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[Branch ~yade-dev/yade/trunk] Rev 2458: 1. Fix a few malformed formulas (my bad) so that LaTeX does not choke on them.

To: Yade developers <yade-dev@xxxxxxxxxxxxxxxxxxx>
From: noreply@xxxxxxxxxxxxx
Date: Fri, 01 Oct 2010 22:31:22 -0000
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Sender: bounces@xxxxxxxxxxxxx

------------------------------------------------------------
revno: 2458
committer: Chiara Modenese <chia@engs-018373>
branch nick: yade
timestamp: Fri 2010-10-01 23:30:00 +0100
message:
  1. Fix a few malformed formulas (my bad) so that LaTeX does not choke on them.
modified:
  doc/sphinx/introduction.rst
  doc/sphinx/prog.rst
  doc/sphinx/yadeSphinx.py
  pkg/dem/Engine/GlobalEngine/NozzleFactory.hpp
  py/_utils.cpp


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=== modified file 'doc/sphinx/introduction.rst'
--- doc/sphinx/introduction.rst	2010-09-30 18:00:41 +0000
+++ doc/sphinx/introduction.rst	2010-10-01 22:30:00 +0000
@@ -456,7 +456,7 @@
 
 hides 3 internal dispatchers within the :yref:`InteractionLoop` engine; they all operate on interactions and are, for performance reasons, put together:
 
-:yref:`InteractionGeometryDispatcher`
+:yref:`IGeomDispatcher`
 	uses the first set of functors (``Ig2``), which are dispatched based on combination of ``2`` :yref:`Shapes<Shapes>` objects. Dispatched functor resolves exact collision configuration and creates :yref:`IGeom<Interaction::geom>` (whence ``Ig`` in the name) associated with the interaction, if there is collision. The functor might as well fail on approximate interactions, indicating there is no real contact between the bodies, even if they did overlap in the approximate collision detection.
 
 	#. The first functor, :yref:`Ig2_Sphere_Sphere_Dem3DofGeom`, is called on interaction of 2 :yref:`Spheres<Sphere>` and creates :yref:`Dem3DofGeom` instance, if appropriate.
@@ -465,7 +465,7 @@
 
 	All ``Ig2`` functors derive from :yref:`IGeomFunctor` (they are documented at the same place).
 
-:yref:`InteractionPhysicsDispatcher`
+:yref:`IPhysDispatcher`
 	dispatches to the second set of functors based on combination of ``2`` :yref:`Materials<Material>`; these functors return return :yref:`IPhys` instance (the ``Ip`` prefix). In our case, there is only 1 functor used, :yref:`Ip2_FrictMat_FrictMat_FrictPhys`, which create :yref:`FrictPhys` from 2 :yref:`FrictMat's<FrictMat>`.
 	
 	``Ip2`` functors are derived from :yref:`IPhysFunctor`.

=== modified file 'doc/sphinx/prog.rst'
--- doc/sphinx/prog.rst	2010-09-30 18:00:41 +0000
+++ doc/sphinx/prog.rst	2010-10-01 22:30:00 +0000
@@ -11,6 +11,7 @@
 .. _scons-parameters:
 Pre-build configuration
 -----------------------
+
 We use ``\$`` to denote build variable in strings in this section; in SCons script, they can be used either by writing ``\$variable`` in strings passed to SCons functions, or obtained as attribute of the ``Environment`` instance ``env``, i.e. ``env['variable']``; we use the formed in running text here.
 
 In order to allow parallel installation of multiple yade versions, the installation location follows the pattern ``\$PREFIX/lib/yade\$SUFFIX`` for libraries and ``\$PREFIX/bin/yade\$SUFFIX`` for executables (in the following, we will refer only to the first one). ``\$SUFFIX`` takes the form ``-\$version\$variant``, which further allows multiple different builds of the same version (typically, optimized and debug builds). For instance, the default debug build of version 0.5 would be  installed in ``/usr/local/lib/yade-0.5-dbg/``, the executable being ``/usr/local/bin/yade-0.5-dbg``.
@@ -894,10 +895,10 @@
 
 There are currenly 4 predefined dispatchers (see `dispatcher-names`_) and corresponding functor types. They are inherit from template instantiations of ``Dispatcher1D`` or ``Dispatcher2D`` (for functors, ``Functor1D`` or ``Functor2D``). These templates themselves derive from ``DynlibDispatcher`` (for dispatchers) and ``FunctorWrapper`` (for functors).
 
