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------------------------------------------------------------
revno: 3725
committer: Christian Jakob <jakob@xxxxxxxxxxxxxxxxxxx>
timestamp: Wed 2013-10-02 16:08:10 +0200
message:
  fixing/updating refs and links in users manual - part 1
modified:
  doc/sphinx/user.rst


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=== modified file 'doc/sphinx/user.rst'
--- doc/sphinx/user.rst	2013-10-02 12:58:57 +0000
+++ doc/sphinx/user.rst	2013-10-02 14:08:10 +0000
@@ -179,7 +179,7 @@
 	
 -> :yref:`getRoundness()<BodyContainer.getRoundness>` returns roundness coefficient RC of a packing or a part of the packing
 
-.. note:: Have a look at ``examples/clumps/`` folder. There you will find some examples, that show usage of different functions for clumps.
+.. note:: Have a look at :ysrc:`examples/clumps/` folder. There you will find some examples, that show usage of different functions for clumps.
 
 
 Sphere packings
@@ -268,7 +268,7 @@
 #. :yref:`yade.pack.gtsSurface2Facets` function can create the triangulated surface (from :yref:`Facet` particles) in the simulation itself, as shown in the funnel example. (Triangulated surface can also be imported directly from a STL file using :yref:`yade.ymport.stl`.)
 #. :yref:`yade._packPredicates.inGtsSurface` predicate can be created, using the surface as boundary representation of the enclosed volume.
 
-The :ysrc:`scripts/test/gts-horse.py` (img. img-horse_) shows both possibilities; first, a GTS surface is imported::
+The :ysrc:`scripts/gts-horse/gts-horse.py` (img. img-horse_) shows both possibilities; first, a GTS surface is imported::
 
 	import gts
 	surf=gts.read(open('horse.coarse.gts'))
@@ -287,7 +287,7 @@
 .. figure:: fig/horse.png
 	:width: 8cm
 
-	Imported GTS surface (horse) used as packing predicate (top) and surface constructed from :yref:`facets<yade.facet>` (bottom). See http://www.youtube.com/watch?v=PZVruIlUX1A for movie of this simulation.
+	Imported GTS surface (horse) used as packing predicate (top) and surface constructed from :yref:`facets<yade.utils.facet>` (bottom). See http://www.youtube.com/watch?v=PZVruIlUX1A for movie of this simulation.
 
 
 Boolean operations on predicates
@@ -317,7 +317,7 @@
 Algorithms presented below operate on geometric spheres, defined by their center and radius. With a few exception documented below, the procedure is as follows:
 
 #. Sphere positions and radii are computed (some functions use volume predicate for this, some do not)
-#. :yref:`yade.sphere` is called for each position and radius computed; it receives extra `keyword arguments <http://docs.python.org/glossary.html#term-keyword-argument>`_ of the packing function (i.e. arguments that the packing function doesn't specify in its definition; they are noted ``**kw``). Each :yref:`yade.sphere` call creates actual :yref:`Body` objects with :yref:`Sphere` :yref:`shape<Shape>`. List of :yref:`Body` objects is returned.
+#. :yref:`sphere<yade.utils.sphere>` is called for each position and radius computed; it receives extra `keyword arguments <http://docs.python.org/glossary.html#term-keyword-argument>`_ of the packing function (i.e. arguments that the packing function doesn't specify in its definition; they are noted ``**kw``). Each :yref:`sphere<yade.utils.sphere>` call creates actual :yref:`Body` objects with :yref:`Sphere` :yref:`shape<Shape>`. List of :yref:`Body` objects is returned.
 #. List returned from the packing function can be added to simulation using ``O.bodies.append``.
 
 Taking the example of pierced box::
@@ -325,7 +325,7 @@
 	pred=pack.inAlignedBox((-2,-2,-2),(2,2,2))-pack.inCylinder((0,-2,0),(0,2,0),1)
 	spheres=pack.randomDensePack(pred,spheresInCell=2000,radius=.1,rRelFuzz=.4,wire=True,color=(0,0,1),material=1)
 
-Keyword arguments ``wire``, ``color`` and ``material`` are not declared in :yref:`yade.pack.randomDensePack`, therefore will be passed to :yref:`yade.sphere`, where they are also documented. ``spheres`` is now list of :yref:`Body` objects, which we add to the simulation::
+Keyword arguments ``wire``, ``color`` and ``material`` are not declared in :yref:`yade.pack.randomDensePack`, therefore will be passed to :yref:`sphere<yade.utils.sphere>`, where they are also documented. ``spheres`` is now list of :yref:`Body` objects, which we add to the simulation::
 
 	O.bodies.append(spheres)
 
@@ -369,7 +369,7 @@
 GenGeo
 	is library (python module) for packing generation developed with `ESyS-Particle <http://www.launchpad.net/esys-particle>`_. It creates packing by random insertion of spheres with given radius range. Inserted spheres touch each other exactly and, more importantly, they also touch the boundary, if in its neighbourhood. Boundary is represented as special object of the GenGeo library (Sphere, cylinder, box, convex polyhedron, …). Therefore, GenGeo cannot be used with volume represented by yade predicates as explained above.
 
