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------------------------------------------------------------
revno: 3747
committer: Jerome Duriez <jerome.duriez@xxxxxxxxxxxxxxx>
timestamp: Tue 2013-11-05 11:52:25 +0100
message:
  Some corrections in the JCFpm doc (hyperlinks...)
modified:
  pkg/dem/JointedCohesiveFrictionalPM.cpp
  pkg/dem/JointedCohesiveFrictionalPM.hpp
  pkg/dem/VTKRecorder.hpp


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=== modified file 'pkg/dem/JointedCohesiveFrictionalPM.cpp'
--- pkg/dem/JointedCohesiveFrictionalPM.cpp	2013-11-04 14:20:24 +0000
+++ pkg/dem/JointedCohesiveFrictionalPM.cpp	2013-11-05 10:52:25 +0000
@@ -254,7 +254,6 @@
 			Real jSigT1	= yade1->jointTensileStrength;
 			Real jSigT2	= yade2->jointTensileStrength;
 			
-			//contactPhysics->frictionAngle = (jointFrictionAngle>=0 ? jointFrictionAngle : std::min(f1,f2)); 
 			contactPhysics->tanFrictionAngle = std::tan(std::min(jf1,jf2));
 			
 			//contactPhysics->kn = jointNormalStiffness*2.*R1*R2/(R1+R2); // very first expression from Luc

=== modified file 'pkg/dem/JointedCohesiveFrictionalPM.hpp'
--- pkg/dem/JointedCohesiveFrictionalPM.hpp	2013-11-04 14:20:24 +0000
+++ pkg/dem/JointedCohesiveFrictionalPM.hpp	2013-11-05 10:52:25 +0000
@@ -10,16 +10,16 @@
 /** This class holds information associated with each body state*/
 class JCFpmState: public State {
 	YADE_CLASS_BASE_DOC_ATTRS_CTOR(JCFpmState,State,"JCFpm state information about each body.",
-		((int,tensBreak,0,,"number of tensile breakages. [-]"))
-                ((int,shearBreak,0,,"number of shear breakages. [-]"))
-		((int,noIniLinks,0,,"number of initial cohesive interactions. [-]"))
-		((Real,tensBreakRel,0,,"relative number (in [0;1]) of tensile breakages (compared with noIniLinks). [-]"))
-		((Real,shearBreakRel,0,,"relative number (in [0;1]) of shear breakages (compared with noIniLinks). [-]"))
-		((bool,onJoint,false,,"identifies if the particle is on a joint surface."))
-		((int,joint,0,,"indicates the number of joint surfaces to which the particle belongs (0-> no joint, 1->1 joint, etc..). [-]"))
-		((Vector3r,jointNormal1,Vector3r::Zero(),,"specifies the normal direction to the joint plane 1. Rk: the ideal here would be to create a vector of vector wich size is defined by the joint integer (as much joint normals as joints). However, it needs to make the pushback function works with python since joint detection is done through a python script. lines 272 to 312 of cpp file should therefore be adapted. [-]"))
-		((Vector3r,jointNormal2,Vector3r::Zero(),,"specifies the normal direction to the joint plane 2. [-]"))
-		((Vector3r,jointNormal3,Vector3r::Zero(),,"specifies the normal direction to the joint plane 3. [-]"))
+		((int,tensBreak,0,,"Number of tensile breakages. [-]"))
+		((int,shearBreak,0,,"Number of shear breakages. [-]"))
+		((int,noIniLinks,0,,"Number of initial cohesive interactions. [-]"))
+		((Real,tensBreakRel,0,,"Relative number (in [0;1], compared with :yref:noIniLinks) of tensile breakages. [-]"))
+		((Real,shearBreakRel,0,,"Relative number (in [0;1], compared with :yref:noIniLinks) of shear breakages. [-]"))
+		((bool,onJoint,false,,"Identifies if the particle is on a joint surface."))
+		((int,joint,0,,"Indicates the number of joint surfaces to which the particle belongs (0-> no joint, 1->1 joint, etc..). [-]"))
+		((Vector3r,jointNormal1,Vector3r::Zero(),,"Specifies the normal direction to the joint plane 1. Rk: the ideal here would be to create a vector of vector wich size is defined by the joint integer (as much joint normals as joints). However, it needs to make the pushback function works with python since joint detection is done through a python script. lines 272 to 312 of cpp file should therefore be adapted. [-]"))
+		((Vector3r,jointNormal2,Vector3r::Zero(),,"Specifies the normal direction to the joint plane 2. [-]"))
+		((Vector3r,jointNormal3,Vector3r::Zero(),,"Specifies the normal direction to the joint plane 3. [-]"))
                 ,
 		createIndex();
 	);
@@ -33,17 +33,16 @@
 		virtual shared_ptr<State> newAssocState() const { return shared_ptr<State>(new JCFpmState); }
 		virtual bool stateTypeOk(State* s) const { return (bool)dynamic_cast<JCFpmState*>(s); }
 		