-Example: InteractionGeometryDispatcher
+Example: IGeomDispatcher
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Let's take (the most complicated perhaps) :yref:`InteractionGeometryDispatcher`. :yref:`IGeomFunctor`, which is dispatched based on types of 2 :yref:`Shape` instances (a :yref:`Functor`), takes a number of arguments and returns bool. The functor "call" is always provided by its overridden ``Functor::go`` method; it always receives the dispatched instances as first argument(s) (2 Ã— ``const shared_ptr<Shape>&``) and a number of other arguments it needs:
+Let's take (the most complicated perhaps) :yref:`IGeomDispatcher`. :yref:`IGeomFunctor`, which is dispatched based on types of 2 :yref:`Shape` instances (a :yref:`Functor`), takes a number of arguments and returns bool. The functor "call" is always provided by its overridden ``Functor::go`` method; it always receives the dispatched instances as first argument(s) (2 Ã— ``const shared_ptr<Shape>&``) and a number of other arguments it needs:
 
 .. code-block:: c++
 
@@ -917,7 +918,7 @@
 
 .. code-block:: c++
 
-	class InteractionGeometryDispatcher: public Dispatcher2D<	
+	class IGeomDispatcher: public Dispatcher2D<	
 	   Shape,                       // 1st class for dispatch
 	   Shape,                       // 2nd class for dispatch
 	   IGeomFunctor,  // functor type
@@ -1003,14 +1004,14 @@
 
 Classes entering the dispatch mechanism must provide for fast identification of themselves and of their parent class. [#rttiindex]_ This is called class indexing and all such classes derive from :yref:`Indexable`. There are ``top-level`` Indexables (types that the dispatchers accept) and each derived class registers its index related to this top-level Indexable. Currently, there are:
 
-============================ ===========================
-Top-level Indexable          used by
-============================ ===========================
-:yref:`Shape`                :yref:`BoundFunctor`, :yref:`InteractionGeometryDispatcher`
-:yref:`Material`             :yref:`InteractionPhysicsDispatcher`
-:yref:`IPhys`   :yref:`LawDispatcher`
-:yref:`IGeom`  :yref:`LawDispatcher`
-============================ ===========================
+==================== ===========================
+Top-level Indexable  used by
+==================== ===========================
+:yref:`Shape`        :yref:`BoundFunctor`, :yref:`IGeomDispatcher`
+:yref:`Material`     :yref:`IPhysDispatcher`
+:yref:`IPhys`        :yref:`LawDispatcher`
+:yref:`IGeom`        :yref:`LawDispatcher`
+==================== ===========================
 
 The top-level Indexable must use the ``REGISTER_INDEX_COUNTER`` macro, which sets up the machinery for identifying types of derived classes; they must then use the ``REGISTER_CLASS_INDEX`` macro *and* call ``createIndex()`` in their constructor. For instance, taking the :yref:`Shape` class (which is a top-level Indexable):
 
@@ -1077,7 +1078,7 @@
 
 .. ipython::
 
-	Yade [3]: ig=InteractionGeometryDispatcher([
+	Yade [3]: ig=IGeomDispatcher([
 	   ...:    Ig2_Sphere_Sphere_Dem3DofGeom(),
 	   ...:    Ig2_Facet_Sphere_Dem3DofGeom(),
 	   ...:    Ig2_Wall_Sphere_Dem3DofGeom()
@@ -1106,7 +1107,7 @@
 
 OpenGL functors
 ^^^^^^^^^^^^^^^
-OpenGL rendering is being done also by 1D functors (dispatched for the type to be rendered). Since it is sufficient to have exactly one class for each rendered type, the functors are found automatically. Their base functor types are ``GlShapeFunctor``, ``GlBoundFunctor``, ``GlInteractionGeometryFunctor`` and so on. These classes register the type they render using the ``RENDERS`` macro:
+OpenGL rendering is being done also by 1D functors (dispatched for the type to be rendered). Since it is sufficient to have exactly one class for each rendered type, the functors are found automatically. Their base functor types are ``GlShapeFunctor``, ``GlBoundFunctor``, ``GlIGeomFunctor`` and so on. These classes register the type they render using the ``RENDERS`` macro:
 
