Dear all, Yade 0.95.0 is available for download [1]. The Ubuntu stable packages [2] and Debian packages for experimental branch [3] are ready. The full changelog is attached.
Thanks all, who contributed in this version. [1] https://launchpad.net/yade/trunk/0.90/+download/yade-0.95.0.tar.gz [2] https://launchpad.net/~yade-pkg/+archive/stable [3] https://buildd.debian.org/status/package.php?p=yade&suite=experimental Anton
Anton Gladky (41):
Remove RELEASE file.
Fix compilation warning.
Fix typo in git-command.
Remove doxygen from installation section.
Add notification message for yade-batch.
Enable SnapshotEngine.
Minor fix in documentation.
Fix pack.py as suggested by Kneib François.
Remove all Py_BEGIN_ALLOW_THREADS and Py_END_ALLOW_THREADS to prevent
race conditions in python-bindings. (Closes LP:1056684)
Return back some Py_BEGIN_ALLOW_THREADS, as the previous commit freezes
autotests.
Add url to Chen`s thesis.
Add Tran`s publications.
Remove duplicate.
Minor fix in references.
Search numpy during configuration step.
Search loki-library and headers during compilation step.
Resize interactionsOnBody, if it is necessary. (Closes: LP:1105177)
Fix compilation.
Add omp.h header into ParallelEngine
AddNUMPY_INCLUDE_DIRS to cmake.
Remove --debug option from yade-batch template.
Remove debug-option from yade-batch.
Fix import of Image-module in Ubuntu Raring.
Fix segmentation fault in bodyNumInteractionsHistogram. (Closes:
LP:1087680)
Use default {CMAKE_CXX_FLAGS_DEBUG for Debug-build instead of hardcoded.
Make the bug LP:1087680 visible again.
Fix segmentation fault in bodyNumInteractionsHistogram.
Return back the opportunity to keep all interaction pointers for each body
Use interaction pointers in body class instead of iteration over all
interactions in body::py_intrs.
Add visualisation to Jakob`s scripts.
Merge pull request #32 from jakob-ifgt/master
Merge pull request #33 from jakob-ifgt/master
Add python-argparse into installation section.
Merge pull request #34 from jakob-ifgt/master
Remove scripts/debian as it is maintained in Debian itself
Remove extra/boost_python_len.hpp as it was for very old boost-versions.
Remove extra/foreach.hpp_local. Not used anywhere.
Remove site_scons. Forgotten during cmake-migration.
Remove convexHull2d. Was blocked.
Remove boost-python-indexing-suite-v2-noSymlinkHeaders.
0.95.0
Bruno Chareyre (68):
Give the git clone adress that will work always (previous one is blocked
at 3SR lab)
enable setting FlowEngine by number of steps or by deformation aplitude
a fix in bibtex
-remove excess verbosity
- add thread number attribute to change the number of thread of
interactionLoop dynamicaly during simulations. Also usefull combined with
parallel engine (for fine grain tuning of thread number in each subprocess)
1. Add thread number to parallel engine, can be changed dynamicaly.
Uncouples the number of threads in parallel engines and in slaves. 2.
Enable nested parallel regions (disabled on many systems by default) else the
parallel engine is doing no good
1. Replace one loop on cells by an optimized vector<Cell> iterator 2.
Clean an horrible block of code (not only ugly, it was also slow)
- introduce a position buffer for faster updates of volumes
Use retriangulation conditions more consistently. The solvers are not
swapped before a given fraction of the permutation interval now, to reduce
overheads.
small change in the initialization logic, now defining the two position
buffers if "first"
make ompThread an attribute of Engine, as it likely to be used more and
more in the future. It is then inherited by InteractionLoop and ParallelEngine
Parallelize volume updates and the computation of fluid forces
fix a typo introduced in previous commit, giving compile error in
FlowEngine
remove traces of the SpherePadder module, which is broken and
unmaintained (with author's agreement)
make grids periodic
use EpsVolPercent_RTRG consistently in periodic flow: negative value is
ignored, just like the non-periodic case
Adapt setContactProperties to pass argument in radians to
Shop::setContactFriction
-fix conversion mistake (radian/degree)
update variable names to denote the unit of friction angle (rad), and
make this explicit in the documentation
- include elasticity in the normal lubrication force - fix ompThreads
assignment in flow engine, resulting in numThreads=-1 by default, then
"libgomp: Out of memory"
Fix the F9-F12 keys binding for IPython>=0.12
-add the correct prefactor in normal lubrication relation -overlap
the two triangulations during one iteration in order to have the "previous"
forces defined in the normal lubrication equation
Update the documentation of the ompThreads attribute.
