker(markerNumber=markerB1,outputVariableType=exu.OutputVariableType.Position))
@@ -223,21 +224,14 @@ You can view and download this file on Github: `bicycleIftommBenchmark.py <https
    #add joints:
    useJoints = True
    if useJoints:
-       oJointRW = mbs.AddObject(GenericJoint(markerNumbers=[markerR, markerB1],
-                                             constrainedAxes=[1,1,1,1,0,1],
-                                             rotationMarker0=RotationMatrixZ(pi*0.5),
-                                             visualization=VGenericJoint(axesRadius=0.5*dY, axesLength=5*dY)))
-       
-       oJointFW = mbs.AddObject(GenericJoint(markerNumbers=[markerF, markerH3],
-                                             constrainedAxes=[1,1,1,1,0,1],
-                                             rotationMarker0=RotationMatrixZ(pi*0.5),
-                                             visualization=VGenericJoint(axesRadius=0.5*dY, axesLength=5*dY)))
-       
-       oJointSteer = mbs.AddObject(GenericJoint(markerNumbers=[markerB2, markerH2],
-                                             constrainedAxes=[1,1,1,1,1,0],
-                                             rotationMarker0=RotationMatrixY(-lam),
-                                             rotationMarker1=RotationMatrixY(-lam),
-                                             visualization=VGenericJoint(axesRadius=0.5*dY, axesLength=3*5*dY)))
+       oJointRW = mbs.CreateRevoluteJoint(bodyNumbers=[bR, bB], position=P1, axis=[0,1,0],
+                               axisRadius=0.5*dY, axisLength=5*dY)
+       oJointFW = mbs.CreateRevoluteJoint(bodyNumbers=[bF, bH], position=P3, axis=[0,1,0],
+                               axisRadius=0.5*dY, axisLength=5*dY)
+       oJointSteer = mbs.CreateRevoluteJoint(bodyNumbers=[bB, bH], 
+                                             position=P2-bCOM, useGlobalFrame=False,
+                                             axis=RotationMatrixY(-lam) @ [0,0,1],
+                                             axisRadius=0.5*dY, axisLength=5*dY)[0]
    #%%++++++++++++++++++++++++++++++++++++++++++++++++
    #add 'rolling disc' for wheels:
    cStiffness = 5e4*10 #spring stiffness: 50N==>F/k = u = 0.001m (penetration)
@@ -363,7 +357,7 @@ You can view and download this file on Github: `bicycleIftommBenchmark.py <https
    print("pB1=",pB1)
    simulationSettings = exu.SimulationSettings() #takes currently set values or default values
    
-   tEnd = 5*4
+   tEnd = 5
    h=0.001  #use small step size to detext contact switching
    
    simulationSettings.timeIntegration.numberOfSteps = int(tEnd/h)

docs/RST/Examples/cartesianSpringDamper.rst

@@ -58,7 +58,7 @@ You can view and download this file on Github: `cartesianSpringDamper.py <https:
                        physicsMass=mass)
    
    ## create spring damper  between objectGround and massPoint
-   mbs.CreateCartesianSpringDamper(bodyList=[objectGround, massPoint],
+   mbs.CreateCartesianSpringDamper(bodyNumbers=[objectGround, massPoint],
                                    stiffness = [k,k,k], 
                                    damping   = [d,0,0], 
                                    offset    = [L,0,0])

docs/RST/Examples/cartesianSpringDamperUserFunction.rst

@@ -58,7 +58,7 @@ You can view and download this file on Github: `cartesianSpringDamperUserFunctio
                        physicsMass=mass)
    
    ## create spring damper between ground and mass point
-   csd = mbs.CreateCartesianSpringDamper(bodyList=[objectGround, massPoint],
+   csd = mbs.CreateCartesianSpringDamper(bodyNumbers=[objectGround, massPoint],
                                    stiffness = [k,k,k], 
                                    damping   = [d,0,0],
                                    offset    = [L,0,0])

docs/RST/Examples/gyroStability.rst

@@ -63,32 +63,30 @@ You can view and download this file on Github: `gyroStability.py <https://github
        iCylSum = iCyl1.Translated([0,0.5*L,0]) + iCyl0
        com = iCylSum.COM()
        iCylSum = iCylSum.Translated(-com)
-       
-       # print(iCyl0)
-       # print(iCyl1)
-       # print(iCylSum)
    
        #graphics for body
+       color = [graphics.color.red, graphics.color.lawngreen, graphics.color.steelblue][i]
        gCyl0 = graphics.SolidOfRevolution(pAxis=[0,0,0]-com, vAxis=[2*L,0,0], 
                                               contour = [[-L,-r],[L,-r],[L,-0.5*r],[-L,-0.5*r],], 
-                                              color= graphics.color.steelblue, nTiles= 32, smoothContour=False)
-       gCyl1 = graphics.Cylinder(pAxis=[-L,0,0]-com, vAxis=[2*L,0,0],radius=0.5*w, color=graphics.color.steelblue, nTiles=32)
-       gCyl2 = graphics.Cylinder(pAxis=[0,0,0]-com, vAxis=[0,L,0],radius=0.5*w, color=graphics.color.steelblue, nTiles=32)
+                                              color= color, nTiles= 32, smoothContour=False)
+       gCyl1 = graphics.Cylinder(pAxis=[-L,0,0]-com, vAxis=[2*L,0,0],radius=0.5*w, color=color, nTiles=32)
+       gCyl2 = graphics.Cylinder(pAxis=[0,0,0]-com, vAxis=[0,L,0],radius=0.5*w, color=color, nTiles=32)
        gCOM = graphics.Basis(origin=[0,0,0],length = 1.25*L)
        
        nodeType = exu.NodeType.RotationRotationVector
        if doImplicit:
            nodeType = exu.NodeType.RotationEulerParameters
            