 .. code-block:: c++
 
@@ -1328,8 +1329,8 @@
 	ForceReseter                        400               9449Î¼s              0.01%      
 	BoundDispatcher                     400            1171770Î¼s              1.15%      
 	InsertionSortCollider               400            9433093Î¼s              9.24%      
-	InteractionGeometryDispatcher       400           15177607Î¼s             14.87%      
-	InteractionPhysicsDispatcher        400            9518738Î¼s              9.33%      
+	IGeomDispatcher       400           15177607Î¼s             14.87%      
+	IPhysDispatcher        400            9518738Î¼s              9.33%      
 	LawDispatcher                       400           64810867Î¼s             63.49%      
 	  Law2_Dem3DofGeom_CpmPhys_Cpm                                                     
 	    setup                           4926145            7649131Î¼s             15.25%  
@@ -1605,7 +1606,7 @@
 
 #. Collider erases interactions that were requested for being erased (see below).
 
-#. :yref:`InteractionLoop` (via :yref:`InteractionGeometryDispatcher`) calls appropriate :yref:`IGeomFunctor` based on :yref:`Shape` combination of both bodies, if such functor exists. For real interactions, the functor updates associated :yref:`IGeom`. For potential interactions, the functor returns
+#. :yref:`InteractionLoop` (via :yref:`IGeomDispatcher`) calls appropriate :yref:`IGeomFunctor` based on :yref:`Shape` combination of both bodies, if such functor exists. For real interactions, the functor updates associated :yref:`IGeom`. For potential interactions, the functor returns
 
 	``false``
 		if there is no geometrical overlap, and the interaction will stillremain potential-only
@@ -1620,7 +1621,7 @@
 	.. note::
 		If there is no functor suitable to handle given combination of :yref:`shapes<Shape>`, the interaction will be left in potential state, without raising any error.
 
-#. For real interactions (already existing or jsut created in last step), :yref:`InteractionLoop` (via :yref:`InteractionPhysicsDispatcher`) calls appropriate :yref:`IPhysFunctor` based on :yref:`Material` combination of both bodies. The functor *must* update (or create, if it doesn't exist yet) associated :yref:`IPhys` instance. It is an error if no suitable functor is found, and an exception will be thrown.
+#. For real interactions (already existing or jsut created in last step), :yref:`InteractionLoop` (via :yref:`IPhysDispatcher`) calls appropriate :yref:`IPhysFunctor` based on :yref:`Material` combination of both bodies. The functor *must* update (or create, if it doesn't exist yet) associated :yref:`IPhys` instance. It is an error if no suitable functor is found, and an exception will be thrown.
 
 #. For real interactions, :yref:`InteractionLoop` (via :yref:`LawDispatcher`) calls appropriate :yref:`LawFunctor` based on combintation of :yref:`IGeom` and :yref:`IPhys` of the interaction. Again, it is an error if no functor capable of handling it is found.
 

=== modified file 'doc/sphinx/yadeSphinx.py'
--- doc/sphinx/yadeSphinx.py	2010-09-30 18:00:41 +0000
+++ doc/sphinx/yadeSphinx.py	2010-10-01 22:30:00 +0000
@@ -131,7 +131,7 @@
 	sect('Constitutive laws','',['LawFunctor','LawDispatcher'])+
 	sect('Callbacks','',['BodyCallback','IntrCallback'])+
 	sect('Preprocessors','',['FileGenerator'])+
-	sect('Rendering','',['OpenGLRenderer','GlShapeFunctor','GlStateFunctor','GlBoundFunctor','GlInteractionGeometryFunctor','GlInteractionPhysicsFunctor'])+ # ,'GlShapeDispatcher','GlStateDispatcher','GlBoundDispatcher','GlInteractionGeometryDispatcher','GlInteractionPhysicsDispatcher'])+
+	sect('Rendering','',['OpenGLRenderer','GlShapeFunctor','GlStateFunctor','GlBoundFunctor','GlIGeomFunctor','GlIPhysFunctor'])+ # ,'GlShapeDispatcher','GlStateDispatcher','GlBoundDispatcher','GlIGeomDispatcher','GlIPhysDispatcher'])+
 	sect('Simulation data','',['Omega','BodyContainer','InteractionContainer','ForceContainer','MaterialContainer','Scene','Cell'])
 	+"""
 Other classes