- fix again the offset of ids in SpherePack.toSimulation (previous fix
was assuming two bodies per clump)
- fix https://bugs.launchpad.net/yade/+bug/923929 again, as shown by
François it could still happen in some cases (see example in the bug report)
- remove the check/throw when generating aperiodic 2D packings, since the
algorithm actually support that.
Define O.engine with a default list at startup, with example script and
notes in the documentation.
remove utils prefix
- Updates and improvements in the triax-tutorial material - smallfix
in a note in introduction.rst
fixed version of the triax script for clumps
Remove first iteration form "--performance" option measurements
-transfer the normal lubrication force correctly when retriangulating
-doc fix
-fix the sign of the normal lubrication force in the periodic case
fix compile warning (actually fix the functions as well, as they were not
returning results at all!)
- doc fix
-remove remaining debug lines
periodic update of publications
fix a typo in bibtex file, +1 ref
- one fix in articles, yet more references in conferences
fix/add Tran's reference
- use "orientation" parameter in utils.box (fix bug/1111514)
- improved version of TriaxialStressController, controling not onlt
stress but also strain rate - making the interface more similar (but still
not exactly like) PeriTriaxController. - TriaxialCompressionEngine and
ThreeDTriaxialEngine become almost useless - reflected in the example
script which now uses only TriaxialStressController
-micro-fix (no need to define an initial timestep)
-code cleaning
- fix the default value of orientation in utils.box. [1,0,0,0] is NOT a
quaternion.
-add a few python bindings to the periodic engine for manipulations of
the internal tesselation
-fix the detection of (not) already computed tesselation
-make volume() functional also when PeriodicFlow is actually in use
uncouple the compilation of flow code and linsolv, so that it is possible
to effectively compile the flow engines without cholmod
remove useless "sigma_iso" and "isAxisymetric" members from TTController
- make an old engine deprecated, not compiled now, to be removed later
more #ifdef guards, to allow flow engine without linsolv
remove sigma_iso from the triax example script
fix syntax error in a doc string (blocking the buildbot
https://yade-dem.org/buildbot/builders/yade-full/builds/1741/steps/shell_3/logs/stdio)
-deprecation warnings in ThreeD and TriaxialCompression engines
-change the default value of FlowEngine::pressureForce, a flow engine is
supposed to compute a flow by default...
smallfix in example script
- 3 new references
- add "Open Source Discrete Element Method" explicitely in the home page,
google has to find us
nicer documentation of equations for stiffness definition
remove useless #define
- ship a copy of ipython_directive.py from ipython/HEAD for ipython 0.13
ipython version was checked in two different places, forgot the second
one. Still no confirmation of the fix.
- some lines comited by mistake, sorry for that.
- escape crash on non-iterable __doc__ (some qt class) - define new
attributes needed for ipython_directives.py >= 0.13 - fix existing *.rst to
use strictly 3 blank spaces in multiline directives (i.e. " ...:")
- reference name Tran2012a appearing twice -> renaming Tran2012b
- re-introduce the @supress of Christian (removed during experiments)
Christian Jakob (21):
add addToClump() method in yadeWrapper
improvements in clump logic - part 1
Improvements in clump logic - part 2
Added new example script, that show usage of addToClump() and
releaseFromClump()
Improvements in clump logic - part 3 + 4.
shorten the code of replaceByClumps()
add a check of python input for replaceByClumps() method
further improvements in clump logic
some fixes in documentation of wrapper and state
fix documentation of clumpTemplate in utils.py
Merge remote branch 'upstream/master'
let replaceByClumps return a list of tuples with new clump ids and
associated sphere ids
Merge remote branch 'upstream/master'
avgNumInteractions now takes care of clumps
some improvements for previous commit
doc fix in utils.py and exclude unused Clump.hpp in _utils.cpp
updated documentation of clumps in user manual and small fixes in doc in
yadeWrapper
Merge branch 'master' of github.com:yade/trunk
bug fix in replaceByClumps, that could lead to set negative masses on
bodies and shorten the code
yet another doc improvement in wrapper and user manual concerning
replaceByClumps method
replaced errors by warnings in addToClump and releaseFromClump in wrapper
Donia Marzougui (5):
Fix the computation of viscous forces by using the correct positions
of bodies (updated in buildTriangulation), and fix some variable names.
