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------------------------------------------------------------
revno: 3610
committer: Christian Jakob <jakob@xxxxxxxxxxxxxxxxxxx>
timestamp: Thu 2015-03-05 09:18:57 +0100
message:
  improve/fix documentation about clumps
modified:
  doc/sphinx/user.rst
  py/wrapper/yadeWrapper.cpp


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=== modified file 'doc/sphinx/user.rst'
--- doc/sphinx/user.rst	2014-07-10 09:57:20 +0000
+++ doc/sphinx/user.rst	2015-03-05 08:18:57 +0000
@@ -152,7 +152,7 @@
 
 * Another option is to replace :yref:`standalone<Body.isStandalone>` spheres from a given packing (see :yref:`SpherePack<yade._packSpheres.SpherePack>` and :yref:`makeCloud<yade._packSpheres.SpherePack.makeCloud>`) by clumps using clump templates.
 
-This is done by a function called :yref:`replaceByClumps()<BodyContainer.replaceByClumps>`. This function takes a list of :yref:`clumpTemplates()<yade.clumpTemplate>` and a list of amounts and replaces spheres by clumps. The volume of a new clump will be the same as the volume of the sphere, that was replaced (clump volume/mass/inertia is accounting for overlaps assuming that there are only pair overlaps).
+This is done by a function called :yref:`replaceByClumps()<BodyContainer.replaceByClumps>`. This function takes a list of :yref:`clumpTemplates()<yade.utils.clumpTemplate>` and a list of amounts and replaces spheres by clumps. The volume of a new clump will be the same as the volume of the sphere, that was replaced (clump volume/mass/inertia is accounting for overlaps assuming that there are only pair overlaps).
 
 -> :yref:`replaceByClumps()<yade.wrapper.BodyContainer.replaceByClumps>` returns a list of tuples: ``[(clumpId1,[memberId1,memberId2,...]),(clumpId2,[memberId1,memberId2,...]),...]``
 