=== modified file 'pkg/dem/Engine/GlobalEngine/NozzleFactory.hpp'
--- pkg/dem/Engine/GlobalEngine/NozzleFactory.hpp	2010-09-30 18:00:41 +0000
+++ pkg/dem/Engine/GlobalEngine/NozzleFactory.hpp	2010-10-01 22:30:00 +0000
@@ -31,7 +31,7 @@
 
 class DragForceApplier: public GlobalEngine{
 	public: virtual void action();
-	YADE_CLASS_BASE_DOC_ATTRS(DragForceApplier,GlobalEngine,"Apply `drag force <http://en.wikipedia.org/wiki/Drag_equation>`__ on particles, decelerating them proportionally to their linear velocities. The applied force reads\n\n.. math:: \\begin{equation}F_{d}=-\\frac{\\vec{v}}{|\\vec{v}|}\\frac{1}{2}\\rho|\\vec{v}|^2 C_d A\\end{equation}\n\nwhere $\\rho$ is the medium density (:yref:`density<DragForceApplier.density>`), $v$ is particle's velocity,  $A$ is particle projected area (disc), $C_d$ is the drag coefficient (0.47 for :yref:`Sphere`), \n\n.. note:: Drag force is only applied to spherical particles.\n\n.. warn:: Not tested.",
+	YADE_CLASS_BASE_DOC_ATTRS(DragForceApplier,GlobalEngine,"Apply `drag force <http://en.wikipedia.org/wiki/Drag_equation>`__ on particles, decelerating them proportionally to their linear velocities. The applied force reads\n\n.. math:: F_{d}=-\\frac{\\vec{v}}{|\\vec{v}|}\\frac{1}{2}\\rho|\\vec{v}|^2 C_d A\n\nwhere $\\rho$ is the medium density (:yref:`density<DragForceApplier.density>`), $v$ is particle's velocity,  $A$ is particle projected area (disc), $C_d$ is the drag coefficient (0.47 for :yref:`Sphere`), \n\n.. note:: Drag force is only applied to spherical particles.\n\n.. warn:: Not tested.",
 		((Real,density,0,,"Density of the medium."))
 	);
 };

