yade-dev team mailing list archive

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------------------------------------------------------------
revno: 3868
committer: Jan Stransky <jan.stransky@xxxxxxxxxxx>
timestamp: Wed 2014-04-02 17:19:41 +0200
message:
  fixed some errors and warnings for documentation build
modified:
  doc/references.bib
  doc/sphinx/installation.rst
  doc/sphinx/user.rst
  doc/yade-articles.bib
  doc/yade-conferences.bib
  pkg/common/Gl1_NormPhys.hpp
  pkg/dem/ConcretePM.hpp
  py/_polyhedra_utils.cpp


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=== modified file 'doc/references.bib'
--- doc/references.bib	2014-01-29 16:26:55 +0000
+++ doc/references.bib	2014-04-02 15:19:41 +0000
@@ -659,7 +659,7 @@
 
 @article{Lambert2008,
 	title={Comparison between two capillary forces models},
-	author={Lambert, Pierre and Chau, Alexandre and Delchambre, Alain and R{\'e}gnier, St{\'e}phane},
+	author={Lambert, Pierre and Chau, Alexandre and Delchambre, Alain and Régnier, Stéphane},
 	journal={Langmuir},
 	volume={24},
 	number={7},

=== modified file 'doc/sphinx/installation.rst'
--- doc/sphinx/installation.rst	2014-02-28 13:03:16 +0000
+++ doc/sphinx/installation.rst	2014-04-02 15:19:41 +0000
@@ -125,8 +125,10 @@
 Most of the list above is very likely already packaged for your distribution. In case you are confronted
 with some errors concerning not available packages (e.g. Package libmetis-dev is not available) it may be necessary 
 to add yade external ppa from https://launchpad.net/~yade-users/+archive/external::
+
 	sudo add-apt-repository ppa:yade-users/external 
 	sudo apt-get update 
+
 The following commands have to be executed in command line of corresponding 
 distributions. Just copy&paste to the terminal. To perform commands you 
 should have root privileges

=== modified file 'doc/sphinx/user.rst'
--- doc/sphinx/user.rst	2014-03-13 12:57:08 +0000
+++ doc/sphinx/user.rst	2014-04-02 15:19:41 +0000
@@ -1380,7 +1380,7 @@
 	O.saveGnuplot(O.tags['id']+'/'+'graph1')
 
 Controlling parallel computation
--------------------------------
+--------------------------------
 
 Default total number of available cores is determined from ``/proc/cpuinfo`` (provided by Linux kernel); in addition, if ``OMP_NUM_THREADS`` environment variable is set, minimum of these two is taken. The ``-j``/``--jobs`` option can be used to override this number.
 
@@ -1391,7 +1391,7 @@
 If number of cores for a job exceeds total number of cores, warning is issued and only the total number of cores is used instead.
 
 Merging gnuplot from individual jobs
--------------------------------------
+------------------------------------
 
 Frequently, it is desirable to obtain single figure for all jobs in the batch, for comparison purposes. Somewhat heiristic way for this functionality is provided by the batch system. ``yade-batch`` must be run with the ``--gnuplot`` option, specifying some file name that will be used for the merged figure::
 

=== modified file 'doc/yade-articles.bib'
--- doc/yade-articles.bib	2014-04-01 13:18:38 +0000
+++ doc/yade-articles.bib	2014-04-02 15:19:41 +0000
@@ -366,7 +366,7 @@
 	author = {Puckett, J.G. and Lechenault, F. and Daniels, K.E.},
 	journal = {Physical Review E},
 	volume = {83},
-	issue = {4},
+	number = {4},
 	pages = {041301},
 	year = {2011},
 	doi = {10.1103/PhysRevE.83.041301},
@@ -595,7 +595,7 @@
 	author = {Hilton, J. E. and Tordesillas, A.},
 	journal = {Phys. Rev. E},
 	volume = {88},
-	issue = {6},
+	number = {6},
 	pages = {062203},
 	numpages = {8},
 	year = {2013},

=== modified file 'doc/yade-conferences.bib'
--- doc/yade-conferences.bib	2014-01-13 17:49:25 +0000
+++ doc/yade-conferences.bib	2014-04-02 15:19:41 +0000
@@ -521,7 +521,7 @@
 	url = {https://www.yade-dem.org/publi/APC000193.pdf}
 }
 
-@InProceedings{ Hilton2013,
+@InProceedings{ Hilton2013b,
 	author = {J. E. Hilton and P. W. Cleary and A. Tordesillas},
 	title = {Unitary stick-slip motion in granular beds},
 	publisher = {AIP},