Remove fictious spheres from the computation of edge surfaces (employed
in the computation of viscous forces)
Correct the computation of the viscous and normal stress per particle.
Correct the sign of some parameters in the computation of the viscous
forces.
Correct the normal lubrication force.
Francois Kneib (24):
Continue the implementation of grids : - add GridConnexion Aabb -
add GridNode-GridNode Ig2 functor : Ig2_GridNode_GridNode_GridNodeGeom6D -
add GridNode-GridNode contact geometry : GridNodeGeom6D - add an example
script : examples/grids/Simple_Grid_Falling.py - update utils.py (minor
change)
Add the possibility of avoiding the contact detection between a group of
particle. -> the vector "avoidSelfInteractionMasks" contains a list of
masks : all particles having the same mask will not collide if this mask is
inside this list. -> the "mayCollide" method now check this too. ->
avoidSelfInteractionMasks can be set in python with a list of int.
Add the Sphere-GridConnection frictionnal contact : -> new contact
geometry : ScGridCoGeom -> new Ig2 : Ig2_Sphere_GridConnection_ScGridCoGeom
-> new Law2 : Law2_ScGridCoGeom_FrictPhys_CundallStrack -> update
utils.py to handle the new contact type (using avoidSelfInteractionMasks)
Merge branch 'master' of github.com:yade/trunk
Add the contact following and avoid multiple contact when a sphere is
sliding on a grid.
-Grids : Fix some minor bugs in
Ig2_Sphere_GridConnection_ScGridCoGeom::go(...). -Collider : Change the
vector of masks "avoidSelfInteractionMasks" to a single mask
"avoidSelfInteractionMask".
Create and correct documentation.
Grids : - modify the rendering. - Apply correct DEM laws in
utils.py to set right kn, ks, kr, and ktw. Now the grid behavior no longer
depends on the spacial discretization you make.
Modified setContactFriction method. Now it has to be used with an
angle in radian unit, no longer in degrees.
Try to fix documentation in this files, everywere "yref" appears in the
online documentation.
Fix Grid periodicity, and allow periodic sphere-grid contacts.
Disable a boring warning into the grid construction.
Fix a bug in SpherePack.toSimulation. There was a big problem when you
tried to add clumped SpherePack (with makeClumpCloud() for example).
Corrected toSimulation() (for the last time I hope :-) ).
Fix a bug in growParticles(...) method. Growing a clump is now really
homothetic. Before that, growing clumps seemed to be homothetic but at the next
timestep the original position of members was reseted.
Add Inelastic ChainedCylinder behavior law (by Ignacio Olmedo).
Create inelastic material and related physics, Ip2 and Law2. Example script
and complete documentation will come soon.
Add the ability to save to a file a SpherePack containing some Clumps.
Into SpherePack : now the toFile method writes a fifth column containing the
clump number (-1 if the sphere isn't clumped). The fromFile method uses the new
information to append clumped Spheres. Into Shop : loadSpheresFromFile
method is modified to read and return the fifth column. Old files with 4
columns are still compatible. Into CapillaryTriaxialTest and
CohesiveTriaxialTest : Shop::loadSpheresFromFile is sometimes used here, so
remove the clumpId information to match the "BasicSphere" typedef.
getStress(...) method : exclude gridNode-gridNode contacts for the stress
computing. growParticles(...) method : avoid growing gridNode and
gridConnection.
Fix some Grids bugs.
A minor spelling correction.
Add a little class summary and explanations into Grid.hpp. Fix a bug
into utils.py when creating a Grid in a non-periodic scene.
In the sphinx documentation, add the https GitHub read-only method : git
clone https://github.com/yade/trunk.git
Avoid GridNode-GridNode contact stiffnesses (kn and ks) to be changed
when the growParticles(...) method is used. (GridNodes are not concerned by
this method).
Add a missing space in the dependencies code lines.
François Kneib (1):
Correct a remaining bug into the toSimulation() python function.
Jan Stransky (9):
little modifications
added example script for CombinedKinematicEngine
little modifications of ConcretePM
modification of ConcretePM, improved utils.intrsOfEachBody function
improved yade executable: optparse->argparse, yade executable is now
loadable as python module
modified yade executable, fixing bug 1134422
complete optparse->argparse, --generate-manpage should work
improvement of ConcretePM, remover warnings in pack module
(randomDensePack and randomPeriPack functions)
modified ConcretePM, corrected Peri3dController related examples
Jan Stránský (1):
minor changes
françois (1):
makeClumpCloud(...) now takes a "seed" parameter to generate always the
same pack.
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