=== modified file 'py/_utils.cpp'
--- py/_utils.cpp	2010-09-30 18:00:41 +0000
+++ py/_utils.cpp	2010-10-01 22:30:00 +0000
@@ -467,6 +467,6 @@
 	py::def("flipCell",&Shop::flipCell,(py::arg("flip")=Matrix3r(Matrix3r::Zero())),"Flip periodic cell so that angles between $R^3$ axes and transformed axes are as small as possible. This function relies on the fact that periodic cell defines by repetition or its corners regular grid of points in $R^3$; however, all cells generating identical grid are equivalent and can be flipped one over another. This necessiatates adjustment of :yref:`Interaction.cellDist` for interactions that cross boundary and didn't before (or vice versa), and re-initialization of collider. The *flip* argument can be used to specify desired flip: integers, each column for one axis; if zero matrix, best fit (minimizing the angles) is computed automatically.\n\nIn c++, this function is accessible as ``Shop::flipCell``.\n\n.. warning::\n\t This function is currently broken and should not be used.");
 	py::def("getViscoelasticFromSpheresInteraction",getViscoelasticFromSpheresInteraction,(py::arg("m"),py::arg("tc"),py::arg("en"),py::arg("es")),"Get viscoelastic interaction parameters from analytical solution of a pair spheres collision problem. \n\n:Parameters:\n\t`m` : float\n\t\tsphere mass\n\t`tc` : float\n\t\tcollision time\n\t`en` : float\n\t\tnormal restitution coefficient\n\t`es` : float\n\t\ttangential restitution coefficient.\n\n\n:return: \n\tdict with keys:\n\n\tkn : float\n\t\tnormal elastic coefficient computed as:\n\n.. math:: k_n=\\frac{m}{t_c^2}\\left(\\pi^2+(\\ln e_n)^2\\right)\n\n\tcn : float\n\t\tnormal viscous coefficient computed as:\n\n.. math:: c_n=-\\frac{2m}{t_c}\\ln e_n\n\n\n\tkt : float\n\t\ttangential elastic coefficient computed as:\n\n.. math:: k_t=\\frac27\\frac{m}{t_c^2}\\left(\\pi^2+(\\ln e_t)^2\\right)\n\n\tct : float\n\t\ttangential viscous coefficient computed as:\n\n.. math:: c_t=-\\frac27\\frac{m}{t_c}\\ln e_t.\n\n\nFor details see [Pournin2001]_. ");
 	py::def("stressTensorOfPeriodicCell",Shop__stressTensorOfPeriodicCell,(py::args("smallStrains")=false),"Compute overall (macroscopic) stress of periodic cell using equation published in [Kuhl2001]_:\n\n.. math:: \\vec{\\sigma}=\\frac{1}{V}\\sum_cl^c[\\vec{N}^cf_N^c+\\vec{T}^{cT}\\cdot\\vec{f}^c_T],\n\nwhere $V$ is volume of the cell, $l^c$ length of interaction $c$, $f^c_N$ normal force and $\\vec{f}^c_T$ shear force. Sumed are values over all interactions $c$. $\\vec{N}^c$ and $\\vec{T}^{cT}$ are projection tensors (see the original publication for more details):\n\n.. math:: \\vec{N}=\\vec{n}\\otimes\\vec{n}\\rightarrow N_{ij}=n_in_j\n\n.. math:: \\vec{T}^T=\\vec{I}_{sym}\\cdot\\vec{n}-\\vec{n}\\otimes\\vec{n}\\otimes\\vec{n}\\rightarrow T^T_{ijk}=\\frac{1}{2}(\\delta_{ik}\\delta_{jl}+\\delta_{il}\\delta_{jk})n_l-n_in_jn_k\n\n.. math:: \\vec{T}^T\\cdot\\vec{f}_T\\equiv T^T_{ijk}f_k=(\\delta_{ik}n_j/2+\\delta_{jk}n_i/2-n_in_jn_k)f_k=n_jf_i/2+n_if_j/2-n_in_jn_kf_k,\n\nwhere $n$ is unit vector oriented along the interaction (:yref:`normal<GenericSpheresContact::normal>`) and $\\delta$ is Kronecker's delta. As $\\vec{n}$ and $\\vec{f}_T$ are perpendicular (therfore $n_if_i=0$) we can write\n\n.. math:: \\sigma_{ij}=\\frac{1}{V}\\sum l[n_in_jf_N+n_jf^T_i/2+n_if^T_j/2]\n\n:param bool smallStrains: if false (large strains), real values of volume and interaction lengths are computed. If true, only :yref:`refLength<Dem3DofGeom::refLength>` of interactions and initial volume are computed (can save some time).\n\n:return: macroscopic stress tensor as Matrix3");
-	py::def("normalShearStressTensors",Shop__normalShearStressTensors,(py::args("compressionPositive")=false),"Compute overall stress tensor of the periodic cell decomposed in 2 parts, one contributed by normal forces, the other by shear forces. The formulation can be found in [Thornton2000]_, eq. (3):\n\n.. math:: \\tensor{sigma}_{ij}=\\frac{2}{V}\\sum R N \\vec{n}_i \\vec{n}_j+\frac{2}{V}\\sum R T \\vec{n}_i\\vec{t}_j\n\nwhere $V$ is the cell volume, $R$ is \"contact radius\" (in our implementation, current distance between particle centroids), $\\vec{n}$ is the normal vector, $\\vec{t}$ is a vector perpendicular to $\\vec{n}$, $N$ and $T$ are norms of normal and shear forces.");
+	py::def("normalShearStressTensors",Shop__normalShearStressTensors,(py::args("compressionPositive")=false),"Compute overall stress tensor of the periodic cell decomposed in 2 parts, one contributed by normal forces, the other by shear forces. The formulation can be found in [Thornton2000]_, eq. (3):\n\n.. math:: \\tens{sigma}_{ij}=\\frac{2}{V}\\sum R N \\vec{n}_i \\vec{n}_j+\\frac{2}{V}\\sum R T \\vec{n}_i\\vec{t}_j\n\nwhere $V$ is the cell volume, $R$ is \"contact radius\" (in our implementation, current distance between particle centroids), $\\vec{n}$ is the normal vector, $\\vec{t}$ is a vector perpendicular to $\\vec{n}$, $N$ and $T$ are norms of normal and shear forces.");
 	py::def("maxOverlapRatio",maxOverlapRatio,"Return maximum overlap ration in interactions (with :yref:`ScGeom`) of two :yref:`spheres<Sphere>`. The ratio is computed as $\\frac{u_N}{2(r_1 r_2)/r_1+r_2}$, where $u_N$ is the current overlap distance and $r_1$, $r_2$ are radii of the two spheres in contact.");
 }