=== modified file 'pkg/common/Gl1_NormPhys.hpp'
--- pkg/common/Gl1_NormPhys.hpp	2012-09-21 19:03:18 +0000
+++ pkg/common/Gl1_NormPhys.hpp	2014-04-02 15:19:41 +0000
@@ -11,16 +11,17 @@
 		static GLUquadric* gluQuadric; // needed for gluCylinder, initialized by ::go if no initialized yet
 	public:
 		virtual void go(const shared_ptr<IPhys>&,const shared_ptr<Interaction>&,const shared_ptr<Body>&,const shared_ptr<Body>&,bool wireFrame);
-	YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_NormPhys,GlIPhysFunctor,"Renders :yref:`NormPhys` objects as cylinders of which diameter and color depends on :yref:`NormPhys::normForce` magnitude.",
-		((Real,maxFn,0,,"Value of :yref:`NormPhys.normalForce` corresponding to :yref:`maxDiameter<Gl1_NormPhys.maxDiameter>`. This value will be increased (but *not decreased* ) automatically."))
+	YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_NormPhys,GlIPhysFunctor,"Renders :yref:`NormPhys` objects as cylinders of which diameter and color depends on :yref:`NormPhys.normalForce` magnitude.",
+		// changed doc maxDiameter -> maxRadius ((Real,maxFn,0,,"Value of :yref:`NormPhys.normalForce` corresponding to :yref:`maxDiameter<Gl1_NormPhys.maxDiameter>`. This value will be increased (but *not decreased* ) automatically."))
+		((Real,maxFn,0,,"Value of :yref:`NormPhys.normalForce` corresponding to :yref:`maxRadius<Gl1_NormPhys.maxRadius>`. This value will be increased (but *not decreased* ) automatically."))
 		((int,signFilter,0,,"If non-zero, only display contacts with negative (-1) or positive (+1) normal forces; if zero, all contacts will be displayed."))
 		((Real,refRadius,std::numeric_limits<Real>::infinity(),,"Reference (minimum) particle radius; used only if :yref:`maxRadius<Gl1_NormPhys.maxRadius>` is negative. This value will be decreased (but *not increased* ) automatically. |yupdate|"))
 		((Real,maxRadius,-1,,"Cylinder radius corresponding to the maximum normal force. If negative, auto-updated :yref:`refRadius<Gl1_NormPhys.refRadius>` will be used instead."))
-		((int,slices,6,,"Number of sphere slices; (see `glutCylinder reference <http://www.opengl.org/sdk/docs/man/xhtml/gluCylinder.xml>`__)"))
-		((int,stacks,1,,"Number of sphere stacks; (see `glutCylinder reference <http://www.opengl.org/sdk/docs/man/xhtml/gluCylinder.xml>`__)"))
+		((int,slices,6,,"Number of sphere slices; (see `glutCylinder reference <http://www.opengl.org/sdk/docs/man/xhtml/gluCylinder.xml>`_)"))
+		((int,stacks,1,,"Number of sphere stacks; (see `glutCylinder reference <http://www.opengl.org/sdk/docs/man/xhtml/gluCylinder.xml>`_)"))
 		// strong/weak fabric attributes
-		((Real,maxWeakFn,NaN,,"Value that divides contacts by their normal force into the ``weak fabric'' and ``strong fabric''. This value is set as side-effect by :yref:`utils.fabricTensor`."))
-		((int,weakFilter,0,,"If non-zero, only display contacts belonging to the ``weak'' (-1) or ``strong'' (+1) fabric."))
+		((Real,maxWeakFn,NaN,,"Value that divides contacts by their normal force into the 'weak fabric' and 'strong fabric'. This value is set as side-effect by :yref:`utils.fabricTensor`."))
+		((int,weakFilter,0,,"If non-zero, only display contacts belonging to the 'weak' (-1) or 'strong' (+1) fabric."))
 		((Real,weakScale,1.,,"If :yref:`maxWeakFn<Gl1_NormPhys.maxWeakFn>` is set, scale radius of the weak fabric by this amount (usually smaller than 1). If zero, 1 pixel line is displayed. Colors are not affected by this value."))
 	);
 	RENDERS(NormPhys);

=== modified file 'pkg/dem/ConcretePM.hpp'
--- pkg/dem/ConcretePM.hpp	2013-08-14 08:59:42 +0000
+++ pkg/dem/ConcretePM.hpp	2014-04-02 15:19:41 +0000
@@ -311,7 +311,7 @@
 			((bool,epsT,false,,"Show shear strain "))
 			((bool,epsTAxes,false,,"Show axes of shear plane "))
 			((bool,normal,false,,"Show contact normal"))
-			((Real,colorStrainRatio,-1,,"If positive, set the interaction (wire) color based on $\\eps_N$ normalized by $\\eps_0$ × `colorStrainRatio` ($\\eps_0$ = :yref:`CpmPhys.epsCrackOnset` ). Otherwise, color based on the residual strength."))
+			((Real,colorStrainRatio,-1,,"If positive, set the interaction (wire) color based on $\\eps_N$ normalized by $\\eps_0$ × :yref:`colorStrainRatio<CpmPhys.colorStrainRatio>` ($\\eps_0$ = :yref:`CpmPhys.epsCrackOnset` ). Otherwise, color based on the residual strength."))
 			((bool,epsNLabel,false,,"Numerically show normal strain"))
 		);
 	};

=== modified file 'py/_polyhedra_utils.cpp'
--- py/_polyhedra_utils.cpp	2013-10-15 16:14:46 +0000
+++ py/_polyhedra_utils.cpp	2014-04-02 15:19:41 +0000
@@ -367,7 +367,7 @@
 	py::def("SieveCurve",SieveCurve,"save sieve curve coordinates into file");
 	py::def("SizeOfPolyhedra",SizeOfPolyhedra,"returns max, middle an min size in perpendicular directions");
 	py::def("SizeRatio",SizeRatio,"save sizes of polyhedra into file");
-	py::def("convexHull",convexHull,"....");
+	py::def("convexHull",convexHull,"");
 	py::def("Split",Split,"split polyhedron perpendicularly to given direction direction");
 }