-	YADE_CLASS_BASE_DOC_ATTRS_CTOR(JCFpmMat,FrictMat,"possibly jointed cohesive frictional material, for use with other JCFpm classes",
-		((int,type,0,,"if particles of two different types interact, it will be with friction only (no cohesion).[-]"))
-		//((Real,alpha,0.,,"defines the shear to normal stiffness ratio ks/kn in the matrix."))
-		((Real,tensileStrength,0.,,"defines the maximum admissible normal force in traction in the matrix (:yref:`JCFpmPhys.FnMax`=tensileStrength*:yref:`JCFpmPhys.crossSection`). [Pa]"))
-		((Real,cohesion,0.,,"defines the maximum admissible tangential force in shear, for Fn=0, in the matrix (:yref:`JCFpmPhys.FsMax`=cohesion*:yref:`JCFpmPhys.crossSection`). [Pa]"))
-		((Real,jointNormalStiffness,0.,,"defines the normal stiffness on the joint surface. [Pa/m]"))
-		((Real,jointShearStiffness,0.,,"defines the shear stiffness on the joint surface. [Pa/m]"))
-		((Real,jointTensileStrength,0.,,"defines the :yref:`maximum admissible normal force in traction<JCFpmPhys.FnMax>` on the joint surface. [Pa]"))
-		((Real,jointCohesion,0.,,"defines the :yref:`maximum admissible tangential force in shear<JCFpmPhys.FsMax>`, for Fn=0, on the joint surface. [Pa]"))
-		((Real,jointFrictionAngle,-1,,"defines Coulomb friction on the joint surface. [rad]"))
-		((Real,jointDilationAngle,0,,"defines the dilatancy of the joint surface (only valid for :yref:`smooth contact logic<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.smoothJoint`). [rad]"))	
+	YADE_CLASS_BASE_DOC_ATTRS_CTOR(JCFpmMat,FrictMat,"Possibly jointed, cohesive frictional material, for use with other JCFpm classes",
+		((Real,cohesion,0.,,"Defines the maximum admissible tangential force in shear, for Fn=0, in the matrix (:yref:`FsMax<JCFpmPhys.FsMax>` = cohesion*:yref:`crossSection<JCFpmPhys.crossSection>`). [Pa]"))
+		((Real,jointCohesion,0.,,"Defines the :yref:`maximum admissible tangential force in shear<JCFpmPhys.FsMax>`, for Fn=0, on the joint surface. [Pa]"))
+		((Real,jointDilationAngle,0,,"Defines the dilatancy of the joint surface (only valid for :yref:`smooth contact logic<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.smoothJoint>`). [rad]"))	
+		((Real,jointFrictionAngle,-1,,"Defines Coulomb friction on the joint surface. [rad]"))
+		((Real,jointNormalStiffness,0.,,"Defines the normal stiffness on the joint surface. [Pa/m]"))
+		((Real,jointShearStiffness,0.,,"Defines the shear stiffness on the joint surface. [Pa/m]"))
+		((Real,jointTensileStrength,0.,,"Defines the :yref:`maximum admissible normal force in traction<JCFpmPhys.FnMax>` on the joint surface. [Pa]"))
+		((int,type,0,,"If particles of two different types interact, it will be with friction only (no cohesion).[-]"))
+		((Real,tensileStrength,0.,,"Defines the maximum admissible normal force in traction in the matrix (:yref:`FnMax<JCFpmPhys.FnMax>` = tensileStrength*:yref:`crossSection<JCFpmPhys.crossSection>`). [Pa]"))
 		,
 		createIndex();
 	);
@@ -56,7 +55,7 @@
 	public:
 		virtual ~JCFpmPhys();
 