=== modified file 'py/wrapper/yadeWrapper.cpp'
--- py/wrapper/yadeWrapper.cpp	2014-12-01 18:20:51 +0000
+++ py/wrapper/yadeWrapper.cpp	2015-03-05 08:18:57 +0000
@@ -892,12 +892,12 @@
 		.def("append",&pyBodyContainer::append,"Append one Body instance, return its id.")
 		.def("append",&pyBodyContainer::appendList,"Append list of Body instance, return list of ids")
 		.def("appendClumped",&pyBodyContainer::appendClump,(py::arg("discretization")=0),"Append given list of bodies as a clump (rigid aggregate); returns a tuple of ``(clumpId,[memberId1,memberId2,...])``. Clump masses and inertia are adapted automatically (for details see :yref:`clump()<BodyContainer.clump>`).")
-		.def("clump",&pyBodyContainer::clump,(py::arg("discretization")=0),"Clump given bodies together (creating a rigid aggregate); returns ``clumpId``. Clump masses and inertia are adapted automatically when discretization>0. If clump members are overlapping this is done by integration/summation over mass points using a regular grid of cells (number of grid cells in one direction is defined as $R_{min}/discretization$, where $R_{min}$ is minimum clump member radius). For non-overlapping members inertia of the clump is the sum of inertias from members. If discretization<=0 sum of inertias from members is used (faster, but inaccurate).")
-		.def("updateClumpProperties",&pyBodyContainer::updateClumpProperties,(py::arg("excludeList")=py::list(),py::arg("discretization")=5),"Update clump properties mass, volume and inertia (for details of 'discretization' value see :yref:`clump()<BodyContainer.clump>`). Clumps can be excluded from the calculation by giving a list of ids: *O.bodies.updateProperties([ids])*.")
+		.def("clump",&pyBodyContainer::clump,(py::arg("discretization")=0),"Clump given bodies together (creating a rigid aggregate); returns ``clumpId``. Clump masses and inertia are adapted automatically when discretization>0. If clump members are overlapping this is done by integration/summation over mass points using a regular grid of cells (grid cells length is defined as $R_{min}/discretization$, where $R_{min}$ is minimum clump member radius). For non-overlapping members inertia of the clump is the sum of inertias from members. If discretization<=0 sum of inertias from members is used (faster, but inaccurate).")
+		.def("updateClumpProperties",&pyBodyContainer::updateClumpProperties,(py::arg("excludeList")=py::list(),py::arg("discretization")=5),"Manually force Yade to update clump properties mass, volume and inertia (for details of 'discretization' value see :yref:`clump()<BodyContainer.clump>`). Can be used, when clumps are modified or erased during a simulation. Clumps can be excluded from the calculation by giving a list of ids: *O.bodies.updateProperties([ids])*.")
 		.def("addToClump",&pyBodyContainer::addToClump,(py::arg("discretization")=0),"Add body b (or a list of bodies) to an existing clump c. c must be clump and b may not be a clump member of c. Clump masses and inertia are adapted automatically (for details see :yref:`clump()<BodyContainer.clump>`).\n\nSee :ysrc:`examples/clumps/addToClump-example.py` for an example script.\n\n.. note:: If b is a clump itself, then all members will be added to c and b will be deleted. If b is a clump member of clump d, then all members from d will be added to c and d will be deleted. If you need to add just clump member b, :yref:`release<BodyContainer.releaseFromClump>` this member from d first.")
 		.def("releaseFromClump",&pyBodyContainer::releaseFromClump,(py::arg("discretization")=0),"Release body b from clump c. b must be a clump member of c. Clump masses and inertia are adapted automatically (for details see :yref:`clump()<BodyContainer.clump>`).\n\nSee :ysrc:`examples/clumps/releaseFromClump-example.py` for an example script.\n\n.. note:: If c contains only 2 members b will not be released and a warning will appear. In this case clump c should be :yref:`erased<BodyContainer.erase>`.")
 		.def("replaceByClumps",&pyBodyContainer::replaceByClumps,(py::arg("discretization")=0),"Replace spheres by clumps using a list of clump templates and a list of amounts; returns a list of tuples: ``[(clumpId1,[memberId1,memberId2,...]),(clumpId2,[memberId1,memberId2,...]),...]``. A new clump will have the same volume as the sphere, that was replaced. Clump masses and inertia are adapted automatically (for details see :yref:`clump()<BodyContainer.clump>`). \n\n\t *O.bodies.replaceByClumps( [utils.clumpTemplate([1,1],[.5,.5])] , [.9] ) #will replace 90 % of all standalone spheres by 'dyads'*\n\nSee :ysrc:`examples/clumps/replaceByClumps-example.py` for an example script.")
-		.def("getRoundness",&pyBodyContainer::getRoundness,(py::arg("excludeList")=py::list()),"Returns roundness coefficient RC = R2/R1. R1 is the theoretical radius of a sphere, with same volume as clump. R2 is the minimum radius of a sphere, that imbeds clump. If just spheres are present RC = 1. If clumps are present 0 < RC < 1. Bodies can be excluded from the calculation by giving a list of ids: *O.bodies.getRoundness([ids])*.\n\nSee :ysrc:`examples/clumps/replaceByClumps-example.py` for an example script.")
+		.def("getRoundness",&pyBodyContainer::getRoundness,(py::arg("excludeList")=py::list()),"Returns roundness coefficient RC = R2/R1. R1 is the equivalent sphere radius of a clump. R2 is the minimum radius of a sphere, that imbeds the clump. If just spheres are present RC = 1. If clumps are present 0 < RC < 1. Bodies can be excluded from the calculation by giving a list of ids: *O.bodies.getRoundness([ids])*.\n\nSee :ysrc:`examples/clumps/replaceByClumps-example.py` for an example script.")
 		.def("clear", &pyBodyContainer::clear,"Remove all bodies (interactions not checked)")
 		.def("erase", &pyBodyContainer::erase,(py::arg("eraseClumpMembers")=0),"Erase body with the given id; all interaction will be deleted by InteractionLoop in the next step. If a clump is erased use *O.bodies.erase(clumpId,True)* to erase the clump AND its members.")
 		.def("replace",&pyBodyContainer::replace);