-       [n0,b0]=AddRigidBody(mainSys = mbs,
-                            inertia = iCylSum, #includes COM
-                            nodeType = nodeType,
-                            position = p0,
-                            rotationMatrix = np.diag([1,1,1]),
-                            angularVelocity = omega0,
-                            gravity = g,
-                            graphicsDataList = [gCyl1, gCyl2, gCOM])
-   
+       result0 = mbs.CreateRigidBody(
+           referencePosition = p0,
+           initialAngularVelocity = omega0,
+           inertia = iCylSum,
+           gravity = g,
+           nodeType = nodeType,
+           graphicsDataList = [gCyl1, gCyl2, gCOM],
+           returnDict = True
+       )
+       n0, b0 = result0['nodeNumber'], result0['bodyNumber']
        sAngVel = mbs.AddSensor(SensorNode(nodeNumber=n0, fileName='solution/gyroAngVel'+str(i)+'.txt',
                                           outputVariableType=exu.OutputVariableType.AngularVelocityLocal))
        sAngle = mbs.AddSensor(SensorNode(nodeNumber=n0, fileName='solution/gyroAngle'+str(i)+'.txt',

docs/RST/Examples/multiMbsTest.rst

@@ -48,26 +48,16 @@ You can view and download this file on Github: `multiMbsTest.py <https://github.
                                             axis0=[0,0,1], axis1=[0,0,0*1], radius=[0.05,0.05], 
                                             thickness = 0.1, width = [0.12,0.12], color=color0)
        
-       [n0,b0]=AddRigidBody(mainSys = mbs,
-                            inertia = iCube0,
-                            nodeType = str(exu.NodeType.RotationEulerParameters),
-                            position = pMid0,
-                            rotationMatrix = np.diag([1,1,1]),
-                            angularVelocity = [0,0,0],
-                            gravity = g,
-                            graphicsDataList = [graphicsBody0])
-       
+       b0 = mbs.CreateRigidBody(referencePosition = pMid0,
+                                inertia = iCube0,
+                                gravity = g,
+                                graphicsDataList = [graphicsBody0])
+   
        #ground body and marker
-       oGround = mbs.AddObject(ObjectGround())
-       markerGround = mbs.AddMarker(MarkerBodyRigid(bodyNumber=oGround, localPosition=p0))
-       
-       #markers for rigid body:
-       markerBody0J0 = mbs.AddMarker(MarkerBodyRigid(bodyNumber=b0, localPosition=[-0.5*bodyDim[0],0,0]))
-       
-       #revolute joint (free z-axis)
-       mbs.AddObject(GenericJoint(markerNumbers=[markerGround, markerBody0J0], 
-                                  constrainedAxes=[1,1,1,1,1,0],
-                                  visualization=VObjectJointGeneric(axesRadius=0.01, axesLength=0.1)))
+       oGround = mbs.CreateGround()
+       mbs.CreateRevoluteJoint(bodyNumbers=[oGround, b0], 
+                               position=p0, axis=[0,0,1],
+                               axisRadius=0.01, axisLength=0.1)
        mbs.Assemble()
    
    def Simulate(SC, mbs):

docs/RST/Examples/openAIgymNLinkContinuous.rst

@@ -133,7 +133,7 @@ You can view and download this file on Github: `openAIgymNLinkContinuous.py <htt
            masscart = 1.
            massarm = 0.1
            total_mass = massarm + masscart
-           armInertia = self.length**2*0.5*massarm
+           armInertia = self.length**2*0.5*massarm #for a rod with equally distributed mass, correctly, it would read self.length**2*massarm/3; using here the values of previous research
            
            # environment variables  and force magnitudes and are taken from the  
            # paper "Reliability evaluation of reinforcement learning methods for 
@@ -145,9 +145,9 @@ You can view and download this file on Github: `openAIgymNLinkContinuous.py <htt
            if self.nLinks == 3: 
                self.force_mag = self.force_mag*1.5 
                thresholdFactor = 2
-           if self.nLinks == 4: 
-               self.force_mag = self.force_mag*3
-               thresholdFactor = 5
+           if self.nLinks >= 4: 
+               self.force_mag = self.force_mag*2.5
+               thresholdFactor = 2.5
    
            if self.flagContinuous: 
                self.force_mag *= 2 #continuous controller can have larger max value
@@ -331,6 +331,10 @@ You can view and download this file on Github: `openAIgymNLinkContinuous.py <htt
            reward = 1 - 0.5 * abs(self.state[0])/self.x_threshold
            for i in range(self.nLinks):
                reward -=  0.5 * abs(self.state[i+1]) / (self.theta_threshold_radians*self.nLinks)
+           
+           if self.nLinks > 2: #larger weight on last link!
+               reward -=  5. * 0.5 * abs(self.state[self.nTotalLinks-1]) / self.theta_threshold_radians
+               
            if reward < 0: reward = 0
    
            return reward 
@@ -506,9 +510,9 @@ You can view and download this file on Github: `openAIgymNLinkContinuous.py <htt
            #only load and test
            if False: 
                if flagContinuous and modelType == 'A2C': 
-                   model = SAC.load("solution/" + modelName)
-               else: 
                    model = A2C.load("solution/" + modelName)
+               else: 
+                   model = SAC.load("solution/" + modelName)
            
            env = InvertedNPendulumEnv(thresholdFactor=5) #larger threshold for testing
            solutionFile='solution/learningCoordinates.txt'