-	Packings generated by this module can be imported directly via :yref:`yade.ymport.gengeo`, or from saved file via :yref:`yade.ymport.gengeoFile`. There is an example script :ysrc:`scripts/test/genCylLSM.py`. Full documentation for GenGeo can be found at `ESyS documentation website <http://esys.esscc.uq.edu.au/docs.html>`_.
+	Packings generated by this module can be imported directly via :yref:`yade.ymport.gengeo`, or from saved file via :yref:`yade.ymport.gengeoFile`. There is an example script :ysrc:`examples/test/genCylLSM.py`. Full documentation for GenGeo can be found at `ESyS documentation website <http://esys.esscc.uq.edu.au/docs.html>`_.
 
 	To our knowledge, the GenGeo library is not currently packaged. It can be downloaded from current subversion repository ::
 
@@ -394,9 +394,9 @@
 Triangulated surfaces
 =====================
 
-Yade integrates with the the `GNU Triangulated Surface library <http://gts.sourceforge.net>`_, exposed in python via the 3rd party :yref:`external:gts` module. GTS provides variety of functions for surface manipulation (coarsening, tesselation, simplification, import), to be found in its documentation.
+Yade integrates with the the `GNU Triangulated Surface library <http://gts.sourceforge.net>`_, exposed in python via GTS module. GTS provides variety of functions for surface manipulation (coarsening, tesselation, simplification, import), to be found in its documentation.
 
-GTS surfaces are geometrical objects, which can be inserted into simulation as set of particles whose :yref:`Body.shape` is of type :yref:`Facet` -- single triangulation elements. :yref:`pack.gtsSurface2Facets` can be used to convert GTS surface triangulation into list of :yref:`bodies<Body>` ready to be inserted into simulation via ``O.bodies.append``.
+GTS surfaces are geometrical objects, which can be inserted into simulation as set of particles whose :yref:`Body.shape` is of type :yref:`Facet` -- single triangulation elements. :yref:`yade.pack.gtsSurface2Facets` can be used to convert GTS surface triangulation into list of :yref:`bodies<Body>` ready to be inserted into simulation via ``O.bodies.append``.
 
 Facet particles are created by default as non-:yref:`Body.dynamic` (they have zero inertial mass). That means that  they are fixed in space and will not move if subject to forces. You can however
 
@@ -424,7 +424,7 @@
 Parametric construction
 ------------------------
 
-The :yref:`external:gts` module provides convenient way of creating surface by vertices, edges and triangles.
+The GTS module provides convenient way of creating surface by vertices, edges and triangles.
 
 Frequently, though, the surface can be conveniently described as surface between polylines in space. For instance, cylinder is surface between two polygons (closed polylines). The :yref:`yade.pack.sweptPolylines2gtsSurface` offers the functionality of connecting several polylines with triangulation.
 
@@ -497,7 +497,7 @@
 Individual interactions on demand
 ----------------------------------
 
-It is possible to create an interaction between a pair of particles independently of collision detection using :yref:`yade.createInteraction`. This function looks for and uses matching ``Ig2`` and ``Ip2`` functors. Interaction will be created regardless of distance between given particles (by passing a special parameter to the ``Ig2`` functor to force creation of the interaction even without any geometrical contact). Appropriate constitutive law should be used to avoid deletion of the interaction at the next simulation step.
+It is possible to create an interaction between a pair of particles independently of collision detection using :yref:`createInteraction<yade.utils.createInteraction>`. This function looks for and uses matching ``Ig2`` and ``Ip2`` functors. Interaction will be created regardless of distance between given particles (by passing a special parameter to the ``Ig2`` functor to force creation of the interaction even without any geometrical contact). Appropriate constitutive law should be used to avoid deletion of the interaction at the next simulation step.
 
 .. ipython::
 
@@ -525,7 +525,7 @@
 	# created by functors in InteractionLoop
 	Yade [2]: i.geom, i.phys
 
-This method will be rather slow if many interaction are to be created (the functor lookup will be repeated for each of them). In such case, ask on yade-dev@xxxxxxxxxxxxxxxxxxx to have the :yref:`yade.createInteraction` function accept list of pairs id's as well.
+This method will be rather slow if many interaction are to be created (the functor lookup will be repeated for each of them). In such case, ask on yade-dev@xxxxxxxxxxxxxxxxxxx to have the :yref:`createInteraction<yade.utils.createInteraction>` function accept list of pairs id's as well.
 
 Base engines
 =============