-		YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(JCFpmPhys,NormShearPhys,"representation of a single interaction of the JCFpm type, storage for relevant parameters",
+		YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(JCFpmPhys,NormShearPhys,"Representation of a single interaction of the JCFpm type, storage for relevant parameters",
 			((Real,initD,0,,"equilibrium distance for interacting particles. Computed as the interparticular distance at first contact detection."))
 			((bool,isCohesive,false,,"If false, particles interact in a frictional way. If true, particles are bonded regarding the given :yref:`cohesion<JCFpmMat.cohesion>` and :yref:`tensile strength<JCFpmMat.tensileStrength>` (or their jointed variants)."))
 			((bool,more,false,,"specifies if the interaction is crossed by more than 3 joints. If true, interaction is deleted (temporary solution)."))
@@ -65,9 +64,8 @@
 			((Real,crossSection,0,,"crossSection=pi*Rmin^2. [m2]"))
 			((Real,FnMax,0,,"computed from :yref:`tensile strength<JCFpmMat.tensileStrength>` (or joint variant) to define the maximum admissible normal force in traction. [N]"))
 			((Real,FsMax,0,,"computed from :yref:`cohesion<JCFpmMat.cohesion>` (or jointCohesion) to define the maximum admissible tangential force in shear, for Fn=0. [N]"))
-			((Vector3r,jointNormal,Vector3r::Zero(),,"normal direction to the joint, deduced from e.g. <JCFpmState.jointNormal1>."))
+			((Vector3r,jointNormal,Vector3r::Zero(),,"normal direction to the joint, deduced from e.g. :yref:`<JCFpmState.jointNormal1>`."))
 			((Real,jointCumulativeSliding,0,,"sliding distance for particles interacting on a joint. Used, when :yref:`<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.smoothJoint>` is true, to take into account dilatancy due to shearing. [-]"))
-			//((Real,dilationAngle,0,,"defines the dilatancy of the joint surface. [rad]"))
 			((Real,tanDilationAngle,0,,"tangent of the angle defining the dilatancy of the joint surface (auto. computed from :yref:`JCFpmMat.jointDilationAngle`). [-]"))
 			((Real,dilation,0,,"defines the normal displacement in the joint after sliding treshold. [m]"))
 			,
@@ -87,7 +85,7 @@
 		FUNCTOR2D(JCFpmMat,JCFpmMat);
 		DECLARE_LOGGER;
 		
-		YADE_CLASS_BASE_DOC_ATTRS(Ip2_JCFpmMat_JCFpmMat_JCFpmPhys,IPhysFunctor,"converts 2 JCFpmMat instances to JCFpmPhys with corresponding parameters.",
+		YADE_CLASS_BASE_DOC_ATTRS(Ip2_JCFpmMat_JCFpmMat_JCFpmPhys,IPhysFunctor,"Converts 2 :yref:`JCFpmMat` instances to one :yref:`JCFpmPhys` instance, with corresponding parameters.",
 			((int,cohesiveTresholdIteration,1,,"should new contacts be cohesive? They will before this iter, they won't afterward."))
 		);
 		
@@ -101,10 +99,10 @@
 		FUNCTOR2D(ScGeom,JCFpmPhys);
 
 		YADE_CLASS_BASE_DOC_ATTRS(Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM,LawFunctor,"Interaction law for cohesive frictional material, e.g. rock, possibly presenting joint surfaces. Joint surfaces can be defined in a preprocessing phase through .stl meshes (see ref for details of the procedure), and can be mechanically described with a smooth contact logic [Ivars2011]_ (implemented in Yade in [Scholtes2012]_).",
+			((string,Key,"",,"string specifying the name of saved file 'cracks___.txt', when :yref:`recordCracks<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.recordCracks>` is true."))
+			((bool,cracksFileExist,false,,"if true (and if :yref:`recordCracks<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.recordCracks>`), data are appended to an existing 'cracksKey' text file; otherwise its content is reset."))
 			((bool,smoothJoint,false,,"if true, interactions of particles belonging to joint surface (:yref:`JCFpmPhys.isOnJoint`) are handled according to a smooth contact logic [Ivars2011]_, [Scholtes2012]_."))
-			((bool,recordCracks,false,,"if true a text file cracksKey.txt (see below) will be created (apparition iteration, position, type (tensile or shear), cross section and contact normal)."))
-			((string,Key,"",,"string specifying the name of saved file 'cracks___.txt', when :yref:`recordCracks<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.`recordCracks>` is true."))
-			((bool,cracksFileExist,false,,"if true (and if :yref:`recordCracks<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.`recordCracks>`), data are appended to an existing 'cracks...' text file; otherwise its content is reset."))
+			((bool,recordCracks,false,,"if true a text file cracksKey.txt (see :yref:`Key<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.Key>`) will be created. It contains : apparition iteration, position, type (tensile or shear), cross section and contact normal."))
 		);
 		DECLARE_LOGGER;	
 };

=== modified file 'pkg/dem/VTKRecorder.hpp'
--- pkg/dem/VTKRecorder.hpp	2013-11-04 14:55:45 +0000
+++ pkg/dem/VTKRecorder.hpp	2013-11-05 10:52:25 +0000
@@ -24,7 +24,7 @@
 		#endif
 		((string,fileName,"",,"Base file name; it will be appended with {spheres,intrs,facets}-243100.vtu (unless *multiblock* is ``True``) depending on active recorders and step number (243100 in this case). It can contain slashes, but the directory must exist already."))
 		((vector<string>,recorders,vector<string>(1,string("all")),,"List of active recorders (as strings). ``all`` (the default value) enables all base and generic recorders.\n\n.. admonition:: Base recorders\n\n\tBase recorders save the geometry (unstructured grids) on which other data is defined. They are implicitly activated by many of the other recorders. Each of them creates a new file (or a block, if :yref:`multiblock <VTKRecorder.multiblock>` is set).\n\n\t``spheres``\n\t\tSaves positions and radii (``radii``) of :yref:`spherical<Sphere>` particles.\n\t``facets``\n\t\tSave :yref:`facets<Facet>` positions (vertices).\n\t``boxes``\n\t\tSave :yref:`boxes<Box>` positions (edges).\n\t``intr``\n\t\tStore interactions as lines between nodes at respective particles positions. Additionally stores magnitude of normal (``forceN``) and shear (``absForceT``) forces on interactions (the :yref:`geom<Interaction.geom> must be of type :yref:`NormShearPhys`). \n\n.. admonition:: Generic recorders\n\n\tGeneric recorders do not depend on specific model being used and save commonly useful data.\n\n\t``id``\n\t\tSaves id's (field ``id``) of spheres; active only if ``spheres`` is active.\n\t``mass``\n\t\tSaves masses (field ``mass``) of spheres; active only if ``spheres`` is active.\n\t``clumpId``\n\t\tSaves id's of clumps to which each sphere belongs (field ``clumpId``); active only if ``spheres`` is active.\n\t``colors``\n\t\tSaves colors of :yref:`spheres<Sphere>` and of :yref:`facets<Facet>` (field ``color``); only active if ``spheres`` or ``facets`` are activated.\n\t``mask``\n\t\tSaves groupMasks of :yref:`spheres<Sphere>` and of :yref:`facets<Facet>` (field ``mask``); only active if ``spheres`` or ``facets`` are activated.\n\t``materialId``\n\t\tSaves materialID of :yref:`spheres<Sphere>` and of :yref:`facets<Facet>`; only active if ``spheres`` or ``facets`` are activated.\n\t``velocity``\n\t\tSaves linear and angular velocities of spherical particles as Vector3 and length(fields ``linVelVec``, ``linVelLen`` and ``angVelVec``, ``angVelLen`` respectively``); only effective with ``spheres``.\n\t``stress``\n\t\tSaves stresses of :yref:`spheres<Sphere>` and of :yref:`facets<Facet>`  as Vector3 and length; only active if ``spheres`` or ``facets`` are activated.\n\n.. admonition:: Specific recorders\n\n\tThe following should only be activated in appropriate cases, otherwise crashes can occur due to violation of type presuppositions.\n\n\t``cpm``\n\t\tSaves data pertaining to the :yref:`concrete model<Law2_ScGeom_CpmPhys_Cpm>`: ``cpmDamage`` (normalized residual strength averaged on particle), ``cpmStress`` (stress on particle); ``intr`` is activated automatically by ``cpm``\n\t``wpm``\n\t\tSaves data pertaining to the :yref:`wire particle model<Law2_ScGeom_WirePhys_WirePM>`: ``wpmForceNFactor`` shows the loading factor for the wire, e.g. normal force divided by threshold normal force.\n\t``jcfpm``\n\t\tSaves data pertaining to the :yref:`rock (smooth)-jointed model<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM>`: ``damage`` is defined by :yref:`JCFpmState.tensBreak` + :yref:`JCFpmState.shearBreak`; ``intr`` is activated automatically by ``jcfpm``, and :yref:`on joint<JCFpmPhys.isOnJoint>` or :yref:`cohesive<JCFpmPhys.isCohesive>` interactions can be vizualized.\n\t``cracks``\n\t\tSaves other data pertaining to the :yref:`rock model<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM>`: ``cracks`` shows locations where cohesive bonds failed during the simulation, with their types (0/1  for tensile/shear breakages), their sizes (0.5*(R1+R2)), and their normal directions. The :yref:`corresponding attribute<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.recordCracks>` has to be activated, and Key attributes have to be consistent.\n\n"))
-		((string,Key,"",,"Necessary if :yref:`recorders` contains 'cracks'. A string specifying the name of file 'cracks___.txt' that is considered in this case (see :yref:`corresponding attribute<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.Key>`."))
+		((string,Key,"",,"Necessary if :yref:`recorders<VTKRecorder.recorders>` contains 'cracks'. A string specifying the name of file 'cracks___.txt' that is considered in this case (see :yref:`corresponding attribute<Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.Key>`)."))
 		((int,mask,0,,"If mask defined, only bodies with corresponding groupMask will be exported. If 0, all bodies will be exported.")),
 		/*ctor*/
 		initRun=true;